3155 lines
3.0 MiB
3155 lines
3.0 MiB
##fileformat=VCFv4.0
|
|
##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_exome_agilent_designed_120.targets.interval_list] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[soap.filtered.vcf, /home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v9/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE variantmergeoption=UNION rod_priority_list=soap,gatk printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set"
|
|
##FILTER=<ID=BadSOAPSNP,Description="QUAL < 20 || RankSumP < 0.01">
|
|
##FILTER=<ID=ESPStandard,Description="AB 0.75 || QD 5.0 || HRun 3 || SB -0.10">
|
|
##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual > 0.04">
|
|
##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP)) 0.1)">
|
|
##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
|
|
##FILTER=<ID=LowQual,Description="Low quality">
|
|
##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
|
|
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
|
|
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
|
|
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
|
|
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
|
|
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
|
##GenomicAnnotator="analysis_type=GenomicAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[soap_gatk.vcf, /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt] rodToIntervalTrackName=variant BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null logging_level=info log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub vcfOutput=null sampleName=null select=[Ljava.lang.String;@638bd7f1 join=[Ljava.lang.String;@720e4245 oneToMany=false maxJoinTableSize=500000 ignoreFilteredSites=false"
|
|
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
|
|
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
|
|
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
|
|
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
|
|
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
|
|
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
|
|
##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position. ">
|
|
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
|
|
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
|
|
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
|
|
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
|
|
##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
|
|
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
|
|
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
|
|
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
|
|
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/NA12878.WEx.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_exome_agilent_designed_120.targets.interval_list] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod, interval,Intervals,/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_exome_agilent_designed_120.targets.interval_list] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod hapmap=null hapmap_chip=null out=null err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=10000 num_threads=1 interval_merging=ALL read_group_black_list=null genotype_model=JOINT_ESTIMATE base_model=EMPIRICAL heterozygosity=7.8E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null platform=null min_base_quality_score=20 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 cap_base_quality_by_mapping_quality=false"
|
|
##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=[/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_exome_agilent_designed_120.targets.interval_list] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/GA2.WEx.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/GA2.WEx.cleaned.indels.10.mask, interval,Intervals,/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_exome_agilent_designed_120.targets.interval_list] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Indel NO_HEADER=false"
|
|
##VariantsToVCF="analysis_type=VariantsToVCF input_file=[] sample_metadata=[] read_buffer_size=null phone_home=DEV read_filter=[] intervals=[/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_exome_agilent_designed_120.targets.interval_list] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[calls.soapsnp] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null"
|
|
##reference=Homo_sapiens_assembly18.fasta
|
|
##source=VariantOptimizer
|
|
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
|
|
chr1 867694 . T C 11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=24;DB;DP=5;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=99.00;MQ0=0;OQ=81.73;QD=16.35;RankSumP=1.00000;SB=-49.69;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1027T>C;refseq.codonCoord=343;refseq.end=867694;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1107;refseq.name=NM_152486;refseq.name2=SAMD11;refseq.positionType=CDS;refseq.proteinCoordStr=p.W343R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=-38;refseq.start=867694;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=filterInsoap-gatk GT 1/1
|
|
chr1 871477 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=2.43617e-08;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1856A>C;refseq.codonCoord=619;refseq.end=871477;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1915;refseq.name=NM_015658;refseq.name2=NOC2L;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y619S;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=53;refseq.start=871477;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 1/0
|
|
chr1 871490 . G A 72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=18;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=8.35;MQ=97.97;MQ0=1;OQ=2002.85;QD=23.02;RankSumP=1.00000;SB=-547.28;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1843C>T;refseq.codonCoord=615;refseq.end=871490;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1902;refseq.name=NM_015658;refseq.name2=NOC2L;refseq.positionType=CDS;refseq.proteinCoordStr=p.L615L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=40;refseq.start=871490;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/1
|
|
chr1 873762 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=315;Dels=0.00;HRun=2;HaplotypeScore=15.11;MQ=91.05;MQ0=15;OQ=5231.78;QD=16.61;RankSumP=0.200390;SB=-1533.02;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1528A>C;refseq.codonCoord=510;refseq.end=873762;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1587;refseq.name=NM_015658;refseq.name2=NOC2L;refseq.positionType=CDS;refseq.proteinCoordStr=p.N510H;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-30;refseq.start=873762;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 877664 . A G 197.22 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=105;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=92.52;MQ0=4;OQ=3931.65;QD=37.44;RankSumP=1.00000;SB=-1152.13;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1182T>C;refseq.codonCoord=394;refseq.end=877664;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1241;refseq.name=NM_015658;refseq.name2=NOC2L;refseq.positionType=CDS;refseq.proteinCoordStr=p.T394T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-10;refseq.spliceInfo=splice-donor_-10;refseq.start=877664;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 878502 . T C 228.12 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=148;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=84.04;MQ0=5;OQ=5658.62;QD=38.23;RankSumP=1.00000;SB=-1972.80;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.918A>G;refseq.codonCoord=306;refseq.end=878502;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=977;refseq.name=NM_015658;refseq.name2=NOC2L;refseq.positionType=CDS;refseq.proteinCoordStr=p.E306E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=30;refseq.start=878502;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 878522 . T C 293.17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=111;Dels=0.00;HRun=1;HaplotypeScore=2.70;MQ=84.65;MQ0=4;OQ=4266.78;QD=38.44;RankSumP=1.00000;SB=-907.71;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.898A>G;refseq.codonCoord=300;refseq.end=878522;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=957;refseq.name=NM_015658;refseq.name2=NOC2L;refseq.positionType=CDS;refseq.proteinCoordStr=p.I300V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=878522;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 887188 . G C 80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=146;Dels=0.00;HRun=1;HaplotypeScore=5.20;MQ=98.78;MQ0=0;OQ=6699.32;QD=45.89;RankSumP=1.00000;SB=-2186.94;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.609G>C;refseq.codonCoord=203;refseq.end=887188;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=716;refseq.name=NM_198317;refseq.name2=KLHL17;refseq.positionType=CDS;refseq.proteinCoordStr=p.A203A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-103;refseq.start=887188;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 890423 . A C 62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.500000;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1918A>C;refseq.codonCoord=640;refseq.end=890423;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2025;refseq.name=NM_198317;refseq.name2=KLHL17;refseq.positionType=CDS;refseq.proteinCoordStr=p.T640P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=218;refseq.start=890423;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=soap GT 0/1
|
|
chr1 898188 . A C 22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.0113507;SecondBestBaseQ=16;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1123A>C;refseq.codingCoordStr_2=c.1087A>C;refseq.codonCoord_1=375;refseq.codonCoord_2=363;refseq.end_1=898188;refseq.end_2=898188;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1158;refseq.mrnaCoord_2=1122;refseq.name2_1=PLEKHN1;refseq.name2_2=PLEKHN1;refseq.name_1=NM_001160184;refseq.name_2=NM_032129;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T375P;refseq.proteinCoordStr_2=p.T363P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-66;refseq.spliceDist_2=-66;refseq.start_1=898188;refseq.start_2=898188;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=soap GT 0/1
|
|
chr1 899282 . C T 79.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=70.00;QD=17.50;RankSumP=0.500000;SB=-46.55;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1536C>T;refseq.codingCoordStr_2=c.1641C>T;refseq.codonCoord_1=512;refseq.codonCoord_2=547;refseq.end_1=899282;refseq.end_2=899282;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1571;refseq.mrnaCoord_2=1676;refseq.name2_1=PLEKHN1;refseq.name2_2=PLEKHN1;refseq.name_1=NM_001160184;refseq.name_2=NM_032129;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D512D;refseq.proteinCoordStr_2=p.D547D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-13;refseq.spliceDist_2=-13;refseq.start_1=899282;refseq.start_2=899282;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 0/1
|
|
chr1 939471 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=98.11;MQ0=0;OQ=551.25;QD=11.25;RankSumP=0.559709;SB=-179.21;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.248G>A;refseq.codonCoord=83;refseq.end=939471;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=355;refseq.name=NM_005101;refseq.name2=ISG15;refseq.positionType=CDS;refseq.proteinCoordStr=p.S83N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=245;refseq.start=939471;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/0
|
|
chr1 939517 . A G 158.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=97.07;MQ0=0;OQ=1471.70;QD=32.70;RankSumP=1.00000;SB=-444.52;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.294A>G;refseq.codonCoord=98;refseq.end=939517;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=401;refseq.name=NM_005101;refseq.name2=ISG15;refseq.positionType=CDS;refseq.proteinCoordStr=p.V98V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-266;refseq.start=939517;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 971794 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=6.89;MQ=97.02;MQ0=0;OQ=672.99;QD=8.63;RankSumP=0.0799027;SB=-261.89;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3066A>G;refseq.codonCoord=1022;refseq.end=971794;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3116;refseq.name=NM_198576;refseq.name2=AGRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1022S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=155;refseq.start=971794;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 0/1
|
|
chr1 972857 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=142;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=98.91;MQ0=0;OQ=2022.81;QD=14.25;RankSumP=0.128650;SB=-782.59;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3558T>C;refseq.codonCoord=1186;refseq.end=972857;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3608;refseq.name=NM_198576;refseq.name2=AGRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.F1186F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=42;refseq.start=972857;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/0
|
|
chr1 974165 . T C 28.08 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=95.26;MQ0=0;QD=1.56;RankSumP=0.0318358;SB=-0.97;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4161T>C;refseq.codonCoord=1387;refseq.end=974165;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4211;refseq.name=NM_198576;refseq.name2=AGRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1387T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=56;refseq.start=974165;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 976748 . T G 14 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=21;HRun=2;RankSumP=0.546167;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5423T>G;refseq.codonCoord=1808;refseq.end=976748;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5473;refseq.name=NM_198576;refseq.name2=AGRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1808G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=53;refseq.start=976748;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 980143 . C T 75.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=23;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=96.71;MQ0=0;OQ=129.22;QD=21.54;RankSumP=1.00000;SB=-44.55;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6057C>T;refseq.codonCoord=2019;refseq.end=980143;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6107;refseq.name=NM_198576;refseq.name2=AGRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.D2019D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=77;refseq.start=980143;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=filterInsoap-gatk GT 1/1
|
|
chr1 1105747 . C T 18.35 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=24;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=99.00;MQ0=0;QD=1.41;RankSumP=0.461538;SB=-30.49;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.528C>T;refseq.codingCoordStr_2=c.309C>T;refseq.codonCoord_1=176;refseq.codonCoord_2=103;refseq.end_1=1105747;refseq.end_2=1105747;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=679;refseq.mrnaCoord_2=486;refseq.name2_1=TTLL10;refseq.name2_2=TTLL10;refseq.name_1=NM_001130045;refseq.name_2=NM_153254;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S176S;refseq.proteinCoordStr_2=p.S103S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.start_1=1105747;refseq.start_2=1105747;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=FilteredInAll GT 0/1
|
|
chr1 1105812 . A G 34.75 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DP=8;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=99.00;MQ0=0;QD=4.34;RankSumP=0.542857;SB=-41.66;SecondBestBaseQ=18;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.593A>G;refseq.codingCoordStr_2=c.374A>G;refseq.codonCoord_1=198;refseq.codonCoord_2=125;refseq.end_1=1105812;refseq.end_2=1105812;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=744;refseq.mrnaCoord_2=551;refseq.name2_1=TTLL10;refseq.name2_2=TTLL10;refseq.name_1=NM_001130045;refseq.name_2=NM_153254;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K198R;refseq.proteinCoordStr_2=p.K125R;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=-33;refseq.spliceDist_2=-33;refseq.start_1=1105812;refseq.start_2=1105812;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=soap-filterIngatk GT 0/1
|
|
chr1 1148494 . A G 146.17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=277;Dels=0.00;HRun=0;HaplotypeScore=13.07;MQ=98.55;MQ0=0;OQ=9166.54;QD=33.09;RankSumP=1.00000;SB=-2683.31;SecondBestBaseQ=8;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.570T>C;refseq.codingCoordStr_2=c.570T>C;refseq.codonCoord_1=190;refseq.codonCoord_2=190;refseq.end_1=1148494;refseq.end_2=1148494;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=899;refseq.mrnaCoord_2=899;refseq.name2_1=SDF4;refseq.name2_2=SDF4;refseq.name_1=NM_016176;refseq.name_2=NM_016547;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D190D;refseq.proteinCoordStr_2=p.D190D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=-8;refseq.spliceDist_2=-8;refseq.spliceInfo_1=splice-donor_-8;refseq.spliceInfo_2=splice-donor_-8;refseq.start_1=1148494;refseq.start_2=1148494;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=Intersection GT 1/1
|
|
chr1 1169279 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=3;RankSumP=1.98460e-05;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.449T>G;refseq.codonCoord=150;refseq.end=1169279;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=481;refseq.name=NM_001014980;refseq.name2=FAM132A;refseq.positionType=CDS;refseq.proteinCoordStr=p.V150G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=70;refseq.start=1169279;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 1234787 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=15;HRun=1;RankSumP=0.00108523;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.414T>G;refseq.codonCoord=138;refseq.end=1234787;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=444;refseq.name=NM_153339;refseq.name2=PUSL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C138W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-60;refseq.start=1234787;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 1/0
|
|
chr1 1237357 . T C 32 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=97.85;MQ0=0;OQ=433.16;QD=28.88;RankSumP=1.00000;SB=-122.88;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1641A>G;refseq.codonCoord=547;refseq.end=1237357;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1699;refseq.name=NM_017871;refseq.name2=CPSF3L;refseq.positionType=CDS;refseq.proteinCoordStr=p.P547P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=34;refseq.start=1237357;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 1239050 . G A 96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=367;Dels=0.00;HRun=3;HaplotypeScore=10.95;MQ=98.92;MQ0=0;OQ=15506.08;QD=42.25;RankSumP=1.00000;SB=-6976.91;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.882C>T;refseq.codonCoord=294;refseq.end=1239050;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=940;refseq.name=NM_017871;refseq.name2=CPSF3L;refseq.positionType=CDS;refseq.proteinCoordStr=p.F294F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-76;refseq.start=1239050;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/1
|
|
chr1 1244704 . C G 79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=60;Dels=0.00;HRun=3;HaplotypeScore=2.00;MQ=99.00;MQ0=0;OQ=2745.50;QD=45.76;RankSumP=1.00000;SB=-934.63;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.264G>C;refseq.codonCoord=88;refseq.end=1244704;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=322;refseq.name=NM_017871;refseq.name2=CPSF3L;refseq.positionType=CDS;refseq.proteinCoordStr=p.G88G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=64;refseq.start=1244704;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 1267396 . T C 65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=52.72;MQ0=15;OQ=251.83;QD=9.33;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.366A>G;refseq.codonCoord=122;refseq.end=1267396;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=413;refseq.name=NM_004421;refseq.name2=DVL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P122P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=4;refseq.spliceInfo=splice-acceptor_4;refseq.start=1267396;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 1280139 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=78.50;MQ0=7;OQ=447.40;QD=11.47;RankSumP=0.477552;SB=-81.78;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.735G>C;refseq.codonCoord=245;refseq.end=1280139;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=766;refseq.name=NM_032348;refseq.name2=MXRA8;refseq.positionType=CDS;refseq.proteinCoordStr=p.V245V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-215;refseq.start=1280139;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 1413144 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DP=501;Dels=0.00;HRun=0;HaplotypeScore=177.01;MQ=27.85;MQ0=98;OQ=4836.61;QD=9.65;RankSumP=0.0240713;SB=-631.13;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1253G>A;refseq.codonCoord=418;refseq.end=1413144;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1354;refseq.name=NM_031921;refseq.name2=ATAD3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.R418Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-14;refseq.start=1413144;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap-filterIngatk GT 1/0
|
|
chr1 1415583 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1421A>C;refseq.codonCoord=474;refseq.end=1415583;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1522;refseq.name=NM_031921;refseq.name2=ATAD3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.D474A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=84;refseq.start=1415583;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 1469207 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.388A>C;refseq.codonCoord=130;refseq.end=1469207;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=713;refseq.name=NM_014188;refseq.name2=SSU72;refseq.positionType=CDS;refseq.proteinCoordStr=p.T130P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=24;refseq.start=1469207;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 1541790 . T C 56 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=98.68;MQ0=0;OQ=935.87;QD=24.63;RankSumP=1.00000;SB=-446.54;SecondBestBaseQ=2;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_2=c.214T>C;refseq.codingCoordStr_3=c.214T>C;refseq.codingCoordStr_4=c.214T>C;refseq.codingCoordStr_5=c.-90T>C;refseq.codingCoordStr_6=c.214T>C;refseq.codonCoord_2=72;refseq.codonCoord_3=72;refseq.codonCoord_4=72;refseq.codonCoord_6=72;refseq.end_1=1541790;refseq.end_2=1541790;refseq.end_3=1541790;refseq.end_4=1541790;refseq.end_5=1541790;refseq.end_6=1541790;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_6=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=259;refseq.mrnaCoord_2=259;refseq.mrnaCoord_3=259;refseq.mrnaCoord_4=259;refseq.mrnaCoord_5=276;refseq.mrnaCoord_6=259;refseq.name2_1=MIB2;refseq.name2_2=MIB2;refseq.name2_3=MIB2;refseq.name2_4=MIB2;refseq.name2_5=MIB2;refseq.name2_6=MIB2;refseq.name_1=NR_033183;refseq.name_2=NM_001170686;refseq.name_3=NM_001170687;refseq.name_4=NM_001170688;refseq.name_5=NM_001170689;refseq.name_6=NM_080875;refseq.numMatchingRecords=6;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=utr5;refseq.positionType_6=CDS;refseq.proteinCoordStr_2=p.F72L;refseq.proteinCoordStr_3=p.F72L;refseq.proteinCoordStr_4=p.F72L;refseq.proteinCoordStr_6=p.F72L;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceAA_4=Phe;refseq.referenceAA_6=Phe;refseq.referenceCodon_2=TTC;refseq.referenceCodon_3=TTC;refseq.referenceCodon_4=TTC;refseq.referenceCodon_6=TTC;refseq.spliceDist_1=40;refseq.spliceDist_2=40;refseq.spliceDist_3=40;refseq.spliceDist_4=40;refseq.spliceDist_5=40;refseq.spliceDist_6=40;refseq.start_1=1541790;refseq.start_2=1541790;refseq.start_3=1541790;refseq.start_4=1541790;refseq.start_5=1541790;refseq.start_6=1541790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_6=Leu;refseq.variantCodon_2=CTC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_6=CTC;set=Intersection GT 1/1
|
|
chr1 1548655 . T C 77.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=99.00;MQ0=0;OQ=1226.82;QD=30.67;RankSumP=1.00000;SB=-574.39;SecondBestBaseQ=0;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_4=c.305T>C;refseq.codingCoordStr_5=c.305T>C;refseq.codingCoordStr_6=c.305T>C;refseq.codonCoord_4=102;refseq.codonCoord_5=102;refseq.codonCoord_6=102;refseq.end_1=1548663;refseq.end_2=1548663;refseq.end_3=1548655;refseq.end_4=1548655;refseq.end_5=1548655;refseq.end_6=1548655;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_3=*;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_3=350;refseq.mrnaCoord_4=350;refseq.mrnaCoord_5=350;refseq.mrnaCoord_6=350;refseq.name2_1=MIB2;refseq.name2_2=MIB2;refseq.name2_3=MIB2;refseq.name2_4=MIB2;refseq.name2_5=MIB2;refseq.name2_6=MIB2;refseq.name_1=NM_001170687;refseq.name_2=NM_001170689;refseq.name_3=NR_033183;refseq.name_4=NM_001170686;refseq.name_5=NM_001170688;refseq.name_6=NM_080875;refseq.numMatchingRecords=6;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=non_coding_exon;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_4=p.M102T;refseq.proteinCoordStr_5=p.M102T;refseq.proteinCoordStr_6=p.M102T;refseq.referenceAA_4=Met;refseq.referenceAA_5=Met;refseq.referenceAA_6=Met;refseq.referenceCodon_4=ATG;refseq.referenceCodon_5=ATG;refseq.referenceCodon_6=ATG;refseq.spliceDist_3=24;refseq.spliceDist_4=24;refseq.spliceDist_5=24;refseq.spliceDist_6=24;refseq.start_1=1541868;refseq.start_2=1541868;refseq.start_3=1548655;refseq.start_4=1548655;refseq.start_5=1548655;refseq.start_6=1548655;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_4=Thr;refseq.variantAA_5=Thr;refseq.variantAA_6=Thr;refseq.variantCodon_4=ACG;refseq.variantCodon_5=ACG;refseq.variantCodon_6=ACG;set=Intersection GT 1/1
|
|
chr1 1656035 rs61777509 C T 21.24 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=266;Dels=0.00;HRun=0;HaplotypeScore=3.48;MQ=3.81;MQ0=257;QD=0.08;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.686G>A;refseq.codonCoord=229;refseq.end=1656035;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1102;refseq.name=NM_182838;refseq.name2=SLC35E2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R229H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-47;refseq.start=1656035;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:193,73:7:-7.51,-2.11,-18.34:54.04
|
|
chr1 1660274 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.405G>C;refseq.codonCoord=135;refseq.end=1660274;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=821;refseq.name=NM_182838;refseq.name2=SLC35E2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R135R;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-54;refseq.start=1660274;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=FilteredInAll GT 1/0
|
|
chr1 1660591 . G C 14.23 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=7.46;MQ0=237;QD=0.06;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.266C>G;refseq.codonCoord=89;refseq.end=1660591;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=682;refseq.name=NM_182838;refseq.name2=SLC35E2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T89R;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-57;refseq.start=1660591;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:238,1:2:-5.29,-0.60,-4.55:39.45
|
|
chr1 1675900 . G T 80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=121;Dels=0.00;HRun=2;HaplotypeScore=2.37;MQ=98.70;MQ0=0;OQ=4577.40;QD=37.83;RankSumP=1.00000;SB=-1439.30;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.786C>A;refseq.codonCoord=262;refseq.end=1675900;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1008;refseq.name=NM_023018;refseq.name2=NADK;refseq.positionType=CDS;refseq.proteinCoordStr=p.N262K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-58;refseq.start=1675900;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/1
|
|
chr1 1746724 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.29A>G;refseq.codonCoord=10;refseq.end=1746724;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=361;refseq.name=NM_002074;refseq.name2=GNB1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E10G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-29;refseq.start=1746724;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 1876879 . A G 89 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=369;Dels=0.00;HRun=2;HaplotypeScore=9.54;MQ=97.48;MQ0=0;OQ=15204.63;QD=41.20;RankSumP=1.00000;SB=-7137.72;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2287T>C;refseq.codonCoord=763;refseq.end=1876879;refseq.frame=0;refseq.functionalClass=readthrough;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2443;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.*763Q;refseq.referenceAA=Stop;refseq.referenceCodon=TAG;refseq.spliceDist=271;refseq.start=1876879;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 1876952 . G C 28 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;HRun=3;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2214C>G;refseq.codonCoord=738;refseq.end=1876952;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2370;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.G738G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=198;refseq.start=1876952;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=soap GT 1/1
|
|
chr1 1876955 . C G 120.64 BadSOAPSNP;ESPStandard;Indel AC=1;AF=0.50;AN=2;BestBaseQ=34;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=90.00;MQ0=0;QD=3.66;RankSumP=0.0666667;SB=-3.99;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2211G>C;refseq.codonCoord=737;refseq.end=1876955;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2367;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.A737A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=195;refseq.start=1876955;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 1876965 . G T 5 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=2;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2201C>A;refseq.codonCoord=734;refseq.end=1876965;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2357;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.P734Q;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=185;refseq.start=1876965;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=FilteredInAll GT 1/1
|
|
chr1 1876967 . C G 1 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=2;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2199G>C;refseq.codonCoord=733;refseq.end=1876967;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2355;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.K733N;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=183;refseq.start=1876967;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 1/1
|
|
chr1 1876970 . G T 5 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=10;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2196C>A;refseq.codonCoord=732;refseq.end=1876970;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2352;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.A732A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=180;refseq.start=1876970;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=FilteredInAll GT 1/1
|
|
chr1 1876972 . C G 8 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=17;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2194G>C;refseq.codonCoord=732;refseq.end=1876972;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2350;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.A732P;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=178;refseq.start=1876972;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/1
|
|
chr1 1876973 . C T 43.58 ESPStandard;Indel;LowQual AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=7.63;MQ=97.85;MQ0=0;QD=1.36;SB=32.13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2193G>A;refseq.codonCoord=731;refseq.end=1876973;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2349;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q731Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=177;refseq.start=1876973;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:27,5:26:-15.47,-7.83,-86.63:76.42
|
|
chr1 1877105 . G A 360.63 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=98.18;MQ0=0;OQ=4470.76;QD=40.28;RankSumP=1.00000;SB=-2186.73;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2061C>T;refseq.codonCoord=687;refseq.end=1877105;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2217;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.A687A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=45;refseq.start=1877105;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 1878053 . C A 428.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=99.00;MQ0=0;OQ=3632.02;QD=38.64;RankSumP=1.00000;SB=-1456.70;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1882G>T;refseq.codonCoord=628;refseq.end=1878053;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2038;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.G628C;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=31;refseq.start=1878053;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 1/1
|
|
chr1 1886300 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=5.22;MQ=98.26;MQ0=0;OQ=868.20;QD=11.89;RankSumP=0.330848;SB=-381.06;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1462C>T;refseq.codonCoord=488;refseq.end=1886300;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1618;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.L488L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=61;refseq.start=1886300;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/0
|
|
chr1 1887682 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1389C>A;refseq.codonCoord=463;refseq.end=1887682;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1545;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y463*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-13;refseq.start=1887682;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=FilteredInAll GT 0/1
|
|
chr1 1890092 . T C 139.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=149;Dels=0.00;HRun=0;HaplotypeScore=6.36;MQ=97.63;MQ0=0;OQ=2198.36;QD=14.75;RankSumP=0.361408;SB=-690.24;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1087A>G;refseq.codonCoord=363;refseq.end=1890092;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1243;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.I363V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=41;refseq.start=1890092;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 1906750 . C T 228.29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=255;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=98.76;MQ0=0;OQ=4459.86;QD=17.49;RankSumP=0.484359;SB=-1443.83;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.435G>A;refseq.codonCoord=145;refseq.end=1906750;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=591;refseq.name=NM_001080484;refseq.name2=KIAA1751;refseq.positionType=CDS;refseq.proteinCoordStr=p.L145L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=40;refseq.start=1906750;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 0/1
|
|
chr1 1946897 . T C 76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=24;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=2.52;MQ=97.79;MQ0=0;OQ=1785.40;QD=28.80;RankSumP=1.00000;SB=-478.40;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.330T>C;refseq.codonCoord=110;refseq.end=1946897;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=425;refseq.name=NM_000815;refseq.name2=GABRD;refseq.positionType=CDS;refseq.proteinCoordStr=p.G110G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=81;refseq.start=1946897;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 1980867 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.311G>C;refseq.codonCoord=104;refseq.end=1980867;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=472;refseq.name=NM_002744;refseq.name2=PRKCZ;refseq.positionType=CDS;refseq.proteinCoordStr=p.G104A;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-24;refseq.start=1980867;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 2056602 . T G 0.01 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=204;Dels=0.00;HRun=1;HaplotypeScore=6.21;MQ=98.42;MQ0=0;OQ=582.95;QD=2.86;RankSumP=0.00000;SB=269.90;SecondBestBaseQ=22;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.-174T>G;refseq.codingCoordStr_2=c.-174T>G;refseq.codingCoordStr_3=c.376T>G;refseq.codonCoord_3=126;refseq.end_1=2056602;refseq.end_2=2056602;refseq.end_3=2056602;refseq.frame_3=0;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=325;refseq.mrnaCoord_2=222;refseq.mrnaCoord_3=537;refseq.name2_1=PRKCZ;refseq.name2_2=PRKCZ;refseq.name2_3=PRKCZ;refseq.name_1=NM_001033581;refseq.name_2=NM_001033582;refseq.name_3=NM_002744;refseq.numMatchingRecords=3;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.Y126D;refseq.referenceAA_3=Tyr;refseq.referenceCodon_3=TAC;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.spliceDist_3=42;refseq.start_1=2056602;refseq.start_2=2056602;refseq.start_3=2056602;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Asp;refseq.variantCodon_3=GAC;set=FilteredInAll GT 1/0
|
|
chr1 2150876 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.811A>C;refseq.codonCoord=271;refseq.end=2150876;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=883;refseq.name=NM_003036;refseq.name2=SKI;refseq.positionType=CDS;refseq.proteinCoordStr=p.T271P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-159;refseq.start=2150876;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 2329933 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=97.45;MQ0=0;OQ=465.51;QD=12.58;RankSumP=0.640061;SB=-249.07;SecondBestBaseQ=26;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.418G>C;refseq.codingCoordStr_2=c.418G>C;refseq.codonCoord_1=140;refseq.codonCoord_2=140;refseq.end_1=2329933;refseq.end_2=2329933;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=487;refseq.mrnaCoord_2=487;refseq.name2_1=PEX10;refseq.name2_2=PEX10;refseq.name_1=NM_002617;refseq.name_2=NM_153818;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G140R;refseq.proteinCoordStr_2=p.G140R;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=-183;refseq.spliceDist_2=-183;refseq.start_1=2329933;refseq.start_2=2329933;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;set=Intersection GT 1/0
|
|
chr1 2330060 . T C 156.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=114;Dels=0.00;HRun=0;HaplotypeScore=3.20;MQ=98.87;MQ0=0;OQ=1800.17;QD=15.79;RankSumP=0.484429;SB=-635.71;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.291A>G;refseq.codingCoordStr_2=c.291A>G;refseq.codonCoord_1=97;refseq.codonCoord_2=97;refseq.end_1=2330060;refseq.end_2=2330060;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=360;refseq.mrnaCoord_2=360;refseq.name2_1=PEX10;refseq.name2_2=PEX10;refseq.name_1=NM_002617;refseq.name_2=NM_153818;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T97T;refseq.proteinCoordStr_2=p.T97T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=98;refseq.spliceDist_2=98;refseq.start_1=2330060;refseq.start_2=2330060;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 1/0
|
|
chr1 2434274 . G A 104.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.38;MQ=98.65;MQ0=0;OQ=748.76;QD=12.27;RankSumP=0.193878;SB=-372.84;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1640C>T;refseq.codonCoord=547;refseq.end=2434274;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1649;refseq.name=NM_018216;refseq.name2=PANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.A547V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=65;refseq.start=2434274;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 2442429 . T C 129.87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=225;Dels=0.00;HRun=1;HaplotypeScore=10.77;MQ=98.68;MQ0=0;OQ=4577.08;QD=20.34;RankSumP=0.357412;SB=-1341.94;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.393A>G;refseq.codonCoord=131;refseq.end=2442429;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=402;refseq.name=NM_018216;refseq.name2=PANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.K131K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-30;refseq.start=2442429;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/0
|
|
chr1 2480088 . C T 189.84 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=163;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=99.00;MQ0=0;OQ=2484.29;QD=15.24;RankSumP=0.412654;SB=-363.44;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.721G>A;refseq.codonCoord=241;refseq.end=2480088;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1020;refseq.name=NM_003820;refseq.name2=TNFRSF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.V241I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-6;refseq.spliceInfo=splice-donor_-6;refseq.start=2480088;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 0/1
|
|
chr1 2486265 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=98.37;MQ0=0;OQ=632.80;QD=12.17;RankSumP=0.0554813;SB=-331.25;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.50A>G;refseq.codonCoord=17;refseq.end=2486265;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=349;refseq.name=NM_003820;refseq.name2=TNFRSF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.K17R;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-20;refseq.start=2486265;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/0
|
|
chr1 2508234 . C T 18.35 ESPStandard;LowQual AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.03;MQ0=0;QD=1.53;SB=-35.51;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.50C>T;refseq.codonCoord=17;refseq.end=2508234;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=126;refseq.name=NM_152371;refseq.name2=C1orf93;refseq.positionType=CDS;refseq.proteinCoordStr=p.A17V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-14;refseq.start=2508234;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:10,2:11:-8.42,-3.31,-33.55:51.12
|
|
chr1 2512902 . C G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=483;Dels=0.00;HRun=2;HaplotypeScore=62.06;MQ=97.52;MQ0=0;OQ=76.19;QD=0.16;RankSumP=0.00000;SB=748.51;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2194G>C;refseq.codonCoord=732;refseq.end=2512902;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2408;refseq.name=NM_033467;refseq.name2=MMEL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A732P;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=31;refseq.start=2512902;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 2928125 . C T 226.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.52;MQ0=0;OQ=1141.93;QD=18.72;RankSumP=0.666966;SB=-538.13;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.15C>T;refseq.codonCoord=5;refseq.end=2928125;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=220;refseq.name=NM_080431;refseq.name2=ACTRT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.H5H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=220;refseq.start=2928125;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 0/1
|
|
chr1 2928429 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=278;Dels=0.00;HRun=1;HaplotypeScore=21.32;MQ=98.46;MQ0=0;OQ=5338.24;QD=19.20;RankSumP=0.0297766;SB=-1429.83;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.319C>T;refseq.codonCoord=107;refseq.end=2928429;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=524;refseq.name=NM_080431;refseq.name2=ACTRT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L107L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=524;refseq.start=2928429;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 2928557 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=126;Dels=0.00;HRun=1;HaplotypeScore=10.63;MQ=98.41;MQ0=0;OQ=1832.32;QD=14.54;RankSumP=0.00761714;SB=-476.58;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.447T>G;refseq.codonCoord=149;refseq.end=2928557;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=652;refseq.name=NM_080431;refseq.name2=ACTRT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S149S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=652;refseq.start=2928557;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=filterInsoap-gatk GT 1/0
|
|
chr1 2928784 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=41;Dels=0.00;HRun=2;HaplotypeScore=1.16;MQ=98.33;MQ0=0;OQ=478.84;QD=11.68;RankSumP=0.113638;SB=-247.82;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.674T>G;refseq.codonCoord=225;refseq.end=2928784;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=879;refseq.name=NM_080431;refseq.name2=ACTRT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L225W;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-544;refseq.start=2928784;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/0
|
|
chr1 3311983 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1097A>C;refseq.codingCoordStr_2=c.1097A>C;refseq.codonCoord_1=366;refseq.codonCoord_2=366;refseq.end_1=3311983;refseq.end_2=3311983;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1179;refseq.mrnaCoord_2=1179;refseq.name2_1=PRDM16;refseq.name2_2=PRDM16;refseq.name_1=NM_022114;refseq.name_2=NM_199454;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H366P;refseq.proteinCoordStr_2=p.H366P;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=65;refseq.spliceDist_2=65;refseq.start_1=3311983;refseq.start_2=3311983;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 3311985 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1099G>C;refseq.codingCoordStr_2=c.1099G>C;refseq.codonCoord_1=367;refseq.codonCoord_2=367;refseq.end_1=3311985;refseq.end_2=3311985;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1181;refseq.mrnaCoord_2=1181;refseq.name2_1=PRDM16;refseq.name2_2=PRDM16;refseq.name_1=NM_022114;refseq.name_2=NM_199454;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A367P;refseq.proteinCoordStr_2=p.A367P;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=67;refseq.spliceDist_2=67;refseq.start_1=3311985;refseq.start_2=3311985;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 3318218 . T C 336.78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=102;Dels=0.00;HRun=1;HaplotypeScore=2.59;MQ=98.23;MQ0=0;OQ=4028.92;QD=39.50;RankSumP=1.00000;SB=-1668.53;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1597T>C;refseq.codingCoordStr_2=c.1597T>C;refseq.codonCoord_1=533;refseq.codonCoord_2=533;refseq.end_1=3318218;refseq.end_2=3318218;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1679;refseq.mrnaCoord_2=1679;refseq.name2_1=PRDM16;refseq.name2_2=PRDM16;refseq.name_1=NM_022114;refseq.name_2=NM_199454;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S533P;refseq.proteinCoordStr_2=p.S533P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCG;refseq.referenceCodon_2=TCG;refseq.spliceDist_1=411;refseq.spliceDist_2=411;refseq.start_1=3318218;refseq.start_2=3318218;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCG;refseq.variantCodon_2=CCG;set=Intersection GT 1/1
|
|
chr1 3318519 . C T 112.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=5.15;MQ=98.73;MQ0=0;OQ=1541.46;QD=13.76;RankSumP=0.111948;SB=-457.89;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1898C>T;refseq.codingCoordStr_2=c.1898C>T;refseq.codonCoord_1=633;refseq.codonCoord_2=633;refseq.end_1=3318519;refseq.end_2=3318519;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1980;refseq.mrnaCoord_2=1980;refseq.name2_1=PRDM16;refseq.name2_2=PRDM16;refseq.name_1=NM_022114;refseq.name_2=NM_199454;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P633L;refseq.proteinCoordStr_2=p.P633L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.spliceDist_1=-706;refseq.spliceDist_2=-706;refseq.start_1=3318519;refseq.start_2=3318519;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;set=Intersection GT 0/1
|
|
chr1 3379587 . C T 221.44 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=177;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=98.89;MQ0=0;OQ=2483.15;QD=14.03;RankSumP=0.351299;SB=-1028.98;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1108C>T;refseq.codonCoord=370;refseq.end=3379587;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1356;refseq.name=NM_014448;refseq.name2=ARHGEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.H370Y;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-68;refseq.start=3379587;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 0/1
|
|
chr1 3384316 . T C 200.77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=155;Dels=0.00;HRun=1;HaplotypeScore=3.84;MQ=98.49;MQ0=0;OQ=5625.47;QD=36.29;RankSumP=1.00000;SB=-2309.52;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1491T>C;refseq.codonCoord=497;refseq.end=3384316;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1739;refseq.name=NM_014448;refseq.name2=ARHGEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.S497S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=18;refseq.start=3384316;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 3384899 . G A 282.03 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=4.54;MQ=98.82;MQ0=0;OQ=2348.39;QD=15.45;RankSumP=0.0478186;SB=-1070.95;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1677G>A;refseq.codonCoord=559;refseq.end=3384899;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1925;refseq.name=NM_014448;refseq.name2=ARHGEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.V559V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=52;refseq.start=3384899;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/0
|
|
chr1 3386922 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=3.35;MQ=98.48;MQ0=0;OQ=1293.20;QD=14.70;RankSumP=0.496366;SB=-528.76;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2041G>A;refseq.codonCoord=681;refseq.end=3386922;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2289;refseq.name=NM_014448;refseq.name2=ARHGEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.E681K;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=51;refseq.start=3386922;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/0
|
|
chr1 3400840 . T G 58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.357143;SecondBestBaseQ=22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4084A>C;refseq.codonCoord=1362;refseq.end=3400840;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4311;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1362P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-46;refseq.start=3400840;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=soap GT 1/0
|
|
chr1 3400842 . C G 23 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=1;RankSumP=0.345238;SecondBestBaseQ=19;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4082G>C;refseq.codonCoord=1361;refseq.end=3400842;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4309;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1361A;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-48;refseq.start=3400842;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=soap GT 1/0
|
|
chr1 3400879 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=6.92980e-06;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4045T>C;refseq.codonCoord=1349;refseq.end=3400879;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4272;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1349P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=45;refseq.start=3400879;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 3411757 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=98.02;MQ0=0;OQ=160.14;QD=6.96;RankSumP=0.537934;SB=-70.34;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2063T>C;refseq.codonCoord=688;refseq.end=3411757;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2290;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.L688P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=3411757;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 0/1
|
|
chr1 3414248 . G A 255.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=285;Dels=0.00;HRun=0;HaplotypeScore=9.18;MQ=98.00;MQ0=0;OQ=5857.64;QD=20.55;RankSumP=0.0233239;SB=-2515.97;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1760C>T;refseq.codonCoord=587;refseq.end=3414248;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1987;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.P587L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-30;refseq.start=3414248;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/0
|
|
chr1 3418020 . T G 128.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=95.74;MQ0=0;OQ=1355.12;QD=35.66;RankSumP=1.00000;SB=-512.85;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1068A>C;refseq.codonCoord=356;refseq.end=3418020;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1295;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.T356T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-47;refseq.start=3418020;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 3418468 . G A 303.59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=127;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=98.85;MQ0=0;OQ=4126.18;QD=32.49;RankSumP=1.00000;SB=-1877.39;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.938C>T;refseq.codonCoord=313;refseq.end=3418468;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1165;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.A313V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-39;refseq.start=3418468;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 3486339 . T C 55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=96.92;MQ0=0;OQ=782.61;QD=30.10;RankSumP=1.00000;SB=-77.36;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.391A>G;refseq.codonCoord=131;refseq.end=3486339;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=618;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S131G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=15;refseq.start=3486339;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 3501794 . A G 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=23;DB;DP=172;Dels=0.00;HRun=0;HaplotypeScore=42.06;MQ=92.72;MQ0=0;OQ=1213.32;QD=7.05;RankSumP=0.00905981;SB=-259.30;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.344T>C;refseq.codonCoord=115;refseq.end=3501794;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=571;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.M115T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-33;refseq.start=3501794;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=FilteredInAll GT 0/1
|
|
chr1 3501842 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.296T>G;refseq.codonCoord=99;refseq.end=3501842;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=523;refseq.name=NM_001409;refseq.name2=MEGF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.V99G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=30;refseq.start=3501842;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 3532172 . T G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=189;Dels=0.00;HRun=2;HaplotypeScore=24.92;MQ=98.61;MQ0=0;OQ=137.14;QD=0.73;RankSumP=0.00000;SB=203.67;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.329T>G;refseq.codonCoord=110;refseq.end=3532172;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=410;refseq.name=NM_182752;refseq.name2=TPRG1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.V110G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=36;refseq.start=3532172;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 3537996 . T C 138.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=10.36;MQ=96.87;MQ0=0;OQ=3523.46;QD=25.17;RankSumP=1.00000;SB=-1024.82;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1134A>G;refseq.codonCoord=378;refseq.end=3537996;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1242;refseq.name=NM_017818;refseq.name2=WDR8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A378A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=86;refseq.start=3537996;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 3538692 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=146;Dels=0.00;HRun=2;HaplotypeScore=2.60;MQ=99.00;MQ0=0;OQ=2834.57;QD=19.41;RankSumP=0.270425;SB=-383.05;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.993C>G;refseq.codonCoord=331;refseq.end=3538692;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1101;refseq.name=NM_017818;refseq.name2=WDR8;refseq.positionType=CDS;refseq.proteinCoordStr=p.I331M;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-56;refseq.start=3538692;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 3628534 . C T 200.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=217;Dels=0.00;HRun=0;HaplotypeScore=7.26;MQ=98.33;MQ0=0;OQ=8064.29;QD=37.16;RankSumP=1.00000;SB=-3764.34;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.372C>T;refseq.codingCoordStr_2=c.372C>T;refseq.codingCoordStr_3=c.372C>T;refseq.codingCoordStr_4=c.519C>T;refseq.codonCoord_1=124;refseq.codonCoord_2=124;refseq.codonCoord_3=124;refseq.codonCoord_4=173;refseq.end_1=3628534;refseq.end_2=3628534;refseq.end_3=3628534;refseq.end_4=3628534;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=606;refseq.mrnaCoord_2=606;refseq.mrnaCoord_3=606;refseq.mrnaCoord_4=629;refseq.name2_1=TP73;refseq.name2_2=TP73;refseq.name2_3=TP73;refseq.name2_4=TP73;refseq.name_1=NM_001126240;refseq.name_2=NM_001126241;refseq.name_3=NM_001126242;refseq.name_4=NM_005427;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T124T;refseq.proteinCoordStr_2=p.T124T;refseq.proteinCoordStr_3=p.T124T;refseq.proteinCoordStr_4=p.T173T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.spliceDist_1=90;refseq.spliceDist_2=90;refseq.spliceDist_3=90;refseq.spliceDist_4=90;refseq.start_1=3628534;refseq.start_2=3628534;refseq.start_3=3628534;refseq.start_4=3628534;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=ACT;refseq.variantCodon_4=ACT;set=Intersection GT 1/1
|
|
chr1 3659032 . C T 264.24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=418;Dels=0.00;HRun=0;HaplotypeScore=6.74;MQ=98.22;MQ0=0;OQ=7943.27;QD=19.00;RankSumP=0.114800;SB=-2293.81;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.127C>T;refseq.codonCoord=43;refseq.end=3659032;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=208;refseq.name=NM_152492;refseq.name2=CCDC27;refseq.positionType=CDS;refseq.proteinCoordStr=p.R43C;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-192;refseq.start=3659032;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 0/1
|
|
chr1 3659061 . A G 126.45 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=487;Dels=0.00;HRun=0;HaplotypeScore=14.13;MQ=98.10;MQ0=0;OQ=17183.11;QD=35.28;RankSumP=1.00000;SB=-7476.21;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.156A>G;refseq.codonCoord=52;refseq.end=3659061;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=237;refseq.name=NM_152492;refseq.name2=CCDC27;refseq.positionType=CDS;refseq.proteinCoordStr=p.P52P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-163;refseq.start=3659061;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 3659065 . C G 34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=493;Dels=0.00;HRun=0;HaplotypeScore=21.17;MQ=98.02;MQ0=0;OQ=22590.29;QD=45.82;RankSumP=1.00000;SB=-9634.98;SecondBestBaseQ=24;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.160C>G;refseq.codonCoord=54;refseq.end=3659065;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=241;refseq.name=NM_152492;refseq.name2=CCDC27;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q54E;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-159;refseq.start=3659065;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 3667793 . T C 355.71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1884.80;QD=36.96;RankSumP=1.00000;SB=-755.97;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.800T>C;refseq.codonCoord=267;refseq.end=3667793;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=881;refseq.name=NM_152492;refseq.name2=CCDC27;refseq.positionType=CDS;refseq.proteinCoordStr=p.M267T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-62;refseq.start=3667793;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 3669635 . C T 55.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=112.55;QD=12.51;RankSumP=0.0571429;SB=-77.07;SecondBestBaseQ=22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1058C>T;refseq.codonCoord=353;refseq.end=3669635;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1139;refseq.name=NM_152492;refseq.name2=CCDC27;refseq.positionType=CDS;refseq.proteinCoordStr=p.T353M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=104;refseq.start=3669635;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 3693570 . G A 102.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=2.89;MQ=99.00;MQ0=0;OQ=1916.61;QD=18.43;RankSumP=0.0619562;SB=-381.39;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.780C>T;refseq.codonCoord=260;refseq.end=3693570;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=808;refseq.name=NM_020710;refseq.name2=LRRC47;refseq.positionType=CDS;refseq.proteinCoordStr=p.V260V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=165;refseq.start=3693570;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/0
|
|
chr1 3742996 . A T 145.32 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=482;Dels=0.00;HRun=0;HaplotypeScore=11.61;MQ=98.53;MQ0=0;OQ=18280.65;QD=37.93;RankSumP=1.00000;SB=-8844.58;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1240T>A;refseq.codonCoord=414;refseq.end=3742996;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1599;refseq.name=NM_014704;refseq.name2=KIAA0562;refseq.positionType=CDS;refseq.proteinCoordStr=p.L414I;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=-78;refseq.start=3742996;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/1
|
|
chr1 3745535 . T C 299.39 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=388;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=98.86;MQ0=0;OQ=16588.12;QD=42.75;RankSumP=1.00000;SB=-4985.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.744A>G;refseq.codonCoord=248;refseq.end=3745535;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1103;refseq.name=NM_014704;refseq.name2=KIAA0562;refseq.positionType=CDS;refseq.proteinCoordStr=p.E248E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=9;refseq.spliceInfo=splice-acceptor_9;refseq.start=3745535;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 3751339 . C T 449.94 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=163;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=98.76;MQ0=0;OQ=6845.24;QD=42.00;RankSumP=1.00000;SB=-2435.80;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.558G>A;refseq.codonCoord=186;refseq.end=3751339;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=917;refseq.name=NM_014704;refseq.name2=KIAA0562;refseq.positionType=CDS;refseq.proteinCoordStr=p.T186T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=3751339;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 3790102 . A G 432.91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=99.00;MQ0=0;OQ=4434.70;QD=36.35;RankSumP=1.00000;SB=-1956.10;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.954A>G;refseq.codonCoord=318;refseq.end=3790102;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1277;refseq.name=NM_004402;refseq.name2=DFFB;refseq.positionType=CDS;refseq.proteinCoordStr=p.P318P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=172;refseq.start=3790102;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 3797453 . G C 114.36 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=157;Dels=0.00;HRun=1;HaplotypeScore=1.75;MQ=98.15;MQ0=0;OQ=7569.01;QD=48.21;RankSumP=1.00000;SB=-3729.38;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.158C>G;refseq.codonCoord=53;refseq.end=3797453;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=265;refseq.name=NM_207356;refseq.name2=C1orf174;refseq.positionType=CDS;refseq.proteinCoordStr=p.T53R;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=29;refseq.start=3797453;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 1/1
|
|
chr1 4671913 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=96.88;MQ0=0;OQ=191.76;QD=6.61;RankSumP=0.517302;SB=-105.97;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.123T>C;refseq.codingCoordStr_2=c.123T>C;refseq.codonCoord_1=41;refseq.codonCoord_2=41;refseq.end_1=4671913;refseq.end_2=4671913;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=504;refseq.mrnaCoord_2=504;refseq.name2_1=AJAP1;refseq.name2_2=AJAP1;refseq.name_1=NM_001042478;refseq.name_2=NM_018836;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C41C;refseq.proteinCoordStr_2=p.C41C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.start_1=4671913;refseq.start_2=4671913;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=Intersection GT 1/0
|
|
chr1 4672577 . G A 293.28 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=5.26;MQ=98.92;MQ0=0;OQ=6291.46;QD=41.39;RankSumP=1.00000;SB=-2174.75;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.787G>A;refseq.codingCoordStr_2=c.787G>A;refseq.codonCoord_1=263;refseq.codonCoord_2=263;refseq.end_1=4672577;refseq.end_2=4672577;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1168;refseq.mrnaCoord_2=1168;refseq.name2_1=AJAP1;refseq.name2_2=AJAP1;refseq.name_1=NM_001042478;refseq.name_2=NM_018836;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G263R;refseq.proteinCoordStr_2=p.G263R;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=-43;refseq.spliceDist_2=-43;refseq.start_1=4672577;refseq.start_2=4672577;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=Intersection GT 1/1
|
|
chr1 6081149 . A G 277.52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.74;MQ0=0;OQ=5649.23;QD=37.17;RankSumP=1.00000;SB=-2525.35;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1032A>G;refseq.codingCoordStr_2=c.990A>G;refseq.codonCoord_1=344;refseq.codonCoord_2=330;refseq.end_1=6081149;refseq.end_2=6081149;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1210;refseq.mrnaCoord_2=1168;refseq.name2_1=KCNAB2;refseq.name2_2=KCNAB2;refseq.name_1=NM_003636;refseq.name_2=NM_172130;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S344S;refseq.proteinCoordStr_2=p.S330S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=18;refseq.spliceDist_2=18;refseq.start_1=6081149;refseq.start_2=6081149;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;set=Intersection GT 1/1
|
|
chr1 6106679 . A G 234.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=3.06;MQ=96.50;MQ0=0;OQ=3368.72;QD=35.09;RankSumP=1.00000;SB=-1078.71;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4615T>C;refseq.codonCoord=1539;refseq.end=6106679;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4715;refseq.name=NM_015557;refseq.name2=CHD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1539P;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=76;refseq.start=6106679;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 6108496 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4088A>G;refseq.codonCoord=1363;refseq.end=6108496;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4188;refseq.name=NM_015557;refseq.name2=CHD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1363G;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=6108496;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 6119456 . A G 347.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.25;MQ0=0;OQ=2017.69;QD=36.03;RankSumP=1.00000;SB=-854.06;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2493T>C;refseq.codonCoord=831;refseq.end=6119456;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2593;refseq.name=NM_015557;refseq.name2=CHD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.I831I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=57;refseq.start=6119456;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 6131553 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=3;RankSumP=4.30255e-07;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1331A>C;refseq.codonCoord=444;refseq.end=6131553;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1431;refseq.name=NM_015557;refseq.name2=CHD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.N444T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-53;refseq.start=6131553;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 6131950 . T C 371.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=98.13;MQ0=0;OQ=4064.67;QD=37.29;RankSumP=1.00000;SB=-598.45;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1104A>G;refseq.codonCoord=368;refseq.end=6131950;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1204;refseq.name=NM_015557;refseq.name2=CHD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.V368V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-58;refseq.start=6131950;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 6133770 . G A 80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=156;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=98.32;MQ0=0;OQ=6027.96;QD=38.64;RankSumP=1.00000;SB=-2840.62;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.903C>T;refseq.codonCoord=301;refseq.end=6133770;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1003;refseq.name=NM_015557;refseq.name2=CHD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.F301F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=33;refseq.start=6133770;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/1
|
|
chr1 6138323 . C G 321.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=142;Dels=0.00;HRun=0;HaplotypeScore=9.73;MQ=98.66;MQ0=0;OQ=2863.17;QD=20.16;RankSumP=0.339134;SB=-1347.76;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.429G>C;refseq.codonCoord=143;refseq.end=6138323;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=529;refseq.name=NM_015557;refseq.name2=CHD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.L143L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=42;refseq.start=6138323;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/0
|
|
chr1 6191927 . A G 36.49 BadSOAPSNP;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=9.12;RankSumP=0.333333;SB=-10.00;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.564A>G;refseq.codonCoord=188;refseq.end=6191927;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=738;refseq.name=NM_207396;refseq.name2=RNF207;refseq.positionType=CDS;refseq.proteinCoordStr=p.A188A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=13;refseq.start=6191927;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=FilteredInAll GT 0/1
|
|
chr1 6195793 . C T 195.03 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=189;Dels=0.00;HRun=0;HaplotypeScore=10.64;MQ=98.35;MQ0=0;OQ=3136.08;QD=16.59;RankSumP=0.375582;SB=-1147.57;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1615C>T;refseq.codonCoord=539;refseq.end=6195793;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1789;refseq.name=NM_207396;refseq.name2=RNF207;refseq.positionType=CDS;refseq.proteinCoordStr=p.R539C;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-38;refseq.start=6195793;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 0/1
|
|
chr1 6201001 . A G 392.06 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.57;MQ0=0;OQ=3085.34;QD=36.73;RankSumP=1.00000;SB=-1306.79;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1718A>G;refseq.codonCoord=573;refseq.end=6201001;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1892;refseq.name=NM_207396;refseq.name2=RNF207;refseq.positionType=CDS;refseq.proteinCoordStr=p.N573S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-16;refseq.start=6201001;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 6201957 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.16;MQ=97.65;MQ0=0;OQ=653.17;QD=20.41;RankSumP=0.299276;SB=-191.63;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1808G>C;refseq.codonCoord=603;refseq.end=6201957;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1982;refseq.name=NM_207396;refseq.name2=RNF207;refseq.positionType=CDS;refseq.proteinCoordStr=p.G603A;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=75;refseq.start=6201957;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 6227981 . G A 3 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=18;HRun=0;RankSumP=0.333333;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.388G>A;refseq.codonCoord=130;refseq.end=6227981;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=453;refseq.name=NM_001024598;refseq.name2=HES3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A130T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=225;refseq.start=6227981;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 6423361 . T C 4 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=0;RankSumP=0.321429;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.764T>C;refseq.codonCoord=255;refseq.end=6423361;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=932;refseq.name=NM_031475;refseq.name2=ESPN;refseq.positionType=CDS;refseq.proteinCoordStr=p.V255A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=89;refseq.start=6423361;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=FilteredInAll GT 1/0
|
|
chr1 6423672 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=6.34531e-08;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.950A>C;refseq.codonCoord=317;refseq.end=6423672;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1118;refseq.name=NM_031475;refseq.name2=ESPN;refseq.positionType=CDS;refseq.proteinCoordStr=p.H317P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-41;refseq.start=6423672;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 6427287 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1150T>C;refseq.codonCoord=384;refseq.end=6427287;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1318;refseq.name=NM_031475;refseq.name2=ESPN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S384P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-43;refseq.start=6427287;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 6427290 . T C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=20;DP=218;Dels=0.00;HRun=2;HaplotypeScore=17.33;MQ=60.37;MQ0=6;OQ=110.09;QD=0.50;RankSumP=0.00000;SB=278.95;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1153T>C;refseq.codonCoord=385;refseq.end=6427290;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1321;refseq.name=NM_031475;refseq.name2=ESPN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S385P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-40;refseq.start=6427290;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 6453232 . T C 26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=8;HRun=2;RankSumP=0.639155;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.1769A>G;refseq.codingCoordStr_2=c.1601A>G;refseq.codingCoordStr_3=c.1601A>G;refseq.codingCoordStr_4=c.1601A>G;refseq.codingCoordStr_5=c.1832A>G;refseq.codonCoord_1=590;refseq.codonCoord_2=534;refseq.codonCoord_3=534;refseq.codonCoord_4=534;refseq.codonCoord_5=611;refseq.end_1=6453232;refseq.end_2=6453232;refseq.end_3=6453232;refseq.end_4=6453232;refseq.end_5=6453232;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=1870;refseq.mrnaCoord_2=1824;refseq.mrnaCoord_3=1807;refseq.mrnaCoord_4=1752;refseq.mrnaCoord_5=2330;refseq.name2_1=PLEKHG5;refseq.name2_2=PLEKHG5;refseq.name2_3=PLEKHG5;refseq.name2_4=PLEKHG5;refseq.name2_5=PLEKHG5;refseq.name_1=NM_001042663;refseq.name_2=NM_001042664;refseq.name_3=NM_001042665;refseq.name_4=NM_020631;refseq.name_5=NM_198681;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.E590G;refseq.proteinCoordStr_2=p.E534G;refseq.proteinCoordStr_3=p.E534G;refseq.proteinCoordStr_4=p.E534G;refseq.proteinCoordStr_5=p.E611G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceAA_4=Glu;refseq.referenceAA_5=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.referenceCodon_4=GAG;refseq.referenceCodon_5=GAG;refseq.spliceDist_1=59;refseq.spliceDist_2=59;refseq.spliceDist_3=59;refseq.spliceDist_4=59;refseq.spliceDist_5=59;refseq.start_1=6453232;refseq.start_2=6453232;refseq.start_3=6453232;refseq.start_4=6453232;refseq.start_5=6453232;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantAA_5=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;refseq.variantCodon_5=GGG;set=soap GT 1/0
|
|
chr1 6536978 . A C 9.27 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=5;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=123.82;QD=24.76;RankSumP=1.00000;SB=-88.01;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.172T>G;refseq.codonCoord=58;refseq.end=6536978;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=268;refseq.name=NM_024654;refseq.name2=NOL9;refseq.positionType=CDS;refseq.proteinCoordStr=p.S58A;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-225;refseq.start=6536978;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=filterInsoap-gatk GT 1/1
|
|
chr1 6537002 rs6693400 A G 42.83 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=21.42;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.148T>C;refseq.codonCoord=50;refseq.end=6537002;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=244;refseq.name=NM_024654;refseq.name2=NOL9;refseq.positionType=CDS;refseq.proteinCoordStr=p.W50R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=244;refseq.start=6537002;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:0,2:2:-7.69,-0.60,-0.00:6.02
|
|
chr1 6537122 . G A 183.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=20;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=5.37;MQ=97.82;MQ0=0;OQ=1356.94;QD=23.00;RankSumP=1.00000;SB=-456.52;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.28C>T;refseq.codonCoord=10;refseq.end=6537122;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=124;refseq.name=NM_024654;refseq.name2=NOL9;refseq.positionType=CDS;refseq.proteinCoordStr=p.R10W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=124;refseq.start=6537122;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/1
|
|
chr1 6557818 . A G 296 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.87;MQ0=0;OQ=3425.79;QD=39.38;RankSumP=1.00000;SB=-1165.81;SecondBestBaseQ=2;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.1039A>G;refseq.codingCoordStr_4=c.1039A>G;refseq.codonCoord_3=347;refseq.codonCoord_4=347;refseq.end_1=6559051;refseq.end_2=6559051;refseq.end_3=6557818;refseq.end_4=6557818;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_3=1039;refseq.mrnaCoord_4=1039;refseq.name2_1=TAS1R1;refseq.name2_2=TAS1R1;refseq.name2_3=TAS1R1;refseq.name2_4=TAS1R1;refseq.name_1=NM_177540;refseq.name_2=NM_177541;refseq.name_3=NM_138697;refseq.name_4=NM_177539;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_3=p.K347E;refseq.proteinCoordStr_4=p.K347E;refseq.referenceAA_3=Lys;refseq.referenceAA_4=Lys;refseq.referenceCodon_3=AAG;refseq.referenceCodon_4=AAG;refseq.spliceDist_3=-222;refseq.spliceDist_4=-222;refseq.start_1=6553873;refseq.start_2=6553873;refseq.start_3=6557818;refseq.start_4=6557818;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_3=Glu;refseq.variantAA_4=Glu;refseq.variantCodon_3=GAG;refseq.variantCodon_4=GAG;set=Intersection GT 1/1
|
|
chr1 6561571 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_2=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.1866C>T;refseq.codingCoordStr_3=c.*89C>T;refseq.codingCoordStr_4=c.1104C>T;refseq.codonCoord_2=622;refseq.codonCoord_4=368;refseq.end_1=6561932;refseq.end_2=6561571;refseq.end_3=6561571;refseq.end_4=6561571;refseq.frame_2=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=true;refseq.mrnaCoord_2=1866;refseq.mrnaCoord_3=1532;refseq.mrnaCoord_4=1104;refseq.name2_1=TAS1R1;refseq.name2_2=TAS1R1;refseq.name2_3=TAS1R1;refseq.name2_4=TAS1R1;refseq.name_1=NM_177541;refseq.name_2=NM_138697;refseq.name_3=NM_177539;refseq.name_4=NM_177540;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=utr3;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.F622F;refseq.proteinCoordStr_4=p.F368F;refseq.referenceAA_2=Phe;refseq.referenceAA_4=Phe;refseq.referenceCodon_2=TTC;refseq.referenceCodon_4=TTC;refseq.spliceDist_2=272;refseq.spliceDist_3=272;refseq.spliceDist_4=272;refseq.start_1=6559728;refseq.start_2=6561571;refseq.start_3=6561571;refseq.start_4=6561571;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Phe;refseq.variantAA_4=Phe;refseq.variantCodon_2=TTT;refseq.variantCodon_4=TTT;set=FilteredInAll GT 0/1
|
|
chr1 6563935 . G A 63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=159.75;QD=6.95;RankSumP=0.617546;SB=-54.97;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.679G>A;refseq.codonCoord=227;refseq.end=6563935;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=882;refseq.name=NM_005341;refseq.name2=ZBTB48;refseq.positionType=CDS;refseq.proteinCoordStr=p.G227S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-12;refseq.start=6563935;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=soap-filterIngatk GT 1/0
|
|
chr1 6582092 . G A 159.71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=97.76;MQ0=0;OQ=1525.15;QD=16.23;RankSumP=0.279349;SB=-719.63;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1029C>T;refseq.codonCoord=343;refseq.end=6582092;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1081;refseq.name=NM_014851;refseq.name2=KLHL21;refseq.positionType=CDS;refseq.proteinCoordStr=p.S343S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=6582092;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/0
|
|
chr1 6627222 . A G 268.35 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=249;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.73;MQ0=0;OQ=9501.73;QD=38.16;RankSumP=1.00000;SB=-4392.11;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1080T>C;refseq.codonCoord=360;refseq.end=6627222;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1186;refseq.name=NM_018198;refseq.name2=DNAJC11;refseq.positionType=CDS;refseq.proteinCoordStr=p.G360G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-18;refseq.start=6627222;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 6628462 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.868A>C;refseq.codonCoord=290;refseq.end=6628462;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=974;refseq.name=NM_018198;refseq.name2=DNAJC11;refseq.positionType=CDS;refseq.proteinCoordStr=p.T290P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-27;refseq.start=6628462;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 7646351 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1157T>G;refseq.codonCoord=386;refseq.end=7646351;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1364;refseq.name=NM_015215;refseq.name2=CAMTA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V386G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=352;refseq.start=7646351;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 7646544 . G A 222.71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=306;Dels=0.00;HRun=0;HaplotypeScore=14.03;MQ=98.58;MQ0=0;OQ=5652.55;QD=18.47;RankSumP=0.198017;SB=-2285.85;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1350G>A;refseq.codonCoord=450;refseq.end=7646544;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1557;refseq.name=NM_015215;refseq.name2=CAMTA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S450S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=545;refseq.start=7646544;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/0
|
|
chr1 7792635 . T C 173.10 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=470;Dels=0.00;HRun=0;HaplotypeScore=13.49;MQ=98.52;MQ0=0;OQ=16020.80;QD=34.09;RankSumP=1.00000;SB=-4813.09;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1335T>C;refseq.codonCoord=445;refseq.end=7792635;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1510;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.S445S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-34;refseq.start=7792635;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 7809226 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2033T>G;refseq.codonCoord=678;refseq.end=7809226;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2208;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V678G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=100;refseq.start=7809226;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 7809835 . G A 58.26 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.81;MQ=97.69;MQ0=0;OQ=1909.75;QD=28.94;RankSumP=1.00000;SB=-759.02;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2235G>A;refseq.codonCoord=745;refseq.end=7809835;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2410;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P745P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=71;refseq.start=7809835;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 7810011 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=4;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2411T>C;refseq.codonCoord=804;refseq.end=7810011;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2586;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L804P;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=247;refseq.start=7810011;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 7810080 . T C 264.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=318;Dels=0.00;HRun=1;HaplotypeScore=6.82;MQ=98.45;MQ0=0;OQ=11617.47;QD=36.53;RankSumP=1.00000;SB=-2944.67;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2480T>C;refseq.codonCoord=827;refseq.end=7810080;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2655;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L827P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=316;refseq.start=7810080;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 7812528 . C T 270.80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=470;Dels=0.00;HRun=0;HaplotypeScore=6.63;MQ=96.65;MQ0=0;OQ=18747.60;QD=39.89;RankSumP=1.00000;SB=-7202.27;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2907C>T;refseq.codonCoord=969;refseq.end=7812528;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3082;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T969T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=45;refseq.start=7812528;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 7812611 . T G 27 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.0457059;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2990T>G;refseq.codonCoord=997;refseq.end=7812611;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3165;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.M997R;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=128;refseq.start=7812611;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=soap GT 1/0
|
|
chr1 7812613 . A G 68 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.0315822;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2992A>G;refseq.codonCoord=998;refseq.end=7812613;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3167;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.K998E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=130;refseq.start=7812613;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=soap GT 0/1
|
|
chr1 7812640 . G A 26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.426684;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3019G>A;refseq.codonCoord=1007;refseq.end=7812640;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3194;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1007T;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=157;refseq.start=7812640;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=soap GT 1/0
|
|
chr1 7812642 . T A 41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=0;RankSumP=0.477476;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3021T>A;refseq.codonCoord=1007;refseq.end=7812642;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3196;refseq.name=NM_016831;refseq.name2=PER3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1007A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=159;refseq.start=7812642;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=soap GT 1/0
|
|
chr1 7836017 . G A 282.14 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=338;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=98.71;MQ0=0;OQ=14254.42;QD=42.17;RankSumP=1.00000;SB=-5480.57;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.62C>T;refseq.codonCoord=21;refseq.end=7836017;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=122;refseq.name=NM_021995;refseq.name2=UTS2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T21M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-64;refseq.start=7836017;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/1
|
|
chr1 7922617 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.25G>T;refseq.codonCoord=9;refseq.end=7922617;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=153;refseq.name=NM_001561;refseq.name2=TNFRSF9;refseq.positionType=CDS;refseq.proteinCoordStr=p.V9L;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-76;refseq.start=7922617;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=FilteredInAll GT 1/0
|
|
chr1 8312971 . G C 223.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=97.83;MQ0=0;OQ=2191.79;QD=19.06;RankSumP=0.352093;SB=-991.40;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.831G>C;refseq.codonCoord=277;refseq.end=8312971;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=831;refseq.name=NM_001080397;refseq.name2=SLC45A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L277L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=116;refseq.start=8312971;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 0/1
|
|
chr1 8313082 . A G 106.50 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.62;MQ0=0;OQ=1003.30;QD=32.36;RankSumP=1.00000;SB=-342.13;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.942A>G;refseq.codonCoord=314;refseq.end=8313082;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=942;refseq.name=NM_001080397;refseq.name2=SLC45A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P314P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=227;refseq.start=8313082;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 8318147 . G T 133.30 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=117;Dels=0.00;HRun=0;HaplotypeScore=7.94;MQ=98.26;MQ0=0;OQ=1583.26;QD=13.53;RankSumP=0.136484;SB=-307.72;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1507G>T;refseq.codonCoord=503;refseq.end=8318147;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1507;refseq.name=NM_001080397;refseq.name2=SLC45A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A503S;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=64;refseq.start=8318147;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 0/1
|
|
chr1 8341231 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=99.00;MQ0=0;OQ=315.85;QD=9.02;RankSumP=0.506590;SB=-175.16;SecondBestBaseQ=26;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.3951G>T;refseq.codingCoordStr_2=c.2289G>T;refseq.codingCoordStr_3=c.3951G>T;refseq.codonCoord_1=1317;refseq.codonCoord_2=763;refseq.codonCoord_3=1317;refseq.end_1=8341231;refseq.end_2=8341231;refseq.end_3=8341231;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=4576;refseq.mrnaCoord_2=2875;refseq.mrnaCoord_3=4761;refseq.name2_1=RERE;refseq.name2_2=RERE;refseq.name2_3=RERE;refseq.name_1=NM_001042681;refseq.name_2=NM_001042682;refseq.name_3=NM_012102;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R1317R;refseq.proteinCoordStr_2=p.R763R;refseq.proteinCoordStr_3=p.R1317R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.referenceCodon_3=CGG;refseq.spliceDist_1=333;refseq.spliceDist_2=333;refseq.spliceDist_3=333;refseq.start_1=8341231;refseq.start_2=8341231;refseq.start_3=8341231;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;refseq.variantCodon_3=CGT;set=Intersection GT 1/0
|
|
chr1 8341237 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.73;MQ=99.00;MQ0=0;OQ=382.38;QD=9.80;RankSumP=0.178167;SB=-205.63;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.3945A>G;refseq.codingCoordStr_2=c.2283A>G;refseq.codingCoordStr_3=c.3945A>G;refseq.codonCoord_1=1315;refseq.codonCoord_2=761;refseq.codonCoord_3=1315;refseq.end_1=8341237;refseq.end_2=8341237;refseq.end_3=8341237;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=4570;refseq.mrnaCoord_2=2869;refseq.mrnaCoord_3=4755;refseq.name2_1=RERE;refseq.name2_2=RERE;refseq.name2_3=RERE;refseq.name_1=NM_001042681;refseq.name_2=NM_001042682;refseq.name_3=NM_012102;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R1315R;refseq.proteinCoordStr_2=p.R761R;refseq.proteinCoordStr_3=p.R1315R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.referenceCodon_3=CGA;refseq.spliceDist_1=327;refseq.spliceDist_2=327;refseq.spliceDist_3=327;refseq.start_1=8341237;refseq.start_2=8341237;refseq.start_3=8341237;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;set=Intersection GT 1/0
|
|
chr1 8348487 . T C 149.14 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=3.47;MQ=99.00;MQ0=0;OQ=1669.45;QD=13.04;RankSumP=0.0780778;SB=-548.76;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1419A>G;refseq.codingCoordStr_2=c.-244A>G;refseq.codingCoordStr_3=c.1419A>G;refseq.codonCoord_1=473;refseq.codonCoord_3=473;refseq.end_1=8348487;refseq.end_2=8348487;refseq.end_3=8348487;refseq.frame_1=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2044;refseq.mrnaCoord_2=343;refseq.mrnaCoord_3=2229;refseq.name2_1=RERE;refseq.name2_2=RERE;refseq.name2_3=RERE;refseq.name_1=NM_001042681;refseq.name_2=NM_001042682;refseq.name_3=NM_012102;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=utr5;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.T473T;refseq.proteinCoordStr_3=p.T473T;refseq.referenceAA_1=Thr;refseq.referenceAA_3=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_3=ACA;refseq.spliceDist_1=-29;refseq.spliceDist_2=-29;refseq.spliceDist_3=-29;refseq.start_1=8348487;refseq.start_2=8348487;refseq.start_3=8348487;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_3=ACG;set=Intersection GT 1/0
|
|
chr1 8638883 . G A 5 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.206213;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.61C>T;refseq.codingCoordStr_2=c.61C>T;refseq.codonCoord_1=21;refseq.codonCoord_2=21;refseq.end_1=8638883;refseq.end_2=8638883;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=686;refseq.mrnaCoord_2=871;refseq.name2_1=RERE;refseq.name2_2=RERE;refseq.name_1=NM_001042681;refseq.name_2=NM_012102;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R21*;refseq.proteinCoordStr_2=p.R21*;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.spliceDist_1=205;refseq.spliceDist_2=205;refseq.start_1=8638883;refseq.start_2=8638883;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantCodon_1=TGA;refseq.variantCodon_2=TGA;set=FilteredInAll GT 1/0
|
|
chr1 8931993 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=98.80;MQ0=0;OQ=1241.57;QD=10.80;RankSumP=0.325768;SB=-545.26;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.164C>T;refseq.codonCoord=55;refseq.end=8931993;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=188;refseq.name=NM_001215;refseq.name2=CA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.T55M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=85;refseq.start=8931993;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 8932031 . A C 140.14 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=4.31;MQ=98.88;MQ0=0;OQ=2146.28;QD=12.55;RankSumP=0.280833;SB=-664.48;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.202A>C;refseq.codonCoord=68;refseq.end=8932031;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=226;refseq.name=NM_001215;refseq.name2=CA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.M68L;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-58;refseq.start=8932031;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 0/1
|
|
chr1 8985978 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=3;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1507A>C;refseq.codonCoord=503;refseq.end=8985978;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1507;refseq.name=NM_207420;refseq.name2=SLC2A7;refseq.positionType=CDS;refseq.proteinCoordStr=p.T503P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-33;refseq.start=8985978;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 8987425 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=65;Dels=0.00;HRun=1;HaplotypeScore=3.22;MQ=98.86;MQ0=0;OQ=610.44;QD=9.39;RankSumP=0.695078;SB=-215.42;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1293C>T;refseq.codonCoord=431;refseq.end=8987425;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1293;refseq.name=NM_207420;refseq.name2=SLC2A7;refseq.positionType=CDS;refseq.proteinCoordStr=p.I431I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-28;refseq.start=8987425;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 9088272 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=157;Dels=0.00;HRun=0;HaplotypeScore=6.77;MQ=98.36;MQ0=0;OQ=3051.96;QD=19.44;RankSumP=0.0275394;SB=-1423.49;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.652C>T;refseq.codonCoord=218;refseq.end=9088272;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=795;refseq.name=NM_024980;refseq.name2=GPR157;refseq.positionType=CDS;refseq.proteinCoordStr=p.R218C;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=55;refseq.start=9088272;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 1/0
|
|
chr1 9228032 . A C 176.61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=248;Dels=0.00;HRun=1;HaplotypeScore=4.27;MQ=98.57;MQ0=0;OQ=4987.31;QD=20.11;RankSumP=0.481493;SB=-1651.32;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.452A>C;refseq.codonCoord=151;refseq.end=9228032;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=725;refseq.name=NM_004285;refseq.name2=H6PD;refseq.positionType=CDS;refseq.proteinCoordStr=p.D151A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-176;refseq.start=9228032;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 9229620 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=638;Dels=0.00;HRun=0;HaplotypeScore=22.04;MQ=98.42;MQ0=0;OQ=11771.97;QD=18.45;RankSumP=0.496064;SB=-4681.19;SecondBestBaseQ=23;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.636G>A;refseq.codonCoord=212;refseq.end=9229620;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=909;refseq.name=NM_004285;refseq.name2=H6PD;refseq.positionType=CDS;refseq.proteinCoordStr=p.A212A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=9;refseq.spliceInfo=splice-acceptor_9;refseq.start=9229620;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 9229725 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=234;Dels=0.00;HRun=1;HaplotypeScore=17.08;MQ=98.54;MQ0=0;OQ=2493.18;QD=10.65;RankSumP=0.231987;SB=-1167.14;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.741T>C;refseq.codonCoord=247;refseq.end=9229725;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1014;refseq.name=NM_004285;refseq.name2=H6PD;refseq.positionType=CDS;refseq.proteinCoordStr=p.A247A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-5;refseq.spliceInfo=splice-donor_-5;refseq.start=9229725;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/0
|
|
chr1 9246497 . G A 173.08 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=150;Dels=0.00;HRun=0;HaplotypeScore=13.18;MQ=98.77;MQ0=0;OQ=2117.39;QD=14.12;RankSumP=0.397194;SB=-1019.44;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1358G>A;refseq.codonCoord=453;refseq.end=9246497;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1631;refseq.name=NM_004285;refseq.name2=H6PD;refseq.positionType=CDS;refseq.proteinCoordStr=p.R453Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=343;refseq.start=9246497;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 9246800 . C T 80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=99.00;MQ0=0;OQ=201.09;QD=9.58;RankSumP=0.0394466;SB=-76.27;SecondBestBaseQ=23;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1661C>T;refseq.codonCoord=554;refseq.end=9246800;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1934;refseq.name=NM_004285;refseq.name2=H6PD;refseq.positionType=CDS;refseq.proteinCoordStr=p.P554L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=646;refseq.start=9246800;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 0/1
|
|
chr1 9247158 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=201;Dels=0.00;HRun=0;HaplotypeScore=9.59;MQ=98.11;MQ0=0;OQ=2441.87;QD=12.15;RankSumP=0.282694;SB=-634.63;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2019T>C;refseq.codonCoord=673;refseq.end=9247158;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2292;refseq.name=NM_004285;refseq.name2=H6PD;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y673Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=1004;refseq.start=9247158;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/0
|
|
chr1 9247257 . A G 102.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=97.56;MQ0=0;OQ=620.21;QD=16.76;RankSumP=0.493482;SB=-164.69;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2118A>G;refseq.codonCoord=706;refseq.end=9247257;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2391;refseq.name=NM_004285;refseq.name2=H6PD;refseq.positionType=CDS;refseq.proteinCoordStr=p.S706S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=1103;refseq.start=9247257;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 0/1
|
|
chr1 9701445 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1127A>G;refseq.codonCoord=376;refseq.end=9701445;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1335;refseq.name=NM_005026;refseq.name2=PIK3CD;refseq.positionType=CDS;refseq.proteinCoordStr=p.E376G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=107;refseq.start=9701445;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 9718625 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=184;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=99.03;MQ0=0;OQ=3984.49;QD=21.65;RankSumP=0.366058;SB=-1690.32;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1639G>A;refseq.codingCoordStr_2=c.1609G>A;refseq.codonCoord_1=547;refseq.codonCoord_2=537;refseq.end_1=9718625;refseq.end_2=9718625;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2398;refseq.mrnaCoord_2=2368;refseq.name2_1=CLSTN1;refseq.name2_2=CLSTN1;refseq.name_1=NM_001009566;refseq.name_2=NM_014944;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G547R;refseq.proteinCoordStr_2=p.G537R;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=63;refseq.spliceDist_2=63;refseq.start_1=9718625;refseq.start_2=9718625;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=Intersection GT 0/1
|
|
chr1 10241239 . C G 109.19 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=204;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.88;MQ0=0;OQ=5059.89;QD=24.80;RankSumP=0.316268;SB=-1158.15;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.285C>G;refseq.codingCoordStr_2=c.285C>G;refseq.codonCoord_1=95;refseq.codonCoord_2=95;refseq.end_1=10241239;refseq.end_2=10241239;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=537;refseq.name2_1=KIF1B;refseq.name2_2=KIF1B;refseq.name_1=NM_015074;refseq.name_2=NM_183416;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A95A;refseq.proteinCoordStr_2=p.A95A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=-79;refseq.spliceDist_2=-79;refseq.start_1=10241239;refseq.start_2=10241239;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/0
|
|
chr1 10287199 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.3369A>C;refseq.codonCoord_2=1123;refseq.end_1=10302677;refseq.end_2=10287199;refseq.frame_2=2;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=3621;refseq.name2_1=KIF1B;refseq.name2_2=KIF1B;refseq.name_1=NM_015074;refseq.name_2=NM_183416;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.K1123N;refseq.referenceAA_2=Lys;refseq.referenceCodon_2=AAA;refseq.spliceDist_2=1392;refseq.start_1=10279902;refseq.start_2=10287199;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Asn;refseq.variantCodon_2=AAC;set=FilteredInAll GT 0/1
|
|
chr1 10357911 . C A 364.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=358;Dels=0.00;HRun=0;HaplotypeScore=5.69;MQ=98.94;MQ0=0;OQ=7074.49;QD=19.76;RankSumP=0.329394;SB=-2183.47;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5163C>A;refseq.codonCoord=1721;refseq.end=10357911;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5415;refseq.name=NM_015074;refseq.name2=KIF1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1721T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=12;refseq.start=10357911;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 10383072 . T C 108.23 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=414;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=85.82;MQ0=37;OQ=6587.61;QD=15.91;RankSumP=0.353726;SB=-2641.79;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.120T>C;refseq.codonCoord=40;refseq.end=10383072;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=210;refseq.name=NM_002631;refseq.name2=PGD;refseq.positionType=CDS;refseq.proteinCoordStr=p.D40D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=36;refseq.start=10383072;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/0
|
|
chr1 10395757 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.706A>C;refseq.codonCoord=236;refseq.end=10395757;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=796;refseq.name=NM_002631;refseq.name2=PGD;refseq.positionType=CDS;refseq.proteinCoordStr=p.T236P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=52;refseq.start=10395757;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 0/1
|
|
chr1 10395783 . C T 265.81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=271;Dels=0.00;HRun=0;HaplotypeScore=6.22;MQ=97.00;MQ0=3;OQ=4963.60;QD=18.32;RankSumP=0.339314;SB=-1791.56;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.732C>T;refseq.codonCoord=244;refseq.end=10395783;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=822;refseq.name=NM_002631;refseq.name2=PGD;refseq.positionType=CDS;refseq.proteinCoordStr=p.D244D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=78;refseq.start=10395783;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 10434176 . T C 167.10 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=99.00;MQ0=0;OQ=2547.66;QD=33.97;RankSumP=1.00000;SB=-1138.13;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.405T>C;refseq.codingCoordStr_2=c.432T>C;refseq.codonCoord_1=135;refseq.codonCoord_2=144;refseq.end_1=10434176;refseq.end_2=10434176;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=565;refseq.mrnaCoord_2=848;refseq.name2_1=CORT;refseq.name2_2=APITD1;refseq.name_1=NM_001302;refseq.name_2=NM_198544;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S135S;refseq.proteinCoordStr_2=p.S144S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCT;refseq.referenceCodon_2=TCT;refseq.spliceDist_1=156;refseq.spliceDist_2=156;refseq.start_1=10434176;refseq.start_2=10434176;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=Intersection GT 1/1
|
|
chr1 10445772 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.713C>G;refseq.codingCoordStr_2=c.713C>G;refseq.codonCoord_1=238;refseq.codonCoord_2=238;refseq.end_1=10445772;refseq.end_2=10445772;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=811;refseq.mrnaCoord_2=811;refseq.name2_1=DFFA;refseq.name2_2=DFFA;refseq.name_1=NM_004401;refseq.name_2=NM_213566;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A238G;refseq.proteinCoordStr_2=p.A238G;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=-71;refseq.spliceDist_2=82;refseq.start_1=10445772;refseq.start_2=10445772;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 10518928 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=106;Dels=0.00;HRun=2;HaplotypeScore=3.14;MQ=98.61;MQ0=0;OQ=1511.65;QD=14.26;RankSumP=0.340405;SB=-375.76;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.156C>T;refseq.codonCoord=52;refseq.end=10518928;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=177;refseq.name=NM_004565;refseq.name2=PEX14;refseq.positionType=CDS;refseq.proteinCoordStr=p.F52F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-14;refseq.start=10518928;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 0/1
|
|
chr1 10627612 . C G 23 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=1.25862e-06;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3817G>C;refseq.codonCoord=1273;refseq.end=10627612;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4137;refseq.name=NM_001079843;refseq.name2=CASZ1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1273P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-52;refseq.start=10627612;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 10627697 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.48;MQ=98.14;MQ0=0;OQ=664.19;QD=9.63;RankSumP=0.392793;SB=-147.56;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3732C>T;refseq.codonCoord=1244;refseq.end=10627697;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4052;refseq.name=NM_001079843;refseq.name2=CASZ1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C1244C;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=36;refseq.start=10627697;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/0
|
|
chr1 10630729 . A G 17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=14;DB;DP=13;Dels=0.00;HRun=2;HaplotypeScore=3.70;MQ=99.00;MQ0=0;OQ=107.49;QD=8.27;RankSumP=0.100000;SB=-6.99;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3213T>C;refseq.codingCoordStr_2=c.3213T>C;refseq.codonCoord_1=1071;refseq.codonCoord_2=1071;refseq.end_1=10630729;refseq.end_2=10630729;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3533;refseq.mrnaCoord_2=3533;refseq.name2_1=CASZ1;refseq.name2_2=CASZ1;refseq.name_1=NM_001079843;refseq.name_2=NM_017766;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F1071F;refseq.proteinCoordStr_2=p.F1071F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.spliceDist_1=55;refseq.spliceDist_2=55;refseq.start_1=10630729;refseq.start_2=10630729;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;set=filterInsoap-gatk GT 0/1
|
|
chr1 10636352 . T C 124.89 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=96.91;MQ0=0;OQ=919.45;QD=32.84;RankSumP=1.00000;SB=-193.67;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2349A>G;refseq.codingCoordStr_2=c.2349A>G;refseq.codonCoord_1=783;refseq.codonCoord_2=783;refseq.end_1=10636352;refseq.end_2=10636352;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2669;refseq.mrnaCoord_2=2669;refseq.name2_1=CASZ1;refseq.name2_2=CASZ1;refseq.name_1=NM_001079843;refseq.name_2=NM_017766;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S783S;refseq.proteinCoordStr_2=p.S783S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=-332;refseq.spliceDist_2=-332;refseq.start_1=10636352;refseq.start_2=10636352;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;set=Intersection GT 1/1
|
|
chr1 10641199 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1362A>C;refseq.codingCoordStr_2=c.1362A>C;refseq.codonCoord_1=454;refseq.codonCoord_2=454;refseq.end_1=10641199;refseq.end_2=10641199;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1682;refseq.mrnaCoord_2=1682;refseq.name2_1=CASZ1;refseq.name2_2=CASZ1;refseq.name_1=NM_001079843;refseq.name_2=NM_017766;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K454N;refseq.proteinCoordStr_2=p.K454N;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.start_1=10641199;refseq.start_2=10641199;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=FilteredInAll GT 1/0
|
|
chr1 10648085 . G A 211.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.06;MQ=98.32;MQ0=0;OQ=888.36;QD=15.86;RankSumP=0.393004;SB=-406.15;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.147C>T;refseq.codingCoordStr_2=c.147C>T;refseq.codonCoord_1=49;refseq.codonCoord_2=49;refseq.end_1=10648085;refseq.end_2=10648085;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=467;refseq.mrnaCoord_2=467;refseq.name2_1=CASZ1;refseq.name2_2=CASZ1;refseq.name_1=NM_001079843;refseq.name_2=NM_017766;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D49D;refseq.proteinCoordStr_2=p.D49D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=131;refseq.spliceDist_2=131;refseq.start_1=10648085;refseq.start_2=10648085;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 1/0
|
|
chr1 11010111 . G A 90 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=637;Dels=0.00;HRun=0;HaplotypeScore=30.25;MQ=98.94;MQ0=0;OQ=26737.74;QD=41.97;RankSumP=1.00000;SB=-12640.25;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1479C>T;refseq.codonCoord=493;refseq.end=11010111;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1500;refseq.name=NM_006610;refseq.name2=MASP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S493S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=182;refseq.start=11010111;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 11013503 . C A 285.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=243;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=98.48;MQ0=0;OQ=9091.35;QD=37.41;RankSumP=1.00000;SB=-3750.76;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1111G>T;refseq.codonCoord=371;refseq.end=11013503;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1132;refseq.name=NM_006610;refseq.name2=MASP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D371Y;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=24;refseq.start=11013503;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 11041903 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.254A>C;refseq.codonCoord=85;refseq.end=11041903;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=345;refseq.name=NM_003132;refseq.name2=SRM;refseq.positionType=CDS;refseq.proteinCoordStr=p.N85T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-35;refseq.start=11041903;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 11042486 . T C 156.67 PASS AC=2;AF=1.00;AN=2;BestBaseQ=18;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=7.30;MQ=92.92;MQ0=0;OQ=922.59;QD=18.09;RankSumP=1.00000;SB=-45.69;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.102A>G;refseq.codonCoord=34;refseq.end=11042486;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=193;refseq.name=NM_003132;refseq.name2=SRM;refseq.positionType=CDS;refseq.proteinCoordStr=p.S34S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-66;refseq.start=11042486;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/1
|
|
chr1 11054804 . G A 176.29 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=381;Dels=0.00;HRun=1;HaplotypeScore=7.47;MQ=98.69;MQ0=0;OQ=15695.04;QD=41.19;RankSumP=1.00000;SB=-4573.23;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2169C>T;refseq.codingCoordStr_2=c.2094C>T;refseq.codonCoord_1=723;refseq.codonCoord_2=698;refseq.end_1=11054804;refseq.end_2=11054804;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2219;refseq.mrnaCoord_2=2144;refseq.name2_1=EXOSC10;refseq.name2_2=EXOSC10;refseq.name_1=NM_001001998;refseq.name_2=NM_002685;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R723R;refseq.proteinCoordStr_2=p.R698R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.start_1=11054804;refseq.start_2=11054804;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=Intersection GT 1/1
|
|
chr1 11063774 . C G 70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=148;Dels=0.00;HRun=2;HaplotypeScore=12.48;MQ=98.57;MQ0=0;OQ=6027.65;QD=40.73;RankSumP=1.00000;SB=-1902.74;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1389G>C;refseq.codingCoordStr_2=c.1389G>C;refseq.codonCoord_1=463;refseq.codonCoord_2=463;refseq.end_1=11063774;refseq.end_2=11063774;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1439;refseq.mrnaCoord_2=1439;refseq.name2_1=EXOSC10;refseq.name2_2=EXOSC10;refseq.name_1=NM_001001998;refseq.name_2=NM_002685;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P463P;refseq.proteinCoordStr_2=p.P463P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=-49;refseq.spliceDist_2=-49;refseq.start_1=11063774;refseq.start_2=11063774;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=Intersection GT 1/1
|
|
chr1 11090823 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.chr=chr1;refseq.codingCoordStr=c.7634+2;refseq.end=11090823;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=false;refseq.name=NM_004958;refseq.name2=MTOR;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=11090823;refseq.transcriptStrand=-;set=FilteredInAll GT 0/1
|
|
chr1 11127645 . C T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=518;Dels=0.00;HRun=1;HaplotypeScore=6.82;MQ=98.68;MQ0=0;OQ=21863.85;QD=42.21;RankSumP=1.00000;SB=-10618.77;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4731G>A;refseq.codonCoord=1577;refseq.end=11127645;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4852;refseq.name=NM_004958;refseq.name2=MTOR;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1577A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-34;refseq.start=11127645;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 11181930 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=4;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4225A>C;refseq.codonCoord=1409;refseq.end=11181930;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4346;refseq.name=NM_004958;refseq.name2=MTOR;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1409P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-29;refseq.start=11181930;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 11211345 . G A 309.14 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=4.48;MQ=98.73;MQ0=0;OQ=4857.52;QD=40.48;RankSumP=1.00000;SB=-1314.20;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2997C>T;refseq.codonCoord=999;refseq.end=11211345;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3118;refseq.name=NM_004958;refseq.name2=MTOR;refseq.positionType=CDS;refseq.proteinCoordStr=p.N999N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-34;refseq.start=11211345;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/1
|
|
chr1 11224301 . A G 341 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1456.37;QD=37.34;RankSumP=1.00000;SB=-480.46;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1437T>C;refseq.codonCoord=479;refseq.end=11224301;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1558;refseq.name=NM_004958;refseq.name2=MTOR;refseq.positionType=CDS;refseq.proteinCoordStr=p.D479D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=25;refseq.start=11224301;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 11239610 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.471T>G;refseq.codonCoord=157;refseq.end=11239610;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=592;refseq.name=NM_004958;refseq.name2=MTOR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G157G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-34;refseq.start=11239610;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 11484180 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=97.42;MQ0=0;OQ=354.81;QD=10.75;RankSumP=0.223942;SB=-134.08;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.544G>A;refseq.codonCoord=182;refseq.end=11484180;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=682;refseq.name=NM_020780;refseq.name2=PTCHD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G182S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=547;refseq.start=11484180;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/0
|
|
chr1 11502057 . G A 431.85 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.52;MQ0=0;OQ=3107.23;QD=37.89;RankSumP=1.00000;SB=-1256.66;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1948G>A;refseq.codonCoord=650;refseq.end=11502057;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2086;refseq.name=NM_020780;refseq.name2=PTCHD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A650T;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=59;refseq.start=11502057;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 11651481 . G A 199.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=132;Dels=0.00;HRun=1;HaplotypeScore=4.97;MQ=85.50;MQ0=1;OQ=2018.16;QD=15.29;RankSumP=0.303565;SB=-859.89;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.179G>A;refseq.codonCoord=60;refseq.end=11651481;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=345;refseq.name=NM_018438;refseq.name2=FBXO6;refseq.positionType=CDS;refseq.proteinCoordStr=p.R60Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-108;refseq.start=11651481;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 11659517 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.307A>C;refseq.codingCoordStr_2=c.307A>C;refseq.codonCoord_1=103;refseq.codonCoord_2=103;refseq.end_1=11659517;refseq.end_2=11659517;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=528;refseq.mrnaCoord_2=495;refseq.name2_1=MAD2L2;refseq.name2_2=MAD2L2;refseq.name_1=NM_001127325;refseq.name_2=NM_006341;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T103P;refseq.proteinCoordStr_2=p.T103P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-26;refseq.spliceDist_2=-26;refseq.start_1=11659517;refseq.start_2=11659517;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 11692058 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.591A>C;refseq.codonCoord=197;refseq.end=11692058;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=731;refseq.name=NM_198545;refseq.name2=C1orf187;refseq.positionType=CDS;refseq.proteinCoordStr=p.A197A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-52;refseq.start=11692058;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 11694575 . A G 213.52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=129;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=98.82;MQ0=0;OQ=2041.21;QD=15.82;RankSumP=0.256857;SB=-666.88;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.723A>G;refseq.codonCoord=241;refseq.end=11694575;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=863;refseq.name=NM_198545;refseq.name2=C1orf187;refseq.positionType=CDS;refseq.proteinCoordStr=p.L241L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=-35;refseq.start=11694575;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 11777044 . G A 86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=442;Dels=0.00;HRun=2;HaplotypeScore=9.05;MQ=98.81;MQ0=0;OQ=18840.73;QD=42.63;RankSumP=1.00000;SB=-9377.11;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1305C>T;refseq.codonCoord=435;refseq.end=11777044;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1534;refseq.name=NM_005957;refseq.name2=MTHFR;refseq.positionType=CDS;refseq.proteinCoordStr=p.F435F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-43;refseq.start=11777044;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/1
|
|
chr1 11777063 . T G 194.11 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=404;Dels=0.00;HRun=0;HaplotypeScore=15.24;MQ=98.76;MQ0=0;OQ=9030.42;QD=22.35;RankSumP=0.340334;SB=-3893.93;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1286A>C;refseq.codonCoord=429;refseq.end=11777063;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1515;refseq.name=NM_005957;refseq.name2=MTHFR;refseq.positionType=CDS;refseq.proteinCoordStr=p.E429A;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-62;refseq.start=11777063;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 11777483 . G A 176.94 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=930.59;QD=15.01;RankSumP=0.135750;SB=-481.45;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1056C>T;refseq.codonCoord=352;refseq.end=11777483;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1285;refseq.name=NM_005957;refseq.name2=MTHFR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S352S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=25;refseq.start=11777483;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/0
|
|
chr1 11778965 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=10.92;MQ=98.29;MQ0=0;OQ=1179.99;QD=11.68;RankSumP=0.0973272;SB=-591.31;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.665C>T;refseq.codonCoord=222;refseq.end=11778965;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=894;refseq.name=NM_005957;refseq.name2=MTHFR;refseq.positionType=CDS;refseq.proteinCoordStr=p.A222V;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=79;refseq.start=11778965;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 11779042 . A C 34 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.500023;SecondBestBaseQ=11;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.588T>G;refseq.codonCoord=196;refseq.end=11779042;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=817;refseq.name=NM_005957;refseq.name2=MTHFR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G196G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=11779042;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=soap GT 0/1
|
|
chr1 11785644 . G A 218.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=13.62;MQ=98.31;MQ0=0;OQ=2161.23;QD=19.30;RankSumP=0.359644;SB=-772.61;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.117C>T;refseq.codonCoord=39;refseq.end=11785644;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=346;refseq.name=NM_005957;refseq.name2=MTHFR;refseq.positionType=CDS;refseq.proteinCoordStr=p.P39P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-120;refseq.start=11785644;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/0
|
|
chr1 11807142 . A G 63 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=98.81;MQ0=0;OQ=1011.20;QD=32.62;RankSumP=1.00000;SB=-500.50;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.593A>G;refseq.codingCoordStr_2=c.593A>G;refseq.codingCoordStr_3=c.593A>G;refseq.codingCoordStr_4=c.593A>G;refseq.codonCoord_1=198;refseq.codonCoord_2=198;refseq.codonCoord_3=198;refseq.codonCoord_4=198;refseq.end_1=11807142;refseq.end_2=11807142;refseq.end_3=11807142;refseq.end_4=11807142;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=706;refseq.mrnaCoord_2=706;refseq.mrnaCoord_3=706;refseq.mrnaCoord_4=706;refseq.name2_1=CLCN6;refseq.name2_2=CLCN6;refseq.name2_3=CLCN6;refseq.name2_4=CLCN6;refseq.name_1=NM_001286;refseq.name_2=NM_021735;refseq.name_3=NM_021736;refseq.name_4=NM_021737;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.E198G;refseq.proteinCoordStr_2=p.E198G;refseq.proteinCoordStr_3=p.E198G;refseq.proteinCoordStr_4=p.E198G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceAA_4=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.referenceCodon_4=GAG;refseq.spliceDist_1=13;refseq.spliceDist_2=13;refseq.spliceDist_3=13;refseq.spliceDist_4=13;refseq.start_1=11807142;refseq.start_2=11807142;refseq.start_3=11807142;refseq.start_4=11807142;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;set=Intersection GT 1/1
|
|
chr1 11937499 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.605A>C;refseq.codonCoord=202;refseq.end=11937499;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=696;refseq.name=NM_000302;refseq.name2=PLOD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H202P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=26;refseq.start=11937499;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 11937502 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.608G>C;refseq.codonCoord=203;refseq.end=11937502;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=699;refseq.name=NM_000302;refseq.name2=PLOD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R203P;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=29;refseq.start=11937502;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 11986764 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1287+2;refseq.codingCoordStr_2=c.1287+2;refseq.end_1=11986764;refseq.end_2=11986764;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.name2_1=MFN2;refseq.name2_2=MFN2;refseq.name_1=NM_001127660;refseq.name_2=NM_014874;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-donor_2;refseq.spliceInfo_2=splice-donor_2;refseq.start_1=11986764;refseq.start_2=11986764;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;set=FilteredInAll GT 1/0
|
|
chr1 12005513 . A G 404.08 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.85;MQ0=0;OQ=2627.31;QD=41.05;RankSumP=1.00000;SB=-934.70;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.499A>G;refseq.codonCoord=167;refseq.end=12005513;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=679;refseq.name=NM_021933;refseq.name2=MIIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.K167E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=37;refseq.start=12005513;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 12046263 . G A 14 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=50.14;QD=25.07;RankSumP=0.666667;SB=-49.56;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.21G>A;refseq.codonCoord=7;refseq.end=12046263;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=243;refseq.name=NM_001243;refseq.name2=TNFRSF8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A7A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-43;refseq.start=12046263;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=filterInsoap-gatk GT 1/0
|
|
chr1 12067139 . A C 27 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=4;RankSumP=0.500000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.95A>C;refseq.codonCoord=32;refseq.end=12067139;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=317;refseq.name=NM_001243;refseq.name2=TNFRSF8;refseq.positionType=CDS;refseq.proteinCoordStr=p.N32T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=32;refseq.start=12067139;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap GT 0/1
|
|
chr1 12098316 . C T 436.21 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=396;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=98.83;MQ0=0;OQ=16111.86;QD=40.69;RankSumP=1.00000;SB=-3212.07;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.889C>T;refseq.codonCoord=297;refseq.end=12098316;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1111;refseq.name=NM_001243;refseq.name2=TNFRSF8;refseq.positionType=CDS;refseq.proteinCoordStr=p.R297C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-58;refseq.start=12098316;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/1
|
|
chr1 12120884 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=4.44;MQ=96.21;MQ0=0;OQ=745.73;QD=12.43;RankSumP=0.200217;SB=-186.61;SecondBestBaseQ=26;refseq.changesAA_1=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1347T>C;refseq.codingCoordStr_2=c.-43T>C;refseq.codonCoord_1=449;refseq.end_1=12120884;refseq.end_2=12120884;refseq.frame_1=2;refseq.functionalClass_1=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.mrnaCoord_1=1569;refseq.mrnaCoord_2=244;refseq.name2_1=TNFRSF8;refseq.name2_2=TNFRSF8;refseq.name_1=NM_001243;refseq.name_2=NM_152942;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=utr5;refseq.proteinCoordStr_1=p.S449S;refseq.referenceAA_1=Ser;refseq.referenceCodon_1=AGT;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.start_1=12120884;refseq.start_2=12120884;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantCodon_1=AGC;set=Intersection GT 1/0
|
|
chr1 12171529 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=6.25;MQ=98.38;MQ0=0;OQ=563.14;QD=6.19;RankSumP=0.455539;SB=-181.52;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.168A>G;refseq.codonCoord=56;refseq.end=12171529;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=257;refseq.name=NM_001066;refseq.name2=TNFRSF1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.K56K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-11;refseq.start=12171529;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 0/1
|
|
chr1 12175542 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=187;Dels=0.00;HRun=2;HaplotypeScore=5.15;MQ=98.40;MQ0=0;OQ=2015.62;QD=10.78;RankSumP=0.0282041;SB=-677.39;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.587T>G;refseq.codonCoord=196;refseq.end=12175542;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=676;refseq.name=NM_001066;refseq.name2=TNFRSF1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.M196R;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=36;refseq.start=12175542;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 1/0
|
|
chr1 12239689 . T G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=475;Dels=0.00;HRun=2;HaplotypeScore=32.66;MQ=98.45;MQ0=0;OQ=70.18;QD=0.15;RankSumP=0.00000;SB=802.60;SecondBestBaseQ=16;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.899T>G;refseq.codingCoordStr_2=c.899T>G;refseq.codonCoord_1=300;refseq.codonCoord_2=300;refseq.end_1=12239689;refseq.end_2=12239689;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1040;refseq.mrnaCoord_2=1040;refseq.name2_1=VPS13D;refseq.name2_2=VPS13D;refseq.name_1=NM_015378;refseq.name_2=NM_018156;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V300G;refseq.proteinCoordStr_2=p.V300G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-43;refseq.spliceDist_2=-43;refseq.start_1=12239689;refseq.start_2=12239689;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 12259991 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3759C>A;refseq.codingCoordStr_2=c.3759C>A;refseq.codonCoord_1=1253;refseq.codonCoord_2=1253;refseq.end_1=12259991;refseq.end_2=12259991;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3900;refseq.mrnaCoord_2=3900;refseq.name2_1=VPS13D;refseq.name2_2=VPS13D;refseq.name_1=NM_015378;refseq.name_2=NM_018156;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y1253*;refseq.proteinCoordStr_2=p.Y1253*;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-692;refseq.spliceDist_2=-692;refseq.start_1=12259991;refseq.start_2=12259991;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantCodon_1=TAA;refseq.variantCodon_2=TAA;set=FilteredInAll GT 1/0
|
|
chr1 12324455 . A C 59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=282;Dels=0.00;HRun=2;HaplotypeScore=5.63;MQ=98.44;MQ0=0;OQ=10676.91;QD=37.86;RankSumP=1.00000;SB=-3474.46;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.8658A>C;refseq.codingCoordStr_2=c.8583A>C;refseq.codonCoord_1=2886;refseq.codonCoord_2=2861;refseq.end_1=12324455;refseq.end_2=12324455;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=8799;refseq.mrnaCoord_2=8724;refseq.name2_1=VPS13D;refseq.name2_2=VPS13D;refseq.name_1=NM_015378;refseq.name_2=NM_018156;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P2886P;refseq.proteinCoordStr_2=p.P2861P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.start_1=12324455;refseq.start_2=12324455;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=Intersection GT 1/1
|
|
chr1 12561551 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=121;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=98.02;MQ0=0;OQ=1442.84;QD=11.92;RankSumP=0.0445705;SB=-625.54;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.480A>G;refseq.codonCoord=160;refseq.end=12561551;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=947;refseq.name=NM_004753;refseq.name2=DHRS3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P160P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=21;refseq.start=12561551;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/0
|
|
chr1 12698931 . A T 113.09 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=359;Dels=0.00;HRun=1;HaplotypeScore=9.51;MQ=98.69;MQ0=0;OQ=14443.69;QD=40.23;RankSumP=1.00000;SB=-7046.90;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1A>T;refseq.codingCoordStr_2=c.-7A>T;refseq.codonCoord_1=1;refseq.end_1=12698931;refseq.end_2=12698931;refseq.frame_1=0;refseq.functionalClass_1=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.mrnaCoord_1=227;refseq.mrnaCoord_2=227;refseq.name2_1=AADACL3;refseq.name2_2=AADACL3;refseq.name_1=NM_001103169;refseq.name_2=NM_001103170;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=utr5;refseq.proteinCoordStr_1=p.M1L;refseq.referenceAA_1=Met;refseq.referenceCodon_1=ATG;refseq.spliceDist_1=-4;refseq.spliceDist_2=-4;refseq.spliceInfo_1=splice-donor_-4;refseq.spliceInfo_2=splice-donor_-4;refseq.start_1=12698931;refseq.start_2=12698931;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.uorfChange_2=-1;refseq.variantAA_1=Leu;refseq.variantCodon_1=TTG;set=Intersection GT 1/1
|
|
chr1 12702147 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=162;Dels=0.00;HRun=3;HaplotypeScore=5.00;MQ=98.35;MQ0=0;OQ=2579.34;QD=15.92;RankSumP=0.0424003;SB=-1039.46;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.81T>C;refseq.codonCoord_2=27;refseq.end_1=12703461;refseq.end_2=12702147;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=314;refseq.name2_1=AADACL3;refseq.name2_2=AADACL3;refseq.name_1=NM_001103169;refseq.name_2=NM_001103170;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.D27D;refseq.referenceAA_2=Asp;refseq.referenceCodon_2=GAT;refseq.spliceDist_2=84;refseq.start_1=12698945;refseq.start_2=12702147;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Asp;refseq.variantCodon_2=GAC;set=Intersection GT 1/0
|
|
chr1 12702205 . T C 124.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=326;Dels=0.00;HRun=2;HaplotypeScore=8.54;MQ=98.44;MQ0=0;OQ=5384.35;QD=16.52;RankSumP=0.0302761;SB=-1970.76;SecondBestBaseQ=32;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.139T>C;refseq.codonCoord_2=47;refseq.end_1=12703461;refseq.end_2=12702205;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=372;refseq.name2_1=AADACL3;refseq.name2_2=AADACL3;refseq.name_1=NM_001103169;refseq.name_2=NM_001103170;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S47P;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCC;refseq.spliceDist_2=-76;refseq.start_1=12698945;refseq.start_2=12702205;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCC;set=Intersection GT 1/0
|
|
chr1 12728989 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.24A>C;refseq.codonCoord=8;refseq.end=12728989;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=240;refseq.name=NM_152290;refseq.name2=C1orf158;refseq.positionType=CDS;refseq.proteinCoordStr=p.P8P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-88;refseq.start=12728989;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 12775990 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.357776;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.27A>C;refseq.codonCoord=9;refseq.end=12775990;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=130;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L9L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=52;refseq.start=12775990;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=soap GT 0/1
|
|
chr1 12776096 . A C 4 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.517244;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.133A>C;refseq.codonCoord=45;refseq.end=12776096;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=236;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S45R;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-155;refseq.start=12776096;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=FilteredInAll GT 0/1
|
|
chr1 12776131 . T G 61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.683137;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.168T>G;refseq.codonCoord=56;refseq.end=12776131;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=271;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V56V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-120;refseq.start=12776131;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=soap GT 1/0
|
|
chr1 12776655 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=1073;Dels=0.00;HRun=0;HaplotypeScore=17.14;MQ=41.10;MQ0=249;OQ=6160.66;QD=5.74;RankSumP=0.424929;SB=-1103.86;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.292T>C;refseq.codonCoord=98;refseq.end=12776655;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=395;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.W98R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=5;refseq.spliceInfo=splice-acceptor_5;refseq.start=12776655;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/0
|
|
chr1 12776677 . T A 0.01 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1423;Dels=0.00;HRun=0;HaplotypeScore=27.14;MQ=40.70;MQ0=180;OQ=9834.77;QD=6.91;SB=-2401.36;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.314T>A;refseq.codonCoord=105;refseq.end=12776677;refseq.frame=1;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=417;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L105*;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=27;refseq.start=12776677;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TAG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1163,258:1152:-982.48,-346.88,-3698.94:99
|
|
chr1 12776684 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1495;Dels=0.00;HRun=0;HaplotypeScore=35.76;MQ=40.34;MQ0=161;OQ=9845.03;QD=6.59;SB=-2558.63;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.321T>C;refseq.codonCoord=107;refseq.end=12776684;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=424;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D107D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=34;refseq.start=12776684;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1215,278:1240:-983.50,-373.42,-4227.45:99
|
|
chr1 12776692 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1536;Dels=0.00;HRun=1;HaplotypeScore=26.71;MQ=40.20;MQ0=131;OQ=10930.90;QD=7.12;SB=-2920.72;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.329A>G;refseq.codonCoord=110;refseq.end=12776692;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=432;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E110G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=42;refseq.start=12776692;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1252,284:1321:-1092.09,-397.76,-4714.49:99
|
|
chr1 12776749 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=1156;Dels=0.00;HRun=0;HaplotypeScore=31.93;MQ=30.86;MQ0=235;OQ=2901.73;QD=2.51;RankSumP=0.477501;SB=608.99;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.386C>T;refseq.codonCoord=129;refseq.end=12776749;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=489;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T129M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=99;refseq.start=12776749;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=soap-filterIngatk GT 0/1
|
|
chr1 12776775 . T C 52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1184;Dels=0.00;HRun=1;HaplotypeScore=23.42;MQ=22.06;MQ0=617;OQ=908.02;QD=0.77;RankSumP=0.346154;SB=379.03;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.412T>C;refseq.codonCoord=138;refseq.end=12776775;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=515;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C138R;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=125;refseq.start=12776775;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=soap-filterIngatk GT 1/0
|
|
chr1 12776943 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.320625;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.580T>C;refseq.codonCoord=194;refseq.end=12776943;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=683;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y194H;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-287;refseq.start=12776943;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap GT 1/0
|
|
chr1 12776988 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.491653;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.625G>C;refseq.codonCoord=209;refseq.end=12776988;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=728;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E209Q;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-242;refseq.start=12776988;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap GT 0/1
|
|
chr1 12777001 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1564;Dels=0.00;HRun=0;HaplotypeScore=27.09;MQ=36.61;MQ0=579;OQ=9030.07;QD=5.77;RankSumP=0.450890;SB=-3123.39;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.638G>A;refseq.codonCoord=213;refseq.end=12777001;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=741;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R213H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-229;refseq.start=12777001;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 1/0
|
|
chr1 12777061 . A C 96 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1448;Dels=0.00;HRun=0;HaplotypeScore=38.53;MQ=48.78;MQ0=817;OQ=629.53;QD=0.43;RankSumP=0.240827;SB=-135.92;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.698A>C;refseq.codonCoord=233;refseq.end=12777061;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=801;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N233T;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-169;refseq.start=12777061;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=soap-filterIngatk GT 0/1
|
|
chr1 12777066 rs1063775 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=1339;Dels=0.00;HRun=1;HaplotypeScore=37.18;MQ=51.38;MQ0=734;OQ=534.56;QD=0.40;SB=-250.54;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.703C>G;refseq.codonCoord=235;refseq.end=12777066;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=806;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R235G;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-164;refseq.start=12777066;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1058,280:560:-225.41,-168.67,-2409.03:99
|
|
chr1 12778234 . C T 15 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=0;RankSumP=0.649725;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.927C>T;refseq.codonCoord=309;refseq.end=12778234;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1030;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D309D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=61;refseq.start=12778234;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 0/1
|
|
chr1 12778235 . A G 15 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=0;RankSumP=0.692582;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.928A>G;refseq.codonCoord=310;refseq.end=12778235;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1031;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M310V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=62;refseq.start=12778235;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT 0/1
|
|
chr1 12778422 . C G 80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=315;Dels=0.00;HRun=1;HaplotypeScore=6.92;MQ=17.39;MQ0=235;OQ=2348.56;QD=7.46;RankSumP=1.00000;SB=-461.31;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1115C>G;refseq.codonCoord=372;refseq.end=12778422;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1218;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A372G;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=249;refseq.start=12778422;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 12778432 . G C 97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=274;Dels=0.00;HRun=0;HaplotypeScore=3.62;MQ=18.59;MQ0=200;OQ=2485.51;QD=9.07;RankSumP=1.00000;SB=-696.02;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1125G>C;refseq.codonCoord=375;refseq.end=12778432;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1228;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R375R;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=259;refseq.start=12778432;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/1
|
|
chr1 12778597 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1658;Dels=0.00;HRun=0;HaplotypeScore=32.04;MQ=15.84;MQ0=1034;OQ=16239.50;QD=9.79;RankSumP=0.478295;SB=-5512.14;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1290C>G;refseq.codonCoord=430;refseq.end=12778597;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1393;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F430L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-214;refseq.start=12778597;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=soap-filterIngatk GT 1/0
|
|
chr1 12778666 . C T 61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.381342;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1359C>T;refseq.codonCoord=453;refseq.end=12778666;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1462;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G453G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-145;refseq.start=12778666;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap GT 0/1
|
|
chr1 12778698 . C T 84 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=1077;Dels=0.00;HRun=0;HaplotypeScore=23.41;MQ=12.29;MQ0=797;OQ=3991.71;QD=3.71;RankSumP=1.00000;SB=-1375.76;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1391C>T;refseq.codonCoord=464;refseq.end=12778698;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1494;refseq.name=NM_023013;refseq.name2=PRAMEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P464L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-113;refseq.start=12778698;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 12829862 . G C 8611.57 ESPStandard;SnpCluster AC=1;AF=0.50;AN=2;DP=1220;Dels=0.00;HRun=0;HaplotypeScore=423.79;MQ=68.52;MQ0=93;QD=7.06;SB=290.95;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.868C>G;refseq.codingCoordStr_2=c.868C>G;refseq.codonCoord_1=290;refseq.codonCoord_2=290;refseq.end_1=12829862;refseq.end_2=12829862;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1094;refseq.mrnaCoord_2=963;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q290E;refseq.proteinCoordStr_2=p.Q290E;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-15;refseq.spliceDist_2=-40;refseq.start_1=12829862;refseq.start_2=12829862;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1015,205:1041:-860.16,-313.47,-4347.41:99
|
|
chr1 12829869 . G C 12060.83 SnpCluster AC=1;AF=0.50;AN=2;DP=1295;Dels=0.00;HRun=0;HaplotypeScore=450.21;MQ=69.68;MQ0=102;QD=9.31;SB=-2796.50;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.861C>G;refseq.codingCoordStr_2=c.861C>G;refseq.codonCoord_1=287;refseq.codonCoord_2=287;refseq.end_1=12829869;refseq.end_2=12829869;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1087;refseq.mrnaCoord_2=956;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T287T;refseq.proteinCoordStr_2=p.T287T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-22;refseq.spliceDist_2=-47;refseq.start_1=12829869;refseq.start_2=12829869;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1005,288:1098:-1205.08,-330.63,-4301.46:99
|
|
chr1 12829871 . T C 19873.22 SnpCluster AC=1;AF=0.50;AN=2;DP=1323;Dels=0.00;HRun=0;HaplotypeScore=470.22;MQ=69.87;MQ0=109;QD=15.02;SB=-3744.21;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.859A>G;refseq.codingCoordStr_2=c.859A>G;refseq.codonCoord_1=287;refseq.codonCoord_2=287;refseq.end_1=12829871;refseq.end_2=12829871;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1085;refseq.mrnaCoord_2=954;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T287A;refseq.proteinCoordStr_2=p.T287A;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-24;refseq.spliceDist_2=-49;refseq.start_1=12829871;refseq.start_2=12829871;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:773,550:1126:-1986.32,-339.08,-2702.53:99
|
|
chr1 12829872 . G C 12614.21 SnpCluster AC=1;AF=0.50;AN=2;DP=1325;Dels=0.00;HRun=1;HaplotypeScore=470.73;MQ=70.09;MQ0=107;QD=9.52;SB=-3488.02;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.858C>G;refseq.codingCoordStr_2=c.858C>G;refseq.codonCoord_1=286;refseq.codonCoord_2=286;refseq.end_1=12829872;refseq.end_2=12829872;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1084;refseq.mrnaCoord_2=953;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S286R;refseq.proteinCoordStr_2=p.S286R;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=-25;refseq.spliceDist_2=-50;refseq.start_1=12829872;refseq.start_2=12829872;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1033,292:1119:-1260.42,-337.00,-4235.66:99
|
|
chr1 12829903 . T C 0.57 PASS AC=1;AF=0.50;AN=2;DP=1624;Dels=0.00;HRun=2;HaplotypeScore=10.99;MQ=76.55;MQ0=78;OQ=9795.76;QD=6.03;SB=-1211.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.827A>G;refseq.codingCoordStr_2=c.827A>G;refseq.codonCoord_1=276;refseq.codonCoord_2=276;refseq.end_1=12829903;refseq.end_2=12829903;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1053;refseq.mrnaCoord_2=922;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E276G;refseq.proteinCoordStr_2=p.E276G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-56;refseq.spliceDist_2=-81;refseq.start_1=12829903;refseq.start_2=12829903;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=gatk GT:AD:DP:GL:GQ 0/1:1379,244:1360:-978.58,-409.64,-4744.51:99
|
|
chr1 12829937 rs2359486 C T 7691.21 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=1428;Dels=0.00;HRun=1;HaplotypeScore=399.25;MQ=83.23;MQ0=58;QD=5.39;SB=-569.09;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.793G>A;refseq.codingCoordStr_2=c.793G>A;refseq.codonCoord_1=265;refseq.codonCoord_2=265;refseq.end_1=12829937;refseq.end_2=12829937;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1019;refseq.mrnaCoord_2=888;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D265N;refseq.proteinCoordStr_2=p.D265N;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-90;refseq.spliceDist_2=-115;refseq.start_1=12829937;refseq.start_2=12829937;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1242,185:1148:-768.12,-345.65,-4154.82:99
|
|
chr1 12829938 rs2359485 A G 7097.65 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=1420;Dels=0.00;HRun=0;HaplotypeScore=387.89;MQ=83.28;MQ0=55;QD=5.00;SB=-602.02;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.792T>C;refseq.codingCoordStr_2=c.792T>C;refseq.codonCoord_1=264;refseq.codonCoord_2=264;refseq.end_1=12829938;refseq.end_2=12829938;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1018;refseq.mrnaCoord_2=887;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D264D;refseq.proteinCoordStr_2=p.D264D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=-91;refseq.spliceDist_2=-116;refseq.start_1=12829938;refseq.start_2=12829938;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1237,182:1144:-708.77,-344.52,-4101.04:99
|
|
chr1 12829945 . T C 14187 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=1373;Dels=0.00;HRun=5;HaplotypeScore=337.02;MQ=83.54;MQ0=29;QD=10.33;RankSumP=0.0849102;SB=-3297.44;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.785A>G;refseq.codingCoordStr_2=c.785A>G;refseq.codonCoord_1=262;refseq.codonCoord_2=262;refseq.end_1=12829945;refseq.end_2=12829945;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1011;refseq.mrnaCoord_2=880;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q262R;refseq.proteinCoordStr_2=p.Q262R;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-98;refseq.spliceDist_2=-123;refseq.start_1=12829945;refseq.start_2=12829945;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;set=soap-filterIngatk GT 1/0
|
|
chr1 12829957 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1132;Dels=0.00;HRun=0;HaplotypeScore=109.26;MQ=82.85;MQ0=9;OQ=12685.65;QD=11.21;RankSumP=0.0336072;SB=-1710.64;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.773T>A;refseq.codingCoordStr_2=c.773T>A;refseq.codonCoord_1=258;refseq.codonCoord_2=258;refseq.end_1=12829957;refseq.end_2=12829957;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=999;refseq.mrnaCoord_2=868;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V258D;refseq.proteinCoordStr_2=p.V258D;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=-110;refseq.spliceDist_2=-135;refseq.start_1=12829957;refseq.start_2=12829957;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=soap-filterIngatk GT 0/1
|
|
chr1 12829972 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=897;Dels=0.00;HRun=0;HaplotypeScore=105.51;MQ=78.59;MQ0=11;OQ=8362.35;QD=9.32;SB=-613.64;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.758C>T;refseq.codingCoordStr_2=c.758C>T;refseq.codonCoord_1=253;refseq.codonCoord_2=253;refseq.end_1=12829972;refseq.end_2=12829972;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=984;refseq.mrnaCoord_2=853;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P253L;refseq.proteinCoordStr_2=p.P253L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=-125;refseq.spliceDist_2=-150;refseq.start_1=12829972;refseq.start_2=12829972;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:567,329:732:-835.23,-220.41,-2240.35:99
|
|
chr1 12829995 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=651;Dels=0.00;HRun=0;HaplotypeScore=39.77;MQ=67.94;MQ0=16;OQ=982.57;QD=1.51;SB=772.53;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.735A>T;refseq.codingCoordStr_2=c.735A>T;refseq.codonCoord_1=245;refseq.codonCoord_2=245;refseq.end_1=12829995;refseq.end_2=12829995;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=961;refseq.mrnaCoord_2=830;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E245D;refseq.proteinCoordStr_2=p.E245D;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=-148;refseq.spliceDist_2=-173;refseq.start_1=12829995;refseq.start_2=12829995;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:566,83:597:-281.32,-179.78,-2143.22:99
|
|
chr1 12830364 rs1737104 T C 0.01 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=225;Dels=0.00;HRun=2;HaplotypeScore=2.56;MQ=69.88;MQ0=14;OQ=929.50;QD=4.13;SB=324.10;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.366A>G;refseq.codingCoordStr_2=c.366A>G;refseq.codonCoord_1=122;refseq.codonCoord_2=122;refseq.end_1=12830364;refseq.end_2=12830364;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=592;refseq.mrnaCoord_2=461;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G122G;refseq.proteinCoordStr_2=p.G122G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=-517;refseq.spliceDist_2=461;refseq.start_1=12830364;refseq.start_2=12830364;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:178,47:200:-156.47,-60.23,-676.77:99
|
|
chr1 12830368 rs1737105 T C 0.05 PASS AC=1;AF=0.50;AN=2;DB;DP=215;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=66.21;MQ0=15;OQ=1271.07;QD=5.91;SB=278.95;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.362A>G;refseq.codingCoordStr_2=c.362A>G;refseq.codonCoord_1=121;refseq.codonCoord_2=121;refseq.end_1=12830368;refseq.end_2=12830368;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=588;refseq.mrnaCoord_2=457;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D121G;refseq.proteinCoordStr_2=p.D121G;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=-521;refseq.spliceDist_2=457;refseq.start_1=12830368;refseq.start_2=12830368;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=gatk GT:AD:DP:GL:GQ 0/1:161,54:189:-187.31,-56.92,-596.84:99
|
|
chr1 12830385 . A C 2546.90 ESPStandard;SnpCluster AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=0;HaplotypeScore=23.53;MQ=60.10;MQ0=4;QD=11.32;SB=87.72;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.345T>G;refseq.codingCoordStr_2=c.345T>G;refseq.codonCoord_1=115;refseq.codonCoord_2=115;refseq.end_1=12830385;refseq.end_2=12830385;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=571;refseq.mrnaCoord_2=440;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F115L;refseq.proteinCoordStr_2=p.F115L;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.spliceDist_1=526;refseq.spliceDist_2=440;refseq.start_1=12830385;refseq.start_2=12830385;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=TTG;refseq.variantCodon_2=TTG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:133,92:196:-316.99,-59.02,-473.61:99
|
|
chr1 12830389 . C T 3923.41 SnpCluster AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=0;HaplotypeScore=26.54;MQ=59.52;MQ0=3;QD=16.91;SB=-120.58;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.341G>A;refseq.codingCoordStr_2=c.341G>A;refseq.codonCoord_1=114;refseq.codonCoord_2=114;refseq.end_1=12830389;refseq.end_2=12830389;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=567;refseq.mrnaCoord_2=436;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G114D;refseq.proteinCoordStr_2=p.G114D;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=522;refseq.spliceDist_2=436;refseq.start_1=12830389;refseq.start_2=12830389;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:132,100:214:-391.34,-64.44,-491.71:99
|
|
chr1 12830390 . C T 4141.55 SnpCluster AC=1;AF=0.50;AN=2;DP=237;Dels=0.00;HRun=0;HaplotypeScore=26.54;MQ=59.02;MQ0=3;QD=17.47;SB=-95.60;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.340G>A;refseq.codingCoordStr_2=c.340G>A;refseq.codonCoord_1=114;refseq.codonCoord_2=114;refseq.end_1=12830390;refseq.end_2=12830390;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=566;refseq.mrnaCoord_2=435;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G114S;refseq.proteinCoordStr_2=p.G114S;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=521;refseq.spliceDist_2=435;refseq.start_1=12830390;refseq.start_2=12830390;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:133,104:217:-413.15,-65.35,-489.79:99
|
|
chr1 12830424 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=437;Dels=0.00;HRun=0;HaplotypeScore=6.63;MQ=65.65;MQ0=3;OQ=11961.16;QD=27.37;RankSumP=0.484447;SB=-2665.52;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.306G>A;refseq.codingCoordStr_2=c.306G>A;refseq.codonCoord_1=102;refseq.codonCoord_2=102;refseq.end_1=12830424;refseq.end_2=12830424;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=532;refseq.mrnaCoord_2=401;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A102A;refseq.proteinCoordStr_2=p.A102A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=487;refseq.spliceDist_2=401;refseq.start_1=12830424;refseq.start_2=12830424;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 0/1
|
|
chr1 12830472 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=685;Dels=0.00;HRun=1;HaplotypeScore=11.84;MQ=60.52;MQ0=11;OQ=6762.73;QD=9.87;RankSumP=0.495582;SB=-2141.82;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.258A>G;refseq.codingCoordStr_2=c.258A>G;refseq.codonCoord_1=86;refseq.codonCoord_2=86;refseq.end_1=12830472;refseq.end_2=12830472;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=484;refseq.mrnaCoord_2=353;refseq.name2_1=HNRNPCL1;refseq.name2_2=LOC649330;refseq.name_1=NM_001013631;refseq.name_2=NM_001146181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A86A;refseq.proteinCoordStr_2=p.A86A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=439;refseq.spliceDist_2=353;refseq.start_1=12830472;refseq.start_2=12830472;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/0
|
|
chr1 12842581 . A C 30 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.430335;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.734A>C;refseq.codonCoord=245;refseq.end=12842581;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=821;refseq.name=NM_023014;refseq.name2=PRAMEF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y245S;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-133;refseq.start=12842581;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=soap GT 0/1
|
|
chr1 12844086 . C G 47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.404040;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1290C>G;refseq.codonCoord=430;refseq.end=12844086;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1377;refseq.name=NM_023014;refseq.name2=PRAMEF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.F430L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-266;refseq.start=12844086;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=soap GT 1/0
|
|
chr1 12844126 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.518717;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1330T>G;refseq.codonCoord=444;refseq.end=12844126;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1417;refseq.name=NM_023014;refseq.name2=PRAMEF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.F444V;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-226;refseq.start=12844126;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=soap GT 1/0
|
|
chr1 12844187 . C T 11 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=32;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1391C>T;refseq.codonCoord=464;refseq.end=12844187;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1478;refseq.name=NM_023014;refseq.name2=PRAMEF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P464L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-165;refseq.start=12844187;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT 1/1
|
|
chr1 12862097 . C T 5 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.166667;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1292G>A;refseq.codonCoord=431;refseq.end=12862097;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1363;refseq.name=NM_001009611;refseq.name2=PRAMEF4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S431N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=417;refseq.start=12862097;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 0/1
|
|
chr1 12862135 . G C 22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.333333;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1254C>G;refseq.codonCoord=418;refseq.end=12862135;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1325;refseq.name=NM_001009611;refseq.name2=PRAMEF4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P418P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=379;refseq.start=12862135;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=soap GT 0/1
|
|
chr1 12862491 . A C 28 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.750000;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.898T>G;refseq.codonCoord=300;refseq.end=12862491;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=969;refseq.name=NM_001009611;refseq.name2=PRAMEF4;refseq.positionType=CDS;refseq.proteinCoordStr=p.F300V;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=23;refseq.start=12862491;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=soap GT 0/1
|
|
chr1 12864706 . C T 43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=1305;Dels=0.00;HRun=1;HaplotypeScore=33.78;MQ=18.46;MQ0=531;OQ=11889.79;QD=9.11;RankSumP=1.00000;SB=-3501.82;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.431G>A;refseq.codonCoord=144;refseq.end=12864706;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=502;refseq.name=NM_001009611;refseq.name2=PRAMEF4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R144K;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=138;refseq.start=12864706;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/1
|
|
chr1 12864760 . C G 74 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.750000;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.377G>C;refseq.codonCoord=126;refseq.end=12864760;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=448;refseq.name=NM_001009611;refseq.name2=PRAMEF4;refseq.positionType=CDS;refseq.proteinCoordStr=p.C126S;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=84;refseq.start=12864760;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=soap GT 1/0
|
|
chr1 12864766 . T C 71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.632576;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.371A>G;refseq.codonCoord=124;refseq.end=12864766;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=442;refseq.name=NM_001009611;refseq.name2=PRAMEF4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H124R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=78;refseq.start=12864766;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=soap GT 1/0
|
|
chr1 12875383 . T G 27 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.466667;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1376A>C;refseq.codonCoord=459;refseq.end=12875383;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1449;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.N459T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-70;refseq.start=12875383;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap GT 1/0
|
|
chr1 12875431 . T C 3 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=3;RankSumP=0.166667;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1328A>G;refseq.codonCoord=443;refseq.end=12875431;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1401;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.E443G;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-118;refseq.start=12875431;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=FilteredInAll GT 1/0
|
|
chr1 12875555 rs1736772 C G 12.86 LowQual AC=1;AF=0.50;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=70.00;MQ0=1;QD=6.43;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1204G>C;refseq.codonCoord=402;refseq.end=12875555;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1277;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.G402R;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-242;refseq.start=12875555;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1,1:1:-4.55,-0.30,-0.00:1.76
|
|
chr1 12875747 . C G 19.14 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=12.25;MQ=1.17;MQ0=289;QD=0.07;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1012G>C;refseq.codonCoord=338;refseq.end=12875747;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1085;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.E338Q;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=146;refseq.start=12875747;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:270,20:1:-5.19,-0.30,-0.00:1.76
|
|
chr1 12877046 . T C 66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.750000;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.824A>G;refseq.codonCoord=275;refseq.end=12877046;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=897;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.K275R;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-43;refseq.start=12877046;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=soap GT 1/0
|
|
chr1 12877063 . G A 14 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.539394;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.807C>T;refseq.codonCoord=269;refseq.end=12877063;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=880;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.P269P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-60;refseq.start=12877063;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=FilteredInAll GT 1/0
|
|
chr1 12877112 . C T 6 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.400000;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.758G>A;refseq.codonCoord=253;refseq.end=12877112;refseq.frame=1;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=831;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.W253*;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=-109;refseq.start=12877112;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAG;set=FilteredInAll GT 0/1
|
|
chr1 12877535 . A G 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=26;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.335T>C;refseq.codonCoord=112;refseq.end=12877535;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=408;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.F112S;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=48;refseq.start=12877535;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 1/1
|
|
chr1 12878048 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.352587;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.218T>C;refseq.codonCoord=73;refseq.end=12878048;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=291;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.L73P;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=-70;refseq.start=12878048;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=soap GT 0/1
|
|
chr1 12878079 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.0603825;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.187A>C;refseq.codonCoord=63;refseq.end=12878079;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=260;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.S63R;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-101;refseq.start=12878079;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=soap GT 1/0
|
|
chr1 12878123 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.423888;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.143G>A;refseq.codonCoord=48;refseq.end=12878123;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=216;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.R48H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-145;refseq.start=12878123;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap GT 0/1
|
|
chr1 12878135 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.143383;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.131T>C;refseq.codonCoord=44;refseq.end=12878135;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=204;refseq.name=NM_001039361;refseq.name2=PRAMEF10;refseq.positionType=CDS;refseq.proteinCoordStr=p.F44S;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=156;refseq.start=12878135;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=soap GT 0/1
|
|
chr1 12902316 . G A 6 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=534;Dels=0.00;HRun=0;HaplotypeScore=6.17;MQ=8.39;MQ0=484;OQ=248.70;QD=0.47;RankSumP=1.00000;SB=-75.07;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.921G>A;refseq.codingCoordStr_2=c.921G>A;refseq.codonCoord_1=307;refseq.codonCoord_2=307;refseq.end_1=12902316;refseq.end_2=12902316;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1004;refseq.mrnaCoord_2=921;refseq.name2_1=PRAMEF8;refseq.name2_2=PRAMEF7;refseq.name_1=NM_001012276;refseq.name_2=NM_001012277;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S307S;refseq.proteinCoordStr_2=p.S307S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCG;refseq.referenceCodon_2=TCG;refseq.spliceDist_1=58;refseq.spliceDist_2=58;refseq.start_1=12902316;refseq.start_2=12902316;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCA;refseq.variantCodon_2=TCA;set=filterInsoap-gatk GT 1/1
|
|
chr1 12902415 . A G 11 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=2;RankSumP=0.700000;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1020A>G;refseq.codingCoordStr_2=c.1020A>G;refseq.codonCoord_1=340;refseq.codonCoord_2=340;refseq.end_1=12902415;refseq.end_2=12902415;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1103;refseq.mrnaCoord_2=1020;refseq.name2_1=PRAMEF8;refseq.name2_2=PRAMEF7;refseq.name_1=NM_001012276;refseq.name_2=NM_001012277;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T340T;refseq.proteinCoordStr_2=p.T340T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=157;refseq.spliceDist_2=157;refseq.start_1=12902415;refseq.start_2=12902415;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=FilteredInAll GT 0/1
|
|
chr1 12902432 . T C 12 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=491;Dels=0.00;HRun=0;HaplotypeScore=18.76;MQ=16.36;MQ0=322;OQ=718.70;QD=1.46;RankSumP=1.00000;SB=-90.12;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1037T>C;refseq.codingCoordStr_2=c.1037T>C;refseq.codonCoord_1=346;refseq.codonCoord_2=346;refseq.end_1=12902432;refseq.end_2=12902432;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1120;refseq.mrnaCoord_2=1037;refseq.name2_1=PRAMEF8;refseq.name2_2=PRAMEF7;refseq.name_1=NM_001012276;refseq.name_2=NM_001012277;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V346A;refseq.proteinCoordStr_2=p.V346A;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=174;refseq.spliceDist_2=174;refseq.start_1=12902432;refseq.start_2=12902432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=filterInsoap-gatk GT 1/1
|
|
chr1 12921380 rs28482402 G A 11.18 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=1756;Dels=0.00;HRun=0;HaplotypeScore=91.80;MQ=0.50;MQ0=1755;QD=0.01;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1143C>T;refseq.codonCoord=381;refseq.end=12921380;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1229;refseq.name=NM_001010889;refseq.name2=PRAMEF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.N381N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=274;refseq.start=12921380;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1303,453:1:-4.37,-0.30,-0.00:1.76
|
|
chr1 12923773 . C T 36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1752;Dels=0.00;HRun=0;HaplotypeScore=40.69;MQ=4.26;MQ0=1724;OQ=941.49;QD=0.54;RankSumP=0.421098;SB=-10.00;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.497G>A;refseq.codonCoord=166;refseq.end=12923773;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=583;refseq.name=NM_001010889;refseq.name2=PRAMEF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.C166Y;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=210;refseq.start=12923773;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=soap-filterIngatk GT 0/1
|
|
chr1 12923899 . C G 10 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=2798;Dels=0.00;HRun=1;HaplotypeScore=74.29;MQ=19.24;MQ0=1202;OQ=33492.16;QD=11.97;RankSumP=0.268164;SB=-13969.29;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.371G>C;refseq.codonCoord=124;refseq.end=12923899;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=457;refseq.name=NM_001010889;refseq.name2=PRAMEF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.C124S;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=84;refseq.start=12923899;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 1/0
|
|
chr1 12924656 rs2994117 G A 12.11 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=196;Dels=0.00;HRun=2;HaplotypeScore=1.90;MQ=2.00;MQ0=195;QD=0.06;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.280C>T;refseq.codonCoord=94;refseq.end=12924656;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=366;refseq.name=NM_001010889;refseq.name2=PRAMEF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.H94Y;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-8;refseq.spliceInfo=splice-donor_-8;refseq.start=12924656;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:172,24:1:-4.47,-0.30,-0.00:1.76
|
|
chr1 12924897 rs61779383 T C 43.84 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=1616;Dels=0.00;HRun=3;HaplotypeScore=865.82;MQ=0.81;MQ0=1614;QD=0.03;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.39A>G;refseq.codonCoord=13;refseq.end=12924897;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=125;refseq.name=NM_001010889;refseq.name2=PRAMEF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.A13A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=61;refseq.start=12924897;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:905,710:2:-7.79,-0.60,-0.00:6.02
|
|
chr1 12958834 . T A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=2;RankSumP=0.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.319T>A;refseq.codonCoord=107;refseq.end=12958834;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=319;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.L107M;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=26;refseq.start=12958834;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=FilteredInAll GT 1/0
|
|
chr1 12959034 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.519C>G;refseq.codonCoord=173;refseq.end=12959034;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=519;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.V173V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=226;refseq.start=12959034;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT 1/0
|
|
chr1 12959174 . C T 41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=1080;Dels=0.00;HRun=0;HaplotypeScore=27.56;MQ=21.26;MQ0=349;OQ=20257.82;QD=18.76;RankSumP=1.00000;SB=-8995.55;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.659C>T;refseq.codonCoord=220;refseq.end=12959174;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=659;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.P220L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-214;refseq.start=12959174;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 12959241 . C T 45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=817;Dels=0.00;HRun=0;HaplotypeScore=10.64;MQ=19.07;MQ0=384;OQ=2240.05;QD=2.74;RankSumP=0.452121;SB=-757.69;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.726C>T;refseq.codonCoord=242;refseq.end=12959241;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=726;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.S242S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-147;refseq.start=12959241;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 0/1
|
|
chr1 12959323 . T A 17 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.808T>A;refseq.codonCoord=270;refseq.end=12959323;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=808;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y270N;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-65;refseq.start=12959323;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 1/1
|
|
chr1 12960451 . T A 14 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.929T>A;refseq.codonCoord=310;refseq.end=12960451;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=929;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.V310E;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=57;refseq.start=12960451;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=FilteredInAll GT 1/1
|
|
chr1 12960464 . T C 14 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.942T>C;refseq.codonCoord=314;refseq.end=12960464;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=942;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.C314C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=70;refseq.start=12960464;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=FilteredInAll GT 1/1
|
|
chr1 12960612 . C G 6 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=3;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1090C>G;refseq.codonCoord=364;refseq.end=12960612;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1090;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.R364G;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=218;refseq.start=12960612;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/1
|
|
chr1 12960615 . G T 6 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1093G>T;refseq.codonCoord=365;refseq.end=12960615;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1093;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.D365Y;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=221;refseq.start=12960615;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=FilteredInAll GT 1/1
|
|
chr1 12960651 rs56088861 T C 0.32 PASS AC=2;AF=1.00;AN=2;DB;DP=612;Dels=0.00;HRun=1;HaplotypeScore=20.49;MQ=2.88;MQ0=597;OQ=266.64;QD=0.44;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1129T>C;refseq.codonCoord=377;refseq.end=12960651;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1129;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.C377R;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=257;refseq.start=12960651;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=gatk GT:AD:DP:GL:GQ 1/1:391,219:8:-30.25,-2.41,-0.00:24.07
|
|
chr1 12960706 rs55830102 G C 0.82 PASS AC=2;AF=1.00;AN=2;DB;DP=808;Dels=0.00;HRun=0;HaplotypeScore=17.24;MQ=2.50;MQ0=793;OQ=326.92;QD=0.40;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1184G>C;refseq.codonCoord=395;refseq.end=12960706;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1184;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.G395A;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-263;refseq.start=12960706;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=gatk GT:AD:DP:GL:GQ 1/1:390,418:8:-36.28,-2.41,-0.00:24.08
|
|
chr1 12960762 . T C 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=18;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1240T>C;refseq.codonCoord=414;refseq.end=12960762;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1240;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y414H;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-207;refseq.start=12960762;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT 1/1
|
|
chr1 12960914 . G T 90 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.732684;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1392G>T;refseq.codonCoord=464;refseq.end=12960914;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1392;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.T464T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-55;refseq.start=12960914;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=soap GT 0/1
|
|
chr1 12960937 . T C 20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.614011;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1415T>C;refseq.codonCoord=472;refseq.end=12960937;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1415;refseq.name=NM_001100631;refseq.name2=PRAMEF22;refseq.positionType=CDS;refseq.proteinCoordStr=p.F472S;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-32;refseq.start=12960937;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=soap GT 1/0
|
|
chr1 13201474 . C A 71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.416667;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1392G>T;refseq.codingCoordStr_2=c.1392G>T;refseq.codonCoord_1=464;refseq.codonCoord_2=464;refseq.end_1=13201474;refseq.end_2=13201474;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1413;refseq.mrnaCoord_2=1392;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T464T;refseq.proteinCoordStr_2=p.T464T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.spliceDist_1=520;refseq.spliceDist_2=-55;refseq.start_1=13201474;refseq.start_2=13201474;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;set=soap GT 1/0
|
|
chr1 13201682 rs55830102 C G 0.26 PASS AC=2;AF=1.00;AN=2;DB;DP=829;Dels=0.00;HRun=0;HaplotypeScore=23.42;MQ=2.85;MQ0=813;OQ=396.82;QD=0.48;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1184G>C;refseq.codingCoordStr_2=c.1184G>C;refseq.codonCoord_1=395;refseq.codonCoord_2=395;refseq.end_1=13201682;refseq.end_2=13201682;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1205;refseq.mrnaCoord_2=1184;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G395A;refseq.proteinCoordStr_2=p.G395A;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=312;refseq.spliceDist_2=-263;refseq.start_1=13201682;refseq.start_2=13201682;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=gatk GT:AD:DP:GL:GQ 1/1:406,421:10:-43.27,-3.01,-0.00:30.10
|
|
chr1 13201737 rs56088861 A G 0.06 PASS AC=2;AF=1.00;AN=2;DB;DP=604;Dels=0.00;HRun=1;HaplotypeScore=25.00;MQ=3.34;MQ0=587;OQ=396.67;QD=0.66;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1129T>C;refseq.codingCoordStr_2=c.1129T>C;refseq.codonCoord_1=377;refseq.codonCoord_2=377;refseq.end_1=13201737;refseq.end_2=13201737;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1150;refseq.mrnaCoord_2=1129;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C377R;refseq.proteinCoordStr_2=p.C377R;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=257;refseq.spliceDist_2=257;refseq.start_1=13201737;refseq.start_2=13201737;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=gatk GT:AD:DP:GL:GQ 1/1:362,239:11:-43.25,-3.31,-0.00:33.11
|
|
chr1 13201773 . C A 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1093G>T;refseq.codingCoordStr_2=c.1093G>T;refseq.codonCoord_1=365;refseq.codonCoord_2=365;refseq.end_1=13201773;refseq.end_2=13201773;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1114;refseq.mrnaCoord_2=1093;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D365Y;refseq.proteinCoordStr_2=p.D365Y;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=221;refseq.spliceDist_2=221;refseq.start_1=13201773;refseq.start_2=13201773;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;set=FilteredInAll GT 1/1
|
|
chr1 13201776 . G C 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=3;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1090C>G;refseq.codingCoordStr_2=c.1090C>G;refseq.codonCoord_1=364;refseq.codonCoord_2=364;refseq.end_1=13201776;refseq.end_2=13201776;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1111;refseq.mrnaCoord_2=1090;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R364G;refseq.proteinCoordStr_2=p.R364G;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.spliceDist_1=218;refseq.spliceDist_2=218;refseq.start_1=13201776;refseq.start_2=13201776;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/1
|
|
chr1 13201924 . A G 3 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.942T>C;refseq.codingCoordStr_2=c.942T>C;refseq.codonCoord_1=314;refseq.codonCoord_2=314;refseq.end_1=13201924;refseq.end_2=13201924;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=963;refseq.mrnaCoord_2=942;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C314C;refseq.proteinCoordStr_2=p.C314C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=70;refseq.spliceDist_2=70;refseq.start_1=13201924;refseq.start_2=13201924;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=FilteredInAll GT 1/1
|
|
chr1 13201937 rs56101354 A T 40.29 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=426;Dels=0.00;HRun=0;HaplotypeScore=11.88;MQ=2.02;MQ0=424;QD=0.09;SB=-45.99;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.929T>A;refseq.codingCoordStr_2=c.929T>A;refseq.codonCoord_1=310;refseq.codonCoord_2=310;refseq.end_1=13201937;refseq.end_2=13201937;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=950;refseq.mrnaCoord_2=929;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V310E;refseq.proteinCoordStr_2=p.V310E;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=57;refseq.spliceDist_2=57;refseq.start_1=13201937;refseq.start_2=13201937;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:164,256:2:-7.44,-0.60,-0.00:6.02
|
|
chr1 13203065 . A T 8 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.333333;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.808T>A;refseq.codingCoordStr_2=c.808T>A;refseq.codonCoord_1=270;refseq.codonCoord_2=270;refseq.end_1=13203065;refseq.end_2=13203065;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=829;refseq.mrnaCoord_2=808;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y270N;refseq.proteinCoordStr_2=p.Y270N;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-65;refseq.spliceDist_2=-65;refseq.start_1=13203065;refseq.start_2=13203065;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=FilteredInAll GT 0/1
|
|
chr1 13203193 . A C 3 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.680T>G;refseq.codingCoordStr_2=c.680T>G;refseq.codonCoord_1=227;refseq.codonCoord_2=227;refseq.end_1=13203193;refseq.end_2=13203193;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=701;refseq.mrnaCoord_2=680;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I227S;refseq.proteinCoordStr_2=p.I227S;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=-193;refseq.spliceDist_2=-193;refseq.start_1=13203193;refseq.start_2=13203193;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;set=FilteredInAll GT 1/1
|
|
chr1 13203214 . G A 3 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.659C>T;refseq.codingCoordStr_2=c.659C>T;refseq.codonCoord_1=220;refseq.codonCoord_2=220;refseq.end_1=13203214;refseq.end_2=13203214;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=680;refseq.mrnaCoord_2=659;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P220L;refseq.proteinCoordStr_2=p.P220L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=-214;refseq.spliceDist_2=-214;refseq.start_1=13203214;refseq.start_2=13203214;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=FilteredInAll GT 1/1
|
|
chr1 13203354 . G C 35 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.388455;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.519C>G;refseq.codingCoordStr_2=c.519C>G;refseq.codonCoord_1=173;refseq.codonCoord_2=173;refseq.end_1=13203354;refseq.end_2=13203354;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=540;refseq.mrnaCoord_2=519;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V173V;refseq.proteinCoordStr_2=p.V173V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=226;refseq.spliceDist_2=226;refseq.start_1=13203354;refseq.start_2=13203354;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=soap GT 0/1
|
|
chr1 13203471 . C T 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.402G>A;refseq.codingCoordStr_2=c.402G>A;refseq.codonCoord_1=134;refseq.codonCoord_2=134;refseq.end_1=13203471;refseq.end_2=13203471;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=423;refseq.mrnaCoord_2=402;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R134R;refseq.proteinCoordStr_2=p.R134R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=AGG;refseq.referenceCodon_2=AGG;refseq.spliceDist_1=109;refseq.spliceDist_2=109;refseq.start_1=13203471;refseq.start_2=13203471;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGA;refseq.variantCodon_2=AGA;set=FilteredInAll GT 1/1
|
|
chr1 13204125 . G T 30 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;HRun=0;RankSumP=0.619048;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.134C>A;refseq.codingCoordStr_2=c.134C>A;refseq.codonCoord_1=45;refseq.codonCoord_2=45;refseq.end_1=13204125;refseq.end_2=13204125;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=155;refseq.mrnaCoord_2=134;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A45D;refseq.proteinCoordStr_2=p.A45D;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=155;refseq.spliceDist_2=134;refseq.start_1=13204125;refseq.start_2=13204125;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=soap GT 0/1
|
|
chr1 13204132 . C T 28 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.100000;SecondBestBaseQ=21;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.127G>A;refseq.codingCoordStr_2=c.127G>A;refseq.codonCoord_1=43;refseq.codonCoord_2=43;refseq.end_1=13204132;refseq.end_2=13204132;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=148;refseq.mrnaCoord_2=127;refseq.name2_1=PRAMEF3;refseq.name2_2=PRAMEF22;refseq.name_1=NM_001013692;refseq.name_2=NM_001100631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V43M;refseq.proteinCoordStr_2=p.V43M;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=148;refseq.spliceDist_2=127;refseq.start_1=13204132;refseq.start_2=13204132;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;set=soap GT 0/1
|
|
chr1 13237491 . C T 10.16 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=1401;Dels=0.00;HRun=1;HaplotypeScore=30.18;MQ=0.61;MQ0=1400;QD=0.01;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.14C>T;refseq.codingCoordStr_2=c.14C>T;refseq.codonCoord_1=5;refseq.codonCoord_2=5;refseq.end_1=13237491;refseq.end_2=13237491;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=100;refseq.mrnaCoord_2=114;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T5I;refseq.proteinCoordStr_2=p.T5I;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=36;refseq.spliceDist_2=36;refseq.start_1=13237491;refseq.start_2=13237491;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1329,71:1:-4.26,-0.30,-0.00:1.76
|
|
chr1 13237513 . T G 48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.0767677;SecondBestBaseQ=21;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.36T>G;refseq.codingCoordStr_2=c.36T>G;refseq.codonCoord_1=12;refseq.codonCoord_2=12;refseq.end_1=13237513;refseq.end_2=13237513;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=122;refseq.mrnaCoord_2=136;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L12L;refseq.proteinCoordStr_2=p.L12L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTT;refseq.referenceCodon_2=CTT;refseq.spliceDist_1=58;refseq.spliceDist_2=58;refseq.start_1=13237513;refseq.start_2=13237513;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=soap GT 1/0
|
|
chr1 13237516 . A G 36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.727273;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.39A>G;refseq.codingCoordStr_2=c.39A>G;refseq.codonCoord_1=13;refseq.codonCoord_2=13;refseq.end_1=13237516;refseq.end_2=13237516;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=125;refseq.mrnaCoord_2=139;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A13A;refseq.proteinCoordStr_2=p.A13A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=61;refseq.spliceDist_2=61;refseq.start_1=13237516;refseq.start_2=13237516;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=soap GT 0/1
|
|
chr1 13238508 . A G 15 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.365A>G;refseq.codingCoordStr_2=c.365A>G;refseq.codonCoord_1=122;refseq.codonCoord_2=122;refseq.end_1=13238508;refseq.end_2=13238508;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=451;refseq.mrnaCoord_2=465;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H122R;refseq.proteinCoordStr_2=p.H122R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=78;refseq.spliceDist_2=78;refseq.start_1=13238508;refseq.start_2=13238508;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=FilteredInAll GT 1/1
|
|
chr1 13238514 . G C 25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.529412;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.371G>C;refseq.codingCoordStr_2=c.371G>C;refseq.codonCoord_1=124;refseq.codonCoord_2=124;refseq.end_1=13238514;refseq.end_2=13238514;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=457;refseq.mrnaCoord_2=471;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C124S;refseq.proteinCoordStr_2=p.C124S;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=84;refseq.spliceDist_2=84;refseq.start_1=13238514;refseq.start_2=13238514;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=soap GT 0/1
|
|
chr1 13238640 rs7419099 G A 42.02 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=950;Dels=0.00;HRun=0;HaplotypeScore=33.35;MQ=1.03;MQ0=948;QD=0.04;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.497G>A;refseq.codingCoordStr_2=c.497G>A;refseq.codonCoord_1=166;refseq.codonCoord_2=166;refseq.end_1=13238640;refseq.end_2=13238640;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=583;refseq.mrnaCoord_2=597;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C166Y;refseq.proteinCoordStr_2=p.C166Y;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=210;refseq.spliceDist_2=210;refseq.start_1=13238640;refseq.start_2=13238640;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:863,85:2:-7.61,-0.60,-0.00:6.02
|
|
chr1 13241032 . C T 3 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1143C>T;refseq.codingCoordStr_2=c.1143C>T;refseq.codonCoord_1=381;refseq.codonCoord_2=381;refseq.end_1=13241032;refseq.end_2=13241032;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1229;refseq.mrnaCoord_2=1243;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N381N;refseq.proteinCoordStr_2=p.N381N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=274;refseq.spliceDist_2=274;refseq.start_1=13241032;refseq.start_2=13241032;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=FilteredInAll GT 1/1
|
|
chr1 13241033 . A G 3 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1144A>G;refseq.codingCoordStr_2=c.1144A>G;refseq.codonCoord_1=382;refseq.codonCoord_2=382;refseq.end_1=13241033;refseq.end_2=13241033;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1230;refseq.mrnaCoord_2=1244;refseq.name2_1=PRAMEF6;refseq.name2_2=PRAMEF5;refseq.name_1=NM_001010889;refseq.name_2=NM_001013407;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T382A;refseq.proteinCoordStr_2=p.T382A;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=275;refseq.spliceDist_2=275;refseq.start_1=13241033;refseq.start_2=13241033;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=FilteredInAll GT 1/1
|
|
chr1 13296661 rs2933094 T C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=1123;Dels=0.00;HRun=1;HaplotypeScore=45.18;MQ=1.09;MQ0=1120;OQ=90.01;QD=0.08;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.72T>C;refseq.codingCoordStr_2=c.72T>C;refseq.codonCoord_1=24;refseq.codonCoord_2=24;refseq.end_1=13296661;refseq.end_2=13296661;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=166;refseq.mrnaCoord_2=166;refseq.name2_1=PRAMEF9;refseq.name2_2=PRAMEF15;refseq.name_1=NM_001010890;refseq.name_2=NM_001098376;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A24A;refseq.proteinCoordStr_2=p.A24A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=88;refseq.spliceDist_2=88;refseq.start_1=13296661;refseq.start_2=13296661;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:778,343:3:-12.49,-0.90,-0.00:9.03
|
|
chr1 13296875 rs2994117 C T 11.07 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=448;Dels=0.00;HRun=2;HaplotypeScore=79.35;MQ=1.42;MQ0=447;QD=0.02;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.286C>T;refseq.codingCoordStr_2=c.286C>T;refseq.codonCoord_1=96;refseq.codonCoord_2=96;refseq.end_1=13296875;refseq.end_2=13296875;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=380;refseq.mrnaCoord_2=380;refseq.name2_1=PRAMEF9;refseq.name2_2=PRAMEF15;refseq.name_1=NM_001010890;refseq.name_2=NM_001098376;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R96C;refseq.proteinCoordStr_2=p.R96C;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGT;refseq.referenceCodon_2=CGT;refseq.spliceDist_1=-8;refseq.spliceDist_2=-8;refseq.spliceInfo_1=splice-donor_-8;refseq.spliceInfo_2=splice-donor_-8;refseq.start_1=13296875;refseq.start_2=13296875;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:282,163:1:-4.36,-0.30,-0.00:1.76
|
|
chr1 13297664 rs2153358 A C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=1045;Dels=0.00;HRun=0;HaplotypeScore=31.50;MQ=1.80;MQ0=1040;OQ=153.26;QD=0.15;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.404A>C;refseq.codingCoordStr_2=c.404A>C;refseq.codonCoord_1=135;refseq.codonCoord_2=135;refseq.end_1=13297664;refseq.end_2=13297664;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=498;refseq.mrnaCoord_2=498;refseq.name2_1=PRAMEF9;refseq.name2_2=PRAMEF15;refseq.name_1=NM_001010890;refseq.name_2=NM_001098376;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K135T;refseq.proteinCoordStr_2=p.K135T;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=111;refseq.spliceDist_2=111;refseq.start_1=13297664;refseq.start_2=13297664;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACA;refseq.variantCodon_2=ACA;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:918,126:5:-18.89,-1.51,-0.00:15.05
|
|
chr1 13297697 rs2488535 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=1624;Dels=0.00;HRun=0;HaplotypeScore=40.72;MQ=1.73;MQ0=1616;OQ=61.09;QD=0.04;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.437G>A;refseq.codingCoordStr_2=c.437G>A;refseq.codonCoord_1=146;refseq.codonCoord_2=146;refseq.end_1=13297697;refseq.end_2=13297697;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=531;refseq.mrnaCoord_2=531;refseq.name2_1=PRAMEF9;refseq.name2_2=PRAMEF15;refseq.name_1=NM_001010890;refseq.name_2=NM_001098376;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R146Q;refseq.proteinCoordStr_2=p.R146Q;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.spliceDist_1=144;refseq.spliceDist_2=144;refseq.start_1=13297697;refseq.start_2=13297697;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1481,139:8:-11.80,-2.41,-18.88:93.92
|
|
chr1 13320707 rs61745371 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=412;Dels=0.00;HRun=0;HaplotypeScore=59.93;MQ=2.84;MQ0=406;OQ=110.95;QD=0.27;SB=-3.98;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1211T>C;refseq.codonCoord=404;refseq.end=13320707;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1394;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.I404T;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=489;refseq.start=13320707;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:388,24:6:-16.19,-1.81,-8.01:62.05
|
|
chr1 13320767 rs61738672 A G 22.49 ESPStandard;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=622;Dels=0.00;HRun=3;HaplotypeScore=24.98;MQ=2.37;MQ0=613;QD=0.04;SB=2.04;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1151T>C;refseq.codonCoord=384;refseq.end=13320767;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1334;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.L384P;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=429;refseq.start=13320767;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:599,22:6:-7.34,-1.81,-17.17:55.31
|
|
chr1 13320771 rs6700727 C T 25.22 ESPStandard;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=623;Dels=0.00;HRun=0;HaplotypeScore=62.17;MQ=2.47;MQ0=614;QD=0.04;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1147G>A;refseq.codonCoord=383;refseq.end=13320771;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1330;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.A383T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=425;refseq.start=13320771;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:602,20:6:-7.61,-1.81,-16.27:58.05
|
|
chr1 13320772 rs2142947 G C 39.04 ESPStandard;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=634;Dels=0.00;HRun=1;HaplotypeScore=63.16;MQ=2.45;MQ0=625;QD=0.06;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1146C>G;refseq.codonCoord=382;refseq.end=13320772;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1329;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.F382L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=424;refseq.start=13320772;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:612,22:6:-8.99,-1.81,-18.17:71.87
|
|
chr1 13320786 . C T 20 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=655;Dels=0.00;HRun=1;HaplotypeScore=17.90;MQ=1.49;MQ0=650;OQ=52.02;QD=0.08;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1132G>A;refseq.codonCoord=378;refseq.end=13320786;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1315;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.D378N;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=410;refseq.start=13320786;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/1
|
|
chr1 13320870 . A G 74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=575;Dels=0.00;HRun=0;HaplotypeScore=15.63;MQ=23.15;MQ0=205;OQ=14322.39;QD=24.91;RankSumP=1.00000;SB=-5955.79;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1048T>C;refseq.codonCoord=350;refseq.end=13320870;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1231;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.L350L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=326;refseq.start=13320870;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 13320938 . T C 75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=714;Dels=0.00;HRun=0;HaplotypeScore=10.29;MQ=11.40;MQ0=671;OQ=1044.50;QD=1.46;RankSumP=1.00000;SB=-213.42;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.980A>G;refseq.codonCoord=327;refseq.end=13320938;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1163;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.H327R;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=258;refseq.start=13320938;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/1
|
|
chr1 13321134 rs1063787 T C 174.22 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=1080;Dels=0.00;HRun=0;HaplotypeScore=14.10;MQ=2.04;MQ0=1075;QD=0.16;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.784A>G;refseq.codonCoord=262;refseq.end=13321134;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=967;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.M262V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=62;refseq.start=13321134;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:533,547:5:-20.98,-1.51,-0.00:15.05
|
|
chr1 13321135 . G A 161.19 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=1061;Dels=0.00;HRun=0;HaplotypeScore=13.68;MQ=2.06;MQ0=1056;QD=0.15;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.783C>T;refseq.codonCoord=261;refseq.end=13321135;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=966;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.D261D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=61;refseq.start=13321135;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:521,535:5:-19.68,-1.51,-0.00:15.05
|
|
chr1 13321138 rs1063786 T C 164.22 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=1034;Dels=0.00;HRun=1;HaplotypeScore=16.92;MQ=2.09;MQ0=1029;QD=0.16;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.780A>G;refseq.codonCoord=260;refseq.end=13321138;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=963;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.E260E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=58;refseq.start=13321138;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:504,529:5:-19.98,-1.51,-0.00:15.05
|
|
chr1 13322310 . G C 15.75 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=1113;Dels=0.00;HRun=1;HaplotypeScore=23.26;MQ=0.72;MQ0=1112;QD=0.01;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.703C>G;refseq.codonCoord=235;refseq.end=13322310;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=886;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.R235G;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-20;refseq.start=13322310;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:589,522:1:-4.85,-0.30,-0.00:1.76
|
|
chr1 13322388 rs61778604 G C -0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=1015;Dels=0.00;HRun=0;HaplotypeScore=128.08;MQ=1.84;MQ0=1011;OQ=141.54;QD=0.14;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.625C>G;refseq.codonCoord=209;refseq.end=13322388;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=808;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q209E;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-98;refseq.start=13322388;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:566,80:4:-17.69,-1.20,-0.00:12.04
|
|
chr1 13322684 . T C 10.53 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=612;Dels=0.00;HRun=1;HaplotypeScore=50.17;MQ=1.09;MQ0=611;QD=0.02;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.329A>G;refseq.codonCoord=110;refseq.end=13322684;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=512;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.E110G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=42;refseq.start=13322684;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:580,32:1:-4.30,-0.30,-0.00:1.76
|
|
chr1 13323385 rs1063756 T C 0.03 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=708;Dels=0.00;HRun=3;HaplotypeScore=15.20;MQ=2.83;MQ0=700;OQ=227.94;QD=0.32;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.39A>G;refseq.codonCoord=13;refseq.end=13323385;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=222;refseq.name=NM_001099854;refseq.name2=PRAMEF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.A13A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=144;refseq.start=13323385;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:354,354:7:-26.37,-2.11,-0.00:21.07
|
|
chr1 13370159 . G A 32 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DP=300;Dels=0.00;HRun=0;HaplotypeScore=9.15;MQ=4.95;MQ0=281;OQ=436.17;QD=1.45;RankSumP=1.00000;SB=-133.67;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.869G>A;refseq.codonCoord=290;refseq.end=13370159;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=899;refseq.name=NM_001045480;refseq.name2=PRAMEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.C290Y;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=3;refseq.spliceInfo=splice-acceptor_3;refseq.start=13370159;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/1
|
|
chr1 13370171 . C T 38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DP=388;Dels=0.00;HRun=0;HaplotypeScore=11.55;MQ=4.35;MQ0=369;OQ=461.61;QD=1.19;RankSumP=1.00000;SB=-144.01;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.881C>T;refseq.codonCoord=294;refseq.end=13370171;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=911;refseq.name=NM_001045480;refseq.name2=PRAMEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.P294L;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=15;refseq.start=13370171;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/1
|
|
chr1 13370213 . A G 14 BadSOAPSNP;FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;BestBaseQ=25;DP=539;Dels=0.00;HRun=2;HaplotypeScore=6.32;MQ=3.08;MQ0=529;OQ=57.40;QD=0.11;RankSumP=1.00000;SB=-27.89;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.923A>G;refseq.codonCoord=308;refseq.end=13370213;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=953;refseq.name=NM_001045480;refseq.name2=PRAMEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q308R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=57;refseq.start=13370213;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=FilteredInAll GT 1/1
|
|
chr1 13370267 . A G 11 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.977A>G;refseq.codonCoord=326;refseq.end=13370267;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1007;refseq.name=NM_001045480;refseq.name2=PRAMEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.H326R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=111;refseq.start=13370267;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=FilteredInAll GT 1/1
|
|
chr1 13370292 . T C 5 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1002T>C;refseq.codonCoord=334;refseq.end=13370292;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1032;refseq.name=NM_001045480;refseq.name2=PRAMEF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.T334T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=136;refseq.start=13370292;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/1
|
|
chr1 13394608 . C G 0.03 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=520;Dels=0.00;HRun=0;HaplotypeScore=8.11;MQ=1.90;MQ0=517;OQ=57.30;QD=0.11;SB=-53.92;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.49C>G;refseq.codingCoordStr_2=c.49C>G;refseq.codonCoord_1=17;refseq.codonCoord_2=17;refseq.end_1=13394608;refseq.end_2=13394608;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=148;refseq.mrnaCoord_2=59;refseq.name2_1=PRAMEF20;refseq.name2_2=PRAMEF21;refseq.name_1=NM_001099852;refseq.name_2=NM_001100114;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L17V;refseq.proteinCoordStr_2=p.L17V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=53;refseq.spliceDist_2=59;refseq.start_1=13394608;refseq.start_2=13394608;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:491,29:2:-9.14,-0.60,-0.00:6.02
|
|
chr1 13394620 . G C 19.14 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=441;Dels=0.00;HRun=1;HaplotypeScore=39.04;MQ=1.48;MQ0=439;QD=0.04;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.61G>C;refseq.codingCoordStr_2=c.61G>C;refseq.codonCoord_1=21;refseq.codonCoord_2=21;refseq.end_1=13394620;refseq.end_2=13394620;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=160;refseq.mrnaCoord_2=71;refseq.name2_1=PRAMEF20;refseq.name2_2=PRAMEF21;refseq.name_1=NM_001099852;refseq.name_2=NM_001100114;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E21Q;refseq.proteinCoordStr_2=p.E21Q;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=65;refseq.spliceDist_2=71;refseq.start_1=13394620;refseq.start_2=13394620;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:422,18:1:-5.19,-0.30,-0.00:1.76
|
|
chr1 13394622 . G A 10.16 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=431;Dels=0.00;HRun=1;HaplotypeScore=38.20;MQ=1.50;MQ0=429;QD=0.02;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.63G>A;refseq.codingCoordStr_2=c.63G>A;refseq.codonCoord_1=21;refseq.codonCoord_2=21;refseq.end_1=13394622;refseq.end_2=13394622;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=162;refseq.mrnaCoord_2=73;refseq.name2_1=PRAMEF20;refseq.name2_2=PRAMEF21;refseq.name_1=NM_001099852;refseq.name_2=NM_001100114;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E21E;refseq.proteinCoordStr_2=p.E21E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=67;refseq.spliceDist_2=73;refseq.start_1=13394622;refseq.start_2=13394622;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:418,12:1:-4.26,-0.30,-0.00:1.76
|
|
chr1 13541562 rs61745371 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=474;Dels=0.00;HRun=0;HaplotypeScore=43.89;MQ=2.60;MQ0=468;OQ=114.95;QD=0.24;SB=-3.98;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1355T>C;refseq.codingCoordStr_2=c.1211T>C;refseq.codonCoord_1=452;refseq.codonCoord_2=404;refseq.end_1=13541562;refseq.end_2=13541562;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1458;refseq.mrnaCoord_2=1394;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I452T;refseq.proteinCoordStr_2=p.I404T;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=489;refseq.spliceDist_2=489;refseq.start_1=13541562;refseq.start_2=13541562;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:450,24:6:-16.59,-1.81,-8.51:67.05
|
|
chr1 13541622 rs61738672 A G 20.51 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=723;Dels=0.00;HRun=3;HaplotypeScore=22.66;MQ=2.16;MQ0=715;QD=0.03;SB=2.04;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1295T>C;refseq.codingCoordStr_2=c.1151T>C;refseq.codonCoord_1=432;refseq.codonCoord_2=384;refseq.end_1=13541622;refseq.end_2=13541622;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1398;refseq.mrnaCoord_2=1334;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L432P;refseq.proteinCoordStr_2=p.L384P;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTA;refseq.referenceCodon_2=CTA;refseq.spliceDist_1=429;refseq.spliceDist_2=429;refseq.start_1=13541622;refseq.start_2=13541622;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:715,7:6:-7.14,-1.81,-17.17:53.31
|
|
chr1 13541989 rs1063787 T C 135.51 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=941;Dels=0.00;HRun=0;HaplotypeScore=43.50;MQ=1.96;MQ0=937;QD=0.14;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.928A>G;refseq.codingCoordStr_2=c.784A>G;refseq.codonCoord_1=310;refseq.codonCoord_2=262;refseq.end_1=13541989;refseq.end_2=13541989;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1031;refseq.mrnaCoord_2=967;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.M310V;refseq.proteinCoordStr_2=p.M262V;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=62;refseq.spliceDist_2=62;refseq.start_1=13541989;refseq.start_2=13541989;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:481,457:4:-17.08,-1.20,-0.00:12.04
|
|
chr1 13541990 . G A 125.88 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=930;Dels=0.00;HRun=0;HaplotypeScore=47.08;MQ=1.97;MQ0=926;QD=0.14;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.927C>T;refseq.codingCoordStr_2=c.783C>T;refseq.codonCoord_1=309;refseq.codonCoord_2=261;refseq.end_1=13541990;refseq.end_2=13541990;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1030;refseq.mrnaCoord_2=966;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D309D;refseq.proteinCoordStr_2=p.D261D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=61;refseq.spliceDist_2=61;refseq.start_1=13541990;refseq.start_2=13541990;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:470,455:4:-16.12,-1.20,-0.00:12.04
|
|
chr1 13541993 rs1063786 T C 129.51 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=920;Dels=0.00;HRun=1;HaplotypeScore=46.34;MQ=1.98;MQ0=916;QD=0.14;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.924A>G;refseq.codingCoordStr_2=c.780A>G;refseq.codonCoord_1=308;refseq.codonCoord_2=260;refseq.end_1=13541993;refseq.end_2=13541993;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1027;refseq.mrnaCoord_2=963;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E308E;refseq.proteinCoordStr_2=p.E260E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=58;refseq.spliceDist_2=58;refseq.start_1=13541993;refseq.start_2=13541993;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:469,451:4:-16.48,-1.20,-0.00:12.04
|
|
chr1 13543165 . G C 16.73 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=1138;Dels=0.00;HRun=1;HaplotypeScore=24.55;MQ=0.74;MQ0=1137;QD=0.01;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.703C>G;refseq.codingCoordStr_2=c.703C>G;refseq.codonCoord_1=235;refseq.codonCoord_2=235;refseq.end_1=13543165;refseq.end_2=13543165;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=806;refseq.mrnaCoord_2=886;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R235G;refseq.proteinCoordStr_2=p.R235G;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.spliceDist_1=-164;refseq.spliceDist_2=-20;refseq.start_1=13543165;refseq.start_2=13543165;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:619,518:1:-4.95,-0.30,-0.00:1.76
|
|
chr1 13543243 rs61778604 G C 14.78 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=918;Dels=0.00;HRun=0;HaplotypeScore=95.22;MQ=0.93;MQ0=914;QD=0.02;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.625C>G;refseq.codingCoordStr_2=c.625C>G;refseq.codonCoord_1=209;refseq.codonCoord_2=209;refseq.end_1=13543243;refseq.end_2=13543243;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=728;refseq.mrnaCoord_2=808;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q209E;refseq.proteinCoordStr_2=p.Q209E;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-242;refseq.spliceDist_2=-98;refseq.start_1=13543243;refseq.start_2=13543243;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:498,82:1:-4.75,-0.30,-0.00:1.76
|
|
chr1 13543364 rs1856642 A G 0.09 PASS AC=2;AF=1.00;AN=2;DB;DP=838;Dels=0.00;HRun=1;HaplotypeScore=24.01;MQ=1.36;MQ0=834;OQ=80.17;QD=0.10;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.504T>C;refseq.codingCoordStr_2=c.504T>C;refseq.codonCoord_1=168;refseq.codonCoord_2=168;refseq.end_1=13543364;refseq.end_2=13543364;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=607;refseq.mrnaCoord_2=687;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F168F;refseq.proteinCoordStr_2=p.F168F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.spliceDist_1=217;refseq.spliceDist_2=217;refseq.start_1=13543364;refseq.start_2=13543364;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;set=gatk GT:AD:DP:GL:GQ 1/1:604,234:3:-11.51,-0.90,-0.00:9.03
|
|
chr1 13543456 rs61778607 A G 10.28 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=860;Dels=0.00;HRun=1;HaplotypeScore=23.16;MQ=0.92;MQ0=859;QD=0.01;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.412T>C;refseq.codingCoordStr_2=c.412T>C;refseq.codonCoord_1=138;refseq.codonCoord_2=138;refseq.end_1=13543456;refseq.end_2=13543456;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=515;refseq.mrnaCoord_2=595;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C138R;refseq.proteinCoordStr_2=p.C138R;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=125;refseq.spliceDist_2=125;refseq.start_1=13543456;refseq.start_2=13543456;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:493,367:1:-4.27,-0.30,-0.00:1.76
|
|
chr1 13543541 rs1063762 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=640;Dels=0.00;HRun=0;HaplotypeScore=44.90;MQ=1.87;MQ0=637;OQ=72.17;QD=0.11;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.327T>C;refseq.codingCoordStr_2=c.327T>C;refseq.codonCoord_1=109;refseq.codonCoord_2=109;refseq.end_1=13543541;refseq.end_2=13543541;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=430;refseq.mrnaCoord_2=510;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D109D;refseq.proteinCoordStr_2=p.D109D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=40;refseq.spliceDist_2=40;refseq.start_1=13543541;refseq.start_2=13543541;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:560,79:3:-10.71,-0.90,-0.00:9.03
|
|
chr1 13544125 rs4083405 G C 19.14 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=794;Dels=0.00;HRun=0;HaplotypeScore=16.26;MQ=1.06;MQ0=793;QD=0.02;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.154C>G;refseq.codingCoordStr_2=c.154C>G;refseq.codonCoord_1=52;refseq.codonCoord_2=52;refseq.end_1=13544125;refseq.end_2=13544125;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=257;refseq.mrnaCoord_2=337;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L52V;refseq.proteinCoordStr_2=p.L52V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=-134;refseq.spliceDist_2=-134;refseq.start_1=13544125;refseq.start_2=13544125;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:494,300:1:-5.19,-0.30,-0.00:1.76
|
|
chr1 13544240 rs1063756 T C 0.04 PASS AC=2;AF=1.00;AN=2;DB;DP=688;Dels=0.00;HRun=3;HaplotypeScore=11.57;MQ=3.39;MQ0=678;OQ=308.81;QD=0.45;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.39A>G;refseq.codingCoordStr_2=c.39A>G;refseq.codonCoord_1=13;refseq.codonCoord_2=13;refseq.end_1=13544240;refseq.end_2=13544240;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=142;refseq.mrnaCoord_2=222;refseq.name2_1=PRAMEF13;refseq.name2_2=PRAMEF14;refseq.name_1=NM_001024661;refseq.name_2=NM_001099854;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A13A;refseq.proteinCoordStr_2=p.A13A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=64;refseq.spliceDist_2=144;refseq.start_1=13544240;refseq.start_2=13544240;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=gatk GT:AD:DP:GL:GQ 1/1:326,362:9:-34.47,-2.71,-0.00:27.09
|
|
chr1 13568374 . C G 65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=1246;Dels=0.00;HRun=0;HaplotypeScore=31.09;MQ=2.07;MQ0=1227;OQ=255.83;QD=0.21;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1178G>C;refseq.codingCoordStr_2=c.1178G>C;refseq.codonCoord_1=393;refseq.codonCoord_2=393;refseq.end_1=13568374;refseq.end_2=13568374;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1225;refseq.mrnaCoord_2=1225;refseq.name2_1=PRAMEF19;refseq.name2_2=PRAMEF18;refseq.name_1=NM_001099790;refseq.name_2=NM_001099850;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G393A;refseq.proteinCoordStr_2=p.G393A;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=312;refseq.spliceDist_2=312;refseq.start_1=13568374;refseq.start_2=13568374;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=soap-filterIngatk GT 1/1
|
|
chr1 13568403 . G A 77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=1435;Dels=0.00;HRun=3;HaplotypeScore=45.64;MQ=10.36;MQ0=1192;OQ=6060.87;QD=4.22;RankSumP=1.00000;SB=-922.74;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1149C>T;refseq.codingCoordStr_2=c.1149C>T;refseq.codonCoord_1=383;refseq.codonCoord_2=383;refseq.end_1=13568403;refseq.end_2=13568403;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1196;refseq.mrnaCoord_2=1196;refseq.name2_1=PRAMEF19;refseq.name2_2=PRAMEF18;refseq.name_1=NM_001099790;refseq.name_2=NM_001099850;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C383C;refseq.proteinCoordStr_2=p.C383C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=283;refseq.spliceDist_2=283;refseq.start_1=13568403;refseq.start_2=13568403;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;set=soap-filterIngatk GT 1/1
|
|
chr1 13568561 . T C 20 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=762;Dels=0.00;HRun=0;HaplotypeScore=32.48;MQ=16.33;MQ0=730;OQ=1098.09;QD=1.44;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.991A>G;refseq.codingCoordStr_2=c.991A>G;refseq.codonCoord_1=331;refseq.codonCoord_2=331;refseq.end_1=13568561;refseq.end_2=13568561;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1038;refseq.mrnaCoord_2=1038;refseq.name2_1=PRAMEF19;refseq.name2_2=PRAMEF18;refseq.name_1=NM_001099790;refseq.name_2=NM_001099850;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T331A;refseq.proteinCoordStr_2=p.T331A;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=125;refseq.spliceDist_2=125;refseq.start_1=13568561;refseq.start_2=13568561;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=soap-filterIngatk GT 1/1
|
|
chr1 13568609 rs2359294 A G 0.02 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=451;Dels=0.00;HRun=3;HaplotypeScore=3.97;MQ=8.99;MQ0=442;OQ=320.31;QD=0.71;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.943T>C;refseq.codingCoordStr_2=c.943T>C;refseq.codonCoord_1=315;refseq.codonCoord_2=315;refseq.end_1=13568609;refseq.end_2=13568609;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=990;refseq.mrnaCoord_2=990;refseq.name2_1=PRAMEF19;refseq.name2_2=PRAMEF18;refseq.name_1=NM_001099790;refseq.name_2=NM_001099850;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.W315R;refseq.proteinCoordStr_2=p.W315R;refseq.referenceAA_1=Trp;refseq.referenceAA_2=Trp;refseq.referenceCodon_1=TGG;refseq.referenceCodon_2=TGG;refseq.spliceDist_1=77;refseq.spliceDist_2=77;refseq.start_1=13568609;refseq.start_2=13568609;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:369,82:9:-35.62,-2.71,-0.00:27.09
|
|
chr1 13568616 rs2359295 A G 0.07 PASS AC=2;AF=1.00;AN=2;DB;DP=438;Dels=0.00;HRun=1;HaplotypeScore=3.49;MQ=7.80;MQ0=430;OQ=260.64;QD=0.60;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.936T>C;refseq.codingCoordStr_2=c.936T>C;refseq.codonCoord_1=312;refseq.codonCoord_2=312;refseq.end_1=13568616;refseq.end_2=13568616;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=983;refseq.mrnaCoord_2=983;refseq.name2_1=PRAMEF19;refseq.name2_2=PRAMEF18;refseq.name_1=NM_001099790;refseq.name_2=NM_001099850;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C312C;refseq.proteinCoordStr_2=p.C312C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=70;refseq.spliceDist_2=70;refseq.start_1=13568616;refseq.start_2=13568616;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=gatk GT:AD:DP:GL:GQ 1/1:372,66:8:-29.65,-2.41,-0.00:24.07
|
|
chr1 13568634 rs2101624 A T 0.24 PASS AC=2;AF=1.00;AN=2;DB;DP=386;Dels=0.00;HRun=1;HaplotypeScore=6.78;MQ=5.53;MQ0=380;OQ=223.20;QD=0.58;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.918T>A;refseq.codingCoordStr_2=c.918T>A;refseq.codonCoord_1=306;refseq.codonCoord_2=306;refseq.end_1=13568634;refseq.end_2=13568634;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=965;refseq.mrnaCoord_2=965;refseq.name2_1=PRAMEF19;refseq.name2_2=PRAMEF18;refseq.name_1=NM_001099790;refseq.name_2=NM_001099850;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D306E;refseq.proteinCoordStr_2=p.D306E;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=52;refseq.spliceDist_2=52;refseq.start_1=13568634;refseq.start_2=13568634;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=gatk GT:AD:DP:GL:GQ 1/1:346,40:6:-25.89,-1.81,-0.00:18.06
|
|
chr1 13568641 rs2101625 G A 0.76 PASS AC=2;AF=1.00;AN=2;DB;DP=343;Dels=0.00;HRun=1;HaplotypeScore=12.97;MQ=5.86;MQ0=337;OQ=219.62;QD=0.64;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.911C>T;refseq.codingCoordStr_2=c.911C>T;refseq.codonCoord_1=304;refseq.codonCoord_2=304;refseq.end_1=13568641;refseq.end_2=13568641;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=958;refseq.mrnaCoord_2=958;refseq.name2_1=PRAMEF19;refseq.name2_2=PRAMEF18;refseq.name_1=NM_001099790;refseq.name_2=NM_001099850;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S304F;refseq.proteinCoordStr_2=p.S304F;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCC;refseq.referenceCodon_2=TCC;refseq.spliceDist_1=45;refseq.spliceDist_2=45;refseq.start_1=13568641;refseq.start_2=13568641;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;set=gatk GT:AD:DP:GL:GQ 1/1:321,22:6:-25.53,-1.81,-0.00:18.06
|
|
chr1 13615447 . C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=517;Dels=0.00;HRun=0;HaplotypeScore=34.72;MQ=2.64;MQ0=513;OQ=106.98;QD=0.21;SB=-56.93;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.49C>G;refseq.codingCoordStr_2=c.49C>G;refseq.codonCoord_1=17;refseq.codonCoord_2=17;refseq.end_1=13615447;refseq.end_2=13615447;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=148;refseq.mrnaCoord_2=59;refseq.name2_1=PRAMEF20;refseq.name2_2=PRAMEF21;refseq.name_1=NM_001099852;refseq.name_2=NM_001100114;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L17V;refseq.proteinCoordStr_2=p.L17V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=53;refseq.spliceDist_2=59;refseq.start_1=13615447;refseq.start_2=13615447;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:488,29:3:-14.19,-0.90,-0.00:9.03
|
|
chr1 13615459 . G C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=447;Dels=0.00;HRun=1;HaplotypeScore=34.62;MQ=2.46;MQ0=444;OQ=66.76;QD=0.15;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.61G>C;refseq.codingCoordStr_2=c.61G>C;refseq.codonCoord_1=21;refseq.codonCoord_2=21;refseq.end_1=13615459;refseq.end_2=13615459;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=160;refseq.mrnaCoord_2=71;refseq.name2_1=PRAMEF20;refseq.name2_2=PRAMEF21;refseq.name_1=NM_001099852;refseq.name_2=NM_001100114;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E21Q;refseq.proteinCoordStr_2=p.E21Q;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=65;refseq.spliceDist_2=71;refseq.start_1=13615459;refseq.start_2=13615459;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:428,18:2:-10.08,-0.60,-0.00:6.02
|
|
chr1 13615461 . G A 48.02 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=441;Dels=0.00;HRun=1;HaplotypeScore=35.72;MQ=2.47;MQ0=438;QD=0.11;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.63G>A;refseq.codingCoordStr_2=c.63G>A;refseq.codonCoord_1=21;refseq.codonCoord_2=21;refseq.end_1=13615461;refseq.end_2=13615461;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=162;refseq.mrnaCoord_2=73;refseq.name2_1=PRAMEF20;refseq.name2_2=PRAMEF21;refseq.name_1=NM_001099852;refseq.name_2=NM_001100114;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E21E;refseq.proteinCoordStr_2=p.E21E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=67;refseq.spliceDist_2=73;refseq.start_1=13615461;refseq.start_2=13615461;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:426,13:2:-8.21,-0.60,-0.00:6.02
|
|
chr1 13813451 . C G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=548;Dels=0.00;HRun=1;HaplotypeScore=14.30;MQ=98.83;MQ0=0;OQ=23090.12;QD=42.14;RankSumP=1.00000;SB=-9891.95;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.314C>G;refseq.codingCoordStr_2=c.314C>G;refseq.codingCoordStr_3=c.668C>G;refseq.codingCoordStr_4=c.668C>G;refseq.codonCoord_1=105;refseq.codonCoord_2=105;refseq.codonCoord_3=223;refseq.codonCoord_4=223;refseq.end_1=13813451;refseq.end_2=13813451;refseq.end_3=13813451;refseq.end_4=13813451;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=541;refseq.mrnaCoord_2=541;refseq.mrnaCoord_3=717;refseq.mrnaCoord_4=717;refseq.name2_1=PDPN;refseq.name2_2=PDPN;refseq.name2_3=PDPN;refseq.name2_4=PDPN;refseq.name_1=NM_001006624;refseq.name_2=NM_001006625;refseq.name_3=NM_006474;refseq.name_4=NM_198389;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.A105G;refseq.proteinCoordStr_2=p.A105G;refseq.proteinCoordStr_3=p.A223G;refseq.proteinCoordStr_4=p.A223G;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.referenceCodon_3=GCA;refseq.referenceCodon_4=GCA;refseq.spliceDist_1=-43;refseq.spliceDist_2=-37;refseq.spliceDist_3=-43;refseq.spliceDist_4=-37;refseq.start_1=13813451;refseq.start_2=13813451;refseq.start_3=13813451;refseq.start_4=13813451;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;refseq.variantCodon_3=GGA;refseq.variantCodon_4=GGA;set=Intersection GT 1/1
|
|
chr1 13977726 . T A 108.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=122;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=98.75;MQ0=0;OQ=1755.00;QD=14.39;RankSumP=0.318138;SB=-424.47;SecondBestBaseQ=32;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.246T>A;refseq.codingCoordStr_3=c.849T>A;refseq.codingCoordStr_4=c.849T>A;refseq.codonCoord_2=82;refseq.codonCoord_3=283;refseq.codonCoord_4=283;refseq.end_1=14015498;refseq.end_2=13977726;refseq.end_3=13977726;refseq.end_4=13977726;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_2=445;refseq.mrnaCoord_3=1705;refseq.mrnaCoord_4=1705;refseq.name2_1=PRDM2;refseq.name2_2=PRDM2;refseq.name2_3=PRDM2;refseq.name2_4=PRDM2;refseq.name_1=NM_001135610;refseq.name_2=NM_001007257;refseq.name_3=NM_012231;refseq.name_4=NM_015866;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.D82E;refseq.proteinCoordStr_3=p.D283E;refseq.proteinCoordStr_4=p.D283E;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceCodon_2=GAT;refseq.referenceCodon_3=GAT;refseq.referenceCodon_4=GAT;refseq.spliceDist_2=227;refseq.spliceDist_3=227;refseq.spliceDist_4=227;refseq.start_1=13948580;refseq.start_2=13977726;refseq.start_3=13977726;refseq.start_4=13977726;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantAA_4=Glu;refseq.variantCodon_2=GAA;refseq.variantCodon_3=GAA;refseq.variantCodon_4=GAA;set=Intersection GT 1/0
|
|
chr1 13977885 . G A 184.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=300;Dels=0.00;HRun=1;HaplotypeScore=9.03;MQ=98.97;MQ0=0;OQ=6468.73;QD=21.56;RankSumP=0.399673;SB=-2057.38;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.405G>A;refseq.codingCoordStr_3=c.1008G>A;refseq.codingCoordStr_4=c.1008G>A;refseq.codonCoord_2=135;refseq.codonCoord_3=336;refseq.codonCoord_4=336;refseq.end_1=14015498;refseq.end_2=13977885;refseq.end_3=13977885;refseq.end_4=13977885;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_2=604;refseq.mrnaCoord_3=1864;refseq.mrnaCoord_4=1864;refseq.name2_1=PRDM2;refseq.name2_2=PRDM2;refseq.name2_3=PRDM2;refseq.name2_4=PRDM2;refseq.name_1=NM_001135610;refseq.name_2=NM_001007257;refseq.name_3=NM_012231;refseq.name_4=NM_015866;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.E135E;refseq.proteinCoordStr_3=p.E336E;refseq.proteinCoordStr_4=p.E336E;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceAA_4=Glu;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.referenceCodon_4=GAG;refseq.spliceDist_2=386;refseq.spliceDist_3=386;refseq.spliceDist_4=386;refseq.start_1=13948580;refseq.start_2=13977885;refseq.start_3=13977885;refseq.start_4=13977885;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantAA_4=Glu;refseq.variantCodon_2=GAA;refseq.variantCodon_3=GAA;refseq.variantCodon_4=GAA;set=Intersection GT 1/0
|
|
chr1 13981701 . A G 157.09 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=98.86;MQ0=0;OQ=1352.73;QD=13.80;RankSumP=0.426089;SB=-677.73;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.4221A>G;refseq.codingCoordStr_3=c.4824A>G;refseq.codingCoordStr_4=c.4824A>G;refseq.codonCoord_2=1407;refseq.codonCoord_3=1608;refseq.codonCoord_4=1608;refseq.end_1=14015498;refseq.end_2=13981701;refseq.end_3=13981701;refseq.end_4=13981701;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_2=4420;refseq.mrnaCoord_3=5680;refseq.mrnaCoord_4=5680;refseq.name2_1=PRDM2;refseq.name2_2=PRDM2;refseq.name2_3=PRDM2;refseq.name2_4=PRDM2;refseq.name_1=NM_001135610;refseq.name_2=NM_001007257;refseq.name_3=NM_012231;refseq.name_4=NM_015866;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.S1407S;refseq.proteinCoordStr_3=p.S1608S;refseq.proteinCoordStr_4=p.S1608S;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.referenceCodon_4=TCA;refseq.spliceDist_2=-213;refseq.spliceDist_3=-213;refseq.spliceDist_4=-213;refseq.start_1=13948580;refseq.start_2=13981701;refseq.start_3=13981701;refseq.start_4=13981701;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_2=TCG;refseq.variantCodon_3=TCG;refseq.variantCodon_4=TCG;set=Intersection GT 0/1
|
|
chr1 14015590 . A G 196.61 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=246;Dels=0.00;HRun=1;HaplotypeScore=5.84;MQ=99.00;MQ0=0;OQ=8394.67;QD=34.12;RankSumP=1.00000;SB=-2866.32;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.593A>G;refseq.codingCoordStr_2=c.5118A>G;refseq.codonCoord_1=198;refseq.codonCoord_2=1706;refseq.end_1=14015590;refseq.end_2=14015590;refseq.frame_1=1;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=719;refseq.mrnaCoord_2=5974;refseq.name2_1=PRDM2;refseq.name2_2=PRDM2;refseq.name_1=NM_001135610;refseq.name_2=NM_012231;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q198R;refseq.proteinCoordStr_2=p.P1706P;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=-63;refseq.spliceDist_2=-63;refseq.start_1=14015590;refseq.start_2=14015590;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Pro;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CCG;set=Intersection GT 1/1
|
|
chr1 15259266 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=0;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.646A>C;refseq.codingCoordStr_2=c.910A>C;refseq.codingCoordStr_3=c.646A>C;refseq.codingCoordStr_4=c.928A>C;refseq.codingCoordStr_5=c.928A>C;refseq.codonCoord_1=216;refseq.codonCoord_2=304;refseq.codonCoord_3=216;refseq.codonCoord_4=310;refseq.codonCoord_5=310;refseq.end_1=15259266;refseq.end_2=15259266;refseq.end_3=15259266;refseq.end_4=15259266;refseq.end_5=15259266;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=957;refseq.mrnaCoord_2=1146;refseq.mrnaCoord_3=947;refseq.mrnaCoord_4=1209;refseq.mrnaCoord_5=1209;refseq.name2_1=KAZ;refseq.name2_2=KAZ;refseq.name2_3=KAZ;refseq.name2_4=KAZ;refseq.name2_5=KAZ;refseq.name_1=NM_001017999;refseq.name_2=NM_001018000;refseq.name_3=NM_001018001;refseq.name_4=NM_015209;refseq.name_5=NM_201628;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.S216R;refseq.proteinCoordStr_2=p.S304R;refseq.proteinCoordStr_3=p.S216R;refseq.proteinCoordStr_4=p.S310R;refseq.proteinCoordStr_5=p.S310R;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceAA_5=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.referenceCodon_3=AGC;refseq.referenceCodon_4=AGC;refseq.referenceCodon_5=AGC;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.spliceDist_3=12;refseq.spliceDist_4=12;refseq.spliceDist_5=12;refseq.start_1=15259266;refseq.start_2=15259266;refseq.start_3=15259266;refseq.start_4=15259266;refseq.start_5=15259266;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantAA_5=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;refseq.variantCodon_3=CGC;refseq.variantCodon_4=CGC;refseq.variantCodon_5=CGC;set=FilteredInAll GT 0/1
|
|
chr1 15259267 . G C 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=4;RankSumP=1.50996e-08;SecondBestBaseQ=21;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.647G>C;refseq.codingCoordStr_2=c.911G>C;refseq.codingCoordStr_3=c.647G>C;refseq.codingCoordStr_4=c.929G>C;refseq.codingCoordStr_5=c.929G>C;refseq.codonCoord_1=216;refseq.codonCoord_2=304;refseq.codonCoord_3=216;refseq.codonCoord_4=310;refseq.codonCoord_5=310;refseq.end_1=15259267;refseq.end_2=15259267;refseq.end_3=15259267;refseq.end_4=15259267;refseq.end_5=15259267;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=958;refseq.mrnaCoord_2=1147;refseq.mrnaCoord_3=948;refseq.mrnaCoord_4=1210;refseq.mrnaCoord_5=1210;refseq.name2_1=KAZ;refseq.name2_2=KAZ;refseq.name2_3=KAZ;refseq.name2_4=KAZ;refseq.name2_5=KAZ;refseq.name_1=NM_001017999;refseq.name_2=NM_001018000;refseq.name_3=NM_001018001;refseq.name_4=NM_015209;refseq.name_5=NM_201628;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.S216T;refseq.proteinCoordStr_2=p.S304T;refseq.proteinCoordStr_3=p.S216T;refseq.proteinCoordStr_4=p.S310T;refseq.proteinCoordStr_5=p.S310T;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceAA_5=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.referenceCodon_3=AGC;refseq.referenceCodon_4=AGC;refseq.referenceCodon_5=AGC;refseq.spliceDist_1=13;refseq.spliceDist_2=13;refseq.spliceDist_3=13;refseq.spliceDist_4=13;refseq.spliceDist_5=13;refseq.start_1=15259267;refseq.start_2=15259267;refseq.start_3=15259267;refseq.start_4=15259267;refseq.start_5=15259267;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantAA_5=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;refseq.variantCodon_3=ACC;refseq.variantCodon_4=ACC;refseq.variantCodon_5=ACC;set=FilteredInAll GT 0/1
|
|
chr1 15418664 . G A 195.71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=99.00;MQ0=0;OQ=1607.58;QD=14.23;RankSumP=0.351736;SB=-702.65;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.600G>A;refseq.codingCoordStr_2=c.600G>A;refseq.codingCoordStr_3=c.600G>A;refseq.codingCoordStr_4=c.600G>A;refseq.codonCoord_1=200;refseq.codonCoord_2=200;refseq.codonCoord_3=200;refseq.codonCoord_4=200;refseq.end_1=15418664;refseq.end_2=15418664;refseq.end_3=15418664;refseq.end_4=15418664;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1119;refseq.mrnaCoord_2=1046;refseq.mrnaCoord_3=1088;refseq.mrnaCoord_4=1015;refseq.name2_1=TMEM51;refseq.name2_2=TMEM51;refseq.name2_3=TMEM51;refseq.name2_4=TMEM51;refseq.name_1=NM_001136216;refseq.name_2=NM_001136217;refseq.name_3=NM_001136218;refseq.name_4=NM_018022;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.P200P;refseq.proteinCoordStr_2=p.P200P;refseq.proteinCoordStr_3=p.P200P;refseq.proteinCoordStr_4=p.P200P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.referenceCodon_3=CCG;refseq.referenceCodon_4=CCG;refseq.spliceDist_1=256;refseq.spliceDist_2=256;refseq.spliceDist_3=256;refseq.spliceDist_4=256;refseq.start_1=15418664;refseq.start_2=15418664;refseq.start_3=15418664;refseq.start_4=15418664;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;refseq.variantCodon_3=CCA;refseq.variantCodon_4=CCA;set=Intersection GT 1/0
|
|
chr1 15685019 . A G 79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=15.93;MQ=98.18;MQ0=0;OQ=3693.63;QD=32.98;RankSumP=1.00000;SB=-1561.14;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.530A>G;refseq.codonCoord=177;refseq.end=15685019;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=555;refseq.name=NM_015849;refseq.name2=CELA2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q177R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=37;refseq.start=15685019;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/1
|
|
chr1 15686423 . T C 217.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=277;Dels=0.00;HRun=0;HaplotypeScore=8.58;MQ=98.10;MQ0=0;OQ=4503.58;QD=16.26;RankSumP=0.422240;SB=-1451.11;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.696T>C;refseq.codonCoord=232;refseq.end=15686423;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=721;refseq.name=NM_015849;refseq.name2=CELA2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.H232H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=57;refseq.start=15686423;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/0
|
|
chr1 15825810 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.198G>T;refseq.codonCoord=66;refseq.end=15825810;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=294;refseq.name=NM_032341;refseq.name2=DDI2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L66F;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=60;refseq.start=15825810;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 0/1
|
|
chr1 15969521 . C T 76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=368;Dels=0.00;HRun=1;HaplotypeScore=11.89;MQ=97.96;MQ0=0;OQ=13544.05;QD=36.80;RankSumP=1.00000;SB=-6531.45;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.572C>T;refseq.codingCoordStr_2=c.281C>T;refseq.codingCoordStr_3=c.572C>T;refseq.codonCoord_1=191;refseq.codonCoord_2=94;refseq.codonCoord_3=191;refseq.end_1=15969521;refseq.end_2=15969521;refseq.end_3=15969521;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=779;refseq.mrnaCoord_2=301;refseq.mrnaCoord_3=871;refseq.name2_1=FBLIM1;refseq.name2_2=FBLIM1;refseq.name2_3=FBLIM1;refseq.name_1=NM_001024215;refseq.name_2=NM_001024216;refseq.name_3=NM_017556;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S191F;refseq.proteinCoordStr_2=p.S94F;refseq.proteinCoordStr_3=p.S191F;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCC;refseq.referenceCodon_2=TCC;refseq.referenceCodon_3=TCC;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.spliceDist_3=31;refseq.start_1=15969521;refseq.start_2=15969521;refseq.start_3=15969521;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;refseq.variantCodon_3=TTC;set=Intersection GT 1/1
|
|
chr1 16075658 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=1;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.779G>A;refseq.codonCoord=260;refseq.end=16075658;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=983;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S260N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-103;refseq.start=16075658;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 1/0
|
|
chr1 16075659 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=0;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.780C>A;refseq.codonCoord=260;refseq.end=16075659;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=984;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S260R;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-102;refseq.start=16075659;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=FilteredInAll GT 1/0
|
|
chr1 16128594 . T C 242.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1070.48;QD=39.65;RankSumP=1.00000;SB=-249.10;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3272T>C;refseq.codonCoord=1091;refseq.end=16128594;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3476;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1091P;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=1422;refseq.start=16128594;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 16130247 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=5.02957e-09;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4925T>G;refseq.codonCoord=1642;refseq.end=16130247;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5129;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1642G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=3075;refseq.start=16130247;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 16132400 . A G 219.87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=164;Dels=0.00;HRun=0;HaplotypeScore=4.97;MQ=98.67;MQ0=0;OQ=5171.52;QD=31.53;RankSumP=1.00000;SB=-2113.85;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7078A>G;refseq.codonCoord=2360;refseq.end=16132400;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=7282;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.N2360D;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-2949;refseq.start=16132400;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 16136580 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10362A>C;refseq.codonCoord=3454;refseq.end=16136580;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10566;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.K3454N;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-148;refseq.start=16136580;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 0/1
|
|
chr1 16136917 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10533C>G;refseq.codonCoord=3511;refseq.end=16136917;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10737;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.G3511G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=24;refseq.start=16136917;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 16137051 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10667A>G;refseq.codonCoord=3556;refseq.end=16137051;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10871;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.E3556G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-38;refseq.start=16137051;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 16138491 . T A 102.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=169;Dels=0.00;HRun=0;HaplotypeScore=9.64;MQ=98.69;MQ0=0;OQ=3802.56;QD=22.50;RankSumP=0.491140;SB=-814.17;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10977T>A;refseq.codonCoord=3659;refseq.end=16138491;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=11181;refseq.name=NM_015001;refseq.name2=SPEN;refseq.positionType=CDS;refseq.proteinCoordStr=p.I3659I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=114;refseq.start=16138491;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/0
|
|
chr1 16144837 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=6.98;MQ=94.25;MQ0=0;OQ=318.72;QD=5.22;RankSumP=0.553629;SB=-62.30;SecondBestBaseQ=15;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.621T>C;refseq.codonCoord=207;refseq.end=16144837;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=860;refseq.name=NM_003443;refseq.name2=ZBTB17;refseq.positionType=CDS;refseq.proteinCoordStr=p.A207A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-41;refseq.start=16144837;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 16205243 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=3;RankSumP=1.64411e-07;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.325A>C;refseq.codonCoord=109;refseq.end=16205243;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=393;refseq.name=NM_178840;refseq.name2=C1orf64;refseq.positionType=CDS;refseq.proteinCoordStr=p.T109P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=243;refseq.start=16205243;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 16214824 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=98.60;MQ0=0;OQ=767.21;QD=11.80;RankSumP=0.101664;SB=-284.46;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.351T>C;refseq.codonCoord=117;refseq.end=16214824;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1178;refseq.name=NM_014424;refseq.name2=HSPB7;refseq.positionType=CDS;refseq.proteinCoordStr=p.T117T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=18;refseq.start=16214824;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 16216947 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.34;MQ=99.00;MQ0=0;OQ=488.03;QD=13.56;RankSumP=0.631450;SB=-257.58;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.99T>C;refseq.codonCoord=33;refseq.end=16216947;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=926;refseq.name=NM_014424;refseq.name2=HSPB7;refseq.positionType=CDS;refseq.proteinCoordStr=p.A33A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-101;refseq.start=16216947;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 16216989 . G A 87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=347.49;QD=13.36;RankSumP=0.0965757;SB=-144.59;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.57C>T;refseq.codonCoord=19;refseq.end=16216989;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=884;refseq.name=NM_014424;refseq.name2=HSPB7;refseq.positionType=CDS;refseq.proteinCoordStr=p.S19S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-143;refseq.start=16216989;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/0
|
|
chr1 16223862 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=238;Dels=0.00;HRun=3;HaplotypeScore=20.73;MQ=67.50;MQ0=0;OQ=2282.38;QD=9.59;RankSumP=0.00745984;SB=-1151.77;SecondBestBaseQ=23;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.247A>G;refseq.codingCoordStr_2=c.247A>G;refseq.codonCoord_1=83;refseq.codonCoord_2=83;refseq.end_1=16223862;refseq.end_2=16223862;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=327;refseq.mrnaCoord_2=327;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R83G;refseq.proteinCoordStr_2=p.R83G;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=AGG;refseq.referenceCodon_2=AGG;refseq.spliceDist_1=18;refseq.spliceDist_2=18;refseq.start_1=16223862;refseq.start_2=16223862;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=filterInsoap-gatk GT 0/1
|
|
chr1 16227177 . A T 99.94 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=284;Dels=0.00;HRun=1;HaplotypeScore=12.56;MQ=98.48;MQ0=0;OQ=6133.84;QD=21.60;RankSumP=0.370158;SB=-1605.17;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.944A>T;refseq.codingCoordStr_2=c.944A>T;refseq.codonCoord_1=315;refseq.codonCoord_2=315;refseq.end_1=16227177;refseq.end_2=16227177;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1024;refseq.mrnaCoord_2=1024;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y315F;refseq.proteinCoordStr_2=p.Y315F;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-25;refseq.spliceDist_2=-25;refseq.start_1=16227177;refseq.start_2=16227177;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;set=Intersection GT 0/1
|
|
chr1 16229084 rs7411607 C G 2.52 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=2.15;MQ=92.87;MQ0=0;OQ=286.91;QD=9.26;SB=-140.56;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1335C>G;refseq.codingCoordStr_2=c.1335C>G;refseq.codonCoord_1=445;refseq.codonCoord_2=445;refseq.end_1=16229084;refseq.end_2=16229084;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1415;refseq.mrnaCoord_2=1415;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A445A;refseq.proteinCoordStr_2=p.A445A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=38;refseq.spliceDist_2=38;refseq.start_1=16229084;refseq.start_2=16229084;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=gatk GT:AD:DP:GL:GQ 0/1:21,10:26:-39.81,-7.83,-77.01:99
|
|
chr1 16229088 rs1805152 G A 32.67 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=91.65;MQ0=0;OQ=359.34;QD=10.57;SB=-161.65;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1339G>A;refseq.codingCoordStr_2=c.1339G>A;refseq.codonCoord_1=447;refseq.codonCoord_2=447;refseq.end_1=16229088;refseq.end_2=16229088;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1419;refseq.mrnaCoord_2=1419;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A447T;refseq.proteinCoordStr_2=p.A447T;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.start_1=16229088;refseq.start_2=16229088;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=gatk GT:AD:DP:GL:GQ 0/1:21,13:28:-47.65,-8.44,-59.42:99
|
|
chr1 16229109 rs34471231 A G 3.61 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.55;MQ=92.67;MQ0=0;OQ=405.27;QD=9.21;SB=-211.57;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1360A>G;refseq.codingCoordStr_2=c.1360A>G;refseq.codonCoord_1=454;refseq.codonCoord_2=454;refseq.end_1=16229109;refseq.end_2=16229109;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1440;refseq.mrnaCoord_2=1440;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T454A;refseq.proteinCoordStr_2=p.T454A;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=-49;refseq.spliceDist_2=-49;refseq.start_1=16229109;refseq.start_2=16229109;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=gatk GT:AD:DP:GL:GQ 0/1:29,15:40:-55.86,-12.05,-104.89:99
|
|
chr1 16229118 rs35747151 G A 0.03 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=92.45;MQ0=0;OQ=185.29;QD=4.31;SB=20.09;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1369G>A;refseq.codingCoordStr_2=c.1369G>A;refseq.codonCoord_1=457;refseq.codonCoord_2=457;refseq.end_1=16229118;refseq.end_2=16229118;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1449;refseq.mrnaCoord_2=1449;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V457I;refseq.proteinCoordStr_2=p.V457I;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=-40;refseq.spliceDist_2=-40;refseq.start_1=16229118;refseq.start_2=16229118;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:33,10:31:-31.15,-9.34,-88.45:99
|
|
chr1 16229120 rs35154011 T C 0.05 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=93.07;MQ0=0;OQ=183.25;QD=4.47;SB=-0.56;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1371T>C;refseq.codingCoordStr_2=c.1371T>C;refseq.codonCoord_1=457;refseq.codonCoord_2=457;refseq.end_1=16229120;refseq.end_2=16229120;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1451;refseq.mrnaCoord_2=1451;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V457V;refseq.proteinCoordStr_2=p.V457V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=-38;refseq.spliceDist_2=-38;refseq.start_1=16229120;refseq.start_2=16229120;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=gatk GT:AD:DP:GL:GQ 0/1:27,14:30:-30.65,-9.04,-91.27:99
|
|
chr1 16229734 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=175;Dels=0.00;HRun=0;HaplotypeScore=15.41;MQ=59.79;MQ0=66;OQ=1422.98;QD=8.13;RankSumP=0.162780;SB=-496.50;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1600C>T;refseq.codingCoordStr_2=c.1600C>T;refseq.codonCoord_1=534;refseq.codonCoord_2=534;refseq.end_1=16229734;refseq.end_2=16229734;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1680;refseq.mrnaCoord_2=1680;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R534W;refseq.proteinCoordStr_2=p.R534W;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.spliceDist_1=-23;refseq.spliceDist_2=-23;refseq.start_1=16229734;refseq.start_2=16229734;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Trp;refseq.variantAA_2=Trp;refseq.variantCodon_1=TGG;refseq.variantCodon_2=TGG;set=Intersection GT 0/1
|
|
chr1 16232724 . C T 131.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=134;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=30.63;MQ0=4;OQ=1969.71;QD=14.70;RankSumP=0.123400;SB=-907.58;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2045C>T;refseq.codingCoordStr_2=c.2048C>T;refseq.codonCoord_1=682;refseq.codonCoord_2=683;refseq.end_1=16232724;refseq.end_2=16232724;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2125;refseq.mrnaCoord_2=2128;refseq.name2_1=CLCNKA;refseq.name2_2=CLCNKA;refseq.name_1=NM_001042704;refseq.name_2=NM_004070;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P682L;refseq.proteinCoordStr_2=p.P683L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.start_1=16232724;refseq.start_2=16232724;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 0/1
|
|
chr1 16247120 . G C 176.24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=5.42;MQ=97.44;MQ0=0;OQ=1346.74;QD=19.81;RankSumP=0.338381;SB=-48.46;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.492G>C;refseq.codonCoord=164;refseq.end=16247120;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=628;refseq.name=NM_000085;refseq.name2=CLCNKB;refseq.positionType=CDS;refseq.proteinCoordStr=p.G164G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=16247120;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 16247650 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;DB;DP=186;Dels=0.00;HRun=1;HaplotypeScore=21.29;MQ=62.16;MQ0=94;OQ=1314.45;QD=7.07;RankSumP=0.0619009;SB=-3.98;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.641C>G;refseq.codonCoord=214;refseq.end=16247650;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=777;refseq.name=NM_000085;refseq.name2=CLCNKB;refseq.positionType=CDS;refseq.proteinCoordStr=p.A214G;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-15;refseq.start=16247650;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 16247651 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=181;Dels=0.00;HRun=1;HaplotypeScore=17.95;MQ=62.95;MQ0=90;OQ=869.64;QD=4.80;RankSumP=0.327531;SB=-3.98;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.642A>C;refseq.codonCoord=214;refseq.end=16247651;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=778;refseq.name=NM_000085;refseq.name2=CLCNKB;refseq.positionType=CDS;refseq.proteinCoordStr=p.A214A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-14;refseq.start=16247651;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 16248778 rs34188929 C T 0.32 PASS AC=1;AF=0.50;AN=2;DB;DP=434;Dels=0.00;HRun=0;HaplotypeScore=12.45;MQ=20.28;MQ0=408;OQ=183.82;QD=0.42;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.860C>T;refseq.codingCoordStr_2=c.353C>T;refseq.codonCoord_1=287;refseq.codonCoord_2=118;refseq.end_1=16248778;refseq.end_2=16248778;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=996;refseq.mrnaCoord_2=536;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A287V;refseq.proteinCoordStr_2=p.A118V;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=-7;refseq.spliceDist_2=-7;refseq.spliceInfo_1=splice-donor_-7;refseq.spliceInfo_2=splice-donor_-7;refseq.start_1=16248778;refseq.start_2=16248778;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=gatk GT:AD:DP:GL:GQ 0/1:374,59:24:-28.89,-7.23,-67.46:99
|
|
chr1 16248906 . T C 41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=92.85;MQ0=0;OQ=330.55;QD=10.02;RankSumP=0.730369;SB=-97.96;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.876T>C;refseq.codingCoordStr_2=c.369T>C;refseq.codonCoord_1=292;refseq.codonCoord_2=123;refseq.end_1=16248906;refseq.end_2=16248906;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1012;refseq.mrnaCoord_2=552;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C292C;refseq.proteinCoordStr_2=p.C123C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=10;refseq.spliceDist_2=10;refseq.spliceInfo_1=splice-acceptor_10;refseq.spliceInfo_2=splice-acceptor_10;refseq.start_1=16248906;refseq.start_2=16248906;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=Intersection GT 1/0
|
|
chr1 16250586 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=823;Dels=0.00;HRun=0;HaplotypeScore=13.46;MQ=96.40;MQ0=4;OQ=15346.55;QD=18.65;RankSumP=0.0116494;SB=-6148.69;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1254C>T;refseq.codingCoordStr_2=c.747C>T;refseq.codonCoord_1=418;refseq.codonCoord_2=249;refseq.end_1=16250586;refseq.end_2=16250586;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1390;refseq.mrnaCoord_2=930;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T418T;refseq.proteinCoordStr_2=p.T249T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=27;refseq.spliceDist_2=27;refseq.start_1=16250586;refseq.start_2=16250586;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;set=Intersection GT 0/1
|
|
chr1 16250587 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=828;Dels=0.00;HRun=0;HaplotypeScore=13.31;MQ=96.41;MQ0=4;OQ=14842.34;QD=17.93;RankSumP=6.82858e-05;SB=-5491.85;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1255A>G;refseq.codingCoordStr_2=c.748A>G;refseq.codonCoord_1=419;refseq.codonCoord_2=250;refseq.end_1=16250587;refseq.end_2=16250587;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1391;refseq.mrnaCoord_2=931;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I419V;refseq.proteinCoordStr_2=p.I250V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.start_1=16250587;refseq.start_2=16250587;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=filterInsoap-gatk GT 0/1
|
|
chr1 16250802 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=94.56;MQ0=1;OQ=494.50;QD=14.54;RankSumP=0.528480;SB=-109.92;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1308C>T;refseq.codingCoordStr_2=c.801C>T;refseq.codonCoord_1=436;refseq.codonCoord_2=267;refseq.end_1=16250802;refseq.end_2=16250802;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1444;refseq.mrnaCoord_2=984;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I436I;refseq.proteinCoordStr_2=p.I267I;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=11;refseq.spliceDist_2=11;refseq.start_1=16250802;refseq.start_2=16250802;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;set=Intersection GT 0/1
|
|
chr1 16251312 . A T 129.09 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=297;Dels=0.00;HRun=0;HaplotypeScore=10.81;MQ=83.64;MQ0=2;OQ=4199.62;QD=14.14;RankSumP=0.0250061;SB=-1650.08;SecondBestBaseQ=27;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1441A>T;refseq.codingCoordStr_2=c.934A>T;refseq.codonCoord_1=481;refseq.codonCoord_2=312;refseq.end_1=16251312;refseq.end_2=16251312;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1577;refseq.mrnaCoord_2=1117;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T481S;refseq.proteinCoordStr_2=p.T312S;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=33;refseq.spliceDist_2=33;refseq.start_1=16251312;refseq.start_2=16251312;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=Intersection GT 0/1
|
|
chr1 16252783 . T C 191.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=323;Dels=0.00;HRun=0;HaplotypeScore=3.01;MQ=79.05;MQ0=67;OQ=8282.70;QD=25.64;RankSumP=1.00000;SB=-2474.66;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1685T>C;refseq.codingCoordStr_2=c.1178T>C;refseq.codonCoord_1=562;refseq.codonCoord_2=393;refseq.end_1=16252783;refseq.end_2=16252783;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1821;refseq.mrnaCoord_2=1361;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.M562T;refseq.proteinCoordStr_2=p.M393T;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=63;refseq.spliceDist_2=63;refseq.start_1=16252783;refseq.start_2=16252783;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 1/1
|
|
chr1 16252830 . A G 134.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=213;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=57.96;MQ0=57;OQ=5354.57;QD=25.14;RankSumP=1.00000;SB=-1179.65;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1732A>G;refseq.codingCoordStr_2=c.1225A>G;refseq.codonCoord_1=578;refseq.codonCoord_2=409;refseq.end_1=16252830;refseq.end_2=16252830;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1868;refseq.mrnaCoord_2=1408;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K578E;refseq.proteinCoordStr_2=p.K409E;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=-25;refseq.spliceDist_2=-25;refseq.start_1=16252830;refseq.start_2=16252830;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 1/1
|
|
chr1 16252839 . C T 75.45 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=205;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=56.61;MQ0=47;OQ=5963.25;QD=29.09;RankSumP=1.00000;SB=-1589.53;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1741C>T;refseq.codingCoordStr_2=c.1234C>T;refseq.codonCoord_1=581;refseq.codonCoord_2=412;refseq.end_1=16252839;refseq.end_2=16252839;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1877;refseq.mrnaCoord_2=1417;refseq.name2_1=CLCNKB;refseq.name2_2=CLCNKB;refseq.name_1=NM_000085;refseq.name_2=NM_001165945;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L581L;refseq.proteinCoordStr_2=p.L412L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=-16;refseq.spliceDist_2=-16;refseq.start_1=16252839;refseq.start_2=16252839;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=TTG;refseq.variantCodon_2=TTG;set=Intersection GT 1/1
|
|
chr1 16257718 . C A 46 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=47.56;MQ0=5;OQ=329.63;QD=9.99;RankSumP=0.428571;SB=-105.79;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.644G>T;refseq.codonCoord=215;refseq.end=16257718;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=834;refseq.name=NM_182623;refseq.name2=FAM131C;refseq.positionType=CDS;refseq.proteinCoordStr=p.S215I;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=82;refseq.start=16257718;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/0
|
|
chr1 16259034 . G C 57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=86.12;MQ0=2;OQ=1714.58;QD=34.99;RankSumP=1.00000;SB=-692.70;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.368C>G;refseq.codonCoord=123;refseq.end=16259034;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=558;refseq.name=NM_182623;refseq.name2=FAM131C;refseq.positionType=CDS;refseq.proteinCoordStr=p.P123R;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-84;refseq.start=16259034;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/1
|
|
chr1 16261233 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=175;Dels=0.00;HRun=1;HaplotypeScore=6.00;MQ=61.05;MQ0=8;OQ=2186.06;QD=12.49;RankSumP=0.100213;SB=-1110.97;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.216A>G;refseq.codonCoord=72;refseq.end=16261233;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=406;refseq.name=NM_182623;refseq.name2=FAM131C;refseq.positionType=CDS;refseq.proteinCoordStr=p.R72R;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=42;refseq.start=16261233;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 1/0
|
|
chr1 16336980 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1267A>C;refseq.codonCoord=423;refseq.end=16336980;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1404;refseq.name=NM_004431;refseq.name2=EPHA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T423P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-46;refseq.start=16336980;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 16337260 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=1.84;MQ=99.00;MQ0=0;OQ=904.28;QD=19.24;RankSumP=0.718034;SB=-375.35;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.987C>T;refseq.codonCoord=329;refseq.end=16337260;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1124;refseq.name=NM_004431;refseq.name2=EPHA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P329P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=16337260;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/0
|
|
chr1 16347517 . G C 1 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.500000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.766C>G;refseq.codonCoord=256;refseq.end=16347517;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=903;refseq.name=NM_004431;refseq.name2=EPHA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P256A;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-58;refseq.start=16347517;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 16347519 . A C 55 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=3.65564e-07;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.764T>G;refseq.codonCoord=255;refseq.end=16347519;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=901;refseq.name=NM_004431;refseq.name2=EPHA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V255G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-60;refseq.start=16347519;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 16347710 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=505.38;QD=8.57;RankSumP=0.727520;SB=-219.42;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.573G>A;refseq.codonCoord=191;refseq.end=16347710;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=710;refseq.name=NM_004431;refseq.name2=EPHA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L191L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-251;refseq.start=16347710;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 0/1
|
|
chr1 16347713 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=473.74;QD=8.03;RankSumP=0.0746050;SB=-186.78;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.570G>A;refseq.codonCoord=190;refseq.end=16347713;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=707;refseq.name=NM_004431;refseq.name2=EPHA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A190A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-254;refseq.start=16347713;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 16450495 . G C 247.01 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=98.49;MQ0=0;OQ=3459.48;QD=46.13;RankSumP=1.00000;SB=-1215.72;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1411C>G;refseq.codonCoord=471;refseq.end=16450495;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1627;refseq.name=NM_018994;refseq.name2=FBXO42;refseq.positionType=CDS;refseq.proteinCoordStr=p.P471A;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=373;refseq.start=16450495;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 16608719 . T C 223.32 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=99.00;MQ0=0;OQ=2256.56;QD=35.82;RankSumP=1.00000;SB=-789.13;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.551A>G;refseq.codonCoord=184;refseq.end=16608719;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1034;refseq.name=NM_198546;refseq.name2=SPATA21;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q184R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-37;refseq.start=16608719;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/1
|
|
chr1 17121119 . A G 6 PASS AC=2;AF=1.00;AN=2;BestBaseQ=20;DB;DP=5;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=135.23;QD=27.05;RankSumP=1.00000;SB=-51.69;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.19A>G;refseq.codonCoord=7;refseq.end=17121119;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=88;refseq.name=NM_014675;refseq.name2=CROCC;refseq.positionType=CDS;refseq.proteinCoordStr=p.R7G;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-42;refseq.start=17121119;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=filterInsoap-gatk GT 1/1
|
|
chr1 17147924 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=166;Dels=0.00;HRun=0;HaplotypeScore=26.68;MQ=37.67;MQ0=48;OQ=74.40;QD=0.45;SB=59.20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2752C>T;refseq.codonCoord=918;refseq.end=17147924;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2821;refseq.name=NM_014675;refseq.name2=CROCC;refseq.positionType=CDS;refseq.proteinCoordStr=p.R918W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=44;refseq.start=17147924;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:109,51:86:-36.63,-25.91,-285.57:99
|
|
chr1 17153333 . C T 88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.464220;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3215C>T;refseq.codonCoord=1072;refseq.end=17153333;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3284;refseq.name=NM_014675;refseq.name2=CROCC;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1072M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=29;refseq.start=17153333;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=soap GT 0/1
|
|
chr1 17155160 . G A 60 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=99.00;MQ0=0;OQ=79.88;QD=13.31;RankSumP=0.642857;SB=-47.65;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3786G>A;refseq.codonCoord=1262;refseq.end=17155160;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3855;refseq.name=NM_014675;refseq.name2=CROCC;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1262G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-79;refseq.start=17155160;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 17165158 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=129;Dels=0.00;HRun=1;HaplotypeScore=5.08;MQ=98.90;MQ0=0;OQ=2041.88;QD=15.83;RankSumP=0.254264;SB=-870.61;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4653G>A;refseq.codonCoord=1551;refseq.end=17165158;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4722;refseq.name=NM_014675;refseq.name2=CROCC;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1551S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-44;refseq.start=17165158;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/0
|
|
chr1 17168266 . T C 78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=98.82;MQ0=0;OQ=1349.21;QD=30.66;RankSumP=1.00000;SB=-618.40;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5145T>C;refseq.codonCoord=1715;refseq.end=17168266;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5214;refseq.name=NM_014675;refseq.name2=CROCC;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1715A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=69;refseq.start=17168266;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 17174367 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=210;Dels=0.00;HRun=0;HaplotypeScore=7.76;MQ=98.93;MQ0=0;OQ=2294.50;QD=10.93;RankSumP=0.405230;SB=-1028.34;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.429T>C;refseq.codingCoordStr_2=c.429T>C;refseq.codingCoordStr_3=c.432T>C;refseq.codingCoordStr_4=c.432T>C;refseq.codonCoord_1=143;refseq.codonCoord_2=143;refseq.codonCoord_3=144;refseq.codonCoord_4=144;refseq.end_1=17174367;refseq.end_2=17174367;refseq.end_3=17174367;refseq.end_4=17174367;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=543;refseq.mrnaCoord_2=562;refseq.mrnaCoord_3=565;refseq.mrnaCoord_4=546;refseq.name2_1=MFAP2;refseq.name2_2=MFAP2;refseq.name2_3=MFAP2;refseq.name2_4=MFAP2;refseq.name_1=NM_001135247;refseq.name_2=NM_001135248;refseq.name_3=NM_002403;refseq.name_4=NM_017459;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.H143H;refseq.proteinCoordStr_2=p.H143H;refseq.proteinCoordStr_3=p.H144H;refseq.proteinCoordStr_4=p.H144H;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceAA_4=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.referenceCodon_3=CAT;refseq.referenceCodon_4=CAT;refseq.spliceDist_1=-17;refseq.spliceDist_2=-17;refseq.spliceDist_3=-17;refseq.spliceDist_4=-17;refseq.start_1=17174367;refseq.start_2=17174367;refseq.start_3=17174367;refseq.start_4=17174367;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantAA_4=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;refseq.variantCodon_4=CAC;set=Intersection GT 0/1
|
|
chr1 17185330 . C T 120.07 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.75;MQ=98.73;MQ0=0;OQ=1387.07;QD=32.26;RankSumP=1.00000;SB=-271.86;SecondBestBaseQ=10;refseq.changesAA_1=false;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.3501G>A;refseq.codingCoordStr_2=c.3214G>A;refseq.codingCoordStr_3=c.3516G>A;refseq.codonCoord_1=1167;refseq.codonCoord_2=1072;refseq.codonCoord_3=1172;refseq.end_1=17185330;refseq.end_2=17185330;refseq.end_3=17185330;refseq.frame_1=2;refseq.frame_2=0;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3691;refseq.mrnaCoord_2=3404;refseq.mrnaCoord_3=3706;refseq.name2_1=ATP13A2;refseq.name2_2=ATP13A2;refseq.name2_3=ATP13A2;refseq.name_1=NM_001141973;refseq.name_2=NM_001141974;refseq.name_3=NM_022089;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P1167P;refseq.proteinCoordStr_2=p.A1072T;refseq.proteinCoordStr_3=p.P1172P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=CCG;refseq.spliceDist_1=111;refseq.spliceDist_2=111;refseq.spliceDist_3=111;refseq.start_1=17185330;refseq.start_2=17185330;refseq.start_3=17185330;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=ACC;refseq.variantCodon_3=CCA;set=Intersection GT 1/1
|
|
chr1 17185930 . G A 155.81 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=98.63;MQ0=0;OQ=2557.15;QD=31.57;RankSumP=1.00000;SB=-931.66;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.3177C>T;refseq.codingCoordStr_2=c.3060C>T;refseq.codingCoordStr_3=c.3192C>T;refseq.codonCoord_1=1059;refseq.codonCoord_2=1020;refseq.codonCoord_3=1064;refseq.end_1=17185930;refseq.end_2=17185930;refseq.end_3=17185930;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3367;refseq.mrnaCoord_2=3250;refseq.mrnaCoord_3=3382;refseq.name2_1=ATP13A2;refseq.name2_2=ATP13A2;refseq.name2_3=ATP13A2;refseq.name_1=NM_001141973;refseq.name_2=NM_001141974;refseq.name_3=NM_022089;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A1059A;refseq.proteinCoordStr_2=p.A1020A;refseq.proteinCoordStr_3=p.A1064A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GCC;refseq.spliceDist_1=-44;refseq.spliceDist_2=-44;refseq.spliceDist_3=-44;refseq.start_1=17185930;refseq.start_2=17185930;refseq.start_3=17185930;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;refseq.variantCodon_3=GCT;set=Intersection GT 1/1
|
|
chr1 17186241 . C T 71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=9.09;MQ=97.63;MQ0=0;OQ=3564.01;QD=28.29;RankSumP=1.00000;SB=-926.93;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2955G>A;refseq.codingCoordStr_2=c.2838G>A;refseq.codingCoordStr_3=c.2970G>A;refseq.codonCoord_1=985;refseq.codonCoord_2=946;refseq.codonCoord_3=990;refseq.end_1=17186241;refseq.end_2=17186241;refseq.end_3=17186241;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3145;refseq.mrnaCoord_2=3028;refseq.mrnaCoord_3=3160;refseq.name2_1=ATP13A2;refseq.name2_2=ATP13A2;refseq.name2_3=ATP13A2;refseq.name_1=NM_001141973;refseq.name_2=NM_001141974;refseq.name_3=NM_022089;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V985V;refseq.proteinCoordStr_2=p.V946V;refseq.proteinCoordStr_3=p.V990V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.spliceDist_1=111;refseq.spliceDist_2=111;refseq.spliceDist_3=111;refseq.start_1=17186241;refseq.start_2=17186241;refseq.start_3=17186241;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;refseq.variantCodon_3=GTA;set=Intersection GT 1/1
|
|
chr1 17187529 . G A 311.79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.53;MQ0=0;OQ=3002.09;QD=37.06;RankSumP=1.00000;SB=-1138.37;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2622C>T;refseq.codingCoordStr_2=c.2505C>T;refseq.codingCoordStr_3=c.2637C>T;refseq.codonCoord_1=874;refseq.codonCoord_2=835;refseq.codonCoord_3=879;refseq.end_1=17187529;refseq.end_2=17187529;refseq.end_3=17187529;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2812;refseq.mrnaCoord_2=2695;refseq.mrnaCoord_3=2827;refseq.name2_1=ATP13A2;refseq.name2_2=ATP13A2;refseq.name2_3=ATP13A2;refseq.name_1=NM_001141973;refseq.name_2=NM_001141974;refseq.name_3=NM_022089;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.G874G;refseq.proteinCoordStr_2=p.G835G;refseq.proteinCoordStr_3=p.G879G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.referenceCodon_3=GGC;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.spliceDist_3=28;refseq.start_1=17187529;refseq.start_2=17187529;refseq.start_3=17187529;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;refseq.variantCodon_3=GGT;set=Intersection GT 1/1
|
|
chr1 17191598 . G A 259.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.15;MQ=97.04;MQ0=0;OQ=1605.23;QD=36.48;RankSumP=1.00000;SB=-747.43;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1800C>T;refseq.codingCoordStr_2=c.1800C>T;refseq.codingCoordStr_3=c.1815C>T;refseq.codonCoord_1=600;refseq.codonCoord_2=600;refseq.codonCoord_3=605;refseq.end_1=17191598;refseq.end_2=17191598;refseq.end_3=17191598;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1990;refseq.mrnaCoord_2=1990;refseq.mrnaCoord_3=2005;refseq.name2_1=ATP13A2;refseq.name2_2=ATP13A2;refseq.name2_3=ATP13A2;refseq.name_1=NM_001141973;refseq.name_2=NM_001141974;refseq.name_3=NM_022089;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P600P;refseq.proteinCoordStr_2=p.P600P;refseq.proteinCoordStr_3=p.P605P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.spliceDist_1=-31;refseq.spliceDist_2=-31;refseq.spliceDist_3=-31;refseq.start_1=17191598;refseq.start_2=17191598;refseq.start_3=17191598;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;set=Intersection GT 1/1
|
|
chr1 17192709 . A C 23 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=3;RankSumP=0.510212;SecondBestBaseQ=15;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1734+2;refseq.codingCoordStr_2=c.1734+2;refseq.codingCoordStr_3=c.1749+2;refseq.end_1=17192709;refseq.end_2=17192709;refseq.end_3=17192709;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.name2_1=ATP13A2;refseq.name2_2=ATP13A2;refseq.name2_3=ATP13A2;refseq.name_1=NM_001141973;refseq.name_2=NM_001141974;refseq.name_3=NM_022089;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceDist_3=2;refseq.spliceInfo_1=splice-donor_2;refseq.spliceInfo_2=splice-donor_2;refseq.spliceInfo_3=splice-donor_2;refseq.start_1=17192709;refseq.start_2=17192709;refseq.start_3=17192709;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;set=soap GT 0/1
|
|
chr1 17253084 . G T 193.78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=15;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=8.09;MQ=97.96;MQ0=0;OQ=992.63;QD=16.27;RankSumP=1.00000;SB=-430.57;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.18C>A;refseq.codonCoord=6;refseq.end=17253084;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=169;refseq.name=NM_003000;refseq.name2=SDHB;refseq.positionType=CDS;refseq.proteinCoordStr=p.A6A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-55;refseq.start=17253084;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 17269290 . T C 352.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=139;Dels=0.00;HRun=1;HaplotypeScore=1.77;MQ=99.00;MQ0=0;OQ=5717.91;QD=41.14;RankSumP=1.00000;SB=-2744.62;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1644A>G;refseq.codonCoord=548;refseq.end=17269290;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1726;refseq.name=NM_007365;refseq.name2=PADI2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L548L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=9;refseq.spliceInfo=splice-acceptor_9;refseq.start=17269290;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 17274842 . C T 340.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=172;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=98.70;MQ0=0;OQ=6739.56;QD=39.18;RankSumP=1.00000;SB=-1275.71;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1374G>A;refseq.codonCoord=458;refseq.end=17274842;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1456;refseq.name=NM_007365;refseq.name2=PADI2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A458A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=64;refseq.start=17274842;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 17278396 . G A 353.34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=4.46;MQ=98.79;MQ0=0;OQ=3756.82;QD=38.33;RankSumP=1.00000;SB=-1521.67;SecondBestBaseQ=10;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1260C>T;refseq.codonCoord=420;refseq.end=17278396;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1342;refseq.name=NM_007365;refseq.name2=PADI2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N420N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-51;refseq.start=17278396;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/1
|
|
chr1 17428095 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=96.94;MQ0=0;OQ=232.13;QD=9.29;RankSumP=0.392222;SB=-97.78;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.891G>T;refseq.codonCoord=297;refseq.end=17428095;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=983;refseq.name=NM_013358;refseq.name2=PADI1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T297T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-39;refseq.start=17428095;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 0/1
|
|
chr1 17482035 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=187;Dels=0.00;HRun=0;HaplotypeScore=8.34;MQ=98.61;MQ0=0;OQ=2396.71;QD=12.82;RankSumP=0.113367;SB=-381.68;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1869G>T;refseq.codonCoord=623;refseq.end=17482035;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1909;refseq.name=NM_016233;refseq.name2=PADI3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P623P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=108;refseq.start=17482035;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 17612173 . G A 138.81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=4.94;MQ=97.99;MQ0=0;OQ=1424.48;QD=18.26;RankSumP=0.217772;SB=-554.10;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1296C>T;refseq.codingCoordStr_2=c.1296C>T;refseq.codonCoord_1=432;refseq.codonCoord_2=432;refseq.end_1=17612173;refseq.end_2=17612173;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1343;refseq.mrnaCoord_2=1484;refseq.name2_1=RCC2;refseq.name2_2=RCC2;refseq.name_1=NM_001136204;refseq.name_2=NM_018715;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I432I;refseq.proteinCoordStr_2=p.I432I;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=-18;refseq.spliceDist_2=-18;refseq.start_1=17612173;refseq.start_2=17612173;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;set=Intersection GT 1/0
|
|
chr1 17863639 . T C 62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=122;Dels=0.01;HRun=3;HaplotypeScore=13.24;MQ=98.34;MQ0=0;OQ=3960.06;QD=32.46;RankSumP=1.00000;SB=-1674.51;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2854T>C;refseq.codingCoordStr_2=c.2971T>C;refseq.codonCoord_1=952;refseq.codonCoord_2=991;refseq.end_1=17863639;refseq.end_2=17863639;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2897;refseq.mrnaCoord_2=3130;refseq.name2_1=ARHGEF10L;refseq.name2_2=ARHGEF10L;refseq.name_1=NM_001011722;refseq.name_2=NM_018125;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.W952R;refseq.proteinCoordStr_2=p.W991R;refseq.referenceAA_1=Trp;refseq.referenceAA_2=Trp;refseq.referenceCodon_1=TGG;refseq.referenceCodon_2=TGG;refseq.spliceDist_1=-39;refseq.spliceDist_2=-39;refseq.start_1=17863639;refseq.start_2=17863639;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;set=Intersection GT 1/1
|
|
chr1 17895952 . C T 289.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=168;Dels=0.00;HRun=0;HaplotypeScore=7.36;MQ=98.64;MQ0=0;OQ=6455.73;QD=38.43;RankSumP=1.00000;SB=-2952.38;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3213C>T;refseq.codingCoordStr_2=c.3330C>T;refseq.codonCoord_1=1071;refseq.codonCoord_2=1110;refseq.end_1=17895952;refseq.end_2=17895952;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3256;refseq.mrnaCoord_2=3489;refseq.name2_1=ARHGEF10L;refseq.name2_2=ARHGEF10L;refseq.name_1=NM_001011722;refseq.name_2=NM_018125;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N1071N;refseq.proteinCoordStr_2=p.N1110N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=23;refseq.spliceDist_2=23;refseq.start_1=17895952;refseq.start_2=17895952;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 1/1
|
|
chr1 17896096 . T C 99.85 PASS AC=2;AF=1.00;AN=2;BestBaseQ=24;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=92.25;MQ0=0;OQ=828.20;QD=29.58;RankSumP=1.00000;SB=-433.51;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3357T>C;refseq.codingCoordStr_2=c.3474T>C;refseq.codonCoord_1=1119;refseq.codonCoord_2=1158;refseq.end_1=17896096;refseq.end_2=17896096;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3400;refseq.mrnaCoord_2=3633;refseq.name2_1=ARHGEF10L;refseq.name2_2=ARHGEF10L;refseq.name_1=NM_001011722;refseq.name_2=NM_018125;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D1119D;refseq.proteinCoordStr_2=p.D1158D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=167;refseq.spliceDist_2=167;refseq.start_1=17896096;refseq.start_2=17896096;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=Intersection GT 1/1
|
|
chr1 17896277 . A G 78.56 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.99;MQ=98.16;MQ0=0;OQ=1014.97;QD=25.37;RankSumP=1.00000;SB=-483.49;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3538A>G;refseq.codingCoordStr_2=c.3655A>G;refseq.codonCoord_1=1180;refseq.codonCoord_2=1219;refseq.end_1=17896277;refseq.end_2=17896277;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3581;refseq.mrnaCoord_2=3814;refseq.name2_1=ARHGEF10L;refseq.name2_2=ARHGEF10L;refseq.name_1=NM_001011722;refseq.name_2=NM_018125;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I1180V;refseq.proteinCoordStr_2=p.I1219V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=348;refseq.spliceDist_2=348;refseq.start_1=17896277;refseq.start_2=17896277;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=Intersection GT 1/1
|
|
chr1 17896464 . G A 97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.36;MQ0=0;OQ=265.70;QD=9.84;RankSumP=0.639857;SB=-74.27;SecondBestBaseQ=29;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.*2G>A;refseq.codingCoordStr_2=c.*2G>A;refseq.end_1=17896464;refseq.end_2=17896464;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.mrnaCoord_1=3768;refseq.mrnaCoord_2=4001;refseq.name2_1=ARHGEF10L;refseq.name2_2=ARHGEF10L;refseq.name_1=NM_001011722;refseq.name_2=NM_018125;refseq.numMatchingRecords=2;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.spliceDist_1=-494;refseq.spliceDist_2=-494;refseq.start_1=17896464;refseq.start_2=17896464;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;set=Intersection GT 1/0
|
|
chr1 18022097 . G T 110.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=132;Dels=0.00;HRun=1;HaplotypeScore=1.74;MQ=98.42;MQ0=0;OQ=1989.01;QD=15.07;RankSumP=0.500000;SB=-407.41;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7G>T;refseq.codonCoord=3;refseq.end=18022097;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=223;refseq.name=NM_030812;refseq.name2=ACTL8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A3S;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=31;refseq.start=18022097;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 0/1
|
|
chr1 18022153 . C A 328.24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=265;Dels=0.00;HRun=0;HaplotypeScore=9.39;MQ=98.47;MQ0=0;OQ=4594.81;QD=17.34;RankSumP=0.272367;SB=-1328.10;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.63C>A;refseq.codonCoord=21;refseq.end=18022153;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=279;refseq.name=NM_030812;refseq.name2=ACTL8;refseq.positionType=CDS;refseq.proteinCoordStr=p.G21G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=87;refseq.start=18022153;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 18025169 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=91;Dels=0.00;HRun=3;HaplotypeScore=1.11;MQ=98.59;MQ0=0;OQ=2004.31;QD=22.03;RankSumP=0.0956292;SB=-737.75;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.669C>T;refseq.codonCoord=223;refseq.end=18025169;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=885;refseq.name=NM_030812;refseq.name2=ACTL8;refseq.positionType=CDS;refseq.proteinCoordStr=p.D223D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=321;refseq.start=18025169;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 18490948 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.185T>G;refseq.codonCoord=62;refseq.end=18490948;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=568;refseq.name=NM_032880;refseq.name2=IGSF21;refseq.positionType=CDS;refseq.proteinCoordStr=p.V62G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=18490948;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 18564305 . T G 15 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=4.66862e-06;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.542T>G;refseq.codonCoord=181;refseq.end=18564305;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=925;refseq.name=NM_032880;refseq.name2=IGSF21;refseq.positionType=CDS;refseq.proteinCoordStr=p.V181G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=18564305;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 18680123 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=151;Dels=0.00;HRun=1;HaplotypeScore=14.64;MQ=98.22;MQ0=0;OQ=2226.56;QD=14.75;RankSumP=0.0944004;SB=-516.80;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.61G>T;refseq.codonCoord=21;refseq.end=18680123;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=113;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.V21L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=113;refseq.start=18680123;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 18680207 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=96.99;MQ0=0;OQ=575.72;QD=14.76;RankSumP=0.454178;SB=-171.79;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.145G>C;refseq.codonCoord=49;refseq.end=18680207;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=197;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G49R;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=197;refseq.start=18680207;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 0/1
|
|
chr1 18680342 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.58;MQ0=0;OQ=496.23;QD=16.01;RankSumP=0.305706;SB=-193.24;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.280G>A;refseq.codonCoord=94;refseq.end=18680342;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=332;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G94S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=332;refseq.start=18680342;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/0
|
|
chr1 18680368 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=98.63;MQ0=0;OQ=458.75;QD=13.11;RankSumP=0.162266;SB=-125.07;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.306C>T;refseq.codonCoord=102;refseq.end=18680368;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=358;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G102G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=358;refseq.start=18680368;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 0/1
|
|
chr1 18680484 . C G 111.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=98.09;MQ0=0;OQ=1333.12;QD=19.90;RankSumP=0.0526206;SB=-298.53;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.422C>G;refseq.codonCoord=141;refseq.end=18680484;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=474;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.P141R;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=474;refseq.start=18680484;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/0
|
|
chr1 18680643 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=219;Dels=0.00;HRun=4;HaplotypeScore=9.84;MQ=98.64;MQ0=0;OQ=4413.61;QD=20.15;RankSumP=0.207158;SB=-1610.44;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.581G>C;refseq.codonCoord=194;refseq.end=18680643;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=633;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.R194P;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=633;refseq.start=18680643;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 18680656 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=225;Dels=0.00;HRun=2;HaplotypeScore=9.32;MQ=98.65;MQ0=0;OQ=3135.91;QD=13.94;RankSumP=0.232122;SB=-1286.10;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.594A>G;refseq.codonCoord=198;refseq.end=18680656;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=646;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G198G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=646;refseq.start=18680656;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 0/1
|
|
chr1 18680879 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=98.78;MQ0=0;OQ=1464.66;QD=18.78;RankSumP=0.344955;SB=-274.97;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.817C>A;refseq.codonCoord=273;refseq.end=18680879;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=869;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.H273N;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=869;refseq.start=18680879;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 18681052 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=10.00;MQ=96.11;MQ0=0;OQ=614.39;QD=11.82;RankSumP=0.358701;SB=-72.75;SecondBestBaseQ=20;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.990T>A;refseq.codonCoord=330;refseq.end=18681052;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1042;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.A330A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=1042;refseq.start=18681052;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 18681113 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=96.05;MQ0=0;OQ=1067.09;QD=15.69;RankSumP=0.458321;SB=-376.86;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1051A>C;refseq.codonCoord=351;refseq.end=18681113;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1103;refseq.name=NM_152375;refseq.name2=KLHDC7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T351P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=1103;refseq.start=18681113;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 18899826 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=99.00;MQ0=0;OQ=430.72;QD=7.98;RankSumP=0.388831;SB=-118.73;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.879A>G;refseq.codingCoordStr_2=c.879A>G;refseq.codingCoordStr_3=c.873A>G;refseq.codonCoord_1=293;refseq.codonCoord_2=293;refseq.codonCoord_3=291;refseq.end_1=18899826;refseq.end_2=18899826;refseq.end_3=18899826;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1477;refseq.mrnaCoord_2=1477;refseq.mrnaCoord_3=1471;refseq.name2_1=PAX7;refseq.name2_2=PAX7;refseq.name2_3=PAX7;refseq.name_1=NM_001135254;refseq.name_2=NM_002584;refseq.name_3=NM_013945;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P293P;refseq.proteinCoordStr_2=p.P293P;refseq.proteinCoordStr_3=p.P291P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.referenceCodon_3=CCA;refseq.spliceDist_1=-74;refseq.spliceDist_2=-74;refseq.spliceDist_3=-74;refseq.start_1=18899826;refseq.start_2=18899826;refseq.start_3=18899826;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCG;refseq.variantCodon_2=CCG;refseq.variantCodon_3=CCG;set=Intersection GT 0/1
|
|
chr1 19039315 . T G 17 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.115244;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1885A>C;refseq.codonCoord=629;refseq.end=19039315;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1886;refseq.name=NM_152232;refseq.name2=TAS1R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T629P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=294;refseq.start=19039315;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 19048433 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=4.74;MQ=98.58;MQ0=0;OQ=1463.17;QD=11.99;RankSumP=0.0492273;SB=-365.23;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1456A>G;refseq.codonCoord=486;refseq.end=19048433;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1457;refseq.name=NM_152232;refseq.name2=TAS1R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.I486V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-12;refseq.start=19048433;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 19053602 . G C 143.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=152;Dels=0.00;HRun=1;HaplotypeScore=2.74;MQ=98.22;MQ0=0;OQ=2467.44;QD=16.23;RankSumP=0.105861;SB=-1191.25;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.949C>G;refseq.codonCoord=317;refseq.end=19053602;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=950;refseq.name=NM_152232;refseq.name2=TAS1R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R317G;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-309;refseq.start=19053602;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 19053669 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=97;Dels=0.00;HRun=2;HaplotypeScore=2.95;MQ=99.00;MQ0=0;OQ=1137.60;QD=11.73;RankSumP=0.222614;SB=-566.52;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.882T>G;refseq.codonCoord=294;refseq.end=19053669;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=883;refseq.name=NM_152232;refseq.name2=TAS1R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T294T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-376;refseq.start=19053669;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 0/1
|
|
chr1 19053980 . T C 152.32 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=222;Dels=0.00;HRun=0;HaplotypeScore=7.93;MQ=98.68;MQ0=0;OQ=3213.62;QD=14.48;RankSumP=0.228270;SB=-1183.66;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.571A>G;refseq.codonCoord=191;refseq.end=19053980;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=572;refseq.name=NM_152232;refseq.name2=TAS1R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.I191V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=88;refseq.start=19053980;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 19056664 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=294;Dels=0.00;HRun=0;HaplotypeScore=16.52;MQ=98.52;MQ0=0;OQ=4447.40;QD=15.13;RankSumP=0.320459;SB=-1354.96;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.231T>C;refseq.codonCoord=77;refseq.end=19056664;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=232;refseq.name=NM_152232;refseq.name2=TAS1R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.F77F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=49;refseq.start=19056664;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 0/1
|
|
chr1 19058716 . G C 252.16 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=263;Dels=0.00;HRun=0;HaplotypeScore=12.69;MQ=98.67;MQ0=0;OQ=6044.90;QD=22.98;RankSumP=0.163801;SB=-2306.47;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.26C>G;refseq.codonCoord=9;refseq.end=19058716;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=27;refseq.name=NM_152232;refseq.name2=TAS1R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S9C;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=27;refseq.start=19058716;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 0/1
|
|
chr1 19074543 . A G 290.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=2568.54;QD=33.36;RankSumP=1.00000;SB=-1276.52;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1200T>C;refseq.codingCoordStr_2=c.1380T>C;refseq.codingCoordStr_3=c.1380T>C;refseq.codonCoord_1=400;refseq.codonCoord_2=460;refseq.codonCoord_3=460;refseq.end_1=19074543;refseq.end_2=19074543;refseq.end_3=19074543;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1516;refseq.mrnaCoord_2=1656;refseq.mrnaCoord_3=1656;refseq.name2_1=ALDH4A1;refseq.name2_2=ALDH4A1;refseq.name2_3=ALDH4A1;refseq.name_1=NM_001161504;refseq.name_2=NM_003748;refseq.name_3=NM_170726;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.D400D;refseq.proteinCoordStr_2=p.D460D;refseq.proteinCoordStr_3=p.D460D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.referenceCodon_3=GAT;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.spliceDist_3=42;refseq.start_1=19074543;refseq.start_2=19074543;refseq.start_3=19074543;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;refseq.variantCodon_3=GAC;set=Intersection GT 1/1
|
|
chr1 19075483 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=96.50;MQ0=0;OQ=697.38;QD=23.25;RankSumP=0.709148;SB=-303.23;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1071C>T;refseq.codingCoordStr_2=c.1251C>T;refseq.codingCoordStr_3=c.1251C>T;refseq.codonCoord_1=357;refseq.codonCoord_2=417;refseq.codonCoord_3=417;refseq.end_1=19075483;refseq.end_2=19075483;refseq.end_3=19075483;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1387;refseq.mrnaCoord_2=1527;refseq.mrnaCoord_3=1527;refseq.name2_1=ALDH4A1;refseq.name2_2=ALDH4A1;refseq.name2_3=ALDH4A1;refseq.name_1=NM_001161504;refseq.name_2=NM_003748;refseq.name_3=NM_170726;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A357A;refseq.proteinCoordStr_2=p.A417A;refseq.proteinCoordStr_3=p.A417A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GCC;refseq.spliceDist_1=66;refseq.spliceDist_2=66;refseq.spliceDist_3=66;refseq.start_1=19075483;refseq.start_2=19075483;refseq.start_3=19075483;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;refseq.variantCodon_3=GCT;set=Intersection GT 1/0
|
|
chr1 19075504 . T C 145.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=20;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=95.40;MQ0=0;OQ=403.72;QD=19.22;RankSumP=1.00000;SB=-111.04;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1050A>G;refseq.codingCoordStr_2=c.1230A>G;refseq.codingCoordStr_3=c.1230A>G;refseq.codonCoord_1=350;refseq.codonCoord_2=410;refseq.codonCoord_3=410;refseq.end_1=19075504;refseq.end_2=19075504;refseq.end_3=19075504;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1366;refseq.mrnaCoord_2=1506;refseq.mrnaCoord_3=1506;refseq.name2_1=ALDH4A1;refseq.name2_2=ALDH4A1;refseq.name2_3=ALDH4A1;refseq.name_1=NM_001161504;refseq.name_2=NM_003748;refseq.name_3=NM_170726;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S350S;refseq.proteinCoordStr_2=p.S410S;refseq.proteinCoordStr_3=p.S410S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.spliceDist_1=45;refseq.spliceDist_2=45;refseq.spliceDist_3=45;refseq.start_1=19075504;refseq.start_2=19075504;refseq.start_3=19075504;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;refseq.variantCodon_3=TCG;set=filterInsoap-gatk GT 1/1
|
|
chr1 19075513 . T C 147.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=14;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=94.54;MQ0=0;OQ=311.89;QD=18.35;RankSumP=1.00000;SB=-122.05;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1041A>G;refseq.codingCoordStr_2=c.1221A>G;refseq.codingCoordStr_3=c.1221A>G;refseq.codonCoord_1=347;refseq.codonCoord_2=407;refseq.codonCoord_3=407;refseq.end_1=19075513;refseq.end_2=19075513;refseq.end_3=19075513;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1357;refseq.mrnaCoord_2=1497;refseq.mrnaCoord_3=1497;refseq.name2_1=ALDH4A1;refseq.name2_2=ALDH4A1;refseq.name2_3=ALDH4A1;refseq.name_1=NM_001161504;refseq.name_2=NM_003748;refseq.name_3=NM_170726;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A347A;refseq.proteinCoordStr_2=p.A407A;refseq.proteinCoordStr_3=p.A407A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.referenceCodon_3=GCA;refseq.spliceDist_1=36;refseq.spliceDist_2=36;refseq.spliceDist_3=36;refseq.start_1=19075513;refseq.start_2=19075513;refseq.start_3=19075513;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;refseq.variantCodon_3=GCG;set=filterInsoap-gatk GT 1/1
|
|
chr1 19076584 . C G 142.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=2.75;MQ=99.00;MQ0=0;OQ=2037.66;QD=21.68;RankSumP=0.116785;SB=-983.85;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.870G>C;refseq.codingCoordStr_2=c.1050G>C;refseq.codingCoordStr_3=c.1050G>C;refseq.codonCoord_1=290;refseq.codonCoord_2=350;refseq.codonCoord_3=350;refseq.end_1=19076584;refseq.end_2=19076584;refseq.end_3=19076584;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1186;refseq.mrnaCoord_2=1326;refseq.mrnaCoord_3=1326;refseq.name2_1=ALDH4A1;refseq.name2_2=ALDH4A1;refseq.name2_3=ALDH4A1;refseq.name_1=NM_001161504;refseq.name_2=NM_003748;refseq.name_3=NM_170726;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A290A;refseq.proteinCoordStr_2=p.A350A;refseq.proteinCoordStr_3=p.A350A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.referenceCodon_3=GCG;refseq.spliceDist_1=-88;refseq.spliceDist_2=-88;refseq.spliceDist_3=-88;refseq.start_1=19076584;refseq.start_2=19076584;refseq.start_3=19076584;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;refseq.variantCodon_3=GCC;set=Intersection GT 1/0
|
|
chr1 19283716 . A G 366.53 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=240;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=98.89;MQ0=0;OQ=8882.60;QD=37.01;RankSumP=1.00000;SB=-3437.21;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.14877T>C;refseq.codonCoord=4959;refseq.end=19283716;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=14881;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H4959H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=64;refseq.start=19283716;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 19283755 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.184102;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.14838T>C;refseq.codonCoord=4946;refseq.end=19283755;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=14842;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.C4946C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=25;refseq.start=19283755;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=FilteredInAll GT 0/1
|
|
chr1 19285848 . T A 249.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=211;Dels=0.00;HRun=1;HaplotypeScore=8.22;MQ=98.76;MQ0=0;OQ=8222.60;QD=38.97;RankSumP=1.00000;SB=-2997.13;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.14599A>T;refseq.codonCoord=4867;refseq.end=19285848;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=14603;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.M4867L;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=55;refseq.start=19285848;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/1
|
|
chr1 19287891 . C T 56.32 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=285;Dels=0.00;HRun=2;HaplotypeScore=3.95;MQ=98.93;MQ0=0;OQ=11524.02;QD=40.44;RankSumP=1.00000;SB=-4864.95;SecondBestBaseQ=6;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.14379G>A;refseq.codonCoord=4793;refseq.end=19287891;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=14383;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.K4793K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-52;refseq.start=19287891;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/1
|
|
chr1 19288057 . A C 40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.500005;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.14213T>G;refseq.codonCoord=4738;refseq.end=19288057;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=14217;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V4738G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=19288057;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap GT 0/1
|
|
chr1 19295691 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=6.62423e-09;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.13431T>G;refseq.codonCoord=4477;refseq.end=19295691;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=13435;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G4477G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=41;refseq.start=19295691;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 19306036 . A G 211.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=110;Dels=0.00;HRun=0;HaplotypeScore=6.89;MQ=98.74;MQ0=0;OQ=3849.82;QD=35.00;RankSumP=1.00000;SB=-1165.30;SecondBestBaseQ=13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.12117T>C;refseq.codonCoord=4039;refseq.end=19306036;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=12121;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V4039V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=12;refseq.start=19306036;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 19314653 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10889A>C;refseq.codonCoord=3630;refseq.end=19314653;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=10893;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.D3630A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=66;refseq.start=19314653;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 19320339 . G T 50 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=2.55032e-05;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10072C>A;refseq.codonCoord=3358;refseq.end=19320339;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=10076;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q3358K;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-70;refseq.start=19320339;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 0/1
|
|
chr1 19320406 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.81;MQ=94.73;MQ0=0;OQ=600.53;QD=12.51;RankSumP=0.752777;SB=-177.35;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10005A>G;refseq.codonCoord=3335;refseq.end=19320406;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=10009;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.A3335A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=110;refseq.start=19320406;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/0
|
|
chr1 19320430 . C G 318.63 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=95.24;MQ0=0;OQ=1611.99;QD=43.57;RankSumP=1.00000;SB=-658.01;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9981G>C;refseq.codonCoord=3327;refseq.end=19320430;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=9985;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.L3327L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=86;refseq.start=19320430;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/1
|
|
chr1 19338174 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=4.62741e-09;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8721C>G;refseq.codonCoord=2907;refseq.end=19338174;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=8725;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2907G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-11;refseq.start=19338174;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 19347084 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7619A>C;refseq.codonCoord=2540;refseq.end=19347084;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7623;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2540P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-11;refseq.start=19347084;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 19364402 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4240A>C;refseq.codonCoord=1414;refseq.end=19364402;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4244;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1414P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=29;refseq.start=19364402;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 19372147 . T C 345.36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=231;Dels=0.00;HRun=0;HaplotypeScore=4.56;MQ=98.77;MQ0=0;OQ=4434.88;QD=19.20;RankSumP=0.0234507;SB=-1283.10;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3319A>G;refseq.codonCoord=1107;refseq.end=19372147;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3323;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1107A;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=28;refseq.start=19372147;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/0
|
|
chr1 19372541 . G A 166.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=2.97;MQ=99.00;MQ0=0;OQ=1290.46;QD=17.68;RankSumP=0.433365;SB=-628.60;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3144C>T;refseq.codonCoord=1048;refseq.end=19372541;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3148;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1048S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-22;refseq.start=19372541;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/0
|
|
chr1 19396859 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.785A>C;refseq.codonCoord=262;refseq.end=19396859;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=789;refseq.name=NM_020765;refseq.name2=UBR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.N262T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=34;refseq.start=19396859;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 19426426 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.306557;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2170C>T;refseq.codonCoord=724;refseq.end=19426426;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2213;refseq.name=NM_015047;refseq.name2=KIAA0090;refseq.positionType=CDS;refseq.proteinCoordStr=p.R724C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-33;refseq.start=19426426;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=FilteredInAll GT 1/0
|
|
chr1 19430033 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1956T>C;refseq.codonCoord=652;refseq.end=19430033;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1999;refseq.name=NM_015047;refseq.name2=KIAA0090;refseq.positionType=CDS;refseq.proteinCoordStr=p.F652F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=12;refseq.start=19430033;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=FilteredInAll GT 0/1
|
|
chr1 19437925 . C T 164.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=378;Dels=0.00;HRun=1;HaplotypeScore=9.57;MQ=98.90;MQ0=0;OQ=7946.68;QD=21.02;RankSumP=0.387613;SB=-2471.28;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1040G>A;refseq.codonCoord=347;refseq.end=19437925;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1083;refseq.name=NM_015047;refseq.name2=KIAA0090;refseq.positionType=CDS;refseq.proteinCoordStr=p.S347N;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=14;refseq.start=19437925;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 19437931 . C G 132.95 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=362;Dels=0.00;HRun=0;HaplotypeScore=18.50;MQ=98.89;MQ0=0;OQ=8473.00;QD=23.41;RankSumP=0.190487;SB=-2899.84;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1034G>C;refseq.codonCoord=345;refseq.end=19437931;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1077;refseq.name=NM_015047;refseq.name2=KIAA0090;refseq.positionType=CDS;refseq.proteinCoordStr=p.S345T;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=19437931;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/0
|
|
chr1 19439468 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=158;Dels=0.00;HRun=1;HaplotypeScore=4.92;MQ=98.17;MQ0=0;OQ=1776.08;QD=11.24;RankSumP=0.148632;SB=-388.69;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.696G>A;refseq.codonCoord=232;refseq.end=19439468;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=739;refseq.name=NM_015047;refseq.name2=KIAA0090;refseq.positionType=CDS;refseq.proteinCoordStr=p.E232E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=60;refseq.start=19439468;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 19442693 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.chr=chr1;refseq.codingCoordStr=c.380+2;refseq.end=19442693;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=false;refseq.name=NM_015047;refseq.name2=KIAA0090;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=19442693;refseq.transcriptStrand=-;set=FilteredInAll GT 0/1
|
|
chr1 19455126 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.185A>C;refseq.codonCoord=62;refseq.end=19455126;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=440;refseq.name=NM_016183;refseq.name2=MRTO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H62P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=19455126;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 19456591 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=103;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=98.54;MQ0=0;OQ=1351.07;QD=13.12;RankSumP=0.0590109;SB=-598.28;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.330G>A;refseq.codonCoord=110;refseq.end=19456591;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=585;refseq.name=NM_016183;refseq.name2=MRTO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.E110E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-12;refseq.start=19456591;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/0
|
|
chr1 19457794 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=504;Dels=0.00;HRun=2;HaplotypeScore=16.74;MQ=97.85;MQ0=0;OQ=10695.21;QD=21.22;RankSumP=0.189994;SB=-3932.41;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.603G>A;refseq.codonCoord=201;refseq.end=19457794;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=858;refseq.name=NM_016183;refseq.name2=MRTO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.K201K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=33;refseq.start=19457794;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/0
|
|
chr1 19469599 . G C 44.67 ESPStandard;LowQual AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=1;HaplotypeScore=5.04;MQ=34.58;MQ0=12;QD=0.30;SB=-25.05;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.440C>G;refseq.codingCoordStr_2=c.440C>G;refseq.codonCoord_1=147;refseq.codonCoord_2=147;refseq.end_1=19469599;refseq.end_2=19469599;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=440;refseq.mrnaCoord_2=440;refseq.name2_1=AKR7L;refseq.name2_2=AKR7L;refseq.name_1=NM_001145289;refseq.name_2=NM_201252;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A147G;refseq.proteinCoordStr_2=p.A147G;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=38;refseq.spliceDist_2=38;refseq.start_1=19469599;refseq.start_2=19469599;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:127,24:104:-39.07,-31.32,-471.49:77.50
|
|
chr1 19483828 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=401;Dels=0.00;HRun=1;HaplotypeScore=15.96;MQ=95.72;MQ0=4;OQ=8627.32;QD=21.51;RankSumP=0.353644;SB=-2735.79;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.643A>G;refseq.codonCoord=215;refseq.end=19483828;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=720;refseq.name=NM_012067;refseq.name2=AKR7A3;refseq.positionType=CDS;refseq.proteinCoordStr=p.N215D;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=39;refseq.start=19483828;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/0
|
|
chr1 19485064 . C T 38.18 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=104;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=36.73;MQ0=3;OQ=1263.03;QD=12.14;RankSumP=0.534928;SB=-300.79;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.412G>A;refseq.codonCoord=138;refseq.end=19485064;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=489;refseq.name=NM_012067;refseq.name2=AKR7A3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V138M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=19485064;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 19822649 . T C 195.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=170;Dels=0.00;HRun=0;HaplotypeScore=3.44;MQ=91.37;MQ0=2;OQ=2814.07;QD=16.55;RankSumP=0.460871;SB=-897.66;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.207T>C;refseq.codonCoord=69;refseq.end=19822649;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=280;refseq.name=NM_001032363;refseq.name2=C1orf151;refseq.positionType=CDS;refseq.proteinCoordStr=p.H69H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-16;refseq.start=19822649;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/0
|
|
chr1 19864855 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=21;HRun=2;RankSumP=0.000631265;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.22A>C;refseq.codonCoord=8;refseq.end=19864855;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=489;refseq.name=NM_000871;refseq.name2=HTR6;refseq.positionType=CDS;refseq.proteinCoordStr=p.T8P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=489;refseq.start=19864855;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 19893580 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=98.47;MQ0=0;OQ=374.12;QD=8.50;RankSumP=0.286991;SB=-135.62;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1434T>C;refseq.codonCoord=478;refseq.end=19893580;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1676;refseq.name=NM_181719;refseq.name2=TMCO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R478R;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=52;refseq.start=19893580;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 0/1
|
|
chr1 19893581 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=98.47;MQ0=0;OQ=423.02;QD=9.61;RankSumP=0.638190;SB=-147.56;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1433G>A;refseq.codonCoord=478;refseq.end=19893581;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1675;refseq.name=NM_181719;refseq.name2=TMCO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R478H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=51;refseq.start=19893581;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 0/1
|
|
chr1 19970409 . G A 211.77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=98.35;MQ0=0;OQ=11426.88;QD=41.10;RankSumP=1.00000;SB=-5288.83;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.333C>T;refseq.codonCoord=111;refseq.end=19970409;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=575;refseq.name=NM_181719;refseq.name2=TMCO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.D111D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-22;refseq.start=19970409;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 19970518 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.224A>G;refseq.codonCoord=75;refseq.end=19970518;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=466;refseq.name=NM_181719;refseq.name2=TMCO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.E75G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=45;refseq.start=19970518;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 19970528 . G T 102.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=20;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=4.56;MQ=97.46;MQ0=0;OQ=1504.00;QD=20.89;RankSumP=1.00000;SB=-444.30;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.214C>A;refseq.codonCoord=72;refseq.end=19970528;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=456;refseq.name=NM_181719;refseq.name2=TMCO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q72K;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=35;refseq.start=19970528;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 20013523 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=1.15811e-06;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.659A>C;refseq.codonCoord=220;refseq.end=20013523;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=836;refseq.name=NM_019062;refseq.name2=RNF186;refseq.positionType=CDS;refseq.proteinCoordStr=p.H220P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-415;refseq.start=20013523;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 20013560 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=125;Dels=0.00;HRun=0;HaplotypeScore=8.61;MQ=98.68;MQ0=0;OQ=1281.72;QD=10.25;RankSumP=0.139419;SB=-469.86;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.622C>A;refseq.codonCoord=208;refseq.end=20013560;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=799;refseq.name=NM_019062;refseq.name2=RNF186;refseq.positionType=CDS;refseq.proteinCoordStr=p.P208T;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-452;refseq.start=20013560;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 20013870 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=98.31;MQ0=0;OQ=719.84;QD=12.85;RankSumP=0.504331;SB=-301.23;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.312G>A;refseq.codonCoord=104;refseq.end=20013870;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=489;refseq.name=NM_019062;refseq.name2=RNF186;refseq.positionType=CDS;refseq.proteinCoordStr=p.A104A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=489;refseq.start=20013870;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 20014115 . C T 109.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=95.84;MQ0=0;OQ=566.64;QD=13.18;RankSumP=0.540947;SB=-302.19;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.67G>A;refseq.codonCoord=23;refseq.end=20014115;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=244;refseq.name=NM_019062;refseq.name2=RNF186;refseq.positionType=CDS;refseq.proteinCoordStr=p.A23T;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=244;refseq.start=20014115;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 0/1
|
|
chr1 20096739 . G A 270 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=314;Dels=0.00;HRun=0;HaplotypeScore=7.86;MQ=98.88;MQ0=0;OQ=6168.31;QD=19.64;RankSumP=0.236917;SB=-2114.49;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.603G>A;refseq.codonCoord=201;refseq.end=20096739;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=722;refseq.name=NM_015207;refseq.name2=OTUD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T201T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-4;refseq.spliceInfo=splice-donor_-4;refseq.start=20096739;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 20177516 . G A 76 PASS AC=1;AF=0.50;AN=2;BestBaseQ=10;HRun=2;RankSumP=0.289860;SecondBestBaseQ=10;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.129C>T;refseq.codingCoordStr_2=c.129C>T;refseq.codingCoordStr_3=c.129C>T;refseq.codingCoordStr_4=c.129C>T;refseq.codonCoord_1=43;refseq.codonCoord_2=43;refseq.codonCoord_3=43;refseq.codonCoord_4=43;refseq.end_1=20177516;refseq.end_2=20177516;refseq.end_3=20177516;refseq.end_4=20177516;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=424;refseq.mrnaCoord_2=393;refseq.mrnaCoord_3=313;refseq.mrnaCoord_4=347;refseq.name2_1=PLA2G2A;refseq.name2_2=PLA2G2A;refseq.name2_3=PLA2G2A;refseq.name2_4=PLA2G2A;refseq.name_1=NM_000300;refseq.name_2=NM_001161727;refseq.name_3=NM_001161728;refseq.name_4=NM_001161729;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.F43F;refseq.proteinCoordStr_2=p.F43F;refseq.proteinCoordStr_3=p.F43F;refseq.proteinCoordStr_4=p.F43F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceAA_4=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.referenceCodon_3=TTC;refseq.referenceCodon_4=TTC;refseq.spliceDist_1=-57;refseq.spliceDist_2=-57;refseq.spliceDist_3=-57;refseq.spliceDist_4=-57;refseq.start_1=20177516;refseq.start_2=20177516;refseq.start_3=20177516;refseq.start_4=20177516;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantAA_4=Phe;refseq.variantCodon_1=TTT;refseq.variantCodon_2=TTT;refseq.variantCodon_3=TTT;refseq.variantCodon_4=TTT;set=soap GT 1/0
|
|
chr1 20314641 . T C 158.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=370;Dels=0.00;HRun=1;HaplotypeScore=5.14;MQ=98.77;MQ0=0;OQ=7002.16;QD=18.92;RankSumP=0.0140335;SB=-2771.59;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.238A>G;refseq.codonCoord=80;refseq.end=20314641;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=255;refseq.name=NM_012400;refseq.name2=PLA2G2D;refseq.positionType=CDS;refseq.proteinCoordStr=p.S80G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=53;refseq.start=20314641;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/0
|
|
chr1 20699803 . C T 102.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=266;Dels=0.00;HRun=1;HaplotypeScore=13.09;MQ=98.83;MQ0=0;OQ=5386.63;QD=20.25;RankSumP=0.432858;SB=-2274.73;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1026G>A;refseq.codonCoord=342;refseq.end=20699803;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1183;refseq.name=NM_024544;refseq.name2=MUL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A342A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=697;refseq.start=20699803;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 20832817 . C T 5.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=5;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=92.14;MQ0=0;OQ=109.87;QD=21.97;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.189C>T;refseq.codonCoord=63;refseq.end=20832817;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=283;refseq.name=NM_032409;refseq.name2=PINK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L63L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-199;refseq.start=20832817;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=filterInsoap-gatk GT 1/1
|
|
chr1 20836995 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.461A>G;refseq.codonCoord=154;refseq.end=20836995;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=555;refseq.name=NM_032409;refseq.name2=PINK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E154G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=74;refseq.start=20836995;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 20860460 . G C 228.71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=4.29;MQ=97.50;MQ0=0;OQ=1723.74;QD=39.18;RankSumP=1.00000;SB=-387.75;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.22C>G;refseq.codonCoord=8;refseq.end=20860460;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=165;refseq.name=NM_005216;refseq.name2=DDOST;refseq.positionType=CDS;refseq.proteinCoordStr=p.R8G;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=165;refseq.start=20860460;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 1/1
|
|
chr1 20865406 . G C 161.83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=289;Dels=0.00;HRun=1;HaplotypeScore=9.72;MQ=98.46;MQ0=0;OQ=12262.17;QD=42.43;RankSumP=1.00000;SB=-4852.30;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2796C>G;refseq.codingCoordStr_2=c.2799C>G;refseq.codonCoord_1=932;refseq.codonCoord_2=933;refseq.end_1=20865406;refseq.end_2=20865406;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2914;refseq.mrnaCoord_2=2917;refseq.name2_1=KIF17;refseq.name2_2=KIF17;refseq.name_1=NM_001122819;refseq.name_2=NM_020816;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D932E;refseq.proteinCoordStr_2=p.D933E;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=6;refseq.spliceDist_2=6;refseq.spliceInfo_1=splice-acceptor_6;refseq.spliceInfo_2=splice-acceptor_6;refseq.start_1=20865406;refseq.start_2=20865406;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 1/1
|
|
chr1 20885150 . C T 62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=136.91;QD=8.56;RankSumP=0.478896;SB=-42.64;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1995G>A;refseq.codingCoordStr_2=c.1995G>A;refseq.codonCoord_1=665;refseq.codonCoord_2=665;refseq.end_1=20885150;refseq.end_2=20885150;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2113;refseq.mrnaCoord_2=2113;refseq.name2_1=KIF17;refseq.name2_2=KIF17;refseq.name_1=NM_001122819;refseq.name_2=NM_020816;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A665A;refseq.proteinCoordStr_2=p.A665A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=-25;refseq.spliceDist_2=-25;refseq.start_1=20885150;refseq.start_2=20885150;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 0/1
|
|
chr1 20897488 . C T 362.83 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=256;Dels=0.00;HRun=0;HaplotypeScore=4.95;MQ=98.84;MQ0=0;OQ=4976.56;QD=19.44;RankSumP=0.197781;SB=-1653.16;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1204G>A;refseq.codingCoordStr_2=c.1204G>A;refseq.codonCoord_1=402;refseq.codonCoord_2=402;refseq.end_1=20897488;refseq.end_2=20897488;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1322;refseq.mrnaCoord_2=1322;refseq.name2_1=KIF17;refseq.name2_2=KIF17;refseq.name_1=NM_001122819;refseq.name_2=NM_020816;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V402M;refseq.proteinCoordStr_2=p.V402M;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-30;refseq.spliceDist_2=-30;refseq.start_1=20897488;refseq.start_2=20897488;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;set=Intersection GT 0/1
|
|
chr1 20923486 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.368T>G;refseq.codingCoordStr_2=c.620T>G;refseq.codonCoord_1=123;refseq.codonCoord_2=207;refseq.end_1=20923486;refseq.end_2=20923486;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=993;refseq.mrnaCoord_2=1122;refseq.name2_1=SH2D5;refseq.name2_2=SH2D5;refseq.name_1=NM_001103160;refseq.name_2=NM_001103161;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V123G;refseq.proteinCoordStr_2=p.V207G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-11;refseq.spliceDist_2=-11;refseq.start_1=20923486;refseq.start_2=20923486;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 20923545 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=98.68;MQ0=0;OQ=819.66;QD=18.21;RankSumP=0.427261;SB=-141.14;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.309G>A;refseq.codingCoordStr_2=c.561G>A;refseq.codonCoord_1=103;refseq.codonCoord_2=187;refseq.end_1=20923545;refseq.end_2=20923545;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=934;refseq.mrnaCoord_2=1063;refseq.name2_1=SH2D5;refseq.name2_2=SH2D5;refseq.name_1=NM_001103160;refseq.name_2=NM_001103161;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q103Q;refseq.proteinCoordStr_2=p.Q187Q;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-70;refseq.spliceDist_2=-70;refseq.start_1=20923545;refseq.start_2=20923545;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;set=Intersection GT 0/1
|
|
chr1 21009825 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4569A>C;refseq.codonCoord=1523;refseq.end=21009825;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5150;refseq.name=NM_003760;refseq.name2=EIF4G3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1523H;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-8;refseq.spliceInfo=splice-donor_-8;refseq.start=21009825;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=FilteredInAll GT 1/0
|
|
chr1 21039991 . A G 263.06 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=403;Dels=0.00;HRun=0;HaplotypeScore=5.03;MQ=98.71;MQ0=0;OQ=16330.26;QD=40.52;RankSumP=1.00000;SB=-7285.95;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3838T>C;refseq.codonCoord=1280;refseq.end=21039991;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4419;refseq.name=NM_003760;refseq.name2=EIF4G3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1280L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=-56;refseq.start=21039991;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/1
|
|
chr1 21085313 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2224C>A;refseq.codonCoord=742;refseq.end=21085313;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2805;refseq.name=NM_003760;refseq.name2=EIF4G3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q742K;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-33;refseq.start=21085313;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 0/1
|
|
chr1 21471913 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=4;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.323A>C;refseq.codingCoordStr_2=c.311A>C;refseq.codingCoordStr_3=c.350A>C;refseq.codingCoordStr_4=c.359A>C;refseq.codonCoord_1=108;refseq.codonCoord_2=104;refseq.codonCoord_3=117;refseq.codonCoord_4=120;refseq.end_1=21471913;refseq.end_2=21471913;refseq.end_3=21471913;refseq.end_4=21471913;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=579;refseq.mrnaCoord_2=474;refseq.mrnaCoord_3=425;refseq.mrnaCoord_4=434;refseq.name2_1=ECE1;refseq.name2_2=ECE1;refseq.name2_3=ECE1;refseq.name2_4=ECE1;refseq.name_1=NM_001113347;refseq.name_2=NM_001113348;refseq.name_3=NM_001113349;refseq.name_4=NM_001397;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.D108A;refseq.proteinCoordStr_2=p.D104A;refseq.proteinCoordStr_3=p.D117A;refseq.proteinCoordStr_4=p.D120A;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.referenceCodon_3=GAC;refseq.referenceCodon_4=GAC;refseq.spliceDist_1=79;refseq.spliceDist_2=79;refseq.spliceDist_3=79;refseq.spliceDist_4=79;refseq.start_1=21471913;refseq.start_2=21471913;refseq.start_3=21471913;refseq.start_4=21471913;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;refseq.variantCodon_3=GCC;refseq.variantCodon_4=GCC;set=FilteredInAll GT 1/0
|
|
chr1 21667975 . A G 254.63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=161;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=97.77;MQ0=0;OQ=2975.22;QD=18.48;RankSumP=0.107771;SB=-776.88;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.341A>G;refseq.codonCoord=114;refseq.end=21667975;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=691;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y114C;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-3;refseq.spliceInfo=splice-donor_-3;refseq.start=21667975;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 0/1
|
|
chr1 21670711 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.265589;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.509A>G;refseq.codonCoord=170;refseq.end=21670711;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=859;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q170R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=63;refseq.start=21670711;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=soap GT 0/1
|
|
chr1 21670741 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.0735131;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.539A>G;refseq.codonCoord=180;refseq.end=21670741;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=889;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.N180S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=93;refseq.start=21670741;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=soap GT 0/1
|
|
chr1 21672511 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=883;Dels=0.00;HRun=1;HaplotypeScore=12.97;MQ=87.80;MQ0=83;OQ=15999.37;QD=18.12;RankSumP=0.0435458;SB=-6383.06;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.786G>A;refseq.codonCoord=262;refseq.end=21672511;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1136;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.E262E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=52;refseq.start=21672511;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/0
|
|
chr1 21680694 . C T 7 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.223875;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1451C>T;refseq.codonCoord=484;refseq.end=21680694;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1801;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P484L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=18;refseq.start=21680694;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT 0/1
|
|
chr1 21680746 . G A 12 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=291;Dels=0.00;HRun=1;HaplotypeScore=7.46;MQ=17.62;MQ0=163;OQ=2870.73;QD=9.87;RankSumP=0.108392;SB=-944.94;SecondBestBaseQ=12;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1503G>A;refseq.codonCoord=501;refseq.end=21680746;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1853;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.S501S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=70;refseq.start=21680746;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=filterInsoap-gatk GT 1/0
|
|
chr1 21680794 . A C 57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=0;RankSumP=0.500000;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1551A>C;refseq.codonCoord=517;refseq.end=21680794;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1901;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.G517G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-56;refseq.start=21680794;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=soap GT 0/1
|
|
chr1 21680810 . T C 66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=0;RankSumP=0.500000;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1567T>C;refseq.codonCoord=523;refseq.end=21680810;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1917;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L523L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-40;refseq.start=21680810;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=soap GT 1/0
|
|
chr1 21681601 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.753884;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1644G>C;refseq.codonCoord=548;refseq.end=21681601;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1994;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.K548N;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-15;refseq.start=21681601;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=soap GT 0/1
|
|
chr1 21682337 . T C 130.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=69.76;MQ0=16;OQ=2223.13;QD=32.69;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1773T>C;refseq.codonCoord=591;refseq.end=21682337;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2123;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y591Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=115;refseq.start=21682337;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/1
|
|
chr1 21682437 rs4466620 T C 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=737;Dels=0.00;HRun=2;HaplotypeScore=15.03;MQ=6.85;MQ0=729;OQ=152.89;QD=0.21;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1873T>C;refseq.codonCoord=625;refseq.end=21682437;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2223;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.F625L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=215;refseq.start=21682437;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=gatk GT:AD:DP:GL:GQ 0/1:206,530:7:-20.68,-2.11,-8.54:64.27
|
|
chr1 21682463 rs4291471 C G 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=797;Dels=0.00;HRun=0;HaplotypeScore=24.12;MQ=5.38;MQ0=781;OQ=64.41;QD=0.08;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1899C>G;refseq.codonCoord=633;refseq.end=21682463;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2249;refseq.name=NM_032264;refseq.name2=NBPF3;refseq.positionType=CDS;refseq.proteinCoordStr=p.H633Q;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=241;refseq.start=21682463;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=gatk GT:AD:DP:GL:GQ 0/1:620,174:16:-14.54,-4.82,-68.50:97.24
|
|
chr1 21762222 . T C 149.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=114;Dels=0.00;HRun=0;HaplotypeScore=6.35;MQ=97.86;MQ0=0;OQ=3570.32;QD=31.32;RankSumP=1.00000;SB=-1038.76;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.330T>C;refseq.codingCoordStr_2=c.330T>C;refseq.codonCoord_1=110;refseq.codonCoord_2=110;refseq.end_1=21762222;refseq.end_2=21762222;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=587;refseq.mrnaCoord_2=549;refseq.name2_1=ALPL;refseq.name2_2=ALPL;refseq.name_1=NM_000478;refseq.name_2=NM_001127501;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S110S;refseq.proteinCoordStr_2=p.S110S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGT;refseq.referenceCodon_2=AGT;refseq.spliceDist_1=33;refseq.spliceDist_2=33;refseq.start_1=21762222;refseq.start_2=21762222;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;set=Intersection GT 1/1
|
|
chr1 21776718 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=2.22;MQ=97.50;MQ0=0;OQ=264.32;QD=11.49;RankSumP=0.108473;SB=-44.67;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1565T>C;refseq.codingCoordStr_2=c.1565T>C;refseq.codonCoord_1=522;refseq.codonCoord_2=522;refseq.end_1=21776718;refseq.end_2=21776718;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1822;refseq.mrnaCoord_2=1784;refseq.name2_1=ALPL;refseq.name2_2=ALPL;refseq.name_1=NM_000478;refseq.name_2=NM_001127501;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V522A;refseq.proteinCoordStr_2=p.V522A;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=256;refseq.spliceDist_2=256;refseq.start_1=21776718;refseq.start_2=21776718;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/0
|
|
chr1 21813142 . C T 149.21 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=5.73;MQ=97.92;MQ0=0;OQ=1457.90;QD=13.38;RankSumP=0.115108;SB=-400.34;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.319G>A;refseq.codingCoordStr_2=c.511G>A;refseq.codingCoordStr_3=c.319G>A;refseq.codonCoord_1=107;refseq.codonCoord_2=171;refseq.codonCoord_3=107;refseq.end_1=21813142;refseq.end_2=21813142;refseq.end_3=21813142;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=684;refseq.mrnaCoord_2=544;refseq.mrnaCoord_3=577;refseq.name2_1=RAP1GAP;refseq.name2_2=RAP1GAP;refseq.name2_3=RAP1GAP;refseq.name_1=NM_001145657;refseq.name_2=NM_001145658;refseq.name_3=NM_002885;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A107T;refseq.proteinCoordStr_2=p.A171T;refseq.proteinCoordStr_3=p.A107T;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.referenceCodon_3=GCT;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.spliceDist_3=28;refseq.start_1=21813142;refseq.start_2=21813142;refseq.start_3=21813142;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=ACT;set=Intersection GT 0/1
|
|
chr1 21816407 . G A 181.53 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=528.10;QD=17.04;RankSumP=0.360552;SB=-271.78;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.270C>T;refseq.codingCoordStr_2=c.462C>T;refseq.codingCoordStr_3=c.270C>T;refseq.codonCoord_1=90;refseq.codonCoord_2=154;refseq.codonCoord_3=90;refseq.end_1=21816407;refseq.end_2=21816407;refseq.end_3=21816407;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=635;refseq.mrnaCoord_2=495;refseq.mrnaCoord_3=528;refseq.name2_1=RAP1GAP;refseq.name2_2=RAP1GAP;refseq.name2_3=RAP1GAP;refseq.name_1=NM_001145657;refseq.name_2=NM_001145658;refseq.name_3=NM_002885;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Y90Y;refseq.proteinCoordStr_2=p.Y154Y;refseq.proteinCoordStr_3=p.Y90Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.spliceDist_1=-22;refseq.spliceDist_2=-22;refseq.spliceDist_3=-22;refseq.start_1=21816407;refseq.start_2=21816407;refseq.start_3=21816407;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;refseq.variantCodon_3=TAT;set=Intersection GT 1/0
|
|
chr1 21818117 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=98.16;MQ0=0;OQ=423.64;QD=9.01;RankSumP=0.724131;SB=-133.65;SecondBestBaseQ=24;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.54G>A;refseq.codingCoordStr_2=c.246G>A;refseq.codingCoordStr_3=c.54G>A;refseq.codonCoord_1=18;refseq.codonCoord_2=82;refseq.codonCoord_3=18;refseq.end_1=21818117;refseq.end_2=21818117;refseq.end_3=21818117;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=419;refseq.mrnaCoord_2=279;refseq.mrnaCoord_3=312;refseq.name2_1=RAP1GAP;refseq.name2_2=RAP1GAP;refseq.name2_3=RAP1GAP;refseq.name_1=NM_001145657;refseq.name_2=NM_001145658;refseq.name_3=NM_002885;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P18P;refseq.proteinCoordStr_2=p.P82P;refseq.proteinCoordStr_3=p.P18P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.referenceCodon_3=CCG;refseq.spliceDist_1=-13;refseq.spliceDist_2=-13;refseq.spliceDist_3=-13;refseq.start_1=21818117;refseq.start_2=21818117;refseq.start_3=21818117;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;refseq.variantCodon_3=CCA;set=Intersection GT 0/1
|
|
chr1 21981957 . G A 260.22 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.21;MQ0=0;OQ=659.71;QD=34.72;RankSumP=1.00000;SB=-284.88;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.81C>T;refseq.codingCoordStr_2=c.81C>T;refseq.codonCoord_1=27;refseq.codonCoord_2=27;refseq.end_1=21981957;refseq.end_2=21981957;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=319;refseq.mrnaCoord_2=319;refseq.name2_1=USP48;refseq.name2_2=USP48;refseq.name_1=NM_001032730;refseq.name_2=NM_032236;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H27H;refseq.proteinCoordStr_2=p.H27H;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=-54;refseq.spliceDist_2=-54;refseq.start_1=21981957;refseq.start_2=21981957;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAT;refseq.variantCodon_2=CAT;set=Intersection GT 1/1
|
|
chr1 22013793 . A C 6 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=5;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=123.82;QD=24.76;RankSumP=1.00000;SB=-89.14;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.401A>C;refseq.codonCoord=134;refseq.end=22013793;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=588;refseq.name=NM_001013693;refseq.name2=LDLRAD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N134T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-111;refseq.start=22013793;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=filterInsoap-gatk GT 1/1
|
|
chr1 22015061 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.550T>G;refseq.codonCoord=184;refseq.end=22015061;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=737;refseq.name=NM_001013693;refseq.name2=LDLRAD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C184G;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=39;refseq.start=22015061;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 22029118 . T G 16 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=1.18573e-06;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.11725A>C;refseq.codonCoord=3909;refseq.end=22029118;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=11765;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T3909P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-46;refseq.start=22029118;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 22032601 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10924A>C;refseq.codonCoord=3642;refseq.end=22032601;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=10964;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T3642P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-55;refseq.start=22032601;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 22047738 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7722A>C;refseq.codonCoord=2574;refseq.end=22047738;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7762;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L2574F;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=-16;refseq.start=22047738;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=FilteredInAll GT 1/0
|
|
chr1 22058700 . T G 70 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=65;Dels=0.00;HRun=2;HaplotypeScore=11.30;MQ=96.67;MQ0=0;QD=0.71;RankSumP=2.65575e-06;SB=74.24;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5239A>C;refseq.codonCoord=1747;refseq.end=22058700;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5279;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1747P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-55;refseq.start=22058700;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 22064041 . G A 33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=21;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=98.44;MQ0=0;OQ=463.77;QD=27.28;RankSumP=1.00000;SB=-181.68;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4508C>T;refseq.codonCoord=1503;refseq.end=22064041;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4548;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1503V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=113;refseq.start=22064041;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 22072469 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3779G>C;refseq.codonCoord=1260;refseq.end=22072469;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3819;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1260A;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-15;refseq.start=22072469;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 22079236 . T C 394.05 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=166;Dels=0.00;HRun=0;HaplotypeScore=3.70;MQ=98.81;MQ0=0;OQ=6103.07;QD=36.77;RankSumP=1.00000;SB=-1561.90;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2294A>G;refseq.codonCoord=765;refseq.end=22079236;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2334;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N765S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-50;refseq.start=22079236;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/1
|
|
chr1 22079529 . G A 429.72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=98.09;MQ0=0;OQ=6324.77;QD=36.99;RankSumP=1.00000;SB=-1839.59;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2109C>T;refseq.codonCoord=703;refseq.end=22079529;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2149;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A703A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-87;refseq.start=22079529;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 22079822 . T C 65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=97.80;MQ0=0;OQ=1303.38;QD=28.33;RankSumP=1.00000;SB=-565.29;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1912A>G;refseq.codonCoord=638;refseq.end=22079822;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1952;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.M638V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-87;refseq.start=22079822;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 22086714 . A G 388.98 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=98.43;MQ0=0;OQ=3543.58;QD=35.08;RankSumP=1.00000;SB=-1320.87;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.744T>C;refseq.codonCoord=248;refseq.end=22086714;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=784;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L248L;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=41;refseq.start=22086714;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/1
|
|
chr1 22089695 . G A 101.68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=130;Dels=0.00;HRun=2;HaplotypeScore=6.63;MQ=98.49;MQ0=0;OQ=4977.72;QD=38.29;RankSumP=1.00000;SB=-1715.73;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.324C>T;refseq.codonCoord=108;refseq.end=22089695;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=364;refseq.name=NM_005529;refseq.name2=HSPG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.F108F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-31;refseq.start=22089695;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/1
|
|
chr1 22179927 . C T 100.57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=8.57;MQ=48.06;MQ0=31;OQ=1124.72;QD=14.61;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.153C>T;refseq.codonCoord=51;refseq.end=22179927;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=268;refseq.name=NM_007352;refseq.name2=CELA3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.S51S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=24;refseq.start=22179927;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/1
|
|
chr1 22179945 . C G 83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=107;Dels=0.00;HRun=0;HaplotypeScore=18.33;MQ=49.92;MQ0=35;OQ=1398.46;QD=13.07;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.171C>G;refseq.codonCoord=57;refseq.end=22179945;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=286;refseq.name=NM_007352;refseq.name2=CELA3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T57T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=42;refseq.start=22179945;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 22180125 . C T 404.19 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=96.05;MQ0=0;OQ=2967.57;QD=39.57;RankSumP=1.00000;SB=-791.04;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.235C>T;refseq.codonCoord=79;refseq.end=22180125;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=350;refseq.name=NM_007352;refseq.name2=CELA3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.R79W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=22180125;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/1
|
|
chr1 22182849 . G C 81 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=224;Dels=0.00;HRun=2;HaplotypeScore=6.06;MQ=33.26;MQ0=87;OQ=3990.08;QD=17.81;RankSumP=1.00000;SB=-293.23;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.438G>C;refseq.codonCoord=146;refseq.end=22182849;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=553;refseq.name=NM_007352;refseq.name2=CELA3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P146P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-62;refseq.start=22182849;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 22183312 . G C 95.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=162;Dels=0.00;HRun=2;HaplotypeScore=4.55;MQ=91.80;MQ0=0;OQ=6640.09;QD=40.99;RankSumP=1.00000;SB=-1830.57;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.543G>C;refseq.codonCoord=181;refseq.end=22183312;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=658;refseq.name=NM_007352;refseq.name2=CELA3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P181P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=44;refseq.start=22183312;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 22183411 . T C 297.43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=438;Dels=0.00;HRun=0;HaplotypeScore=8.81;MQ=54.14;MQ0=156;OQ=8308.83;QD=18.97;RankSumP=1.00000;SB=-2920.10;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.642T>C;refseq.codonCoord=214;refseq.end=22183411;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=757;refseq.name=NM_007352;refseq.name2=CELA3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.N214N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-1;refseq.spliceInfo=splice-donor_-1;refseq.start=22183411;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 22185748 . T C 103.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=153;Dels=0.00;HRun=0;HaplotypeScore=3.90;MQ=82.51;MQ0=20;OQ=4593.61;QD=30.02;RankSumP=1.00000;SB=-1394.90;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.780T>C;refseq.codonCoord=260;refseq.end=22185748;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=895;refseq.name=NM_007352;refseq.name2=CELA3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.I260I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-16;refseq.start=22185748;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 22204595 . T C 47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;DB;DP=606;Dels=0.00;HRun=0;HaplotypeScore=71.55;MQ=57.39;MQ0=102;OQ=1354.92;QD=2.24;RankSumP=0.374199;SB=105.76;SecondBestBaseQ=18;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.198T>C;refseq.codonCoord=66;refseq.end=22204595;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=217;refseq.name=NM_005747;refseq.name2=CELA3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.D66D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-30;refseq.start=22204595;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=soap-filterIngatk GT 1/0
|
|
chr1 22204835 . G C 10.81 ESPStandard;LowQual AC=1;AF=0.50;AN=2;DP=248;Dels=0.00;HRun=0;HaplotypeScore=17.41;MQ=81.47;MQ0=23;QD=0.04;SB=170.55;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.321G>C;refseq.codonCoord=107;refseq.end=22204835;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=340;refseq.name=NM_005747;refseq.name2=CELA3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.L107L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-42;refseq.start=22204835;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:228,13:182:-59.17,-54.85,-804.99:43.27
|
|
chr1 22208864 . C G 316.95 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=267;Dels=0.00;HRun=1;HaplotypeScore=4.92;MQ=84.78;MQ0=8;OQ=10024.27;QD=37.54;RankSumP=1.00000;SB=-3473.58;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.722C>G;refseq.codonCoord=241;refseq.end=22208864;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=741;refseq.name=NM_005747;refseq.name2=CELA3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.A241G;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-74;refseq.start=22208864;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 22208892 . C T 87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=236;Dels=0.00;HRun=0;HaplotypeScore=32.29;MQ=84.60;MQ0=11;OQ=8003.59;QD=33.91;RankSumP=1.00000;SB=-2550.27;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.750C>T;refseq.codonCoord=250;refseq.end=22208892;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=769;refseq.name=NM_005747;refseq.name2=CELA3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.P250P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-46;refseq.start=22208892;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 22208895 . G A 61 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=233;Dels=0.00;HRun=0;HaplotypeScore=31.19;MQ=83.73;MQ0=12;OQ=8067.23;QD=34.62;RankSumP=1.00000;SB=-2394.81;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.753G>A;refseq.codonCoord=251;refseq.end=22208895;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=772;refseq.name=NM_005747;refseq.name2=CELA3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T251T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-43;refseq.start=22208895;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 22708264 . A G 295.08 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=550;Dels=0.00;HRun=0;HaplotypeScore=9.53;MQ=98.78;MQ0=0;OQ=10437.83;QD=18.98;RankSumP=0.317750;SB=-3405.52;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1784A>G;refseq.codingCoordStr_2=c.1784A>G;refseq.codonCoord_1=595;refseq.codonCoord_2=595;refseq.end_1=22708264;refseq.end_2=22708264;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2295;refseq.mrnaCoord_2=2007;refseq.name2_1=ZBTB40;refseq.name2_2=ZBTB40;refseq.name_1=NM_001083621;refseq.name_2=NM_014870;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y595C;refseq.proteinCoordStr_2=p.Y595C;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-50;refseq.spliceDist_2=-50;refseq.start_1=22708264;refseq.start_2=22708264;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=Intersection GT 0/1
|
|
chr1 22719296 . G A 434.07 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=161;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=98.60;MQ0=0;OQ=6519.97;QD=40.50;RankSumP=1.00000;SB=-3215.16;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2989G>A;refseq.codingCoordStr_2=c.2989G>A;refseq.codonCoord_1=997;refseq.codonCoord_2=997;refseq.end_1=22719296;refseq.end_2=22719296;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3500;refseq.mrnaCoord_2=3212;refseq.name2_1=ZBTB40;refseq.name2_2=ZBTB40;refseq.name_1=NM_001083621;refseq.name_2=NM_014870;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V997M;refseq.proteinCoordStr_2=p.V997M;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-60;refseq.spliceDist_2=-60;refseq.start_1=22719296;refseq.start_2=22719296;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;set=Intersection GT 1/1
|
|
chr1 22725302 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=236;Dels=0.00;HRun=2;HaplotypeScore=4.64;MQ=98.61;MQ0=0;OQ=4538.25;QD=19.23;RankSumP=0.170187;SB=-1356.22;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3546G>C;refseq.codingCoordStr_2=c.3546G>C;refseq.codonCoord_1=1182;refseq.codonCoord_2=1182;refseq.end_1=22725302;refseq.end_2=22725302;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4057;refseq.mrnaCoord_2=3769;refseq.name2_1=ZBTB40;refseq.name2_2=ZBTB40;refseq.name_1=NM_001083621;refseq.name_2=NM_014870;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P1182P;refseq.proteinCoordStr_2=p.P1182P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=21;refseq.spliceDist_2=21;refseq.start_1=22725302;refseq.start_2=22725302;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=Intersection GT 0/1
|
|
chr1 22788340 . T C 78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=100;Dels=0.00;HRun=2;HaplotypeScore=8.01;MQ=98.30;MQ0=0;OQ=3706.34;QD=37.06;RankSumP=1.00000;SB=-738.92;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1369T>C;refseq.codonCoord_2=457;refseq.end_1=22792395;refseq.end_2=22788340;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1494;refseq.name2_1=EPHA8;refseq.name2_2=EPHA8;refseq.name_1=NM_020526;refseq.name_2=NM_001006943;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S457P;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCA;refseq.spliceDist_2=-360;refseq.start_1=22788297;refseq.start_2=22788340;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCA;set=Intersection GT 1/1
|
|
chr1 22792475 . A G 42 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.500000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1385A>G;refseq.codonCoord=462;refseq.end=22792475;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1510;refseq.name=NM_020526;refseq.name2=EPHA8;refseq.positionType=CDS;refseq.proteinCoordStr=p.E462G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-56;refseq.start=22792475;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=soap GT 0/1
|
|
chr1 22792681 . C G 300.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=98.62;MQ0=0;OQ=2313.62;QD=39.89;RankSumP=1.00000;SB=-822.58;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1518C>G;refseq.codonCoord=506;refseq.end=22792681;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1643;refseq.name=NM_020526;refseq.name2=EPHA8;refseq.positionType=CDS;refseq.proteinCoordStr=p.T506T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=78;refseq.start=22792681;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 22799828 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=64;Dels=0.00;HRun=0;HaplotypeScore=5.06;MQ=97.76;MQ0=0;OQ=929.31;QD=14.52;RankSumP=0.0446368;SB=-438.41;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2476G>A;refseq.codonCoord=826;refseq.end=22799828;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2601;refseq.name=NM_020526;refseq.name2=EPHA8;refseq.positionType=CDS;refseq.proteinCoordStr=p.V826M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-63;refseq.start=22799828;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/0
|
|
chr1 22984091 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=18;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.746T>G;refseq.codingCoordStr_2=c.746T>G;refseq.codonCoord_1=249;refseq.codonCoord_2=249;refseq.end_1=22984091;refseq.end_2=22984091;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=891;refseq.mrnaCoord_2=891;refseq.name2_1=EPHB2;refseq.name2_2=EPHB2;refseq.name_1=NM_004442;refseq.name_2=NM_017449;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V249G;refseq.proteinCoordStr_2=p.V249G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-66;refseq.spliceDist_2=-66;refseq.start_1=22984091;refseq.start_2=22984091;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 22984093 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.748C>G;refseq.codingCoordStr_2=c.748C>G;refseq.codonCoord_1=250;refseq.codonCoord_2=250;refseq.end_1=22984093;refseq.end_2=22984093;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=893;refseq.mrnaCoord_2=893;refseq.name2_1=EPHB2;refseq.name2_2=EPHB2;refseq.name_1=NM_004442;refseq.name_2=NM_017449;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P250A;refseq.proteinCoordStr_2=p.P250A;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=-64;refseq.spliceDist_2=-64;refseq.start_1=22984093;refseq.start_2=22984093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=FilteredInAll GT 1/0
|
|
chr1 23081512 . G A 144.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=183;Dels=0.00;HRun=0;HaplotypeScore=13.13;MQ=99.00;MQ0=0;OQ=2830.60;QD=15.47;RankSumP=0.364384;SB=-1195.02;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1377G>A;refseq.codingCoordStr_2=c.1377G>A;refseq.codonCoord_1=459;refseq.codonCoord_2=459;refseq.end_1=23081512;refseq.end_2=23081512;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1522;refseq.mrnaCoord_2=1522;refseq.name2_1=EPHB2;refseq.name2_2=EPHB2;refseq.name_1=NM_004442;refseq.name_2=NM_017449;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P459P;refseq.proteinCoordStr_2=p.P459P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=-52;refseq.spliceDist_2=-52;refseq.start_1=23081512;refseq.start_2=23081512;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=Intersection GT 1/0
|
|
chr1 23091985 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1450A>C;refseq.codingCoordStr_2=c.1450A>C;refseq.codonCoord_1=484;refseq.codonCoord_2=484;refseq.end_1=23091985;refseq.end_2=23091985;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1595;refseq.mrnaCoord_2=1595;refseq.name2_1=EPHB2;refseq.name2_2=EPHB2;refseq.name_1=NM_004442;refseq.name_2=NM_017449;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T484P;refseq.proteinCoordStr_2=p.T484P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.start_1=23091985;refseq.start_2=23091985;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=FilteredInAll GT 0/1
|
|
chr1 23092080 . T C 156.86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=363;Dels=0.00;HRun=0;HaplotypeScore=10.85;MQ=98.63;MQ0=0;OQ=13483.94;QD=37.15;RankSumP=1.00000;SB=-6344.29;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1545T>C;refseq.codingCoordStr_2=c.1545T>C;refseq.codonCoord_1=515;refseq.codonCoord_2=515;refseq.end_1=23092080;refseq.end_2=23092080;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1690;refseq.mrnaCoord_2=1690;refseq.name2_1=EPHB2;refseq.name2_2=EPHB2;refseq.name_1=NM_004442;refseq.name_2=NM_017449;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G515G;refseq.proteinCoordStr_2=p.G515G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=-47;refseq.spliceDist_2=-47;refseq.start_1=23092080;refseq.start_2=23092080;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=Intersection GT 1/1
|
|
chr1 23278176 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1974A>C;refseq.codingCoordStr_2=c.1902A>C;refseq.codonCoord_1=658;refseq.codonCoord_2=634;refseq.end_1=23278176;refseq.end_2=23278176;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2123;refseq.mrnaCoord_2=2051;refseq.name2_1=KDM1A;refseq.name2_2=KDM1A;refseq.name_1=NM_001009999;refseq.name_2=NM_015013;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P658P;refseq.proteinCoordStr_2=p.P634P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=-82;refseq.spliceDist_2=-82;refseq.start_1=23278176;refseq.start_2=23278176;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 23278634 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2057T>G;refseq.codingCoordStr_2=c.1985T>G;refseq.codonCoord_1=686;refseq.codonCoord_2=662;refseq.end_1=23278634;refseq.end_2=23278634;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2206;refseq.mrnaCoord_2=2134;refseq.name2_1=KDM1A;refseq.name2_2=KDM1A;refseq.name_1=NM_001009999;refseq.name_2=NM_015013;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V686G;refseq.proteinCoordStr_2=p.V662G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.start_1=23278634;refseq.start_2=23278634;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 23280554 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2199A>G;refseq.codingCoordStr_2=c.2127A>G;refseq.codonCoord_1=733;refseq.codonCoord_2=709;refseq.end_1=23280554;refseq.end_2=23280554;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2348;refseq.mrnaCoord_2=2276;refseq.name2_1=KDM1A;refseq.name2_2=KDM1A;refseq.name_1=NM_001009999;refseq.name_2=NM_015013;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G733G;refseq.proteinCoordStr_2=p.G709G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=29;refseq.spliceDist_2=29;refseq.start_1=23280554;refseq.start_2=23280554;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 23290740 . C T 342.84 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=179;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=99.00;MQ0=0;OQ=7003.64;QD=39.13;RankSumP=1.00000;SB=-3248.11;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2602G>A;refseq.codingCoordStr_2=c.2602G>A;refseq.codonCoord_1=868;refseq.codonCoord_2=868;refseq.end_1=23290740;refseq.end_2=23290740;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2920;refseq.mrnaCoord_2=2986;refseq.name2_1=LUZP1;refseq.name2_2=LUZP1;refseq.name_1=NM_001142546;refseq.name_2=NM_033631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D868N;refseq.proteinCoordStr_2=p.D868N;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-471;refseq.spliceDist_2=-471;refseq.start_1=23290740;refseq.start_2=23290740;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=Intersection GT 1/1
|
|
chr1 23291848 . G A 291.26 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=235;Dels=0.00;HRun=0;HaplotypeScore=8.39;MQ=98.70;MQ0=0;OQ=9008.59;QD=38.33;RankSumP=1.00000;SB=-3390.55;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1494C>T;refseq.codingCoordStr_2=c.1494C>T;refseq.codonCoord_1=498;refseq.codonCoord_2=498;refseq.end_1=23291848;refseq.end_2=23291848;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1812;refseq.mrnaCoord_2=1878;refseq.name2_1=LUZP1;refseq.name2_2=LUZP1;refseq.name_1=NM_001142546;refseq.name_2=NM_033631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S498S;refseq.proteinCoordStr_2=p.S498S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=-1579;refseq.spliceDist_2=-1579;refseq.start_1=23291848;refseq.start_2=23291848;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 1/1
|
|
chr1 23291961 . G T 192.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.96;MQ0=0;OQ=1765.62;QD=36.03;RankSumP=1.00000;SB=-277.62;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1381C>A;refseq.codingCoordStr_2=c.1381C>A;refseq.codonCoord_1=461;refseq.codonCoord_2=461;refseq.end_1=23291961;refseq.end_2=23291961;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1699;refseq.mrnaCoord_2=1765;refseq.name2_1=LUZP1;refseq.name2_2=LUZP1;refseq.name_1=NM_001142546;refseq.name_2=NM_033631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q461K;refseq.proteinCoordStr_2=p.Q461K;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=1500;refseq.spliceDist_2=1500;refseq.start_1=23291961;refseq.start_2=23291961;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/1
|
|
chr1 23291970 . C T 329.15 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.96;MQ0=0;OQ=1913.20;QD=40.71;RankSumP=1.00000;SB=-272.33;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1372G>A;refseq.codingCoordStr_2=c.1372G>A;refseq.codonCoord_1=458;refseq.codonCoord_2=458;refseq.end_1=23291970;refseq.end_2=23291970;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1690;refseq.mrnaCoord_2=1756;refseq.name2_1=LUZP1;refseq.name2_2=LUZP1;refseq.name_1=NM_001142546;refseq.name_2=NM_033631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G458S;refseq.proteinCoordStr_2=p.G458S;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=1491;refseq.spliceDist_2=1491;refseq.start_1=23291970;refseq.start_2=23291970;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;set=Intersection GT 1/1
|
|
chr1 23292442 . T C 262.77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=439;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=98.89;MQ0=0;OQ=17274.51;QD=39.35;RankSumP=1.00000;SB=-5942.56;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.900A>G;refseq.codingCoordStr_2=c.900A>G;refseq.codonCoord_1=300;refseq.codonCoord_2=300;refseq.end_1=23292442;refseq.end_2=23292442;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1218;refseq.mrnaCoord_2=1284;refseq.name2_1=LUZP1;refseq.name2_2=LUZP1;refseq.name_1=NM_001142546;refseq.name_2=NM_033631;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T300T;refseq.proteinCoordStr_2=p.T300T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=1019;refseq.spliceDist_2=1019;refseq.start_1=23292442;refseq.start_2=23292442;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 1/1
|
|
chr1 23510056 . G T 0.02 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=187;Dels=0.00;HRun=1;HaplotypeScore=16.99;MQ=97.87;MQ0=0;OQ=281.77;QD=1.51;RankSumP=0.00000;SB=224.77;SecondBestBaseQ=13;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1077C>A;refseq.codingCoordStr_2=c.1389C>A;refseq.codingCoordStr_3=c.1086C>A;refseq.codingCoordStr_4=c.1380C>A;refseq.codonCoord_1=359;refseq.codonCoord_2=463;refseq.codonCoord_3=362;refseq.codonCoord_4=460;refseq.end_1=23510056;refseq.end_2=23510056;refseq.end_3=23510056;refseq.end_4=23510056;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.functionalClass_3=nonsense;refseq.functionalClass_4=nonsense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1373;refseq.mrnaCoord_2=1548;refseq.mrnaCoord_3=1382;refseq.mrnaCoord_4=1539;refseq.name2_1=HNRNPR;refseq.name2_2=HNRNPR;refseq.name2_3=HNRNPR;refseq.name2_4=HNRNPR;refseq.name_1=NM_001102397;refseq.name_2=NM_001102398;refseq.name_3=NM_001102399;refseq.name_4=NM_005826;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.Y359*;refseq.proteinCoordStr_2=p.Y463*;refseq.proteinCoordStr_3=p.Y362*;refseq.proteinCoordStr_4=p.Y460*;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceAA_4=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.referenceCodon_4=TAC;refseq.spliceDist_1=91;refseq.spliceDist_2=91;refseq.spliceDist_3=91;refseq.spliceDist_4=91;refseq.start_1=23510056;refseq.start_2=23510056;refseq.start_3=23510056;refseq.start_4=23510056;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantAA_3=Stop;refseq.variantAA_4=Stop;refseq.variantCodon_1=TAA;refseq.variantCodon_2=TAA;refseq.variantCodon_3=TAA;refseq.variantCodon_4=TAA;set=FilteredInAll GT 0/1
|
|
chr1 23561469 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.993G>A;refseq.codingCoordStr_2=c.993G>A;refseq.codonCoord_1=331;refseq.codonCoord_2=331;refseq.end_1=23561469;refseq.end_2=23561469;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1552;refseq.mrnaCoord_2=1374;refseq.name2_1=ZNF436;refseq.name2_2=ZNF436;refseq.name_1=NM_001077195;refseq.name_2=NM_030634;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E331E;refseq.proteinCoordStr_2=p.E331E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=833;refseq.spliceDist_2=833;refseq.start_1=23561469;refseq.start_2=23561469;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=FilteredInAll GT 0/1
|
|
chr1 23568739 . G A 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=8.89;MQ=98.66;MQ0=0;OQ=2383.08;QD=31.36;RankSumP=1.00000;SB=-277.65;SecondBestBaseQ=3;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.-354C>T;refseq.codingCoordStr_3=c.362G>A;refseq.codonCoord_3=121;refseq.end_1=23570208;refseq.end_2=23568739;refseq.end_3=23568739;refseq.frame_3=1;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=206;refseq.mrnaCoord_3=689;refseq.name2_1=C1orf213;refseq.name2_2=ZNF436;refseq.name2_3=C1orf213;refseq.name_1=NM_001008896;refseq.name_2=NM_001077195;refseq.name_3=NM_138479;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=utr5;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.R121Q;refseq.referenceAA_3=Arg;refseq.referenceCodon_3=CGA;refseq.spliceDist_2=206;refseq.spliceDist_3=689;refseq.start_1=23568604;refseq.start_2=23568739;refseq.start_3=23568739;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=+;refseq.variantAA_3=Gln;refseq.variantCodon_3=CAA;set=Intersection GT 1/1
|
|
chr1 23640783 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=235;Dels=0.00;HRun=0;HaplotypeScore=4.75;MQ=98.74;MQ0=0;OQ=4050.86;QD=17.24;RankSumP=0.124328;SB=-1380.10;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.672C>T;refseq.codingCoordStr_2=c.699C>T;refseq.codonCoord_1=224;refseq.codonCoord_2=233;refseq.end_1=23640783;refseq.end_2=23640783;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=796;refseq.mrnaCoord_2=823;refseq.name2_1=ASAP3;refseq.name2_2=ASAP3;refseq.name_1=NM_001143778;refseq.name_2=NM_017707;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A224A;refseq.proteinCoordStr_2=p.A233A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.start_1=23640783;refseq.start_2=23640783;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=Intersection GT 1/0
|
|
chr1 23758085 . T C 427.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=98.70;MQ0=0;OQ=3428.64;QD=36.47;RankSumP=1.00000;SB=-1494.35;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.313A>G;refseq.codonCoord=105;refseq.end=23758085;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=718;refseq.name=NM_002167;refseq.name2=ID3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T105A;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=13;refseq.start=23758085;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 23950038 . C T 255.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=5.96;MQ=98.53;MQ0=0;OQ=1451.67;QD=15.44;RankSumP=0.485196;SB=-728.21;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.434C>T;refseq.codonCoord=145;refseq.end=23950038;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=494;refseq.name=NM_003198;refseq.name2=TCEB3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T145M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=117;refseq.start=23950038;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 24007308 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=615;Dels=0.00;HRun=0;HaplotypeScore=18.97;MQ=98.89;MQ0=0;OQ=23551.04;QD=38.29;RankSumP=1.00000;SB=-11071.12;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.654A>G;refseq.codingCoordStr_2=c.441A>G;refseq.codonCoord_1=218;refseq.codonCoord_2=147;refseq.end_1=24007308;refseq.end_2=24007308;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=698;refseq.mrnaCoord_2=485;refseq.name2_1=HMGCL;refseq.name2_2=HMGCL;refseq.name_1=NM_000191;refseq.name_2=NM_001166059;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L218L;refseq.proteinCoordStr_2=p.L147L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTA;refseq.referenceCodon_2=CTA;refseq.spliceDist_1=93;refseq.spliceDist_2=93;refseq.start_1=24007308;refseq.start_2=24007308;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 1/1
|
|
chr1 24045227 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=5.39241e-09;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1184T>G;refseq.codonCoord=395;refseq.end=24045227;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1267;refseq.name=NM_000147;refseq.name2=FUCA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V395G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=24;refseq.start=24045227;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 24062307 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.566T>C;refseq.codonCoord=189;refseq.end=24062307;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=649;refseq.name=NM_000147;refseq.name2=FUCA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F189S;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=42;refseq.start=24062307;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 0/1
|
|
chr1 24073681 . G C 64 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=6.47;MQ=97.74;MQ0=0;OQ=3858.73;QD=44.87;RankSumP=1.00000;SB=-1716.28;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1014C>G;refseq.codonCoord=338;refseq.end=24073681;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1141;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T338T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-634;refseq.start=24073681;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 24073696 . C T 204.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=97.49;MQ0=0;OQ=2992.74;QD=41.57;RankSumP=1.00000;SB=-1471.87;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.999G>A;refseq.codonCoord=333;refseq.end=24073696;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1126;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P333P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-649;refseq.start=24073696;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 24073849 . A G 242.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=153;Dels=0.00;HRun=1;HaplotypeScore=1.88;MQ=98.86;MQ0=0;OQ=6478.63;QD=42.34;RankSumP=1.00000;SB=-3018.56;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.846T>C;refseq.codonCoord=282;refseq.end=24073849;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=973;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A282A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-802;refseq.start=24073849;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 24073944 . A G 232.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=5.02;MQ=98.35;MQ0=0;OQ=5530.26;QD=35.45;RankSumP=1.00000;SB=-2619.70;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.751T>C;refseq.codonCoord=251;refseq.end=24073944;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=878;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L251L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=796;refseq.start=24073944;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 24074035 . C T 332.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.86;MQ0=0;OQ=4897.02;QD=39.81;RankSumP=1.00000;SB=-2191.37;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.660G>A;refseq.codonCoord=220;refseq.end=24074035;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=787;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V220V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=705;refseq.start=24074035;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/1
|
|
chr1 24074230 . G A 259.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=4.74;MQ=98.41;MQ0=0;OQ=4736.76;QD=38.83;RankSumP=1.00000;SB=-2070.34;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.465C>T;refseq.codonCoord=155;refseq.end=24074230;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=592;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G155G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=510;refseq.start=24074230;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 1/1
|
|
chr1 24074506 . T C 221.87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=127;Dels=0.00;HRun=0;HaplotypeScore=4.24;MQ=97.41;MQ0=0;OQ=4305.30;QD=33.90;RankSumP=1.00000;SB=-1479.63;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.189A>G;refseq.codonCoord=63;refseq.end=24074506;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=316;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q63Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=234;refseq.start=24074506;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 24074507 . T C 212.83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=97.65;MQ0=0;OQ=4421.77;QD=32.75;RankSumP=1.00000;SB=-1251.50;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.188A>G;refseq.codonCoord=63;refseq.end=24074507;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=315;refseq.name=NM_001841;refseq.name2=CNR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q63R;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=233;refseq.start=24074507;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/1
|
|
chr1 24160695 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.725968;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.161C>G;refseq.codonCoord=54;refseq.end=24160695;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=573;refseq.name=NM_017761;refseq.name2=PNRC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A54G;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=179;refseq.start=24160695;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap GT 1/0
|
|
chr1 24160712 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=4;RankSumP=0.506882;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.178C>A;refseq.codonCoord=60;refseq.end=24160712;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=590;refseq.name=NM_017761;refseq.name2=PNRC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q60K;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=196;refseq.start=24160712;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=soap GT 1/0
|
|
chr1 24160780 . G C 51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.591919;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.246G>C;refseq.codonCoord=82;refseq.end=24160780;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=658;refseq.name=NM_017761;refseq.name2=PNRC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R82S;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=264;refseq.start=24160780;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=soap GT 0/1
|
|
chr1 24266150 . C T 151.98 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=98.51;MQ0=0;OQ=686.06;QD=14.29;RankSumP=0.524006;SB=-313.75;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3371G>A;refseq.codonCoord=1124;refseq.end=24266150;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3534;refseq.name=NM_152372;refseq.name2=MYOM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1124Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=16;refseq.start=24266150;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 24267398 . A G 209.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=234;Dels=0.00;HRun=1;HaplotypeScore=3.42;MQ=98.83;MQ0=0;OQ=4206.58;QD=17.98;RankSumP=0.384300;SB=-861.31;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3197T>C;refseq.codonCoord=1066;refseq.end=24267398;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3360;refseq.name=NM_152372;refseq.name2=MYOM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.I1066T;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=47;refseq.start=24267398;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 24273260 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2945C>A;refseq.codonCoord=982;refseq.end=24273260;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3108;refseq.name=NM_152372;refseq.name2=MYOM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A982E;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-24;refseq.start=24273260;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=FilteredInAll GT 0/1
|
|
chr1 24281752 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=90;Dels=0.00;HRun=1;HaplotypeScore=10.58;MQ=98.43;MQ0=0;OQ=984.91;QD=10.94;RankSumP=0.0166731;SB=-436.88;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2010G>A;refseq.codonCoord=670;refseq.end=24281752;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2173;refseq.name=NM_152372;refseq.name2=MYOM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.E670E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=40;refseq.start=24281752;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 24288646 . T C 38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=35;Dels=0.00;HRun=3;HaplotypeScore=1.59;MQ=99.00;MQ0=0;OQ=1274.43;QD=36.41;RankSumP=1.00000;SB=-656.93;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1583A>G;refseq.codonCoord=528;refseq.end=24288646;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1746;refseq.name=NM_152372;refseq.name2=MYOM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.D528G;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-32;refseq.start=24288646;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 24288720 . C T 132.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=98.98;MQ0=0;OQ=704.82;QD=14.68;RankSumP=0.102608;SB=-276.27;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1509G>A;refseq.codonCoord=503;refseq.end=24288720;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1672;refseq.name=NM_152372;refseq.name2=MYOM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P503P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=23;refseq.start=24288720;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 24320530 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.02;MQ0=0;OQ=944.07;QD=20.52;RankSumP=0.686157;SB=-444.82;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1077C>T;refseq.codonCoord=359;refseq.end=24320530;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1116;refseq.name=NM_021258;refseq.name2=IL22RA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V359V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=285;refseq.start=24320530;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/0
|
|
chr1 24327275 . C T 329.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=260;Dels=0.00;HRun=0;HaplotypeScore=10.47;MQ=98.78;MQ0=0;OQ=5151.82;QD=19.81;RankSumP=0.345773;SB=-1469.90;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.613G>A;refseq.codonCoord=205;refseq.end=24327275;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=652;refseq.name=NM_021258;refseq.name2=IL22RA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V205I;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-58;refseq.start=24327275;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 24333384 . T G 50 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=217;Dels=0.00;HRun=2;HaplotypeScore=6.92;MQ=98.65;MQ0=0;OQ=8702.00;QD=40.10;RankSumP=1.00000;SB=-4120.57;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.435A>C;refseq.codonCoord=145;refseq.end=24333384;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=474;refseq.name=NM_021258;refseq.name2=IL22RA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P145P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=80;refseq.start=24333384;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 24356695 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=137;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=98.93;MQ0=0;OQ=2225.97;QD=16.25;RankSumP=0.133686;SB=-366.86;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1075C>T;refseq.codingCoordStr_2=c.988C>T;refseq.codingCoordStr_3=c.*209C>T;refseq.codonCoord_1=359;refseq.codonCoord_2=330;refseq.end_1=24356695;refseq.end_2=24356695;refseq.end_3=24356695;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.mrnaCoord_1=1088;refseq.mrnaCoord_2=1001;refseq.mrnaCoord_3=957;refseq.name2_1=IL28RA;refseq.name2_2=IL28RA;refseq.name2_3=IL28RA;refseq.name_1=NM_170743;refseq.name_2=NM_173064;refseq.name_3=NM_173065;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=utr3;refseq.proteinCoordStr_1=p.H359Y;refseq.proteinCoordStr_2=p.H330Y;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=274;refseq.spliceDist_2=187;refseq.spliceDist_3=274;refseq.start_1=24356695;refseq.start_2=24356695;refseq.start_3=24356695;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;set=Intersection GT 1/0
|
|
chr1 24368672 . G A 266.81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=326;Dels=0.00;HRun=0;HaplotypeScore=6.94;MQ=98.34;MQ0=0;OQ=6249.85;QD=19.17;RankSumP=0.00431832;SB=-1669.27;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.189C>T;refseq.codingCoordStr_2=c.189C>T;refseq.codingCoordStr_3=c.189C>T;refseq.codonCoord_1=63;refseq.codonCoord_2=63;refseq.codonCoord_3=63;refseq.end_1=24368672;refseq.end_2=24368672;refseq.end_3=24368672;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=202;refseq.mrnaCoord_2=202;refseq.mrnaCoord_3=202;refseq.name2_1=IL28RA;refseq.name2_2=IL28RA;refseq.name2_3=IL28RA;refseq.name_1=NM_170743;refseq.name_2=NM_173064;refseq.name_3=NM_173065;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P63P;refseq.proteinCoordStr_2=p.P63P;refseq.proteinCoordStr_3=p.P63P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.spliceDist_1=7;refseq.spliceDist_2=7;refseq.spliceDist_3=7;refseq.spliceInfo_1=splice-acceptor_7;refseq.spliceInfo_2=splice-acceptor_7;refseq.spliceInfo_3=splice-acceptor_7;refseq.start_1=24368672;refseq.start_2=24368672;refseq.start_3=24368672;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;set=filterInsoap-gatk GT 1/0
|
|
chr1 24530650 . C G 347.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=303;Dels=0.00;HRun=0;HaplotypeScore=10.81;MQ=98.82;MQ0=0;OQ=6175.19;QD=20.38;RankSumP=0.445177;SB=-2072.02;SecondBestBaseQ=32;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.180C>G;refseq.codingCoordStr_3=c.165C>G;refseq.codonCoord_2=60;refseq.codonCoord_3=55;refseq.end_1=24533711;refseq.end_2=24530650;refseq.end_3=24530650;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=226;refseq.mrnaCoord_3=326;refseq.name2_1=GRHL3;refseq.name2_2=GRHL3;refseq.name2_3=GRHL3;refseq.name_1=NM_198174;refseq.name_2=NM_021180;refseq.name_3=NM_198173;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.D60E;refseq.proteinCoordStr_3=p.D55E;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceCodon_2=GAC;refseq.referenceCodon_3=GAC;refseq.spliceDist_2=-40;refseq.spliceDist_3=-40;refseq.start_1=24522205;refseq.start_2=24530650;refseq.start_3=24530650;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantCodon_2=GAG;refseq.variantCodon_3=GAG;set=Intersection GT 1/0
|
|
chr1 24541254 . C G 194.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=98.89;MQ0=0;OQ=1966.44;QD=19.86;RankSumP=0.483972;SB=-217.22;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1125C>G;refseq.codingCoordStr_2=c.1110C>G;refseq.codingCoordStr_3=c.831C>G;refseq.codonCoord_1=375;refseq.codonCoord_2=370;refseq.codonCoord_3=277;refseq.end_1=24541254;refseq.end_2=24541254;refseq.end_3=24541254;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1171;refseq.mrnaCoord_2=1271;refseq.mrnaCoord_3=984;refseq.name2_1=GRHL3;refseq.name2_2=GRHL3;refseq.name2_3=GRHL3;refseq.name_1=NM_021180;refseq.name_2=NM_198173;refseq.name_3=NM_198174;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V375V;refseq.proteinCoordStr_2=p.V370V;refseq.proteinCoordStr_3=p.V277V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.referenceCodon_3=GTC;refseq.spliceDist_1=63;refseq.spliceDist_2=63;refseq.spliceDist_3=63;refseq.start_1=24541254;refseq.start_2=24541254;refseq.start_3=24541254;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;refseq.variantCodon_3=GTG;set=Intersection GT 1/0
|
|
chr1 24553502 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=335;Dels=0.00;HRun=1;HaplotypeScore=4.27;MQ=98.80;MQ0=0;OQ=5042.33;QD=15.05;RankSumP=0.0358706;SB=-1983.98;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1761C>T;refseq.codingCoordStr_2=c.1746C>T;refseq.codingCoordStr_3=c.1467C>T;refseq.codonCoord_1=587;refseq.codonCoord_2=582;refseq.codonCoord_3=489;refseq.end_1=24553502;refseq.end_2=24553502;refseq.end_3=24553502;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1807;refseq.mrnaCoord_2=1907;refseq.mrnaCoord_3=1620;refseq.name2_1=GRHL3;refseq.name2_2=GRHL3;refseq.name2_3=GRHL3;refseq.name_1=NM_021180;refseq.name_2=NM_198173;refseq.name_3=NM_198174;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V587V;refseq.proteinCoordStr_2=p.V582V;refseq.proteinCoordStr_3=p.V489V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.referenceCodon_3=GTC;refseq.spliceDist_1=52;refseq.spliceDist_2=52;refseq.spliceDist_3=52;refseq.start_1=24553502;refseq.start_2=24553502;refseq.start_3=24553502;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;refseq.variantCodon_3=GTT;set=Intersection GT 0/1
|
|
chr1 24641203 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=177;Dels=0.00;HRun=0;HaplotypeScore=4.14;MQ=98.93;MQ0=0;OQ=2952.88;QD=16.68;RankSumP=0.0388287;SB=-1383.36;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.234G>A;refseq.codonCoord=78;refseq.end=24641203;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=641;refseq.name=NM_020448;refseq.name2=NIPAL3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L78L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=72;refseq.start=24641203;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/0
|
|
chr1 24868365 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1904T>G;refseq.codonCoord=635;refseq.end=24868365;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2128;refseq.name=NM_005839;refseq.name2=SRRM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V635G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=165;refseq.start=24868365;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 24870675 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.chr=chr1;refseq.codingCoordStr=c.2610+2;refseq.end=24870675;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_005839;refseq.name2=SRRM1;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=24870675;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 25101550 . T G 46 PASS AC=1;AF=0.50;AN=2;BestBaseQ=19;HRun=2;RankSumP=0.0165598;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.940A>C;refseq.codingCoordStr_2=c.898A>C;refseq.codonCoord_1=314;refseq.codonCoord_2=300;refseq.end_1=25101550;refseq.end_2=25101550;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1379;refseq.mrnaCoord_2=1309;refseq.name2_1=RUNX3;refseq.name2_2=RUNX3;refseq.name_1=NM_001031680;refseq.name_2=NM_004350;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T314P;refseq.proteinCoordStr_2=p.T300P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=195;refseq.spliceDist_2=195;refseq.start_1=25101550;refseq.start_2=25101550;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=soap GT 1/0
|
|
chr1 25427306 . G A 222.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=286;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=98.93;MQ0=0;OQ=5310.10;QD=18.57;RankSumP=0.376019;SB=-1743.35;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.266C>T;refseq.codingCoordStr_2=c.140C>T;refseq.codonCoord_1=89;refseq.codonCoord_2=47;refseq.end_1=25427306;refseq.end_2=25427306;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=321;refseq.mrnaCoord_2=195;refseq.name2_1=SYF2;refseq.name2_2=SYF2;refseq.name_1=NM_015484;refseq.name_2=NM_207170;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A89V;refseq.proteinCoordStr_2=p.A47V;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=25427306;refseq.start_2=25427306;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=Intersection GT 1/0
|
|
chr1 25483688 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.186G>T;refseq.codingCoordStr_2=c.186G>T;refseq.codonCoord_1=62;refseq.codonCoord_2=62;refseq.end_1=25483688;refseq.end_2=25483688;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=244;refseq.mrnaCoord_2=244;refseq.name2_1=RHD;refseq.name2_2=RHD;refseq.name_1=NM_001127691;refseq.name_2=NM_016124;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L62F;refseq.proteinCoordStr_2=p.L62F;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTG;refseq.referenceCodon_2=TTG;refseq.spliceDist_1=38;refseq.spliceDist_2=38;refseq.start_1=25483688;refseq.start_2=25483688;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTT;refseq.variantCodon_2=TTT;set=FilteredInAll GT 0/1
|
|
chr1 25489838 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.168092;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.455A>C;refseq.codingCoordStr_2=c.455A>C;refseq.codonCoord_1=152;refseq.codonCoord_2=152;refseq.end_1=25489838;refseq.end_2=25489838;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=513;refseq.mrnaCoord_2=513;refseq.name2_1=RHD;refseq.name2_2=RHD;refseq.name_1=NM_001127691;refseq.name_2=NM_016124;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N152T;refseq.proteinCoordStr_2=p.N152T;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-32;refseq.spliceDist_2=-32;refseq.start_1=25489838;refseq.start_2=25489838;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=soap GT 0/1
|
|
chr1 25502505 . C G 10 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=5;HRun=3;RankSumP=0.214291;SecondBestBaseQ=3;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.907C>G;refseq.codingCoordStr_2=c.907C>G;refseq.codonCoord_1=303;refseq.codonCoord_2=303;refseq.end_1=25502505;refseq.end_2=25502505;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=965;refseq.mrnaCoord_2=965;refseq.name2_1=RHD;refseq.name2_2=RHD;refseq.name_1=NM_001127691;refseq.name_2=NM_016124;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L303V;refseq.proteinCoordStr_2=p.L303V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=-33;refseq.spliceDist_2=-33;refseq.start_1=25502505;refseq.start_2=25502505;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT 1/0
|
|
chr1 25502530 . A C 59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=11;HRun=2;RankSumP=0.103492;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.932A>C;refseq.codingCoordStr_2=c.932A>C;refseq.codonCoord_1=311;refseq.codonCoord_2=311;refseq.end_1=25502530;refseq.end_2=25502530;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=990;refseq.mrnaCoord_2=990;refseq.name2_1=RHD;refseq.name2_2=RHD;refseq.name_1=NM_001127691;refseq.name_2=NM_016124;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y311S;refseq.proteinCoordStr_2=p.Y311S;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-8;refseq.spliceDist_2=-8;refseq.spliceInfo_1=splice-donor_-8;refseq.spliceInfo_2=splice-donor_-8;refseq.start_1=25502530;refseq.start_2=25502530;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=soap GT 0/1
|
|
chr1 25520983 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.373829;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1170T>C;refseq.codonCoord_2=390;refseq.end_1=25527965;refseq.end_2=25520983;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1228;refseq.name2_1=RHD;refseq.name2_2=RHD;refseq.name_1=NM_001127691;refseq.name_2=NM_016124;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.L390L;refseq.referenceAA_2=Leu;refseq.referenceCodon_2=CTT;refseq.spliceDist_2=17;refseq.start_1=25502548;refseq.start_2=25520983;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Leu;refseq.variantCodon_2=CTC;set=soap GT 1/0
|
|
chr1 25521006 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.603353;SecondBestBaseQ=32;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1193A>T;refseq.codonCoord_2=398;refseq.end_1=25527965;refseq.end_2=25521006;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1251;refseq.name2_1=RHD;refseq.name2_2=RHD;refseq.name_1=NM_001127691;refseq.name_2=NM_016124;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.E398V;refseq.referenceAA_2=Glu;refseq.referenceCodon_2=GAG;refseq.spliceDist_2=-35;refseq.start_1=25502548;refseq.start_2=25521006;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Val;refseq.variantCodon_2=GTG;set=soap GT 0/1
|
|
chr1 25542054 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.109T>G;refseq.codonCoord=37;refseq.end=25542054;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=259;refseq.name=NM_014313;refseq.name2=TMEM50A;refseq.positionType=CDS;refseq.proteinCoordStr=p.W37G;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=16;refseq.start=25542054;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 25569579 . A T 79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.554424;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1193T>A;refseq.codingCoordStr_2=c.740T>A;refseq.codingCoordStr_3=c.798T>A;refseq.codingCoordStr_4=c.1059T>A;refseq.codonCoord_1=398;refseq.codonCoord_2=247;refseq.codonCoord_3=266;refseq.codonCoord_4=353;refseq.end_1=25569579;refseq.end_2=25569579;refseq.end_3=25569579;refseq.end_4=25569579;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=nonsense;refseq.functionalClass_4=nonsense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1279;refseq.mrnaCoord_2=826;refseq.mrnaCoord_3=884;refseq.mrnaCoord_4=1145;refseq.name2_1=RHCE;refseq.name2_2=RHCE;refseq.name2_3=RHCE;refseq.name2_4=RHCE;refseq.name_1=NM_020485;refseq.name_2=NM_138616;refseq.name_3=NM_138617;refseq.name_4=NM_138618;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.V398E;refseq.proteinCoordStr_2=p.V247E;refseq.proteinCoordStr_3=p.C266*;refseq.proteinCoordStr_4=p.C353*;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=TGT;refseq.referenceCodon_4=TGT;refseq.spliceDist_1=-35;refseq.spliceDist_2=-35;refseq.spliceDist_3=-35;refseq.spliceDist_4=-35;refseq.start_1=25569579;refseq.start_2=25569579;refseq.start_3=25569579;refseq.start_4=25569579;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantAA_3=Stop;refseq.variantAA_4=Stop;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;refseq.variantCodon_3=TGA;refseq.variantCodon_4=TGA;set=soap GT 0/1
|
|
chr1 25569602 . G A 73 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.402079;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1170C>T;refseq.codingCoordStr_2=c.717C>T;refseq.codingCoordStr_3=c.775C>T;refseq.codingCoordStr_4=c.1036C>T;refseq.codonCoord_1=390;refseq.codonCoord_2=239;refseq.codonCoord_3=259;refseq.codonCoord_4=346;refseq.end_1=25569602;refseq.end_2=25569602;refseq.end_3=25569602;refseq.end_4=25569602;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=nonsense;refseq.functionalClass_4=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1256;refseq.mrnaCoord_2=803;refseq.mrnaCoord_3=861;refseq.mrnaCoord_4=1122;refseq.name2_1=RHCE;refseq.name2_2=RHCE;refseq.name2_3=RHCE;refseq.name2_4=RHCE;refseq.name_1=NM_020485;refseq.name_2=NM_138616;refseq.name_3=NM_138617;refseq.name_4=NM_138618;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.L390L;refseq.proteinCoordStr_2=p.L239L;refseq.proteinCoordStr_3=p.Q259*;refseq.proteinCoordStr_4=p.Q346*;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Gln;refseq.referenceAA_4=Gln;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.referenceCodon_3=CAA;refseq.referenceCodon_4=CAA;refseq.spliceDist_1=17;refseq.spliceDist_2=17;refseq.spliceDist_3=17;refseq.spliceDist_4=17;refseq.start_1=25569602;refseq.start_2=25569602;refseq.start_3=25569602;refseq.start_4=25569602;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Stop;refseq.variantAA_4=Stop;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;refseq.variantCodon_3=TAA;refseq.variantCodon_4=TAA;set=soap GT 1/0
|
|
chr1 25601705 . G T 10 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.463282;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.455C>A;refseq.codingCoordStr_2=c.455C>A;refseq.codingCoordStr_3=c.455C>A;refseq.codingCoordStr_4=c.455C>A;refseq.codonCoord_1=152;refseq.codonCoord_2=152;refseq.codonCoord_3=152;refseq.codonCoord_4=152;refseq.end_1=25601705;refseq.end_2=25601705;refseq.end_3=25601705;refseq.end_4=25601705;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=541;refseq.mrnaCoord_2=541;refseq.mrnaCoord_3=541;refseq.mrnaCoord_4=541;refseq.name2_1=RHCE;refseq.name2_2=RHCE;refseq.name2_3=RHCE;refseq.name2_4=RHCE;refseq.name_1=NM_020485;refseq.name_2=NM_138616;refseq.name_3=NM_138617;refseq.name_4=NM_138618;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T152N;refseq.proteinCoordStr_2=p.T152N;refseq.proteinCoordStr_3=p.T152N;refseq.proteinCoordStr_4=p.T152N;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.spliceDist_1=-32;refseq.spliceDist_2=-32;refseq.spliceDist_3=-32;refseq.spliceDist_4=-32;refseq.start_1=25601705;refseq.start_2=25601705;refseq.start_3=25601705;refseq.start_4=25601705;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantAA_3=Asn;refseq.variantAA_4=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;refseq.variantCodon_3=AAC;refseq.variantCodon_4=AAC;set=FilteredInAll GT 0/1
|
|
chr1 25619817 . G C 17 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.600000;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.48C>G;refseq.codingCoordStr_2=c.48C>G;refseq.codingCoordStr_3=c.48C>G;refseq.codingCoordStr_4=c.48C>G;refseq.codonCoord_1=16;refseq.codonCoord_2=16;refseq.codonCoord_3=16;refseq.codonCoord_4=16;refseq.end_1=25619817;refseq.end_2=25619817;refseq.end_3=25619817;refseq.end_4=25619817;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=134;refseq.mrnaCoord_2=134;refseq.mrnaCoord_3=134;refseq.mrnaCoord_4=134;refseq.name2_1=RHCE;refseq.name2_2=RHCE;refseq.name2_3=RHCE;refseq.name2_4=RHCE;refseq.name_1=NM_020485;refseq.name_2=NM_138616;refseq.name_3=NM_138617;refseq.name_4=NM_138618;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.C16W;refseq.proteinCoordStr_2=p.C16W;refseq.proteinCoordStr_3=p.C16W;refseq.proteinCoordStr_4=p.C16W;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.referenceCodon_3=TGC;refseq.referenceCodon_4=TGC;refseq.spliceDist_1=-101;refseq.spliceDist_2=-101;refseq.spliceDist_3=-101;refseq.spliceDist_4=-101;refseq.start_1=25619817;refseq.start_2=25619817;refseq.start_3=25619817;refseq.start_4=25619817;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Trp;refseq.variantAA_2=Trp;refseq.variantAA_3=Trp;refseq.variantAA_4=Trp;refseq.variantCodon_1=TGG;refseq.variantCodon_2=TGG;refseq.variantCodon_3=TGG;refseq.variantCodon_4=TGG;set=FilteredInAll GT 0/1
|
|
chr1 25630258 . T G 31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.500001;SecondBestBaseQ=15;refseq.chr=chr1;refseq.codingCoordStr=c.80+2;refseq.end=25630258;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_018202;refseq.name2=TMEM57;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=25630258;refseq.transcriptStrand=+;set=soap GT 1/0
|
|
chr1 26004241 . G A 145.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=97.60;MQ0=0;OQ=1455.06;QD=33.07;RankSumP=1.00000;SB=-152.20;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.425G>A;refseq.codingCoordStr_2=c.323G>A;refseq.codonCoord_1=142;refseq.codonCoord_2=108;refseq.end_1=26004241;refseq.end_2=26004241;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=480;refseq.mrnaCoord_2=378;refseq.name2_1=SEPN1;refseq.name2_2=SEPN1;refseq.name_1=NM_020451;refseq.name_2=NM_206926;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C142Y;refseq.proteinCoordStr_2=p.C108Y;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.start_1=26004241;refseq.start_2=26004241;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;set=Intersection GT 1/1
|
|
chr1 26010849 . T C 55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=98.31;MQ0=0;OQ=1105.66;QD=36.86;RankSumP=1.00000;SB=-488.58;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1173T>C;refseq.codingCoordStr_2=c.1071T>C;refseq.codonCoord_1=391;refseq.codonCoord_2=357;refseq.end_1=26010849;refseq.end_2=26010849;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1228;refseq.mrnaCoord_2=1126;refseq.name2_1=SEPN1;refseq.name2_2=SEPN1;refseq.name_1=NM_020451;refseq.name_2=NM_206926;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P391P;refseq.proteinCoordStr_2=p.P357P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.spliceDist_1=81;refseq.spliceDist_2=81;refseq.start_1=26010849;refseq.start_2=26010849;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=Intersection GT 1/1
|
|
chr1 26013160 . C A 81 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=98.70;MQ0=0;OQ=2386.80;QD=35.62;RankSumP=1.00000;SB=-866.83;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1506C>A;refseq.codingCoordStr_2=c.1404C>A;refseq.codonCoord_1=502;refseq.codonCoord_2=468;refseq.end_1=26013160;refseq.end_2=26013160;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1561;refseq.mrnaCoord_2=1459;refseq.name2_1=SEPN1;refseq.name2_2=SEPN1;refseq.name_1=NM_020451;refseq.name_2=NM_206926;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N502K;refseq.proteinCoordStr_2=p.N468K;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=6;refseq.spliceDist_2=6;refseq.spliceInfo_1=splice-acceptor_6;refseq.spliceInfo_2=splice-acceptor_6;refseq.start_1=26013160;refseq.start_2=26013160;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=Intersection GT 1/1
|
|
chr1 26230254 . G A 190.63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=194;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=98.48;MQ0=0;OQ=3970.14;QD=20.46;RankSumP=0.297560;SB=-1330.37;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1146G>A;refseq.codonCoord=382;refseq.end=26230254;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2013;refseq.name=NM_004455;refseq.name2=EXTL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L382L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=45;refseq.start=26230254;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/0
|
|
chr1 26257590 . T C 209.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=321;Dels=0.00;HRun=1;HaplotypeScore=2.63;MQ=98.92;MQ0=0;OQ=5942.46;QD=18.51;RankSumP=0.318730;SB=-928.52;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.709A>G;refseq.codonCoord=237;refseq.end=26257590;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=845;refseq.name=NM_032588;refseq.name2=TRIM63;refseq.positionType=CDS;refseq.proteinCoordStr=p.K237E;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=112;refseq.start=26257590;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/0
|
|
chr1 26360527 . A G 108.70 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=99.00;MQ0=0;OQ=343.77;QD=14.32;RankSumP=0.509994;SB=-37.93;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.158A>G;refseq.codonCoord=53;refseq.end=26360527;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=345;refseq.name=NM_024869;refseq.name2=GRRP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H53R;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=238;refseq.start=26360527;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 0/1
|
|
chr1 26369238 . T C 25.04 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=19;DB;DP=6;Dels=0.00;HRun=1;HaplotypeScore=1.21;MQ=94.28;MQ0=0;QD=4.17;RankSumP=0.633333;SB=-7.00;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.177T>C;refseq.codonCoord=59;refseq.end=26369238;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=264;refseq.name=NM_015871;refseq.name2=ZNF593;refseq.positionType=CDS;refseq.proteinCoordStr=p.G59G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-24;refseq.start=26369238;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 26387899 . T G 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=16;HRun=3;RankSumP=0.00228049;SecondBestBaseQ=9;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1740T>G;refseq.codonCoord_2=580;refseq.end_1=26387899;refseq.end_2=26387899;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1778;refseq.mrnaCoord_2=1798;refseq.name2_1=CNKSR1;refseq.name2_2=CNKSR1;refseq.name_1=NR_023345;refseq.name_2=NM_006314;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.G580G;refseq.referenceAA_2=Gly;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=50;refseq.spliceDist_2=50;refseq.start_1=26387899;refseq.start_2=26387899;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 26454678 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=488;Dels=0.00;HRun=1;HaplotypeScore=3.09;MQ=98.90;MQ0=0;OQ=10377.30;QD=21.26;RankSumP=0.494580;SB=-3725.27;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.638G>A;refseq.codonCoord=213;refseq.end=26454678;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=769;refseq.name=NM_022778;refseq.name2=CCDC21;refseq.positionType=CDS;refseq.proteinCoordStr=p.S213N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-266;refseq.start=26454678;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/0
|
|
chr1 26481401 . A G 20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=8;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=91.70;MQ0=0;OQ=66.44;QD=8.30;RankSumP=0.100000;SB=-35.93;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1179T>C;refseq.codingCoordStr_2=c.1440T>C;refseq.codingCoordStr_3=c.1539T>C;refseq.codonCoord_1=393;refseq.codonCoord_2=480;refseq.codonCoord_3=513;refseq.end_1=26481401;refseq.end_2=26481401;refseq.end_3=26481401;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1327;refseq.mrnaCoord_2=1807;refseq.mrnaCoord_3=1812;refseq.name2_1=UBXN11;refseq.name2_2=UBXN11;refseq.name2_3=UBXN11;refseq.name_1=NM_001077262;refseq.name_2=NM_145345;refseq.name_3=NM_183008;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P393P;refseq.proteinCoordStr_2=p.P480P;refseq.proteinCoordStr_3=p.P513P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.spliceDist_1=-42;refseq.spliceDist_2=-42;refseq.spliceDist_3=-42;refseq.start_1=26481401;refseq.start_2=26481401;refseq.start_3=26481401;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;set=Intersection GT 0/1
|
|
chr1 26481415 . G A 20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=90.61;MQ0=0;OQ=74.88;QD=10.70;RankSumP=0.666667;SB=-37.64;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1165C>T;refseq.codingCoordStr_2=c.1426C>T;refseq.codingCoordStr_3=c.1525C>T;refseq.codonCoord_1=389;refseq.codonCoord_2=476;refseq.codonCoord_3=509;refseq.end_1=26481415;refseq.end_2=26481415;refseq.end_3=26481415;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1313;refseq.mrnaCoord_2=1793;refseq.mrnaCoord_3=1798;refseq.name2_1=UBXN11;refseq.name2_2=UBXN11;refseq.name2_3=UBXN11;refseq.name_1=NM_001077262;refseq.name_2=NM_145345;refseq.name_3=NM_183008;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P389S;refseq.proteinCoordStr_2=p.P476S;refseq.proteinCoordStr_3=p.P509S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.spliceDist_1=-56;refseq.spliceDist_2=-56;refseq.spliceDist_3=-56;refseq.start_1=26481415;refseq.start_2=26481415;refseq.start_3=26481415;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;refseq.variantCodon_3=TCC;set=Intersection GT 1/0
|
|
chr1 26481439 . G A 55 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=94.83;MQ0=0;OQ=96.73;QD=8.79;RankSumP=0.542857;SB=2.03;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1141C>T;refseq.codingCoordStr_2=c.1402C>T;refseq.codingCoordStr_3=c.1501C>T;refseq.codonCoord_1=381;refseq.codonCoord_2=468;refseq.codonCoord_3=501;refseq.end_1=26481439;refseq.end_2=26481439;refseq.end_3=26481439;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1289;refseq.mrnaCoord_2=1769;refseq.mrnaCoord_3=1774;refseq.name2_1=UBXN11;refseq.name2_2=UBXN11;refseq.name2_3=UBXN11;refseq.name_1=NM_001077262;refseq.name_2=NM_145345;refseq.name_3=NM_183008;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P381S;refseq.proteinCoordStr_2=p.P468S;refseq.proteinCoordStr_3=p.P501S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.spliceDist_1=-80;refseq.spliceDist_2=-80;refseq.spliceDist_3=-80;refseq.start_1=26481439;refseq.start_2=26481439;refseq.start_3=26481439;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;refseq.variantCodon_3=TCC;set=Intersection GT 1/0
|
|
chr1 26481846 . C T 240.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=145;Dels=0.00;HRun=0;HaplotypeScore=5.10;MQ=99.00;MQ0=0;OQ=2115.18;QD=14.59;RankSumP=0.0534604;SB=-863.36;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.813G>A;refseq.codingCoordStr_2=c.1074G>A;refseq.codingCoordStr_3=c.1173G>A;refseq.codonCoord_1=271;refseq.codonCoord_2=358;refseq.codonCoord_3=391;refseq.end_1=26481846;refseq.end_2=26481846;refseq.end_3=26481846;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=961;refseq.mrnaCoord_2=1441;refseq.mrnaCoord_3=1446;refseq.name2_1=UBXN11;refseq.name2_2=UBXN11;refseq.name2_3=UBXN11;refseq.name_1=NM_001077262;refseq.name_2=NM_145345;refseq.name_3=NM_183008;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.T271T;refseq.proteinCoordStr_2=p.T358T;refseq.proteinCoordStr_3=p.T391T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.referenceCodon_3=ACG;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.spliceDist_3=22;refseq.start_1=26481846;refseq.start_2=26481846;refseq.start_3=26481846;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACA;refseq.variantCodon_2=ACA;refseq.variantCodon_3=ACA;set=Intersection GT 0/1
|
|
chr1 26483478 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=7.10;MQ=98.63;MQ0=0;OQ=772.35;QD=10.44;RankSumP=0.316866;SB=-181.81;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.575T>G;refseq.codingCoordStr_2=c.836T>G;refseq.codingCoordStr_3=c.935T>G;refseq.codonCoord_1=192;refseq.codonCoord_2=279;refseq.codonCoord_3=312;refseq.end_1=26483478;refseq.end_2=26483478;refseq.end_3=26483478;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=723;refseq.mrnaCoord_2=1203;refseq.mrnaCoord_3=1208;refseq.name2_1=UBXN11;refseq.name2_2=UBXN11;refseq.name2_3=UBXN11;refseq.name_1=NM_001077262;refseq.name_2=NM_145345;refseq.name_3=NM_183008;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.L192R;refseq.proteinCoordStr_2=p.L279R;refseq.proteinCoordStr_3=p.L312R;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.spliceDist_1=-39;refseq.spliceDist_2=-39;refseq.spliceDist_3=-39;refseq.start_1=26483478;refseq.start_2=26483478;refseq.start_3=26483478;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;set=Intersection GT 0/1
|
|
chr1 26500065 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=564;Dels=0.00;HRun=1;HaplotypeScore=25.17;MQ=98.44;MQ0=0;OQ=6600.47;QD=11.70;RankSumP=8.48466e-06;SB=-1001.24;SecondBestBaseQ=28;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.138A>G;refseq.codingCoordStr_3=c.138A>G;refseq.codonCoord_2=46;refseq.codonCoord_3=46;refseq.end_1=26500761;refseq.end_2=26500065;refseq.end_3=26500065;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=286;refseq.mrnaCoord_3=411;refseq.name2_1=UBXN11;refseq.name2_2=UBXN11;refseq.name2_3=UBXN11;refseq.name_1=NM_145345;refseq.name_2=NM_001077262;refseq.name_3=NM_183008;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.S46S;refseq.proteinCoordStr_3=p.S46S;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.spliceDist_2=38;refseq.spliceDist_3=38;refseq.start_1=26497151;refseq.start_2=26500065;refseq.start_3=26500065;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_2=TCG;refseq.variantCodon_3=TCG;set=filterInsoap-gatk GT 1/0
|
|
chr1 26519279 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.85A>C;refseq.codonCoord=29;refseq.end=26519279;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=183;refseq.name=NM_001803;refseq.name2=CD52;refseq.positionType=CDS;refseq.proteinCoordStr=p.T29P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=31;refseq.start=26519279;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 26519313 . A G 304.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=325;Dels=0.00;HRun=0;HaplotypeScore=10.02;MQ=97.74;MQ0=0;OQ=5205.92;QD=16.02;RankSumP=0.214690;SB=-1990.49;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.119A>G;refseq.codonCoord=40;refseq.end=26519313;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=217;refseq.name=NM_001803;refseq.name2=CD52;refseq.positionType=CDS;refseq.proteinCoordStr=p.N40S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=65;refseq.start=26519313;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 26519317 . A G 193.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=336;Dels=0.00;HRun=0;HaplotypeScore=17.72;MQ=97.86;MQ0=0;OQ=5278.83;QD=15.71;RankSumP=0.234952;SB=-1953.44;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.123A>G;refseq.codonCoord=41;refseq.end=26519317;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=221;refseq.name=NM_001803;refseq.name2=CD52;refseq.positionType=CDS;refseq.proteinCoordStr=p.I41M;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=69;refseq.start=26519317;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 26659214 . G A 348.58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=392;Dels=0.00;HRun=0;HaplotypeScore=9.66;MQ=98.96;MQ0=0;OQ=6962.06;QD=17.76;RankSumP=0.0694949;SB=-1686.37;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.757G>A;refseq.codingCoordStr_2=c.757G>A;refseq.codonCoord_1=253;refseq.codonCoord_2=253;refseq.end_1=26659214;refseq.end_2=26659214;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=878;refseq.mrnaCoord_2=878;refseq.name2_1=DHDDS;refseq.name2_2=DHDDS;refseq.name_1=NM_024887;refseq.name_2=NM_205861;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V253M;refseq.proteinCoordStr_2=p.V253M;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-9;refseq.spliceDist_2=-9;refseq.spliceInfo_1=splice-donor_-9;refseq.spliceInfo_2=splice-donor_-9;refseq.start_1=26659214;refseq.start_2=26659214;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;set=Intersection GT 1/0
|
|
chr1 26752507 . T C 212.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=153;Dels=0.00;HRun=1;HaplotypeScore=4.16;MQ=98.81;MQ0=0;OQ=5634.12;QD=36.82;RankSumP=1.00000;SB=-2218.31;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.534T>C;refseq.codingCoordStr_2=c.507T>C;refseq.codonCoord_1=178;refseq.codonCoord_2=169;refseq.end_1=26752507;refseq.end_2=26752507;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=583;refseq.mrnaCoord_2=670;refseq.name2_1=RPS6KA1;refseq.name2_2=RPS6KA1;refseq.name_1=NM_001006665;refseq.name_2=NM_002953;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A178A;refseq.proteinCoordStr_2=p.A169A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=39;refseq.spliceDist_2=39;refseq.start_1=26752507;refseq.start_2=26752507;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/1
|
|
chr1 26978698 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5722A>C;refseq.codingCoordStr_2=c.5071A>C;refseq.codonCoord_1=1908;refseq.codonCoord_2=1691;refseq.end_1=26978698;refseq.end_2=26978698;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=6095;refseq.mrnaCoord_2=5444;refseq.name2_1=ARID1A;refseq.name2_2=ARID1A;refseq.name_1=NM_006015;refseq.name_2=NM_139135;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T1908P;refseq.proteinCoordStr_2=p.T1691P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=598;refseq.spliceDist_2=598;refseq.start_1=26978698;refseq.start_2=26978698;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=FilteredInAll GT 0/1
|
|
chr1 26979751 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.6775T>G;refseq.codingCoordStr_2=c.6124T>G;refseq.codonCoord_1=2259;refseq.codonCoord_2=2042;refseq.end_1=26979751;refseq.end_2=26979751;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=7148;refseq.mrnaCoord_2=6497;refseq.name2_1=ARID1A;refseq.name2_2=ARID1A;refseq.name_1=NM_006015;refseq.name_2=NM_139135;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L2259V;refseq.proteinCoordStr_2=p.L2042V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTG;refseq.referenceCodon_2=TTG;refseq.spliceDist_1=-1438;refseq.spliceDist_2=-1438;refseq.start_1=26979751;refseq.start_2=26979751;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT 1/0
|
|
chr1 27047710 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.156501;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.521G>T;refseq.codonCoord=174;refseq.end=27047710;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=616;refseq.name=NM_032283;refseq.name2=ZDHHC18;refseq.positionType=CDS;refseq.proteinCoordStr=p.R174L;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=25;refseq.start=27047710;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT 0/1
|
|
chr1 27051883 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=1;RankSumP=1.17772e-07;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.989A>C;refseq.codonCoord=330;refseq.end=27051883;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1084;refseq.name=NM_032283;refseq.name2=ZDHHC18;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y330S;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=53;refseq.start=27051883;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 0/1
|
|
chr1 27083308 . T C 104.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=151;Dels=0.00;HRun=1;HaplotypeScore=3.75;MQ=98.62;MQ0=0;OQ=4749.32;QD=31.45;RankSumP=1.00000;SB=-2299.13;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.790A>G;refseq.codonCoord=264;refseq.end=27083308;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1072;refseq.name=NM_018066;refseq.name2=GPN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R264G;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=61;refseq.start=27083308;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 27142028 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=4;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.626T>G;refseq.codonCoord=209;refseq.end=27142028;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=742;refseq.name=NM_006600;refseq.name2=NUDC;refseq.positionType=CDS;refseq.proteinCoordStr=p.V209G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=80;refseq.start=27142028;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 27151108 . G A 88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=171.65;QD=8.17;RankSumP=0.185110;SB=-101.55;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.351C>T;refseq.codonCoord=117;refseq.end=27151108;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=444;refseq.name=NM_152365;refseq.name2=C1orf172;refseq.positionType=CDS;refseq.proteinCoordStr=p.D117D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=383;refseq.start=27151108;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/0
|
|
chr1 27151140 . G A 80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.24;MQ0=0;OQ=127.04;QD=7.94;RankSumP=0.722090;SB=-74.30;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.319C>T;refseq.codonCoord=107;refseq.end=27151140;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=412;refseq.name=NM_152365;refseq.name2=C1orf172;refseq.positionType=CDS;refseq.proteinCoordStr=p.R107W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=351;refseq.start=27151140;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/0
|
|
chr1 27211690 . G T 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.59C>A;refseq.codonCoord=20;refseq.end=27211690;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=231;refseq.name=NM_052943;refseq.name2=FAM46B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T20K;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-206;refseq.start=27211690;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=FilteredInAll GT 1/1
|
|
chr1 27299383 . T C 301.57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=98.88;MQ0=0;OQ=3215.58;QD=33.85;RankSumP=1.00000;SB=-768.12;SecondBestBaseQ=2;refseq.chr=chr1;refseq.codingCoordStr=c.*2A>G;refseq.end=27299383;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.mrnaCoord=3076;refseq.name=NM_003047;refseq.name2=SLC9A1;refseq.positionType=utr3;refseq.spliceDist=340;refseq.start=27299383;refseq.transcriptStrand=-;set=Intersection GT 1/1
|
|
chr1 27299628 . T C 354.82 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=211;Dels=0.00;HRun=1;HaplotypeScore=3.64;MQ=98.68;MQ0=0;OQ=8368.22;QD=39.66;RankSumP=1.00000;SB=-2555.36;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2205A>G;refseq.codonCoord=735;refseq.end=27299628;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2831;refseq.name=NM_003047;refseq.name2=SLC9A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E735E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=95;refseq.start=27299628;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 27353344 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=98.60;MQ0=0;OQ=920.01;QD=10.82;RankSumP=0.398429;SB=-269.27;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.69T>C;refseq.codonCoord=23;refseq.end=27353344;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=695;refseq.name=NM_003047;refseq.name2=SLC9A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V23V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-284;refseq.start=27353344;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 0/1
|
|
chr1 27552384 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=19;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=6.03;MQ=98.29;MQ0=0;OQ=478.12;QD=10.87;RankSumP=0.0365116;SB=-159.70;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1331A>G;refseq.codonCoord=444;refseq.end=27552384;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1498;refseq.name=NM_032872;refseq.name2=SYTL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q444R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=24;refseq.start=27552384;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 0/1
|
|
chr1 27552879 . A G 228.58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=5.01;MQ=98.77;MQ0=0;OQ=1602.02;QD=15.11;RankSumP=0.417329;SB=-557.66;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1602A>G;refseq.codonCoord=534;refseq.end=27552879;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1769;refseq.name=NM_032872;refseq.name2=SYTL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E534E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=89;refseq.start=27552879;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 0/1
|
|
chr1 27559879 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1958T>G;refseq.codonCoord=653;refseq.end=27559879;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2207;refseq.name=NM_004672;refseq.name2=MAP3K6;refseq.positionType=CDS;refseq.proteinCoordStr=p.V653G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=38;refseq.start=27559879;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 27560053 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=4.80;MQ=97.25;MQ0=0;OQ=482.71;QD=8.94;RankSumP=0.567459;SB=-178.53;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1866C>A;refseq.codonCoord=622;refseq.end=27560053;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2115;refseq.name=NM_004672;refseq.name2=MAP3K6;refseq.positionType=CDS;refseq.proteinCoordStr=p.N622K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=34;refseq.start=27560053;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 0/1
|
|
chr1 27581725 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.48;MQ0=0;OQ=808.50;QD=19.72;RankSumP=0.494417;SB=-176.64;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.108T>C;refseq.codonCoord=36;refseq.end=27581725;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=184;refseq.name=NM_207397;refseq.name2=CD164L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.F36F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=20;refseq.start=27581725;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 0/1
|
|
chr1 27746690 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00102838;SecondBestBaseQ=13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4524A>C;refseq.codonCoord=1508;refseq.end=27746690;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5493;refseq.name=NM_001029882;refseq.name2=AHDC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1508P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-332;refseq.start=27746690;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 27748411 . C T 390.66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=98.67;MQ0=0;OQ=2648.60;QD=36.28;RankSumP=1.00000;SB=-1009.37;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2803G>A;refseq.codonCoord=935;refseq.end=27748411;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3772;refseq.name=NM_001029882;refseq.name2=AHDC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A935T;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-2053;refseq.start=27748411;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 27749069 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=97.54;MQ0=0;OQ=288.58;QD=12.02;RankSumP=0.308171;SB=-162.86;SecondBestBaseQ=24;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2145G>T;refseq.codonCoord=715;refseq.end=27749069;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3114;refseq.name=NM_001029882;refseq.name2=AHDC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P715P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=2219;refseq.start=27749069;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/0
|
|
chr1 28040250 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.410T>G;refseq.codingCoordStr_3=c.-17T>G;refseq.codonCoord_2=137;refseq.end_1=28042273;refseq.end_2=28040250;refseq.end_3=28040250;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.mrnaCoord_2=464;refseq.mrnaCoord_3=819;refseq.name2_1=PPP1R8;refseq.name2_2=PPP1R8;refseq.name2_3=PPP1R8;refseq.name_1=NM_002713;refseq.name_2=NM_014110;refseq.name_3=NM_138558;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=utr5;refseq.proteinCoordStr_2=p.V137G;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTG;refseq.spliceDist_2=-83;refseq.spliceDist_3=-83;refseq.start_1=28037961;refseq.start_2=28040250;refseq.start_3=28040250;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 28040252 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=3;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.412A>G;refseq.codingCoordStr_3=c.-15A>G;refseq.codonCoord_2=138;refseq.end_1=28042273;refseq.end_2=28040252;refseq.end_3=28040252;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.mrnaCoord_2=466;refseq.mrnaCoord_3=821;refseq.name2_1=PPP1R8;refseq.name2_2=PPP1R8;refseq.name2_3=PPP1R8;refseq.name_1=NM_002713;refseq.name_2=NM_014110;refseq.name_3=NM_138558;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=utr5;refseq.proteinCoordStr_2=p.K138E;refseq.referenceAA_2=Lys;refseq.referenceCodon_2=AAA;refseq.spliceDist_2=-81;refseq.spliceDist_3=-81;refseq.start_1=28037961;refseq.start_2=28040252;refseq.start_3=28040252;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Glu;refseq.variantCodon_2=GAA;set=FilteredInAll GT 0/1
|
|
chr1 28081892 . A G 250.24 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=110;Dels=0.00;HRun=1;HaplotypeScore=5.08;MQ=98.59;MQ0=0;OQ=3970.79;QD=36.10;RankSumP=1.00000;SB=-1184.84;SecondBestBaseQ=0;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.1470A>G;refseq.codonCoord_3=490;refseq.end_1=28084382;refseq.end_2=28084382;refseq.end_3=28081892;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=1498;refseq.name2_1=C1orf38;refseq.name2_2=C1orf38;refseq.name2_3=C1orf38;refseq.name_1=NM_001039477;refseq.name_2=NM_004848;refseq.name_3=NM_001105556;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.L490L;refseq.referenceAA_3=Leu;refseq.referenceCodon_3=CTA;refseq.spliceDist_3=-250;refseq.start_1=28075837;refseq.start_2=28079163;refseq.start_3=28081892;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Leu;refseq.variantCodon_3=CTG;set=Intersection GT 1/1
|
|
chr1 28081949 . T C 204.41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=98.52;MQ0=0;OQ=2141.98;QD=33.47;RankSumP=1.00000;SB=-1057.70;SecondBestBaseQ=2;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.1527T>C;refseq.codonCoord_3=509;refseq.end_1=28084382;refseq.end_2=28084382;refseq.end_3=28081949;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=1555;refseq.name2_1=C1orf38;refseq.name2_2=C1orf38;refseq.name2_3=C1orf38;refseq.name_1=NM_001039477;refseq.name_2=NM_004848;refseq.name_3=NM_001105556;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.V509V;refseq.referenceAA_3=Val;refseq.referenceCodon_3=GTT;refseq.spliceDist_3=-193;refseq.start_1=28075837;refseq.start_2=28079163;refseq.start_3=28081949;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Val;refseq.variantCodon_3=GTC;set=Intersection GT 1/1
|
|
chr1 28081953 . A G 301.59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=98.48;MQ0=0;OQ=2268.55;QD=38.45;RankSumP=1.00000;SB=-1156.47;SecondBestBaseQ=0;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.1531A>G;refseq.codonCoord_3=511;refseq.end_1=28084382;refseq.end_2=28084382;refseq.end_3=28081953;refseq.frame_3=0;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=1559;refseq.name2_1=C1orf38;refseq.name2_2=C1orf38;refseq.name2_3=C1orf38;refseq.name_1=NM_001039477;refseq.name_2=NM_004848;refseq.name_3=NM_001105556;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.K511E;refseq.referenceAA_3=Lys;refseq.referenceCodon_3=AAG;refseq.spliceDist_3=-189;refseq.start_1=28075837;refseq.start_2=28079163;refseq.start_3=28081953;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Glu;refseq.variantCodon_3=GAG;set=Intersection GT 1/1
|
|
chr1 28159252 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=0;RankSumP=0.666667;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.85A>G;refseq.codonCoord=29;refseq.end=28159252;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=162;refseq.name=NM_018053;refseq.name2=XKR8;refseq.positionType=CDS;refseq.proteinCoordStr=p.T29A;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=162;refseq.start=28159252;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 28166299 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=261;Dels=0.00;HRun=0;HaplotypeScore=11.36;MQ=98.62;MQ0=0;OQ=2757.54;QD=10.57;RankSumP=0.492355;SB=-641.44;SecondBestBaseQ=28;refseq.chr=chr1;refseq.codingCoordStr=c.*1G>A;refseq.end=28166299;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=false;refseq.mrnaCoord=1266;refseq.name=NM_018053;refseq.name2=XKR8;refseq.positionType=utr3;refseq.spliceDist=699;refseq.start=28166299;refseq.transcriptStrand=+;set=Intersection GT 1/0
|
|
chr1 28349915 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=3;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.205A>C;refseq.codingCoordStr_2=c.205A>C;refseq.codingCoordStr_3=c.205A>C;refseq.codingCoordStr_4=c.205A>C;refseq.codonCoord_1=69;refseq.codonCoord_2=69;refseq.codonCoord_3=69;refseq.codonCoord_4=69;refseq.end_1=28349915;refseq.end_2=28349915;refseq.end_3=28349915;refseq.end_4=28349915;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=596;refseq.mrnaCoord_2=540;refseq.mrnaCoord_3=448;refseq.mrnaCoord_4=396;refseq.name2_1=PTAFR;refseq.name2_2=PTAFR;refseq.name2_3=PTAFR;refseq.name2_4=PTAFR;refseq.name_1=NM_000952;refseq.name_2=NM_001164721;refseq.name_3=NM_001164722;refseq.name_4=NM_001164723;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T69P;refseq.proteinCoordStr_2=p.T69P;refseq.proteinCoordStr_3=p.T69P;refseq.proteinCoordStr_4=p.T69P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.spliceDist_1=243;refseq.spliceDist_2=243;refseq.spliceDist_3=243;refseq.spliceDist_4=243;refseq.start_1=28349915;refseq.start_2=28349915;refseq.start_3=28349915;refseq.start_4=28349915;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;set=FilteredInAll GT 1/0
|
|
chr1 28400429 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.679C>A;refseq.codonCoord=227;refseq.end=28400429;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=712;refseq.name=NM_014280;refseq.name2=DNAJC8;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q227K;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=40;refseq.start=28400429;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 0/1
|
|
chr1 28436866 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=157;Dels=0.00;HRun=2;HaplotypeScore=8.64;MQ=98.77;MQ0=0;OQ=2505.74;QD=15.96;RankSumP=0.241938;SB=-564.20;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.187A>G;refseq.codingCoordStr_3=c.*1312A>G;refseq.codonCoord_2=63;refseq.end_1=28436924;refseq.end_2=28436866;refseq.end_3=28436866;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.mrnaCoord_2=271;refseq.mrnaCoord_3=1579;refseq.name2_1=ATPIF1;refseq.name2_2=ATPIF1;refseq.name2_3=ATPIF1;refseq.name_1=NM_016311;refseq.name_2=NM_178190;refseq.name_3=NM_178191;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=utr3;refseq.proteinCoordStr_2=p.R63G;refseq.referenceAA_2=Arg;refseq.referenceCodon_2=AGG;refseq.spliceDist_2=8;refseq.spliceDist_3=-333;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=28435561;refseq.start_2=28436866;refseq.start_3=28436866;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=Intersection GT 0/1
|
|
chr1 28471466 . C G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=140;Dels=0.00;HRun=1;HaplotypeScore=29.01;MQ=98.07;MQ0=0;OQ=97.13;QD=0.69;RankSumP=0.00000;SB=278.98;SecondBestBaseQ=19;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.439C>G;refseq.codonCoord=147;refseq.end=28471466;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=792;refseq.name=NM_031459;refseq.name2=SESN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L147V;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=85;refseq.start=28471466;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT 1/0
|
|
chr1 28471467 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.440T>G;refseq.codonCoord=147;refseq.end=28471467;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=793;refseq.name=NM_031459;refseq.name2=SESN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L147R;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=86;refseq.start=28471467;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=FilteredInAll GT 1/0
|
|
chr1 28672967 . C A 159.65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=206;Dels=0.00;HRun=0;HaplotypeScore=3.63;MQ=98.60;MQ0=0;OQ=3031.42;QD=14.72;RankSumP=0.340716;SB=-1321.03;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1138C>A;refseq.codingCoordStr_2=c.1168C>A;refseq.codonCoord_1=380;refseq.codonCoord_2=390;refseq.end_1=28672967;refseq.end_2=28672967;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1420;refseq.mrnaCoord_2=1403;refseq.name2_1=PHACTR4;refseq.name2_2=PHACTR4;refseq.name_1=NM_001048183;refseq.name_2=NM_023923;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L380I;refseq.proteinCoordStr_2=p.L390I;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTA;refseq.referenceCodon_2=CTA;refseq.spliceDist_1=-284;refseq.spliceDist_2=-284;refseq.start_1=28672967;refseq.start_2=28672967;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATA;refseq.variantCodon_2=ATA;set=Intersection GT 1/0
|
|
chr1 28734223 . G A 257.60 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=141;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=98.84;MQ0=0;OQ=2086.19;QD=14.80;RankSumP=0.303933;SB=-1060.01;SecondBestBaseQ=32;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_3=c.609G>A;refseq.codingCoordStr_4=c.567G>A;refseq.codingCoordStr_5=c.516G>A;refseq.codingCoordStr_6=c.516G>A;refseq.codonCoord_3=203;refseq.codonCoord_4=189;refseq.codonCoord_5=172;refseq.codonCoord_6=172;refseq.end_1=28734223;refseq.end_2=28734223;refseq.end_3=28734223;refseq.end_4=28734223;refseq.end_5=28734223;refseq.end_6=28734223;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=*;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeAlternate_5=A;refseq.haplotypeAlternate_6=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=919;refseq.mrnaCoord_2=915;refseq.mrnaCoord_3=694;refseq.mrnaCoord_4=652;refseq.mrnaCoord_5=776;refseq.mrnaCoord_6=601;refseq.name2_1=SNHG3-RCC1;refseq.name2_2=SNHG3-RCC1;refseq.name2_3=RCC1;refseq.name2_4=RCC1;refseq.name2_5=SNHG3-RCC1;refseq.name2_6=RCC1;refseq.name_1=NR_030725;refseq.name_2=NR_030726;refseq.name_3=NM_001048194;refseq.name_4=NM_001048195;refseq.name_5=NM_001048199;refseq.name_6=NM_001269;refseq.numMatchingRecords=6;refseq.positionType_1=non_coding_exon;refseq.positionType_2=non_coding_exon;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_3=p.V203V;refseq.proteinCoordStr_4=p.V189V;refseq.proteinCoordStr_5=p.V172V;refseq.proteinCoordStr_6=p.V172V;refseq.referenceAA_3=Val;refseq.referenceAA_4=Val;refseq.referenceAA_5=Val;refseq.referenceAA_6=Val;refseq.referenceCodon_3=GTG;refseq.referenceCodon_4=GTG;refseq.referenceCodon_5=GTG;refseq.referenceCodon_6=GTG;refseq.spliceDist_1=-23;refseq.spliceDist_2=-23;refseq.spliceDist_3=-23;refseq.spliceDist_4=-23;refseq.spliceDist_5=-23;refseq.spliceDist_6=-23;refseq.start_1=28734223;refseq.start_2=28734223;refseq.start_3=28734223;refseq.start_4=28734223;refseq.start_5=28734223;refseq.start_6=28734223;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantCodon_3=GTA;refseq.variantCodon_4=GTA;refseq.variantCodon_5=GTA;refseq.variantCodon_6=GTA;set=Intersection GT 1/0
|
|
chr1 28889233 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.424137;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.189G>A;refseq.codingCoordStr_2=c.159G>A;refseq.codonCoord_1=63;refseq.codonCoord_2=53;refseq.end_1=28889233;refseq.end_2=28889233;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=327;refseq.mrnaCoord_2=294;refseq.name2_1=GMEB1;refseq.name2_2=GMEB1;refseq.name_1=NM_006582;refseq.name_2=NM_024482;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T63T;refseq.proteinCoordStr_2=p.T53T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.spliceDist_1=-53;refseq.spliceDist_2=31;refseq.start_1=28889233;refseq.start_2=28889233;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACA;refseq.variantCodon_2=ACA;set=FilteredInAll GT 1/0
|
|
chr1 29011562 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=222.56;QD=13.91;RankSumP=0.522455;SB=-6.99;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.80G>T;refseq.codonCoord=27;refseq.end=29011562;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=322;refseq.name=NM_000911;refseq.name2=OPRD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C27F;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-148;refseq.start=29011562;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 0/1
|
|
chr1 29062184 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=2.12;MQ=98.31;MQ0=0;OQ=703.51;QD=12.56;RankSumP=0.00465618;SB=-376.92;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.921C>T;refseq.codonCoord=307;refseq.end=29062184;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1163;refseq.name=NM_000911;refseq.name2=OPRD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G307G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=344;refseq.start=29062184;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=filterInsoap-gatk GT 0/1
|
|
chr1 29252249 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.1683A>C;refseq.codingCoordStr_2=c.1683A>C;refseq.codingCoordStr_3=c.1056A>C;refseq.codingCoordStr_4=c.1056A>C;refseq.codingCoordStr_5=c.1056A>C;refseq.codingCoordStr_6=c.1578A>C;refseq.codonCoord_1=561;refseq.codonCoord_2=561;refseq.codonCoord_3=352;refseq.codonCoord_4=352;refseq.codonCoord_5=352;refseq.codonCoord_6=526;refseq.end_1=29252249;refseq.end_2=29252249;refseq.end_3=29252249;refseq.end_4=29252249;refseq.end_5=29252249;refseq.end_6=29252249;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1810;refseq.mrnaCoord_2=1883;refseq.mrnaCoord_3=1793;refseq.mrnaCoord_4=1873;refseq.mrnaCoord_5=1890;refseq.mrnaCoord_6=1705;refseq.name2_1=EPB41;refseq.name2_2=EPB41;refseq.name2_3=EPB41;refseq.name2_4=EPB41;refseq.name2_5=EPB41;refseq.name2_6=EPB41;refseq.name_1=NM_001166005;refseq.name_2=NM_001166006;refseq.name_3=NM_001166007;refseq.name_4=NM_004437;refseq.name_5=NM_203342;refseq.name_6=NM_203343;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.A561A;refseq.proteinCoordStr_2=p.A561A;refseq.proteinCoordStr_3=p.A352A;refseq.proteinCoordStr_4=p.A352A;refseq.proteinCoordStr_5=p.A352A;refseq.proteinCoordStr_6=p.A526A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceAA_5=Ala;refseq.referenceAA_6=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.referenceCodon_3=GCA;refseq.referenceCodon_4=GCA;refseq.referenceCodon_5=GCA;refseq.referenceCodon_6=GCA;refseq.spliceDist_1=47;refseq.spliceDist_2=47;refseq.spliceDist_3=47;refseq.spliceDist_4=47;refseq.spliceDist_5=47;refseq.spliceDist_6=47;refseq.start_1=29252249;refseq.start_2=29252249;refseq.start_3=29252249;refseq.start_4=29252249;refseq.start_5=29252249;refseq.start_6=29252249;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;refseq.variantCodon_3=GCC;refseq.variantCodon_4=GCC;refseq.variantCodon_5=GCC;refseq.variantCodon_6=GCC;set=FilteredInAll GT 0/1
|
|
chr1 29347928 rs2230678 C T 27.32 ESPStandard;LowQual AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=3.90;SB=-37.53;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1066G>A;refseq.codonCoord=356;refseq.end=29347928;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1439;refseq.name=NM_005626;refseq.name2=SFRS4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G356S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=398;refseq.start=29347928;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:5,2:7:-8.12,-2.11,-21.13:60.15
|
|
chr1 29347981 . C G 57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=96.23;MQ0=0;OQ=64.81;QD=4.63;RankSumP=0.393939;SB=-6.99;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1013G>C;refseq.codonCoord=338;refseq.end=29347981;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1386;refseq.name=NM_005626;refseq.name2=SFRS4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G338A;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=345;refseq.start=29347981;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/0
|
|
chr1 29348235 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=418;Dels=0.00;HRun=0;HaplotypeScore=51.83;MQ=98.28;MQ0=0;OQ=7180.88;QD=17.18;RankSumP=0.151116;SB=-25.97;SecondBestBaseQ=24;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.759A>C;refseq.codonCoord=253;refseq.end=29348235;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1132;refseq.name=NM_005626;refseq.name2=SFRS4;refseq.positionType=CDS;refseq.proteinCoordStr=p.E253D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=91;refseq.start=29348235;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/0
|
|
chr1 29402286 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.71;MQ0=0;OQ=751.44;QD=9.51;RankSumP=0.174719;SB=-377.09;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.369A>G;refseq.codingCoordStr_2=c.597A>G;refseq.codonCoord_1=123;refseq.codonCoord_2=199;refseq.end_1=29402286;refseq.end_2=29402286;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=760;refseq.mrnaCoord_2=633;refseq.name2_1=MECR;refseq.name2_2=MECR;refseq.name_1=NM_001024732;refseq.name_2=NM_016011;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A123A;refseq.proteinCoordStr_2=p.A199A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=47;refseq.spliceDist_2=47;refseq.start_1=29402286;refseq.start_2=29402286;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/0
|
|
chr1 29415224 . A G 165.38 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=169;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=98.36;MQ0=0;OQ=2391.70;QD=14.15;RankSumP=0.467154;SB=-890.50;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.58T>C;refseq.codingCoordStr_2=c.286T>C;refseq.codonCoord_1=20;refseq.codonCoord_2=96;refseq.end_1=29415224;refseq.end_2=29415224;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=449;refseq.mrnaCoord_2=322;refseq.name2_1=MECR;refseq.name2_2=MECR;refseq.name_1=NM_001024732;refseq.name_2=NM_016011;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F20L;refseq.proteinCoordStr_2=p.F96L;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.start_1=29415224;refseq.start_2=29415224;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;set=Intersection GT 0/1
|
|
chr1 29474688 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1286G>C;refseq.codingCoordStr_2=c.1286G>C;refseq.codingCoordStr_3=c.1286G>C;refseq.codonCoord_1=429;refseq.codonCoord_2=429;refseq.codonCoord_3=429;refseq.end_1=29474688;refseq.end_2=29474688;refseq.end_3=29474688;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1396;refseq.mrnaCoord_2=1396;refseq.mrnaCoord_3=1396;refseq.name2_1=PTPRU;refseq.name2_2=PTPRU;refseq.name2_3=PTPRU;refseq.name_1=NM_005704;refseq.name_2=NM_133177;refseq.name_3=NM_133178;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S429T;refseq.proteinCoordStr_2=p.S429T;refseq.proteinCoordStr_3=p.S429T;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.referenceCodon_3=AGC;refseq.spliceDist_1=142;refseq.spliceDist_2=142;refseq.spliceDist_3=142;refseq.start_1=29474688;refseq.start_2=29474688;refseq.start_3=29474688;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;refseq.variantCodon_3=ACC;set=FilteredInAll GT 0/1
|
|
chr1 29510603 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2936A>G;refseq.codingCoordStr_2=c.2924A>G;refseq.codingCoordStr_3=c.2906A>G;refseq.codonCoord_1=979;refseq.codonCoord_2=975;refseq.codonCoord_3=969;refseq.end_1=29510603;refseq.end_2=29510603;refseq.end_3=29510603;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3046;refseq.mrnaCoord_2=3034;refseq.mrnaCoord_3=3016;refseq.name2_1=PTPRU;refseq.name2_2=PTPRU;refseq.name2_3=PTPRU;refseq.name_1=NM_005704;refseq.name_2=NM_133177;refseq.name_3=NM_133178;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E979G;refseq.proteinCoordStr_2=p.E975G;refseq.proteinCoordStr_3=p.E969G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.spliceDist_1=49;refseq.spliceDist_2=49;refseq.spliceDist_3=49;refseq.start_1=29510603;refseq.start_2=29510603;refseq.start_3=29510603;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=FilteredInAll GT 0/1
|
|
chr1 29511659 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=1;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.3111C>A;refseq.codingCoordStr_2=c.3099C>A;refseq.codingCoordStr_3=c.3081C>A;refseq.codonCoord_1=1037;refseq.codonCoord_2=1033;refseq.codonCoord_3=1027;refseq.end_1=29511659;refseq.end_2=29511659;refseq.end_3=29511659;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.functionalClass_3=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3221;refseq.mrnaCoord_2=3209;refseq.mrnaCoord_3=3191;refseq.name2_1=PTPRU;refseq.name2_2=PTPRU;refseq.name2_3=PTPRU;refseq.name_1=NM_005704;refseq.name_2=NM_133177;refseq.name_3=NM_133178;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Y1037*;refseq.proteinCoordStr_2=p.Y1033*;refseq.proteinCoordStr_3=p.Y1027*;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.spliceDist_1=9;refseq.spliceDist_2=9;refseq.spliceDist_3=9;refseq.spliceInfo_1=splice-acceptor_9;refseq.spliceInfo_2=splice-acceptor_9;refseq.spliceInfo_3=splice-acceptor_9;refseq.start_1=29511659;refseq.start_2=29511659;refseq.start_3=29511659;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantAA_3=Stop;refseq.variantCodon_1=TAA;refseq.variantCodon_2=TAA;refseq.variantCodon_3=TAA;set=FilteredInAll GT 1/0
|
|
chr1 30961488 . A G 151.94 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=227;Dels=0.00;HRun=1;HaplotypeScore=5.37;MQ=98.84;MQ0=0;OQ=2975.00;QD=13.11;RankSumP=0.159069;SB=-1456.94;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1062T>C;refseq.codonCoord=354;refseq.end=30961488;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1096;refseq.name=NM_002379;refseq.name2=MATN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T354T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-146;refseq.start=30961488;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 30987951 . T C 209.35 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=202;Dels=0.00;HRun=1;HaplotypeScore=4.57;MQ=98.85;MQ0=0;OQ=2927.33;QD=14.49;RankSumP=0.366060;SB=-1263.44;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.120A>G;refseq.codonCoord=40;refseq.end=30987951;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=211;refseq.name=NM_006762;refseq.name2=LAPTM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.S40S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=33;refseq.start=30987951;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/0
|
|
chr1 31119986 . C T 266.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=176;Dels=0.00;HRun=1;HaplotypeScore=5.07;MQ=98.92;MQ0=0;OQ=2944.90;QD=16.73;RankSumP=0.0315152;SB=-1433.24;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.907G>A;refseq.codonCoord=303;refseq.end=31119986;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=954;refseq.name=NM_014654;refseq.name2=SDC3;refseq.positionType=CDS;refseq.proteinCoordStr=p.D303N;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=37;refseq.start=31119986;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 31122234 . C T 37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=94.00;MQ0=0;OQ=91.37;QD=6.09;RankSumP=0.425641;SB=-41.63;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.622G>A;refseq.codonCoord=208;refseq.end=31122234;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=669;refseq.name=NM_014654;refseq.name2=SDC3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V208I;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-249;refseq.start=31122234;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 0/1
|
|
chr1 31124100 . G A 269.14 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=98.76;MQ0=0;OQ=2176.43;QD=18.93;RankSumP=0.300161;SB=-704.32;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.213C>T;refseq.codonCoord=71;refseq.end=31124100;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=260;refseq.name=NM_014654;refseq.name2=SDC3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P71P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-44;refseq.start=31124100;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/0
|
|
chr1 31199335 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=1.94783e-08;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2404T>C;refseq.codingCoordStr_2=c.2404T>C;refseq.codonCoord_1=802;refseq.codonCoord_2=802;refseq.end_1=31199335;refseq.end_2=31199335;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2517;refseq.mrnaCoord_2=2517;refseq.name2_1=PUM1;refseq.name2_2=PUM1;refseq.name_1=NM_001020658;refseq.name_2=NM_014676;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S802P;refseq.proteinCoordStr_2=p.S802P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCC;refseq.referenceCodon_2=TCC;refseq.spliceDist_1=81;refseq.spliceDist_2=81;refseq.start_1=31199335;refseq.start_2=31199335;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 31199402 . A G 446.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=97.39;MQ0=0;OQ=3962.68;QD=37.38;RankSumP=1.00000;SB=-1848.90;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2337T>C;refseq.codingCoordStr_2=c.2337T>C;refseq.codonCoord_1=779;refseq.codonCoord_2=779;refseq.end_1=31199402;refseq.end_2=31199402;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2450;refseq.mrnaCoord_2=2450;refseq.name2_1=PUM1;refseq.name2_2=PUM1;refseq.name_1=NM_001020658;refseq.name_2=NM_014676;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N779N;refseq.proteinCoordStr_2=p.N779N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=14;refseq.spliceDist_2=14;refseq.start_1=31199402;refseq.start_2=31199402;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=Intersection GT 1/1
|
|
chr1 31304863 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.138G>C;refseq.codingCoordStr_2=c.138G>C;refseq.codonCoord_1=46;refseq.codonCoord_2=46;refseq.end_1=31304863;refseq.end_2=31304863;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=251;refseq.mrnaCoord_2=251;refseq.name2_1=PUM1;refseq.name2_2=PUM1;refseq.name_1=NM_001020658;refseq.name_2=NM_014676;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A46A;refseq.proteinCoordStr_2=p.A46A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=149;refseq.spliceDist_2=149;refseq.start_1=31304863;refseq.start_2=31304863;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=FilteredInAll GT 1/0
|
|
chr1 31669195 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=96.75;MQ0=0;OQ=116.97;QD=4.18;RankSumP=0.217497;SB=-79.29;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.108C>T;refseq.codonCoord=36;refseq.end=31669195;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=258;refseq.name=NM_178865;refseq.name2=SERINC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T36T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=69;refseq.start=31669195;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=soap-filterIngatk GT 0/1
|
|
chr1 31670821 . T C 140.99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=324;Dels=0.00;HRun=2;HaplotypeScore=5.75;MQ=98.13;MQ0=0;OQ=5644.95;QD=17.42;RankSumP=0.0631501;SB=-2148.95;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.450T>C;refseq.codonCoord=150;refseq.end=31670821;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=600;refseq.name=NM_178865;refseq.name2=SERINC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.I150I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-23;refseq.start=31670821;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/0
|
|
chr1 31678492 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=0;RankSumP=3.77679e-05;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1105G>C;refseq.codonCoord=369;refseq.end=31678492;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1255;refseq.name=NM_178865;refseq.name2=SERINC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V369L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=92;refseq.start=31678492;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT 0/1
|
|
chr1 31678493 . T A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=0;RankSumP=6.41427e-05;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1106T>A;refseq.codonCoord=369;refseq.end=31678493;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1256;refseq.name=NM_178865;refseq.name2=SERINC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V369E;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=93;refseq.start=31678493;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=FilteredInAll GT 1/0
|
|
chr1 31857491 . C T 304.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.76;MQ0=0;OQ=2465.93;QD=38.53;RankSumP=1.00000;SB=-1178.06;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.111C>T;refseq.codonCoord=37;refseq.end=31857491;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=496;refseq.name=NM_001525;refseq.name2=HCRTR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R37R;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-89;refseq.start=31857491;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/1
|
|
chr1 31865112 . A G 372.09 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=130;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=97.56;MQ0=0;OQ=4474.11;QD=34.42;RankSumP=1.00000;SB=-1712.96;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1222A>G;refseq.codonCoord=408;refseq.end=31865112;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1607;refseq.name=NM_001525;refseq.name2=HCRTR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I408V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=135;refseq.start=31865112;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 31868852 . A G 213.16 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=196;Dels=0.00;HRun=1;HaplotypeScore=6.58;MQ=97.28;MQ0=0;OQ=7957.98;QD=40.60;RankSumP=1.00000;SB=-3773.52;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.804T>C;refseq.codonCoord=268;refseq.end=31868852;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=816;refseq.name=NM_012392;refseq.name2=PEF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I268I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=179;refseq.start=31868852;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 31895236 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4041T>G;refseq.codonCoord=1347;refseq.end=31895236;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4406;refseq.name=NM_001856;refseq.name2=COL16A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1347G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-16;refseq.start=31895236;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 31921158 . A G 79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=113;Dels=0.00;HRun=2;HaplotypeScore=11.57;MQ=98.79;MQ0=0;OQ=3939.49;QD=34.86;RankSumP=1.00000;SB=-1701.90;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2502T>C;refseq.codonCoord=834;refseq.end=31921158;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2867;refseq.name=NM_001856;refseq.name2=COL16A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P834P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=33;refseq.start=31921158;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 31930961 . T C 379.25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=4.20;MQ=98.83;MQ0=0;OQ=3660.69;QD=36.98;RankSumP=1.00000;SB=-1754.05;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1107A>G;refseq.codonCoord=369;refseq.end=31930961;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1472;refseq.name=NM_001856;refseq.name2=COL16A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P369P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=31930961;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 31936793 . T G 345.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=166;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=98.68;MQ0=0;OQ=6175.99;QD=37.20;RankSumP=1.00000;SB=-2021.18;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.268A>C;refseq.codonCoord=90;refseq.end=31936793;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=633;refseq.name=NM_001856;refseq.name2=COL16A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R90R;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=31936793;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/1
|
|
chr1 31938082 . G T 160.59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=280;Dels=0.00;HRun=1;HaplotypeScore=10.68;MQ=98.54;MQ0=0;OQ=10924.83;QD=39.02;RankSumP=1.00000;SB=-4111.23;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.185C>A;refseq.codonCoord=62;refseq.end=31938082;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=550;refseq.name=NM_001856;refseq.name2=COL16A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T62K;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=37;refseq.start=31938082;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 31966234 . T C 14 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=97.65;MQ0=0;OQ=254.90;QD=23.17;RankSumP=1.00000;SB=-47.96;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4551A>G;refseq.codonCoord=1517;refseq.end=31966234;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4905;refseq.name=NM_001703;refseq.name2=BAI2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1517A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-22;refseq.start=31966234;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=filterInsoap-gatk GT 1/1
|
|
chr1 31969234 . C G 36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;DB;DP=11;Dels=0.00;HRun=2;HaplotypeScore=2.12;MQ=96.41;MQ0=0;OQ=112.41;QD=10.22;RankSumP=0.154762;SB=-46.91;SecondBestBaseQ=13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4134G>C;refseq.codonCoord=1378;refseq.end=31969234;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4488;refseq.name=NM_001703;refseq.name2=BAI2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1378P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-247;refseq.start=31969234;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/0
|
|
chr1 31994500 . G A 151.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=4.44;MQ=98.81;MQ0=0;OQ=1769.57;QD=14.87;RankSumP=0.0622783;SB=-783.34;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.525C>T;refseq.codonCoord=175;refseq.end=31994500;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=879;refseq.name=NM_001703;refseq.name2=BAI2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P175P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-314;refseq.start=31994500;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/0
|
|
chr1 32053197 . T C 220.01 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=99.00;MQ0=0;OQ=1209.60;QD=15.12;RankSumP=0.335388;SB=-566.61;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.325A>G;refseq.codonCoord=109;refseq.end=32053197;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=383;refseq.name=NM_144569;refseq.name2=SPOCD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T109A;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=364;refseq.start=32053197;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/0
|
|
chr1 32330073 . A G 99.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=99.00;MQ0=0;OQ=1362.19;QD=12.61;RankSumP=0.0424058;SB=-491.90;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.801A>G;refseq.codonCoord=267;refseq.end=32330073;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=947;refseq.name=NM_018056;refseq.name2=TMEM39B;refseq.positionType=CDS;refseq.proteinCoordStr=p.S267S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-127;refseq.start=32330073;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 0/1
|
|
chr1 32401468 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.957T>G;refseq.codonCoord=319;refseq.end=32401468;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1045;refseq.name=NM_012316;refseq.name2=KPNA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.G319G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-34;refseq.start=32401468;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 32440214 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=13;HRun=2;RankSumP=0.0292071;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.91A>C;refseq.codonCoord=31;refseq.end=32440214;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=223;refseq.name=NM_024296;refseq.name2=CCDC28B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T31P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-74;refseq.start=32440214;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 32445495 . T G 171.53 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=114;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=98.62;MQ0=0;OQ=1563.50;QD=13.71;RankSumP=0.177193;SB=-495.70;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.866T>G;refseq.codingCoordStr_2=c.626T>G;refseq.codonCoord_1=289;refseq.codonCoord_2=209;refseq.end_1=32445495;refseq.end_2=32445495;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=913;refseq.mrnaCoord_2=673;refseq.name2_1=IQCC;refseq.name2_2=IQCC;refseq.name_1=NM_001160042;refseq.name_2=NM_018134;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F289C;refseq.proteinCoordStr_2=p.F209C;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.spliceDist_1=68;refseq.spliceDist_2=68;refseq.start_1=32445495;refseq.start_2=32445495;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=Intersection GT 1/0
|
|
chr1 32485786 . A G 145.16 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=6.03;MQ=97.37;MQ0=0;OQ=1314.14;QD=15.28;RankSumP=0.0236647;SB=-580.26;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.177A>G;refseq.codonCoord=59;refseq.end=32485786;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=382;refseq.name=NM_032648;refseq.name2=FAM167B;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q59Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-85;refseq.start=32485786;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 32514912 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.902T>G;refseq.codingCoordStr_2=c.902T>G;refseq.codonCoord_1=301;refseq.codonCoord_2=301;refseq.end_1=32514912;refseq.end_2=32514912;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1023;refseq.mrnaCoord_2=1040;refseq.name2_1=LCK;refseq.name2_2=LCK;refseq.name_1=NM_001042771;refseq.name_2=NM_005356;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V301G;refseq.proteinCoordStr_2=p.V301G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=-63;refseq.spliceDist_2=-63;refseq.start_1=32514912;refseq.start_2=32514912;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 1/0
|
|
chr1 32831263 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=1;RankSumP=3.08894e-09;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.144C>A;refseq.codonCoord=48;refseq.end=32831263;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=629;refseq.name=NM_001040441;refseq.name2=ZBTB8A;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y48*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=145;refseq.start=32831263;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=FilteredInAll GT 1/0
|
|
chr1 32838534 . G C 76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=358;Dels=0.00;HRun=0;HaplotypeScore=9.68;MQ=98.73;MQ0=0;OQ=17596.99;QD=49.15;RankSumP=1.00000;SB=-7760.72;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1253G>C;refseq.codonCoord=418;refseq.end=32838534;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1738;refseq.name=NM_001040441;refseq.name2=ZBTB8A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G418A;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=260;refseq.start=32838534;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 32906555 . T C 221.25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=381;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=90.58;MQ0=2;OQ=15942.19;QD=41.84;RankSumP=1.00000;SB=-7755.12;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.450T>C;refseq.codingCoordStr_2=c.348T>C;refseq.codingCoordStr_3=c.453T>C;refseq.codonCoord_1=150;refseq.codonCoord_2=116;refseq.codonCoord_3=151;refseq.end_1=32906555;refseq.end_2=32906555;refseq.end_3=32906555;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=609;refseq.mrnaCoord_2=512;refseq.mrnaCoord_3=612;refseq.name2_1=RBBP4;refseq.name2_2=RBBP4;refseq.name2_3=RBBP4;refseq.name_1=NM_001135255;refseq.name_2=NM_001135256;refseq.name_3=NM_005610;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V150V;refseq.proteinCoordStr_2=p.V116V;refseq.proteinCoordStr_3=p.V151V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.referenceCodon_3=GTT;refseq.spliceDist_1=-32;refseq.spliceDist_2=-32;refseq.spliceDist_3=-32;refseq.start_1=32906555;refseq.start_2=32906555;refseq.start_3=32906555;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;refseq.variantCodon_3=GTC;set=Intersection GT 1/1
|
|
chr1 33008213 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.17;MQ=97.15;MQ0=0;OQ=397.75;QD=10.75;RankSumP=0.632290;SB=-200.86;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.846G>A;refseq.codonCoord=282;refseq.end=33008213;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=890;refseq.name=NM_020888;refseq.name2=KIAA1522;refseq.positionType=CDS;refseq.proteinCoordStr=p.A282A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=146;refseq.start=33008213;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 33008238 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.13;MQ=97.60;MQ0=0;OQ=541.53;QD=11.77;RankSumP=0.678288;SB=-152.68;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.871A>G;refseq.codonCoord=291;refseq.end=33008238;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=915;refseq.name=NM_020888;refseq.name2=KIAA1522;refseq.positionType=CDS;refseq.proteinCoordStr=p.M291V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=171;refseq.start=33008238;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 0/1
|
|
chr1 33018389 . C G 309.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=400;Dels=0.00;HRun=0;HaplotypeScore=13.89;MQ=98.68;MQ0=0;OQ=7925.82;QD=19.81;RankSumP=0.257374;SB=-1882.63;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1218G>C;refseq.codonCoord=406;refseq.end=33018389;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2006;refseq.name=NM_003680;refseq.name2=YARS;refseq.positionType=CDS;refseq.proteinCoordStr=p.L406L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=78;refseq.start=33018389;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/0
|
|
chr1 33175102 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=384;Dels=0.00;HRun=1;HaplotypeScore=25.29;MQ=98.61;MQ0=0;OQ=6277.56;QD=16.35;RankSumP=0.499318;SB=-1422.78;SecondBestBaseQ=31;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.*374G>A;refseq.codingCoordStr_2=c.2091G>A;refseq.codonCoord_2=697;refseq.end_1=33175102;refseq.end_2=33175102;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2138;refseq.mrnaCoord_2=2091;refseq.name2_1=RNF19B;refseq.name2_2=RNF19B;refseq.name_1=NM_001127361;refseq.name_2=NM_153341;refseq.numMatchingRecords=2;refseq.positionType_1=utr3;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S697S;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCG;refseq.spliceDist_1=396;refseq.spliceDist_2=346;refseq.start_1=33175102;refseq.start_2=33175102;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ser;refseq.variantCodon_2=TCA;set=Intersection GT 0/1
|
|
chr1 33175129 . G C 160.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=259;Dels=0.00;HRun=0;HaplotypeScore=12.46;MQ=98.80;MQ0=0;OQ=3948.23;QD=15.24;RankSumP=0.338640;SB=-1620.69;SecondBestBaseQ=28;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.*347C>G;refseq.codingCoordStr_2=c.2064C>G;refseq.codonCoord_2=688;refseq.end_1=33175129;refseq.end_2=33175129;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2111;refseq.mrnaCoord_2=2064;refseq.name2_1=RNF19B;refseq.name2_2=RNF19B;refseq.name_1=NM_001127361;refseq.name_2=NM_153341;refseq.numMatchingRecords=2;refseq.positionType_1=utr3;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.P688P;refseq.referenceAA_2=Pro;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=369;refseq.spliceDist_2=319;refseq.start_1=33175129;refseq.start_2=33175129;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCG;set=Intersection GT 0/1
|
|
chr1 33182280 . G A 190.90 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=3.20;MQ=98.56;MQ0=0;OQ=2912.43;QD=18.43;RankSumP=9.85636e-05;SB=-721.35;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1329C>T;refseq.codingCoordStr_2=c.1332C>T;refseq.codonCoord_1=443;refseq.codonCoord_2=444;refseq.end_1=33182280;refseq.end_2=33182280;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1329;refseq.mrnaCoord_2=1332;refseq.name2_1=RNF19B;refseq.name2_2=RNF19B;refseq.name_1=NM_001127361;refseq.name_2=NM_153341;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G443G;refseq.proteinCoordStr_2=p.G444G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=68;refseq.spliceDist_2=68;refseq.start_1=33182280;refseq.start_2=33182280;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=filterInsoap-gatk GT 1/0
|
|
chr1 33251546 . C G 33.76 ESPStandard;LowQual AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=80.81;MQ0=0;QD=0.31;SB=-28.60;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.543G>C;refseq.codingCoordStr_2=c.543G>C;refseq.codonCoord_1=181;refseq.codonCoord_2=181;refseq.end_1=33251546;refseq.end_2=33251546;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=585;refseq.mrnaCoord_2=606;refseq.name2_1=AK2;refseq.name2_2=AK2;refseq.name_1=NM_001625;refseq.name_2=NM_013411;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K181N;refseq.proteinCoordStr_2=p.K181N;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=45;refseq.spliceDist_2=45;refseq.start_1=33251546;refseq.start_2=33251546;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:101,9:104:-37.98,-31.32,-476.63:66.60
|
|
chr1 33274963 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=85.60;MQ0=0;OQ=95.16;QD=3.07;SB=-22.49;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.54C>T;refseq.codingCoordStr_2=c.54C>T;refseq.codonCoord_1=18;refseq.codonCoord_2=18;refseq.end_1=33274963;refseq.end_2=33274963;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=96;refseq.mrnaCoord_2=117;refseq.name2_1=AK2;refseq.name2_2=AK2;refseq.name_1=NM_001625;refseq.name_2=NM_013411;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A18A;refseq.proteinCoordStr_2=p.A18A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=-40;refseq.spliceDist_2=-40;refseq.start_1=33274963;refseq.start_2=33274963;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:23,7:24:-20.03,-7.23,-68.76:99
|
|
chr1 33356208 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1148T>G;refseq.codonCoord=383;refseq.end=33356208;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1735;refseq.name=NM_052998;refseq.name2=ADC;refseq.positionType=CDS;refseq.proteinCoordStr=p.V383G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-97;refseq.start=33356208;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 33419537 . A G 120.01 PASS AC=2;AF=1.00;AN=2;BestBaseQ=18;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=98.29;MQ0=0;OQ=486.34;QD=21.15;RankSumP=1.00000;SB=-219.73;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.84T>C;refseq.codonCoord=28;refseq.end=33419537;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=722;refseq.name=NM_018207;refseq.name2=TRIM62;refseq.positionType=CDS;refseq.proteinCoordStr=p.H28H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-325;refseq.start=33419537;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 33567271 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.604T>C;refseq.codingCoordStr_2=c.2209T>C;refseq.codonCoord_1=202;refseq.codonCoord_2=737;refseq.end_1=33567271;refseq.end_2=33567271;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=956;refseq.mrnaCoord_2=2263;refseq.name2_1=PHC2;refseq.name2_2=PHC2;refseq.name_1=NM_004427;refseq.name_2=NM_198040;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S202P;refseq.proteinCoordStr_2=p.S737P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCC;refseq.referenceCodon_2=TCC;refseq.spliceDist_1=64;refseq.spliceDist_2=64;refseq.start_1=33567271;refseq.start_2=33567271;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 33592620 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=441;Dels=0.00;HRun=1;HaplotypeScore=8.80;MQ=98.14;MQ0=0;OQ=9251.44;QD=20.98;RankSumP=0.126029;SB=-3671.10;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1524G>A;refseq.codonCoord=508;refseq.end=33592620;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1578;refseq.name=NM_198040;refseq.name2=PHC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T508T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-32;refseq.start=33592620;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 33593208 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=3;RankSumP=3.51257e-09;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1210G>C;refseq.codonCoord=404;refseq.end=33593208;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1264;refseq.name=NM_198040;refseq.name2=PHC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A404P;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-180;refseq.start=33593208;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 33605452 . A G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=156;Dels=0.00;HRun=4;HaplotypeScore=2.56;MQ=98.92;MQ0=0;OQ=5524.12;QD=35.41;RankSumP=1.00000;SB=-1949.60;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.828T>C;refseq.codonCoord=276;refseq.end=33605452;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=882;refseq.name=NM_198040;refseq.name2=PHC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P276P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-149;refseq.start=33605452;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 33729739 . T G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=142;Dels=0.00;HRun=3;HaplotypeScore=2.67;MQ=98.18;MQ0=0;OQ=4931.20;QD=34.73;RankSumP=1.00000;SB=-1245.55;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1294T>G;refseq.codonCoord=432;refseq.end=33729739;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1461;refseq.name=NM_145238;refseq.name2=ZSCAN20;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y432D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-151;refseq.start=33729739;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 33732649 . A G 306.47 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.91;MQ0=0;OQ=3643.80;QD=38.76;RankSumP=1.00000;SB=-1732.70;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2118A>G;refseq.codonCoord=706;refseq.end=33732649;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2285;refseq.name=NM_145238;refseq.name2=ZSCAN20;refseq.positionType=CDS;refseq.proteinCoordStr=p.A706A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=245;refseq.start=33732649;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 34057929 . G A 261.80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=4.01;MQ=97.83;MQ0=0;OQ=3022.02;QD=39.76;RankSumP=1.00000;SB=-740.43;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1176C>T;refseq.codonCoord=392;refseq.end=34057929;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1205;refseq.name=NM_052896;refseq.name2=CSMD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A392A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-29;refseq.start=34057929;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 34057968 . C T 86.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=141;Dels=0.00;HRun=2;HaplotypeScore=7.92;MQ=98.49;MQ0=0;OQ=5598.53;QD=39.71;RankSumP=1.00000;SB=-1964.43;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1137G>A;refseq.codonCoord=379;refseq.end=34057968;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1166;refseq.name=NM_052896;refseq.name2=CSMD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K379K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=58;refseq.start=34057968;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/1
|
|
chr1 34102484 . T C 351.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=2289.25;QD=37.53;RankSumP=1.00000;SB=-563.38;SecondBestBaseQ=0;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.105T>C;refseq.codonCoord_3=35;refseq.end_1=34156271;refseq.end_2=34102484;refseq.end_3=34102484;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=*;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=133;refseq.mrnaCoord_3=1848;refseq.name2_1=CSMD2;refseq.name2_2=HMGB4;refseq.name2_3=HMGB4;refseq.name_1=NM_052896;refseq.name_2=NR_033264;refseq.name_3=NM_145205;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=non_coding_exon;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.Y35Y;refseq.referenceAA_3=Tyr;refseq.referenceCodon_3=TAT;refseq.spliceDist_2=34;refseq.spliceDist_3=-495;refseq.start_1=34085195;refseq.start_2=34102484;refseq.start_3=34102484;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Tyr;refseq.variantCodon_3=TAC;set=Intersection GT 1/1
|
|
chr1 34102654 . A C 394.17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=218;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=98.74;MQ0=0;OQ=8655.36;QD=39.70;RankSumP=1.00000;SB=-3768.54;SecondBestBaseQ=2;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.275A>C;refseq.codonCoord_3=92;refseq.end_1=34156271;refseq.end_2=34102654;refseq.end_3=34102654;refseq.frame_3=1;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=*;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=303;refseq.mrnaCoord_3=2018;refseq.name2_1=CSMD2;refseq.name2_2=HMGB4;refseq.name2_3=HMGB4;refseq.name_1=NM_052896;refseq.name_2=NR_033264;refseq.name_3=NM_145205;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=non_coding_exon;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.E92A;refseq.referenceAA_3=Glu;refseq.referenceCodon_3=GAA;refseq.spliceDist_2=204;refseq.spliceDist_3=-325;refseq.start_1=34085195;refseq.start_2=34102654;refseq.start_3=34102654;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Ala;refseq.variantCodon_3=GCA;set=Intersection GT 1/1
|
|
chr1 34174008 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=1.27729e-07;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.532A>C;refseq.codonCoord=178;refseq.end=34174008;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=561;refseq.name=NM_052896;refseq.name2=CSMD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T178P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-61;refseq.start=34174008;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 34440371 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1370A>C;refseq.codingCoordStr_2=c.800A>C;refseq.codonCoord_1=457;refseq.codonCoord_2=267;refseq.end_1=34440371;refseq.end_2=34440371;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2208;refseq.mrnaCoord_2=1199;refseq.name2_1=C1orf94;refseq.name2_2=C1orf94;refseq.name_1=NM_001134734;refseq.name_2=NM_032884;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N457T;refseq.proteinCoordStr_2=p.N267T;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-77;refseq.spliceDist_2=-77;refseq.start_1=34440371;refseq.start_2=34440371;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=FilteredInAll GT 0/1
|
|
chr1 35023662 . A C 39 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=1.31596e-09;SecondBestBaseQ=15;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.712A>C;refseq.codingCoordStr_2=c.712A>C;refseq.codonCoord_1=238;refseq.codonCoord_2=238;refseq.end_1=35023662;refseq.end_2=35023662;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=870;refseq.mrnaCoord_2=1327;refseq.name2_1=GJB3;refseq.name2_2=GJB3;refseq.name_1=NM_001005752;refseq.name_2=NM_024009;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T238P;refseq.proteinCoordStr_2=p.T238P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=737;refseq.spliceDist_2=737;refseq.start_1=35023662;refseq.start_2=35023662;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 35032548 . A G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=631;Dels=0.00;HRun=0;HaplotypeScore=12.59;MQ=98.76;MQ0=0;OQ=24391.31;QD=38.66;RankSumP=1.00000;SB=-11506.98;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.147A>G;refseq.codonCoord=49;refseq.end=35032548;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=235;refseq.name=NM_002060;refseq.name2=GJA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q49Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=164;refseq.start=35032548;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 35032789 . G A 118.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=98.30;MQ0=0;OQ=575.99;QD=18.58;RankSumP=0.108541;SB=-238.93;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.388G>A;refseq.codonCoord=130;refseq.end=35032789;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=476;refseq.name=NM_002060;refseq.name2=GJA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V130I;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=405;refseq.start=35032789;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/0
|
|
chr1 35093549 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=6;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.*338A>G;refseq.codingCoordStr_2=c.*338A>G;refseq.codingCoordStr_3=c.*338A>G;refseq.end_1=35093549;refseq.end_2=35093549;refseq.end_3=35093549;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.mrnaCoord_1=1012;refseq.mrnaCoord_2=905;refseq.mrnaCoord_3=762;refseq.name2_1=C1orf212;refseq.name2_2=C1orf212;refseq.name2_3=C1orf212;refseq.name_1=NM_001164824;refseq.name_2=NM_001164825;refseq.name_3=NM_138428;refseq.numMatchingRecords=3;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.spliceDist_1=622;refseq.spliceDist_2=622;refseq.spliceDist_3=622;refseq.start_1=35093549;refseq.start_2=35093549;refseq.start_3=35093549;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;set=FilteredInAll GT 1/0
|
|
chr1 35142791 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.781T>G;refseq.codonCoord=261;refseq.end=35142791;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=781;refseq.name=NM_001080418;refseq.name2=DLGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.W261G;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=-327;refseq.start=35142791;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 35335552 . G A 80.72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=512;Dels=0.00;HRun=0;HaplotypeScore=4.33;MQ=98.59;MQ0=0;OQ=21727.18;QD=42.44;RankSumP=1.00000;SB=-10671.18;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.217G>A;refseq.codonCoord=73;refseq.end=35335552;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=363;refseq.name=NM_024772;refseq.name2=ZMYM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V73M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=48;refseq.start=35335552;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/1
|
|
chr1 35643236 . T G 18 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=5.07368e-09;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3554T>G;refseq.codonCoord=1185;refseq.end=35643236;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3634;refseq.name=NM_005095;refseq.name2=ZMYM4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1185G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=26;refseq.start=35643236;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 35803801 . G C 12 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=0.0644201;SecondBestBaseQ=14;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2140G>C;refseq.codingCoordStr_2=c.2089G>C;refseq.codingCoordStr_3=c.2140G>C;refseq.codonCoord_1=714;refseq.codonCoord_2=697;refseq.codonCoord_3=714;refseq.end_1=35803801;refseq.end_2=35803801;refseq.end_3=35803801;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2267;refseq.mrnaCoord_2=2199;refseq.mrnaCoord_3=2539;refseq.name2_1=NCDN;refseq.name2_2=NCDN;refseq.name2_3=NCDN;refseq.name_1=NM_001014839;refseq.name_2=NM_001014841;refseq.name_3=NM_014284;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A714P;refseq.proteinCoordStr_2=p.A697P;refseq.proteinCoordStr_3=p.A714P;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GCC;refseq.spliceDist_1=387;refseq.spliceDist_2=387;refseq.spliceDist_3=387;refseq.start_1=35803801;refseq.start_2=35803801;refseq.start_3=35803801;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;set=FilteredInAll GT 0/1
|
|
chr1 35828933 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=0.501998;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1016A>C;refseq.codonCoord=339;refseq.end=35828933;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1224;refseq.name=NM_178548;refseq.name2=TFAP2E;refseq.positionType=CDS;refseq.proteinCoordStr=p.H339P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-31;refseq.start=35828933;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 35986756 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2309G>C;refseq.codonCoord=770;refseq.end=35986756;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2389;refseq.name=NM_022111;refseq.name2=CLSPN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S770T;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=37;refseq.start=35986756;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 36001471 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.621T>G;refseq.codonCoord=207;refseq.end=36001471;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=701;refseq.name=NM_022111;refseq.name2=CLSPN;refseq.positionType=CDS;refseq.proteinCoordStr=p.C207W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=39;refseq.start=36001471;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 0/1
|
|
chr1 36070020 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=3;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1017A>G;refseq.codonCoord=339;refseq.end=36070020;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1207;refseq.name=NM_017629;refseq.name2=EIF2C4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G339G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=21;refseq.start=36070020;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 36079466 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=141;Dels=0.00;HRun=4;HaplotypeScore=18.56;MQ=97.84;MQ0=0;OQ=98.33;QD=0.70;RankSumP=0.00000;SB=194.58;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1838A>C;refseq.codonCoord=613;refseq.end=36079466;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2028;refseq.name=NM_017629;refseq.name2=EIF2C4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H613P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=114;refseq.start=36079466;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 36089158 . A C 190.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=188;Dels=0.00;HRun=1;HaplotypeScore=2.79;MQ=97.94;MQ0=0;OQ=6428.96;QD=34.20;RankSumP=1.00000;SB=-817.85;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2394A>C;refseq.codonCoord=798;refseq.end=36089158;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2584;refseq.name=NM_017629;refseq.name2=EIF2C4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S798S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-84;refseq.start=36089158;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 36140168 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=298;Dels=0.00;HRun=0;HaplotypeScore=9.81;MQ=98.56;MQ0=0;OQ=5292.44;QD=17.76;RankSumP=0.396705;SB=-1896.78;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1173C>T;refseq.codonCoord=391;refseq.end=36140168;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1386;refseq.name=NM_012199;refseq.name2=EIF2C1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y391Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=33;refseq.start=36140168;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 0/1
|
|
chr1 36152387 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1758A>C;refseq.codonCoord=586;refseq.end=36152387;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1971;refseq.name=NM_012199;refseq.name2=EIF2C1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q586H;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=16;refseq.start=36152387;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=FilteredInAll GT 0/1
|
|
chr1 36153558 . A C 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=26;DP=597;Dels=0.00;HRun=4;HaplotypeScore=68.00;MQ=98.15;MQ0=0;OQ=2072.54;QD=3.47;RankSumP=0.000673246;SB=1003.80;SecondBestBaseQ=22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1856A>C;refseq.codonCoord=619;refseq.end=36153558;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2069;refseq.name=NM_012199;refseq.name2=EIF2C1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H619P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=23;refseq.start=36153558;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 36247218 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1015T>C;refseq.codingCoordStr_2=c.313T>C;refseq.codonCoord_1=339;refseq.codonCoord_2=105;refseq.end_1=36247218;refseq.end_2=36247218;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1271;refseq.mrnaCoord_2=1013;refseq.name2_1=EIF2C3;refseq.name2_2=EIF2C3;refseq.name_1=NM_024852;refseq.name_2=NM_177422;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y339H;refseq.proteinCoordStr_2=p.Y105H;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-15;refseq.spliceDist_2=-15;refseq.start_1=36247218;refseq.start_2=36247218;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;set=FilteredInAll GT 1/0
|
|
chr1 36247219 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1016A>C;refseq.codingCoordStr_2=c.314A>C;refseq.codonCoord_1=339;refseq.codonCoord_2=105;refseq.end_1=36247219;refseq.end_2=36247219;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1272;refseq.mrnaCoord_2=1014;refseq.name2_1=EIF2C3;refseq.name2_2=EIF2C3;refseq.name_1=NM_024852;refseq.name_2=NM_177422;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y339S;refseq.proteinCoordStr_2=p.Y105S;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-14;refseq.spliceDist_2=-14;refseq.start_1=36247219;refseq.start_2=36247219;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=FilteredInAll GT 0/1
|
|
chr1 36325685 . G A 34 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.443624;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.914G>A;refseq.codonCoord=305;refseq.end=36325685;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1041;refseq.name=NM_014466;refseq.name2=TEKT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R305H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=59;refseq.start=36325685;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap GT 1/0
|
|
chr1 36326260 . A G 409.13 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=181;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=98.74;MQ0=0;OQ=6642.87;QD=36.70;RankSumP=1.00000;SB=-3026.56;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1179A>G;refseq.codonCoord=393;refseq.end=36326260;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1306;refseq.name=NM_014466;refseq.name2=TEKT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T393T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=100;refseq.start=36326260;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 36329981 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.484C>T;refseq.codonCoord=162;refseq.end=36329981;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=537;refseq.name=NM_017825;refseq.name2=ADPRHL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L162L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-33;refseq.start=36329981;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=FilteredInAll GT 0/1
|
|
chr1 36336052 . T G 13 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=3;RankSumP=0.000265344;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1817A>C;refseq.codonCoord=606;refseq.end=36336052;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1824;refseq.name=NM_005202;refseq.name2=COL8A2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N606T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=1624;refseq.start=36336052;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 36409268 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=4;RankSumP=2.25466e-07;SecondBestBaseQ=12;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.156T>C;refseq.codonCoord=52;refseq.end=36409268;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=372;refseq.name=NM_018067;refseq.name2=MAP7D1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P52P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=110;refseq.start=36409268;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 36415007 . T C 29 PASS AC=2;AF=1.00;AN=2;BestBaseQ=17;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=2.06;MQ=96.28;MQ0=0;OQ=310.86;QD=19.43;RankSumP=1.00000;SB=-73.91;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1356T>C;refseq.codonCoord=452;refseq.end=36415007;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1572;refseq.name=NM_018067;refseq.name2=MAP7D1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S452S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-24;refseq.start=36415007;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 36525020 . C T 270.78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=71.87;MQ0=7;OQ=2558.58;QD=33.67;RankSumP=1.00000;SB=-966.72;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.602C>T;refseq.codonCoord=201;refseq.end=36525020;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=826;refseq.name=NM_005119;refseq.name2=THRAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A201V;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-439;refseq.start=36525020;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 36580068 . C T 199.51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=127;Dels=0.00;HRun=0;HaplotypeScore=4.21;MQ=96.93;MQ0=0;OQ=1940.79;QD=15.28;RankSumP=0.241125;SB=-307.28;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1183G>A;refseq.codonCoord=395;refseq.end=36580068;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1590;refseq.name=NM_032017;refseq.name2=STK40;refseq.positionType=CDS;refseq.proteinCoordStr=p.A395T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=94;refseq.start=36580068;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 36596527 . T C 5 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.303828;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.242A>G;refseq.codonCoord=81;refseq.end=36596527;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=649;refseq.name=NM_032017;refseq.name2=STK40;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q81R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=44;refseq.start=36596527;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=FilteredInAll GT 1/0
|
|
chr1 36658704 . C T 292.67 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=139;Dels=0.00;HRun=0;HaplotypeScore=5.05;MQ=98.68;MQ0=0;OQ=2478.77;QD=17.83;RankSumP=0.306476;SB=-707.34;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.919G>A;refseq.codonCoord=307;refseq.end=36658704;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1035;refseq.name=NM_145047;refseq.name2=OSCP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G307R;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-41;refseq.start=36658704;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 0/1
|
|
chr1 36670654 . T C 163.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=485;Dels=0.00;HRun=0;HaplotypeScore=7.72;MQ=98.71;MQ0=0;OQ=8023.47;QD=16.54;RankSumP=0.0717930;SB=-3023.45;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.391A>G;refseq.codingCoordStr_2=c.391A>G;refseq.codonCoord_1=131;refseq.codonCoord_2=131;refseq.end_1=36670654;refseq.end_2=36670654;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=507;refseq.mrnaCoord_2=507;refseq.name2_1=OSCP1;refseq.name2_2=OSCP1;refseq.name_1=NM_145047;refseq.name_2=NM_206837;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T131A;refseq.proteinCoordStr_2=p.T131A;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-45;refseq.spliceDist_2=-45;refseq.start_1=36670654;refseq.start_2=36670654;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/0
|
|
chr1 36712071 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.366T>C;refseq.codingCoordStr_2=c.366T>C;refseq.codingCoordStr_3=c.366T>C;refseq.codingCoordStr_4=c.366T>C;refseq.codonCoord_1=122;refseq.codonCoord_2=122;refseq.codonCoord_3=122;refseq.codonCoord_4=122;refseq.end_1=36712071;refseq.end_2=36712071;refseq.end_3=36712071;refseq.end_4=36712071;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=544;refseq.mrnaCoord_2=544;refseq.mrnaCoord_3=544;refseq.mrnaCoord_4=544;refseq.name2_1=CSF3R;refseq.name2_2=CSF3R;refseq.name2_3=CSF3R;refseq.name2_4=CSF3R;refseq.name_1=NM_000760;refseq.name_2=NM_156038;refseq.name_3=NM_156039;refseq.name_4=NM_172313;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.P122P;refseq.proteinCoordStr_2=p.P122P;refseq.proteinCoordStr_3=p.P122P;refseq.proteinCoordStr_4=p.P122P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.spliceDist_1=5;refseq.spliceDist_2=5;refseq.spliceDist_3=5;refseq.spliceDist_4=5;refseq.spliceInfo_1=splice-acceptor_5;refseq.spliceInfo_2=splice-acceptor_5;refseq.spliceInfo_3=splice-acceptor_5;refseq.spliceInfo_4=splice-acceptor_5;refseq.start_1=36712071;refseq.start_2=36712071;refseq.start_3=36712071;refseq.start_4=36712071;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;set=FilteredInAll GT 0/1
|
|
chr1 37040188 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2611A>C;refseq.codonCoord=871;refseq.end=37040188;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2746;refseq.name=NM_000831;refseq.name2=GRIK3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T871P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=46;refseq.start=37040188;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 37091856 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1159C>T;refseq.codonCoord=387;refseq.end=37091856;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1294;refseq.name=NM_000831;refseq.name2=GRIK3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R387W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-54;refseq.start=37091856;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 1/0
|
|
chr1 37091857 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=24;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1158G>T;refseq.codonCoord=386;refseq.end=37091857;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1293;refseq.name=NM_000831;refseq.name2=GRIK3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L386F;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=54;refseq.start=37091857;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 1/0
|
|
chr1 37740028 . C G 24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.500000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.497G>C;refseq.codonCoord=166;refseq.end=37740028;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=514;refseq.name=NM_022756;refseq.name2=MEAF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S166T;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-37;refseq.start=37740028;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap GT 1/0
|
|
chr1 37792334 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=15.99;MQ=98.49;MQ0=0;OQ=1338.94;QD=11.16;RankSumP=0.247959;SB=-7.01;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.84G>A;refseq.codonCoord=28;refseq.end=37792334;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=157;refseq.name=NM_024700;refseq.name2=SNIP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V28V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-141;refseq.start=37792334;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 0/1
|
|
chr1 37795903 . C T 100.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=145;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=98.89;MQ0=0;OQ=2074.05;QD=14.30;RankSumP=0.224686;SB=-563.83;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.260C>T;refseq.codonCoord=87;refseq.end=37795903;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=270;refseq.name=NM_003462;refseq.name2=DNALI1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A87V;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-34;refseq.start=37795903;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 0/1
|
|
chr1 37958234 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=121;Dels=0.00;HRun=2;HaplotypeScore=1.32;MQ=98.61;MQ0=0;OQ=1894.26;QD=15.66;RankSumP=0.341636;SB=-604.37;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2496C>T;refseq.codonCoord=832;refseq.end=37958234;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2582;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.F832F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-67;refseq.start=37958234;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/0
|
|
chr1 37958310 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=98.53;MQ0=0;OQ=413.76;QD=8.80;RankSumP=0.532383;SB=-91.55;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2420G>A;refseq.codonCoord=807;refseq.end=37958310;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2506;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.R807Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=37958310;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 37958793 . C G 181.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=97.87;MQ0=0;OQ=611.13;QD=16.98;RankSumP=0.684914;SB=-139.56;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2229G>C;refseq.codonCoord=743;refseq.end=37958793;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2315;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.V743V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=21;refseq.start=37958793;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 37960034 . A G 114.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.70;MQ=95.93;MQ0=0;OQ=588.35;QD=15.48;RankSumP=0.212925;SB=-287.53;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2031T>C;refseq.codonCoord=677;refseq.end=37960034;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2117;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.H677H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=71;refseq.start=37960034;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 0/1
|
|
chr1 37960040 . G A 125.06 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=4.17;MQ=96.38;MQ0=0;OQ=588.07;QD=16.34;RankSumP=0.0824811;SB=-245.52;SecondBestBaseQ=23;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2025C>T;refseq.codonCoord=675;refseq.end=37960040;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2111;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.A675A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=65;refseq.start=37960040;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/0
|
|
chr1 37961327 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=280;Dels=0.00;HRun=0;HaplotypeScore=12.46;MQ=98.70;MQ0=0;OQ=2768.47;QD=9.89;RankSumP=0.249838;SB=-1301.10;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1933G>A;refseq.codonCoord=645;refseq.end=37961327;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2019;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.V645I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-28;refseq.start=37961327;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 0/1
|
|
chr1 37961355 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=232;Dels=0.00;HRun=0;HaplotypeScore=5.40;MQ=98.74;MQ0=0;OQ=2618.58;QD=11.29;RankSumP=0.203803;SB=-1321.76;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1905G>A;refseq.codonCoord=635;refseq.end=37961355;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1991;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.L635L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-56;refseq.start=37961355;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 0/1
|
|
chr1 37961374 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=210;Dels=0.00;HRun=2;HaplotypeScore=7.00;MQ=98.77;MQ0=0;OQ=2019.91;QD=9.62;RankSumP=0.419069;SB=-960.17;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1886T>C;refseq.codonCoord=629;refseq.end=37961374;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1972;refseq.name=NM_001099439;refseq.name2=EPHA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.L629P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=52;refseq.start=37961374;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 0/1
|
|
chr1 37999673 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=97.84;MQ0=0;OQ=713.40;QD=9.51;RankSumP=0.321381;SB=-232.90;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.841T>A;refseq.codingCoordStr_2=c.841T>A;refseq.codonCoord_1=281;refseq.codonCoord_2=281;refseq.end_1=37999673;refseq.end_2=37999673;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=927;refseq.mrnaCoord_2=927;refseq.name2_1=EPHA10;refseq.name2_2=EPHA10;refseq.name_1=NM_001099439;refseq.name_2=NM_173641;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F281I;refseq.proteinCoordStr_2=p.F281I;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.spliceDist_1=-10;refseq.spliceDist_2=670;refseq.spliceInfo_1=splice-donor_-10;refseq.start_1=37999673;refseq.start_2=37999673;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;set=Intersection GT 0/1
|
|
chr1 38000237 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.277A>G;refseq.codingCoordStr_2=c.277A>G;refseq.codonCoord_1=93;refseq.codonCoord_2=93;refseq.end_1=38000237;refseq.end_2=38000237;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=363;refseq.mrnaCoord_2=363;refseq.name2_1=EPHA10;refseq.name2_2=EPHA10;refseq.name_1=NM_001099439;refseq.name_2=NM_173641;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I93V;refseq.proteinCoordStr_2=p.I93V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATA;refseq.referenceCodon_2=ATA;refseq.spliceDist_1=106;refseq.spliceDist_2=106;refseq.start_1=38000237;refseq.start_2=38000237;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=FilteredInAll GT 1/0
|
|
chr1 38060857 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=4;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1290A>C;refseq.codonCoord=430;refseq.end=38060857;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1431;refseq.name=NM_005955;refseq.name2=MTF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P430P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=119;refseq.start=38060857;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 38111382 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=554;Dels=0.00;HRun=0;HaplotypeScore=26.23;MQ=98.89;MQ0=0;OQ=10518.73;QD=18.99;RankSumP=0.414393;SB=-3305.80;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1994T>C;refseq.codonCoord=665;refseq.end=38111382;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2088;refseq.name=NM_005540;refseq.name2=INPP5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.M665T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=43;refseq.start=38111382;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 0/1
|
|
chr1 38121157 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=5;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1340A>G;refseq.codonCoord=447;refseq.end=38121157;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1434;refseq.name=NM_005540;refseq.name2=INPP5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.D447G;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=21;refseq.start=38121157;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 38184032 . G A 151.15 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=3.53;MQ=97.44;MQ0=0;OQ=2189.42;QD=15.64;RankSumP=0.493270;SB=-598.04;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.135C>T;refseq.codonCoord=45;refseq.end=38184032;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=229;refseq.name=NM_005540;refseq.name2=INPP5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.H45H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-18;refseq.start=38184032;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 38207705 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1189T>G;refseq.codonCoord=397;refseq.end=38207705;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1313;refseq.name=NM_006802;refseq.name2=SF3A3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y397D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=19;refseq.start=38207705;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 0/1
|
|
chr1 38207855 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1145A>C;refseq.codonCoord=382;refseq.end=38207855;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1269;refseq.name=NM_006802;refseq.name2=SF3A3;refseq.positionType=CDS;refseq.proteinCoordStr=p.N382T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-26;refseq.start=38207855;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 38222497 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=157;Dels=0.00;HRun=1;HaplotypeScore=9.77;MQ=97.86;MQ0=0;OQ=2123.23;QD=13.52;RankSumP=0.481033;SB=-571.70;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.399A>G;refseq.codonCoord=133;refseq.end=38222497;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=523;refseq.name=NM_006802;refseq.name2=SF3A3;refseq.positionType=CDS;refseq.proteinCoordStr=p.E133E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=23;refseq.start=38222497;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 38236091 . C T 326.18 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=318;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=98.62;MQ0=0;OQ=6198.69;QD=19.49;RankSumP=0.0831082;SB=-2531.03;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.540G>A;refseq.codonCoord=180;refseq.end=38236091;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=766;refseq.name=NM_004468;refseq.name2=FHL3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P180P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=39;refseq.start=38236091;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 39112869 . C T 224.88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=98.96;MQ0=0;OQ=1889.99;QD=15.75;RankSumP=0.488427;SB=-667.62;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1489G>A;refseq.codonCoord=497;refseq.end=39112869;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1770;refseq.name=NM_030772;refseq.name2=GJA9;refseq.positionType=CDS;refseq.proteinCoordStr=p.V497I;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-544;refseq.start=39112869;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 0/1
|
|
chr1 39113449 . A G 217.65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=349;Dels=0.00;HRun=1;HaplotypeScore=5.40;MQ=98.85;MQ0=0;OQ=7138.16;QD=20.45;RankSumP=0.391767;SB=-2525.10;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.909T>C;refseq.codonCoord=303;refseq.end=39113449;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1190;refseq.name=NM_030772;refseq.name2=GJA9;refseq.positionType=CDS;refseq.proteinCoordStr=p.S303S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=1004;refseq.start=39113449;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 0/1
|
|
chr1 39124858 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=129;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1599.61;QD=12.40;RankSumP=0.200485;SB=-795.50;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.817C>A;refseq.codonCoord=273;refseq.end=39124858;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1045;refseq.name=NM_017821;refseq.name2=RHBDL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L273M;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=85;refseq.start=39124858;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 39521508 . G A 177.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=269;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.97;MQ0=0;OQ=11732.97;QD=43.62;RankSumP=1.00000;SB=-5647.07;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.771G>A;refseq.codonCoord=257;refseq.end=39521508;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=976;refseq.name=NM_012090;refseq.name2=MACF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q257Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-53;refseq.start=39521508;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/1
|
|
chr1 39571650 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=3;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2123A>G;refseq.codonCoord_2=708;refseq.end_1=39587726;refseq.end_2=39571650;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=2254;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.E708G;refseq.referenceAA_2=Glu;refseq.referenceCodon_2=GAA;refseq.spliceDist_2=2254;refseq.start_1=39565623;refseq.start_2=39571650;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGA;set=FilteredInAll GT 0/1
|
|
chr1 39579197 . C T 177.86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=243;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.93;MQ0=0;OQ=10385.06;QD=42.74;RankSumP=1.00000;SB=-4671.12;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.5886C>T;refseq.codonCoord_2=1962;refseq.end_1=39587726;refseq.end_2=39579197;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=6017;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.C1962C;refseq.referenceAA_2=Cys;refseq.referenceCodon_2=TGC;refseq.spliceDist_2=-16;refseq.start_1=39565623;refseq.start_2=39579197;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Cys;refseq.variantCodon_2=TGT;set=Intersection GT 1/1
|
|
chr1 39585409 . C A 411.52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=98.87;MQ0=0;OQ=2894.97;QD=39.12;RankSumP=1.00000;SB=-853.52;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.6075C>A;refseq.codonCoord_2=2025;refseq.end_1=39587726;refseq.end_2=39585409;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=6206;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A2025A;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCC;refseq.spliceDist_2=-61;refseq.start_1=39565623;refseq.start_2=39585409;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ala;refseq.variantCodon_2=GCA;set=Intersection GT 1/1
|
|
chr1 39597038 . G A 9 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.312597;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5840G>A;refseq.codingCoordStr_2=c.7346G>A;refseq.codonCoord_1=1947;refseq.codonCoord_2=2449;refseq.end_1=39597038;refseq.end_2=39597038;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=6045;refseq.mrnaCoord_2=7477;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.W1947*;refseq.proteinCoordStr_2=p.W2449*;refseq.referenceAA_1=Trp;refseq.referenceAA_2=Trp;refseq.referenceCodon_1=TGG;refseq.referenceCodon_2=TGG;refseq.spliceDist_1=83;refseq.spliceDist_2=83;refseq.start_1=39597038;refseq.start_2=39597038;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantCodon_1=TAG;refseq.variantCodon_2=TAG;set=FilteredInAll GT 1/0
|
|
chr1 39625577 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=141;Dels=0.00;HRun=0;HaplotypeScore=5.88;MQ=98.35;MQ0=0;OQ=2666.90;QD=18.91;RankSumP=0.132998;SB=-1183.39;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.8290T>C;refseq.codingCoordStr_2=c.9796T>C;refseq.codonCoord_1=2764;refseq.codonCoord_2=3266;refseq.end_1=39625577;refseq.end_2=39625577;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=8495;refseq.mrnaCoord_2=9927;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L2764L;refseq.proteinCoordStr_2=p.L3266L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTG;refseq.referenceCodon_2=TTG;refseq.spliceDist_1=132;refseq.spliceDist_2=132;refseq.start_1=39625577;refseq.start_2=39625577;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 1/0
|
|
chr1 39697455 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.15130T>G;refseq.codingCoordStr_2=c.16636T>G;refseq.codonCoord_1=5044;refseq.codonCoord_2=5546;refseq.end_1=39697455;refseq.end_2=39697455;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=15335;refseq.mrnaCoord_2=16767;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L5044V;refseq.proteinCoordStr_2=p.L5546V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTA;refseq.referenceCodon_2=TTA;refseq.spliceDist_1=-54;refseq.spliceDist_2=-54;refseq.start_1=39697455;refseq.start_2=39697455;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=FilteredInAll GT 1/0
|
|
chr1 39700235 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.15440C>G;refseq.codingCoordStr_2=c.16946C>G;refseq.codonCoord_1=5147;refseq.codonCoord_2=5649;refseq.end_1=39700235;refseq.end_2=39700235;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=15645;refseq.mrnaCoord_2=17077;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A5147G;refseq.proteinCoordStr_2=p.A5649G;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-62;refseq.spliceDist_2=-62;refseq.start_1=39700235;refseq.start_2=39700235;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 1/0
|
|
chr1 39706902 . T G 44.98 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=231;Dels=0.00;HRun=2;HaplotypeScore=19.48;MQ=97.95;MQ0=0;QD=0.19;RankSumP=0.00000;SB=266.89;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.15605T>G;refseq.codingCoordStr_2=c.17129T>G;refseq.codonCoord_1=5202;refseq.codonCoord_2=5710;refseq.end_1=39706902;refseq.end_2=39706902;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=15810;refseq.mrnaCoord_2=17260;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V5202G;refseq.proteinCoordStr_2=p.V5710G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=29;refseq.spliceDist_2=29;refseq.start_1=39706902;refseq.start_2=39706902;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=FilteredInAll GT 1/0
|
|
chr1 39718248 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=166;Dels=0.00;HRun=4;HaplotypeScore=12.54;MQ=98.21;MQ0=0;OQ=58.28;QD=0.35;RankSumP=0.00000;SB=164.56;SecondBestBaseQ=17;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.15886A>C;refseq.codingCoordStr_2=c.17410A>C;refseq.codonCoord_1=5296;refseq.codonCoord_2=5804;refseq.end_1=39718248;refseq.end_2=39718248;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=16091;refseq.mrnaCoord_2=17541;refseq.name2_1=MACF1;refseq.name2_2=MACF1;refseq.name_1=NM_012090;refseq.name_2=NM_033044;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T5296P;refseq.proteinCoordStr_2=p.T5804P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-21;refseq.spliceDist_2=-21;refseq.start_1=39718248;refseq.start_2=39718248;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 39730500 . A G 38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=49.14;MQ0=0;OQ=1155.62;QD=26.87;RankSumP=1.00000;SB=-137.70;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.250A>G;refseq.codonCoord=84;refseq.end=39730500;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=596;refseq.name=NM_181809;refseq.name2=BMP8A;refseq.positionType=CDS;refseq.proteinCoordStr=p.M84V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-85;refseq.start=39730500;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 39760671 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=0;RankSumP=0.650670;SecondBestBaseQ=29;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.878G>A;refseq.codonCoord_2=293;refseq.end_1=39760671;refseq.end_2=39760671;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2505;refseq.mrnaCoord_2=1224;refseq.name2_1=LOC728448;refseq.name2_2=BMP8A;refseq.name_1=NR_003929;refseq.name_2=NM_181809;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.R293H;refseq.referenceAA_2=Arg;refseq.referenceCodon_2=CGC;refseq.spliceDist_1=94;refseq.spliceDist_2=10;refseq.spliceInfo_2=splice-acceptor_10;refseq.start_1=39760671;refseq.start_2=39760671;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_2=His;refseq.variantCodon_2=CAC;set=soap GT 1/0
|
|
chr1 39760732 . T C 18 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=0;RankSumP=0.183489;SecondBestBaseQ=27;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.939T>C;refseq.codonCoord_2=313;refseq.end_1=39760732;refseq.end_2=39760732;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2444;refseq.mrnaCoord_2=1285;refseq.name2_1=LOC728448;refseq.name2_2=BMP8A;refseq.name_1=NR_003929;refseq.name_2=NM_181809;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.L313L;refseq.referenceAA_2=Leu;refseq.referenceCodon_2=CTT;refseq.spliceDist_1=33;refseq.spliceDist_2=-10;refseq.spliceInfo_2=splice-donor_-10;refseq.start_1=39760732;refseq.start_2=39760732;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_2=Leu;refseq.variantCodon_2=CTC;set=FilteredInAll GT 1/0
|
|
chr1 39803446 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=1.26022e-07;SecondBestBaseQ=7;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1164A>G;refseq.codingCoordStr_2=c.1164A>G;refseq.codingCoordStr_3=c.1164A>G;refseq.codonCoord_1=388;refseq.codonCoord_2=388;refseq.codonCoord_3=388;refseq.end_1=39803446;refseq.end_2=39803446;refseq.end_3=39803446;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2062;refseq.mrnaCoord_2=2062;refseq.mrnaCoord_3=2062;refseq.name2_1=PABPC4;refseq.name2_2=PABPC4;refseq.name2_3=PABPC4;refseq.name_1=NM_001135653;refseq.name_2=NM_001135654;refseq.name_3=NM_003819;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.G388G;refseq.proteinCoordStr_2=p.G388G;refseq.proteinCoordStr_3=p.G388G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.referenceCodon_3=GGA;refseq.spliceDist_1=-82;refseq.spliceDist_2=-82;refseq.spliceDist_3=-82;refseq.start_1=39803446;refseq.start_2=39803446;refseq.start_3=39803446;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=FilteredInAll GT 1/0
|
|
chr1 39870915 . T C 224.02 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.60;MQ0=0;OQ=2604.99;QD=35.68;RankSumP=1.00000;SB=-592.34;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.140A>G;refseq.codonCoord=47;refseq.end=39870915;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=191;refseq.name=NM_014571;refseq.name2=HEYL;refseq.positionType=CDS;refseq.proteinCoordStr=p.H47R;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-8;refseq.spliceInfo=splice-donor_-8;refseq.start=39870915;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/1
|
|
chr1 39922229 . G T 246.79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=194;Dels=0.00;HRun=1;HaplotypeScore=3.21;MQ=98.23;MQ0=0;OQ=6767.06;QD=34.88;RankSumP=1.00000;SB=-1918.04;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.345C>A;refseq.codonCoord=115;refseq.end=39922229;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=465;refseq.name=NM_016257;refseq.name2=HPCAL4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R115R;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-34;refseq.start=39922229;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/1
|
|
chr1 39922743 . G A 432.56 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.43;MQ0=0;OQ=3542.26;QD=40.72;RankSumP=1.00000;SB=-1538.41;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.120C>T;refseq.codonCoord=40;refseq.end=39922743;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=240;refseq.name=NM_016257;refseq.name2=HPCAL4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S40S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-43;refseq.start=39922743;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/1
|
|
chr1 39991282 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=131;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=98.93;MQ0=0;OQ=2223.78;QD=16.98;RankSumP=0.375298;SB=-296.21;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.808G>A;refseq.codingCoordStr_2=c.808G>A;refseq.codingCoordStr_3=c.610G>A;refseq.codonCoord_1=270;refseq.codonCoord_2=270;refseq.codonCoord_3=204;refseq.end_1=39991282;refseq.end_2=39991282;refseq.end_3=39991282;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=851;refseq.mrnaCoord_2=851;refseq.mrnaCoord_3=843;refseq.name2_1=PPIE;refseq.name2_2=PPIE;refseq.name2_3=PPIE;refseq.name_1=NM_006112;refseq.name_2=NM_203456;refseq.name_3=NM_203457;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E270K;refseq.proteinCoordStr_2=p.E270K;refseq.proteinCoordStr_3=p.E204K;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.referenceCodon_3=GAA;refseq.spliceDist_1=-30;refseq.spliceDist_2=-30;refseq.spliceDist_3=-30;refseq.start_1=39991282;refseq.start_2=39991282;refseq.start_3=39991282;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantAA_3=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;refseq.variantCodon_3=AAA;set=Intersection GT 1/0
|
|
chr1 40001955 . A G 86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=235;Dels=0.00;HRun=1;HaplotypeScore=9.78;MQ=31.90;MQ0=84;OQ=689.54;QD=2.93;RankSumP=0.466667;SB=-10.55;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.845A>G;refseq.codonCoord_2=282;refseq.end_1=40001960;refseq.end_2=40001955;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=888;refseq.name2_1=BMP8B;refseq.name2_2=PPIE;refseq.name_1=NM_001720;refseq.name_2=NM_203456;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.E282G;refseq.referenceAA_2=Glu;refseq.referenceCodon_2=GAA;refseq.spliceDist_2=8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=40001472;refseq.start_2=40001955;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGA;set=Intersection GT 0/1
|
|
chr1 40001980 . G A 71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.295410;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.939C>T;refseq.codingCoordStr_2=c.870G>A;refseq.codonCoord_1=313;refseq.codonCoord_2=290;refseq.end_1=40001980;refseq.end_2=40001980;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1315;refseq.mrnaCoord_2=913;refseq.name2_1=BMP8B;refseq.name2_2=PPIE;refseq.name_1=NM_001720;refseq.name_2=NM_203456;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L313L;refseq.proteinCoordStr_2=p.P290P;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=-10;refseq.spliceDist_2=33;refseq.spliceInfo_1=splice-donor_-10;refseq.start_1=40001980;refseq.start_2=40001980;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Pro;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CCA;set=soap GT 1/0
|
|
chr1 40026469 . G T 24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=0;RankSumP=0.304762;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.276C>A;refseq.codonCoord=92;refseq.end=40026469;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=652;refseq.name=NM_001720;refseq.name2=BMP8B;refseq.positionType=CDS;refseq.proteinCoordStr=p.G92G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-59;refseq.start=40026469;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=soap GT 0/1
|
|
chr1 40082465 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1129A>C;refseq.codonCoord=377;refseq.end=40082465;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1143;refseq.name=NM_017646;refseq.name2=TRIT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T377P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=13;refseq.start=40082465;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 40121718 . G A 49 PASS AC=2;AF=1.00;AN=2;BestBaseQ=21;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=19.84;MQ=98.21;MQ0=0;OQ=2792.38;QD=23.47;RankSumP=1.00000;SB=-793.54;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.33C>T;refseq.codonCoord=11;refseq.end=40121718;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=47;refseq.name=NM_017646;refseq.name2=TRIT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P11P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=47;refseq.start=40121718;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 40135641 . G C 228.18 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=174;Dels=0.00;HRun=0;HaplotypeScore=4.89;MQ=98.46;MQ0=0;OQ=7855.30;QD=45.15;RankSumP=1.00000;SB=-3582.59;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1085C>G;refseq.codingCoordStr_2=c.1085C>G;refseq.codonCoord_1=362;refseq.codonCoord_2=362;refseq.end_1=40135641;refseq.end_2=40135641;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1666;refseq.mrnaCoord_2=1302;refseq.name2_1=MYCL1;refseq.name2_2=MYCL1;refseq.name_1=NM_001033081;refseq.name_2=NM_001033082;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T362S;refseq.proteinCoordStr_2=p.T362S;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=589;refseq.spliceDist_2=589;refseq.start_1=40135641;refseq.start_2=40135641;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 1/1
|
|
chr1 40305853 . T G 317.97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=133;Dels=0.00;HRun=1;HaplotypeScore=4.43;MQ=95.11;MQ0=0;OQ=5156.44;QD=38.77;RankSumP=1.00000;SB=-1668.24;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.685T>G;refseq.codingCoordStr_2=c.685T>G;refseq.codonCoord_1=229;refseq.codonCoord_2=229;refseq.end_1=40305853;refseq.end_2=40305853;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=896;refseq.mrnaCoord_2=914;refseq.name2_1=CAP1;refseq.name2_2=CAP1;refseq.name_1=NM_001105530;refseq.name_2=NM_006367;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C229G;refseq.proteinCoordStr_2=p.C229G;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=55;refseq.spliceDist_2=55;refseq.start_1=40305853;refseq.start_2=40305853;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=Intersection GT 1/1
|
|
chr1 40305874 . T G 185.30 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=91.53;MQ0=0;OQ=3131.61;QD=37.73;RankSumP=1.00000;SB=-1192.09;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.706T>G;refseq.codingCoordStr_2=c.706T>G;refseq.codonCoord_1=236;refseq.codonCoord_2=236;refseq.end_1=40305874;refseq.end_2=40305874;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=917;refseq.mrnaCoord_2=935;refseq.name2_1=CAP1;refseq.name2_2=CAP1;refseq.name_1=NM_001105530;refseq.name_2=NM_006367;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C236G;refseq.proteinCoordStr_2=p.C236G;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=76;refseq.spliceDist_2=76;refseq.start_1=40305874;refseq.start_2=40305874;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=Intersection GT 1/1
|
|
chr1 40305902 rs6665933 T G 381.76 PASS AC=2;AF=1.00;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=89.10;MQ0=0;OQ=3935.69;QD=38.59;SB=-1575.21;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.734T>G;refseq.codingCoordStr_2=c.734T>G;refseq.codonCoord_1=245;refseq.codonCoord_2=245;refseq.end_1=40305902;refseq.end_2=40305902;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=945;refseq.mrnaCoord_2=963;refseq.name2_1=CAP1;refseq.name2_2=CAP1;refseq.name_1=NM_001105530;refseq.name_2=NM_006367;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I245S;refseq.proteinCoordStr_2=p.I245S;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=-75;refseq.spliceDist_2=-75;refseq.start_1=40305902;refseq.start_2=40305902;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=gatk GT:AD:DP:GL:GQ 1/1:0,102:99:-392.57,-29.81,-0.02:99
|
|
chr1 40305907 rs6665936 T G 204.63 PASS AC=2;AF=1.00;AN=2;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=89.92;MQ0=0;OQ=4023.01;QD=38.68;SB=-1481.53;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.739T>G;refseq.codingCoordStr_2=c.739T>G;refseq.codonCoord_1=247;refseq.codonCoord_2=247;refseq.end_1=40305907;refseq.end_2=40305907;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=950;refseq.mrnaCoord_2=968;refseq.name2_1=CAP1;refseq.name2_2=CAP1;refseq.name_1=NM_001105530;refseq.name_2=NM_006367;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C247G;refseq.proteinCoordStr_2=p.C247G;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=-70;refseq.spliceDist_2=-70;refseq.start_1=40305907;refseq.start_2=40305907;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=gatk GT:AD:DP:GL:GQ 1/1:0,104:101:-401.30,-30.41,-0.02:99
|
|
chr1 40305913 . T G 315.39 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=91.55;MQ0=0;OQ=4338.23;QD=39.08;RankSumP=1.00000;SB=-1308.68;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.745T>G;refseq.codingCoordStr_2=c.745T>G;refseq.codonCoord_1=249;refseq.codonCoord_2=249;refseq.end_1=40305913;refseq.end_2=40305913;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=956;refseq.mrnaCoord_2=974;refseq.name2_1=CAP1;refseq.name2_2=CAP1;refseq.name_1=NM_001105530;refseq.name_2=NM_006367;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y249D;refseq.proteinCoordStr_2=p.Y249D;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAT;refseq.referenceCodon_2=TAT;refseq.spliceDist_1=-64;refseq.spliceDist_2=-64;refseq.start_1=40305913;refseq.start_2=40305913;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 1/1
|
|
chr1 40305934 . T G 278.07 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=6.90;MQ=93.57;MQ0=0;OQ=6307.92;QD=39.92;RankSumP=1.00000;SB=-2563.24;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.766T>G;refseq.codingCoordStr_2=c.766T>G;refseq.codonCoord_1=256;refseq.codonCoord_2=256;refseq.end_1=40305934;refseq.end_2=40305934;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=977;refseq.mrnaCoord_2=995;refseq.name2_1=CAP1;refseq.name2_2=CAP1;refseq.name_1=NM_001105530;refseq.name_2=NM_006367;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S256A;refseq.proteinCoordStr_2=p.S256A;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=-43;refseq.spliceDist_2=-43;refseq.start_1=40305934;refseq.start_2=40305934;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 1/1
|
|
chr1 40434001 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.585A>C;refseq.codonCoord=195;refseq.end=40434001;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=616;refseq.name=NM_012421;refseq.name2=RLF;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q195H;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-23;refseq.start=40434001;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=FilteredInAll GT 0/1
|
|
chr1 40478014 . C G 234.91 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=285;Dels=0.00;HRun=0;HaplotypeScore=11.59;MQ=98.58;MQ0=0;OQ=5967.51;QD=20.94;RankSumP=0.463036;SB=-2284.89;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5053C>G;refseq.codonCoord=1685;refseq.end=40478014;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5084;refseq.name=NM_012421;refseq.name2=RLF;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1685E;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-1167;refseq.start=40478014;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 40478313 . A T 287.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=177;Dels=0.00;HRun=0;HaplotypeScore=6.35;MQ=98.88;MQ0=0;OQ=2750.60;QD=15.54;RankSumP=0.141195;SB=-1102.88;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5352A>T;refseq.codonCoord=1784;refseq.end=40478313;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5383;refseq.name=NM_012421;refseq.name2=RLF;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1784D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-868;refseq.start=40478313;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 40489757 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.453A>C;refseq.codonCoord=151;refseq.end=40489757;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=546;refseq.name=NM_001008740;refseq.name2=TMCO2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K151N;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-196;refseq.start=40489757;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 0/1
|
|
chr1 40496655 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.chr=chr1;refseq.codingCoordStr=c.123+2;refseq.end=40496655;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_005857;refseq.name2=ZMPSTE24;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=40496655;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 40539561 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=3.65611e-06;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1950T>G;refseq.codonCoord=650;refseq.end=40539561;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2020;refseq.name=NM_001852;refseq.name2=COL9A2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G650G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=80;refseq.start=40539561;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 40545710 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DB;DP=129;Dels=0.00;HRun=0;HaplotypeScore=10.09;MQ=98.36;MQ0=0;OQ=1207.47;QD=9.36;RankSumP=0.245393;SB=-109.65;SecondBestBaseQ=22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1003C>G;refseq.codonCoord=335;refseq.end=40545710;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1073;refseq.name=NM_001852;refseq.name2=COL9A2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L335V;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-6;refseq.spliceInfo=splice-donor_-6;refseq.start=40545710;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 0/1
|
|
chr1 40653628 . C G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=674;Dels=0.00;HRun=2;HaplotypeScore=12.32;MQ=98.79;MQ0=0;OQ=30727.56;QD=45.59;RankSumP=1.00000;SB=-8613.26;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.669C>G;refseq.codonCoord=223;refseq.end=40653628;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=734;refseq.name=NM_022733;refseq.name2=SMAP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S223S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-13;refseq.start=40653628;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/1
|
|
chr1 40977156 . C T 305.63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=243;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=98.86;MQ0=0;OQ=4569.07;QD=18.80;RankSumP=0.131633;SB=-1231.08;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.54C>T;refseq.codingCoordStr_2=c.54C>T;refseq.codingCoordStr_3=c.54C>T;refseq.codingCoordStr_4=c.54C>T;refseq.codingCoordStr_5=c.54C>T;refseq.codonCoord_1=18;refseq.codonCoord_2=18;refseq.codonCoord_3=18;refseq.codonCoord_4=18;refseq.codonCoord_5=18;refseq.end_1=40977156;refseq.end_2=40977156;refseq.end_3=40977156;refseq.end_4=40977156;refseq.end_5=40977156;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=360;refseq.mrnaCoord_2=360;refseq.mrnaCoord_3=360;refseq.mrnaCoord_4=737;refseq.mrnaCoord_5=360;refseq.name2_1=NFYC;refseq.name2_2=NFYC;refseq.name2_3=NFYC;refseq.name2_4=NFYC;refseq.name2_5=NFYC;refseq.name_1=NM_001142587;refseq.name_2=NM_001142588;refseq.name_3=NM_001142589;refseq.name_4=NM_001142590;refseq.name_5=NM_014223;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.S18S;refseq.proteinCoordStr_2=p.S18S;refseq.proteinCoordStr_3=p.S18S;refseq.proteinCoordStr_4=p.S18S;refseq.proteinCoordStr_5=p.S18S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceAA_5=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.referenceCodon_3=AGC;refseq.referenceCodon_4=AGC;refseq.referenceCodon_5=AGC;refseq.spliceDist_1=-52;refseq.spliceDist_2=-52;refseq.spliceDist_3=-52;refseq.spliceDist_4=-52;refseq.spliceDist_5=-52;refseq.start_1=40977156;refseq.start_2=40977156;refseq.start_3=40977156;refseq.start_4=40977156;refseq.start_5=40977156;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantAA_5=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;refseq.variantCodon_3=AGT;refseq.variantCodon_4=AGT;refseq.variantCodon_5=AGT;set=Intersection GT 0/1
|
|
chr1 41057674 . T C 274.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=148;Dels=0.00;HRun=1;HaplotypeScore=3.80;MQ=98.97;MQ0=0;OQ=5276.07;QD=35.65;RankSumP=1.00000;SB=-2409.13;SecondBestBaseQ=16;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.777T>C;refseq.codingCoordStr_2=c.777T>C;refseq.codonCoord_1=259;refseq.codonCoord_2=259;refseq.end_1=41057674;refseq.end_2=41057674;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=859;refseq.mrnaCoord_2=859;refseq.name2_1=KCNQ4;refseq.name2_2=KCNQ4;refseq.name_1=NM_004700;refseq.name_2=NM_172163;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A259A;refseq.proteinCoordStr_2=p.A259A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-58;refseq.spliceDist_2=-58;refseq.start_1=41057674;refseq.start_2=41057674;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/1
|
|
chr1 41069415 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=19;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=9.72;MQ=97.48;MQ0=0;OQ=515.00;QD=7.92;RankSumP=0.497141;SB=-231.91;SecondBestBaseQ=18;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1365T>G;refseq.codingCoordStr_2=c.1203T>G;refseq.codonCoord_1=455;refseq.codonCoord_2=401;refseq.end_1=41069415;refseq.end_2=41069415;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1447;refseq.mrnaCoord_2=1285;refseq.name2_1=KCNQ4;refseq.name2_2=KCNQ4;refseq.name_1=NM_004700;refseq.name_2=NM_172163;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H455Q;refseq.proteinCoordStr_2=p.H401Q;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=73;refseq.spliceDist_2=73;refseq.start_1=41069415;refseq.start_2=41069415;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=Intersection GT 1/0
|
|
chr1 41351703 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.codingCoordStr_2=c.554G>C;refseq.codingCoordStr_3=c.371G>C;refseq.codingCoordStr_4=c.584G>C;refseq.codingCoordStr_5=c.371G>C;refseq.codingCoordStr_6=c.371G>C;refseq.codingCoordStr_7=c.413G>C;refseq.codonCoord_2=185;refseq.codonCoord_3=124;refseq.codonCoord_4=195;refseq.codonCoord_5=124;refseq.codonCoord_6=124;refseq.codonCoord_7=138;refseq.end_1=41381126;refseq.end_2=41351703;refseq.end_3=41351703;refseq.end_4=41351703;refseq.end_5=41351703;refseq.end_6=41351703;refseq.end_7=41351703;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.frame_7=1;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.mrnaCoord_2=923;refseq.mrnaCoord_3=995;refseq.mrnaCoord_4=786;refseq.mrnaCoord_5=715;refseq.mrnaCoord_6=810;refseq.mrnaCoord_7=924;refseq.name2_1=SCMH1;refseq.name2_2=SCMH1;refseq.name2_3=SCMH1;refseq.name2_4=SCMH1;refseq.name2_5=SCMH1;refseq.name2_6=SCMH1;refseq.name2_7=SCMH1;refseq.name_1=NM_001172222;refseq.name_2=NM_001031694;refseq.name_3=NM_001172218;refseq.name_4=NM_001172219;refseq.name_5=NM_001172220;refseq.name_6=NM_001172221;refseq.name_7=NM_012236;refseq.numMatchingRecords=7;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.proteinCoordStr_2=p.C185S;refseq.proteinCoordStr_3=p.C124S;refseq.proteinCoordStr_4=p.C195S;refseq.proteinCoordStr_5=p.C124S;refseq.proteinCoordStr_6=p.C124S;refseq.proteinCoordStr_7=p.C138S;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceAA_5=Cys;refseq.referenceAA_6=Cys;refseq.referenceAA_7=Cys;refseq.referenceCodon_2=TGC;refseq.referenceCodon_3=TGC;refseq.referenceCodon_4=TGC;refseq.referenceCodon_5=TGC;refseq.referenceCodon_6=TGC;refseq.referenceCodon_7=TGC;refseq.spliceDist_2=83;refseq.spliceDist_3=83;refseq.spliceDist_4=83;refseq.spliceDist_5=83;refseq.spliceDist_6=83;refseq.spliceDist_7=83;refseq.start_1=41313721;refseq.start_2=41351703;refseq.start_3=41351703;refseq.start_4=41351703;refseq.start_5=41351703;refseq.start_6=41351703;refseq.start_7=41351703;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.transcriptStrand_7=-;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantAA_5=Ser;refseq.variantAA_6=Ser;refseq.variantAA_7=Ser;refseq.variantCodon_2=TCC;refseq.variantCodon_3=TCC;refseq.variantCodon_4=TCC;refseq.variantCodon_5=TCC;refseq.variantCodon_6=TCC;refseq.variantCodon_7=TCC;set=FilteredInAll GT 1/0
|
|
chr1 41748804 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=282.22;QD=17.64;RankSumP=0.587762;SB=-89.31;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.7123C>T;refseq.codingCoordStr_2=c.7126C>T;refseq.codonCoord_1=2375;refseq.codonCoord_2=2376;refseq.end_1=41748804;refseq.end_2=41748804;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=8256;refseq.mrnaCoord_2=8339;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P2375S;refseq.proteinCoordStr_2=p.P2376S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=-534;refseq.spliceDist_2=-534;refseq.start_1=41748804;refseq.start_2=41748804;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=Intersection GT 1/0
|
|
chr1 41748915 . T C 8 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=4;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=90.19;MQ0=0;OQ=95.17;QD=23.79;RankSumP=1.00000;SB=-51.69;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.7012A>G;refseq.codingCoordStr_2=c.7015A>G;refseq.codonCoord_1=2338;refseq.codonCoord_2=2339;refseq.end_1=41748915;refseq.end_2=41748915;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=8145;refseq.mrnaCoord_2=8228;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T2338A;refseq.proteinCoordStr_2=p.T2339A;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=607;refseq.spliceDist_2=610;refseq.start_1=41748915;refseq.start_2=41748915;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=filterInsoap-gatk GT 1/1
|
|
chr1 41748932 . T C 34.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DP=5;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=92.02;MQ0=0;QD=6.81;RankSumP=0.400000;SB=-6.99;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.6995A>G;refseq.codingCoordStr_2=c.6998A>G;refseq.codonCoord_1=2332;refseq.codonCoord_2=2333;refseq.end_1=41748932;refseq.end_2=41748932;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=8128;refseq.mrnaCoord_2=8211;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E2332G;refseq.proteinCoordStr_2=p.E2333G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=590;refseq.spliceDist_2=593;refseq.start_1=41748932;refseq.start_2=41748932;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=soap-filterIngatk GT 1/0
|
|
chr1 41749116 . C T 250.62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=98.35;MQ0=0;OQ=1368.10;QD=17.54;RankSumP=0.412608;SB=-535.10;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.6811G>A;refseq.codingCoordStr_2=c.6814G>A;refseq.codonCoord_1=2271;refseq.codonCoord_2=2272;refseq.end_1=41749116;refseq.end_2=41749116;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=7944;refseq.mrnaCoord_2=8027;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G2271R;refseq.proteinCoordStr_2=p.G2272R;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=406;refseq.spliceDist_2=409;refseq.start_1=41749116;refseq.start_2=41749116;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=Intersection GT 0/1
|
|
chr1 41749394 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=1.23847e-09;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.6533A>C;refseq.codingCoordStr_2=c.6536A>C;refseq.codonCoord_1=2178;refseq.codonCoord_2=2179;refseq.end_1=41749394;refseq.end_2=41749394;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=7666;refseq.mrnaCoord_2=7749;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H2178P;refseq.proteinCoordStr_2=p.H2179P;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=128;refseq.spliceDist_2=131;refseq.start_1=41749394;refseq.start_2=41749394;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 41751153 . T G 11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=6;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=155.14;QD=25.86;RankSumP=1.00000;SB=-91.02;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.6326A>C;refseq.codingCoordStr_2=c.6326A>C;refseq.codonCoord_1=2109;refseq.codonCoord_2=2109;refseq.end_1=41751153;refseq.end_2=41751153;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=7459;refseq.mrnaCoord_2=7539;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D2109A;refseq.proteinCoordStr_2=p.D2109A;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-80;refseq.spliceDist_2=-80;refseq.start_1=41751153;refseq.start_2=41751153;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=filterInsoap-gatk GT 1/1
|
|
chr1 41751412 . C G 67 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=2494.32;QD=47.06;RankSumP=1.00000;SB=-1224.17;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.6067G>C;refseq.codingCoordStr_2=c.6067G>C;refseq.codonCoord_1=2023;refseq.codonCoord_2=2023;refseq.end_1=41751412;refseq.end_2=41751412;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=7200;refseq.mrnaCoord_2=7280;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A2023P;refseq.proteinCoordStr_2=p.A2023P;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-339;refseq.spliceDist_2=-339;refseq.start_1=41751412;refseq.start_2=41751412;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;set=Intersection GT 1/1
|
|
chr1 41751743 . A G 53 PASS AC=2;AF=1.00;AN=2;BestBaseQ=23;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=94.28;MQ0=0;OQ=719.52;QD=25.70;RankSumP=1.00000;SB=-211.81;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5736T>C;refseq.codingCoordStr_2=c.5736T>C;refseq.codonCoord_1=1912;refseq.codonCoord_2=1912;refseq.end_1=41751743;refseq.end_2=41751743;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=6869;refseq.mrnaCoord_2=6949;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A1912A;refseq.proteinCoordStr_2=p.A1912A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=266;refseq.spliceDist_2=266;refseq.start_1=41751743;refseq.start_2=41751743;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/1
|
|
chr1 41763048 . G A 118.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=99.00;MQ0=0;OQ=1577.79;QD=15.78;RankSumP=0.243164;SB=-349.30;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5328C>T;refseq.codingCoordStr_2=c.5328C>T;refseq.codonCoord_1=1776;refseq.codonCoord_2=1776;refseq.end_1=41763048;refseq.end_2=41763048;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=6461;refseq.mrnaCoord_2=6541;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H1776H;refseq.proteinCoordStr_2=p.H1776H;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=-56;refseq.spliceDist_2=-56;refseq.start_1=41763048;refseq.start_2=41763048;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAT;refseq.variantCodon_2=CAT;set=Intersection GT 1/0
|
|
chr1 41818334 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=455;Dels=0.00;HRun=1;HaplotypeScore=17.25;MQ=98.80;MQ0=0;OQ=7884.94;QD=17.33;RankSumP=0.283681;SB=-2030.82;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4722A>G;refseq.codingCoordStr_2=c.4722A>G;refseq.codonCoord_1=1574;refseq.codonCoord_2=1574;refseq.end_1=41818334;refseq.end_2=41818334;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=5855;refseq.mrnaCoord_2=5935;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S1574S;refseq.proteinCoordStr_2=p.S1574S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=-340;refseq.spliceDist_2=-340;refseq.start_1=41818334;refseq.start_2=41818334;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;set=Intersection GT 1/0
|
|
chr1 41819399 . C T 65.09 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=97.24;MQ0=0;OQ=1213.85;QD=33.72;RankSumP=1.00000;SB=-244.32;SecondBestBaseQ=6;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3657G>A;refseq.codingCoordStr_2=c.3657G>A;refseq.codonCoord_1=1219;refseq.codonCoord_2=1219;refseq.end_1=41819399;refseq.end_2=41819399;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4790;refseq.mrnaCoord_2=4870;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q1219Q;refseq.proteinCoordStr_2=p.Q1219Q;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-1405;refseq.spliceDist_2=-1405;refseq.start_1=41819399;refseq.start_2=41819399;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;set=Intersection GT 1/1
|
|
chr1 41819651 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=5.02530e-09;SecondBestBaseQ=7;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3405G>A;refseq.codingCoordStr_2=c.3405G>A;refseq.codonCoord_1=1135;refseq.codonCoord_2=1135;refseq.end_1=41819651;refseq.end_2=41819651;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4538;refseq.mrnaCoord_2=4618;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E1135E;refseq.proteinCoordStr_2=p.E1135E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-1657;refseq.spliceDist_2=-1657;refseq.start_1=41819651;refseq.start_2=41819651;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=FilteredInAll GT 0/1
|
|
chr1 41819795 . C G 189.84 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=168;Dels=0.00;HRun=0;HaplotypeScore=3.50;MQ=98.42;MQ0=0;OQ=4126.60;QD=24.56;RankSumP=0.351025;SB=-1752.89;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3261G>C;refseq.codingCoordStr_2=c.3261G>C;refseq.codonCoord_1=1087;refseq.codonCoord_2=1087;refseq.end_1=41819795;refseq.end_2=41819795;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4394;refseq.mrnaCoord_2=4474;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q1087H;refseq.proteinCoordStr_2=p.Q1087H;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-1801;refseq.spliceDist_2=-1801;refseq.start_1=41819795;refseq.start_2=41819795;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;set=Intersection GT 1/0
|
|
chr1 41821332 . T C 303.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=99.00;MQ0=0;OQ=2551.29;QD=34.48;RankSumP=1.00000;SB=-455.52;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1724A>G;refseq.codingCoordStr_2=c.1724A>G;refseq.codonCoord_1=575;refseq.codonCoord_2=575;refseq.end_1=41821332;refseq.end_2=41821332;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2857;refseq.mrnaCoord_2=2937;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H575R;refseq.proteinCoordStr_2=p.H575R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=2245;refseq.spliceDist_2=2245;refseq.start_1=41821332;refseq.start_2=41821332;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=Intersection GT 1/1
|
|
chr1 41821619 . G A 303.25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=151;Dels=0.00;HRun=0;HaplotypeScore=3.97;MQ=98.63;MQ0=0;OQ=5746.49;QD=38.06;RankSumP=1.00000;SB=-2849.76;SecondBestBaseQ=8;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1437C>T;refseq.codingCoordStr_2=c.1437C>T;refseq.codonCoord_1=479;refseq.codonCoord_2=479;refseq.end_1=41821619;refseq.end_2=41821619;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2570;refseq.mrnaCoord_2=2650;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S479S;refseq.proteinCoordStr_2=p.S479S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=1958;refseq.spliceDist_2=1958;refseq.start_1=41821619;refseq.start_2=41821619;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 1/1
|
|
chr1 41821727 . C G 284.52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=2.48;MQ=97.76;MQ0=0;OQ=5129.47;QD=45.80;RankSumP=1.00000;SB=-1939.20;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1329G>C;refseq.codingCoordStr_2=c.1329G>C;refseq.codonCoord_1=443;refseq.codonCoord_2=443;refseq.end_1=41821727;refseq.end_2=41821727;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2462;refseq.mrnaCoord_2=2542;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L443L;refseq.proteinCoordStr_2=p.L443L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=1850;refseq.spliceDist_2=1850;refseq.start_1=41821727;refseq.start_2=41821727;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;set=Intersection GT 1/1
|
|
chr1 41821747 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=1.40950e-05;SecondBestBaseQ=13;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1309A>C;refseq.codingCoordStr_2=c.1309A>C;refseq.codonCoord_1=437;refseq.codonCoord_2=437;refseq.end_1=41821747;refseq.end_2=41821747;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2442;refseq.mrnaCoord_2=2522;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T437P;refseq.proteinCoordStr_2=p.T437P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=1830;refseq.spliceDist_2=1830;refseq.start_1=41821747;refseq.start_2=41821747;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 41822953 . C T 109.59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.82;MQ0=0;OQ=787.05;QD=13.12;RankSumP=0.219210;SB=-365.44;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.103G>A;refseq.codingCoordStr_2=c.103G>A;refseq.codonCoord_1=35;refseq.codonCoord_2=35;refseq.end_1=41822953;refseq.end_2=41822953;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1236;refseq.mrnaCoord_2=1316;refseq.name2_1=HIVEP3;refseq.name2_2=HIVEP3;refseq.name_1=NM_001127714;refseq.name_2=NM_024503;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V35I;refseq.proteinCoordStr_2=p.V35I;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=624;refseq.spliceDist_2=624;refseq.start_1=41822953;refseq.start_2=41822953;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;set=Intersection GT 0/1
|
|
chr1 42391726 . A G 143.43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=121;Dels=0.00;HRun=0;HaplotypeScore=8.98;MQ=98.07;MQ0=0;OQ=2710.66;QD=22.40;RankSumP=1.00000;SB=-690.92;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.18A>G;refseq.codonCoord=6;refseq.end=42391726;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=48;refseq.name=NM_007102;refseq.name2=GUCA2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.A6A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=48;refseq.start=42391726;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 42466184 . A G 296.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=293;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=98.50;MQ0=0;OQ=11371.83;QD=38.81;RankSumP=1.00000;SB=-4884.77;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.485T>C;refseq.codonCoord=162;refseq.end=42466184;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=676;refseq.name=NM_014947;refseq.name2=FOXJ3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V162A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=41;refseq.start=42466184;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 42939158 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.153668;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.860A>G;refseq.codonCoord=287;refseq.end=42939158;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1031;refseq.name=NM_004559;refseq.name2=YBX1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y287C;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=120;refseq.start=42939158;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=FilteredInAll GT 0/1
|
|
chr1 43068782 . C T 183.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=312;Dels=0.00;HRun=0;HaplotypeScore=8.29;MQ=98.87;MQ0=0;OQ=5195.26;QD=16.65;RankSumP=0.300444;SB=-785.85;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.76C>T;refseq.codingCoordStr_2=c.76C>T;refseq.codonCoord_1=26;refseq.codonCoord_2=26;refseq.end_1=43068782;refseq.end_2=43068782;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=346;refseq.mrnaCoord_2=242;refseq.name2_1=ERMAP;refseq.name2_2=ERMAP;refseq.name_1=NM_001017922;refseq.name_2=NM_018538;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H26Y;refseq.proteinCoordStr_2=p.H26Y;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=-10;refseq.spliceDist_2=-10;refseq.spliceInfo_1=splice-donor_-10;refseq.spliceInfo_2=splice-donor_-10;refseq.start_1=43068782;refseq.start_2=43068782;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;set=Intersection GT 0/1
|
|
chr1 43081029 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.967T>C;refseq.codingCoordStr_2=c.967T>C;refseq.codonCoord_1=323;refseq.codonCoord_2=323;refseq.end_1=43081029;refseq.end_2=43081029;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1237;refseq.mrnaCoord_2=1133;refseq.name2_1=ERMAP;refseq.name2_2=ERMAP;refseq.name_1=NM_001017922;refseq.name_2=NM_018538;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S323P;refseq.proteinCoordStr_2=p.S323P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=255;refseq.spliceDist_2=255;refseq.start_1=43081029;refseq.start_2=43081029;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=FilteredInAll GT 1/0
|
|
chr1 43081031 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.969A>C;refseq.codingCoordStr_2=c.969A>C;refseq.codonCoord_1=323;refseq.codonCoord_2=323;refseq.end_1=43081031;refseq.end_2=43081031;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1239;refseq.mrnaCoord_2=1135;refseq.name2_1=ERMAP;refseq.name2_2=ERMAP;refseq.name_1=NM_001017922;refseq.name_2=NM_018538;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S323S;refseq.proteinCoordStr_2=p.S323S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=257;refseq.spliceDist_2=257;refseq.start_1=43081031;refseq.start_2=43081031;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=FilteredInAll GT 0/1
|
|
chr1 43405123 . C T 306.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=324;Dels=0.00;HRun=0;HaplotypeScore=3.26;MQ=98.76;MQ0=0;OQ=6448.46;QD=19.90;RankSumP=0.165159;SB=-2722.97;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.833G>A;refseq.codingCoordStr_2=c.668G>A;refseq.codonCoord_1=278;refseq.codonCoord_2=223;refseq.end_1=43405123;refseq.end_2=43405123;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=982;refseq.mrnaCoord_2=865;refseq.name2_1=EBNA1BP2;refseq.name2_2=EBNA1BP2;refseq.name_1=NM_001159936;refseq.name_2=NM_006824;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R278H;refseq.proteinCoordStr_2=p.R223H;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.spliceDist_1=-40;refseq.spliceDist_2=-40;refseq.start_1=43405123;refseq.start_2=43405123;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;set=Intersection GT 0/1
|
|
chr1 43409071 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=751;Dels=0.00;HRun=1;HaplotypeScore=16.80;MQ=98.85;MQ0=0;OQ=17876.47;QD=23.80;RankSumP=0.181376;SB=-6222.08;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.555G>C;refseq.codingCoordStr_2=c.390G>C;refseq.codonCoord_1=185;refseq.codonCoord_2=130;refseq.end_1=43409071;refseq.end_2=43409071;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=704;refseq.mrnaCoord_2=587;refseq.name2_1=EBNA1BP2;refseq.name2_2=EBNA1BP2;refseq.name_1=NM_001159936;refseq.name_2=NM_006824;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T185T;refseq.proteinCoordStr_2=p.T130T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.spliceDist_1=-58;refseq.spliceDist_2=-58;refseq.start_1=43409071;refseq.start_2=43409071;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=Intersection GT 1/0
|
|
chr1 43411044 . T A 105.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=6.54;MQ=98.86;MQ0=0;OQ=1774.40;QD=11.67;RankSumP=0.396383;SB=-885.87;SecondBestBaseQ=26;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.33T>A;refseq.codingCoordStr_3=c.33T>A;refseq.codingCoordStr_4=c.33T>A;refseq.codonCoord_2=11;refseq.codonCoord_3=11;refseq.codonCoord_4=11;refseq.end_1=43411044;refseq.end_2=43411044;refseq.end_3=43411044;refseq.end_4=43411044;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=176;refseq.mrnaCoord_2=176;refseq.mrnaCoord_3=111;refseq.mrnaCoord_4=179;refseq.name2_1=WDR65;refseq.name2_2=WDR65;refseq.name2_3=WDR65;refseq.name2_4=WDR65;refseq.name_1=NR_030778;refseq.name_2=NM_001167965;refseq.name_3=NM_001167966;refseq.name_4=NM_152498;refseq.numMatchingRecords=4;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.V11V;refseq.proteinCoordStr_3=p.V11V;refseq.proteinCoordStr_4=p.V11V;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceAA_4=Val;refseq.referenceCodon_2=GTT;refseq.referenceCodon_3=GTT;refseq.referenceCodon_4=GTT;refseq.spliceDist_1=52;refseq.spliceDist_2=52;refseq.spliceDist_3=52;refseq.spliceDist_4=55;refseq.start_1=43411044;refseq.start_2=43411044;refseq.start_3=43411044;refseq.start_4=43411044;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantCodon_2=GTA;refseq.variantCodon_3=GTA;refseq.variantCodon_4=GTA;set=Intersection GT 1/0
|
|
chr1 43420046 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.412T>G;refseq.codingCoordStr_3=c.412T>G;refseq.codingCoordStr_4=c.412T>G;refseq.codonCoord_2=138;refseq.codonCoord_3=138;refseq.codonCoord_4=138;refseq.end_1=43420046;refseq.end_2=43420046;refseq.end_3=43420046;refseq.end_4=43420046;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=646;refseq.mrnaCoord_2=555;refseq.mrnaCoord_3=490;refseq.mrnaCoord_4=558;refseq.name2_1=WDR65;refseq.name2_2=WDR65;refseq.name2_3=WDR65;refseq.name2_4=WDR65;refseq.name_1=NR_030778;refseq.name_2=NM_001167965;refseq.name_3=NM_001167966;refseq.name_4=NM_152498;refseq.numMatchingRecords=4;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.W138G;refseq.proteinCoordStr_3=p.W138G;refseq.proteinCoordStr_4=p.W138G;refseq.referenceAA_2=Trp;refseq.referenceAA_3=Trp;refseq.referenceAA_4=Trp;refseq.referenceCodon_2=TGG;refseq.referenceCodon_3=TGG;refseq.referenceCodon_4=TGG;refseq.spliceDist_1=-63;refseq.spliceDist_2=-63;refseq.spliceDist_3=-63;refseq.spliceDist_4=-63;refseq.start_1=43420046;refseq.start_2=43420046;refseq.start_3=43420046;refseq.start_4=43420046;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;set=FilteredInAll GT 1/0
|
|
chr1 43420050 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=3;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.416A>G;refseq.codingCoordStr_3=c.416A>G;refseq.codingCoordStr_4=c.416A>G;refseq.codonCoord_2=139;refseq.codonCoord_3=139;refseq.codonCoord_4=139;refseq.end_1=43420050;refseq.end_2=43420050;refseq.end_3=43420050;refseq.end_4=43420050;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=650;refseq.mrnaCoord_2=559;refseq.mrnaCoord_3=494;refseq.mrnaCoord_4=562;refseq.name2_1=WDR65;refseq.name2_2=WDR65;refseq.name2_3=WDR65;refseq.name2_4=WDR65;refseq.name_1=NR_030778;refseq.name_2=NM_001167965;refseq.name_3=NM_001167966;refseq.name_4=NM_152498;refseq.numMatchingRecords=4;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.E139G;refseq.proteinCoordStr_3=p.E139G;refseq.proteinCoordStr_4=p.E139G;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceAA_4=Glu;refseq.referenceCodon_2=GAA;refseq.referenceCodon_3=GAA;refseq.referenceCodon_4=GAA;refseq.spliceDist_1=-59;refseq.spliceDist_2=-59;refseq.spliceDist_3=-59;refseq.spliceDist_4=-59;refseq.start_1=43420050;refseq.start_2=43420050;refseq.start_3=43420050;refseq.start_4=43420050;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_2=GGA;refseq.variantCodon_3=GGA;refseq.variantCodon_4=GGA;set=FilteredInAll GT 0/1
|
|
chr1 43422095 . A G 281.03 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=3.30;MQ=98.80;MQ0=0;OQ=2092.49;QD=19.37;RankSumP=0.227890;SB=-726.63;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.721A>G;refseq.codingCoordStr_3=c.721A>G;refseq.codingCoordStr_4=c.721A>G;refseq.codonCoord_2=241;refseq.codonCoord_3=241;refseq.codonCoord_4=241;refseq.end_1=43422095;refseq.end_2=43422095;refseq.end_3=43422095;refseq.end_4=43422095;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=955;refseq.mrnaCoord_2=864;refseq.mrnaCoord_3=799;refseq.mrnaCoord_4=867;refseq.name2_1=WDR65;refseq.name2_2=WDR65;refseq.name2_3=WDR65;refseq.name2_4=WDR65;refseq.name_1=NR_030778;refseq.name_2=NM_001167965;refseq.name_3=NM_001167966;refseq.name_4=NM_152498;refseq.numMatchingRecords=4;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.N241D;refseq.proteinCoordStr_3=p.N241D;refseq.proteinCoordStr_4=p.N241D;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceAA_4=Asn;refseq.referenceCodon_2=AAT;refseq.referenceCodon_3=AAT;refseq.referenceCodon_4=AAT;refseq.spliceDist_1=-41;refseq.spliceDist_2=-41;refseq.spliceDist_3=-41;refseq.spliceDist_4=-41;refseq.start_1=43422095;refseq.start_2=43422095;refseq.start_3=43422095;refseq.start_4=43422095;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantAA_4=Asp;refseq.variantCodon_2=GAT;refseq.variantCodon_3=GAT;refseq.variantCodon_4=GAT;set=Intersection GT 0/1
|
|
chr1 43436805 . C T 113.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=314;Dels=0.00;HRun=2;HaplotypeScore=4.32;MQ=98.42;MQ0=0;OQ=6111.63;QD=19.46;RankSumP=0.345126;SB=-2575.27;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.1329C>T;refseq.codingCoordStr_3=c.1329C>T;refseq.codingCoordStr_4=c.1329C>T;refseq.codonCoord_2=443;refseq.codonCoord_3=443;refseq.codonCoord_4=443;refseq.end_1=43436805;refseq.end_2=43436805;refseq.end_3=43436805;refseq.end_4=43436805;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1563;refseq.mrnaCoord_2=1472;refseq.mrnaCoord_3=1407;refseq.mrnaCoord_4=1475;refseq.name2_1=WDR65;refseq.name2_2=WDR65;refseq.name2_3=WDR65;refseq.name2_4=WDR65;refseq.name_1=NR_030778;refseq.name_2=NM_001167965;refseq.name_3=NM_001167966;refseq.name_4=NM_152498;refseq.numMatchingRecords=4;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.H443H;refseq.proteinCoordStr_3=p.H443H;refseq.proteinCoordStr_4=p.H443H;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceAA_4=His;refseq.referenceCodon_2=CAC;refseq.referenceCodon_3=CAC;refseq.referenceCodon_4=CAC;refseq.spliceDist_1=67;refseq.spliceDist_2=67;refseq.spliceDist_3=67;refseq.spliceDist_4=67;refseq.start_1=43436805;refseq.start_2=43436805;refseq.start_3=43436805;refseq.start_4=43436805;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantAA_4=His;refseq.variantCodon_2=CAT;refseq.variantCodon_3=CAT;refseq.variantCodon_4=CAT;set=Intersection GT 0/1
|
|
chr1 43448054 . G A 303.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=357;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=98.56;MQ0=0;OQ=14875.15;QD=41.67;RankSumP=1.00000;SB=-5126.80;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.1809G>A;refseq.codingCoordStr_3=c.1809G>A;refseq.codingCoordStr_4=c.1809G>A;refseq.codonCoord_2=603;refseq.codonCoord_3=603;refseq.codonCoord_4=603;refseq.end_1=43448054;refseq.end_2=43448054;refseq.end_3=43448054;refseq.end_4=43448054;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=2043;refseq.mrnaCoord_2=1952;refseq.mrnaCoord_3=1887;refseq.mrnaCoord_4=1955;refseq.name2_1=WDR65;refseq.name2_2=WDR65;refseq.name2_3=WDR65;refseq.name2_4=WDR65;refseq.name_1=NR_030778;refseq.name_2=NM_001167965;refseq.name_3=NM_001167966;refseq.name_4=NM_152498;refseq.numMatchingRecords=4;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.S603S;refseq.proteinCoordStr_3=p.S603S;refseq.proteinCoordStr_4=p.S603S;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_2=TCG;refseq.referenceCodon_3=TCG;refseq.referenceCodon_4=TCG;refseq.spliceDist_1=54;refseq.spliceDist_2=54;refseq.spliceDist_3=54;refseq.spliceDist_4=54;refseq.start_1=43448054;refseq.start_2=43448054;refseq.start_3=43448054;refseq.start_4=43448054;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_2=TCA;refseq.variantCodon_3=TCA;refseq.variantCodon_4=TCA;set=Intersection GT 1/1
|
|
chr1 43552151 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=7.28;MQ=97.93;MQ0=0;OQ=817.95;QD=9.74;RankSumP=0.0860249;SB=-206.53;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2334T>C;refseq.codonCoord=778;refseq.end=43552151;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2413;refseq.name=NM_005424;refseq.name2=TIE1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A778A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-76;refseq.start=43552151;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/0
|
|
chr1 43557543 . A G 212.52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=197;Dels=0.00;HRun=1;HaplotypeScore=5.95;MQ=98.35;MQ0=0;OQ=2881.86;QD=14.63;RankSumP=0.00202129;SB=-1402.65;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2973A>G;refseq.codonCoord=991;refseq.end=43557543;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3052;refseq.name=NM_005424;refseq.name2=TIE1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L991L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=51;refseq.start=43557543;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=filterInsoap-gatk GT 0/1
|
|
chr1 43598231 . T C 225.45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=131;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=97.00;MQ0=0;OQ=2356.83;QD=17.99;RankSumP=0.404938;SB=-1018.39;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.432T>C;refseq.codonCoord=144;refseq.end=43598231;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=533;refseq.name=NM_001255;refseq.name2=CDC20;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y144Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=5;refseq.spliceInfo=splice-acceptor_5;refseq.start=43598231;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/0
|
|
chr1 43598289 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.490A>C;refseq.codonCoord=164;refseq.end=43598289;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=591;refseq.name=NM_001255;refseq.name2=CDC20;refseq.positionType=CDS;refseq.proteinCoordStr=p.T164P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=63;refseq.start=43598289;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 43679483 . A G 289.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=104;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=98.63;MQ0=0;OQ=1839.24;QD=17.69;RankSumP=0.444385;SB=-895.63;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4659A>G;refseq.codonCoord=1553;refseq.end=43679483;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5121;refseq.name=NM_015284;refseq.name2=KIAA0467;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1553E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=12;refseq.start=43679483;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 0/1
|
|
chr1 43690224 . G A 360.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=224;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=98.85;MQ0=0;OQ=4236.87;QD=18.91;RankSumP=0.0213665;SB=-1612.48;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.474C>T;refseq.codingCoordStr_2=c.*1486G>A;refseq.codingCoordStr_3=c.474C>T;refseq.codonCoord_1=158;refseq.codonCoord_3=158;refseq.end_1=43690224;refseq.end_2=43690224;refseq.end_3=43690224;refseq.frame_1=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=670;refseq.mrnaCoord_2=9550;refseq.mrnaCoord_3=670;refseq.name2_1=HYI;refseq.name2_2=KIAA0467;refseq.name2_3=HYI;refseq.name_1=NM_001174052;refseq.name_2=NM_015284;refseq.name_3=NM_031207;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=utr3;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.D158D;refseq.proteinCoordStr_3=p.D158D;refseq.referenceAA_1=Asp;refseq.referenceAA_3=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_3=GAC;refseq.spliceDist_1=-32;refseq.spliceDist_2=-668;refseq.spliceDist_3=-32;refseq.start_1=43690224;refseq.start_2=43690224;refseq.start_3=43690224;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=-;refseq.variantAA_1=Asp;refseq.variantAA_3=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_3=GAT;set=Intersection GT 1/0
|
|
chr1 43843808 . G A 391.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=202;Dels=0.00;HRun=0;HaplotypeScore=4.20;MQ=98.93;MQ0=0;OQ=7826.60;QD=38.75;RankSumP=1.00000;SB=-2130.33;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3411G>A;refseq.codingCoordStr_2=c.3384G>A;refseq.codonCoord_1=1137;refseq.codonCoord_2=1128;refseq.end_1=43843808;refseq.end_2=43843808;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3751;refseq.mrnaCoord_2=3724;refseq.name2_1=PTPRF;refseq.name2_2=PTPRF;refseq.name_1=NM_002840;refseq.name_2=NM_130440;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V1137V;refseq.proteinCoordStr_2=p.V1128V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.start_1=43843808;refseq.start_2=43843808;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=Intersection GT 1/1
|
|
chr1 43856094 . T C 135.30 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=97.53;MQ0=0;OQ=1184.13;QD=31.16;RankSumP=1.00000;SB=-243.10;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4296T>C;refseq.codingCoordStr_2=c.4269T>C;refseq.codonCoord_1=1432;refseq.codonCoord_2=1423;refseq.end_1=43856094;refseq.end_2=43856094;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4636;refseq.mrnaCoord_2=4609;refseq.name2_1=PTPRF;refseq.name2_2=PTPRF;refseq.name_1=NM_002840;refseq.name_2=NM_130440;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G1432G;refseq.proteinCoordStr_2=p.G1423G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=-76;refseq.spliceDist_2=-76;refseq.start_1=43856094;refseq.start_2=43856094;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=Intersection GT 1/1
|
|
chr1 43856106 . G A 94.90 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.27;MQ=97.80;MQ0=0;OQ=1191.70;QD=35.05;RankSumP=1.00000;SB=-179.68;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4308G>A;refseq.codingCoordStr_2=c.4281G>A;refseq.codonCoord_1=1436;refseq.codonCoord_2=1427;refseq.end_1=43856106;refseq.end_2=43856106;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4648;refseq.mrnaCoord_2=4621;refseq.name2_1=PTPRF;refseq.name2_2=PTPRF;refseq.name_1=NM_002840;refseq.name_2=NM_130440;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R1436R;refseq.proteinCoordStr_2=p.R1427R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=AGG;refseq.referenceCodon_2=AGG;refseq.spliceDist_1=-64;refseq.spliceDist_2=-64;refseq.start_1=43856106;refseq.start_2=43856106;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGA;refseq.variantCodon_2=AGA;set=Intersection GT 1/1
|
|
chr1 43857326 . C T 44 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=335;Dels=0.00;HRun=0;HaplotypeScore=31.28;MQ=97.21;MQ0=0;OQ=10581.17;QD=31.59;RankSumP=1.00000;SB=-3302.48;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4512C>T;refseq.codingCoordStr_2=c.4485C>T;refseq.codonCoord_1=1504;refseq.codonCoord_2=1495;refseq.end_1=43857326;refseq.end_2=43857326;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4852;refseq.mrnaCoord_2=4825;refseq.name2_1=PTPRF;refseq.name2_2=PTPRF;refseq.name_1=NM_002840;refseq.name_2=NM_130440;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R1504R;refseq.proteinCoordStr_2=p.R1495R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.spliceDist_1=21;refseq.spliceDist_2=21;refseq.start_1=43857326;refseq.start_2=43857326;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=Intersection GT 1/1
|
|
chr1 43858017 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5012T>G;refseq.codingCoordStr_2=c.4985T>G;refseq.codonCoord_1=1671;refseq.codonCoord_2=1662;refseq.end_1=43858017;refseq.end_2=43858017;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=5352;refseq.mrnaCoord_2=5325;refseq.name2_1=PTPRF;refseq.name2_2=PTPRF;refseq.name_1=NM_002840;refseq.name_2=NM_130440;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V1671G;refseq.proteinCoordStr_2=p.V1662G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=80;refseq.spliceDist_2=80;refseq.start_1=43858017;refseq.start_2=43858017;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 43859418 . C T 448.89 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=154;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=98.55;MQ0=0;OQ=6127.85;QD=39.79;RankSumP=1.00000;SB=-2926.82;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5583C>T;refseq.codingCoordStr_2=c.5556C>T;refseq.codonCoord_1=1861;refseq.codonCoord_2=1852;refseq.end_1=43859418;refseq.end_2=43859418;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=5923;refseq.mrnaCoord_2=5896;refseq.name2_1=PTPRF;refseq.name2_2=PTPRF;refseq.name_1=NM_002840;refseq.name_2=NM_130440;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y1861Y;refseq.proteinCoordStr_2=p.Y1852Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=64;refseq.spliceDist_2=64;refseq.start_1=43859418;refseq.start_2=43859418;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;set=Intersection GT 1/1
|
|
chr1 43909844 . C A 261.44 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=245;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=98.98;MQ0=0;OQ=9476.28;QD=38.68;RankSumP=1.00000;SB=-4326.65;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1445C>A;refseq.codonCoord=482;refseq.end=43909844;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1611;refseq.name=NM_014663;refseq.name2=KDM4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.A482E;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=82;refseq.start=43909844;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 44063117 . A G 149.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=111.84;QD=18.64;RankSumP=0.666667;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA_10=true;refseq.changesAA_8=true;refseq.changesAA_9=true;refseq.chr_1=chr1;refseq.chr_10=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.chr_8=chr1;refseq.chr_9=chr1;refseq.codingCoordStr_10=c.289A>G;refseq.codingCoordStr_8=c.382A>G;refseq.codingCoordStr_9=c.337A>G;refseq.codonCoord_10=97;refseq.codonCoord_8=128;refseq.codonCoord_9=113;refseq.end_1=44076467;refseq.end_10=44063117;refseq.end_2=44076467;refseq.end_3=44076467;refseq.end_4=44076467;refseq.end_5=44076467;refseq.end_6=44076467;refseq.end_7=44076467;refseq.end_8=44063117;refseq.end_9=44063117;refseq.frame_10=0;refseq.frame_8=0;refseq.frame_9=0;refseq.functionalClass_10=missense;refseq.functionalClass_8=missense;refseq.functionalClass_9=missense;refseq.haplotypeAlternate_10=G;refseq.haplotypeAlternate_8=G;refseq.haplotypeAlternate_9=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_10=A;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=*;refseq.haplotypeReference_6=*;refseq.haplotypeReference_7=*;refseq.haplotypeReference_8=A;refseq.haplotypeReference_9=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_10=true;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=true;refseq.inCodingRegion_9=true;refseq.mrnaCoord_10=466;refseq.mrnaCoord_8=559;refseq.mrnaCoord_9=514;refseq.name2_1=ST3GAL3;refseq.name2_10=ST3GAL3;refseq.name2_2=ST3GAL3;refseq.name2_3=ST3GAL3;refseq.name2_4=ST3GAL3;refseq.name2_5=ST3GAL3;refseq.name2_6=ST3GAL3;refseq.name2_7=ST3GAL3;refseq.name2_8=ST3GAL3;refseq.name2_9=ST3GAL3;refseq.name_1=NM_006279;refseq.name_10=NM_174971;refseq.name_2=NM_174964;refseq.name_3=NM_174965;refseq.name_4=NM_174966;refseq.name_5=NM_174967;refseq.name_6=NM_174969;refseq.name_7=NM_174970;refseq.name_8=NM_174963;refseq.name_9=NM_174968;refseq.numMatchingRecords=10;refseq.positionType_1=intron;refseq.positionType_10=CDS;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.positionType_4=intron;refseq.positionType_5=intron;refseq.positionType_6=intron;refseq.positionType_7=intron;refseq.positionType_8=CDS;refseq.positionType_9=CDS;refseq.proteinCoordStr_10=p.T97A;refseq.proteinCoordStr_8=p.T128A;refseq.proteinCoordStr_9=p.T113A;refseq.referenceAA_10=Thr;refseq.referenceAA_8=Thr;refseq.referenceAA_9=Thr;refseq.referenceCodon_10=ACA;refseq.referenceCodon_8=ACA;refseq.referenceCodon_9=ACA;refseq.spliceDist_10=-35;refseq.spliceDist_8=-35;refseq.spliceDist_9=-35;refseq.start_1=44053203;refseq.start_10=44063117;refseq.start_2=44053203;refseq.start_3=44053203;refseq.start_4=44053203;refseq.start_5=44053203;refseq.start_6=44053203;refseq.start_7=44053203;refseq.start_8=44063117;refseq.start_9=44063117;refseq.transcriptStrand_1=+;refseq.transcriptStrand_10=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.transcriptStrand_9=+;refseq.variantAA_10=Ala;refseq.variantAA_8=Ala;refseq.variantAA_9=Ala;refseq.variantCodon_10=GCA;refseq.variantCodon_8=GCA;refseq.variantCodon_9=GCA;set=Intersection GT 0/1
|
|
chr1 44173971 . A G 188.81 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=106;Dels=0.00;HRun=1;HaplotypeScore=7.72;MQ=98.89;MQ0=0;OQ=4072.12;QD=38.42;RankSumP=1.00000;SB=-1130.77;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.56A>G;refseq.codingCoordStr_2=c.56A>G;refseq.codingCoordStr_3=c.56A>G;refseq.codingCoordStr_4=c.56A>G;refseq.codonCoord_1=19;refseq.codonCoord_2=19;refseq.codonCoord_3=19;refseq.codonCoord_4=19;refseq.end_1=44173971;refseq.end_2=44173971;refseq.end_3=44173971;refseq.end_4=44173971;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=689;refseq.mrnaCoord_2=354;refseq.mrnaCoord_3=838;refseq.mrnaCoord_4=838;refseq.name2_1=ARTN;refseq.name2_2=ARTN;refseq.name2_3=ARTN;refseq.name2_4=ARTN;refseq.name_1=NM_001136215;refseq.name_2=NM_003976;refseq.name_3=NM_057090;refseq.name_4=NM_057091;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.Q19R;refseq.proteinCoordStr_2=p.Q19R;refseq.proteinCoordStr_3=p.Q19R;refseq.proteinCoordStr_4=p.Q19R;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceAA_4=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.referenceCodon_3=CAG;refseq.referenceCodon_4=CAG;refseq.spliceDist_1=-5;refseq.spliceDist_2=-5;refseq.spliceDist_3=-5;refseq.spliceDist_4=-5;refseq.spliceInfo_1=splice-donor_-5;refseq.spliceInfo_2=splice-donor_-5;refseq.spliceInfo_3=splice-donor_-5;refseq.spliceInfo_4=splice-donor_-5;refseq.start_1=44173971;refseq.start_2=44173971;refseq.start_3=44173971;refseq.start_4=44173971;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;refseq.variantCodon_4=CGG;set=Intersection GT 1/1
|
|
chr1 44188002 . C T 198.31 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=204;Dels=0.00;HRun=0;HaplotypeScore=5.21;MQ=98.75;MQ0=0;OQ=8084.76;QD=39.63;RankSumP=1.00000;SB=-1497.47;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.411C>T;refseq.codonCoord=137;refseq.end=44188002;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1206;refseq.name=NM_014652;refseq.name2=IPO13;refseq.positionType=CDS;refseq.proteinCoordStr=p.D137D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=327;refseq.start=44188002;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 44208901 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=1.07982e-08;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.194T>G;refseq.codingCoordStr_2=c.194T>G;refseq.codonCoord_1=65;refseq.codonCoord_2=65;refseq.end_1=44208901;refseq.end_2=44208901;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=389;refseq.mrnaCoord_2=389;refseq.name2_1=DPH2;refseq.name2_2=DPH2;refseq.name_1=NM_001039589;refseq.name_2=NM_001384;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V65G;refseq.proteinCoordStr_2=p.V65G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=47;refseq.spliceDist_2=47;refseq.start_1=44208901;refseq.start_2=44208901;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 44210179 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.262106;SecondBestBaseQ=27;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1018G>A;refseq.codonCoord_2=340;refseq.end_1=44210406;refseq.end_2=44210179;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1213;refseq.name2_1=DPH2;refseq.name2_2=DPH2;refseq.name_1=NM_001039589;refseq.name_2=NM_001384;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A340T;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCC;refseq.spliceDist_2=-151;refseq.start_1=44209459;refseq.start_2=44210179;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Thr;refseq.variantCodon_2=ACC;set=FilteredInAll GT 1/0
|
|
chr1 44367700 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=265;Dels=0.00;HRun=1;HaplotypeScore=6.97;MQ=98.81;MQ0=0;OQ=7267.16;QD=27.42;RankSumP=0.193562;SB=-1426.69;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.170G>C;refseq.codonCoord=57;refseq.end=44367700;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=228;refseq.name=NM_173484;refseq.name2=KLF17;refseq.positionType=CDS;refseq.proteinCoordStr=p.S57T;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=89;refseq.start=44367700;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 44367997 . A G 189.18 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=121;Dels=0.00;HRun=0;HaplotypeScore=7.56;MQ=98.36;MQ0=0;OQ=1870.21;QD=15.46;RankSumP=0.413048;SB=-234.57;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.467A>G;refseq.codonCoord=156;refseq.end=44367997;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=525;refseq.name=NM_173484;refseq.name2=KLF17;refseq.positionType=CDS;refseq.proteinCoordStr=p.N156S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=386;refseq.start=44367997;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 44368013 . G A 194.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=145;Dels=0.00;HRun=0;HaplotypeScore=6.55;MQ=98.35;MQ0=0;OQ=2812.05;QD=19.39;RankSumP=0.00700147;SB=-765.33;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.483G>A;refseq.codonCoord=161;refseq.end=44368013;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=541;refseq.name=NM_173484;refseq.name2=KLF17;refseq.positionType=CDS;refseq.proteinCoordStr=p.S161S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=402;refseq.start=44368013;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=filterInsoap-gatk GT 1/0
|
|
chr1 44368976 . C T 20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.386320;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1131C>T;refseq.codonCoord=377;refseq.end=44368976;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1189;refseq.name=NM_173484;refseq.name2=KLF17;refseq.positionType=CDS;refseq.proteinCoordStr=p.N377N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-40;refseq.start=44368976;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=soap GT 0/1
|
|
chr1 44368977 . A G 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.377312;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1132A>G;refseq.codonCoord=378;refseq.end=44368977;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1190;refseq.name=NM_173484;refseq.name2=KLF17;refseq.positionType=CDS;refseq.proteinCoordStr=p.N378D;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-39;refseq.start=44368977;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 0/1
|
|
chr1 44883489 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=3;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1320T>C;refseq.codonCoord=440;refseq.end=44883489;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1680;refseq.name=NM_018150;refseq.name2=RNF220;refseq.positionType=CDS;refseq.proteinCoordStr=p.P440P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=44883489;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 44991482 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=149;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=99.00;MQ0=0;OQ=1733.58;QD=11.63;RankSumP=0.317681;SB=-406.07;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.531A>T;refseq.codonCoord=177;refseq.end=44991482;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=646;refseq.name=NM_006845;refseq.name2=KIF2C;refseq.positionType=CDS;refseq.proteinCoordStr=p.R177R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-32;refseq.start=44991482;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 0/1
|
|
chr1 44997585 . A C 370.97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=236;Dels=0.00;HRun=0;HaplotypeScore=6.40;MQ=98.79;MQ0=0;OQ=4540.01;QD=19.24;RankSumP=0.0918535;SB=-1900.29;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1345A>C;refseq.codonCoord=449;refseq.end=44997585;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1460;refseq.name=NM_006845;refseq.name2=KIF2C;refseq.positionType=CDS;refseq.proteinCoordStr=p.I449L;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-23;refseq.start=44997585;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 0/1
|
|
chr1 44998671 . G A 319.62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=136;Dels=0.00;HRun=0;HaplotypeScore=4.97;MQ=97.89;MQ0=0;OQ=2765.36;QD=20.33;RankSumP=0.443929;SB=-1148.51;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1500G>A;refseq.codonCoord=500;refseq.end=44998671;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1615;refseq.name=NM_006845;refseq.name2=KIF2C;refseq.positionType=CDS;refseq.proteinCoordStr=p.A500A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-73;refseq.start=44998671;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 45022594 . C A 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=17;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1297G>T;refseq.codonCoord=433;refseq.end=45022594;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1346;refseq.name=NM_153274;refseq.name2=BEST4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V433L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=149;refseq.start=45022594;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=FilteredInAll GT 1/1
|
|
chr1 45041920 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.17;MQ0=0;OQ=1629.41;QD=14.68;RankSumP=0.361880;SB=-293.32;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1134A>G;refseq.codonCoord=378;refseq.end=45041920;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1234;refseq.name=NM_004073;refseq.name2=PLK3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T378T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-31;refseq.start=45041920;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 0/1
|
|
chr1 45042611 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=87;Dels=0.00;HRun=3;HaplotypeScore=5.59;MQ=98.52;MQ0=0;OQ=1145.44;QD=13.17;RankSumP=0.0203857;SB=-472.27;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1356G>C;refseq.codonCoord=452;refseq.end=45042611;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1456;refseq.name=NM_004073;refseq.name2=PLK3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P452P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=14;refseq.start=45042611;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 0/1
|
|
chr1 45044415 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=245.42;QD=15.34;RankSumP=0.643151;SB=-34.67;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.513A>G;refseq.codonCoord=171;refseq.end=45044415;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1022;refseq.name=NM_001013632;refseq.name2=TCTEX1D4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V171V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-243;refseq.start=45044415;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 45065453 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.85;MQ=98.14;MQ0=0;OQ=582.37;QD=12.13;RankSumP=0.300655;SB=-152.15;SecondBestBaseQ=25;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2487C>T;refseq.codingCoordStr_2=c.2487C>T;refseq.codonCoord_1=829;refseq.codonCoord_2=829;refseq.end_1=45065453;refseq.end_2=45065453;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2499;refseq.mrnaCoord_2=2499;refseq.name2_1=PTCH2;refseq.name2_2=PTCH2;refseq.name_1=NM_001166292;refseq.name_2=NM_003738;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D829D;refseq.proteinCoordStr_2=p.D829D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.start_1=45065453;refseq.start_2=45065453;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 1/0
|
|
chr1 45066105 . A G 275.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=1.27;MQ=99.00;MQ0=0;OQ=4606.62;QD=41.13;RankSumP=1.00000;SB=-767.97;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2055T>C;refseq.codingCoordStr_2=c.2055T>C;refseq.codonCoord_1=685;refseq.codonCoord_2=685;refseq.end_1=45066105;refseq.end_2=45066105;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2067;refseq.mrnaCoord_2=2067;refseq.name2_1=PTCH2;refseq.name2_2=PTCH2;refseq.name_1=NM_001166292;refseq.name_2=NM_003738;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A685A;refseq.proteinCoordStr_2=p.A685A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-4;refseq.spliceDist_2=-4;refseq.spliceInfo_1=splice-donor_-4;refseq.spliceInfo_2=splice-donor_-4;refseq.start_1=45066105;refseq.start_2=45066105;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/1
|
|
chr1 45066130 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.0767741;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2030C>T;refseq.codingCoordStr_2=c.2030C>T;refseq.codonCoord_1=677;refseq.codonCoord_2=677;refseq.end_1=45066130;refseq.end_2=45066130;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2042;refseq.mrnaCoord_2=2042;refseq.name2_1=PTCH2;refseq.name2_2=PTCH2;refseq.name_1=NM_001166292;refseq.name_2=NM_003738;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A677V;refseq.proteinCoordStr_2=p.A677V;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=-29;refseq.spliceDist_2=-29;refseq.start_1=45066130;refseq.start_2=45066130;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=FilteredInAll GT 1/0
|
|
chr1 45066339 . T C 144.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=131;Dels=0.00;HRun=1;HaplotypeScore=2.06;MQ=98.50;MQ0=0;OQ=1833.73;QD=14.00;RankSumP=0.0568304;SB=-795.67;SecondBestBaseQ=25;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1821A>G;refseq.codingCoordStr_2=c.1821A>G;refseq.codonCoord_1=607;refseq.codonCoord_2=607;refseq.end_1=45066339;refseq.end_2=45066339;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1833;refseq.mrnaCoord_2=1833;refseq.name2_1=PTCH2;refseq.name2_2=PTCH2;refseq.name_1=NM_001166292;refseq.name_2=NM_003738;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E607E;refseq.proteinCoordStr_2=p.E607E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=112;refseq.spliceDist_2=112;refseq.start_1=45066339;refseq.start_2=45066339;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 1/0
|
|
chr1 45216625 . G A 296.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=185;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=98.84;MQ0=0;OQ=3961.09;QD=21.41;RankSumP=0.268002;SB=-1604.26;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.243C>T;refseq.codingCoordStr_2=c.243C>T;refseq.codonCoord_1=81;refseq.codonCoord_2=81;refseq.end_1=45216625;refseq.end_2=45216625;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=449;refseq.mrnaCoord_2=449;refseq.name2_1=EIF2B3;refseq.name2_2=EIF2B3;refseq.name_1=NM_001166588;refseq.name_2=NM_020365;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D81D;refseq.proteinCoordStr_2=p.D81D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-52;refseq.spliceDist_2=-52;refseq.start_1=45216625;refseq.start_2=45216625;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 1/0
|
|
chr1 45241763 . A T 217.32 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=353;Dels=0.00;HRun=0;HaplotypeScore=14.28;MQ=98.44;MQ0=0;OQ=6626.63;QD=18.77;RankSumP=0.000140198;SB=-2064.08;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2574T>A;refseq.codonCoord=858;refseq.end=45241763;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2672;refseq.name=NM_024602;refseq.name2=HECTD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P858P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=73;refseq.start=45241763;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=filterInsoap-gatk GT 0/1
|
|
chr1 45242173 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DB;DP=65;Dels=0.00;HRun=3;HaplotypeScore=5.00;MQ=97.67;MQ0=0;OQ=813.25;QD=12.51;RankSumP=0.271960;SB=-410.16;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2370C>T;refseq.codonCoord=790;refseq.end=45242173;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2468;refseq.name=NM_024602;refseq.name2=HECTD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R790R;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=23;refseq.start=45242173;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/0
|
|
chr1 45249250 . G A 76 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.34;MQ=98.21;MQ0=0;OQ=218.94;QD=18.25;RankSumP=0.681818;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.267C>T;refseq.codonCoord=89;refseq.end=45249250;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=365;refseq.name=NM_024602;refseq.name2=HECTD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L89L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-103;refseq.start=45249250;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/0
|
|
chr1 45252296 . A G 281.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=397;Dels=0.00;HRun=0;HaplotypeScore=10.79;MQ=98.40;MQ0=0;OQ=6325.57;QD=15.93;RankSumP=0.178665;SB=-2485.94;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.603A>G;refseq.codonCoord=201;refseq.end=45252296;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=711;refseq.name=NM_000374;refseq.name2=UROD;refseq.positionType=CDS;refseq.proteinCoordStr=p.P201P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-34;refseq.start=45252296;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 0/1
|
|
chr1 45252323 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.630T>G;refseq.codonCoord=210;refseq.end=45252323;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=738;refseq.name=NM_000374;refseq.name2=UROD;refseq.positionType=CDS;refseq.proteinCoordStr=p.G210G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=45252323;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 45257164 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3107A>C;refseq.codonCoord=1036;refseq.end=45257164;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3335;refseq.name=NM_020883;refseq.name2=ZSWIM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1036P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=412;refseq.start=45257164;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 45257495 . T G 24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.500000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2776A>C;refseq.codonCoord=926;refseq.end=45257495;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3004;refseq.name=NM_020883;refseq.name2=ZSWIM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.T926P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=81;refseq.start=45257495;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=soap GT 1/0
|
|
chr1 45444553 . A G 112.51 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=98.03;MQ0=0;OQ=605.99;QD=35.65;RankSumP=1.00000;SB=-299.73;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.57T>C;refseq.codonCoord=19;refseq.end=45444553;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=285;refseq.name=NM_020883;refseq.name2=ZSWIM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.A19A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=285;refseq.start=45444553;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 45570092 . C G 129.67 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.59;MQ0=0;OQ=318.53;QD=15.17;RankSumP=0.669608;SB=-128.70;SecondBestBaseQ=28;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.972G>C;refseq.codingCoordStr_2=c.933G>C;refseq.codingCoordStr_3=c.930G>C;refseq.codingCoordStr_4=c.930G>C;refseq.codingCoordStr_5=c.1014G>C;refseq.codingCoordStr_6=c.1005G>C;refseq.codonCoord_1=324;refseq.codonCoord_2=311;refseq.codonCoord_3=310;refseq.codonCoord_4=310;refseq.codonCoord_5=338;refseq.codonCoord_6=335;refseq.end_1=45570092;refseq.end_2=45570092;refseq.end_3=45570092;refseq.end_4=45570092;refseq.end_5=45570092;refseq.end_6=45570092;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1188;refseq.mrnaCoord_2=1079;refseq.mrnaCoord_3=1076;refseq.mrnaCoord_4=995;refseq.mrnaCoord_5=1230;refseq.mrnaCoord_6=1221;refseq.name2_1=MUTYH;refseq.name2_2=MUTYH;refseq.name2_3=MUTYH;refseq.name2_4=MUTYH;refseq.name2_5=MUTYH;refseq.name2_6=MUTYH;refseq.name_1=NM_001048171;refseq.name_2=NM_001048172;refseq.name_3=NM_001048173;refseq.name_4=NM_001048174;refseq.name_5=NM_001128425;refseq.name_6=NM_012222;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.Q324H;refseq.proteinCoordStr_2=p.Q311H;refseq.proteinCoordStr_3=p.Q310H;refseq.proteinCoordStr_4=p.Q310H;refseq.proteinCoordStr_5=p.Q338H;refseq.proteinCoordStr_6=p.Q335H;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceAA_4=Gln;refseq.referenceAA_5=Gln;refseq.referenceAA_6=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.referenceCodon_3=CAG;refseq.referenceCodon_4=CAG;refseq.referenceCodon_5=CAG;refseq.referenceCodon_6=CAG;refseq.spliceDist_1=17;refseq.spliceDist_2=17;refseq.spliceDist_3=17;refseq.spliceDist_4=17;refseq.spliceDist_5=17;refseq.spliceDist_6=17;refseq.start_1=45570092;refseq.start_2=45570092;refseq.start_3=45570092;refseq.start_4=45570092;refseq.start_5=45570092;refseq.start_6=45570092;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantAA_4=His;refseq.variantAA_5=His;refseq.variantAA_6=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;refseq.variantCodon_4=CAC;refseq.variantCodon_5=CAC;refseq.variantCodon_6=CAC;set=Intersection GT 1/0
|
|
chr1 45581353 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.925T>G;refseq.codonCoord=309;refseq.end=45581353;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1508;refseq.name=NM_025077;refseq.name2=TOE1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C309G;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=13;refseq.start=45581353;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 45845665 . G C 30 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.447801;SecondBestBaseQ=34;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.495G>C;refseq.codingCoordStr_3=c.501G>C;refseq.codonCoord_2=165;refseq.codonCoord_3=167;refseq.end_1=45851417;refseq.end_2=45845665;refseq.end_3=45845665;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=597;refseq.mrnaCoord_3=670;refseq.name2_1=NASP;refseq.name2_2=NASP;refseq.name2_3=NASP;refseq.name_1=NM_152298;refseq.name_2=NM_002482;refseq.name_3=NM_172164;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.L165F;refseq.proteinCoordStr_3=p.L167F;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceCodon_2=TTG;refseq.referenceCodon_3=TTG;refseq.spliceDist_2=86;refseq.spliceDist_3=86;refseq.start_1=45844861;refseq.start_2=45845665;refseq.start_3=45845665;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantCodon_2=TTC;refseq.variantCodon_3=TTC;set=soap GT 0/1
|
|
chr1 45845696 . A T 55 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.223751;SecondBestBaseQ=34;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.526A>T;refseq.codingCoordStr_3=c.532A>T;refseq.codonCoord_2=176;refseq.codonCoord_3=178;refseq.end_1=45851417;refseq.end_2=45845696;refseq.end_3=45845696;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=628;refseq.mrnaCoord_3=701;refseq.name2_1=NASP;refseq.name2_2=NASP;refseq.name2_3=NASP;refseq.name_1=NM_152298;refseq.name_2=NM_002482;refseq.name_3=NM_172164;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.S176C;refseq.proteinCoordStr_3=p.S178C;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_2=AGT;refseq.referenceCodon_3=AGT;refseq.spliceDist_2=117;refseq.spliceDist_3=117;refseq.start_1=45844861;refseq.start_2=45845696;refseq.start_3=45845696;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Cys;refseq.variantAA_3=Cys;refseq.variantCodon_2=TGT;refseq.variantCodon_3=TGT;set=soap GT 0/1
|
|
chr1 45845738 . A G 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.394788;SecondBestBaseQ=34;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.568A>G;refseq.codingCoordStr_3=c.574A>G;refseq.codonCoord_2=190;refseq.codonCoord_3=192;refseq.end_1=45851417;refseq.end_2=45845738;refseq.end_3=45845738;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=670;refseq.mrnaCoord_3=743;refseq.name2_1=NASP;refseq.name2_2=NASP;refseq.name2_3=NASP;refseq.name_1=NM_152298;refseq.name_2=NM_002482;refseq.name_3=NM_172164;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.K190E;refseq.proteinCoordStr_3=p.K192E;refseq.referenceAA_2=Lys;refseq.referenceAA_3=Lys;refseq.referenceCodon_2=AAA;refseq.referenceCodon_3=AAA;refseq.spliceDist_2=159;refseq.spliceDist_3=159;refseq.start_1=45844861;refseq.start_2=45845738;refseq.start_3=45845738;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantCodon_2=GAA;refseq.variantCodon_3=GAA;set=FilteredInAll GT 0/1
|
|
chr1 45845886 . C T 20.76 ESPStandard;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=80.26;MQ0=0;QD=0.90;SB=-30.94;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.716C>T;refseq.codingCoordStr_3=c.722C>T;refseq.codonCoord_2=239;refseq.codonCoord_3=241;refseq.end_1=45851417;refseq.end_2=45845886;refseq.end_3=45845886;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=818;refseq.mrnaCoord_3=891;refseq.name2_1=NASP;refseq.name2_2=NASP;refseq.name2_3=NASP;refseq.name_1=NM_152298;refseq.name_2=NM_002482;refseq.name_3=NM_172164;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.A239V;refseq.proteinCoordStr_3=p.A241V;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_2=GCT;refseq.referenceCodon_3=GCT;refseq.spliceDist_2=307;refseq.spliceDist_3=307;refseq.start_1=45844861;refseq.start_2=45845886;refseq.start_3=45845886;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_2=GTT;refseq.variantCodon_3=GTT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:19,4:22:-11.98,-6.62,-75.28:53.56
|
|
chr1 45846284 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=0;HaplotypeScore=5.49;MQ=82.56;MQ0=1;OQ=115.02;QD=1.01;SB=25.82;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.1114C>A;refseq.codingCoordStr_3=c.1120C>A;refseq.codonCoord_2=372;refseq.codonCoord_3=374;refseq.end_1=45851417;refseq.end_2=45846284;refseq.end_3=45846284;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=1216;refseq.mrnaCoord_3=1289;refseq.name2_1=NASP;refseq.name2_2=NASP;refseq.name2_3=NASP;refseq.name_1=NM_152298;refseq.name_2=NM_002482;refseq.name_3=NM_172164;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.P372T;refseq.proteinCoordStr_3=p.P374T;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_2=CCA;refseq.referenceCodon_3=CCA;refseq.spliceDist_2=-313;refseq.spliceDist_3=-313;refseq.start_1=45844861;refseq.start_2=45846284;refseq.start_3=45846284;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_2=ACA;refseq.variantCodon_3=ACA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:99,15:99:-44.60,-29.81,-349.29:99
|
|
chr1 45846415 . G A 68 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.185094;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.1245G>A;refseq.codingCoordStr_3=c.1251G>A;refseq.codonCoord_2=415;refseq.codonCoord_3=417;refseq.end_1=45851417;refseq.end_2=45846415;refseq.end_3=45846415;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=1347;refseq.mrnaCoord_3=1420;refseq.name2_1=NASP;refseq.name2_2=NASP;refseq.name2_3=NASP;refseq.name_1=NM_152298;refseq.name_2=NM_002482;refseq.name_3=NM_172164;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.R415R;refseq.proteinCoordStr_3=p.R417R;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_2=AGG;refseq.referenceCodon_3=AGG;refseq.spliceDist_2=-182;refseq.spliceDist_3=-182;refseq.start_1=45844861;refseq.start_2=45846415;refseq.start_3=45846415;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_2=AGA;refseq.variantCodon_3=AGA;set=soap GT 1/0
|
|
chr1 45866614 . A G 99.31 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=372;Dels=0.00;HRun=1;HaplotypeScore=10.26;MQ=98.76;MQ0=0;OQ=12904.39;QD=34.69;RankSumP=1.00000;SB=-4745.67;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1326T>C;refseq.codonCoord=442;refseq.end=45866614;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2687;refseq.name=NM_021639;refseq.name2=GPBP1L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S442S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=54;refseq.start=45866614;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 45867859 . T C 130.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=502;Dels=0.00;HRun=1;HaplotypeScore=7.63;MQ=98.73;MQ0=0;OQ=20751.54;QD=41.34;RankSumP=1.00000;SB=-7192.66;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1248A>G;refseq.codonCoord=416;refseq.end=45867859;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2609;refseq.name=NM_021639;refseq.name2=GPBP1L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.K416K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-25;refseq.start=45867859;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 45967962 . T C 231.43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=98.78;MQ0=0;OQ=4309.69;QD=43.10;RankSumP=1.00000;SB=-852.68;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.791A>G;refseq.codingCoordStr_2=c.791A>G;refseq.codonCoord_1=264;refseq.codonCoord_2=264;refseq.end_1=45967962;refseq.end_2=45967962;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1058;refseq.mrnaCoord_2=1058;refseq.name2_1=IPP;refseq.name2_2=IPP;refseq.name_1=NM_001145349;refseq.name_2=NM_005897;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K264R;refseq.proteinCoordStr_2=p.K264R;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=67;refseq.spliceDist_2=67;refseq.start_1=45967962;refseq.start_2=45967962;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGA;refseq.variantCodon_2=AGA;set=Intersection GT 1/1
|
|
chr1 45984510 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.161T>G;refseq.codingCoordStr_2=c.161T>G;refseq.codonCoord_1=54;refseq.codonCoord_2=54;refseq.end_1=45984510;refseq.end_2=45984510;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=428;refseq.mrnaCoord_2=428;refseq.name2_1=IPP;refseq.name2_2=IPP;refseq.name_1=NM_001145349;refseq.name_2=NM_005897;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V54G;refseq.proteinCoordStr_2=p.V54G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=-132;refseq.spliceDist_2=-132;refseq.start_1=45984510;refseq.start_2=45984510;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 0/1
|
|
chr1 46249174 . T G 385.61 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=244;Dels=0.00;HRun=0;HaplotypeScore=2.27;MQ=98.65;MQ0=0;OQ=10181.23;QD=41.73;RankSumP=1.00000;SB=-3858.57;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1164T>G;refseq.codonCoord=388;refseq.end=46249174;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1447;refseq.name=NM_015112;refseq.name2=MAST2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D388E;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-25;refseq.start=46249174;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 46272387 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3730A>C;refseq.codonCoord=1244;refseq.end=46272387;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4013;refseq.name=NM_015112;refseq.name2=MAST2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1244P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=56;refseq.start=46272387;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 46273962 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5034T>G;refseq.codonCoord=1678;refseq.end=46273962;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5317;refseq.name=NM_015112;refseq.name2=MAST2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1678G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-422;refseq.start=46273962;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 46294063 . T A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=2.74649e-05;SecondBestBaseQ=20;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.932A>T;refseq.codingCoordStr_2=c.932A>T;refseq.codonCoord_1=311;refseq.codonCoord_2=311;refseq.end_1=46294063;refseq.end_2=46294063;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1189;refseq.mrnaCoord_2=1688;refseq.name2_1=PIK3R3;refseq.name2_2=PIK3R3;refseq.name_1=NM_001114172;refseq.name_2=NM_003629;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q311L;refseq.proteinCoordStr_2=p.Q311L;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAA;refseq.referenceCodon_2=CAA;refseq.spliceDist_1=-10;refseq.spliceDist_2=-10;refseq.spliceInfo_1=splice-donor_-10;refseq.spliceInfo_2=splice-donor_-10;refseq.start_1=46294063;refseq.start_2=46294063;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=FilteredInAll GT 1/0
|
|
chr1 46423324 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.544A>C;refseq.codonCoord=182;refseq.end=46423324;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1018;refseq.name=NM_005727;refseq.name2=TSPAN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T182P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-51;refseq.start=46423324;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 0/1
|
|
chr1 46427745 . T C 314.12 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.40;MQ0=0;OQ=3212.42;QD=39.66;RankSumP=1.00000;SB=-1557.59;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1867A>G;refseq.codonCoord_2=623;refseq.end_1=46427745;refseq.end_2=46427745;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2518;refseq.mrnaCoord_2=2031;refseq.name2_1=POMGNT1;refseq.name2_2=POMGNT1;refseq.name_1=NR_024332;refseq.name_2=NM_017739;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.M623V;refseq.referenceAA_2=Met;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=-3;refseq.spliceDist_2=-29;refseq.spliceInfo_1=splice-donor_-3;refseq.start_1=46427745;refseq.start_2=46427745;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Val;refseq.variantCodon_2=GTG;set=Intersection GT 1/1
|
|
chr1 46432882 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=417;Dels=0.00;HRun=0;HaplotypeScore=24.94;MQ=98.94;MQ0=0;OQ=16667.97;QD=39.97;RankSumP=1.00000;SB=-5650.31;SecondBestBaseQ=27;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.681A>G;refseq.codonCoord_2=227;refseq.end_1=46432882;refseq.end_2=46432882;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1332;refseq.mrnaCoord_2=845;refseq.name2_1=POMGNT1;refseq.name2_2=POMGNT1;refseq.name_1=NR_024332;refseq.name_2=NM_017739;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.K227K;refseq.referenceAA_2=Lys;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=29;refseq.spliceDist_2=29;refseq.start_1=46432882;refseq.start_2=46432882;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Lys;refseq.variantCodon_2=AAG;set=Intersection GT 1/1
|
|
chr1 46524165 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DP=25;Dels=0.00;HRun=2;HaplotypeScore=17.69;MQ=96.49;MQ0=0;OQ=82.03;QD=3.28;RankSumP=0.501357;SB=11.06;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.951A>C;refseq.codonCoord=317;refseq.end=46524165;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=995;refseq.name=NM_006369;refseq.name2=LRRC41;refseq.positionType=CDS;refseq.proteinCoordStr=p.A317A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-545;refseq.start=46524165;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=soap-filterIngatk GT 1/0
|
|
chr1 46524167 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=1;RankSumP=0.500138;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.949G>C;refseq.codonCoord=317;refseq.end=46524167;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=993;refseq.name=NM_006369;refseq.name2=LRRC41;refseq.positionType=CDS;refseq.proteinCoordStr=p.A317P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-547;refseq.start=46524167;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 46579093 . C G 37 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=21;HRun=1;RankSumP=0.000368367;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8C>G;refseq.codonCoord=3;refseq.end=46579093;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=117;refseq.name=NM_199044;refseq.name2=NSUN4;refseq.positionType=CDS;refseq.proteinCoordStr=p.A3G;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-86;refseq.start=46579093;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 46585330 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.588T>G;refseq.codonCoord=196;refseq.end=46585330;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=697;refseq.name=NM_199044;refseq.name2=NSUN4;refseq.positionType=CDS;refseq.proteinCoordStr=p.C196W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-5;refseq.spliceInfo=splice-donor_-5;refseq.start=46585330;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 1/0
|
|
chr1 46643348 . C A 215.09 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=380;Dels=0.00;HRun=0;HaplotypeScore=11.87;MQ=98.73;MQ0=0;OQ=14170.57;QD=37.29;RankSumP=1.00000;SB=-7035.63;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.385C>A;refseq.codonCoord=129;refseq.end=46643348;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=467;refseq.name=NM_001441;refseq.name2=FAAH;refseq.positionType=CDS;refseq.proteinCoordStr=p.P129T;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-60;refseq.start=46643348;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 46644573 . T C 322.72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=98.73;MQ0=0;OQ=3050.11;QD=33.52;RankSumP=1.00000;SB=-1131.13;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.897T>C;refseq.codonCoord=299;refseq.end=46644573;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=979;refseq.name=NM_001441;refseq.name2=FAAH;refseq.positionType=CDS;refseq.proteinCoordStr=p.C299C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-55;refseq.start=46644573;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 1/1
|
|
chr1 46749304 . C T 282.77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.88;MQ0=0;OQ=1432.57;QD=39.79;RankSumP=1.00000;SB=-741.43;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.459C>T;refseq.codingCoordStr_2=c.444C>T;refseq.codonCoord_1=153;refseq.codonCoord_2=148;refseq.end_1=46749304;refseq.end_2=46749304;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=474;refseq.mrnaCoord_2=459;refseq.name2_1=DMBX1;refseq.name2_2=DMBX1;refseq.name_1=NM_147192;refseq.name_2=NM_172225;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A153A;refseq.proteinCoordStr_2=p.A148A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=111;refseq.spliceDist_2=111;refseq.start_1=46749304;refseq.start_2=46749304;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=Intersection GT 1/1
|
|
chr1 46851224 . T C 83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=24;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.97;MQ=94.29;MQ0=0;OQ=1658.93;QD=30.72;RankSumP=1.00000;SB=-371.57;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.513A>G;refseq.codingCoordStr_2=c.357A>G;refseq.codonCoord_1=171;refseq.codonCoord_2=119;refseq.end_1=46851224;refseq.end_2=46851224;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=570;refseq.mrnaCoord_2=588;refseq.name2_1=MOBKL2C;refseq.name2_2=MOBKL2C;refseq.name_1=NM_145279;refseq.name_2=NM_201403;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A171A;refseq.proteinCoordStr_2=p.A119A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=-62;refseq.spliceDist_2=-62;refseq.start_1=46851224;refseq.start_2=46851224;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/1
|
|
chr1 46853252 . C T 437.31 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=175;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.75;MQ0=0;OQ=7296.88;QD=41.70;RankSumP=1.00000;SB=-1795.71;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.84G>A;refseq.codonCoord_2=28;refseq.end_1=46854959;refseq.end_2=46853252;refseq.frame_2=2;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=141;refseq.name2_1=MOBKL2C;refseq.name2_2=MOBKL2C;refseq.name_1=NM_201403;refseq.name_2=NM_145279;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.M28I;refseq.referenceAA_2=Met;refseq.referenceCodon_2=ATG;refseq.spliceDist_2=-23;refseq.start_1=46851641;refseq.start_2=46853252;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ile;refseq.variantCodon_2=ATA;set=Intersection GT 1/1
|
|
chr1 46853266 . G A 335.02 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=208;Dels=0.00;HRun=1;HaplotypeScore=3.31;MQ=98.79;MQ0=0;OQ=8857.37;QD=42.58;RankSumP=1.00000;SB=-3120.44;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.70C>T;refseq.codonCoord_2=24;refseq.end_1=46854959;refseq.end_2=46853266;refseq.frame_2=0;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=127;refseq.name2_1=MOBKL2C;refseq.name2_2=MOBKL2C;refseq.name_1=NM_201403;refseq.name_2=NM_145279;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.R24*;refseq.referenceAA_2=Arg;refseq.referenceCodon_2=CGA;refseq.spliceDist_2=-37;refseq.start_1=46851641;refseq.start_2=46853266;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Stop;refseq.variantCodon_2=TGA;set=Intersection GT 1/1
|
|
chr1 46853328 . C T 435.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=173;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.74;MQ0=0;OQ=7315.54;QD=42.29;RankSumP=1.00000;SB=-2211.40;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.8G>A;refseq.codonCoord_2=3;refseq.end_1=46854959;refseq.end_2=46853328;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=65;refseq.name2_1=MOBKL2C;refseq.name2_2=MOBKL2C;refseq.name_1=NM_201403;refseq.name_2=NM_145279;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.R3H;refseq.referenceAA_2=Arg;refseq.referenceCodon_2=CGC;refseq.spliceDist_2=65;refseq.start_1=46851641;refseq.start_2=46853328;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=His;refseq.variantCodon_2=CAC;set=Intersection GT 1/1
|
|
chr1 47053334 . A G 5 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=23;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.881A>G;refseq.codingCoordStr_2=c.884A>G;refseq.codonCoord_1=294;refseq.codonCoord_2=295;refseq.end_1=47053334;refseq.end_2=47053334;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=965;refseq.mrnaCoord_2=968;refseq.name2_1=CYP4B1;refseq.name2_2=CYP4B1;refseq.name_1=NM_000779;refseq.name_2=NM_001099772;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D294G;refseq.proteinCoordStr_2=p.D295G;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.start_1=47053334;refseq.start_2=47053334;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 1/1
|
|
chr1 47053335 . T G 8 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.882T>G;refseq.codingCoordStr_2=c.885T>G;refseq.codonCoord_1=294;refseq.codonCoord_2=295;refseq.end_1=47053335;refseq.end_2=47053335;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=966;refseq.mrnaCoord_2=969;refseq.name2_1=CYP4B1;refseq.name2_2=CYP4B1;refseq.name_1=NM_000779;refseq.name_2=NM_001099772;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D294E;refseq.proteinCoordStr_2=p.D295E;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=3;refseq.spliceDist_2=3;refseq.spliceInfo_1=splice-acceptor_3;refseq.spliceInfo_2=splice-acceptor_3;refseq.start_1=47053335;refseq.start_2=47053335;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=FilteredInAll GT 1/1
|
|
chr1 47053446 . G A 144.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=263;Dels=0.00;HRun=0;HaplotypeScore=15.55;MQ=95.78;MQ0=0;OQ=10836.36;QD=41.20;RankSumP=1.00000;SB=-5004.50;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.993G>A;refseq.codingCoordStr_2=c.996G>A;refseq.codonCoord_1=331;refseq.codonCoord_2=332;refseq.end_1=47053446;refseq.end_2=47053446;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1077;refseq.mrnaCoord_2=1080;refseq.name2_1=CYP4B1;refseq.name2_2=CYP4B1;refseq.name_1=NM_000779;refseq.name_2=NM_001099772;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.M331I;refseq.proteinCoordStr_2=p.M332I;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=-78;refseq.spliceDist_2=-78;refseq.start_1=47053446;refseq.start_2=47053446;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATA;refseq.variantCodon_2=ATA;set=Intersection GT 1/1
|
|
chr1 47053471 . C T 324.56 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=243;Dels=0.00;HRun=1;HaplotypeScore=3.62;MQ=97.08;MQ0=0;OQ=10266.62;QD=42.25;RankSumP=1.00000;SB=-4408.07;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1018C>T;refseq.codingCoordStr_2=c.1021C>T;refseq.codonCoord_1=340;refseq.codonCoord_2=341;refseq.end_1=47053471;refseq.end_2=47053471;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1102;refseq.mrnaCoord_2=1105;refseq.name2_1=CYP4B1;refseq.name2_2=CYP4B1;refseq.name_1=NM_000779;refseq.name_2=NM_001099772;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R340C;refseq.proteinCoordStr_2=p.R341C;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGT;refseq.referenceCodon_2=CGT;refseq.spliceDist_1=-53;refseq.spliceDist_2=-53;refseq.start_1=47053471;refseq.start_2=47053471;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;set=Intersection GT 1/1
|
|
chr1 47055359 . C T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=446;Dels=0.00;HRun=0;HaplotypeScore=42.37;MQ=98.43;MQ0=0;OQ=14295.24;QD=32.05;RankSumP=1.00000;SB=-6909.72;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1123C>T;refseq.codingCoordStr_2=c.1126C>T;refseq.codonCoord_1=375;refseq.codonCoord_2=376;refseq.end_1=47055359;refseq.end_2=47055359;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1207;refseq.mrnaCoord_2=1210;refseq.name2_1=CYP4B1;refseq.name2_2=CYP4B1;refseq.name_1=NM_000779;refseq.name_2=NM_001099772;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R375C;refseq.proteinCoordStr_2=p.R376C;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.spliceDist_1=53;refseq.spliceDist_2=53;refseq.start_1=47055359;refseq.start_2=47055359;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=Intersection GT 1/1
|
|
chr1 47168560 . G A 183.04 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=475;Dels=0.00;HRun=1;HaplotypeScore=5.89;MQ=73.78;MQ0=0;OQ=8601.59;QD=18.11;RankSumP=0.255918;SB=-1726.42;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1374C>T;refseq.codonCoord=458;refseq.end=47168560;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1425;refseq.name=NM_000778;refseq.name2=CYP4A11;refseq.positionType=CDS;refseq.proteinCoordStr=p.I458I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=47168560;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 47172554 . G A 31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=381;Dels=0.00;HRun=0;HaplotypeScore=40.70;MQ=14.90;MQ0=372;QD=0.08;RankSumP=0.773810;SB=-10.00;SecondBestBaseQ=23;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.969C>T;refseq.codonCoord=323;refseq.end=47172554;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1020;refseq.name=NM_000778;refseq.name2=CYP4A11;refseq.positionType=CDS;refseq.proteinCoordStr=p.H323H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=72;refseq.start=47172554;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap-filterIngatk GT 1/0
|
|
chr1 47344489 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=337;Dels=0.00;HRun=1;HaplotypeScore=13.50;MQ=61.00;MQ0=84;OQ=1678.37;QD=4.98;RankSumP=0.101297;SB=-556.25;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1170C>T;refseq.codonCoord=390;refseq.end=47344489;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1173;refseq.name=NM_178134;refseq.name2=CYP4Z1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I390I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-32;refseq.start=47344489;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 47344492 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=323;Dels=0.00;HRun=3;HaplotypeScore=13.16;MQ=61.57;MQ0=81;OQ=1707.24;QD=5.29;RankSumP=0.0487252;SB=-549.76;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1173C>T;refseq.codonCoord=391;refseq.end=47344492;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1176;refseq.name=NM_178134;refseq.name2=CYP4Z1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T391T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-29;refseq.start=47344492;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 0/1
|
|
chr1 47353844 . G A 33 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.315543;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1258G>A;refseq.codonCoord=420;refseq.end=47353844;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1261;refseq.name=NM_178134;refseq.name2=CYP4Z1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D420N;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=47353844;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=soap GT 1/0
|
|
chr1 47354940 . A G 30 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.448622;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1298A>G;refseq.codonCoord=433;refseq.end=47354940;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1301;refseq.name=NM_178134;refseq.name2=CYP4Z1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N433S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=32;refseq.start=47354940;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=soap GT 0/1
|
|
chr1 47354953 . A G 47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.570669;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1311A>G;refseq.codonCoord=437;refseq.end=47354953;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1314;refseq.name=NM_178134;refseq.name2=CYP4Z1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I437M;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=-39;refseq.start=47354953;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=soap GT 0/1
|
|
chr1 47380438 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=448;Dels=0.00;HRun=0;HaplotypeScore=28.01;MQ=68.46;MQ0=47;OQ=5547.41;QD=12.38;RankSumP=0.372948;SB=-1530.17;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.454A>T;refseq.codonCoord=152;refseq.end=47380438;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=505;refseq.name=NM_001010969;refseq.name2=CYP4A22;refseq.positionType=CDS;refseq.proteinCoordStr=p.N152Y;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-57;refseq.start=47380438;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 0/1
|
|
chr1 47382076 . T C 135.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=415;Dels=0.00;HRun=1;HaplotypeScore=9.33;MQ=95.69;MQ0=0;OQ=7545.24;QD=18.18;RankSumP=0.404150;SB=-2711.87;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.691T>C;refseq.codonCoord=231;refseq.end=47382076;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=742;refseq.name=NM_001010969;refseq.name2=CYP4A22;refseq.positionType=CDS;refseq.proteinCoordStr=p.C231R;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=56;refseq.start=47382076;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/0
|
|
chr1 47382880 . C T 71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=806;Dels=0.00;HRun=0;HaplotypeScore=57.00;MQ=2.93;MQ0=786;OQ=87.74;QD=0.11;RankSumP=0.176190;SB=-10.00;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.969C>T;refseq.codonCoord=323;refseq.end=47382880;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1020;refseq.name=NM_001010969;refseq.name2=CYP4A22;refseq.positionType=CDS;refseq.proteinCoordStr=p.H323H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=72;refseq.start=47382880;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap-filterIngatk GT 0/1
|
|
chr1 47458042 . T C 62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=14.15;MQ=94.44;MQ0=0;OQ=2066.79;QD=25.20;RankSumP=1.00000;SB=-1049.70;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.933A>G;refseq.codonCoord=311;refseq.end=47458042;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1510;refseq.name=NM_003189;refseq.name2=TAL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.K311K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=392;refseq.start=47458042;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 47489776 . A G 97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=447;Dels=0.00;HRun=2;HaplotypeScore=2.31;MQ=98.99;MQ0=0;OQ=17434.76;QD=39.00;RankSumP=1.00000;SB=-8595.68;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3486T>C;refseq.codingCoordStr_2=c.3483T>C;refseq.codonCoord_1=1162;refseq.codonCoord_2=1161;refseq.end_1=47489776;refseq.end_2=47489776;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3641;refseq.mrnaCoord_2=3638;refseq.name2_1=STIL;refseq.name2_2=STIL;refseq.name_1=NM_001048166;refseq.name_2=NM_003035;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P1162P;refseq.proteinCoordStr_2=p.P1161P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.spliceDist_1=406;refseq.spliceDist_2=406;refseq.start_1=47489776;refseq.start_2=47489776;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=Intersection GT 1/1
|
|
chr1 47507915 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2594A>C;refseq.codingCoordStr_2=c.2594A>C;refseq.codonCoord_1=865;refseq.codonCoord_2=865;refseq.end_1=47507915;refseq.end_2=47507915;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2749;refseq.mrnaCoord_2=2749;refseq.name2_1=STIL;refseq.name2_2=STIL;refseq.name_1=NM_001048166;refseq.name_2=NM_003035;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N865T;refseq.proteinCoordStr_2=p.N865T;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-22;refseq.spliceDist_2=-22;refseq.start_1=47507915;refseq.start_2=47507915;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=FilteredInAll GT 1/0
|
|
chr1 47519193 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1524A>C;refseq.codingCoordStr_2=c.1524A>C;refseq.codonCoord_1=508;refseq.codonCoord_2=508;refseq.end_1=47519193;refseq.end_2=47519193;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1679;refseq.mrnaCoord_2=1679;refseq.name2_1=STIL;refseq.name2_2=STIL;refseq.name_1=NM_001048166;refseq.name_2=NM_003035;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P508P;refseq.proteinCoordStr_2=p.P508P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=276;refseq.spliceDist_2=276;refseq.start_1=47519193;refseq.start_2=47519193;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 47655084 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=318.68;QD=16.77;RankSumP=0.185110;SB=-10.00;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.510C>T;refseq.codonCoord=170;refseq.end=47655084;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=754;refseq.name=NM_012186;refseq.name2=FOXE3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A170A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=754;refseq.start=47655084;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 0/1
|
|
chr1 47676587 . G A 10.16 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=87.00;MQ0=0;QD=10.16;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.193G>A;refseq.codonCoord=65;refseq.end=47676587;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2312;refseq.name=NM_004474;refseq.name2=FOXD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A65T;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=2312;refseq.start=47676587;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:0,1:1:-4.26,-0.30,-0.00:1.76
|
|
chr1 47677496 . G C 194.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=325.72;QD=36.19;RankSumP=1.00000;SB=-186.86;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1102G>C;refseq.codonCoord=368;refseq.end=47677496;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3221;refseq.name=NM_004474;refseq.name2=FOXD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A368P;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-1455;refseq.start=47677496;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 48470320 . T G 379.87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=337;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=98.77;MQ0=0;OQ=13283.71;QD=39.42;RankSumP=1.00000;SB=-3923.56;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.807T>G;refseq.codingCoordStr_2=c.882T>G;refseq.codonCoord_1=269;refseq.codonCoord_2=294;refseq.end_1=48470320;refseq.end_2=48470320;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=859;refseq.mrnaCoord_2=934;refseq.name2_1=SLC5A9;refseq.name2_2=SLC5A9;refseq.name_1=NM_001011547;refseq.name_2=NM_001135181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I269M;refseq.proteinCoordStr_2=p.I294M;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=-91;refseq.spliceDist_2=-91;refseq.start_1=48470320;refseq.start_2=48470320;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;set=Intersection GT 1/1
|
|
chr1 48470338 . C T 214.73 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=270;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=98.83;MQ0=0;OQ=5429.62;QD=20.11;RankSumP=0.178822;SB=-1977.54;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.825C>T;refseq.codingCoordStr_2=c.900C>T;refseq.codonCoord_1=275;refseq.codonCoord_2=300;refseq.end_1=48470338;refseq.end_2=48470338;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=877;refseq.mrnaCoord_2=952;refseq.name2_1=SLC5A9;refseq.name2_2=SLC5A9;refseq.name_1=NM_001011547;refseq.name_2=NM_001135181;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S275S;refseq.proteinCoordStr_2=p.S300S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=-73;refseq.spliceDist_2=-73;refseq.start_1=48470338;refseq.start_2=48470338;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 0/1
|
|
chr1 48537006 . C T 259.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=419;Dels=0.00;HRun=0;HaplotypeScore=6.43;MQ=98.67;MQ0=0;OQ=17175.97;QD=40.99;RankSumP=1.00000;SB=-7570.86;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1433G>A;refseq.codonCoord=478;refseq.end=48537006;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1598;refseq.name=NM_019073;refseq.name2=SPATA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.C478Y;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-142;refseq.start=48537006;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 48997171 . G T 261.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=6.95;MQ=98.01;MQ0=0;OQ=2086.85;QD=17.11;RankSumP=0.154797;SB=-528.95;SecondBestBaseQ=29;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.733C>A;refseq.codonCoord_2=245;refseq.end_1=49105439;refseq.end_2=48997171;refseq.frame_2=0;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=777;refseq.name2_1=AGBL4;refseq.name2_2=BEND5;refseq.name_1=NM_032785;refseq.name_2=NM_024603;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.R245R;refseq.referenceAA_2=Arg;refseq.referenceCodon_2=CGG;refseq.spliceDist_2=-13;refseq.start_1=48901511;refseq.start_2=48997171;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Arg;refseq.variantCodon_2=AGG;set=Intersection GT 0/1
|
|
chr1 50433998 . C T 347.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=265;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=98.84;MQ0=0;OQ=10608.57;QD=40.03;RankSumP=1.00000;SB=-4406.55;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.687C>T;refseq.codingCoordStr_2=c.738C>T;refseq.codingCoordStr_3=c.687C>T;refseq.codingCoordStr_4=c.696C>T;refseq.codingCoordStr_5=c.687C>T;refseq.codonCoord_1=229;refseq.codonCoord_2=246;refseq.codonCoord_3=229;refseq.codonCoord_4=232;refseq.codonCoord_5=229;refseq.end_1=50433998;refseq.end_2=50433998;refseq.end_3=50433998;refseq.end_4=50433998;refseq.end_5=50433998;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=955;refseq.mrnaCoord_2=780;refseq.mrnaCoord_3=769;refseq.mrnaCoord_4=847;refseq.mrnaCoord_5=955;refseq.name2_1=ELAVL4;refseq.name2_2=ELAVL4;refseq.name2_3=ELAVL4;refseq.name2_4=ELAVL4;refseq.name2_5=ELAVL4;refseq.name_1=NM_001144774;refseq.name_2=NM_001144775;refseq.name_3=NM_001144776;refseq.name_4=NM_001144777;refseq.name_5=NM_021952;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.P229P;refseq.proteinCoordStr_2=p.P246P;refseq.proteinCoordStr_3=p.P229P;refseq.proteinCoordStr_4=p.P232P;refseq.proteinCoordStr_5=p.P229P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.referenceCodon_4=CCC;refseq.referenceCodon_5=CCC;refseq.spliceDist_1=-48;refseq.spliceDist_2=-48;refseq.spliceDist_3=-48;refseq.spliceDist_4=-48;refseq.spliceDist_5=-48;refseq.start_1=50433998;refseq.start_2=50433998;refseq.start_3=50433998;refseq.start_4=50433998;refseq.start_5=50433998;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=CCT;set=Intersection GT 1/1
|
|
chr1 50439102 . C T 92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=866;Dels=0.00;HRun=1;HaplotypeScore=11.35;MQ=98.68;MQ0=0;OQ=36693.38;QD=42.37;RankSumP=1.00000;SB=-15598.33;SecondBestBaseQ=2;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.774-8;refseq.codingCoordStr_2=c.825-8;refseq.codingCoordStr_3=c.774-8;refseq.codingCoordStr_4=c.783-8;refseq.codingCoordStr_5=c.808C>T;refseq.codonCoord_5=270;refseq.end_1=50439102;refseq.end_2=50439102;refseq.end_3=50439102;refseq.end_4=50439102;refseq.end_5=50439102;refseq.frame_5=0;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=true;refseq.mrnaCoord_5=1076;refseq.name2_1=ELAVL4;refseq.name2_2=ELAVL4;refseq.name2_3=ELAVL4;refseq.name2_4=ELAVL4;refseq.name2_5=ELAVL4;refseq.name_1=NM_001144774;refseq.name_2=NM_001144775;refseq.name_3=NM_001144776;refseq.name_4=NM_001144777;refseq.name_5=NM_021952;refseq.numMatchingRecords=5;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.positionType_4=intron;refseq.positionType_5=CDS;refseq.proteinCoordStr_5=p.P270S;refseq.referenceAA_5=Pro;refseq.referenceCodon_5=CCC;refseq.spliceDist_1=-8;refseq.spliceDist_2=-8;refseq.spliceDist_3=-8;refseq.spliceDist_4=-8;refseq.spliceDist_5=35;refseq.spliceInfo_1=splice-acceptor_-8;refseq.spliceInfo_2=splice-acceptor_-8;refseq.spliceInfo_3=splice-acceptor_-8;refseq.spliceInfo_4=splice-acceptor_-8;refseq.start_1=50439102;refseq.start_2=50439102;refseq.start_3=50439102;refseq.start_4=50439102;refseq.start_5=50439102;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_5=Ser;refseq.variantCodon_5=TCC;set=Intersection GT 1/1
|
|
chr1 51599509 . T C 282.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=332;Dels=0.00;HRun=0;HaplotypeScore=14.94;MQ=98.87;MQ0=0;OQ=7042.76;QD=21.21;RankSumP=0.131795;SB=-2494.60;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1524A>G;refseq.codingCoordStr_2=c.2466A>G;refseq.codonCoord_1=508;refseq.codonCoord_2=822;refseq.end_1=51599509;refseq.end_2=51599509;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1689;refseq.mrnaCoord_2=2558;refseq.name2_1=EPS15;refseq.name2_2=EPS15;refseq.name_1=NM_001159969;refseq.name_2=NM_001981;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I508M;refseq.proteinCoordStr_2=p.I822M;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATA;refseq.referenceCodon_2=ATA;refseq.spliceDist_1=-79;refseq.spliceDist_2=-79;refseq.start_1=51599509;refseq.start_2=51599509;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;set=Intersection GT 1/0
|
|
chr1 51646539 . G A 280.89 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=288;Dels=0.00;HRun=0;HaplotypeScore=9.19;MQ=98.69;MQ0=0;OQ=11833.08;QD=41.09;RankSumP=1.00000;SB=-4053.44;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.387C>T;refseq.codingCoordStr_2=c.1329C>T;refseq.codonCoord_1=129;refseq.codonCoord_2=443;refseq.end_1=51646539;refseq.end_2=51646539;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=552;refseq.mrnaCoord_2=1421;refseq.name2_1=EPS15;refseq.name2_2=EPS15;refseq.name_1=NM_001159969;refseq.name_2=NM_001981;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y129Y;refseq.proteinCoordStr_2=p.Y443Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=54;refseq.spliceDist_2=54;refseq.start_1=51646539;refseq.start_2=51646539;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;set=Intersection GT 1/1
|
|
chr1 52038830 . G A 80.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=439;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=98.85;MQ0=0;OQ=18939.05;QD=43.14;RankSumP=1.00000;SB=-9200.46;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2427C>T;refseq.codingCoordStr_2=c.2631C>T;refseq.codonCoord_1=809;refseq.codonCoord_2=877;refseq.end_1=52038830;refseq.end_2=52038830;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2749;refseq.mrnaCoord_2=2953;refseq.name2_1=NRD1;refseq.name2_2=NRD1;refseq.name_1=NM_001101662;refseq.name_2=NM_002525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P809P;refseq.proteinCoordStr_2=p.P877P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=-15;refseq.spliceDist_2=-15;refseq.start_1=52038830;refseq.start_2=52038830;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;set=Intersection GT 1/1
|
|
chr1 52063572 . T G 286.68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=229;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=98.77;MQ0=0;OQ=9332.86;QD=40.75;RankSumP=1.00000;SB=-4251.94;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1011A>C;refseq.codingCoordStr_2=c.1215A>C;refseq.codonCoord_1=337;refseq.codonCoord_2=405;refseq.end_1=52063572;refseq.end_2=52063572;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1333;refseq.mrnaCoord_2=1537;refseq.name2_1=NRD1;refseq.name2_2=NRD1;refseq.name_1=NM_001101662;refseq.name_2=NM_002525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G337G;refseq.proteinCoordStr_2=p.G405G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=-26;refseq.spliceDist_2=-26;refseq.start_1=52063572;refseq.start_2=52063572;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=Intersection GT 1/1
|
|
chr1 52078645 . A T 32 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.571429;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.471T>A;refseq.codingCoordStr_2=c.471T>A;refseq.codonCoord_1=157;refseq.codonCoord_2=157;refseq.end_1=52078645;refseq.end_2=52078645;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=793;refseq.mrnaCoord_2=793;refseq.name2_1=NRD1;refseq.name2_2=NRD1;refseq.name_1=NM_001101662;refseq.name_2=NM_002525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D157E;refseq.proteinCoordStr_2=p.D157E;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=130;refseq.spliceDist_2=130;refseq.start_1=52078645;refseq.start_2=52078645;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=soap GT 0/1
|
|
chr1 52078654 . T A 59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.431818;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.462A>T;refseq.codingCoordStr_2=c.462A>T;refseq.codonCoord_1=154;refseq.codonCoord_2=154;refseq.end_1=52078654;refseq.end_2=52078654;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=784;refseq.mrnaCoord_2=784;refseq.name2_1=NRD1;refseq.name2_2=NRD1;refseq.name_1=NM_001101662;refseq.name_2=NM_002525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E154D;refseq.proteinCoordStr_2=p.E154D;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=121;refseq.spliceDist_2=121;refseq.start_1=52078654;refseq.start_2=52078654;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=soap GT 1/0
|
|
chr1 52303121 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.-84A>C;refseq.codingCoordStr_3=c.91A>C;refseq.codonCoord_3=31;refseq.end_1=52303121;refseq.end_2=52303121;refseq.end_3=52303121;refseq.frame_3=0;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=299;refseq.mrnaCoord_2=232;refseq.mrnaCoord_3=299;refseq.name2_1=BTF3L4;refseq.name2_2=BTF3L4;refseq.name2_3=BTF3L4;refseq.name_1=NR_024350;refseq.name_2=NM_001136497;refseq.name_3=NM_152265;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=utr5;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.T31P;refseq.referenceAA_3=Thr;refseq.referenceCodon_3=ACA;refseq.spliceDist_1=37;refseq.spliceDist_2=37;refseq.spliceDist_3=37;refseq.start_1=52303121;refseq.start_2=52303121;refseq.start_3=52303121;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Pro;refseq.variantCodon_3=CCA;set=FilteredInAll GT 0/1
|
|
chr1 52764226 . C T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=366;Dels=0.00;HRun=0;HaplotypeScore=16.40;MQ=98.48;MQ0=0;OQ=15685.44;QD=42.86;RankSumP=1.00000;SB=-5214.51;SecondBestBaseQ=18;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.315G>A;refseq.codingCoordStr_2=c.315G>A;refseq.codingCoordStr_3=c.315G>A;refseq.codonCoord_1=105;refseq.codonCoord_2=105;refseq.codonCoord_3=105;refseq.end_1=52764226;refseq.end_2=52764226;refseq.end_3=52764226;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=549;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=549;refseq.name2_1=ZCCHC11;refseq.name2_2=ZCCHC11;refseq.name2_3=ZCCHC11;refseq.name_1=NM_001009881;refseq.name_2=NM_001009882;refseq.name_3=NM_015269;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P105P;refseq.proteinCoordStr_2=p.P105P;refseq.proteinCoordStr_3=p.P105P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.referenceCodon_3=CCG;refseq.spliceDist_1=-404;refseq.spliceDist_2=-404;refseq.spliceDist_3=-404;refseq.start_1=52764226;refseq.start_2=52764226;refseq.start_3=52764226;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;refseq.variantCodon_3=CCA;set=Intersection GT 1/1
|
|
chr1 52845042 . T C 77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=387;Dels=0.00;HRun=0;HaplotypeScore=20.46;MQ=98.61;MQ0=0;OQ=14421.35;QD=37.26;RankSumP=1.00000;SB=-5535.93;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.237T>C;refseq.codonCoord=79;refseq.end=52845042;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=276;refseq.name=NM_015696;refseq.name2=GPX7;refseq.positionType=CDS;refseq.proteinCoordStr=p.F79F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=99;refseq.start=52845042;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 52931109 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.125A>G;refseq.codonCoord=42;refseq.end=52931109;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=165;refseq.name=NM_023077;refseq.name2=C1orf163;refseq.positionType=CDS;refseq.proteinCoordStr=p.D42G;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=19;refseq.start=52931109;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 52931112 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.122T>G;refseq.codonCoord=41;refseq.end=52931112;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=162;refseq.name=NM_023077;refseq.name2=C1orf163;refseq.positionType=CDS;refseq.proteinCoordStr=p.V41G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=16;refseq.start=52931112;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 53023238 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=125;Dels=0.00;HRun=1;HaplotypeScore=11.10;MQ=98.84;MQ0=0;OQ=1716.46;QD=13.73;RankSumP=0.409395;SB=-708.55;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1194G>A;refseq.codonCoord=398;refseq.end=53023238;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1389;refseq.name=NM_024646;refseq.name2=ZYG11B;refseq.positionType=CDS;refseq.proteinCoordStr=p.G398G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-76;refseq.start=53023238;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 53142945 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=84;Dels=0.00;HRun=1;HaplotypeScore=6.86;MQ=98.96;MQ0=0;OQ=853.59;QD=10.16;RankSumP=0.186463;SB=-404.70;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.570C>A;refseq.codonCoord=190;refseq.end=53142945;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=671;refseq.name=NM_018281;refseq.name2=ECHDC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y190*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-40;refseq.start=53142945;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=Intersection GT 0/1
|
|
chr1 53308066 . G A 348.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.79;MQ0=0;OQ=889.71;QD=38.68;RankSumP=1.00000;SB=-412.54;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.95G>A;refseq.codonCoord=32;refseq.end=53308066;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=102;refseq.name=NM_153703;refseq.name2=PODN;refseq.positionType=CDS;refseq.proteinCoordStr=p.R32H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=53308066;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/1
|
|
chr1 53309854 . G A 117.13 PASS AC=2;AF=1.00;AN=2;BestBaseQ=23;DB;DP=146;Dels=0.00;HRun=0;HaplotypeScore=9.26;MQ=99.00;MQ0=0;OQ=4329.61;QD=29.65;RankSumP=1.00000;SB=-1484.85;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.516G>A;refseq.codonCoord=172;refseq.end=53309854;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=523;refseq.name=NM_153703;refseq.name2=PODN;refseq.positionType=CDS;refseq.proteinCoordStr=p.T172T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-35;refseq.start=53309854;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 53317027 . G A 259.30 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=2.58;MQ=99.00;MQ0=0;OQ=2836.35;QD=31.87;RankSumP=1.00000;SB=-919.04;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1401G>A;refseq.codonCoord=467;refseq.end=53317027;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1408;refseq.name=NM_153703;refseq.name2=PODN;refseq.positionType=CDS;refseq.proteinCoordStr=p.P467P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-256;refseq.start=53317027;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 53317185 . T C 136.53 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=159.66;QD=31.93;RankSumP=1.00000;SB=-91.37;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1559T>C;refseq.codonCoord=520;refseq.end=53317185;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1566;refseq.name=NM_153703;refseq.name2=PODN;refseq.positionType=CDS;refseq.proteinCoordStr=p.V520A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-98;refseq.start=53317185;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=filterInsoap-gatk GT 1/1
|
|
chr1 53326290 . A G 341.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=149;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=97.94;MQ0=0;OQ=5095.10;QD=34.20;RankSumP=1.00000;SB=-1873.41;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1662T>C;refseq.codonCoord=554;refseq.end=53326290;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1830;refseq.name=NM_006671;refseq.name2=SLC1A7;refseq.positionType=CDS;refseq.proteinCoordStr=p.S554S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=198;refseq.start=53326290;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 53326342 . T C 70.02 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=172;Dels=0.00;HRun=2;HaplotypeScore=3.49;MQ=97.74;MQ0=0;OQ=6066.54;QD=35.27;RankSumP=1.00000;SB=-2589.04;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1610A>G;refseq.codonCoord=537;refseq.end=53326342;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1778;refseq.name=NM_006671;refseq.name2=SLC1A7;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q537R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=146;refseq.start=53326342;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/1
|
|
chr1 53330858 . A G 381.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=98.36;MQ0=0;OQ=2269.84;QD=35.47;RankSumP=1.00000;SB=-1155.58;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.987T>C;refseq.codonCoord=329;refseq.end=53330858;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1155;refseq.name=NM_006671;refseq.name2=SLC1A7;refseq.positionType=CDS;refseq.proteinCoordStr=p.R329R;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-45;refseq.start=53330858;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/1
|
|
chr1 53449036 . G A 421.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.29;MQ0=0;OQ=3190.18;QD=41.43;RankSumP=1.00000;SB=-1498.74;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1102G>A;refseq.codonCoord=368;refseq.end=53449036;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1617;refseq.name=NM_000098;refseq.name2=CPT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V368I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-544;refseq.start=53449036;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 53451817 . A G 124.96 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=121;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=98.92;MQ0=0;OQ=1574.68;QD=13.01;RankSumP=0.367617;SB=-433.11;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1939A>G;refseq.codonCoord=647;refseq.end=53451817;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2454;refseq.name=NM_000098;refseq.name2=CPT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.M647V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=294;refseq.start=53451817;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 0/1
|
|
chr1 53454287 . T G 117.22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=2.97;MQ=98.60;MQ0=0;OQ=1069.83;QD=13.89;RankSumP=0.0905738;SB=-481.76;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.369A>C;refseq.codonCoord=123;refseq.end=53454287;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=411;refseq.name=NM_017887;refseq.name2=C1orf123;refseq.positionType=CDS;refseq.proteinCoordStr=p.S123S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=30;refseq.start=53454287;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/0
|
|
chr1 53485315 . C T 289.28 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=262;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.92;MQ0=0;OQ=11319.51;QD=43.20;RankSumP=1.00000;SB=-3837.85;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.2678G>A;refseq.codingCoordStr_2=c.2855G>A;refseq.codingCoordStr_3=c.2066G>A;refseq.codingCoordStr_4=c.2345G>A;refseq.codonCoord_1=893;refseq.codonCoord_2=952;refseq.codonCoord_3=689;refseq.codonCoord_4=782;refseq.end_1=53485315;refseq.end_2=53485315;refseq.end_3=53485315;refseq.end_4=53485315;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=2820;refseq.mrnaCoord_2=2997;refseq.mrnaCoord_3=2208;refseq.mrnaCoord_4=2582;refseq.name2_1=LRP8;refseq.name2_2=LRP8;refseq.name2_3=LRP8;refseq.name2_4=LRP8;refseq.name_1=NM_001018054;refseq.name_2=NM_004631;refseq.name_3=NM_017522;refseq.name_4=NM_033300;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.R893Q;refseq.proteinCoordStr_2=p.R952Q;refseq.proteinCoordStr_3=p.R689Q;refseq.proteinCoordStr_4=p.R782Q;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.referenceCodon_3=CGA;refseq.referenceCodon_4=CGA;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceDist_3=2;refseq.spliceDist_4=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.spliceInfo_3=splice-acceptor_2;refseq.spliceInfo_4=splice-acceptor_2;refseq.start_1=53485315;refseq.start_2=53485315;refseq.start_3=53485315;refseq.start_4=53485315;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantAA_3=Gln;refseq.variantAA_4=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;refseq.variantCodon_3=CAA;refseq.variantCodon_4=CAA;set=Intersection GT 1/1
|
|
chr1 53489004 . G A 272.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=258;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.58;MQ0=0;OQ=10728.87;QD=41.58;RankSumP=1.00000;SB=-4692.58;SecondBestBaseQ=10;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.2622C>T;refseq.codingCoordStr_2=c.2622C>T;refseq.codingCoordStr_3=c.2010C>T;refseq.codingCoordStr_4=c.2112C>T;refseq.codonCoord_1=874;refseq.codonCoord_2=874;refseq.codonCoord_3=670;refseq.codonCoord_4=704;refseq.end_1=53489004;refseq.end_2=53489004;refseq.end_3=53489004;refseq.end_4=53489004;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=2764;refseq.mrnaCoord_2=2764;refseq.mrnaCoord_3=2152;refseq.mrnaCoord_4=2349;refseq.name2_1=LRP8;refseq.name2_2=LRP8;refseq.name2_3=LRP8;refseq.name2_4=LRP8;refseq.name_1=NM_001018054;refseq.name_2=NM_004631;refseq.name_3=NM_017522;refseq.name_4=NM_033300;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.D874D;refseq.proteinCoordStr_2=p.D874D;refseq.proteinCoordStr_3=p.D670D;refseq.proteinCoordStr_4=p.D704D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.referenceCodon_3=GAC;refseq.referenceCodon_4=GAC;refseq.spliceDist_1=-55;refseq.spliceDist_2=-55;refseq.spliceDist_3=-55;refseq.spliceDist_4=-55;refseq.start_1=53489004;refseq.start_2=53489004;refseq.start_3=53489004;refseq.start_4=53489004;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantAA_4=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;refseq.variantCodon_3=GAT;refseq.variantCodon_4=GAT;set=Intersection GT 1/1
|
|
chr1 53496657 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.2131T>C;refseq.codingCoordStr_2=c.2131T>C;refseq.codingCoordStr_3=c.1744T>C;refseq.codingCoordStr_4=c.1621T>C;refseq.codonCoord_1=711;refseq.codonCoord_2=711;refseq.codonCoord_3=582;refseq.codonCoord_4=541;refseq.end_1=53496657;refseq.end_2=53496657;refseq.end_3=53496657;refseq.end_4=53496657;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=2273;refseq.mrnaCoord_2=2273;refseq.mrnaCoord_3=1886;refseq.mrnaCoord_4=1858;refseq.name2_1=LRP8;refseq.name2_2=LRP8;refseq.name2_3=LRP8;refseq.name2_4=LRP8;refseq.name_1=NM_001018054;refseq.name_2=NM_004631;refseq.name_3=NM_017522;refseq.name_4=NM_033300;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.S711P;refseq.proteinCoordStr_2=p.S711P;refseq.proteinCoordStr_3=p.S582P;refseq.proteinCoordStr_4=p.S541P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_1=TCC;refseq.referenceCodon_2=TCC;refseq.referenceCodon_3=TCC;refseq.referenceCodon_4=TCC;refseq.spliceDist_1=75;refseq.spliceDist_2=75;refseq.spliceDist_3=75;refseq.spliceDist_4=75;refseq.start_1=53496657;refseq.start_2=53496657;refseq.start_3=53496657;refseq.start_4=53496657;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;set=FilteredInAll GT 0/1
|
|
chr1 53504903 . G T 66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=214;Dels=0.00;HRun=2;HaplotypeScore=2.16;MQ=98.88;MQ0=0;OQ=8129.31;QD=37.99;RankSumP=1.00000;SB=-3409.68;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1257C>A;refseq.codingCoordStr_2=c.1257C>A;refseq.codingCoordStr_3=c.870C>A;refseq.codingCoordStr_4=c.747C>A;refseq.codonCoord_1=419;refseq.codonCoord_2=419;refseq.codonCoord_3=290;refseq.codonCoord_4=249;refseq.end_1=53504903;refseq.end_2=53504903;refseq.end_3=53504903;refseq.end_4=53504903;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1399;refseq.mrnaCoord_2=1399;refseq.mrnaCoord_3=1012;refseq.mrnaCoord_4=984;refseq.name2_1=LRP8;refseq.name2_2=LRP8;refseq.name2_3=LRP8;refseq.name2_4=LRP8;refseq.name_1=NM_001018054;refseq.name_2=NM_004631;refseq.name_3=NM_017522;refseq.name_4=NM_033300;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.G419G;refseq.proteinCoordStr_2=p.G419G;refseq.proteinCoordStr_3=p.G290G;refseq.proteinCoordStr_4=p.G249G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceAA_4=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.referenceCodon_3=GGC;refseq.referenceCodon_4=GGC;refseq.spliceDist_1=5;refseq.spliceDist_2=5;refseq.spliceDist_3=5;refseq.spliceDist_4=5;refseq.spliceInfo_1=splice-acceptor_5;refseq.spliceInfo_2=splice-acceptor_5;refseq.spliceInfo_3=splice-acceptor_5;refseq.spliceInfo_4=splice-acceptor_5;refseq.start_1=53504903;refseq.start_2=53504903;refseq.start_3=53504903;refseq.start_4=53504903;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;refseq.variantCodon_3=GGA;refseq.variantCodon_4=GGA;set=Intersection GT 1/1
|
|
chr1 53518934 . T G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=20;DP=283;Dels=0.00;HRun=3;HaplotypeScore=28.10;MQ=96.58;MQ0=0;OQ=86.58;QD=0.31;RankSumP=0.00000;SB=369.17;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.409A>C;refseq.codingCoordStr_2=c.409A>C;refseq.codingCoordStr_3=c.409A>C;refseq.codingCoordStr_4=c.409A>C;refseq.codonCoord_1=137;refseq.codonCoord_2=137;refseq.codonCoord_3=137;refseq.codonCoord_4=137;refseq.end_1=53518934;refseq.end_2=53518934;refseq.end_3=53518934;refseq.end_4=53518934;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=551;refseq.mrnaCoord_2=551;refseq.mrnaCoord_3=551;refseq.mrnaCoord_4=646;refseq.name2_1=LRP8;refseq.name2_2=LRP8;refseq.name2_3=LRP8;refseq.name2_4=LRP8;refseq.name_1=NM_001018054;refseq.name_2=NM_004631;refseq.name_3=NM_017522;refseq.name_4=NM_033300;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T137P;refseq.proteinCoordStr_2=p.T137P;refseq.proteinCoordStr_3=p.T137P;refseq.proteinCoordStr_4=p.T137P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.spliceDist_3=42;refseq.spliceDist_4=42;refseq.start_1=53518934;refseq.start_2=53518934;refseq.start_3=53518934;refseq.start_4=53518934;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;set=FilteredInAll GT 1/0
|
|
chr1 53565239 . A C 329.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=245;Dels=0.00;HRun=0;HaplotypeScore=7.99;MQ=98.74;MQ0=0;OQ=4390.62;QD=17.92;RankSumP=0.110200;SB=-1137.02;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.138T>G;refseq.codingCoordStr_2=c.138T>G;refseq.codingCoordStr_3=c.138T>G;refseq.codingCoordStr_4=c.138T>G;refseq.codonCoord_1=46;refseq.codonCoord_2=46;refseq.codonCoord_3=46;refseq.codonCoord_4=46;refseq.end_1=53565239;refseq.end_2=53565239;refseq.end_3=53565239;refseq.end_4=53565239;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=280;refseq.mrnaCoord_2=280;refseq.mrnaCoord_3=280;refseq.mrnaCoord_4=375;refseq.name2_1=LRP8;refseq.name2_2=LRP8;refseq.name2_3=LRP8;refseq.name2_4=LRP8;refseq.name_1=NM_001018054;refseq.name_2=NM_004631;refseq.name_3=NM_017522;refseq.name_4=NM_033300;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.D46E;refseq.proteinCoordStr_2=p.D46E;refseq.proteinCoordStr_3=p.D46E;refseq.proteinCoordStr_4=p.D46E;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.referenceCodon_3=GAT;refseq.referenceCodon_4=GAT;refseq.spliceDist_1=14;refseq.spliceDist_2=14;refseq.spliceDist_3=14;refseq.spliceDist_4=14;refseq.start_1=53565239;refseq.start_2=53565239;refseq.start_3=53565239;refseq.start_4=53565239;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantAA_4=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;refseq.variantCodon_3=GAG;refseq.variantCodon_4=GAG;set=Intersection GT 0/1
|
|
chr1 53832604 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=4.57;MQ=97.21;MQ0=0;OQ=405.60;QD=10.96;RankSumP=0.467674;SB=-40.41;SecondBestBaseQ=23;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.560C>G;refseq.codonCoord=187;refseq.end=53832604;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1127;refseq.name=NM_147193;refseq.name2=GLIS1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A187G;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-236;refseq.start=53832604;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 0/1
|
|
chr1 53832836 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=3.06;MQ=98.46;MQ0=0;OQ=611.38;QD=8.49;RankSumP=0.223539;SB=-170.29;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.328A>G;refseq.codonCoord=110;refseq.end=53832836;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=895;refseq.name=NM_147193;refseq.name2=GLIS1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T110A;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=416;refseq.start=53832836;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/0
|
|
chr1 54377908 . G C 42 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;HRun=0;RankSumP=0.544322;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1223C>G;refseq.codonCoord=408;refseq.end=54377908;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2071;refseq.name=NM_201546;refseq.name2=CDCP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P408R;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=460;refseq.start=54377908;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=soap GT 0/1
|
|
chr1 54377915 . C G 29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=8;RankSumP=0.542857;SecondBestBaseQ=17;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1216G>C;refseq.codonCoord=406;refseq.end=54377915;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2064;refseq.name=NM_201546;refseq.name2=CDCP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A406P;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=453;refseq.start=54377915;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=soap GT 1/0
|
|
chr1 54379392 . C T 242.22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=192;Dels=0.00;HRun=0;HaplotypeScore=2.74;MQ=98.79;MQ0=0;OQ=4147.30;QD=21.60;RankSumP=0.264658;SB=-881.49;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.730G>A;refseq.codonCoord=244;refseq.end=54379392;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1578;refseq.name=NM_201546;refseq.name2=CDCP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G244R;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-34;refseq.start=54379392;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 0/1
|
|
chr1 54379639 . A G 90 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=218;Dels=0.00;HRun=3;HaplotypeScore=9.21;MQ=98.51;MQ0=0;OQ=7023.82;QD=32.22;RankSumP=1.00000;SB=-2438.42;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.483T>C;refseq.codonCoord=161;refseq.end=54379639;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1331;refseq.name=NM_201546;refseq.name2=CDCP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y161Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=56;refseq.start=54379639;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/1
|
|
chr1 54379658 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=4;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.464T>G;refseq.codonCoord=155;refseq.end=54379658;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1312;refseq.name=NM_201546;refseq.name2=CDCP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V155G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=37;refseq.start=54379658;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 0/1
|
|
chr1 54454508 . G C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=298;Dels=0.00;HRun=0;HaplotypeScore=4.08;MQ=98.67;MQ0=0;OQ=14643.51;QD=49.14;RankSumP=1.00000;SB=-3370.24;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1097G>C;refseq.codonCoord=366;refseq.end=54454508;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1174;refseq.name=NM_016491;refseq.name2=MRPL37;refseq.positionType=CDS;refseq.proteinCoordStr=p.C366S;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-98;refseq.start=54454508;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 54848040 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=336.47;QD=8.63;RankSumP=0.668436;SB=-99.58;SecondBestBaseQ=28;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.*667G>A;refseq.codingCoordStr_3=c.1247C>T;refseq.codonCoord_3=416;refseq.end_1=54868984;refseq.end_2=54848040;refseq.end_3=54848040;refseq.frame_3=1;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=2534;refseq.mrnaCoord_3=1379;refseq.name2_1=ACOT11;refseq.name2_2=ACOT11;refseq.name2_3=FAM151A;refseq.name_1=NM_015547;refseq.name_2=NM_147161;refseq.name_3=NM_176782;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=utr3;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.A416V;refseq.referenceAA_3=Ala;refseq.referenceCodon_3=GCG;refseq.spliceDist_2=-549;refseq.spliceDist_3=163;refseq.start_1=54846340;refseq.start_2=54848040;refseq.start_3=54848040;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=-;refseq.variantAA_3=Val;refseq.variantCodon_3=GTG;set=Intersection GT 1/0
|
|
chr1 54848720 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1037T>G;refseq.codonCoord_2=346;refseq.end_1=54868984;refseq.end_2=54848720;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1169;refseq.name2_1=ACOT11;refseq.name2_2=FAM151A;refseq.name_1=NM_015547;refseq.name_2=NM_176782;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V346G;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTT;refseq.spliceDist_2=-48;refseq.start_1=54846340;refseq.start_2=54848720;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGT;set=FilteredInAll GT 0/1
|
|
chr1 54892103 . T G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=479;Dels=0.00;HRun=0;HaplotypeScore=21.64;MQ=98.34;MQ0=0;OQ=16970.48;QD=35.43;RankSumP=1.00000;SB=-7344.36;SecondBestBaseQ=2;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.916T>G;refseq.codonCoord_2=306;refseq.end_1=54892103;refseq.end_2=54892103;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1234;refseq.mrnaCoord_2=1240;refseq.name2_1=C1orf175;refseq.name2_2=C1orf175;refseq.name_1=NR_026782;refseq.name_2=NM_001039464;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.Y306D;refseq.referenceAA_2=Tyr;refseq.referenceCodon_2=TAT;refseq.spliceDist_1=-316;refseq.spliceDist_2=-316;refseq.start_1=54892103;refseq.start_2=54892103;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Asp;refseq.variantCodon_2=GAT;set=Intersection GT 1/1
|
|
chr1 54892134 . A G 91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=507;Dels=0.00;HRun=1;HaplotypeScore=6.09;MQ=98.35;MQ0=0;OQ=19762.37;QD=38.98;RankSumP=1.00000;SB=-9098.59;SecondBestBaseQ=10;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.947A>G;refseq.codonCoord_2=316;refseq.end_1=54892134;refseq.end_2=54892134;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1265;refseq.mrnaCoord_2=1271;refseq.name2_1=C1orf175;refseq.name2_2=C1orf175;refseq.name_1=NR_026782;refseq.name_2=NM_001039464;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.E316G;refseq.referenceAA_2=Glu;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-285;refseq.spliceDist_2=-285;refseq.start_1=54892134;refseq.start_2=54892134;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=Intersection GT 1/1
|
|
chr1 54909117 . T C 429.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=129;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=98.95;MQ0=0;OQ=4680.70;QD=36.28;RankSumP=1.00000;SB=-2146.81;SecondBestBaseQ=35;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1526T>C;refseq.codonCoord_2=509;refseq.end_1=54909117;refseq.end_2=54909117;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1844;refseq.mrnaCoord_2=1850;refseq.name2_1=C1orf175;refseq.name2_2=C1orf175;refseq.name_1=NR_026782;refseq.name_2=NM_001039464;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V509A;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=57;refseq.spliceDist_2=57;refseq.start_1=54909117;refseq.start_2=54909117;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ala;refseq.variantCodon_2=GCG;set=Intersection GT 1/1
|
|
chr1 54912329 . A G 455.35 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=224;Dels=0.00;HRun=0;HaplotypeScore=2.50;MQ=98.64;MQ0=0;OQ=8544.73;QD=38.15;RankSumP=1.00000;SB=-2236.42;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1853A>G;refseq.codonCoord_2=618;refseq.end_1=54912329;refseq.end_2=54912329;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2187;refseq.mrnaCoord_2=2177;refseq.name2_1=C1orf175;refseq.name2_2=C1orf175;refseq.name_1=NR_026782;refseq.name_2=NM_001039464;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.H618R;refseq.referenceAA_2=His;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=69;refseq.spliceDist_2=53;refseq.start_1=54912329;refseq.start_2=54912329;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Arg;refseq.variantCodon_2=CGC;set=Intersection GT 1/1
|
|
chr1 54939430 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=209;Dels=0.00;HRun=1;HaplotypeScore=8.06;MQ=98.94;MQ0=0;OQ=4749.51;QD=22.72;RankSumP=0.378584;SB=-1956.88;SecondBestBaseQ=31;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.3132C>T;refseq.codonCoord_2=1044;refseq.end_1=54939430;refseq.end_2=54939430;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3466;refseq.mrnaCoord_2=3456;refseq.name2_1=C1orf175;refseq.name2_2=C1orf175;refseq.name_1=NR_026782;refseq.name_2=NM_001039464;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.P1044P;refseq.referenceAA_2=Pro;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=27;refseq.spliceDist_2=27;refseq.start_1=54939430;refseq.start_2=54939430;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCT;set=Intersection GT 0/1
|
|
chr1 54940361 . T A 338.45 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=168;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.81;MQ0=0;OQ=6331.12;QD=37.69;RankSumP=1.00000;SB=-2443.30;SecondBestBaseQ=2;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.3296T>A;refseq.codonCoord_2=1099;refseq.end_1=54940361;refseq.end_2=54940361;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3630;refseq.mrnaCoord_2=3620;refseq.name2_1=C1orf175;refseq.name2_2=C1orf175;refseq.name_1=NR_026782;refseq.name_2=NM_001039464;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V1099D;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=11;refseq.spliceDist_2=11;refseq.start_1=54940361;refseq.start_2=54940361;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Asp;refseq.variantCodon_2=GAC;set=Intersection GT 1/1
|
|
chr1 54954888 . T A 294.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=268;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=98.34;MQ0=0;OQ=5795.59;QD=21.63;RankSumP=0.393908;SB=-2391.88;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.139T>A;refseq.codonCoord=47;refseq.end=54954888;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=192;refseq.name=NM_004623;refseq.name2=TTC4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S47T;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=28;refseq.start=54954888;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/0
|
|
chr1 54979673 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1063T>G;refseq.codonCoord=355;refseq.end=54979673;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1116;refseq.name=NM_004623;refseq.name2=TTC4;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y355D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=54979673;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT 1/0
|
|
chr1 54996719 . T C 299.39 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=137;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=97.94;MQ0=0;OQ=2215.61;QD=16.17;RankSumP=0.138752;SB=-1124.20;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.704A>G;refseq.codonCoord=235;refseq.end=54996719;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=787;refseq.name=NM_152268;refseq.name2=PARS2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N235S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=733;refseq.start=54996719;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/0
|
|
chr1 54997339 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=100;Dels=0.00;HRun=3;HaplotypeScore=20.07;MQ=98.23;MQ0=0;OQ=1409.80;QD=14.10;RankSumP=0.121321;SB=-671.38;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.84G>T;refseq.codonCoord=28;refseq.end=54997339;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=167;refseq.name=NM_152268;refseq.name2=PARS2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R28S;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=113;refseq.start=54997339;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/0
|
|
chr1 55024277 . T C 272.66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=96.78;MQ0=0;OQ=3026.35;QD=35.19;RankSumP=1.00000;SB=-1049.05;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.987A>G;refseq.codingCoordStr_2=c.987A>G;refseq.codonCoord_1=329;refseq.codonCoord_2=329;refseq.end_1=55024277;refseq.end_2=55024277;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1092;refseq.mrnaCoord_2=1092;refseq.name2_1=TTC22;refseq.name2_2=TTC22;refseq.name_1=NM_001114108;refseq.name_2=NM_017904;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E329E;refseq.proteinCoordStr_2=p.E329E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=-34;refseq.spliceDist_2=-34;refseq.start_1=55024277;refseq.start_2=55024277;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 1/1
|
|
chr1 55046168 . G T 351.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=2066.24;QD=39.74;RankSumP=1.00000;SB=-421.26;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.376G>T;refseq.codingCoordStr_2=c.376G>T;refseq.codonCoord_1=126;refseq.codonCoord_2=126;refseq.end_1=55046168;refseq.end_2=55046168;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=430;refseq.mrnaCoord_2=430;refseq.name2_1=C1orf177;refseq.name2_2=C1orf177;refseq.name_1=NM_001110533;refseq.name_2=NM_152607;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G126C;refseq.proteinCoordStr_2=p.G126C;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=19;refseq.spliceDist_2=19;refseq.start_1=55046168;refseq.start_2=55046168;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=Intersection GT 1/1
|
|
chr1 55050187 . T C 340.60 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=223;Dels=0.00;HRun=0;HaplotypeScore=4.13;MQ=98.26;MQ0=0;OQ=8393.78;QD=37.64;RankSumP=1.00000;SB=-4034.60;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.613T>C;refseq.codingCoordStr_2=c.613T>C;refseq.codonCoord_1=205;refseq.codonCoord_2=205;refseq.end_1=55050187;refseq.end_2=55050187;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=667;refseq.mrnaCoord_2=667;refseq.name2_1=C1orf177;refseq.name2_2=C1orf177;refseq.name_1=NM_001110533;refseq.name_2=NM_152607;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y205H;refseq.proteinCoordStr_2=p.Y205H;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAT;refseq.referenceCodon_2=TAT;refseq.spliceDist_1=-6;refseq.spliceDist_2=-6;refseq.spliceInfo_1=splice-donor_-6;refseq.spliceInfo_2=splice-donor_-6;refseq.start_1=55050187;refseq.start_2=55050187;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAT;refseq.variantCodon_2=CAT;set=Intersection GT 1/1
|
|
chr1 55092490 . A G 390.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=182;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=98.74;MQ0=0;OQ=7384.60;QD=40.57;RankSumP=1.00000;SB=-1967.23;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1026T>C;refseq.codonCoord=342;refseq.end=55092490;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1155;refseq.name=NM_014762;refseq.name2=DHCR24;refseq.positionType=CDS;refseq.proteinCoordStr=p.I342I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=55092490;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 55230298 . G A 296.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.31;MQ0=0;OQ=2185.50;QD=40.47;RankSumP=1.00000;SB=-948.71;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.567G>A;refseq.codonCoord=189;refseq.end=55230298;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=841;refseq.name=NM_182532;refseq.name2=TMEM61;refseq.positionType=CDS;refseq.proteinCoordStr=p.A189A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=202;refseq.start=55230298;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 55295621 . A G 65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=24;DB;DP=210;Dels=0.00;HRun=1;HaplotypeScore=10.43;MQ=98.70;MQ0=0;OQ=6019.74;QD=28.67;RankSumP=1.00000;SB=-1239.77;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1026A>G;refseq.codonCoord=342;refseq.end=55295621;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1317;refseq.name=NM_174936;refseq.name2=PCSK9;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q342Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=30;refseq.start=55295621;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 55295623 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1028A>C;refseq.codonCoord=343;refseq.end=55295623;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1319;refseq.name=NM_174936;refseq.name2=PCSK9;refseq.positionType=CDS;refseq.proteinCoordStr=p.D343A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=32;refseq.start=55295623;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 55296785 . A G 283.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=329;Dels=0.00;HRun=0;HaplotypeScore=8.47;MQ=98.34;MQ0=0;OQ=12534.44;QD=38.10;RankSumP=1.00000;SB=-6191.47;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1380A>G;refseq.codonCoord=460;refseq.end=55296785;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1671;refseq.name=NM_174936;refseq.name2=PCSK9;refseq.positionType=CDS;refseq.proteinCoordStr=p.V460V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=26;refseq.start=55296785;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 55296825 . G A 317.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=205;Dels=0.00;HRun=0;HaplotypeScore=5.12;MQ=98.18;MQ0=0;OQ=7431.09;QD=36.25;RankSumP=1.00000;SB=-1605.73;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1420G>A;refseq.codonCoord=474;refseq.end=55296825;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1711;refseq.name=NM_174936;refseq.name2=PCSK9;refseq.positionType=CDS;refseq.proteinCoordStr=p.V474I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=66;refseq.start=55296825;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 55301775 . G A 98.78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=23;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=7.64;MQ=97.84;MQ0=0;OQ=2325.67;QD=29.44;RankSumP=1.00000;SB=-880.14;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2009G>A;refseq.codonCoord=670;refseq.end=55301775;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2300;refseq.name=NM_174936;refseq.name2=PCSK9;refseq.positionType=CDS;refseq.proteinCoordStr=p.G670E;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=146;refseq.start=55301775;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 56775215 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=773;Dels=0.00;HRun=0;HaplotypeScore=20.77;MQ=98.63;MQ0=0;OQ=15086.21;QD=19.52;RankSumP=0.0519103;SB=-3750.46;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.297G>A;refseq.codingCoordStr_2=c.297G>A;refseq.codonCoord_1=99;refseq.codonCoord_2=99;refseq.end_1=56775215;refseq.end_2=56775215;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=865;refseq.mrnaCoord_2=798;refseq.name2_1=PPAP2B;refseq.name2_2=PPAP2B;refseq.name_1=NM_003713;refseq.name_2=NM_177414;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A99A;refseq.proteinCoordStr_2=p.A99A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=-1;refseq.spliceDist_2=-1;refseq.spliceInfo_1=splice-donor_-1;refseq.spliceInfo_2=splice-donor_-1;refseq.start_1=56775215;refseq.start_2=56775215;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 0/1
|
|
chr1 56930639 . G A 154.91 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=539;Dels=0.00;HRun=0;HaplotypeScore=6.75;MQ=98.76;MQ0=0;OQ=11080.63;QD=20.56;RankSumP=0.497963;SB=-3759.19;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.351G>A;refseq.codonCoord=117;refseq.end=56930639;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=422;refseq.name=NM_006252;refseq.name2=PRKAA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R117R;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=21;refseq.start=56930639;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/0
|
|
chr1 56992127 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=205;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.40;MQ0=0;OQ=3179.77;QD=15.51;RankSumP=0.400949;SB=-1266.20;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1200G>T;refseq.codonCoord=400;refseq.end=56992127;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1606;refseq.name=NM_001004303;refseq.name2=C1orf168;refseq.positionType=CDS;refseq.proteinCoordStr=p.K400N;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-28;refseq.start=56992127;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 57030405 . T C 267.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=192;Dels=0.00;HRun=0;HaplotypeScore=3.93;MQ=98.59;MQ0=0;OQ=2885.16;QD=15.03;RankSumP=0.235419;SB=-1402.84;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.669A>G;refseq.codonCoord=223;refseq.end=57030405;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1075;refseq.name=NM_001004303;refseq.name2=C1orf168;refseq.positionType=CDS;refseq.proteinCoordStr=p.K223K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-89;refseq.start=57030405;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/0
|
|
chr1 57113315 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=137;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=98.71;MQ0=0;OQ=1663.55;QD=12.14;RankSumP=0.0731497;SB=-494.00;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.277C>A;refseq.codonCoord=93;refseq.end=57113315;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=409;refseq.name=NM_000562;refseq.name2=C8A;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q93K;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-40;refseq.start=57113315;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/0
|
|
chr1 57195072 . C T 403.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=98.90;MQ0=0;OQ=4076.96;QD=43.37;RankSumP=1.00000;SB=-2010.76;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.349G>A;refseq.codonCoord=117;refseq.end=57195072;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=416;refseq.name=NM_000066;refseq.name2=C8B;refseq.positionType=CDS;refseq.proteinCoordStr=p.G117R;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-43;refseq.start=57195072;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/1
|
|
chr1 57253547 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1041T>C;refseq.codonCoord=347;refseq.end=57253547;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1715;refseq.name=NM_021080;refseq.name2=DAB1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F347F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=146;refseq.start=57253547;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=FilteredInAll GT 0/1
|
|
chr1 58744419 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=149;Dels=0.00;HRun=2;HaplotypeScore=2.00;MQ=98.76;MQ0=0;OQ=2338.74;QD=15.70;RankSumP=0.106697;SB=-590.85;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1266C>T;refseq.codonCoord=422;refseq.end=58744419;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1354;refseq.name=NM_145243;refseq.name2=OMA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F422F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=51;refseq.start=58744419;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/0
|
|
chr1 58772300 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=346;Dels=0.00;HRun=4;HaplotypeScore=7.91;MQ=98.99;MQ0=0;OQ=6095.79;QD=17.62;RankSumP=0.374306;SB=-1910.80;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.924C>T;refseq.codonCoord=308;refseq.end=58772300;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1012;refseq.name=NM_145243;refseq.name2=OMA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F308F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=21;refseq.start=58772300;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/0
|
|
chr1 58814769 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=95.87;MQ0=0;OQ=469.23;QD=9.78;RankSumP=0.354648;SB=-208.42;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.648C>A;refseq.codonCoord=216;refseq.end=58814769;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=986;refseq.name=NM_002353;refseq.name2=TACSTD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D216E;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=986;refseq.start=58814769;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 58814976 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=7.34;MQ=98.69;MQ0=0;OQ=1284.00;QD=20.71;RankSumP=0.342232;SB=-639.22;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.441G>C;refseq.codonCoord=147;refseq.end=58814976;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=779;refseq.name=NM_002353;refseq.name2=TACSTD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.E147D;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=779;refseq.start=58814976;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/0
|
|
chr1 58915301 . T C 210.91 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=445;Dels=0.00;HRun=0;HaplotypeScore=13.73;MQ=98.73;MQ0=0;OQ=8342.91;QD=18.75;RankSumP=0.393157;SB=-2986.64;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1275A>G;refseq.codonCoord=425;refseq.end=58915301;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1298;refseq.name=NM_001085487;refseq.name2=MYSM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P425P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=16;refseq.start=58915301;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/0
|
|
chr1 58920514 . T C 266.39 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=401;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=98.84;MQ0=0;OQ=7807.82;QD=19.47;RankSumP=0.113658;SB=-2878.39;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.790A>G;refseq.codonCoord=264;refseq.end=58920514;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=813;refseq.name=NM_001085487;refseq.name2=MYSM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T264A;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=292;refseq.start=58920514;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/0
|
|
chr1 59617059 . G A 291.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=333;Dels=0.00;HRun=0;HaplotypeScore=7.70;MQ=98.33;MQ0=0;OQ=14023.04;QD=42.11;RankSumP=1.00000;SB=-5917.87;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.516G>A;refseq.codingCoordStr_2=c.516G>A;refseq.codonCoord_1=172;refseq.codonCoord_2=172;refseq.end_1=59617059;refseq.end_2=59617059;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=728;refseq.mrnaCoord_2=728;refseq.name2_1=FGGY;refseq.name2_2=FGGY;refseq.name_1=NM_001113411;refseq.name_2=NM_018291;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P172P;refseq.proteinCoordStr_2=p.P172P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=-39;refseq.spliceDist_2=-39;refseq.start_1=59617059;refseq.start_2=59617059;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=Intersection GT 1/1
|
|
chr1 60276350 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=98.62;MQ0=0;OQ=699.40;QD=6.86;RankSumP=0.452853;SB=-86.88;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.765A>G;refseq.codonCoord=255;refseq.end=60276350;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=857;refseq.name=NM_152377;refseq.name2=C1orf87;refseq.positionType=CDS;refseq.proteinCoordStr=p.L255L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=18;refseq.start=60276350;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/0
|
|
chr1 62004619 . C T 149.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=312;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=97.52;MQ0=0;OQ=13057.53;QD=41.85;RankSumP=1.00000;SB=-5943.10;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.270C>T;refseq.codonCoord=90;refseq.end=62004619;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=384;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.I90I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=81;refseq.start=62004619;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/1
|
|
chr1 62004718 . T C 270.05 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=318;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.91;MQ0=0;OQ=13420.67;QD=42.20;RankSumP=1.00000;SB=-4428.44;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.369T>C;refseq.codonCoord=123;refseq.end=62004718;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=483;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.I123I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-16;refseq.start=62004718;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 62033756 . A G 445.61 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=166;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=98.83;MQ0=0;OQ=7003.03;QD=42.19;RankSumP=1.00000;SB=-2580.70;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1198A>G;refseq.codonCoord=400;refseq.end=62033756;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1312;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.I400V;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=30;refseq.start=62033756;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/1
|
|
chr1 62102668 . T G 303.66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=274;Dels=0.00;HRun=0;HaplotypeScore=7.91;MQ=98.70;MQ0=0;OQ=11282.30;QD=41.18;RankSumP=1.00000;SB=-5257.19;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2610T>G;refseq.codonCoord=870;refseq.end=62102668;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2724;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.I870M;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=171;refseq.start=62102668;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/1
|
|
chr1 62152858 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=97.96;MQ0=0;OQ=625.81;QD=12.52;RankSumP=0.491674;SB=-184.20;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3504C>T;refseq.codonCoord=1168;refseq.end=62152858;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3618;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1168N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=12;refseq.start=62152858;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 62152886 . G A 176.81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.11;MQ0=0;OQ=893.85;QD=15.41;RankSumP=0.408570;SB=-461.80;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3532G>A;refseq.codonCoord=1178;refseq.end=62152886;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3646;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1178S;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-39;refseq.start=62152886;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/0
|
|
chr1 62228602 . G A 317.87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=239;Dels=0.00;HRun=0;HaplotypeScore=6.94;MQ=98.80;MQ0=0;OQ=4815.13;QD=20.15;RankSumP=0.477350;SB=-1117.04;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3845G>A;refseq.codonCoord=1282;refseq.end=62228602;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3959;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1282H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-23;refseq.start=62228602;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 62289271 . G C 202.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=293;Dels=0.00;HRun=1;HaplotypeScore=9.26;MQ=98.84;MQ0=0;OQ=5704.53;QD=19.47;RankSumP=0.106176;SB=-1624.45;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4078G>C;refseq.codonCoord=1360;refseq.end=62289271;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4192;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1360L;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=46;refseq.start=62289271;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 0/1
|
|
chr1 62352337 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4486T>C;refseq.codonCoord=1496;refseq.end=62352337;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4600;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1496P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=25;refseq.start=62352337;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 62352395 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4544T>G;refseq.codonCoord=1515;refseq.end=62352395;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4658;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1515G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=83;refseq.start=62352395;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 62352411 . G A 151.73 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=185;Dels=0.00;HRun=1;HaplotypeScore=6.93;MQ=98.57;MQ0=0;OQ=3205.42;QD=17.33;RankSumP=0.455850;SB=-685.73;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4560G>A;refseq.codonCoord=1520;refseq.end=62352411;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4674;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1520E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-96;refseq.start=62352411;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/0
|
|
chr1 62367181 . C T 249.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=476;Dels=0.00;HRun=0;HaplotypeScore=15.27;MQ=98.76;MQ0=0;OQ=7761.33;QD=16.31;RankSumP=0.0174016;SB=-1641.02;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5247C>T;refseq.codonCoord=1749;refseq.end=62367181;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5361;refseq.name=NM_176877;refseq.name2=INADL;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1749N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-25;refseq.start=62367181;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 62445134 . G A 295.21 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=3228.29;QD=42.48;RankSumP=1.00000;SB=-232.78;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.246G>A;refseq.codingCoordStr_2=c.246G>A;refseq.codonCoord_1=82;refseq.codonCoord_2=82;refseq.end_1=62445134;refseq.end_2=62445134;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=681;refseq.mrnaCoord_2=570;refseq.name2_1=L1TD1;refseq.name2_2=L1TD1;refseq.name_1=NM_001164835;refseq.name_2=NM_019079;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G82G;refseq.proteinCoordStr_2=p.G82G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=356;refseq.spliceDist_2=356;refseq.start_1=62445134;refseq.start_2=62445134;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;set=Intersection GT 1/1
|
|
chr1 62448207 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.86;MQ0=0;OQ=557.03;QD=11.60;RankSumP=0.198487;SB=-282.10;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1173C>T;refseq.codingCoordStr_2=c.1173C>T;refseq.codonCoord_1=391;refseq.codonCoord_2=391;refseq.end_1=62448207;refseq.end_2=62448207;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1608;refseq.mrnaCoord_2=1497;refseq.name2_1=L1TD1;refseq.name2_2=L1TD1;refseq.name_1=NM_001164835;refseq.name_2=NM_019079;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A391A;refseq.proteinCoordStr_2=p.A391A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=165;refseq.spliceDist_2=165;refseq.start_1=62448207;refseq.start_2=62448207;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=Intersection GT 0/1
|
|
chr1 62448480 . A G 223.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=223;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.10;MQ0=0;OQ=9006.63;QD=40.39;RankSumP=1.00000;SB=-2995.30;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1446A>G;refseq.codingCoordStr_2=c.1446A>G;refseq.codonCoord_1=482;refseq.codonCoord_2=482;refseq.end_1=62448480;refseq.end_2=62448480;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1881;refseq.mrnaCoord_2=1770;refseq.name2_1=L1TD1;refseq.name2_2=L1TD1;refseq.name_1=NM_001164835;refseq.name_2=NM_019079;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E482E;refseq.proteinCoordStr_2=p.E482E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=438;refseq.spliceDist_2=438;refseq.start_1=62448480;refseq.start_2=62448480;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 1/1
|
|
chr1 62485812 . C G 236.34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=223;Dels=0.00;HRun=0;HaplotypeScore=5.29;MQ=98.37;MQ0=0;OQ=9794.84;QD=43.92;RankSumP=1.00000;SB=-2648.91;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2803G>C;refseq.codonCoord=935;refseq.end=62485812;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3180;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V935L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-81;refseq.start=62485812;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 62485834 . G A 259.92 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=179;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=98.80;MQ0=0;OQ=2873.79;QD=16.05;RankSumP=0.457139;SB=-915.24;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2781C>T;refseq.codonCoord=927;refseq.end=62485834;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3158;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H927H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=99;refseq.start=62485834;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 62501372 . A G 343.94 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=0.52;MQ=99.00;MQ0=0;OQ=3589.08;QD=35.54;RankSumP=1.00000;SB=-772.98;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2519T>C;refseq.codonCoord=840;refseq.end=62501372;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2896;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V840A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-21;refseq.start=62501372;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 62501426 . T C 354.95 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=168;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.52;MQ0=0;OQ=6052.84;QD=36.03;RankSumP=1.00000;SB=-2426.30;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2465A>G;refseq.codonCoord=822;refseq.end=62501426;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2842;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H822R;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-75;refseq.start=62501426;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/1
|
|
chr1 62501449 . T C 274.51 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=7.56;MQ=98.48;MQ0=0;OQ=5862.19;QD=37.58;RankSumP=1.00000;SB=-2565.97;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2442A>G;refseq.codonCoord=814;refseq.end=62501449;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2819;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.K814K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-98;refseq.start=62501449;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 62501506 . G A 373.41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=154;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=98.34;MQ0=0;OQ=5876.00;QD=38.16;RankSumP=1.00000;SB=-2184.34;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2385C>T;refseq.codonCoord=795;refseq.end=62501506;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2762;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P795P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=66;refseq.start=62501506;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 62505009 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=202;Dels=0.00;HRun=0;HaplotypeScore=12.97;MQ=97.92;MQ0=0;OQ=1840.93;QD=9.11;RankSumP=0.454168;SB=-893.93;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2302A>G;refseq.codonCoord=768;refseq.end=62505009;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2679;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.T768A;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-18;refseq.start=62505009;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/0
|
|
chr1 62511492 . T C 130.49 PASS AC=2;AF=1.00;AN=2;BestBaseQ=23;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=97.27;MQ0=0;OQ=804.50;QD=23.66;RankSumP=1.00000;SB=-388.51;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1872A>G;refseq.codonCoord=624;refseq.end=62511492;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2249;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P624P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-29;refseq.start=62511492;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 62511786 . G A 167.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=161;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=98.62;MQ0=0;OQ=2471.61;QD=15.35;RankSumP=0.351479;SB=-1259.65;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1578C>T;refseq.codonCoord=526;refseq.end=62511786;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1955;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S526S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-323;refseq.start=62511786;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/0
|
|
chr1 62512653 . A G 107.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=99.00;MQ0=0;OQ=1625.40;QD=12.22;RankSumP=0.313284;SB=-705.39;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.711T>C;refseq.codonCoord=237;refseq.end=62512653;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1088;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G237G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=695;refseq.start=62512653;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 62512728 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.636T>G;refseq.codonCoord=212;refseq.end=62512728;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1013;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G212G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=620;refseq.start=62512728;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 62513034 . T C 321.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.27;MQ=98.83;MQ0=0;OQ=1657.10;QD=35.26;RankSumP=1.00000;SB=-335.47;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.330A>G;refseq.codonCoord=110;refseq.end=62513034;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=707;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P110P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=314;refseq.start=62513034;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 62513037 . T C 261.10 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.88;MQ0=0;OQ=1373.66;QD=34.34;RankSumP=1.00000;SB=-272.78;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.327A>G;refseq.codonCoord=109;refseq.end=62513037;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=704;refseq.name=NM_181712;refseq.name2=KANK4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S109S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=311;refseq.start=62513037;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/1
|
|
chr1 62695807 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6277A>C;refseq.codonCoord=2093;refseq.end=62695807;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6311;refseq.name=NM_033407;refseq.name2=DOCK7;refseq.positionType=CDS;refseq.proteinCoordStr=p.T2093P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-11;refseq.start=62695807;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 62725658 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=3;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5414A>G;refseq.codonCoord=1805;refseq.end=62725658;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5448;refseq.name=NM_033407;refseq.name2=DOCK7;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1805G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-2;refseq.spliceInfo=splice-donor_-2;refseq.start=62725658;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 63561676 . C T 3 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=89.89;MQ0=0;OQ=66.77;QD=9.54;RankSumP=0.200000;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.359C>T;refseq.codonCoord=120;refseq.end=63561676;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=359;refseq.name=NM_012183;refseq.name2=FOXD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P120L;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=359;refseq.start=63561676;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=filterInsoap-gatk GT 0/1
|
|
chr1 63650226 . C T 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=563;Dels=0.00;HRun=2;HaplotypeScore=57.36;MQ=98.36;MQ0=0;OQ=316.64;QD=0.56;RankSumP=0.00000;SB=817.73;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.722C>T;refseq.codonCoord=241;refseq.end=63650226;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1027;refseq.name=NM_013339;refseq.name2=ALG6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S241F;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=42;refseq.start=63650226;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=FilteredInAll GT 0/1
|
|
chr1 64247576 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.00000;SecondBestBaseQ=19;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.103T>G;refseq.codingCoordStr_2=c.103T>G;refseq.codonCoord_1=35;refseq.codonCoord_2=35;refseq.end_1=64247576;refseq.end_2=64247576;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=502;refseq.mrnaCoord_2=502;refseq.name2_1=ROR1;refseq.name2_2=ROR1;refseq.name_1=NM_001083592;refseq.name_2=NM_005012;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S35A;refseq.proteinCoordStr_2=p.S35A;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.start_1=64247576;refseq.start_2=64247576;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=FilteredInAll GT 1/0
|
|
chr1 64287967 . C T 338.46 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=139;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=98.54;MQ0=0;OQ=5821.93;QD=41.88;RankSumP=1.00000;SB=-2848.63;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.180C>T;refseq.codingCoordStr_2=c.180C>T;refseq.codonCoord_1=60;refseq.codonCoord_2=60;refseq.end_1=64287967;refseq.end_2=64287967;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=579;refseq.mrnaCoord_2=579;refseq.name2_1=ROR1;refseq.name2_2=ROR1;refseq.name_1=NM_001083592;refseq.name_2=NM_005012;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L60L;refseq.proteinCoordStr_2=p.L60L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.spliceDist_1=17;refseq.spliceDist_2=17;refseq.start_1=64287967;refseq.start_2=64287967;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;set=Intersection GT 1/1
|
|
chr1 64380917 . G T 254.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=123;Dels=0.00;HRun=1;HaplotypeScore=2.05;MQ=98.86;MQ0=0;OQ=4871.40;QD=39.60;RankSumP=1.00000;SB=-2371.12;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1170G>T;refseq.codingCoordStr_2=c.1170G>T;refseq.codonCoord_1=390;refseq.codonCoord_2=390;refseq.end_1=64380917;refseq.end_2=64380917;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1569;refseq.mrnaCoord_2=1569;refseq.name2_1=ROR1;refseq.name2_2=ROR1;refseq.name_1=NM_001083592;refseq.name_2=NM_005012;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A390A;refseq.proteinCoordStr_2=p.A390A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=242;refseq.spliceDist_2=-5;refseq.spliceInfo_2=splice-donor_-5;refseq.start_1=64380917;refseq.start_2=64380917;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=Intersection GT 1/1
|
|
chr1 64397430 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=559;Dels=0.00;HRun=1;HaplotypeScore=5.07;MQ=98.73;MQ0=0;OQ=11854.39;QD=21.21;RankSumP=0.307908;SB=-4106.80;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1353A>G;refseq.codonCoord=451;refseq.end=64397430;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1752;refseq.name=NM_005012;refseq.name2=ROR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V451V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-34;refseq.start=64397430;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 0/1
|
|
chr1 64415865 . C T 250.39 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=127;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=98.85;MQ0=0;OQ=2240.33;QD=17.64;RankSumP=0.0876082;SB=-652.62;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1553C>T;refseq.codonCoord=518;refseq.end=64415865;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1952;refseq.name=NM_005012;refseq.name2=ROR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T518M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=167;refseq.start=64415865;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 64416381 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2069T>C;refseq.codonCoord=690;refseq.end=64416381;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2468;refseq.name=NM_005012;refseq.name2=ROR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L690P;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=683;refseq.start=64416381;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 64870897 . G A 263.59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=279;Dels=0.00;HRun=0;HaplotypeScore=9.59;MQ=98.77;MQ0=0;OQ=5541.98;QD=19.86;RankSumP=0.359604;SB=-2180.11;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.519G>A;refseq.codonCoord=173;refseq.end=64870897;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=624;refseq.name=NM_020925;refseq.name2=CACHD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P173P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=28;refseq.start=64870897;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/0
|
|
chr1 64886156 . T C 310.23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=214;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=98.78;MQ0=0;OQ=8144.17;QD=38.06;RankSumP=1.00000;SB=-3978.28;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1088T>C;refseq.codonCoord=363;refseq.end=64886156;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1193;refseq.name=NM_020925;refseq.name2=CACHD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M363T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=85;refseq.start=64886156;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 64917924 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=3;RankSumP=1.05340e-09;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3150A>G;refseq.codonCoord=1050;refseq.end=64917924;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3255;refseq.name=NM_020925;refseq.name2=CACHD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1050G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=59;refseq.start=64917924;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 64919583 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3308A>C;refseq.codonCoord=1103;refseq.end=64919583;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3413;refseq.name=NM_020925;refseq.name2=CACHD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1103A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-24;refseq.start=64919583;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 64929708 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=400;Dels=0.00;HRun=0;HaplotypeScore=11.72;MQ=98.79;MQ0=0;OQ=6801.91;QD=17.00;RankSumP=0.468438;SB=-2535.42;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3548C>G;refseq.codonCoord=1183;refseq.end=64929708;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3653;refseq.name=NM_020925;refseq.name2=CACHD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1183R;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=115;refseq.start=64929708;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/0
|
|
chr1 65083802 . G C 235.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=99.00;MQ0=0;OQ=2063.71;QD=17.20;RankSumP=0.0913991;SB=-492.83;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2097C>G;refseq.codonCoord=699;refseq.end=65083802;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2346;refseq.name=NM_002227;refseq.name2=JAK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A699A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-19;refseq.start=65083802;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 0/1
|
|
chr1 65093838 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=98.98;MQ0=0;OQ=1310.45;QD=14.72;RankSumP=0.126292;SB=-631.60;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1590C>T;refseq.codonCoord=530;refseq.end=65093838;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1839;refseq.name=NM_002227;refseq.name2=JAK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I530I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-59;refseq.start=65093838;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 65107683 . T C 141.04 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=308;Dels=0.00;HRun=2;HaplotypeScore=5.05;MQ=98.79;MQ0=0;OQ=5800.28;QD=18.83;RankSumP=0.0201248;SB=-2332.31;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.546A>G;refseq.codonCoord=182;refseq.end=65107683;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=795;refseq.name=NM_002227;refseq.name2=JAK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G182G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=63;refseq.start=65107683;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 1/0
|
|
chr1 65457136 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=276;Dels=0.00;HRun=2;HaplotypeScore=7.47;MQ=69.03;MQ0=125;OQ=2770.68;QD=10.04;RankSumP=0.195058;SB=-1406.99;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.377G>C;refseq.codingCoordStr_2=c.377G>C;refseq.codingCoordStr_3=c.377G>C;refseq.codonCoord_1=126;refseq.codonCoord_2=126;refseq.codonCoord_3=126;refseq.end_1=65457136;refseq.end_2=65457136;refseq.end_3=65457136;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=735;refseq.mrnaCoord_2=582;refseq.mrnaCoord_3=624;refseq.name2_1=AK3L1;refseq.name2_2=AK3L1;refseq.name2_3=AK3L1;refseq.name_1=NM_001005353;refseq.name_2=NM_013410;refseq.name_3=NM_203464;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R126P;refseq.proteinCoordStr_2=p.R126P;refseq.proteinCoordStr_3=p.R126P;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGT;refseq.referenceCodon_2=CGT;refseq.referenceCodon_3=CGT;refseq.spliceDist_1=-62;refseq.spliceDist_2=-62;refseq.spliceDist_3=-62;refseq.start_1=65457136;refseq.start_2=65457136;refseq.start_3=65457136;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;set=Intersection GT 0/1
|
|
chr1 65831101 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=294;Dels=0.00;HRun=1;HaplotypeScore=16.25;MQ=98.94;MQ0=0;OQ=4882.80;QD=16.61;RankSumP=0.389835;SB=-1714.68;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.668A>G;refseq.codingCoordStr_2=c.668A>G;refseq.codingCoordStr_3=c.668A>G;refseq.codonCoord_1=223;refseq.codonCoord_2=223;refseq.codonCoord_3=223;refseq.end_1=65831101;refseq.end_2=65831101;refseq.end_3=65831101;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=940;refseq.mrnaCoord_2=940;refseq.mrnaCoord_3=940;refseq.name2_1=LEPR;refseq.name2_2=LEPR;refseq.name2_3=LEPR;refseq.name_1=NM_001003679;refseq.name_2=NM_001003680;refseq.name_3=NM_002303;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Q223R;refseq.proteinCoordStr_2=p.Q223R;refseq.proteinCoordStr_3=p.Q223R;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.referenceCodon_3=CAG;refseq.spliceDist_1=-36;refseq.spliceDist_2=-36;refseq.spliceDist_3=-36;refseq.start_1=65831101;refseq.start_2=65831101;refseq.start_3=65831101;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;set=Intersection GT 0/1
|
|
chr1 65839697 . T C 213.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=225;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=98.76;MQ0=0;OQ=4126.22;QD=18.34;RankSumP=0.0957636;SB=-1575.96;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1029T>C;refseq.codingCoordStr_2=c.1029T>C;refseq.codingCoordStr_3=c.1029T>C;refseq.codonCoord_1=343;refseq.codonCoord_2=343;refseq.codonCoord_3=343;refseq.end_1=65839697;refseq.end_2=65839697;refseq.end_3=65839697;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1301;refseq.mrnaCoord_2=1301;refseq.mrnaCoord_3=1301;refseq.name2_1=LEPR;refseq.name2_2=LEPR;refseq.name2_3=LEPR;refseq.name_1=NM_001003679;refseq.name_2=NM_001003680;refseq.name_3=NM_002303;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S343S;refseq.proteinCoordStr_2=p.S343S;refseq.proteinCoordStr_3=p.S343S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=AGT;refseq.referenceCodon_2=AGT;refseq.referenceCodon_3=AGT;refseq.spliceDist_1=35;refseq.spliceDist_2=35;refseq.spliceDist_3=35;refseq.start_1=65839697;refseq.start_2=65839697;refseq.start_3=65839697;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;refseq.variantCodon_3=AGC;set=Intersection GT 1/0
|
|
chr1 66603958 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=166;Dels=0.00;HRun=1;HaplotypeScore=5.47;MQ=98.78;MQ0=0;OQ=2666.96;QD=16.07;RankSumP=0.0412149;SB=-266.85;SecondBestBaseQ=26;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.789G>A;refseq.codingCoordStr_2=c.1260G>A;refseq.codingCoordStr_3=c.1305G>A;refseq.codingCoordStr_4=c.1305G>A;refseq.codonCoord_1=263;refseq.codonCoord_2=420;refseq.codonCoord_3=435;refseq.codonCoord_4=435;refseq.end_1=66603958;refseq.end_2=66603958;refseq.end_3=66603958;refseq.end_4=66603958;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1069;refseq.mrnaCoord_2=1460;refseq.mrnaCoord_3=1496;refseq.mrnaCoord_4=1451;refseq.name2_1=PDE4B;refseq.name2_2=PDE4B;refseq.name2_3=PDE4B;refseq.name2_4=PDE4B;refseq.name_1=NM_001037339;refseq.name_2=NM_001037340;refseq.name_3=NM_001037341;refseq.name_4=NM_002600;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.E263E;refseq.proteinCoordStr_2=p.E420E;refseq.proteinCoordStr_3=p.E435E;refseq.proteinCoordStr_4=p.E435E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceAA_4=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.referenceCodon_4=GAG;refseq.spliceDist_1=21;refseq.spliceDist_2=21;refseq.spliceDist_3=21;refseq.spliceDist_4=21;refseq.start_1=66603958;refseq.start_2=66603958;refseq.start_3=66603958;refseq.start_4=66603958;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantAA_4=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;refseq.variantCodon_3=GAA;refseq.variantCodon_4=GAA;set=Intersection GT 1/0
|
|
chr1 66920284 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=1254.05;QD=21.26;RankSumP=0.655570;SB=-543.12;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.959C>T;refseq.codonCoord=320;refseq.end=66920284;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1176;refseq.name=NM_032291;refseq.name2=SGIP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P320L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=145;refseq.start=66920284;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 0/1
|
|
chr1 66927438 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1335A>C;refseq.codonCoord=445;refseq.end=66927438;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1552;refseq.name=NM_032291;refseq.name2=SGIP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R445R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=20;refseq.start=66927438;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=FilteredInAll GT 0/1
|
|
chr1 67008685 . A T 324.44 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=528;Dels=0.00;HRun=0;HaplotypeScore=10.53;MQ=98.62;MQ0=0;OQ=9654.52;QD=18.29;RankSumP=0.312705;SB=-2956.82;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.147A>T;refseq.codonCoord=49;refseq.end=67008685;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=278;refseq.name=NM_152665;refseq.name2=TCTEX1D1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E49D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=28;refseq.start=67008685;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 67014675 . G A 290.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=199;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=98.91;MQ0=0;OQ=4443.82;QD=22.33;RankSumP=0.319434;SB=-1729.64;SecondBestBaseQ=33;refseq.chr=chr1;refseq.codingCoordStr=c.336+1;refseq.end=67014675;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=false;refseq.name=NM_152665;refseq.name2=TCTEX1D1;refseq.positionType=intron;refseq.spliceDist=1;refseq.spliceInfo=splice-donor_1;refseq.start=67014675;refseq.transcriptStrand=+;set=Intersection GT 1/0
|
|
chr1 67015612 . C A 224.83 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=225;Dels=0.00;HRun=1;HaplotypeScore=7.00;MQ=98.91;MQ0=0;OQ=4371.29;QD=19.43;RankSumP=0.295656;SB=-1277.94;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.427C>A;refseq.codonCoord=143;refseq.end=67015612;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=558;refseq.name=NM_152665;refseq.name2=TCTEX1D1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L143I;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=91;refseq.start=67015612;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 67039344 . T A 266.59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=418;Dels=0.00;HRun=0;HaplotypeScore=5.63;MQ=98.88;MQ0=0;OQ=16153.80;QD=38.65;RankSumP=1.00000;SB=-6841.96;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.149A>T;refseq.codonCoord=50;refseq.end=67039344;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=184;refseq.name=NM_005478;refseq.name2=INSL5;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q50L;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-27;refseq.start=67039344;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 67060633 . C T 337.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=356;Dels=0.00;HRun=0;HaplotypeScore=9.60;MQ=99.01;MQ0=0;OQ=6332.46;QD=17.79;RankSumP=0.421031;SB=-1422.71;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2495G>A;refseq.codonCoord=832;refseq.end=67060633;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2551;refseq.name=NM_024763;refseq.name2=WDR78;refseq.positionType=CDS;refseq.proteinCoordStr=p.R832Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-2;refseq.spliceInfo=splice-donor_-2;refseq.start=67060633;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 67163004 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;DB;DP=131;Dels=0.01;HRun=1;HaplotypeScore=16.45;MQ=98.68;MQ0=0;OQ=1412.05;QD=10.78;RankSumP=0.415084;SB=-419.25;SecondBestBaseQ=20;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.99C>G;refseq.codingCoordStr_2=c.99C>G;refseq.codonCoord_1=33;refseq.codonCoord_2=33;refseq.end_1=67163004;refseq.end_2=67163004;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=155;refseq.mrnaCoord_2=155;refseq.name2_1=WDR78;refseq.name2_2=WDR78;refseq.name_1=NM_024763;refseq.name_2=NM_207014;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C33W;refseq.proteinCoordStr_2=p.C33W;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=-72;refseq.spliceDist_2=-72;refseq.start_1=67163004;refseq.start_2=67163004;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Trp;refseq.variantAA_2=Trp;refseq.variantCodon_1=TGG;refseq.variantCodon_2=TGG;set=Intersection GT 0/1
|
|
chr1 67163056 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=107;Dels=0.00;HRun=0;HaplotypeScore=5.40;MQ=97.07;MQ0=0;OQ=1183.61;QD=11.06;RankSumP=0.178709;SB=-496.66;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.47G>C;refseq.codingCoordStr_2=c.47G>C;refseq.codonCoord_1=16;refseq.codonCoord_2=16;refseq.end_1=67163056;refseq.end_2=67163056;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=103;refseq.mrnaCoord_2=103;refseq.name2_1=WDR78;refseq.name2_2=WDR78;refseq.name_1=NM_024763;refseq.name_2=NM_207014;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G16A;refseq.proteinCoordStr_2=p.G16A;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=103;refseq.spliceDist_2=103;refseq.start_1=67163056;refseq.start_2=67163056;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 1/0
|
|
chr1 67331327 . C T 99.52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=3.98;MQ=98.89;MQ0=0;OQ=1800.85;QD=14.07;RankSumP=0.0807533;SB=-452.32;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1152G>A;refseq.codonCoord=384;refseq.end=67331327;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1263;refseq.name=NM_001013674;refseq.name2=C1orf141;refseq.positionType=CDS;refseq.proteinCoordStr=p.T384T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=549;refseq.start=67331327;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 67333544 . C T 263.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=218;Dels=0.00;HRun=1;HaplotypeScore=3.47;MQ=98.88;MQ0=0;OQ=4259.86;QD=19.54;RankSumP=0.412081;SB=-1434.24;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.565G>A;refseq.codonCoord=189;refseq.end=67333544;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=676;refseq.name=NM_001013674;refseq.name2=C1orf141;refseq.positionType=CDS;refseq.proteinCoordStr=p.V189I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-39;refseq.start=67333544;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 0/1
|
|
chr1 67406400 . G T 148.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=397;Dels=0.00;HRun=0;HaplotypeScore=15.59;MQ=98.87;MQ0=0;OQ=15628.11;QD=39.37;RankSumP=1.00000;SB=-3766.14;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.9G>T;refseq.codonCoord=3;refseq.end=67406400;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=94;refseq.name=NM_144701;refseq.name2=IL23R;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q3H;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=38;refseq.start=67406400;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/1
|
|
chr1 67407653 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.111A>C;refseq.codonCoord=37;refseq.end=67407653;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=196;refseq.name=NM_144701;refseq.name2=IL23R;refseq.positionType=CDS;refseq.proteinCoordStr=p.E37D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=41;refseq.start=67407653;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT 0/1
|
|
chr1 67457975 . T C 213.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=309;Dels=0.00;HRun=1;HaplotypeScore=8.31;MQ=98.86;MQ0=0;OQ=11552.71;QD=37.39;RankSumP=1.00000;SB=-4862.20;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.929T>C;refseq.codonCoord=310;refseq.end=67457975;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1014;refseq.name=NM_144701;refseq.name2=IL23R;refseq.positionType=CDS;refseq.proteinCoordStr=p.L310P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-27;refseq.start=67457975;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 67567907 . T C 91.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=351;Dels=0.00;HRun=1;HaplotypeScore=12.51;MQ=98.92;MQ0=0;OQ=13504.09;QD=38.47;RankSumP=1.00000;SB=-6036.42;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.714T>C;refseq.codonCoord=238;refseq.end=67567907;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1354;refseq.name=NM_001559;refseq.name2=IL12RB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S238S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=50;refseq.start=67567907;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 68376174 . C T 136.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=341;Dels=0.00;HRun=0;HaplotypeScore=21.00;MQ=98.93;MQ0=0;OQ=7313.73;QD=21.45;RankSumP=0.0699171;SB=-2746.19;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1393G>A;refseq.codingCoordStr_2=c.1393G>A;refseq.codonCoord_1=465;refseq.codonCoord_2=465;refseq.end_1=68376174;refseq.end_2=68376174;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1677;refseq.mrnaCoord_2=1677;refseq.name2_1=WLS;refseq.name2_2=WLS;refseq.name_1=NM_001002292;refseq.name_2=NM_024911;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V465I;refseq.proteinCoordStr_2=p.V465I;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.start_1=68376174;refseq.start_2=68376174;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;set=Intersection GT 0/1
|
|
chr1 68397466 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=465;Dels=0.00;HRun=0;HaplotypeScore=26.44;MQ=98.94;MQ0=0;OQ=10508.20;QD=22.60;RankSumP=0.275219;SB=-3015.54;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.432G>A;refseq.codingCoordStr_2=c.432G>A;refseq.codonCoord_1=144;refseq.codonCoord_2=144;refseq.end_1=68397466;refseq.end_2=68397466;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=716;refseq.mrnaCoord_2=716;refseq.name2_1=WLS;refseq.name2_2=WLS;refseq.name_1=NM_001002292;refseq.name_2=NM_024911;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A144A;refseq.proteinCoordStr_2=p.A144A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=53;refseq.spliceDist_2=53;refseq.start_1=68397466;refseq.start_2=68397466;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 0/1
|
|
chr1 68669817 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1168A>C;refseq.codonCoord=390;refseq.end=68669817;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1222;refseq.name=NM_000329;refseq.name2=RPE65;refseq.positionType=CDS;refseq.proteinCoordStr=p.T390P;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=40;refseq.start=68669817;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=FilteredInAll GT 1/0
|
|
chr1 68732937 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=93;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=78.17;MQ0=25;OQ=1169.73;QD=12.58;RankSumP=0.586586;SB=-437.95;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.78A>G;refseq.codingCoordStr_2=c.78A>G;refseq.codonCoord_1=26;refseq.codonCoord_2=26;refseq.end_1=68732937;refseq.end_2=68732937;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=195;refseq.mrnaCoord_2=195;refseq.name2_1=DEPDC1;refseq.name2_2=DEPDC1;refseq.name_1=NM_001114120;refseq.name_2=NM_017779;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A26A;refseq.proteinCoordStr_2=p.A26A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=30;refseq.spliceDist_2=30;refseq.start_1=68732937;refseq.start_2=68732937;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/0
|
|
chr1 70232892 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=337;Dels=0.00;HRun=0;HaplotypeScore=4.89;MQ=98.83;MQ0=0;OQ=7899.41;QD=23.44;RankSumP=0.401556;SB=-2880.92;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.878A>G;refseq.codonCoord=293;refseq.end=70232892;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=908;refseq.name=NM_020794;refseq.name2=LRRC7;refseq.positionType=CDS;refseq.proteinCoordStr=p.N293S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-13;refseq.start=70232892;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 70277520 . C A 13 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.500000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3311C>A;refseq.codonCoord=1104;refseq.end=70277520;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3341;refseq.name=NM_020794;refseq.name2=LRRC7;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1104E;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-545;refseq.start=70277520;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=FilteredInAll GT 1/0
|
|
chr1 70277723 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3514T>G;refseq.codonCoord=1172;refseq.end=70277723;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3544;refseq.name=NM_020794;refseq.name2=LRRC7;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y1172D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-342;refseq.start=70277723;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 1/0
|
|
chr1 70384136 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1744G>C;refseq.codonCoord=582;refseq.end=70384136;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1796;refseq.name=NM_017768;refseq.name2=LRRC40;refseq.positionType=CDS;refseq.proteinCoordStr=p.A582P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=41;refseq.start=70384136;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 70470600 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.399T>G;refseq.codonCoord=133;refseq.end=70470600;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=523;refseq.name=NM_004768;refseq.name2=SFRS11;refseq.positionType=CDS;refseq.proteinCoordStr=p.G133G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-49;refseq.start=70470600;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 71104018 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=393;Dels=0.00;HRun=0;HaplotypeScore=61.88;MQ=98.55;MQ0=0;OQ=8188.18;QD=20.84;RankSumP=0.112466;SB=-2004.92;SecondBestBaseQ=30;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.end_1=71192023;refseq.end_2=71192023;refseq.end_3=71250565;refseq.end_4=71107504;refseq.end_5=71107504;refseq.end_6=71104018;refseq.haplotypeAlternate_6=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=*;refseq.haplotypeReference_6=*;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.mrnaCoord_6=1422;refseq.name2_1=PTGER3;refseq.name2_2=PTGER3;refseq.name2_3=PTGER3;refseq.name2_4=PTGER3;refseq.name2_5=PTGER3;refseq.name2_6=PTGER3;refseq.name_1=NM_198714;refseq.name_2=NM_198716;refseq.name_3=NM_198717;refseq.name_4=NR_028292;refseq.name_5=NR_028293;refseq.name_6=NR_028294;refseq.numMatchingRecords=6;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.positionType_4=non_coding_intron;refseq.positionType_5=non_coding_intron;refseq.positionType_6=non_coding_exon;refseq.spliceDist_6=-59;refseq.start_1=71091141;refseq.start_2=71091141;refseq.start_3=71091141;refseq.start_4=71100679;refseq.start_5=71100679;refseq.start_6=71104018;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;set=soap-filterIngatk GT 1/0
|
|
chr1 71104086 . A G 105.15 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=158;Dels=0.00;HRun=2;HaplotypeScore=2.27;MQ=98.98;MQ0=0;OQ=5681.79;QD=35.96;RankSumP=1.00000;SB=-1425.70;SecondBestBaseQ=0;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.end_1=71192023;refseq.end_2=71192023;refseq.end_3=71250565;refseq.end_4=71107504;refseq.end_5=71107504;refseq.end_6=71104086;refseq.haplotypeAlternate_6=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=*;refseq.haplotypeReference_6=*;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.mrnaCoord_6=1354;refseq.name2_1=PTGER3;refseq.name2_2=PTGER3;refseq.name2_3=PTGER3;refseq.name2_4=PTGER3;refseq.name2_5=PTGER3;refseq.name2_6=PTGER3;refseq.name_1=NM_198714;refseq.name_2=NM_198716;refseq.name_3=NM_198717;refseq.name_4=NR_028292;refseq.name_5=NR_028293;refseq.name_6=NR_028294;refseq.numMatchingRecords=6;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.positionType_4=non_coding_intron;refseq.positionType_5=non_coding_intron;refseq.positionType_6=non_coding_exon;refseq.spliceDist_6=19;refseq.start_1=71091141;refseq.start_2=71091141;refseq.start_3=71091141;refseq.start_4=71100679;refseq.start_5=71100679;refseq.start_6=71104086;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;set=Intersection GT 1/1
|
|
chr1 71212615 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.changesAA_9=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.chr_8=chr1;refseq.chr_9=chr1;refseq.codingCoordStr_7=c.1122A>C;refseq.codingCoordStr_8=c.1122A>C;refseq.codingCoordStr_9=c.1122A>C;refseq.codonCoord_7=374;refseq.codonCoord_8=374;refseq.codonCoord_9=374;refseq.end_1=71250565;refseq.end_2=71250565;refseq.end_3=71250565;refseq.end_4=71250565;refseq.end_5=71250565;refseq.end_6=71250565;refseq.end_7=71212615;refseq.end_8=71212615;refseq.end_9=71212615;refseq.frame_7=2;refseq.frame_8=2;refseq.frame_9=2;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.functionalClass_9=missense;refseq.haplotypeAlternate_7=G;refseq.haplotypeAlternate_8=G;refseq.haplotypeAlternate_9=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=*;refseq.haplotypeReference_6=*;refseq.haplotypeReference_7=T;refseq.haplotypeReference_8=T;refseq.haplotypeReference_9=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.inCodingRegion_9=true;refseq.mrnaCoord_7=1353;refseq.mrnaCoord_8=1353;refseq.mrnaCoord_9=1353;refseq.name2_1=PTGER3;refseq.name2_2=PTGER3;refseq.name2_3=PTGER3;refseq.name2_4=PTGER3;refseq.name2_5=PTGER3;refseq.name2_6=PTGER3;refseq.name2_7=PTGER3;refseq.name2_8=PTGER3;refseq.name2_9=PTGER3;refseq.name_1=NM_198717;refseq.name_2=NR_028293;refseq.name_3=NM_198716;refseq.name_4=NM_198718;refseq.name_5=NR_028292;refseq.name_6=NR_028294;refseq.name_7=NM_001126044;refseq.name_8=NM_198714;refseq.name_9=NM_198719;refseq.numMatchingRecords=9;refseq.positionType_1=intron;refseq.positionType_2=non_coding_intron;refseq.positionType_3=intron;refseq.positionType_4=intron;refseq.positionType_5=non_coding_intron;refseq.positionType_6=non_coding_intron;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.positionType_9=CDS;refseq.proteinCoordStr_7=p.L374F;refseq.proteinCoordStr_8=p.L374F;refseq.proteinCoordStr_9=p.L374F;refseq.referenceAA_7=Leu;refseq.referenceAA_8=Leu;refseq.referenceAA_9=Leu;refseq.referenceCodon_7=TTA;refseq.referenceCodon_8=TTA;refseq.referenceCodon_9=TTA;refseq.spliceDist_7=45;refseq.spliceDist_8=45;refseq.spliceDist_9=45;refseq.start_1=71091141;refseq.start_2=71107601;refseq.start_3=71192071;refseq.start_4=71192071;refseq.start_5=71192071;refseq.start_6=71192071;refseq.start_7=71212615;refseq.start_8=71212615;refseq.start_9=71212615;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.transcriptStrand_7=-;refseq.transcriptStrand_8=-;refseq.transcriptStrand_9=-;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantAA_9=Phe;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC;refseq.variantCodon_9=TTC;set=FilteredInAll GT 1/0
|
|
chr1 71831140 . G A 304.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=210;Dels=0.00;HRun=1;HaplotypeScore=6.50;MQ=98.99;MQ0=0;OQ=8117.06;QD=38.65;RankSumP=1.00000;SB=-2814.07;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.888C>T;refseq.codonCoord=296;refseq.end=71831140;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=988;refseq.name=NM_173808;refseq.name2=NEGR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T296T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-53;refseq.start=71831140;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 72520713 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.53C>G;refseq.codonCoord=18;refseq.end=72520713;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=153;refseq.name=NM_173808;refseq.name2=NEGR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A18G;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-124;refseq.start=72520713;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 74347770 . C T 78.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=103;Dels=0.00;HRun=2;HaplotypeScore=2.00;MQ=98.71;MQ0=0;OQ=4327.25;QD=42.01;RankSumP=1.00000;SB=-1415.75;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.763G>A;refseq.codonCoord=255;refseq.end=74347770;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=955;refseq.name=NM_001105659;refseq.name2=LRRIQ3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A255T;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=56;refseq.start=74347770;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 74438081 . G A 247.08 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=540;Dels=0.00;HRun=0;HaplotypeScore=12.20;MQ=98.61;MQ0=0;OQ=9916.61;QD=18.36;RankSumP=0.0515201;SB=-3712.82;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.228G>A;refseq.codingCoordStr_2=c.228G>A;refseq.codonCoord_1=76;refseq.codonCoord_2=76;refseq.end_1=74438081;refseq.end_2=74438081;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=244;refseq.mrnaCoord_2=265;refseq.name2_1=TNNI3K;refseq.name2_2=FPGT;refseq.name_1=NM_001112808;refseq.name_2=NM_003838;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V76V;refseq.proteinCoordStr_2=p.V76V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-23;refseq.spliceDist_2=-23;refseq.start_1=74438081;refseq.start_2=74438081;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=Intersection GT 1/0
|
|
chr1 74442760 . A G 170.18 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1707.10;QD=14.47;RankSumP=0.370196;SB=-839.47;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.441A>G;refseq.codonCoord_2=147;refseq.end_1=74474363;refseq.end_2=74442760;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=478;refseq.name2_1=TNNI3K;refseq.name2_2=FPGT;refseq.name_1=NM_001112808;refseq.name_2=NM_003838;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.K147K;refseq.referenceAA_2=Lys;refseq.referenceCodon_2=AAA;refseq.spliceDist_2=98;refseq.start_1=74439693;refseq.start_2=74442760;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Lys;refseq.variantCodon_2=AAG;set=Intersection GT 0/1
|
|
chr1 74443662 . C T 123.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=318;Dels=0.00;HRun=0;HaplotypeScore=18.25;MQ=98.79;MQ0=0;OQ=6768.70;QD=21.29;RankSumP=0.000121960;SB=-2670.17;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1343C>T;refseq.codonCoord_2=448;refseq.end_1=74474363;refseq.end_2=74443662;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1380;refseq.name2_1=TNNI3K;refseq.name2_2=FPGT;refseq.name_1=NM_001112808;refseq.name_2=NM_003838;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.P448L;refseq.referenceAA_2=Pro;refseq.referenceCodon_2=CCC;refseq.spliceDist_2=1000;refseq.start_1=74439693;refseq.start_2=74443662;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Leu;refseq.variantCodon_2=CTC;set=filterInsoap-gatk GT 0/1
|
|
chr1 74592336 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1415G>T;refseq.codingCoordStr_2=c.1112G>T;refseq.codonCoord_1=472;refseq.codonCoord_2=371;refseq.end_1=74592336;refseq.end_2=74592336;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1431;refseq.mrnaCoord_2=1163;refseq.name2_1=TNNI3K;refseq.name2_2=TNNI3K;refseq.name_1=NM_001112808;refseq.name_2=NM_015978;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C472F;refseq.proteinCoordStr_2=p.C371F;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=-66;refseq.spliceDist_2=-66;refseq.start_1=74592336;refseq.start_2=74592336;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTT;refseq.variantCodon_2=TTT;set=FilteredInAll GT 0/1
|
|
chr1 74809400 . C T 81 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=592;Dels=0.00;HRun=0;HaplotypeScore=18.19;MQ=98.69;MQ0=0;OQ=24804.92;QD=41.90;RankSumP=1.00000;SB=-7815.39;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4582G>A;refseq.codonCoord=1528;refseq.end=74809400;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4801;refseq.name=NM_001002912;refseq.name2=C1orf173;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1528M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-30;refseq.start=74809400;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/1
|
|
chr1 74809963 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4019T>G;refseq.codonCoord=1340;refseq.end=74809963;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4238;refseq.name=NM_001002912;refseq.name2=C1orf173;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1340G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-593;refseq.start=74809963;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 74810433 . A G 134.92 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=579;Dels=0.00;HRun=0;HaplotypeScore=5.49;MQ=98.77;MQ0=0;OQ=8637.45;QD=14.92;RankSumP=0.397383;SB=-2303.83;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3549T>C;refseq.codonCoord=1183;refseq.end=74810433;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3768;refseq.name=NM_001002912;refseq.name2=C1orf173;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1183S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-1063;refseq.start=74810433;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 74810816 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=471;Dels=0.00;HRun=0;HaplotypeScore=18.27;MQ=98.90;MQ0=0;OQ=10901.54;QD=23.15;RankSumP=0.305954;SB=-4743.07;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3166T>G;refseq.codonCoord=1056;refseq.end=74810816;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3385;refseq.name=NM_001002912;refseq.name2=C1orf173;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1056V;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=948;refseq.start=74810816;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 0/1
|
|
chr1 74870014 . G C 128.06 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=10.78;MQ=98.40;MQ0=0;OQ=7157.76;QD=25.75;RankSumP=0.481032;SB=-2522.85;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.790C>G;refseq.codonCoord=264;refseq.end=74870014;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1009;refseq.name=NM_001002912;refseq.name2=C1orf173;refseq.positionType=CDS;refseq.proteinCoordStr=p.P264A;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-30;refseq.start=74870014;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 74945240 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=658;Dels=0.00;HRun=0;HaplotypeScore=15.69;MQ=98.57;MQ0=0;OQ=14798.45;QD=22.49;RankSumP=0.462434;SB=-5521.39;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.759A>G;refseq.codingCoordStr_2=c.657A>G;refseq.codingCoordStr_3=c.348A>G;refseq.codingCoordStr_4=c.759A>G;refseq.codonCoord_1=253;refseq.codonCoord_2=219;refseq.codonCoord_3=116;refseq.codonCoord_4=253;refseq.end_1=74945240;refseq.end_2=74945240;refseq.end_3=74945240;refseq.end_4=74945240;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1264;refseq.mrnaCoord_2=1123;refseq.mrnaCoord_3=937;refseq.mrnaCoord_4=1225;refseq.name2_1=CRYZ;refseq.name2_2=CRYZ;refseq.name2_3=CRYZ;refseq.name2_4=CRYZ;refseq.name_1=NM_001130042;refseq.name_2=NM_001130043;refseq.name_3=NM_001134759;refseq.name_4=NM_001889;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.E253E;refseq.proteinCoordStr_2=p.E219E;refseq.proteinCoordStr_3=p.E116E;refseq.proteinCoordStr_4=p.E253E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceAA_4=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.referenceCodon_3=GAA;refseq.referenceCodon_4=GAA;refseq.spliceDist_1=27;refseq.spliceDist_2=27;refseq.spliceDist_3=27;refseq.spliceDist_4=27;refseq.start_1=74945240;refseq.start_2=74945240;refseq.start_3=74945240;refseq.start_4=74945240;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantAA_4=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;refseq.variantCodon_3=GAG;refseq.variantCodon_4=GAG;set=Intersection GT 1/0
|
|
chr1 74961427 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=4;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.227T>G;refseq.codingCoordStr_2=c.227T>G;refseq.codingCoordStr_3=c.-21T>G;refseq.codingCoordStr_4=c.227T>G;refseq.codonCoord_1=76;refseq.codonCoord_2=76;refseq.codonCoord_4=76;refseq.end_1=74961427;refseq.end_2=74961427;refseq.end_3=74961427;refseq.end_4=74961427;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=732;refseq.mrnaCoord_2=693;refseq.mrnaCoord_3=569;refseq.mrnaCoord_4=693;refseq.name2_1=CRYZ;refseq.name2_2=CRYZ;refseq.name2_3=CRYZ;refseq.name2_4=CRYZ;refseq.name_1=NM_001130042;refseq.name_2=NM_001130043;refseq.name_3=NM_001134759;refseq.name_4=NM_001889;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=utr5;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.V76G;refseq.proteinCoordStr_2=p.V76G;refseq.proteinCoordStr_4=p.V76G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_4=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_4=GTG;refseq.spliceDist_1=-38;refseq.spliceDist_2=-38;refseq.spliceDist_3=-38;refseq.spliceDist_4=-38;refseq.start_1=74961427;refseq.start_2=74961427;refseq.start_3=74961427;refseq.start_4=74961427;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_4=GGG;set=FilteredInAll GT 0/1
|
|
chr1 74963040 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=463;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=98.62;MQ0=0;OQ=8581.27;QD=18.53;RankSumP=0.00499520;SB=-3610.30;SecondBestBaseQ=34;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.54G>A;refseq.codingCoordStr_3=c.54G>A;refseq.codingCoordStr_4=c.54G>A;refseq.codonCoord_2=18;refseq.codonCoord_3=18;refseq.codonCoord_4=18;refseq.end_1=74971217;refseq.end_2=74963040;refseq.end_3=74963040;refseq.end_4=74963040;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_2=559;refseq.mrnaCoord_3=520;refseq.mrnaCoord_4=520;refseq.name2_1=CRYZ;refseq.name2_2=CRYZ;refseq.name2_3=CRYZ;refseq.name2_4=CRYZ;refseq.name_1=NM_001134759;refseq.name_2=NM_001130042;refseq.name_3=NM_001130043;refseq.name_4=NM_001889;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.G18G;refseq.proteinCoordStr_3=p.G18G;refseq.proteinCoordStr_4=p.G18G;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceAA_4=Gly;refseq.referenceCodon_2=GGG;refseq.referenceCodon_3=GGG;refseq.referenceCodon_4=GGG;refseq.spliceDist_2=-58;refseq.spliceDist_3=-58;refseq.spliceDist_4=-58;refseq.start_1=74961553;refseq.start_2=74963040;refseq.start_3=74963040;refseq.start_4=74963040;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_2=GGA;refseq.variantCodon_3=GGA;refseq.variantCodon_4=GGA;set=filterInsoap-gatk GT 0/1
|
|
chr1 75444964 . A G 144.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=476;Dels=0.00;HRun=1;HaplotypeScore=9.50;MQ=98.89;MQ0=0;OQ=8609.16;QD=18.09;RankSumP=0.409307;SB=-2613.66;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2076T>C;refseq.codonCoord_2=692;refseq.end_1=75449730;refseq.end_2=75444964;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=2220;refseq.name2_1=SLC44A5;refseq.name2_2=SLC44A5;refseq.name_1=NM_001130058;refseq.name_2=NM_152697;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S692S;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCT;refseq.spliceDist_2=29;refseq.start_1=75442117;refseq.start_2=75444964;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ser;refseq.variantCodon_2=TCC;set=Intersection GT 0/1
|
|
chr1 75454099 . T C 418.24 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.28;MQ0=0;OQ=5663.02;QD=41.95;RankSumP=1.00000;SB=-2761.43;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1656A>G;refseq.codingCoordStr_2=c.1656A>G;refseq.codonCoord_1=552;refseq.codonCoord_2=552;refseq.end_1=75454099;refseq.end_2=75454099;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1800;refseq.mrnaCoord_2=1800;refseq.name2_1=SLC44A5;refseq.name2_2=SLC44A5;refseq.name_1=NM_001130058;refseq.name_2=NM_152697;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q552Q;refseq.proteinCoordStr_2=p.Q552Q;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAA;refseq.referenceCodon_2=CAA;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.start_1=75454099;refseq.start_2=75454099;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=Intersection GT 1/1
|
|
chr1 75489513 . C T 262.29 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=296;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=98.75;MQ0=0;OQ=11905.57;QD=40.22;RankSumP=1.00000;SB=-5689.88;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.315G>A;refseq.codingCoordStr_2=c.315G>A;refseq.codonCoord_1=105;refseq.codonCoord_2=105;refseq.end_1=75489513;refseq.end_2=75489513;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=459;refseq.mrnaCoord_2=459;refseq.name2_1=SLC44A5;refseq.name2_2=SLC44A5;refseq.name_1=NM_001130058;refseq.name_2=NM_152697;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V105V;refseq.proteinCoordStr_2=p.V105V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-31;refseq.spliceDist_2=-31;refseq.start_1=75489513;refseq.start_2=75489513;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=Intersection GT 1/1
|
|
chr1 75999610 . A G 170.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=280;Dels=0.00;HRun=1;HaplotypeScore=5.63;MQ=98.93;MQ0=0;OQ=5657.87;QD=20.21;RankSumP=3.89606e-08;SB=-2090.77;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1161A>G;refseq.codingCoordStr_2=c.1173A>G;refseq.codonCoord_1=387;refseq.codonCoord_2=391;refseq.end_1=75999610;refseq.end_2=75999610;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1591;refseq.mrnaCoord_2=1603;refseq.name2_1=ACADM;refseq.name2_2=ACADM;refseq.name_1=NM_000016;refseq.name_2=NM_001127328;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V387V;refseq.proteinCoordStr_2=p.V391V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTA;refseq.referenceCodon_2=GTA;refseq.spliceDist_1=-34;refseq.spliceDist_2=-34;refseq.start_1=75999610;refseq.start_2=75999610;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=filterInsoap-gatk GT 0/1
|
|
chr1 76027816 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.61;MQ0=0;OQ=1978.34;QD=19.02;RankSumP=0.428112;SB=-430.07;SecondBestBaseQ=33;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.end_1=76028214;refseq.end_2=76027816;refseq.haplotypeAlternate_2=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.inCodingRegion_1=false;refseq.mrnaCoord_2=67;refseq.name2_1=RABGGTB;refseq.name2_2=SNORD45B;refseq.name_1=NM_004582;refseq.name_2=NR_002748;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=non_coding_exon;refseq.spliceDist_2=-5;refseq.spliceInfo_2=splice-donor_-5;refseq.start_1=76027640;refseq.start_2=76027816;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;set=Intersection GT 1/0
|
|
chr1 76030480 . A T 423.24 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.04;MQ0=0;OQ=3486.29;QD=40.54;RankSumP=1.00000;SB=-1308.48;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.606A>T;refseq.codonCoord=202;refseq.end=76030480;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=677;refseq.name=NM_004582;refseq.name2=RABGGTB;refseq.positionType=CDS;refseq.proteinCoordStr=p.A202A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=27;refseq.start=76030480;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 76117293 . T C 371.83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=181;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=7120.99;QD=39.34;RankSumP=1.00000;SB=-3318.11;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1569T>C;refseq.codonCoord=523;refseq.end=76117293;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1610;refseq.name=NM_002440;refseq.name2=MSH4;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y523Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=29;refseq.start=76117293;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/1
|
|
chr1 76117299 . A T 317.59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=176;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=7237.66;QD=41.12;RankSumP=1.00000;SB=-3254.81;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1575A>T;refseq.codonCoord=525;refseq.end=76117299;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1616;refseq.name=NM_002440;refseq.name2=MSH4;refseq.positionType=CDS;refseq.proteinCoordStr=p.L525L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=35;refseq.start=76117299;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/1
|
|
chr1 76170560 . C T 277.64 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=152;Dels=0.00;HRun=1;HaplotypeScore=2.99;MQ=98.77;MQ0=0;OQ=6660.03;QD=43.82;RankSumP=1.00000;SB=-2183.30;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.5G>A;refseq.codonCoord_2=2;refseq.end_1=76170560;refseq.end_2=76170560;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=145;refseq.mrnaCoord_2=145;refseq.name2_1=ASB17;refseq.name2_2=ASB17;refseq.name_1=NR_026546;refseq.name_2=NM_080868;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S2N;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=AGT;refseq.spliceDist_1=145;refseq.spliceDist_2=145;refseq.start_1=76170560;refseq.start_2=76170560;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Asn;refseq.variantCodon_2=AAT;set=Intersection GT 1/1
|
|
chr1 76865768 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=864;Dels=0.00;HRun=0;HaplotypeScore=22.59;MQ=98.85;MQ0=0;OQ=14583.09;QD=16.88;RankSumP=0.0940414;SB=-5467.47;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.667C>A;refseq.codonCoord=223;refseq.end=76865768;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=830;refseq.name=NM_152996;refseq.name2=ST6GALNAC3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L223I;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=44;refseq.start=76865768;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 77288565 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.706T>G;refseq.codonCoord=236;refseq.end=77288565;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=881;refseq.name=NM_030965;refseq.name2=ST6GALNAC5;refseq.positionType=CDS;refseq.proteinCoordStr=p.F236V;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=35;refseq.start=77288565;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTT;set=FilteredInAll GT 1/0
|
|
chr1 77407536 . G A 299.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=138;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.71;MQ0=0;OQ=5848.38;QD=42.38;RankSumP=1.00000;SB=-1294.65;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.372C>T;refseq.codonCoord=124;refseq.end=77407536;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=417;refseq.name=NM_005482;refseq.name2=PIGK;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y124Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-4;refseq.spliceInfo=splice-donor_-4;refseq.start=77407536;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 77532166 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=140;Dels=0.00;HRun=1;HaplotypeScore=1.75;MQ=98.54;MQ0=0;OQ=1917.23;QD=13.69;RankSumP=0.229518;SB=-877.31;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.270A>G;refseq.codingCoordStr_2=c.348A>G;refseq.codonCoord_1=90;refseq.codonCoord_2=116;refseq.end_1=77532166;refseq.end_2=77532166;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1296;refseq.mrnaCoord_2=605;refseq.name2_1=AK5;refseq.name2_2=AK5;refseq.name_1=NM_012093;refseq.name_2=NM_174858;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A90A;refseq.proteinCoordStr_2=p.A116A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=-68;refseq.spliceDist_2=-68;refseq.start_1=77532166;refseq.start_2=77532166;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 0/1
|
|
chr1 77536130 . G A 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=204;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=98.89;MQ0=0;OQ=8777.86;QD=43.03;RankSumP=1.00000;SB=-2122.87;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.531G>A;refseq.codingCoordStr_2=c.609G>A;refseq.codonCoord_1=177;refseq.codonCoord_2=203;refseq.end_1=77536130;refseq.end_2=77536130;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1557;refseq.mrnaCoord_2=866;refseq.name2_1=AK5;refseq.name2_2=AK5;refseq.name_1=NM_012093;refseq.name_2=NM_174858;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K177K;refseq.proteinCoordStr_2=p.K203K;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=24;refseq.spliceDist_2=24;refseq.start_1=77536130;refseq.start_2=77536130;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=Intersection GT 1/1
|
|
chr1 77871620 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8C>G;refseq.codonCoord=3;refseq.end=77871620;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=484;refseq.name=NM_015534;refseq.name2=ZZZ3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A3G;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=59;refseq.start=77871620;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 78165034 . G A 218.43 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1667.63;QD=20.09;RankSumP=0.239474;SB=-643.64;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.541G>A;refseq.codingCoordStr_2=c.733G>A;refseq.codonCoord_1=181;refseq.codonCoord_2=245;refseq.end_1=78165034;refseq.end_2=78165034;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=838;refseq.mrnaCoord_2=1030;refseq.name2_1=NEXN;refseq.name2_2=NEXN;refseq.name_1=NM_001172309;refseq.name_2=NM_144573;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G181R;refseq.proteinCoordStr_2=p.G245R;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=46;refseq.spliceDist_2=46;refseq.start_1=78165034;refseq.start_2=78165034;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGA;refseq.variantCodon_2=AGA;set=Intersection GT 1/0
|
|
chr1 78357674 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=195;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=99.00;MQ0=0;OQ=2179.47;QD=11.18;RankSumP=0.415495;SB=-464.88;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.617T>C;refseq.codonCoord=206;refseq.end=78357674;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=807;refseq.name=NM_017655;refseq.name2=GIPC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L206P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=78357674;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/0
|
|
chr1 78731079 . C T 165.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=204;Dels=0.00;HRun=1;HaplotypeScore=6.31;MQ=98.73;MQ0=0;OQ=3984.48;QD=19.53;RankSumP=0.00418101;SB=-1498.44;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.63C>T;refseq.codingCoordStr_2=c.63C>T;refseq.codonCoord_1=21;refseq.codonCoord_2=21;refseq.end_1=78731079;refseq.end_2=78731079;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=329;refseq.mrnaCoord_2=329;refseq.name2_1=PTGFR;refseq.name2_2=PTGFR;refseq.name_1=NM_000959;refseq.name_2=NM_001039585;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T21T;refseq.proteinCoordStr_2=p.T21T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=135;refseq.spliceDist_2=135;refseq.start_1=78731079;refseq.start_2=78731079;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;set=filterInsoap-gatk GT 0/1
|
|
chr1 78866406 . A G 308.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=98.85;MQ0=0;OQ=2357.91;QD=19.17;RankSumP=0.337897;SB=-1095.12;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.218A>G;refseq.codonCoord=73;refseq.end=78866406;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=397;refseq.name=NM_006820;refseq.name2=IFI44L;refseq.positionType=CDS;refseq.proteinCoordStr=p.H73R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=228;refseq.start=78866406;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 0/1
|
|
chr1 78868169 . T C 330.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=194;Dels=0.00;HRun=1;HaplotypeScore=3.92;MQ=98.79;MQ0=0;OQ=8111.84;QD=41.81;RankSumP=1.00000;SB=-2454.66;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.704T>C;refseq.codonCoord=235;refseq.end=78868169;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=883;refseq.name=NM_006820;refseq.name2=IFI44L;refseq.positionType=CDS;refseq.proteinCoordStr=p.I235T;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-20;refseq.start=78868169;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 78879728 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=132;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=98.58;MQ0=0;OQ=1636.22;QD=12.40;RankSumP=0.201364;SB=-483.76;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1170G>T;refseq.codonCoord=390;refseq.end=78879728;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1349;refseq.name=NM_006820;refseq.name2=IFI44L;refseq.positionType=CDS;refseq.proteinCoordStr=p.M390I;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=21;refseq.start=78879728;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 79129948 . G C 101.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=257;Dels=0.00;HRun=1;HaplotypeScore=3.63;MQ=98.79;MQ0=0;OQ=6597.90;QD=25.67;RankSumP=0.449298;SB=-2094.06;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1859C>G;refseq.codonCoord=620;refseq.end=79129948;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2015;refseq.name=NM_022159;refseq.name2=ELTD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A620G;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=18;refseq.start=79129948;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 79165344 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=140;Dels=0.00;HRun=3;HaplotypeScore=4.57;MQ=98.84;MQ0=0;OQ=1880.72;QD=13.43;RankSumP=0.272246;SB=-615.58;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.898G>T;refseq.codonCoord=300;refseq.end=79165344;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1054;refseq.name=NM_022159;refseq.name2=ELTD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V300L;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=21;refseq.start=79165344;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=Intersection GT 1/0
|
|
chr1 82194184 . C T 88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=625;Dels=0.00;HRun=0;HaplotypeScore=15.38;MQ=98.92;MQ0=0;OQ=26544.32;QD=42.47;RankSumP=1.00000;SB=-12876.83;SecondBestBaseQ=6;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1818C>T;refseq.codonCoord=606;refseq.end=82194184;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2034;refseq.name=NM_012302;refseq.name2=LPHN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P606P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=36;refseq.start=82194184;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 84717577 . A G 23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=10;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=291.21;QD=29.12;RankSumP=1.00000;SB=-93.37;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.25A>G;refseq.codonCoord=9;refseq.end=84717577;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=70;refseq.name=NM_025065;refseq.name2=RPF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S9G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=70;refseq.start=84717577;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 84804145 . C G 57 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=12;HRun=1;RankSumP=0.000649371;SecondBestBaseQ=6;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.*84C>G;refseq.codingCoordStr_2=c.664G>C;refseq.codonCoord_2=222;refseq.end_1=84804145;refseq.end_2=84804145;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1663;refseq.mrnaCoord_2=729;refseq.name2_1=SPATA1;refseq.name2_2=CTBS;refseq.name_1=NM_001081472;refseq.name_2=NM_004388;refseq.numMatchingRecords=2;refseq.positionType_1=utr3;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A222P;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=14;refseq.spliceDist_2=-34;refseq.start_1=84804145;refseq.start_2=84804145;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCA;set=FilteredInAll GT 1/0
|
|
chr1 84885791 . T C 303.81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=502;Dels=0.00;HRun=0;HaplotypeScore=8.45;MQ=98.88;MQ0=0;OQ=9496.28;QD=18.92;RankSumP=0.388105;SB=-3276.66;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.1758A>G;refseq.codingCoordStr_2=c.1677A>G;refseq.codingCoordStr_3=c.1677A>G;refseq.codingCoordStr_4=c.1758A>G;refseq.codingCoordStr_5=c.1758A>G;refseq.codonCoord_1=586;refseq.codonCoord_2=559;refseq.codonCoord_3=559;refseq.codonCoord_4=586;refseq.codonCoord_5=586;refseq.end_1=84885791;refseq.end_2=84885791;refseq.end_3=84885791;refseq.end_4=84885791;refseq.end_5=84885791;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=2034;refseq.mrnaCoord_2=1902;refseq.mrnaCoord_3=2030;refseq.mrnaCoord_4=2212;refseq.mrnaCoord_5=2084;refseq.name2_1=SSX2IP;refseq.name2_2=SSX2IP;refseq.name2_3=SSX2IP;refseq.name2_4=SSX2IP;refseq.name2_5=SSX2IP;refseq.name_1=NM_001166293;refseq.name_2=NM_001166294;refseq.name_3=NM_001166295;refseq.name_4=NM_001166417;refseq.name_5=NM_014021;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.A586A;refseq.proteinCoordStr_2=p.A559A;refseq.proteinCoordStr_3=p.A559A;refseq.proteinCoordStr_4=p.A586A;refseq.proteinCoordStr_5=p.A586A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceAA_5=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.referenceCodon_3=GCA;refseq.referenceCodon_4=GCA;refseq.referenceCodon_5=GCA;refseq.spliceDist_1=88;refseq.spliceDist_2=88;refseq.spliceDist_3=88;refseq.spliceDist_4=88;refseq.spliceDist_5=88;refseq.start_1=84885791;refseq.start_2=84885791;refseq.start_3=84885791;refseq.start_4=84885791;refseq.start_5=84885791;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantAA_5=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;refseq.variantCodon_3=GCG;refseq.variantCodon_4=GCG;refseq.variantCodon_5=GCG;set=Intersection GT 1/0
|
|
chr1 84885817 . A G 314.51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=418;Dels=0.00;HRun=0;HaplotypeScore=12.86;MQ=98.79;MQ0=0;OQ=7375.22;QD=17.64;RankSumP=0.427954;SB=-2682.74;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.1732T>C;refseq.codingCoordStr_2=c.1651T>C;refseq.codingCoordStr_3=c.1651T>C;refseq.codingCoordStr_4=c.1732T>C;refseq.codingCoordStr_5=c.1732T>C;refseq.codonCoord_1=578;refseq.codonCoord_2=551;refseq.codonCoord_3=551;refseq.codonCoord_4=578;refseq.codonCoord_5=578;refseq.end_1=84885817;refseq.end_2=84885817;refseq.end_3=84885817;refseq.end_4=84885817;refseq.end_5=84885817;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=2008;refseq.mrnaCoord_2=1876;refseq.mrnaCoord_3=2004;refseq.mrnaCoord_4=2186;refseq.mrnaCoord_5=2058;refseq.name2_1=SSX2IP;refseq.name2_2=SSX2IP;refseq.name2_3=SSX2IP;refseq.name2_4=SSX2IP;refseq.name2_5=SSX2IP;refseq.name_1=NM_001166293;refseq.name_2=NM_001166294;refseq.name_3=NM_001166295;refseq.name_4=NM_001166417;refseq.name_5=NM_014021;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.C578R;refseq.proteinCoordStr_2=p.C551R;refseq.proteinCoordStr_3=p.C551R;refseq.proteinCoordStr_4=p.C578R;refseq.proteinCoordStr_5=p.C578R;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceAA_5=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.referenceCodon_3=TGT;refseq.referenceCodon_4=TGT;refseq.referenceCodon_5=TGT;refseq.spliceDist_1=62;refseq.spliceDist_2=62;refseq.spliceDist_3=62;refseq.spliceDist_4=62;refseq.spliceDist_5=62;refseq.start_1=84885817;refseq.start_2=84885817;refseq.start_3=84885817;refseq.start_4=84885817;refseq.start_5=84885817;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantAA_5=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;refseq.variantCodon_3=CGT;refseq.variantCodon_4=CGT;refseq.variantCodon_5=CGT;set=Intersection GT 0/1
|
|
chr1 85177895 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1039T>G;refseq.codonCoord=347;refseq.end=85177895;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1280;refseq.name=NM_153259;refseq.name2=MCOLN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y347D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-72;refseq.start=85177895;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 0/1
|
|
chr1 85260618 . G A 147.47 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=323;Dels=0.00;HRun=1;HaplotypeScore=4.62;MQ=98.85;MQ0=0;OQ=14075.52;QD=43.58;RankSumP=1.00000;SB=-6962.81;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1149C>T;refseq.codonCoord=383;refseq.end=85260618;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1242;refseq.name=NM_018298;refseq.name2=MCOLN3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L383L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-49;refseq.start=85260618;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/1
|
|
chr1 85362396 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=3;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1986G>A;refseq.codonCoord=662;refseq.end=85362396;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2177;refseq.name=NM_145172;refseq.name2=WDR63;refseq.positionType=CDS;refseq.proteinCoordStr=p.K662K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=5;refseq.spliceInfo=splice-acceptor_5;refseq.start=85362396;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 1/0
|
|
chr1 85514600 . G C 303.78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=3.21;MQ=97.45;MQ0=0;OQ=4358.58;QD=44.48;RankSumP=1.00000;SB=-1929.08;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.24C>G;refseq.codonCoord=8;refseq.end=85514600;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=576;refseq.name=NM_003921;refseq.name2=BCL10;refseq.positionType=CDS;refseq.proteinCoordStr=p.L8L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-34;refseq.start=85514600;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 86148242 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=136;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=98.68;MQ0=0;OQ=3692.09;QD=27.15;RankSumP=0.124058;SB=-1568.25;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2649G>C;refseq.codonCoord=883;refseq.end=86148242;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2691;refseq.name=NM_152890;refseq.name2=COL24A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P883P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-22;refseq.start=86148242;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/0
|
|
chr1 86285124 . C T 209.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=307;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=98.76;MQ0=0;OQ=5969.33;QD=19.44;RankSumP=0.351430;SB=-2333.65;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1922G>A;refseq.codonCoord=641;refseq.end=86285124;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1964;refseq.name=NM_152890;refseq.name2=COL24A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R641H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=17;refseq.start=86285124;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 0/1
|
|
chr1 86330555 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=98.69;MQ0=0;OQ=1821.25;QD=11.53;RankSumP=0.270641;SB=-894.28;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1636C>T;refseq.codonCoord=546;refseq.end=86330555;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1678;refseq.name=NM_152890;refseq.name2=COL24A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P546S;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-18;refseq.start=86330555;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/0
|
|
chr1 86363503 . G A 230.61 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=293;Dels=0.00;HRun=1;HaplotypeScore=3.86;MQ=98.95;MQ0=0;OQ=12381.09;QD=42.26;RankSumP=1.00000;SB=-6036.27;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1104C>T;refseq.codonCoord=368;refseq.end=86363503;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1146;refseq.name=NM_152890;refseq.name2=COL24A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S368S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-388;refseq.start=86363503;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/1
|
|
chr1 86363536 . A G 341.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=260;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=98.96;MQ0=0;OQ=4688.30;QD=18.03;RankSumP=0.0347515;SB=-1840.09;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1071T>C;refseq.codonCoord=357;refseq.end=86363536;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1113;refseq.name=NM_152890;refseq.name2=COL24A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S357S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-421;refseq.start=86363536;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 86364425 . G A 260.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=284;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=5666.03;QD=19.95;RankSumP=0.104293;SB=-2409.29;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.182C>T;refseq.codonCoord=61;refseq.end=86364425;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=224;refseq.name=NM_152890;refseq.name2=COL24A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A61V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=61;refseq.start=86364425;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 86591160 . T C 168.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=98.98;MQ0=0;OQ=1728.94;QD=19.87;RankSumP=0.496088;SB=-738.33;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1383A>G;refseq.codingCoordStr_2=c.1776A>G;refseq.codonCoord_1=461;refseq.codonCoord_2=592;refseq.end_1=86591160;refseq.end_2=86591160;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1990;refseq.mrnaCoord_2=2123;refseq.name2_1=ODF2L;refseq.name2_2=ODF2L;refseq.name_1=NM_001007022;refseq.name_2=NM_020729;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E461E;refseq.proteinCoordStr_2=p.E592E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=-31;refseq.spliceDist_2=-31;refseq.start_1=86591160;refseq.start_2=86591160;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 1/0
|
|
chr1 86592855 . C T 231.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=200;Dels=0.00;HRun=1;HaplotypeScore=4.95;MQ=98.75;MQ0=0;OQ=4266.43;QD=21.33;RankSumP=0.418315;SB=-1500.93;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1233G>A;refseq.codingCoordStr_2=c.1626G>A;refseq.codonCoord_1=411;refseq.codonCoord_2=542;refseq.end_1=86592855;refseq.end_2=86592855;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1840;refseq.mrnaCoord_2=1973;refseq.name2_1=ODF2L;refseq.name2_2=ODF2L;refseq.name_1=NM_001007022;refseq.name_2=NM_020729;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E411E;refseq.proteinCoordStr_2=p.E542E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-55;refseq.spliceDist_2=-55;refseq.start_1=86592855;refseq.start_2=86592855;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=Intersection GT 0/1
|
|
chr1 86594819 . A G 162.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=261;Dels=0.00;HRun=2;HaplotypeScore=7.06;MQ=98.59;MQ0=0;OQ=4780.15;QD=18.31;RankSumP=0.189133;SB=-1798.07;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.934T>C;refseq.codingCoordStr_2=c.1327T>C;refseq.codonCoord_1=312;refseq.codonCoord_2=443;refseq.end_1=86594819;refseq.end_2=86594819;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1541;refseq.mrnaCoord_2=1674;refseq.name2_1=ODF2L;refseq.name2_2=ODF2L;refseq.name_1=NM_001007022;refseq.name_2=NM_020729;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L312L;refseq.proteinCoordStr_2=p.L443L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTG;refseq.referenceCodon_2=TTG;refseq.spliceDist_1=55;refseq.spliceDist_2=55;refseq.start_1=86594819;refseq.start_2=86594819;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 0/1
|
|
chr1 86610746 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.92;MQ0=0;OQ=385.93;QD=11.03;RankSumP=0.610220;SB=-138.54;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.483G>A;refseq.codingCoordStr_2=c.876G>A;refseq.codonCoord_1=161;refseq.codonCoord_2=292;refseq.end_1=86610746;refseq.end_2=86610746;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1090;refseq.mrnaCoord_2=1223;refseq.name2_1=ODF2L;refseq.name2_2=ODF2L;refseq.name_1=NM_001007022;refseq.name_2=NM_020729;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V161V;refseq.proteinCoordStr_2=p.V292V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-45;refseq.spliceDist_2=-45;refseq.start_1=86610746;refseq.start_2=86610746;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=Intersection GT 0/1
|
|
chr1 86620543 . G A 151.86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1584.57;QD=20.32;RankSumP=0.222010;SB=-182.63;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.201C>T;refseq.codingCoordStr_2=c.594C>T;refseq.codonCoord_1=67;refseq.codonCoord_2=198;refseq.end_1=86620543;refseq.end_2=86620543;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=808;refseq.mrnaCoord_2=941;refseq.name2_1=ODF2L;refseq.name2_2=ODF2L;refseq.name_1=NM_001007022;refseq.name_2=NM_020729;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A67A;refseq.proteinCoordStr_2=p.A198A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=-31;refseq.spliceDist_2=-31;refseq.start_1=86620543;refseq.start_2=86620543;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=Intersection GT 1/0
|
|
chr1 86666829 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=320;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=99.00;MQ0=0;OQ=5520.42;QD=17.25;RankSumP=0.229001;SB=-2090.28;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.465C>T;refseq.codonCoord=155;refseq.end=86666829;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=627;refseq.name=NM_006536;refseq.name2=CLCA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y155Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-11;refseq.start=86666829;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 0/1
|
|
chr1 86672920 . T C 243.33 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=172;Dels=0.00;HRun=0;HaplotypeScore=8.15;MQ=98.91;MQ0=0;OQ=2660.22;QD=15.47;RankSumP=0.142565;SB=-700.87;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.876T>C;refseq.codonCoord=292;refseq.end=86672920;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1038;refseq.name=NM_006536;refseq.name2=CLCA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N292N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-97;refseq.start=86672920;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/0
|
|
chr1 86672960 . C G 190.42 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=98.73;MQ0=0;OQ=2315.34;QD=21.84;RankSumP=0.225806;SB=-594.69;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.916C>G;refseq.codonCoord=306;refseq.end=86672960;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1078;refseq.name=NM_006536;refseq.name2=CLCA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q306E;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-57;refseq.start=86672960;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 86711718 . C T 70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=296;Dels=0.00;HRun=2;HaplotypeScore=8.87;MQ=98.73;MQ0=0;OQ=12832.49;QD=43.35;RankSumP=1.00000;SB=-5730.45;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.193C>T;refseq.codonCoord=65;refseq.end=86711718;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=322;refseq.name=NM_001285;refseq.name2=CLCA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L65F;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=31;refseq.start=86711718;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/1
|
|
chr1 86724912 . A G 167.23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=486;Dels=0.00;HRun=0;HaplotypeScore=4.51;MQ=98.84;MQ0=0;OQ=19541.73;QD=40.21;RankSumP=1.00000;SB=-9032.66;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1070A>G;refseq.codonCoord=357;refseq.end=86724912;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1199;refseq.name=NM_001285;refseq.name2=CLCA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N357S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-113;refseq.start=86724912;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/1
|
|
chr1 86731761 . T C 240.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=293;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=98.83;MQ0=0;OQ=10971.80;QD=37.45;RankSumP=1.00000;SB=-5304.48;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1571T>C;refseq.codonCoord=524;refseq.end=86731761;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1700;refseq.name=NM_001285;refseq.name2=CLCA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M524T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=107;refseq.start=86731761;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 86818490 . A T 57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2634A>T;refseq.codonCoord_2=878;refseq.end_1=86818490;refseq.end_2=86818490;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2569;refseq.mrnaCoord_2=2678;refseq.name2_1=CLCA4;refseq.name2_2=CLCA4;refseq.name_1=NR_024602;refseq.name_2=NM_012128;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.T878T;refseq.referenceAA_2=Thr;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=278;refseq.spliceDist_2=278;refseq.start_1=86818490;refseq.start_2=86818490;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Thr;refseq.variantCodon_2=ACT;set=soap GT 1/1
|
|
chr1 86875134 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.chr=chr1;refseq.end=86875134;refseq.haplotypeAlternate=*;refseq.haplotypeReference=*;refseq.mrnaCoord=530;refseq.name=NR_024604;refseq.name2=CLCA3P;refseq.positionType=non_coding_exon;refseq.spliceDist=-46;refseq.start=86875134;refseq.transcriptStrand=+;set=FilteredInAll GT 0/1
|
|
chr1 86980652 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.935T>G;refseq.codonCoord=312;refseq.end=86980652;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1261;refseq.name=NM_016009;refseq.name2=SH3GLB1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V312G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-56;refseq.start=86980652;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 88998564 . T C 151.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=290;Dels=0.00;HRun=2;HaplotypeScore=3.98;MQ=98.95;MQ0=0;OQ=5772.45;QD=19.90;RankSumP=0.340860;SB=-2135.68;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.421T>C;refseq.codonCoord=141;refseq.end=88998564;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=763;refseq.name=NM_006256;refseq.name2=PKN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L141L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=72;refseq.start=88998564;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/0
|
|
chr1 89010144 . C T 104.07 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=102;Dels=0.00;HRun=1;HaplotypeScore=6.56;MQ=98.85;MQ0=0;OQ=1720.33;QD=16.87;RankSumP=0.152933;SB=-408.88;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.979C>T;refseq.codonCoord=327;refseq.end=89010144;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1321;refseq.name=NM_006256;refseq.name2=PKN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L327L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=89010144;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=Intersection GT 0/1
|
|
chr1 89045875 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=229;Dels=0.00;HRun=3;HaplotypeScore=11.35;MQ=98.98;MQ0=0;OQ=4118.56;QD=17.98;RankSumP=0.179525;SB=-889.43;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2010G>A;refseq.codonCoord=670;refseq.end=89045875;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2352;refseq.name=NM_006256;refseq.name2=PKN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K670K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-1;refseq.spliceInfo=splice-donor_-1;refseq.start=89045875;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/0
|
|
chr1 89095570 . G A 145.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=174;Dels=0.00;HRun=1;HaplotypeScore=9.47;MQ=98.96;MQ0=0;OQ=7175.57;QD=41.24;RankSumP=1.00000;SB=-2314.41;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.724C>T;refseq.codonCoord=242;refseq.end=89095570;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=843;refseq.name=NM_001514;refseq.name2=GTF2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.L242L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-94;refseq.start=89095570;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/1
|
|
chr1 89199490 . G A 260.29 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=355;Dels=0.00;HRun=0;HaplotypeScore=9.20;MQ=98.78;MQ0=0;OQ=14719.99;QD=41.46;RankSumP=1.00000;SB=-7188.35;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.735C>T;refseq.codingCoordStr_2=c.633C>T;refseq.codonCoord_1=245;refseq.codonCoord_2=211;refseq.end_1=89199490;refseq.end_2=89199490;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1112;refseq.mrnaCoord_2=1012;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S245S;refseq.proteinCoordStr_2=p.S211S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=-53;refseq.spliceDist_2=-53;refseq.start_1=89199490;refseq.start_2=89199490;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 1/1
|
|
chr1 89200360 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.510A>G;refseq.codingCoordStr_2=c.408A>G;refseq.codonCoord_1=170;refseq.codonCoord_2=136;refseq.end_1=89200360;refseq.end_2=89200360;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=887;refseq.mrnaCoord_2=787;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G170G;refseq.proteinCoordStr_2=p.G136G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=-31;refseq.spliceDist_2=-31;refseq.start_1=89200360;refseq.start_2=89200360;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 89221866 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=586;Dels=0.00;HRun=4;HaplotypeScore=12.06;MQ=55.26;MQ0=170;OQ=1624.95;QD=2.77;RankSumP=0.471506;SB=-102.98;SecondBestBaseQ=32;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.232G>A;refseq.codingCoordStr_4=c.232G>A;refseq.codonCoord_3=78;refseq.codonCoord_4=78;refseq.end_1=89226512;refseq.end_2=89230845;refseq.end_3=89221866;refseq.end_4=89221866;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_3=948;refseq.mrnaCoord_4=848;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name2_3=RBMXL1;refseq.name2_4=RBMXL1;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.name_3=NM_001162536;refseq.name_4=NM_019610;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_3=p.A78T;refseq.proteinCoordStr_4=p.A78T;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceCodon_3=GCC;refseq.referenceCodon_4=GCC;refseq.spliceDist_3=472;refseq.spliceDist_4=472;refseq.start_1=89207749;refseq.start_2=89207749;refseq.start_3=89221866;refseq.start_4=89221866;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantCodon_3=ACC;refseq.variantCodon_4=ACC;set=soap-filterIngatk GT 0/1
|
|
chr1 89221886 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=817;Dels=0.00;HRun=0;HaplotypeScore=12.45;MQ=49.38;MQ0=224;OQ=6413.59;QD=7.85;RankSumP=0.0932971;SB=-900.88;SecondBestBaseQ=33;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.212G>C;refseq.codingCoordStr_4=c.212G>C;refseq.codonCoord_3=71;refseq.codonCoord_4=71;refseq.end_1=89226512;refseq.end_2=89230845;refseq.end_3=89221886;refseq.end_4=89221886;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_3=928;refseq.mrnaCoord_4=828;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name2_3=RBMXL1;refseq.name2_4=RBMXL1;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.name_3=NM_001162536;refseq.name_4=NM_019610;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_3=p.G71A;refseq.proteinCoordStr_4=p.G71A;refseq.referenceAA_3=Gly;refseq.referenceAA_4=Gly;refseq.referenceCodon_3=GGA;refseq.referenceCodon_4=GGA;refseq.spliceDist_3=452;refseq.spliceDist_4=452;refseq.start_1=89207749;refseq.start_2=89207749;refseq.start_3=89221886;refseq.start_4=89221886;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantCodon_3=GCA;refseq.variantCodon_4=GCA;set=Intersection GT 1/0
|
|
chr1 89221978 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=947;Dels=0.00;HRun=0;HaplotypeScore=15.38;MQ=76.86;MQ0=158;OQ=7399.68;QD=7.81;RankSumP=0.251520;SB=-2077.53;SecondBestBaseQ=32;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.120A>G;refseq.codingCoordStr_4=c.120A>G;refseq.codonCoord_3=40;refseq.codonCoord_4=40;refseq.end_1=89226512;refseq.end_2=89230845;refseq.end_3=89221978;refseq.end_4=89221978;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_3=836;refseq.mrnaCoord_4=736;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name2_3=RBMXL1;refseq.name2_4=RBMXL1;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.name_3=NM_001162536;refseq.name_4=NM_019610;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_3=p.I40M;refseq.proteinCoordStr_4=p.I40M;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceCodon_3=ATA;refseq.referenceCodon_4=ATA;refseq.spliceDist_3=360;refseq.spliceDist_4=360;refseq.start_1=89207749;refseq.start_2=89207749;refseq.start_3=89221978;refseq.start_4=89221978;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_3=Met;refseq.variantAA_4=Met;refseq.variantCodon_3=ATG;refseq.variantCodon_4=ATG;set=Intersection GT 1/0
|
|
chr1 89221987 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=907;Dels=0.00;HRun=0;HaplotypeScore=33.99;MQ=79.37;MQ0=112;OQ=7390.59;QD=8.15;RankSumP=0.275178;SB=-1927.30;SecondBestBaseQ=33;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.111A>G;refseq.codingCoordStr_4=c.111A>G;refseq.codonCoord_3=37;refseq.codonCoord_4=37;refseq.end_1=89226512;refseq.end_2=89230845;refseq.end_3=89221987;refseq.end_4=89221987;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_3=827;refseq.mrnaCoord_4=727;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name2_3=RBMXL1;refseq.name2_4=RBMXL1;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.name_3=NM_001162536;refseq.name_4=NM_019610;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_3=p.V37V;refseq.proteinCoordStr_4=p.V37V;refseq.referenceAA_3=Val;refseq.referenceAA_4=Val;refseq.referenceCodon_3=GTA;refseq.referenceCodon_4=GTA;refseq.spliceDist_3=351;refseq.spliceDist_4=351;refseq.start_1=89207749;refseq.start_2=89207749;refseq.start_3=89221987;refseq.start_4=89221987;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantCodon_3=GTG;refseq.variantCodon_4=GTG;set=soap-filterIngatk GT 1/0
|
|
chr1 89222022 rs2893084 T C 0.73 PASS AC=1;AF=0.50;AN=2;DB;DP=900;Dels=0.00;HRun=0;HaplotypeScore=19.38;MQ=76.32;MQ0=125;OQ=1596.06;QD=1.77;SB=-236.32;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.76A>G;refseq.codingCoordStr_4=c.76A>G;refseq.codonCoord_3=26;refseq.codonCoord_4=26;refseq.end_1=89226512;refseq.end_2=89230845;refseq.end_3=89222022;refseq.end_4=89222022;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_3=792;refseq.mrnaCoord_4=692;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name2_3=RBMXL1;refseq.name2_4=RBMXL1;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.name_3=NM_001162536;refseq.name_4=NM_019610;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_3=p.T26A;refseq.proteinCoordStr_4=p.T26A;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_3=ACA;refseq.referenceCodon_4=ACA;refseq.spliceDist_3=316;refseq.spliceDist_4=316;refseq.start_1=89207749;refseq.start_2=89207749;refseq.start_3=89222022;refseq.start_4=89222022;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantCodon_3=GCA;refseq.variantCodon_4=GCA;set=gatk GT:AD:DP:GL:GQ 0/1:695,205:763:-392.65,-229.76,-2893.36:99
|
|
chr1 89222071 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=690;Dels=0.00;HRun=1;HaplotypeScore=11.32;MQ=76.31;MQ0=108;OQ=390.38;QD=0.57;RankSumP=0.436007;SB=384.32;SecondBestBaseQ=33;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.27G>C;refseq.codingCoordStr_4=c.27G>C;refseq.codonCoord_3=9;refseq.codonCoord_4=9;refseq.end_1=89226512;refseq.end_2=89230845;refseq.end_3=89222071;refseq.end_4=89222071;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_3=743;refseq.mrnaCoord_4=643;refseq.name2_1=CCBL2;refseq.name2_2=CCBL2;refseq.name2_3=RBMXL1;refseq.name2_4=RBMXL1;refseq.name_1=NM_001008661;refseq.name_2=NM_001008662;refseq.name_3=NM_001162536;refseq.name_4=NM_019610;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_3=p.K9N;refseq.proteinCoordStr_4=p.K9N;refseq.referenceAA_3=Lys;refseq.referenceAA_4=Lys;refseq.referenceCodon_3=AAG;refseq.referenceCodon_4=AAG;refseq.spliceDist_3=267;refseq.spliceDist_4=267;refseq.start_1=89207749;refseq.start_2=89207749;refseq.start_3=89222071;refseq.start_4=89222071;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_3=Asn;refseq.variantAA_4=Asn;refseq.variantCodon_3=AAC;refseq.variantCodon_4=AAC;set=soap-filterIngatk GT 1/0
|
|
chr1 89247406 . A G 127.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=98.52;MQ0=0;OQ=1215.65;QD=13.21;RankSumP=0.273147;SB=-313.37;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1471T>C;refseq.codonCoord=491;refseq.end=89247406;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1676;refseq.name=NM_018284;refseq.name2=GBP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.C491R;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=89247406;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 0/1
|
|
chr1 89247723 . C T 295.25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=442;Dels=0.00;HRun=0;HaplotypeScore=9.38;MQ=90.65;MQ0=27;OQ=7793.90;QD=17.63;RankSumP=0.367367;SB=-3113.32;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1405G>A;refseq.codonCoord=469;refseq.end=89247723;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1610;refseq.name=NM_018284;refseq.name2=GBP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V469M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=43;refseq.start=89247723;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 89251651 . G A 228.63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=178;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.06;MQ0=0;OQ=3997.23;QD=22.46;RankSumP=0.390718;SB=-1493.35;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.673C>T;refseq.codonCoord=225;refseq.end=89251651;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=878;refseq.name=NM_018284;refseq.name2=GBP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R225W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=48;refseq.start=89251651;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/0
|
|
chr1 89251662 . C T 147.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=170;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=98.02;MQ0=0;OQ=3904.23;QD=22.97;RankSumP=0.344064;SB=-1416.85;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.662G>A;refseq.codonCoord=221;refseq.end=89251662;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=867;refseq.name=NM_018284;refseq.name2=GBP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R221Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=37;refseq.start=89251662;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 0/1
|
|
chr1 89292988 . T C 11 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.601430;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1630A>G;refseq.codonCoord=544;refseq.end=89292988;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1850;refseq.name=NM_002053;refseq.name2=GBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.K544E;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-36;refseq.start=89292988;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=FilteredInAll GT 1/0
|
|
chr1 89294417 . A T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.330696;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1238T>A;refseq.codonCoord=413;refseq.end=89294417;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1458;refseq.name=NM_002053;refseq.name2=GBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V413D;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=83;refseq.start=89294417;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT 0/1
|
|
chr1 89294429 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=449;Dels=0.00;HRun=1;HaplotypeScore=18.49;MQ=31.45;MQ0=340;OQ=1938.24;QD=4.32;RankSumP=0.243126;SB=-607.08;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1226C>G;refseq.codonCoord=409;refseq.end=89294429;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1446;refseq.name=NM_002053;refseq.name2=GBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A409G;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=71;refseq.start=89294429;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 0/1
|
|
chr1 89294439 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.129744;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1216C>T;refseq.codonCoord=406;refseq.end=89294439;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1436;refseq.name=NM_002053;refseq.name2=GBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R406C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=61;refseq.start=89294439;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=FilteredInAll GT 1/0
|
|
chr1 89295234 . G C 75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=401;Dels=0.00;HRun=0;HaplotypeScore=14.93;MQ=75.61;MQ0=11;OQ=17916.52;QD=44.68;RankSumP=1.00000;SB=-7658.54;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1046C>G;refseq.codonCoord=349;refseq.end=89295234;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1266;refseq.name=NM_002053;refseq.name2=GBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T349S;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-110;refseq.start=89295234;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 89352529 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=262;Dels=0.00;HRun=1;HaplotypeScore=5.45;MQ=74.68;MQ0=46;OQ=3173.99;QD=12.11;RankSumP=0.464955;SB=-1306.50;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.907A>G;refseq.codonCoord=303;refseq.end=89352529;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1178;refseq.name=NM_004120;refseq.name2=GBP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S303G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=39;refseq.start=89352529;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/0
|
|
chr1 89355278 . G C 157.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=98.43;MQ0=0;OQ=1869.53;QD=21.01;RankSumP=0.390520;SB=-882.15;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.853C>G;refseq.codonCoord=285;refseq.end=89355278;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1124;refseq.name=NM_004120;refseq.name2=GBP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P285A;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-16;refseq.start=89355278;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 89371625 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=636;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=97.42;MQ0=0;OQ=189.54;QD=0.30;SB=15.31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1566T>C;refseq.codonCoord=522;refseq.end=89371625;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1705;refseq.name=NM_207398;refseq.name2=GBP7;refseq.positionType=CDS;refseq.proteinCoordStr=p.S522S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-97;refseq.start=89371625;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:584,52:627:-211.06,-188.83,-2429.16:99
|
|
chr1 89410166 . G A 180.44 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=300;Dels=0.00;HRun=1;HaplotypeScore=4.60;MQ=98.72;MQ0=0;OQ=6923.36;QD=23.08;RankSumP=0.379063;SB=-2506.58;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.41C>T;refseq.codonCoord=14;refseq.end=89410166;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=180;refseq.name=NM_207398;refseq.name2=GBP7;refseq.positionType=CDS;refseq.proteinCoordStr=p.T14I;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=60;refseq.start=89410166;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 89424659 . T C 1074.87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=402;Dels=0.00;HRun=2;HaplotypeScore=4.41;MQ=96.79;MQ0=0;QD=2.67;RankSumP=0.265595;SB=-467.67;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1652A>G;refseq.codonCoord=551;refseq.end=89424659;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1768;refseq.name=NM_052941;refseq.name2=GBP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.E551G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-56;refseq.start=89424659;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=soap-filterIngatk GT 1/0
|
|
chr1 89424660 . C T 1003.46 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=391;Dels=0.00;HRun=1;HaplotypeScore=4.41;MQ=96.80;MQ0=0;QD=2.57;RankSumP=0.311988;SB=-400.74;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1651G>A;refseq.codonCoord=551;refseq.end=89424660;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1767;refseq.name=NM_052941;refseq.name2=GBP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.E551K;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-57;refseq.start=89424660;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=soap-filterIngatk GT 0/1
|
|
chr1 89424666 rs608339 A T 95.01 ESPStandard;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=356;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=96.70;MQ0=0;QD=0.27;SB=59.33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1645T>A;refseq.codonCoord=549;refseq.end=89424666;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1761;refseq.name=NM_052941;refseq.name2=GBP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.L549M;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-63;refseq.start=89424666;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:258,98:272:-94.70,-81.92,-961.92:99
|
|
chr1 89433579 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=242;Dels=0.00;HRun=1;HaplotypeScore=9.15;MQ=98.72;MQ0=0;OQ=5517.03;QD=22.80;RankSumP=0.184707;SB=-1966.46;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.352G>C;refseq.codonCoord=118;refseq.end=89433579;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=468;refseq.name=NM_052941;refseq.name2=GBP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.D118H;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-12;refseq.start=89433579;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 89500645 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.409984;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1493A>G;refseq.codingCoordStr_2=c.1493A>G;refseq.codonCoord_1=498;refseq.codonCoord_2=498;refseq.end_1=89500645;refseq.end_2=89500645;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1922;refseq.mrnaCoord_2=2030;refseq.name2_1=GBP5;refseq.name2_2=GBP5;refseq.name_1=NM_001134486;refseq.name_2=NM_052942;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K498R;refseq.proteinCoordStr_2=p.K498R;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.start_1=89500645;refseq.start_2=89500645;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=FilteredInAll GT 1/0
|
|
chr1 89619960 . G T 287.91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=210;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.09;MQ0=0;OQ=7633.60;QD=36.35;RankSumP=1.00000;SB=-3400.90;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.991G>T;refseq.codonCoord=331;refseq.end=89619960;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1265;refseq.name=NM_198460;refseq.name2=GBP6;refseq.positionType=CDS;refseq.proteinCoordStr=p.A331S;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=120;refseq.start=89619960;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 89619999 . C T 312.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=236;Dels=0.00;HRun=1;HaplotypeScore=4.29;MQ=97.65;MQ0=0;OQ=8742.99;QD=37.05;RankSumP=1.00000;SB=-3155.36;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1030C>T;refseq.codonCoord=344;refseq.end=89619999;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1304;refseq.name=NM_198460;refseq.name2=GBP6;refseq.positionType=CDS;refseq.proteinCoordStr=p.L344F;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-123;refseq.start=89619999;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 89620032 . A G 197.43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=299;Dels=0.00;HRun=0;HaplotypeScore=8.03;MQ=97.17;MQ0=0;OQ=9928.47;QD=33.21;RankSumP=1.00000;SB=-4073.23;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1063A>G;refseq.codonCoord=355;refseq.end=89620032;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1337;refseq.name=NM_198460;refseq.name2=GBP6;refseq.positionType=CDS;refseq.proteinCoordStr=p.M355V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-90;refseq.start=89620032;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 89622330 . A T 311.02 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.59;MQ0=0;OQ=3492.63;QD=39.24;RankSumP=1.00000;SB=-1677.41;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1559A>T;refseq.codonCoord=520;refseq.end=89622330;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1833;refseq.name=NM_198460;refseq.name2=GBP6;refseq.positionType=CDS;refseq.proteinCoordStr=p.D520V;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=91;refseq.start=89622330;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/1
|
|
chr1 89951331 . A G 217.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=99.00;MQ0=0;OQ=1842.88;QD=36.86;RankSumP=1.00000;SB=-257.73;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.614A>G;refseq.codonCoord=205;refseq.end=89951331;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=856;refseq.name=NM_032270;refseq.name2=LRRC8C;refseq.positionType=CDS;refseq.proteinCoordStr=p.D205G;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=476;refseq.start=89951331;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 90173724 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2509A>C;refseq.codingCoordStr_2=c.2509A>C;refseq.codonCoord_1=837;refseq.codonCoord_2=837;refseq.end_1=90173724;refseq.end_2=90173724;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2934;refseq.mrnaCoord_2=2921;refseq.name2_1=LRRC8D;refseq.name2_2=LRRC8D;refseq.name_1=NM_001134479;refseq.name_2=NM_018103;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T837P;refseq.proteinCoordStr_2=p.T837P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-852;refseq.spliceDist_2=-852;refseq.start_1=90173724;refseq.start_2=90173724;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 90259000 . T G 222.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=364;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=98.76;MQ0=0;OQ=8320.79;QD=22.86;RankSumP=0.327539;SB=-2904.11;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1236T>G;refseq.codonCoord=412;refseq.end=90259000;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1375;refseq.name=NM_182976;refseq.name2=ZNF326;refseq.positionType=CDS;refseq.proteinCoordStr=p.V412V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=62;refseq.start=90259000;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 90265614 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=161;Dels=0.00;HRun=1;HaplotypeScore=4.14;MQ=98.98;MQ0=0;OQ=2933.00;QD=18.22;RankSumP=0.400171;SB=-192.22;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1515G>A;refseq.codonCoord=505;refseq.end=90265614;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1654;refseq.name=NM_182976;refseq.name2=ZNF326;refseq.positionType=CDS;refseq.proteinCoordStr=p.E505E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=114;refseq.start=90265614;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/0
|
|
chr1 91500641 . G A 140.72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=188;Dels=0.00;HRun=0;HaplotypeScore=10.57;MQ=98.90;MQ0=0;OQ=8194.37;QD=43.59;RankSumP=1.00000;SB=-2341.88;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4071C>T;refseq.codonCoord=1357;refseq.end=91500641;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4170;refseq.name=NM_001017975;refseq.name2=HFM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1357A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-16;refseq.start=91500641;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 91554619 . T C 417.47 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=194;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=98.95;MQ0=0;OQ=8224.81;QD=42.40;RankSumP=1.00000;SB=-1773.39;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2815A>G;refseq.codonCoord=939;refseq.end=91554619;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2914;refseq.name=NM_001017975;refseq.name2=HFM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I939V;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=3;refseq.spliceInfo=splice-acceptor_3;refseq.start=91554619;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/1
|
|
chr1 91557475 . G A 188.30 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=427;Dels=0.00;HRun=0;HaplotypeScore=8.10;MQ=98.82;MQ0=0;OQ=18719.76;QD=43.84;RankSumP=1.00000;SB=-8648.19;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2643C>T;refseq.codonCoord=881;refseq.end=91557475;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2742;refseq.name=NM_001017975;refseq.name2=HFM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T881T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-38;refseq.start=91557475;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 91623841 . T C 438.84 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=5089.88;QD=41.38;RankSumP=1.00000;SB=-2303.25;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.633A>G;refseq.codonCoord=211;refseq.end=91623841;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=732;refseq.name=NM_001017975;refseq.name2=HFM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q211Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-122;refseq.start=91623841;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 91632383 . T C 264.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=253;Dels=0.00;HRun=0;HaplotypeScore=8.22;MQ=98.78;MQ0=0;OQ=10693.63;QD=42.27;RankSumP=1.00000;SB=-3749.50;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.349A>G;refseq.codonCoord=117;refseq.end=91632383;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=448;refseq.name=NM_001017975;refseq.name2=HFM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I117V;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-146;refseq.start=91632383;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/1
|
|
chr1 91632389 . A G 335.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=239;Dels=0.00;HRun=1;HaplotypeScore=5.00;MQ=98.92;MQ0=0;OQ=9877.56;QD=41.33;RankSumP=1.00000;SB=-3894.54;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.343T>C;refseq.codonCoord=115;refseq.end=91632389;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=442;refseq.name=NM_001017975;refseq.name2=HFM1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S115P;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-152;refseq.start=91632389;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 91753035 . A G 295.53 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=256;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=98.81;MQ0=0;OQ=9457.08;QD=36.94;RankSumP=1.00000;SB=-3893.56;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.990A>G;refseq.codingCoordStr_2=c.990A>G;refseq.codingCoordStr_3=c.990A>G;refseq.codonCoord_1=330;refseq.codonCoord_2=330;refseq.codonCoord_3=330;refseq.end_1=91753035;refseq.end_2=91753035;refseq.end_3=91753035;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1121;refseq.mrnaCoord_2=1249;refseq.mrnaCoord_3=1155;refseq.name2_1=CDC7;refseq.name2_2=CDC7;refseq.name2_3=CDC7;refseq.name_1=NM_001134419;refseq.name_2=NM_001134420;refseq.name_3=NM_003503;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.T330T;refseq.proteinCoordStr_2=p.T330T;refseq.proteinCoordStr_3=p.T330T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.referenceCodon_3=ACA;refseq.spliceDist_1=72;refseq.spliceDist_2=72;refseq.spliceDist_3=72;refseq.start_1=91753035;refseq.start_2=91753035;refseq.start_3=91753035;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;refseq.variantCodon_3=ACG;set=Intersection GT 1/1
|
|
chr1 91946848 . A G 345.79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=135;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=98.20;MQ0=0;OQ=5477.60;QD=40.57;RankSumP=1.00000;SB=-2595.06;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2247T>C;refseq.codonCoord=749;refseq.end=91946848;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2713;refseq.name=NM_003243;refseq.name2=TGFBR3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T749T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-41;refseq.start=91946848;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 91958245 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=973.97;QD=14.76;RankSumP=0.617261;SB=-279.24;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1206G>A;refseq.codonCoord=402;refseq.end=91958245;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1672;refseq.name=NM_003243;refseq.name2=TGFBR3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P402P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=131;refseq.start=91958245;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 92035462 . T C 71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=96.91;MQ0=0;OQ=2307.52;QD=36.63;RankSumP=1.00000;SB=-1038.83;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.216A>G;refseq.codonCoord=72;refseq.end=92035462;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=682;refseq.name=NM_003243;refseq.name2=TGFBR3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A72A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-31;refseq.start=92035462;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 92201083 . C A 296.34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=321;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.72;MQ0=0;OQ=12642.44;QD=39.38;RankSumP=1.00000;SB=-3582.61;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.184C>A;refseq.codingCoordStr_2=c.184C>A;refseq.codonCoord_1=62;refseq.codonCoord_2=62;refseq.end_1=92201083;refseq.end_2=92201083;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=328;refseq.mrnaCoord_2=533;refseq.name2_1=BRDT;refseq.name2_2=BRDT;refseq.name_1=NM_001726;refseq.name_2=NM_207189;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q62K;refseq.proteinCoordStr_2=p.Q62K;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-9;refseq.spliceDist_2=-9;refseq.spliceInfo_1=splice-donor_-9;refseq.spliceInfo_2=splice-donor_-9;refseq.start_1=92201083;refseq.start_2=92201083;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/1
|
|
chr1 92217845 . C G 280.75 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=392;Dels=0.00;HRun=0;HaplotypeScore=15.42;MQ=98.57;MQ0=0;OQ=6959.82;QD=17.75;RankSumP=0.346204;SB=-2794.68;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1230C>G;refseq.codingCoordStr_2=c.1230C>G;refseq.codonCoord_1=410;refseq.codonCoord_2=410;refseq.end_1=92217845;refseq.end_2=92217845;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1374;refseq.mrnaCoord_2=1579;refseq.name2_1=BRDT;refseq.name2_2=BRDT;refseq.name_1=NM_001726;refseq.name_2=NM_207189;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N410K;refseq.proteinCoordStr_2=p.N410K;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-58;refseq.spliceDist_2=-58;refseq.start_1=92217845;refseq.start_2=92217845;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/0
|
|
chr1 92230431 . C T 351.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.53;MQ0=0;OQ=3178.19;QD=43.54;RankSumP=1.00000;SB=-994.73;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2087C>T;refseq.codingCoordStr_2=c.2087C>T;refseq.codonCoord_1=696;refseq.codonCoord_2=696;refseq.end_1=92230431;refseq.end_2=92230431;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2231;refseq.mrnaCoord_2=2436;refseq.name2_1=BRDT;refseq.name2_2=BRDT;refseq.name_1=NM_001726;refseq.name_2=NM_207189;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P696L;refseq.proteinCoordStr_2=p.P696L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=23;refseq.spliceDist_2=23;refseq.start_1=92230431;refseq.start_2=92230431;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 1/1
|
|
chr1 92367883 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.714T>G;refseq.codonCoord=238;refseq.end=92367883;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=981;refseq.name=NM_183242;refseq.name2=BTBD8;refseq.positionType=CDS;refseq.proteinCoordStr=p.C238W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-39;refseq.start=92367883;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 1/0
|
|
chr1 92719067 . G A 182.06 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=96.29;MQ0=0;OQ=325.06;QD=36.12;RankSumP=1.00000;SB=-50.56;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.465C>T;refseq.codingCoordStr_2=c.465C>T;refseq.codingCoordStr_3=c.465C>T;refseq.codonCoord_1=155;refseq.codonCoord_2=155;refseq.codonCoord_3=155;refseq.end_1=92719067;refseq.end_2=92719067;refseq.end_3=92719067;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=629;refseq.mrnaCoord_2=622;refseq.mrnaCoord_3=715;refseq.name2_1=GFI1;refseq.name2_2=GFI1;refseq.name2_3=GFI1;refseq.name_1=NM_001127215;refseq.name_2=NM_001127216;refseq.name_3=NM_005263;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.C155C;refseq.proteinCoordStr_2=p.C155C;refseq.proteinCoordStr_3=p.C155C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.referenceCodon_3=TGC;refseq.spliceDist_1=167;refseq.spliceDist_2=167;refseq.spliceDist_3=167;refseq.start_1=92719067;refseq.start_2=92719067;refseq.start_3=92719067;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantAA_3=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;refseq.variantCodon_3=TGT;set=filterInsoap-gatk GT 1/1
|
|
chr1 92751942 . A G 299.51 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=190;Dels=0.00;HRun=0;HaplotypeScore=6.16;MQ=98.51;MQ0=0;OQ=7914.35;QD=41.65;RankSumP=1.00000;SB=-3884.57;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2292T>C;refseq.codonCoord=764;refseq.end=92751942;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2302;refseq.name=NM_005665;refseq.name2=EVI5;refseq.positionType=CDS;refseq.proteinCoordStr=p.G764G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=174;refseq.start=92751942;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 92845816 . C A 187.91 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=125;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.61;MQ0=0;OQ=1838.03;QD=14.70;RankSumP=0.295887;SB=-872.16;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1836G>T;refseq.codonCoord=612;refseq.end=92845816;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1846;refseq.name=NM_005665;refseq.name2=EVI5;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q612H;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=57;refseq.start=92845816;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 92862411 . T C 144.44 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=283;Dels=0.00;HRun=1;HaplotypeScore=10.47;MQ=98.66;MQ0=0;OQ=11807.00;QD=41.72;RankSumP=1.00000;SB=-4376.42;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1689A>G;refseq.codonCoord=563;refseq.end=92862411;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1699;refseq.name=NM_005665;refseq.name2=EVI5;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q563Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=69;refseq.start=92862411;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 92863937 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.chr=chr1;refseq.codingCoordStr=c.1620+2;refseq.end=92863937;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=false;refseq.name=NM_005665;refseq.name2=EVI5;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=92863937;refseq.transcriptStrand=-;set=FilteredInAll GT 0/1
|
|
chr1 92933490 . T C 202.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=294;Dels=0.00;HRun=0;HaplotypeScore=12.46;MQ=98.90;MQ0=0;OQ=12308.56;QD=41.87;RankSumP=1.00000;SB=-4021.64;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1006A>G;refseq.codonCoord=336;refseq.end=92933490;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1016;refseq.name=NM_005665;refseq.name2=EVI5;refseq.positionType=CDS;refseq.proteinCoordStr=p.I336V;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-36;refseq.start=92933490;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/1
|
|
chr1 93078905 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=247;Dels=0.00;HRun=2;HaplotypeScore=6.73;MQ=98.95;MQ0=0;OQ=4563.80;QD=18.48;RankSumP=0.167652;SB=-1275.64;SecondBestBaseQ=33;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.end_1=93079900;refseq.end_2=93078905;refseq.haplotypeAlternate_2=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.inCodingRegion_1=false;refseq.mrnaCoord_2=42;refseq.name2_1=RPL5;refseq.name2_2=SNORA66;refseq.name_1=NM_000969;refseq.name_2=NR_002444;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=non_coding_exon;refseq.spliceDist_2=42;refseq.start_1=93078795;refseq.start_2=93078905;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;set=Intersection GT 1/0
|
|
chr1 93353169 . G C 74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=204;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.85;MQ0=0;OQ=10182.95;QD=49.92;RankSumP=1.00000;SB=-4378.55;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.113G>C;refseq.codingCoordStr_2=c.419G>C;refseq.codingCoordStr_3=c.113G>C;refseq.codingCoordStr_4=c.419G>C;refseq.codonCoord_1=38;refseq.codonCoord_2=140;refseq.codonCoord_3=38;refseq.codonCoord_4=140;refseq.end_1=93353169;refseq.end_2=93353169;refseq.end_3=93353169;refseq.end_4=93353169;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=631;refseq.mrnaCoord_2=711;refseq.mrnaCoord_3=430;refseq.mrnaCoord_4=711;refseq.name2_1=MTF2;refseq.name2_2=MTF2;refseq.name2_3=MTF2;refseq.name2_4=MTF2;refseq.name_1=NM_001164391;refseq.name_2=NM_001164392;refseq.name_3=NM_001164393;refseq.name_4=NM_007358;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.C38S;refseq.proteinCoordStr_2=p.C140S;refseq.proteinCoordStr_3=p.C38S;refseq.proteinCoordStr_4=p.C140S;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.referenceCodon_3=TGC;refseq.referenceCodon_4=TGC;refseq.spliceDist_1=37;refseq.spliceDist_2=37;refseq.spliceDist_3=37;refseq.spliceDist_4=37;refseq.start_1=93353169;refseq.start_2=93353169;refseq.start_3=93353169;refseq.start_4=93353169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;refseq.variantCodon_3=TCC;refseq.variantCodon_4=TCC;set=Intersection GT 1/1
|
|
chr1 93392981 . G A 78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=633;Dels=0.00;HRun=1;HaplotypeScore=8.90;MQ=98.90;MQ0=0;OQ=27418.93;QD=43.32;RankSumP=1.00000;SB=-11376.57;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.573C>T;refseq.codingCoordStr_3=c.524C>T;refseq.codonCoord_2=191;refseq.codonCoord_3=175;refseq.end_1=93392981;refseq.end_2=93392981;refseq.end_3=93392981;refseq.frame_2=2;refseq.frame_3=1;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1042;refseq.mrnaCoord_2=1020;refseq.mrnaCoord_3=971;refseq.name2_1=TMED5;refseq.name2_2=TMED5;refseq.name2_3=TMED5;refseq.name_1=NR_030761;refseq.name_2=NM_001167830;refseq.name_3=NM_016040;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.N191N;refseq.proteinCoordStr_3=p.T175I;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Thr;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=ACT;refseq.spliceDist_1=53;refseq.spliceDist_2=53;refseq.spliceDist_3=53;refseq.start_1=93392981;refseq.start_2=93392981;refseq.start_3=93392981;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Asn;refseq.variantAA_3=Ile;refseq.variantCodon_2=AAT;refseq.variantCodon_3=ATT;set=Intersection GT 1/1
|
|
chr1 93418795 . T C 121.83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=97.96;MQ0=0;OQ=1536.65;QD=36.59;RankSumP=1.00000;SB=-272.78;SecondBestBaseQ=0;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.-408A>G;refseq.codingCoordStr_3=c.-408A>G;refseq.codingCoordStr_4=c.120T>C;refseq.codonCoord_4=40;refseq.end_1=93418795;refseq.end_2=93418795;refseq.end_3=93418795;refseq.end_4=93418795;refseq.frame_4=2;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=40;refseq.mrnaCoord_2=40;refseq.mrnaCoord_3=40;refseq.mrnaCoord_4=288;refseq.name2_1=TMED5;refseq.name2_2=TMED5;refseq.name2_3=TMED5;refseq.name2_4=CCDC18;refseq.name_1=NR_030761;refseq.name_2=NM_001167830;refseq.name_3=NM_016040;refseq.name_4=NM_206886;refseq.numMatchingRecords=4;refseq.positionType_1=non_coding_exon;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=CDS;refseq.proteinCoordStr_4=p.L40L;refseq.referenceAA_4=Leu;refseq.referenceCodon_4=CTT;refseq.spliceDist_1=40;refseq.spliceDist_2=40;refseq.spliceDist_3=40;refseq.spliceDist_4=-233;refseq.start_1=93418795;refseq.start_2=93418795;refseq.start_3=93418795;refseq.start_4=93418795;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=+;refseq.variantAA_4=Leu;refseq.variantCodon_4=CTC;set=Intersection GT 1/1
|
|
chr1 93419006 . C T 303.15 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=114;Dels=0.00;HRun=1;HaplotypeScore=2.78;MQ=97.99;MQ0=0;OQ=4330.04;QD=37.98;RankSumP=1.00000;SB=-1150.99;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.331C>T;refseq.codonCoord=111;refseq.end=93419006;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=499;refseq.name=NM_206886;refseq.name2=CCDC18;refseq.positionType=CDS;refseq.proteinCoordStr=p.L111F;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-22;refseq.start=93419006;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 93445311 . A C 433.76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.59;MQ0=0;OQ=4494.32;QD=39.77;RankSumP=1.00000;SB=-1914.28;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1331A>C;refseq.codonCoord=444;refseq.end=93445311;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1499;refseq.name=NM_206886;refseq.name2=CCDC18;refseq.positionType=CDS;refseq.proteinCoordStr=p.N444T;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=60;refseq.start=93445311;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 93821073 . C G 131.98 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=161;Dels=0.00;HRun=1;HaplotypeScore=6.85;MQ=98.86;MQ0=0;OQ=3102.63;QD=19.27;RankSumP=0.377792;SB=-1206.77;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1059G>C;refseq.codonCoord=353;refseq.end=93821073;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1302;refseq.name=NM_003567;refseq.name2=BCAR3;refseq.positionType=CDS;refseq.proteinCoordStr=p.S353S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=26;refseq.start=93821073;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/0
|
|
chr1 94239247 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.30;MQ=99.00;MQ0=0;OQ=645.03;QD=11.73;RankSumP=0.482885;SB=-125.62;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6285T>C;refseq.codonCoord=2095;refseq.end=94239247;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6389;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.D2095D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=3;refseq.spliceInfo=splice-acceptor_3;refseq.start=94239247;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 0/1
|
|
chr1 94240020 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6264C>G;refseq.codonCoord=2088;refseq.end=94240020;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6368;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.C2088W;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-19;refseq.start=94240020;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 0/1
|
|
chr1 94243663 . A G 205.13 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=281;Dels=0.00;HRun=0;HaplotypeScore=7.40;MQ=98.87;MQ0=0;OQ=11040.07;QD=39.29;RankSumP=1.00000;SB=-3473.27;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6069T>C;refseq.codonCoord=2023;refseq.end=94243663;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6173;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.I2023I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=64;refseq.start=94243663;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 94246433 . T C 100.83 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=283;Dels=0.00;HRun=2;HaplotypeScore=6.93;MQ=98.87;MQ0=0;OQ=4150.98;QD=14.67;RankSumP=0.191402;SB=-1274.21;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5844A>G;refseq.codonCoord=1948;refseq.end=94246433;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5948;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1948P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=9;refseq.spliceInfo=splice-acceptor_9;refseq.start=94246433;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/0
|
|
chr1 94246916 . T C 135.22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=698;Dels=0.00;HRun=0;HaplotypeScore=15.83;MQ=98.79;MQ0=0;OQ=14217.90;QD=20.37;RankSumP=0.415620;SB=-4619.17;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5814A>G;refseq.codonCoord=1938;refseq.end=94246916;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5918;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1938L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=-22;refseq.start=94246916;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/0
|
|
chr1 94248976 . C G 110.74 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=146;Dels=0.00;HRun=1;HaplotypeScore=4.71;MQ=98.62;MQ0=0;OQ=3144.33;QD=21.54;RankSumP=0.459199;SB=-787.46;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5682G>C;refseq.codonCoord=1894;refseq.end=94248976;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5786;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1894L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-33;refseq.start=94248976;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/0
|
|
chr1 94285153 . C T 155.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=186;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=98.93;MQ0=0;OQ=4083.43;QD=21.95;RankSumP=0.0167750;SB=-979.43;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2828G>A;refseq.codonCoord=943;refseq.end=94285153;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2932;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R943Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=85;refseq.start=94285153;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 94351136 . T C 451.52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=181;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=98.70;MQ0=0;OQ=7090.23;QD=39.17;RankSumP=1.00000;SB=-2675.17;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.141A>G;refseq.codonCoord=47;refseq.end=94351136;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=245;refseq.name=NM_000350;refseq.name2=ABCA4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P47P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-20;refseq.start=94351136;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 94412035 . C T 96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=688;Dels=0.00;HRun=0;HaplotypeScore=13.71;MQ=98.90;MQ0=0;OQ=28890.72;QD=41.99;RankSumP=1.00000;SB=-12457.53;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3764G>A;refseq.codonCoord=1255;refseq.end=94412035;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4133;refseq.name=NM_004815;refseq.name2=ARHGAP29;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1255D;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=859;refseq.start=94412035;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 94702933 . G A 67 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=172;Dels=0.00;HRun=5;HaplotypeScore=6.18;MQ=98.59;MQ0=0;OQ=7515.48;QD=43.69;RankSumP=1.00000;SB=-3166.43;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.162G>A;refseq.codingCoordStr_2=c.162G>A;refseq.codonCoord_1=54;refseq.codonCoord_2=54;refseq.end_1=94702933;refseq.end_2=94702933;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=264;refseq.mrnaCoord_2=264;refseq.name2_1=ABCD3;refseq.name2_2=ABCD3;refseq.name_1=NM_001122674;refseq.name_2=NM_002858;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K54K;refseq.proteinCoordStr_2=p.K54K;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=15;refseq.spliceDist_2=15;refseq.start_1=94702933;refseq.start_2=94702933;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=Intersection GT 1/1
|
|
chr1 94774188 . A C 280.26 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=168;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.82;MQ0=0;OQ=6298.24;QD=37.49;RankSumP=1.00000;SB=-2604.26;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.333T>G;refseq.codonCoord=111;refseq.end=94774188;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=512;refseq.name=NM_001993;refseq.name2=F3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P111P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-80;refseq.start=94774188;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 95083528 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.992T>C;refseq.codingCoordStr_2=c.848T>C;refseq.codonCoord_1=331;refseq.codonCoord_2=283;refseq.end_1=95083528;refseq.end_2=95083528;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1099;refseq.mrnaCoord_2=1037;refseq.name2_1=SLC44A3;refseq.name2_2=SLC44A3;refseq.name_1=NM_001114106;refseq.name_2=NM_152369;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F331S;refseq.proteinCoordStr_2=p.F283S;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.spliceDist_1=-81;refseq.spliceDist_2=-81;refseq.start_1=95083528;refseq.start_2=95083528;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=FilteredInAll GT 1/0
|
|
chr1 95310910 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.133T>G;refseq.codonCoord=45;refseq.end=95310910;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=186;refseq.name=NM_144988;refseq.name2=ALG14;refseq.positionType=CDS;refseq.proteinCoordStr=p.S45A;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-4;refseq.spliceInfo=splice-donor_-4;refseq.start=95310910;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 95310996 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.47T>G;refseq.codonCoord=16;refseq.end=95310996;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=100;refseq.name=NM_144988;refseq.name2=ALG14;refseq.positionType=CDS;refseq.proteinCoordStr=p.V16G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-90;refseq.start=95310996;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 95482409 . T C 208.97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=300;Dels=0.00;HRun=0;HaplotypeScore=14.15;MQ=98.68;MQ0=0;OQ=11326.57;QD=37.76;RankSumP=1.00000;SB=-5336.49;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.140T>C;refseq.codingCoordStr_2=c.140T>C;refseq.codonCoord_1=47;refseq.codonCoord_2=47;refseq.end_1=95482409;refseq.end_2=95482409;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=216;refseq.mrnaCoord_2=216;refseq.name2_1=RWDD3;refseq.name2_2=RWDD3;refseq.name_1=NM_001128142;refseq.name_2=NM_015485;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V47A;refseq.proteinCoordStr_2=p.V47A;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=55;refseq.spliceDist_2=55;refseq.start_1=95482409;refseq.start_2=95482409;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/1
|
|
chr1 95482527 . T G 350.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=210;Dels=0.00;HRun=0;HaplotypeScore=4.29;MQ=99.00;MQ0=0;OQ=8447.75;QD=40.23;RankSumP=1.00000;SB=-4003.50;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.258T>G;refseq.codingCoordStr_2=c.258T>G;refseq.codonCoord_1=86;refseq.codonCoord_2=86;refseq.end_1=95482527;refseq.end_2=95482527;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=334;refseq.mrnaCoord_2=334;refseq.name2_1=RWDD3;refseq.name2_2=RWDD3;refseq.name_1=NM_001128142;refseq.name_2=NM_015485;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N86K;refseq.proteinCoordStr_2=p.N86K;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=173;refseq.spliceDist_2=173;refseq.start_1=95482527;refseq.start_2=95482527;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/1
|
|
chr1 97045044 . A G 314.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=322;Dels=0.00;HRun=0;HaplotypeScore=4.42;MQ=98.94;MQ0=0;OQ=6985.45;QD=21.69;RankSumP=0.250517;SB=-2608.15;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1113A>G;refseq.codonCoord=371;refseq.end=97045044;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1359;refseq.name=NM_021190;refseq.name2=PTBP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L371L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=35;refseq.start=97045044;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 97753983 . T C 134.98 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=166;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.91;MQ0=0;OQ=4178.85;QD=25.17;RankSumP=0.438696;SB=-1810.66;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1627A>G;refseq.codonCoord=543;refseq.end=97753983;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1764;refseq.name=NM_000110;refseq.name2=DPYD;refseq.positionType=CDS;refseq.proteinCoordStr=p.I543V;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=103;refseq.start=97753983;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/0
|
|
chr1 97754009 . C T 118.51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=205;Dels=0.00;HRun=1;HaplotypeScore=4.99;MQ=98.96;MQ0=0;OQ=2935.86;QD=14.32;RankSumP=0.173906;SB=-1337.21;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1601G>A;refseq.codonCoord=534;refseq.end=97754009;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1738;refseq.name=NM_000110;refseq.name2=DPYD;refseq.positionType=CDS;refseq.proteinCoordStr=p.S534N;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=77;refseq.start=97754009;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 98121473 . G A 307.50 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=277;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=98.34;MQ0=0;OQ=11524.14;QD=41.60;RankSumP=1.00000;SB=-5182.89;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.85C>T;refseq.codingCoordStr_2=c.85C>T;refseq.codonCoord_1=29;refseq.codonCoord_2=29;refseq.end_1=98121473;refseq.end_2=98121473;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=222;refseq.mrnaCoord_2=222;refseq.name2_1=DPYD;refseq.name2_2=DPYD;refseq.name_1=NM_000110;refseq.name_2=NM_001160301;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R29C;refseq.proteinCoordStr_2=p.R29C;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGT;refseq.referenceCodon_2=CGT;refseq.spliceDist_1=46;refseq.spliceDist_2=46;refseq.start_1=98121473;refseq.start_2=98121473;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;set=Intersection GT 1/1
|
|
chr1 98933772 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=167;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=98.95;MQ0=0;OQ=2987.54;QD=17.89;RankSumP=0.391745;SB=-668.10;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.750C>A;refseq.codingCoordStr_2=c.558C>A;refseq.codonCoord_1=250;refseq.codonCoord_2=186;refseq.end_1=98933772;refseq.end_2=98933772;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=802;refseq.mrnaCoord_2=922;refseq.name2_1=SNX7;refseq.name2_2=SNX7;refseq.name_1=NM_015976;refseq.name_2=NM_152238;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F250L;refseq.proteinCoordStr_2=p.F186L;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.spliceDist_1=-89;refseq.spliceDist_2=-89;refseq.start_1=98933772;refseq.start_2=98933772;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=TTA;refseq.variantCodon_2=TTA;set=Intersection GT 1/0
|
|
chr1 98937022 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=351;Dels=0.00;HRun=1;HaplotypeScore=14.77;MQ=96.74;MQ0=1;OQ=6022.29;QD=17.16;RankSumP=0.376407;SB=-2057.45;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1011G>A;refseq.codingCoordStr_2=c.819G>A;refseq.codonCoord_1=337;refseq.codonCoord_2=273;refseq.end_1=98937022;refseq.end_2=98937022;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1063;refseq.mrnaCoord_2=1183;refseq.name2_1=SNX7;refseq.name2_2=SNX7;refseq.name_1=NM_015976;refseq.name_2=NM_152238;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E337E;refseq.proteinCoordStr_2=p.E273E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.start_1=98937022;refseq.start_2=98937022;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=Intersection GT 1/0
|
|
chr1 98998215 . G A 85 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=390;Dels=0.00;HRun=1;HaplotypeScore=10.77;MQ=98.42;MQ0=0;OQ=16787.56;QD=43.05;RankSumP=1.00000;SB=-6842.33;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1296G>A;refseq.codingCoordStr_2=c.951G>A;refseq.codonCoord_1=432;refseq.codonCoord_2=317;refseq.end_1=98998215;refseq.end_2=98998215;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1348;refseq.mrnaCoord_2=1315;refseq.name2_1=SNX7;refseq.name2_2=SNX7;refseq.name_1=NM_015976;refseq.name_2=NM_152238;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E432E;refseq.proteinCoordStr_2=p.E317E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=18;refseq.spliceDist_2=18;refseq.start_1=98998215;refseq.start_2=98998215;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=Intersection GT 1/1
|
|
chr1 99191235 . G C 232.07 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=302;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=98.83;MQ0=0;OQ=6862.53;QD=22.72;RankSumP=0.389605;SB=-2941.95;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.600C>G;refseq.codingCoordStr_2=c.600C>G;refseq.codonCoord_1=200;refseq.codonCoord_2=200;refseq.end_1=99191235;refseq.end_2=99191235;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=822;refseq.mrnaCoord_2=822;refseq.name2_1=LPPR5;refseq.name2_2=LPPR5;refseq.name_1=NM_001010861;refseq.name_2=NM_001037317;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V200V;refseq.proteinCoordStr_2=p.V200V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=-22;refseq.spliceDist_2=-22;refseq.start_1=99191235;refseq.start_2=99191235;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=Intersection GT 0/1
|
|
chr1 100108949 . C T 99.01 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=153;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=2147.85;QD=14.04;RankSumP=0.224082;SB=-786.53;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.894C>T;refseq.codingCoordStr_2=c.894C>T;refseq.codingCoordStr_3=c.894C>T;refseq.codingCoordStr_4=c.894C>T;refseq.codingCoordStr_5=c.843C>T;refseq.codingCoordStr_6=c.846C>T;refseq.codonCoord_1=298;refseq.codonCoord_2=298;refseq.codonCoord_3=298;refseq.codonCoord_4=298;refseq.codonCoord_5=281;refseq.codonCoord_6=282;refseq.end_1=100108949;refseq.end_2=100108949;refseq.end_3=100108949;refseq.end_4=100108949;refseq.end_5=100108949;refseq.end_6=100108949;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeAlternate_6=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1372;refseq.mrnaCoord_2=1294;refseq.mrnaCoord_3=1092;refseq.mrnaCoord_4=1032;refseq.mrnaCoord_5=1105;refseq.mrnaCoord_6=1105;refseq.name2_1=AGL;refseq.name2_2=AGL;refseq.name2_3=AGL;refseq.name2_4=AGL;refseq.name2_5=AGL;refseq.name2_6=AGL;refseq.name_1=NM_000028;refseq.name_2=NM_000642;refseq.name_3=NM_000643;refseq.name_4=NM_000644;refseq.name_5=NM_000645;refseq.name_6=NM_000646;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.L298L;refseq.proteinCoordStr_2=p.L298L;refseq.proteinCoordStr_3=p.L298L;refseq.proteinCoordStr_4=p.L298L;refseq.proteinCoordStr_5=p.L281L;refseq.proteinCoordStr_6=p.L282L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceAA_4=Leu;refseq.referenceAA_5=Leu;refseq.referenceAA_6=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.referenceCodon_3=CTC;refseq.referenceCodon_4=CTC;refseq.referenceCodon_5=CTC;refseq.referenceCodon_6=CTC;refseq.spliceDist_1=48;refseq.spliceDist_2=48;refseq.spliceDist_3=48;refseq.spliceDist_4=48;refseq.spliceDist_5=48;refseq.spliceDist_6=48;refseq.start_1=100108949;refseq.start_2=100108949;refseq.start_3=100108949;refseq.start_4=100108949;refseq.start_5=100108949;refseq.start_6=100108949;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Leu;refseq.variantAA_6=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;refseq.variantCodon_3=CTT;refseq.variantCodon_4=CTT;refseq.variantCodon_5=CTT;refseq.variantCodon_6=CTT;set=Intersection GT 0/1
|
|
chr1 100148976 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=3;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.3821T>C;refseq.codingCoordStr_2=c.3821T>C;refseq.codingCoordStr_3=c.3821T>C;refseq.codingCoordStr_4=c.3821T>C;refseq.codingCoordStr_5=c.3770T>C;refseq.codingCoordStr_6=c.3773T>C;refseq.codonCoord_1=1274;refseq.codonCoord_2=1274;refseq.codonCoord_3=1274;refseq.codonCoord_4=1274;refseq.codonCoord_5=1257;refseq.codonCoord_6=1258;refseq.end_1=100148976;refseq.end_2=100148976;refseq.end_3=100148976;refseq.end_4=100148976;refseq.end_5=100148976;refseq.end_6=100148976;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=4299;refseq.mrnaCoord_2=4221;refseq.mrnaCoord_3=4019;refseq.mrnaCoord_4=3959;refseq.mrnaCoord_5=4032;refseq.mrnaCoord_6=4032;refseq.name2_1=AGL;refseq.name2_2=AGL;refseq.name2_3=AGL;refseq.name2_4=AGL;refseq.name2_5=AGL;refseq.name2_6=AGL;refseq.name_1=NM_000028;refseq.name_2=NM_000642;refseq.name_3=NM_000643;refseq.name_4=NM_000644;refseq.name_5=NM_000645;refseq.name_6=NM_000646;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.I1274T;refseq.proteinCoordStr_2=p.I1274T;refseq.proteinCoordStr_3=p.I1274T;refseq.proteinCoordStr_4=p.I1274T;refseq.proteinCoordStr_5=p.I1257T;refseq.proteinCoordStr_6=p.I1258T;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.spliceDist_1=-16;refseq.spliceDist_2=-16;refseq.spliceDist_3=-16;refseq.spliceDist_4=-16;refseq.spliceDist_5=-16;refseq.spliceDist_6=-16;refseq.start_1=100148976;refseq.start_2=100148976;refseq.start_3=100148976;refseq.start_4=100148976;refseq.start_5=100148976;refseq.start_6=100148976;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantAA_5=Thr;refseq.variantAA_6=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;refseq.variantCodon_3=ACC;refseq.variantCodon_4=ACC;refseq.variantCodon_5=ACC;refseq.variantCodon_6=ACC;set=FilteredInAll GT 1/0
|
|
chr1 100154751 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=7.07432e-05;SecondBestBaseQ=16;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.4357T>G;refseq.codingCoordStr_2=c.4357T>G;refseq.codingCoordStr_3=c.4357T>G;refseq.codingCoordStr_4=c.4357T>G;refseq.codingCoordStr_5=c.4306T>G;refseq.codingCoordStr_6=c.4309T>G;refseq.codonCoord_1=1453;refseq.codonCoord_2=1453;refseq.codonCoord_3=1453;refseq.codonCoord_4=1453;refseq.codonCoord_5=1436;refseq.codonCoord_6=1437;refseq.end_1=100154751;refseq.end_2=100154751;refseq.end_3=100154751;refseq.end_4=100154751;refseq.end_5=100154751;refseq.end_6=100154751;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=4835;refseq.mrnaCoord_2=4757;refseq.mrnaCoord_3=4555;refseq.mrnaCoord_4=4495;refseq.mrnaCoord_5=4568;refseq.mrnaCoord_6=4568;refseq.name2_1=AGL;refseq.name2_2=AGL;refseq.name2_3=AGL;refseq.name2_4=AGL;refseq.name2_5=AGL;refseq.name2_6=AGL;refseq.name_1=NM_000028;refseq.name_2=NM_000642;refseq.name_3=NM_000643;refseq.name_4=NM_000644;refseq.name_5=NM_000645;refseq.name_6=NM_000646;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.W1453G;refseq.proteinCoordStr_2=p.W1453G;refseq.proteinCoordStr_3=p.W1453G;refseq.proteinCoordStr_4=p.W1453G;refseq.proteinCoordStr_5=p.W1436G;refseq.proteinCoordStr_6=p.W1437G;refseq.referenceAA_1=Trp;refseq.referenceAA_2=Trp;refseq.referenceAA_3=Trp;refseq.referenceAA_4=Trp;refseq.referenceAA_5=Trp;refseq.referenceAA_6=Trp;refseq.referenceCodon_1=TGG;refseq.referenceCodon_2=TGG;refseq.referenceCodon_3=TGG;refseq.referenceCodon_4=TGG;refseq.referenceCodon_5=TGG;refseq.referenceCodon_6=TGG;refseq.spliceDist_1=10;refseq.spliceDist_2=10;refseq.spliceDist_3=10;refseq.spliceDist_4=10;refseq.spliceDist_5=10;refseq.spliceDist_6=10;refseq.spliceInfo_1=splice-acceptor_10;refseq.spliceInfo_2=splice-acceptor_10;refseq.spliceInfo_3=splice-acceptor_10;refseq.spliceInfo_4=splice-acceptor_10;refseq.spliceInfo_5=splice-acceptor_10;refseq.spliceInfo_6=splice-acceptor_10;refseq.start_1=100154751;refseq.start_2=100154751;refseq.start_3=100154751;refseq.start_4=100154751;refseq.start_5=100154751;refseq.start_6=100154751;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantAA_5=Gly;refseq.variantAA_6=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;refseq.variantCodon_5=GGG;refseq.variantCodon_6=GGG;set=FilteredInAll GT 1/0
|
|
chr1 100348521 . G A 428.08 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=132;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=5557.95;QD=42.11;RankSumP=1.00000;SB=-2318.59;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.776C>T;refseq.codonCoord=259;refseq.end=100348521;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=917;refseq.name=NM_194292;refseq.name2=SASS6;refseq.positionType=CDS;refseq.proteinCoordStr=p.A259V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-86;refseq.start=100348521;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 100371454 . G A 386.68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=97.60;MQ0=0;OQ=2403.44;QD=38.77;RankSumP=1.00000;SB=-590.35;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.142G>A;refseq.codonCoord=48;refseq.end=100371454;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=161;refseq.name=NM_019083;refseq.name2=CCDC76;refseq.positionType=CDS;refseq.proteinCoordStr=p.A48T;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-6;refseq.spliceInfo=splice-donor_-6;refseq.start=100371454;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 100371455 . C T 372.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=97.60;MQ0=0;OQ=2451.98;QD=39.55;RankSumP=1.00000;SB=-578.76;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.143C>T;refseq.codonCoord=48;refseq.end=100371455;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=162;refseq.name=NM_019083;refseq.name2=CCDC76;refseq.positionType=CDS;refseq.proteinCoordStr=p.A48V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-5;refseq.spliceInfo=splice-donor_-5;refseq.start=100371455;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 100444648 . T C 325.41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=138;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=5661.07;QD=41.02;RankSumP=1.00000;SB=-2580.71;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1150A>G;refseq.codonCoord=384;refseq.end=100444648;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1183;refseq.name=NM_001918;refseq.name2=DBT;refseq.positionType=CDS;refseq.proteinCoordStr=p.S384G;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-60;refseq.start=100444648;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 1/1
|
|
chr1 100513762 . C G 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=2;RankSumP=1.01390e-07;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.674C>G;refseq.codingCoordStr_2=c.635C>G;refseq.codonCoord_1=225;refseq.codonCoord_2=212;refseq.end_1=100513762;refseq.end_2=100513762;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=892;refseq.mrnaCoord_2=853;refseq.name2_1=RTCD1;refseq.name2_2=RTCD1;refseq.name_1=NM_001130841;refseq.name_2=NM_003729;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A225G;refseq.proteinCoordStr_2=p.A212G;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=20;refseq.spliceDist_2=20;refseq.start_1=100513762;refseq.start_2=100513762;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 100969447 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1310A>G;refseq.codingCoordStr_2=c.1034A>G;refseq.codonCoord_1=437;refseq.codonCoord_2=345;refseq.end_1=100969447;refseq.end_2=100969447;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1430;refseq.mrnaCoord_2=1154;refseq.name2_1=VCAM1;refseq.name2_2=VCAM1;refseq.name_1=NM_001078;refseq.name_2=NM_080682;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E437G;refseq.proteinCoordStr_2=p.E345G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=106;refseq.spliceDist_2=106;refseq.start_1=100969447;refseq.start_2=100969447;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 100976337 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2130A>C;refseq.codingCoordStr_2=c.1854A>C;refseq.codonCoord_1=710;refseq.codonCoord_2=618;refseq.end_1=100976337;refseq.end_2=100976337;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2250;refseq.mrnaCoord_2=1974;refseq.name2_1=VCAM1;refseq.name2_2=VCAM1;refseq.name_1=NM_001078;refseq.name_2=NM_080682;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I710I;refseq.proteinCoordStr_2=p.I618I;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATA;refseq.referenceCodon_2=ATA;refseq.spliceDist_1=71;refseq.spliceDist_2=71;refseq.start_1=100976337;refseq.start_2=100976337;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;set=FilteredInAll GT 0/1
|
|
chr1 100976415 . G A 60 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=357;Dels=0.00;HRun=2;HaplotypeScore=5.13;MQ=98.82;MQ0=0;OQ=15257.47;QD=42.74;RankSumP=1.00000;SB=-6296.36;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2208G>A;refseq.codingCoordStr_2=c.1932G>A;refseq.codonCoord_1=736;refseq.codonCoord_2=644;refseq.end_1=100976415;refseq.end_2=100976415;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2328;refseq.mrnaCoord_2=2052;refseq.name2_1=VCAM1;refseq.name2_2=VCAM1;refseq.name_1=NM_001078;refseq.name_2=NM_080682;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K736K;refseq.proteinCoordStr_2=p.K644K;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=149;refseq.spliceDist_2=149;refseq.start_1=100976415;refseq.start_2=100976415;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=Intersection GT 1/1
|
|
chr1 103117970 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.4783A>C;refseq.codingCoordStr_2=c.5131A>C;refseq.codingCoordStr_3=c.5167A>C;refseq.codingCoordStr_4=c.5014A>C;refseq.codonCoord_1=1595;refseq.codonCoord_2=1711;refseq.codonCoord_3=1723;refseq.codonCoord_4=1672;refseq.end_1=103117970;refseq.end_2=103117970;refseq.end_3=103117970;refseq.end_4=103117970;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=5101;refseq.mrnaCoord_2=5449;refseq.mrnaCoord_3=5485;refseq.mrnaCoord_4=5332;refseq.name2_1=COL11A1;refseq.name2_2=COL11A1;refseq.name2_3=COL11A1;refseq.name2_4=COL11A1;refseq.name_1=NM_001168249;refseq.name_2=NM_001854;refseq.name_3=NM_080629;refseq.name_4=NM_080630;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T1595P;refseq.proteinCoordStr_2=p.T1711P;refseq.proteinCoordStr_3=p.T1723P;refseq.proteinCoordStr_4=p.T1672P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.spliceDist_1=91;refseq.spliceDist_2=91;refseq.spliceDist_3=91;refseq.spliceDist_4=91;refseq.start_1=103117970;refseq.start_2=103117970;refseq.start_3=103117970;refseq.start_4=103117970;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;set=FilteredInAll GT 1/0
|
|
chr1 103126726 . A G 165.53 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=178;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.84;MQ0=0;OQ=3072.29;QD=17.26;RankSumP=0.130466;SB=-970.53;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.4255T>C;refseq.codingCoordStr_2=c.4603T>C;refseq.codingCoordStr_3=c.4639T>C;refseq.codingCoordStr_4=c.4486T>C;refseq.codonCoord_1=1419;refseq.codonCoord_2=1535;refseq.codonCoord_3=1547;refseq.codonCoord_4=1496;refseq.end_1=103126726;refseq.end_2=103126726;refseq.end_3=103126726;refseq.end_4=103126726;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=4573;refseq.mrnaCoord_2=4921;refseq.mrnaCoord_3=4957;refseq.mrnaCoord_4=4804;refseq.name2_1=COL11A1;refseq.name2_2=COL11A1;refseq.name2_3=COL11A1;refseq.name2_4=COL11A1;refseq.name_1=NM_001168249;refseq.name_2=NM_001854;refseq.name_3=NM_080629;refseq.name_4=NM_080630;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.S1419P;refseq.proteinCoordStr_2=p.S1535P;refseq.proteinCoordStr_3=p.S1547P;refseq.proteinCoordStr_4=p.S1496P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_1=TCT;refseq.referenceCodon_2=TCT;refseq.referenceCodon_3=TCT;refseq.referenceCodon_4=TCT;refseq.spliceDist_1=-6;refseq.spliceDist_2=-6;refseq.spliceDist_3=-6;refseq.spliceDist_4=-6;refseq.spliceInfo_1=splice-donor_-6;refseq.spliceInfo_2=splice-donor_-6;refseq.spliceInfo_3=splice-donor_-6;refseq.spliceInfo_4=splice-donor_-6;refseq.start_1=103126726;refseq.start_2=103126726;refseq.start_3=103126726;refseq.start_4=103126726;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;set=Intersection GT 0/1
|
|
chr1 103127016 . A G 225.23 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=579;Dels=0.00;HRun=0;HaplotypeScore=6.27;MQ=98.84;MQ0=0;OQ=12250.35;QD=21.16;RankSumP=0.0719995;SB=-3876.39;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.4164T>C;refseq.codingCoordStr_2=c.4512T>C;refseq.codingCoordStr_3=c.4548T>C;refseq.codingCoordStr_4=c.4395T>C;refseq.codonCoord_1=1388;refseq.codonCoord_2=1504;refseq.codonCoord_3=1516;refseq.codonCoord_4=1465;refseq.end_1=103127016;refseq.end_2=103127016;refseq.end_3=103127016;refseq.end_4=103127016;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=4482;refseq.mrnaCoord_2=4830;refseq.mrnaCoord_3=4866;refseq.mrnaCoord_4=4713;refseq.name2_1=COL11A1;refseq.name2_2=COL11A1;refseq.name2_3=COL11A1;refseq.name2_4=COL11A1;refseq.name_1=NM_001168249;refseq.name_2=NM_001854;refseq.name_3=NM_080629;refseq.name_4=NM_080630;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.G1388G;refseq.proteinCoordStr_2=p.G1504G;refseq.proteinCoordStr_3=p.G1516G;refseq.proteinCoordStr_4=p.G1465G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceAA_4=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.referenceCodon_3=GGT;refseq.referenceCodon_4=GGT;refseq.spliceDist_1=-7;refseq.spliceDist_2=-7;refseq.spliceDist_3=-7;refseq.spliceDist_4=-7;refseq.spliceInfo_1=splice-donor_-7;refseq.spliceInfo_2=splice-donor_-7;refseq.spliceInfo_3=splice-donor_-7;refseq.spliceInfo_4=splice-donor_-7;refseq.start_1=103127016;refseq.start_2=103127016;refseq.start_3=103127016;refseq.start_4=103127016;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;refseq.variantCodon_3=GGC;refseq.variantCodon_4=GGC;set=Intersection GT 0/1
|
|
chr1 103178480 . G A 258.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=97.50;MQ0=0;OQ=2128.36;QD=18.84;RankSumP=0.193351;SB=-481.54;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.3027C>T;refseq.codingCoordStr_2=c.3375C>T;refseq.codingCoordStr_3=c.3411C>T;refseq.codingCoordStr_4=c.3258C>T;refseq.codonCoord_1=1009;refseq.codonCoord_2=1125;refseq.codonCoord_3=1137;refseq.codonCoord_4=1086;refseq.end_1=103178480;refseq.end_2=103178480;refseq.end_3=103178480;refseq.end_4=103178480;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=3345;refseq.mrnaCoord_2=3693;refseq.mrnaCoord_3=3729;refseq.mrnaCoord_4=3576;refseq.name2_1=COL11A1;refseq.name2_2=COL11A1;refseq.name2_3=COL11A1;refseq.name2_4=COL11A1;refseq.name_1=NM_001168249;refseq.name_2=NM_001854;refseq.name_3=NM_080629;refseq.name_4=NM_080630;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.D1009D;refseq.proteinCoordStr_2=p.D1125D;refseq.proteinCoordStr_3=p.D1137D;refseq.proteinCoordStr_4=p.D1086D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.referenceCodon_3=GAC;refseq.referenceCodon_4=GAC;refseq.spliceDist_1=-10;refseq.spliceDist_2=-10;refseq.spliceDist_3=-10;refseq.spliceDist_4=-10;refseq.spliceInfo_1=splice-donor_-10;refseq.spliceInfo_2=splice-donor_-10;refseq.spliceInfo_3=splice-donor_-10;refseq.spliceInfo_4=splice-donor_-10;refseq.start_1=103178480;refseq.start_2=103178480;refseq.start_3=103178480;refseq.start_4=103178480;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantAA_4=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;refseq.variantCodon_3=GAT;refseq.variantCodon_4=GAT;set=Intersection GT 1/0
|
|
chr1 103240924 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=300;Dels=0.00;HRun=2;HaplotypeScore=37.46;MQ=96.80;MQ0=0;OQ=465.47;QD=1.55;RankSumP=0.00000;SB=432.39;SecondBestBaseQ=24;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1662T>G;refseq.codingCoordStr_2=c.2010T>G;refseq.codingCoordStr_3=c.2046T>G;refseq.codingCoordStr_4=c.1893T>G;refseq.codonCoord_1=554;refseq.codonCoord_2=670;refseq.codonCoord_3=682;refseq.codonCoord_4=631;refseq.end_1=103240924;refseq.end_2=103240924;refseq.end_3=103240924;refseq.end_4=103240924;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1980;refseq.mrnaCoord_2=2328;refseq.mrnaCoord_3=2364;refseq.mrnaCoord_4=2211;refseq.name2_1=COL11A1;refseq.name2_2=COL11A1;refseq.name2_3=COL11A1;refseq.name2_4=COL11A1;refseq.name_1=NM_001168249;refseq.name_2=NM_001854;refseq.name_3=NM_080629;refseq.name_4=NM_080630;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.G554G;refseq.proteinCoordStr_2=p.G670G;refseq.proteinCoordStr_3=p.G682G;refseq.proteinCoordStr_4=p.G631G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceAA_4=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.referenceCodon_3=GGT;refseq.referenceCodon_4=GGT;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.spliceDist_3=12;refseq.spliceDist_4=12;refseq.start_1=103240924;refseq.start_2=103240924;refseq.start_3=103240924;refseq.start_4=103240924;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;set=FilteredInAll GT 0/1
|
|
chr1 104031684 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.401199;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1446C>T;refseq.codingCoordStr_2=c.1446C>T;refseq.codingCoordStr_3=c.1446C>T;refseq.codingCoordStr_4=c.1446C>T;refseq.codonCoord_1=482;refseq.codonCoord_2=482;refseq.codonCoord_3=482;refseq.codonCoord_4=482;refseq.end_1=104031684;refseq.end_2=104031684;refseq.end_3=104031684;refseq.end_4=104031684;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1718;refseq.mrnaCoord_2=1740;refseq.mrnaCoord_3=1660;refseq.mrnaCoord_4=1741;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.I482I;refseq.proteinCoordStr_2=p.I482I;refseq.proteinCoordStr_3=p.I482I;refseq.proteinCoordStr_4=p.I482I;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.spliceDist_1=100;refseq.spliceDist_2=100;refseq.spliceDist_3=100;refseq.spliceDist_4=100;refseq.start_1=104031684;refseq.start_2=104031684;refseq.start_3=104031684;refseq.start_4=104031684;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantAA_4=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;refseq.variantCodon_3=ATT;refseq.variantCodon_4=ATT;set=soap GT 1/0
|
|
chr1 104031702 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.430499;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1428C>T;refseq.codingCoordStr_2=c.1428C>T;refseq.codingCoordStr_3=c.1428C>T;refseq.codingCoordStr_4=c.1428C>T;refseq.codonCoord_1=476;refseq.codonCoord_2=476;refseq.codonCoord_3=476;refseq.codonCoord_4=476;refseq.end_1=104031702;refseq.end_2=104031702;refseq.end_3=104031702;refseq.end_4=104031702;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1700;refseq.mrnaCoord_2=1722;refseq.mrnaCoord_3=1642;refseq.mrnaCoord_4=1723;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.N476N;refseq.proteinCoordStr_2=p.N476N;refseq.proteinCoordStr_3=p.N476N;refseq.proteinCoordStr_4=p.N476N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceAA_4=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.referenceCodon_4=AAC;refseq.spliceDist_1=82;refseq.spliceDist_2=82;refseq.spliceDist_3=82;refseq.spliceDist_4=82;refseq.start_1=104031702;refseq.start_2=104031702;refseq.start_3=104031702;refseq.start_4=104031702;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantAA_3=Asn;refseq.variantAA_4=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;refseq.variantCodon_3=AAT;refseq.variantCodon_4=AAT;set=soap GT 1/0
|
|
chr1 104031782 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.280712;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1348A>T;refseq.codingCoordStr_2=c.1348A>T;refseq.codingCoordStr_3=c.1348A>T;refseq.codingCoordStr_4=c.1348A>T;refseq.codonCoord_1=450;refseq.codonCoord_2=450;refseq.codonCoord_3=450;refseq.codonCoord_4=450;refseq.end_1=104031782;refseq.end_2=104031782;refseq.end_3=104031782;refseq.end_4=104031782;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1620;refseq.mrnaCoord_2=1642;refseq.mrnaCoord_3=1562;refseq.mrnaCoord_4=1643;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T450S;refseq.proteinCoordStr_2=p.T450S;refseq.proteinCoordStr_3=p.T450S;refseq.proteinCoordStr_4=p.T450S;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.referenceCodon_3=ACA;refseq.referenceCodon_4=ACA;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceDist_3=2;refseq.spliceDist_4=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.spliceInfo_3=splice-acceptor_2;refseq.spliceInfo_4=splice-acceptor_2;refseq.start_1=104031782;refseq.start_2=104031782;refseq.start_3=104031782;refseq.start_4=104031782;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_1=TCA;refseq.variantCodon_2=TCA;refseq.variantCodon_3=TCA;refseq.variantCodon_4=TCA;set=soap GT 1/0
|
|
chr1 104033180 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.183459;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1269C>T;refseq.codingCoordStr_2=c.1269C>T;refseq.codingCoordStr_3=c.1269C>T;refseq.codingCoordStr_4=c.1269C>T;refseq.codonCoord_1=423;refseq.codonCoord_2=423;refseq.codonCoord_3=423;refseq.codonCoord_4=423;refseq.end_1=104033180;refseq.end_2=104033180;refseq.end_3=104033180;refseq.end_4=104033180;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1541;refseq.mrnaCoord_2=1563;refseq.mrnaCoord_3=1483;refseq.mrnaCoord_4=1564;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.N423N;refseq.proteinCoordStr_2=p.N423N;refseq.proteinCoordStr_3=p.N423N;refseq.proteinCoordStr_4=p.N423N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceAA_4=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.referenceCodon_4=AAC;refseq.spliceDist_1=49;refseq.spliceDist_2=49;refseq.spliceDist_3=49;refseq.spliceDist_4=49;refseq.start_1=104033180;refseq.start_2=104033180;refseq.start_3=104033180;refseq.start_4=104033180;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantAA_3=Asn;refseq.variantAA_4=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;refseq.variantCodon_3=AAT;refseq.variantCodon_4=AAT;set=soap GT 1/0
|
|
chr1 104033217 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=3;RankSumP=0.413289;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1232A>T;refseq.codingCoordStr_2=c.1232A>T;refseq.codingCoordStr_3=c.1232A>T;refseq.codingCoordStr_4=c.1232A>T;refseq.codonCoord_1=411;refseq.codonCoord_2=411;refseq.codonCoord_3=411;refseq.codonCoord_4=411;refseq.end_1=104033217;refseq.end_2=104033217;refseq.end_3=104033217;refseq.end_4=104033217;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1504;refseq.mrnaCoord_2=1526;refseq.mrnaCoord_3=1446;refseq.mrnaCoord_4=1527;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.N411I;refseq.proteinCoordStr_2=p.N411I;refseq.proteinCoordStr_3=p.N411I;refseq.proteinCoordStr_4=p.N411I;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceAA_4=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.referenceCodon_3=AAT;refseq.referenceCodon_4=AAT;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.spliceDist_3=12;refseq.spliceDist_4=12;refseq.start_1=104033217;refseq.start_2=104033217;refseq.start_3=104033217;refseq.start_4=104033217;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantAA_4=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;refseq.variantCodon_3=ATT;refseq.variantCodon_4=ATT;set=soap GT 1/0
|
|
chr1 104033414 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.398407;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1145C>T;refseq.codingCoordStr_2=c.1145C>T;refseq.codingCoordStr_3=c.1145C>T;refseq.codingCoordStr_4=c.1145C>T;refseq.codonCoord_1=382;refseq.codonCoord_2=382;refseq.codonCoord_3=382;refseq.codonCoord_4=382;refseq.end_1=104033414;refseq.end_2=104033414;refseq.end_3=104033414;refseq.end_4=104033414;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1417;refseq.mrnaCoord_2=1439;refseq.mrnaCoord_3=1359;refseq.mrnaCoord_4=1440;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T382I;refseq.proteinCoordStr_2=p.T382I;refseq.proteinCoordStr_3=p.T382I;refseq.proteinCoordStr_4=p.T382I;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.referenceCodon_3=ACT;refseq.referenceCodon_4=ACT;refseq.spliceDist_1=44;refseq.spliceDist_2=44;refseq.spliceDist_3=44;refseq.spliceDist_4=44;refseq.start_1=104033414;refseq.start_2=104033414;refseq.start_3=104033414;refseq.start_4=104033414;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantAA_4=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;refseq.variantCodon_3=ATT;refseq.variantCodon_4=ATT;set=soap GT 1/0
|
|
chr1 104033427 . C T 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00528146;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1132G>A;refseq.codingCoordStr_2=c.1132G>A;refseq.codingCoordStr_3=c.1132G>A;refseq.codingCoordStr_4=c.1132G>A;refseq.codonCoord_1=378;refseq.codonCoord_2=378;refseq.codonCoord_3=378;refseq.codonCoord_4=378;refseq.end_1=104033427;refseq.end_2=104033427;refseq.end_3=104033427;refseq.end_4=104033427;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1404;refseq.mrnaCoord_2=1426;refseq.mrnaCoord_3=1346;refseq.mrnaCoord_4=1427;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.D378N;refseq.proteinCoordStr_2=p.D378N;refseq.proteinCoordStr_3=p.D378N;refseq.proteinCoordStr_4=p.D378N;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.referenceCodon_3=GAT;refseq.referenceCodon_4=GAT;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.spliceDist_3=31;refseq.spliceDist_4=31;refseq.start_1=104033427;refseq.start_2=104033427;refseq.start_3=104033427;refseq.start_4=104033427;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantAA_3=Asn;refseq.variantAA_4=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;refseq.variantCodon_3=AAT;refseq.variantCodon_4=AAT;set=FilteredInAll GT 0/1
|
|
chr1 104035653 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.167490;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.981A>T;refseq.codingCoordStr_2=c.981A>T;refseq.codingCoordStr_3=c.981A>T;refseq.codingCoordStr_4=c.981A>T;refseq.codonCoord_1=327;refseq.codonCoord_2=327;refseq.codonCoord_3=327;refseq.codonCoord_4=327;refseq.end_1=104035653;refseq.end_2=104035653;refseq.end_3=104035653;refseq.end_4=104035653;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1253;refseq.mrnaCoord_2=1275;refseq.mrnaCoord_3=1195;refseq.mrnaCoord_4=1276;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.I327I;refseq.proteinCoordStr_2=p.I327I;refseq.proteinCoordStr_3=p.I327I;refseq.proteinCoordStr_4=p.I327I;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceCodon_1=ATA;refseq.referenceCodon_2=ATA;refseq.referenceCodon_3=ATA;refseq.referenceCodon_4=ATA;refseq.spliceDist_1=-21;refseq.spliceDist_2=-21;refseq.spliceDist_3=-21;refseq.spliceDist_4=-21;refseq.start_1=104035653;refseq.start_2=104035653;refseq.start_3=104035653;refseq.start_4=104035653;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantAA_4=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;refseq.variantCodon_3=ATT;refseq.variantCodon_4=ATT;set=soap GT 1/0
|
|
chr1 104035671 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.0270964;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.963C>G;refseq.codingCoordStr_2=c.963C>G;refseq.codingCoordStr_3=c.963C>G;refseq.codingCoordStr_4=c.963C>G;refseq.codonCoord_1=321;refseq.codonCoord_2=321;refseq.codonCoord_3=321;refseq.codonCoord_4=321;refseq.end_1=104035671;refseq.end_2=104035671;refseq.end_3=104035671;refseq.end_4=104035671;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1235;refseq.mrnaCoord_2=1257;refseq.mrnaCoord_3=1177;refseq.mrnaCoord_4=1258;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.G321G;refseq.proteinCoordStr_2=p.G321G;refseq.proteinCoordStr_3=p.G321G;refseq.proteinCoordStr_4=p.G321G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceAA_4=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.referenceCodon_3=GGC;refseq.referenceCodon_4=GGC;refseq.spliceDist_1=-39;refseq.spliceDist_2=-39;refseq.spliceDist_3=-39;refseq.spliceDist_4=-39;refseq.start_1=104035671;refseq.start_2=104035671;refseq.start_3=104035671;refseq.start_4=104035671;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;set=soap GT 0/1
|
|
chr1 104035713 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.399437;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.921G>A;refseq.codingCoordStr_2=c.921G>A;refseq.codingCoordStr_3=c.921G>A;refseq.codingCoordStr_4=c.921G>A;refseq.codonCoord_1=307;refseq.codonCoord_2=307;refseq.codonCoord_3=307;refseq.codonCoord_4=307;refseq.end_1=104035713;refseq.end_2=104035713;refseq.end_3=104035713;refseq.end_4=104035713;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1193;refseq.mrnaCoord_2=1215;refseq.mrnaCoord_3=1135;refseq.mrnaCoord_4=1216;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.A307A;refseq.proteinCoordStr_2=p.A307A;refseq.proteinCoordStr_3=p.A307A;refseq.proteinCoordStr_4=p.A307A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.referenceCodon_3=GCG;refseq.referenceCodon_4=GCG;refseq.spliceDist_1=43;refseq.spliceDist_2=43;refseq.spliceDist_3=43;refseq.spliceDist_4=43;refseq.start_1=104035713;refseq.start_2=104035713;refseq.start_3=104035713;refseq.start_4=104035713;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;refseq.variantCodon_3=GCA;refseq.variantCodon_4=GCA;set=soap GT 0/1
|
|
chr1 104035728 . C T 4 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.296249;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.906G>A;refseq.codingCoordStr_2=c.906G>A;refseq.codingCoordStr_3=c.906G>A;refseq.codingCoordStr_4=c.906G>A;refseq.codonCoord_1=302;refseq.codonCoord_2=302;refseq.codonCoord_3=302;refseq.codonCoord_4=302;refseq.end_1=104035728;refseq.end_2=104035728;refseq.end_3=104035728;refseq.end_4=104035728;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1178;refseq.mrnaCoord_2=1200;refseq.mrnaCoord_3=1120;refseq.mrnaCoord_4=1201;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.M302I;refseq.proteinCoordStr_2=p.M302I;refseq.proteinCoordStr_3=p.M302I;refseq.proteinCoordStr_4=p.M302I;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceAA_3=Met;refseq.referenceAA_4=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.referenceCodon_3=ATG;refseq.referenceCodon_4=ATG;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.spliceDist_3=28;refseq.spliceDist_4=28;refseq.start_1=104035728;refseq.start_2=104035728;refseq.start_3=104035728;refseq.start_4=104035728;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantAA_4=Ile;refseq.variantCodon_1=ATA;refseq.variantCodon_2=ATA;refseq.variantCodon_3=ATA;refseq.variantCodon_4=ATA;set=FilteredInAll GT 0/1
|
|
chr1 104035730 . T C 15 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.326450;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.904A>G;refseq.codingCoordStr_2=c.904A>G;refseq.codingCoordStr_3=c.904A>G;refseq.codingCoordStr_4=c.904A>G;refseq.codonCoord_1=302;refseq.codonCoord_2=302;refseq.codonCoord_3=302;refseq.codonCoord_4=302;refseq.end_1=104035730;refseq.end_2=104035730;refseq.end_3=104035730;refseq.end_4=104035730;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1176;refseq.mrnaCoord_2=1198;refseq.mrnaCoord_3=1118;refseq.mrnaCoord_4=1199;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.M302V;refseq.proteinCoordStr_2=p.M302V;refseq.proteinCoordStr_3=p.M302V;refseq.proteinCoordStr_4=p.M302V;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceAA_3=Met;refseq.referenceAA_4=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.referenceCodon_3=ATG;refseq.referenceCodon_4=ATG;refseq.spliceDist_1=26;refseq.spliceDist_2=26;refseq.spliceDist_3=26;refseq.spliceDist_4=26;refseq.start_1=104035730;refseq.start_2=104035730;refseq.start_3=104035730;refseq.start_4=104035730;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;refseq.variantCodon_3=GTG;refseq.variantCodon_4=GTG;set=FilteredInAll GT 1/0
|
|
chr1 104037558 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.445522;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.631A>C;refseq.codingCoordStr_2=c.631A>C;refseq.codingCoordStr_3=c.631A>C;refseq.codingCoordStr_4=c.631A>C;refseq.codonCoord_1=211;refseq.codonCoord_2=211;refseq.codonCoord_3=211;refseq.codonCoord_4=211;refseq.end_1=104037558;refseq.end_2=104037558;refseq.end_3=104037558;refseq.end_4=104037558;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=903;refseq.mrnaCoord_2=925;refseq.mrnaCoord_3=845;refseq.mrnaCoord_4=926;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.I211L;refseq.proteinCoordStr_2=p.I211L;refseq.proteinCoordStr_3=p.I211L;refseq.proteinCoordStr_4=p.I211L;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.referenceCodon_3=ATT;refseq.referenceCodon_4=ATT;refseq.spliceDist_1=-114;refseq.spliceDist_2=-114;refseq.spliceDist_3=-114;refseq.spliceDist_4=-114;refseq.start_1=104037558;refseq.start_2=104037558;refseq.start_3=104037558;refseq.start_4=104037558;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;refseq.variantCodon_3=CTT;refseq.variantCodon_4=CTT;set=soap GT 1/0
|
|
chr1 104037622 . A G 21 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.376981;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.567T>C;refseq.codingCoordStr_2=c.567T>C;refseq.codingCoordStr_3=c.567T>C;refseq.codingCoordStr_4=c.567T>C;refseq.codonCoord_1=189;refseq.codonCoord_2=189;refseq.codonCoord_3=189;refseq.codonCoord_4=189;refseq.end_1=104037622;refseq.end_2=104037622;refseq.end_3=104037622;refseq.end_4=104037622;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=839;refseq.mrnaCoord_2=861;refseq.mrnaCoord_3=781;refseq.mrnaCoord_4=862;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.Y189Y;refseq.proteinCoordStr_2=p.Y189Y;refseq.proteinCoordStr_3=p.Y189Y;refseq.proteinCoordStr_4=p.Y189Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceAA_4=Tyr;refseq.referenceCodon_1=TAT;refseq.referenceCodon_2=TAT;refseq.referenceCodon_3=TAT;refseq.referenceCodon_4=TAT;refseq.spliceDist_1=54;refseq.spliceDist_2=54;refseq.spliceDist_3=54;refseq.spliceDist_4=54;refseq.start_1=104037622;refseq.start_2=104037622;refseq.start_3=104037622;refseq.start_4=104037622;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantAA_4=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;refseq.variantCodon_3=TAC;refseq.variantCodon_4=TAC;set=soap GT 0/1
|
|
chr1 104039137 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.439886;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.303C>T;refseq.codingCoordStr_2=c.303C>T;refseq.codingCoordStr_3=c.303C>T;refseq.codingCoordStr_4=c.303C>T;refseq.codonCoord_1=101;refseq.codonCoord_2=101;refseq.codonCoord_3=101;refseq.codonCoord_4=101;refseq.end_1=104039137;refseq.end_2=104039137;refseq.end_3=104039137;refseq.end_4=104039137;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=575;refseq.mrnaCoord_2=597;refseq.mrnaCoord_3=517;refseq.mrnaCoord_4=598;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.C101C;refseq.proteinCoordStr_2=p.C101C;refseq.proteinCoordStr_3=p.C101C;refseq.proteinCoordStr_4=p.C101C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.referenceCodon_3=TGC;refseq.referenceCodon_4=TGC;refseq.spliceDist_1=-13;refseq.spliceDist_2=-13;refseq.spliceDist_3=-13;refseq.spliceDist_4=-13;refseq.start_1=104039137;refseq.start_2=104039137;refseq.start_3=104039137;refseq.start_4=104039137;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantAA_3=Cys;refseq.variantAA_4=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;refseq.variantCodon_3=TGT;refseq.variantCodon_4=TGT;set=soap GT 1/0
|
|
chr1 104039241 . G A 18 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.411768;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.199C>T;refseq.codingCoordStr_2=c.199C>T;refseq.codingCoordStr_3=c.199C>T;refseq.codingCoordStr_4=c.199C>T;refseq.codonCoord_1=67;refseq.codonCoord_2=67;refseq.codonCoord_3=67;refseq.codonCoord_4=67;refseq.end_1=104039241;refseq.end_2=104039241;refseq.end_3=104039241;refseq.end_4=104039241;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=471;refseq.mrnaCoord_2=493;refseq.mrnaCoord_3=413;refseq.mrnaCoord_4=494;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.H67Y;refseq.proteinCoordStr_2=p.H67Y;refseq.proteinCoordStr_3=p.H67Y;refseq.proteinCoordStr_4=p.H67Y;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceAA_4=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.referenceCodon_3=CAC;refseq.referenceCodon_4=CAC;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.spliceDist_3=31;refseq.spliceDist_4=31;refseq.start_1=104039241;refseq.start_2=104039241;refseq.start_3=104039241;refseq.start_4=104039241;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantAA_4=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;refseq.variantCodon_3=TAC;refseq.variantCodon_4=TAC;set=FilteredInAll GT 1/0
|
|
chr1 104039245 . G T 86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.400378;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.195C>A;refseq.codingCoordStr_2=c.195C>A;refseq.codingCoordStr_3=c.195C>A;refseq.codingCoordStr_4=c.195C>A;refseq.codonCoord_1=65;refseq.codonCoord_2=65;refseq.codonCoord_3=65;refseq.codonCoord_4=65;refseq.end_1=104039245;refseq.end_2=104039245;refseq.end_3=104039245;refseq.end_4=104039245;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=467;refseq.mrnaCoord_2=489;refseq.mrnaCoord_3=409;refseq.mrnaCoord_4=490;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.A65A;refseq.proteinCoordStr_2=p.A65A;refseq.proteinCoordStr_3=p.A65A;refseq.proteinCoordStr_4=p.A65A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GCC;refseq.referenceCodon_4=GCC;refseq.spliceDist_1=27;refseq.spliceDist_2=27;refseq.spliceDist_3=27;refseq.spliceDist_4=27;refseq.start_1=104039245;refseq.start_2=104039245;refseq.start_3=104039245;refseq.start_4=104039245;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;refseq.variantCodon_3=GCA;refseq.variantCodon_4=GCA;set=soap GT 0/1
|
|
chr1 104039710 . T C 82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.449487;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.75A>G;refseq.codingCoordStr_2=c.75A>G;refseq.codingCoordStr_3=c.75A>G;refseq.codingCoordStr_4=c.75A>G;refseq.codonCoord_1=25;refseq.codonCoord_2=25;refseq.codonCoord_3=25;refseq.codonCoord_4=25;refseq.end_1=104039710;refseq.end_2=104039710;refseq.end_3=104039710;refseq.end_4=104039710;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=347;refseq.mrnaCoord_2=369;refseq.mrnaCoord_3=289;refseq.mrnaCoord_4=370;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.R25R;refseq.proteinCoordStr_2=p.R25R;refseq.proteinCoordStr_3=p.R25R;refseq.proteinCoordStr_4=p.R25R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.referenceCodon_3=CGA;refseq.referenceCodon_4=CGA;refseq.spliceDist_1=-94;refseq.spliceDist_2=-94;refseq.spliceDist_3=-94;refseq.spliceDist_4=-94;refseq.start_1=104039710;refseq.start_2=104039710;refseq.start_3=104039710;refseq.start_4=104039710;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;refseq.variantCodon_4=CGG;set=soap GT 1/0
|
|
chr1 104039730 . A G 37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.708875;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.55T>C;refseq.codingCoordStr_2=c.55T>C;refseq.codingCoordStr_3=c.55T>C;refseq.codingCoordStr_4=c.55T>C;refseq.codonCoord_1=19;refseq.codonCoord_2=19;refseq.codonCoord_3=19;refseq.codonCoord_4=19;refseq.end_1=104039730;refseq.end_2=104039730;refseq.end_3=104039730;refseq.end_4=104039730;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=327;refseq.mrnaCoord_2=349;refseq.mrnaCoord_3=269;refseq.mrnaCoord_4=350;refseq.name2_1=AMY1B;refseq.name2_2=AMY1C;refseq.name2_3=AMY1A;refseq.name2_4=AMY1A;refseq.name_1=NM_001008218;refseq.name_2=NM_001008219;refseq.name_3=NM_001008221;refseq.name_4=NM_004038;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.S19P;refseq.proteinCoordStr_2=p.S19P;refseq.proteinCoordStr_3=p.S19P;refseq.proteinCoordStr_4=p.S19P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.referenceCodon_4=TCA;refseq.spliceDist_1=101;refseq.spliceDist_2=101;refseq.spliceDist_3=101;refseq.spliceDist_4=101;refseq.start_1=104039730;refseq.start_2=104039730;refseq.start_3=104039730;refseq.start_4=104039730;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;refseq.variantCodon_3=CCA;refseq.variantCodon_4=CCA;set=soap GT 0/1
|
|
chr1 107401441 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.91;MQ0=0;OQ=1371.52;QD=12.14;RankSumP=0.107832;SB=-624.50;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.581C>T;refseq.codonCoord=194;refseq.end=107401441;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=652;refseq.name=NM_018137;refseq.name2=PRMT6;refseq.positionType=CDS;refseq.proteinCoordStr=p.A194V;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=652;refseq.start=107401441;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 0/1
|
|
chr1 107986824 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=550;Dels=0.00;HRun=1;HaplotypeScore=14.77;MQ=98.76;MQ0=0;OQ=12694.92;QD=23.08;RankSumP=0.195175;SB=-3906.17;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.174G>C;refseq.codingCoordStr_2=c.1854G>C;refseq.codonCoord_1=58;refseq.codonCoord_2=618;refseq.end_1=107986824;refseq.end_2=107986824;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=247;refseq.mrnaCoord_2=1908;refseq.name2_1=VAV3;refseq.name2_2=VAV3;refseq.name_1=NM_001079874;refseq.name_2=NM_006113;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q58H;refseq.proteinCoordStr_2=p.Q618H;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=-61;refseq.spliceDist_2=-61;refseq.start_1=107986824;refseq.start_2=107986824;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;set=Intersection GT 1/0
|
|
chr1 108109250 . T A 312.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=226;Dels=0.00;HRun=0;HaplotypeScore=5.81;MQ=98.82;MQ0=0;OQ=9073.71;QD=40.15;RankSumP=1.00000;SB=-2934.63;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.892A>T;refseq.codonCoord=298;refseq.end=108109250;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=946;refseq.name=NM_006113;refseq.name2=VAV3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T298S;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-30;refseq.start=108109250;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/1
|
|
chr1 108114781 . C T 95 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=113;Dels=0.00;HRun=4;HaplotypeScore=3.33;MQ=98.72;MQ0=0;OQ=4841.99;QD=42.85;RankSumP=1.00000;SB=-631.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.648G>A;refseq.codonCoord=216;refseq.end=108114781;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=702;refseq.name=NM_006113;refseq.name2=VAV3;refseq.positionType=CDS;refseq.proteinCoordStr=p.K216K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-1;refseq.spliceInfo=splice-donor_-1;refseq.start=108114781;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/1
|
|
chr1 108483331 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1121A>G;refseq.codingCoordStr_2=c.1064A>G;refseq.codonCoord_1=374;refseq.codonCoord_2=355;refseq.end_1=108483331;refseq.end_2=108483331;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1335;refseq.mrnaCoord_2=1184;refseq.name2_1=SLC25A24;refseq.name2_2=SLC25A24;refseq.name_1=NM_013386;refseq.name_2=NM_213651;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D374G;refseq.proteinCoordStr_2=p.D355G;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=23;refseq.spliceDist_2=23;refseq.start_1=108483331;refseq.start_2=108483331;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 1/0
|
|
chr1 108505357 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=282;Dels=0.00;HRun=1;HaplotypeScore=13.96;MQ=98.88;MQ0=0;OQ=6099.17;QD=21.63;RankSumP=0.250451;SB=-1664.25;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.480G>A;refseq.codingCoordStr_2=c.423G>A;refseq.codonCoord_1=160;refseq.codonCoord_2=141;refseq.end_1=108505357;refseq.end_2=108505357;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=694;refseq.mrnaCoord_2=543;refseq.name2_1=SLC25A24;refseq.name2_2=SLC25A24;refseq.name_1=NM_013386;refseq.name_2=NM_213651;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E160E;refseq.proteinCoordStr_2=p.E141E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-31;refseq.spliceDist_2=-31;refseq.start_1=108505357;refseq.start_2=108505357;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=Intersection GT 0/1
|
|
chr1 108530007 . T C 137.88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.74;MQ0=0;OQ=803.01;QD=21.70;RankSumP=0.664314;SB=-352.49;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.276A>G;refseq.codingCoordStr_2=c.219A>G;refseq.codonCoord_1=92;refseq.codonCoord_2=73;refseq.end_1=108530007;refseq.end_2=108530007;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=490;refseq.mrnaCoord_2=339;refseq.name2_1=SLC25A24;refseq.name2_2=SLC25A24;refseq.name_1=NM_013386;refseq.name_2=NM_213651;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K92K;refseq.proteinCoordStr_2=p.K73K;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=-35;refseq.spliceDist_2=-35;refseq.start_1=108530007;refseq.start_2=108530007;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/0
|
|
chr1 108904676 . C G 31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=9;HRun=1;RankSumP=0.458109;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.103C>G;refseq.codonCoord=35;refseq.end=108904676;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=183;refseq.name=NM_001010883;refseq.name2=FAM102B;refseq.positionType=CDS;refseq.proteinCoordStr=p.L35V;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-35;refseq.start=108904676;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=soap GT 1/0
|
|
chr1 109070096 . T C 181.95 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=407;Dels=0.00;HRun=1;HaplotypeScore=7.63;MQ=98.80;MQ0=0;OQ=16385.31;QD=40.26;RankSumP=1.00000;SB=-6397.90;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1058T>C;refseq.codonCoord=353;refseq.end=109070096;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1058;refseq.name=NM_001144937;refseq.name2=FNDC7;refseq.positionType=CDS;refseq.proteinCoordStr=p.V353A;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-54;refseq.start=109070096;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 109074979 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=488;Dels=0.00;HRun=2;HaplotypeScore=6.65;MQ=98.99;MQ0=0;OQ=8926.37;QD=18.29;RankSumP=0.237637;SB=-3132.63;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1785A>G;refseq.codonCoord=595;refseq.end=109074979;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1785;refseq.name=NM_001144937;refseq.name2=FNDC7;refseq.positionType=CDS;refseq.proteinCoordStr=p.G595G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-95;refseq.start=109074979;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 0/1
|
|
chr1 109140384 . G C 258.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=249;Dels=0.00;HRun=0;HaplotypeScore=4.35;MQ=98.82;MQ0=0;OQ=4903.54;QD=19.69;RankSumP=0.418801;SB=-1652.73;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1116G>C;refseq.codonCoord=372;refseq.end=109140384;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1191;refseq.name=NM_007269;refseq.name2=STXBP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L372L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=109140384;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 0/1
|
|
chr1 109167809 . C T 364.68 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=311;Dels=0.00;HRun=0;HaplotypeScore=9.15;MQ=98.58;MQ0=0;OQ=6052.29;QD=19.46;RankSumP=0.0352182;SB=-2400.35;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1961G>A;refseq.codonCoord=654;refseq.end=109167809;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2230;refseq.name=NM_152763;refseq.name2=AKNAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C654Y;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=25;refseq.start=109167809;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 0/1
|
|
chr1 109171438 . G T 72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=38;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=98.75;MQ0=0;OQ=1456.09;QD=38.32;RankSumP=1.00000;SB=-442.48;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1848C>A;refseq.codonCoord=616;refseq.end=109171438;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2117;refseq.name=NM_152763;refseq.name2=AKNAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N616K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=109171438;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/1
|
|
chr1 109178593 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=96.45;MQ0=0;OQ=399.10;QD=8.49;RankSumP=0.595575;SB=-5.84;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1745G>T;refseq.codonCoord=582;refseq.end=109178593;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2014;refseq.name=NM_152763;refseq.name2=AKNAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G582V;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-2;refseq.spliceInfo=splice-donor_-2;refseq.start=109178593;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 109196087 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=640;Dels=0.00;HRun=0;HaplotypeScore=17.38;MQ=98.77;MQ0=0;OQ=12984.53;QD=20.29;RankSumP=0.481709;SB=-5334.91;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.723A>G;refseq.codonCoord=241;refseq.end=109196087;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=992;refseq.name=NM_152763;refseq.name2=AKNAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A241A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-271;refseq.start=109196087;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/0
|
|
chr1 109196628 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=465;Dels=0.00;HRun=1;HaplotypeScore=13.85;MQ=99.00;MQ0=0;OQ=10101.03;QD=21.72;RankSumP=0.485039;SB=-3625.51;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.182G>A;refseq.codonCoord=61;refseq.end=109196628;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=451;refseq.name=NM_152763;refseq.name2=AKNAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S61N;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=285;refseq.start=109196628;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 109268274 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=1;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1730A>C;refseq.codonCoord=577;refseq.end=109268274;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2226;refseq.name=NM_013296;refseq.name2=GPSM2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N577T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-86;refseq.start=109268274;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 0/1
|
|
chr1 109278989 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1482C>A;refseq.codingCoordStr_2=c.1332C>A;refseq.codonCoord_1=494;refseq.codonCoord_2=444;refseq.end_1=109278989;refseq.end_2=109278989;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1612;refseq.mrnaCoord_2=1472;refseq.name2_1=CLCC1;refseq.name2_2=CLCC1;refseq.name_1=NM_001048210;refseq.name_2=NM_015127;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A494A;refseq.proteinCoordStr_2=p.A444A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=99;refseq.spliceDist_2=99;refseq.start_1=109278989;refseq.start_2=109278989;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=FilteredInAll GT 0/1
|
|
chr1 109281501 . G T 228.26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=448;Dels=0.00;HRun=0;HaplotypeScore=15.42;MQ=98.48;MQ0=0;OQ=6927.62;QD=15.46;RankSumP=0.0657570;SB=-2046.09;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1104C>A;refseq.codingCoordStr_2=c.954C>A;refseq.codonCoord_1=368;refseq.codonCoord_2=318;refseq.end_1=109281501;refseq.end_2=109281501;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1234;refseq.mrnaCoord_2=1094;refseq.name2_1=CLCC1;refseq.name2_2=CLCC1;refseq.name_1=NM_001048210;refseq.name_2=NM_015127;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S368R;refseq.proteinCoordStr_2=p.S318R;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=63;refseq.spliceDist_2=63;refseq.start_1=109281501;refseq.start_2=109281501;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGA;refseq.variantCodon_2=AGA;set=Intersection GT 0/1
|
|
chr1 109287719 . A G 120.07 PASS AC=2;AF=1.00;AN=2;BestBaseQ=23;DB;DP=158;Dels=0.00;HRun=1;HaplotypeScore=9.88;MQ=93.36;MQ0=0;OQ=3934.05;QD=24.90;RankSumP=1.00000;SB=-1094.69;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.603T>C;refseq.codingCoordStr_2=c.453T>C;refseq.codonCoord_1=201;refseq.codonCoord_2=151;refseq.end_1=109287719;refseq.end_2=109287719;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=733;refseq.mrnaCoord_2=593;refseq.name2_1=CLCC1;refseq.name2_2=CLCC1;refseq.name_1=NM_001048210;refseq.name_2=NM_015127;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T201T;refseq.proteinCoordStr_2=p.T151T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.start_1=109287719;refseq.start_2=109287719;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=Intersection GT 1/1
|
|
chr1 109287720 . G T 40 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=24;DP=159;Dels=0.00;HRun=1;HaplotypeScore=6.39;MQ=93.25;MQ0=0;OQ=224.81;QD=1.41;RankSumP=0.000171221;SB=218.74;SecondBestBaseQ=15;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.602C>A;refseq.codingCoordStr_2=c.452C>A;refseq.codonCoord_1=201;refseq.codonCoord_2=151;refseq.end_1=109287720;refseq.end_2=109287720;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=732;refseq.mrnaCoord_2=592;refseq.name2_1=CLCC1;refseq.name2_2=CLCC1;refseq.name_1=NM_001048210;refseq.name_2=NM_015127;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T201N;refseq.proteinCoordStr_2=p.T151N;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=41;refseq.spliceDist_2=41;refseq.start_1=109287720;refseq.start_2=109287720;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=FilteredInAll GT 0/1
|
|
chr1 109452171 . A T 27.08 BadSOAPSNP;ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=240;Dels=0.00;HRun=2;HaplotypeScore=27.41;MQ=4.29;MQ0=232;QD=0.11;RankSumP=0.440090;SB=-10.00;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.57T>A;refseq.codonCoord=19;refseq.end=109452171;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=237;refseq.name=NM_001122961;refseq.name2=C1orf194;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y19*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=12;refseq.start=109452171;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=FilteredInAll GT 0/1
|
|
chr1 109506141 . A G 341.60 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=202;Dels=0.00;HRun=0;HaplotypeScore=4.35;MQ=98.40;MQ0=0;OQ=7018.21;QD=34.74;RankSumP=1.00000;SB=-2653.37;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.256A>G;refseq.codonCoord=86;refseq.end=109506141;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=477;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.I86V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-19;refseq.start=109506141;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 109536821 . T C 281.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=299;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=98.16;MQ0=0;OQ=11007.76;QD=36.82;RankSumP=1.00000;SB=-4657.32;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1749T>C;refseq.codonCoord=583;refseq.end=109536821;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1970;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.G583G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=66;refseq.start=109536821;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 109536921 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1849A>C;refseq.codonCoord=617;refseq.end=109536921;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2070;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.T617P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-99;refseq.start=109536921;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 109536939 . A C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=308;Dels=0.00;HRun=4;HaplotypeScore=8.15;MQ=97.31;MQ0=0;OQ=12568.90;QD=40.81;RankSumP=1.00000;SB=-6078.80;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1867A>C;refseq.codonCoord=623;refseq.end=109536939;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2088;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.T623P;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-81;refseq.start=109536939;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 109538586 . C T 271.25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=343;Dels=0.00;HRun=0;HaplotypeScore=11.23;MQ=98.46;MQ0=0;OQ=13661.31;QD=39.83;RankSumP=1.00000;SB=-5447.79;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1968C>T;refseq.codonCoord=656;refseq.end=109538586;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2189;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.N656N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=21;refseq.start=109538586;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/1
|
|
chr1 109538613 . G A 128.64 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=377;Dels=0.00;HRun=1;HaplotypeScore=8.18;MQ=98.72;MQ0=0;OQ=15733.65;QD=41.73;RankSumP=1.00000;SB=-7107.08;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1995G>A;refseq.codonCoord=665;refseq.end=109538613;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2216;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.P665P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=48;refseq.start=109538613;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 109538655 . T C 130.99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=332;Dels=0.00;HRun=1;HaplotypeScore=9.62;MQ=98.99;MQ0=0;OQ=12220.92;QD=36.81;RankSumP=1.00000;SB=-5760.25;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2037T>C;refseq.codonCoord=679;refseq.end=109538655;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2258;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.T679T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-85;refseq.start=109538655;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 109538695 . C T 300.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=300;Dels=0.00;HRun=1;HaplotypeScore=3.96;MQ=98.89;MQ0=0;OQ=12726.10;QD=42.42;RankSumP=1.00000;SB=-4932.58;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2077C>T;refseq.codonCoord=693;refseq.end=109538695;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2298;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.L693L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-45;refseq.start=109538695;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/1
|
|
chr1 109544008 . G A 302.95 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=247;Dels=0.00;HRun=0;HaplotypeScore=8.13;MQ=98.70;MQ0=0;OQ=9963.61;QD=40.34;RankSumP=1.00000;SB=-4231.95;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2511G>A;refseq.codonCoord=837;refseq.end=109544008;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2732;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.S837S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=109544008;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/1
|
|
chr1 109544127 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=4;refseq.chr=chr1;refseq.codingCoordStr=c.2628+2;refseq.end=109544127;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=109544127;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 109547141 . T C 72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=216;Dels=0.00;HRun=2;HaplotypeScore=8.63;MQ=98.71;MQ0=0;OQ=8157.86;QD=37.77;RankSumP=1.00000;SB=-3277.26;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3026T>C;refseq.codonCoord=1009;refseq.end=109547141;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3247;refseq.name=NM_020775;refseq.name2=KIAA1324;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1009P;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=53;refseq.start=109547141;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 109595775 . T C 429.39 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=196;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=98.93;MQ0=0;OQ=7321.76;QD=37.36;RankSumP=1.00000;SB=-2603.08;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1551T>C;refseq.codonCoord=517;refseq.end=109595775;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1612;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S517S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=1612;refseq.start=109595775;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 109596549 . T C 291.64 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=269;Dels=0.00;HRun=0;HaplotypeScore=4.05;MQ=98.45;MQ0=0;OQ=9575.81;QD=35.60;RankSumP=1.00000;SB=-4150.25;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2325T>C;refseq.codonCoord=775;refseq.end=109596549;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2386;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y775Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-986;refseq.start=109596549;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/1
|
|
chr1 109596773 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=3;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2549T>G;refseq.codonCoord=850;refseq.end=109596773;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2610;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V850G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-762;refseq.start=109596773;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 109597131 . T C 142.27 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=7.71;MQ=99.00;MQ0=0;OQ=1862.46;QD=38.01;RankSumP=1.00000;SB=-600.24;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2907T>C;refseq.codonCoord=969;refseq.end=109597131;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2968;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.F969F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=-404;refseq.start=109597131;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 109603197 . A C 36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.0812958;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3931A>C;refseq.codonCoord=1311;refseq.end=109603197;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3992;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1311P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-28;refseq.start=109603197;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=soap GT 0/1
|
|
chr1 109609910 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=4;RankSumP=1.37974e-09;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5758A>C;refseq.codonCoord=1920;refseq.end=109609910;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5819;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1920P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=31;refseq.start=109609910;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 109611723 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=301;Dels=0.00;HRun=1;HaplotypeScore=20.55;MQ=98.33;MQ0=0;OQ=6000.83;QD=19.94;RankSumP=1.63009e-06;SB=-2255.30;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6044G>A;refseq.codonCoord=2015;refseq.end=109611723;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6105;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2015K;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=31;refseq.start=109611723;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=filterInsoap-gatk GT 1/0
|
|
chr1 109611724 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=303;Dels=0.00;HRun=0;HaplotypeScore=20.55;MQ=98.33;MQ0=0;OQ=6142.38;QD=20.27;RankSumP=5.89160e-05;SB=-2371.86;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6045G>A;refseq.codonCoord=2015;refseq.end=109611724;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6106;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2015R;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=32;refseq.start=109611724;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=filterInsoap-gatk GT 1/0
|
|
chr1 109612067 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=95;Dels=0.00;HRun=2;HaplotypeScore=3.02;MQ=98.69;MQ0=0;OQ=1219.90;QD=12.84;RankSumP=0.439359;SB=-380.06;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6180C>A;refseq.codonCoord=2060;refseq.end=109612067;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6241;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2060R;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=72;refseq.start=109612067;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/0
|
|
chr1 109617699 . A C 129.77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=24;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=89.49;MQ0=0;OQ=213.38;QD=19.40;RankSumP=1.00000;SB=-92.14;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8628A>C;refseq.codonCoord=2876;refseq.end=109617699;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=8689;refseq.name=NM_001408;refseq.name2=CELSR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2876G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-117;refseq.start=109617699;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=filterInsoap-gatk GT 1/1
|
|
chr1 109639376 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DP=90;Dels=0.00;HRun=1;HaplotypeScore=4.13;MQ=99.00;MQ0=0;OQ=1305.11;QD=14.50;RankSumP=0.438404;SB=-199.87;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.934C>T;refseq.codonCoord=312;refseq.end=109639376;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=984;refseq.name=NM_001010985;refseq.name2=MYBPHL;refseq.positionType=CDS;refseq.proteinCoordStr=p.H312Y;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=67;refseq.start=109639376;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/0
|
|
chr1 109640441 . C T 121.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.10;MQ0=0;OQ=1580.25;QD=15.80;RankSumP=0.453284;SB=-666.67;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.805G>A;refseq.codonCoord=269;refseq.end=109640441;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=855;refseq.name=NM_001010985;refseq.name2=MYBPHL;refseq.positionType=CDS;refseq.proteinCoordStr=p.D269N;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-63;refseq.start=109640441;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 0/1
|
|
chr1 109640956 . A G 91.52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=386;Dels=0.00;HRun=1;HaplotypeScore=5.06;MQ=98.19;MQ0=0;OQ=15879.04;QD=41.14;RankSumP=1.00000;SB=-7775.76;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.702T>C;refseq.codonCoord=234;refseq.end=109640956;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=752;refseq.name=NM_001010985;refseq.name2=MYBPHL;refseq.positionType=CDS;refseq.proteinCoordStr=p.T234T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-29;refseq.start=109640956;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 109641261 . C A 310.29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=244;Dels=0.00;HRun=0;HaplotypeScore=7.13;MQ=98.91;MQ0=0;OQ=4281.73;QD=17.55;RankSumP=0.214576;SB=-909.61;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.504G>T;refseq.codonCoord=168;refseq.end=109641261;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=554;refseq.name=NM_001010985;refseq.name2=MYBPHL;refseq.positionType=CDS;refseq.proteinCoordStr=p.P168P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-67;refseq.start=109641261;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/0
|
|
chr1 109667165 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1936C>A;refseq.codonCoord=646;refseq.end=109667165;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1985;refseq.name=NM_002959;refseq.name2=SORT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R646S;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-89;refseq.start=109667165;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT 0/1
|
|
chr1 109669098 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1780A>C;refseq.codonCoord=594;refseq.end=109669098;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1829;refseq.name=NM_002959;refseq.name2=SORT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T594P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-55;refseq.start=109669098;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 109686298 . T G 160.80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=142;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.64;MQ0=0;OQ=5822.55;QD=41.00;RankSumP=1.00000;SB=-514.08;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.969A>C;refseq.codonCoord=323;refseq.end=109686298;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1018;refseq.name=NM_002959;refseq.name2=SORT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T323T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=109686298;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 109698626 . A G 97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=483;Dels=0.00;HRun=0;HaplotypeScore=21.20;MQ=98.82;MQ0=0;OQ=20400.82;QD=42.24;RankSumP=1.00000;SB=-6723.61;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.594T>C;refseq.codonCoord=198;refseq.end=109698626;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=643;refseq.name=NM_002959;refseq.name2=SORT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F198F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=51;refseq.start=109698626;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 109851768 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=4;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1290T>G;refseq.codonCoord=430;refseq.end=109851768;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1672;refseq.name=NM_020703;refseq.name2=AMIGO1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G430G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-800;refseq.start=109851768;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 109972419 . T C 412.71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=190;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=98.94;MQ0=0;OQ=6844.69;QD=36.02;RankSumP=1.00000;SB=-2267.39;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1434T>C;refseq.codingCoordStr_2=c.1191T>C;refseq.codingCoordStr_3=c.1077T>C;refseq.codonCoord_1=478;refseq.codonCoord_2=397;refseq.codonCoord_3=359;refseq.end_1=109972419;refseq.end_2=109972419;refseq.end_3=109972419;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1794;refseq.mrnaCoord_2=1623;refseq.mrnaCoord_3=1285;refseq.name2_1=AMPD2;refseq.name2_2=AMPD2;refseq.name2_3=AMPD2;refseq.name_1=NM_004037;refseq.name_2=NM_139156;refseq.name_3=NM_203404;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.H478H;refseq.proteinCoordStr_2=p.H397H;refseq.proteinCoordStr_3=p.H359H;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.referenceCodon_3=CAT;refseq.spliceDist_1=-4;refseq.spliceDist_2=-4;refseq.spliceDist_3=-4;refseq.spliceInfo_1=splice-donor_-4;refseq.spliceInfo_2=splice-donor_-4;refseq.spliceInfo_3=splice-donor_-4;refseq.start_1=109972419;refseq.start_2=109972419;refseq.start_3=109972419;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;set=Intersection GT 1/1
|
|
chr1 109974445 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2213A>C;refseq.codingCoordStr_2=c.1970A>C;refseq.codingCoordStr_3=c.1856A>C;refseq.codonCoord_1=738;refseq.codonCoord_2=657;refseq.codonCoord_3=619;refseq.end_1=109974445;refseq.end_2=109974445;refseq.end_3=109974445;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2573;refseq.mrnaCoord_2=2402;refseq.mrnaCoord_3=2064;refseq.name2_1=AMPD2;refseq.name2_2=AMPD2;refseq.name2_3=AMPD2;refseq.name_1=NM_004037;refseq.name_2=NM_139156;refseq.name_3=NM_203404;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.N738T;refseq.proteinCoordStr_2=p.N657T;refseq.proteinCoordStr_3=p.N619T;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.spliceDist_1=68;refseq.spliceDist_2=68;refseq.spliceDist_3=68;refseq.start_1=109974445;refseq.start_2=109974445;refseq.start_3=109974445;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;refseq.variantCodon_3=ACC;set=FilteredInAll GT 0/1
|
|
chr1 109975298 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=273.49;QD=12.43;RankSumP=0.554391;SB=-110.79;SecondBestBaseQ=32;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.*1G>T;refseq.codingCoordStr_2=c.*1G>T;refseq.codingCoordStr_3=c.*1G>T;refseq.end_1=109975298;refseq.end_2=109975298;refseq.end_3=109975298;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.mrnaCoord_1=3001;refseq.mrnaCoord_2=2830;refseq.mrnaCoord_3=2492;refseq.name2_1=AMPD2;refseq.name2_2=AMPD2;refseq.name2_3=AMPD2;refseq.name_1=NM_004037;refseq.name_2=NM_139156;refseq.name_3=NM_203404;refseq.numMatchingRecords=3;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.spliceDist_1=211;refseq.spliceDist_2=211;refseq.spliceDist_3=211;refseq.start_1=109975298;refseq.start_2=109975298;refseq.start_3=109975298;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;set=Intersection GT 0/1
|
|
chr1 110003222 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=994;Dels=0.00;HRun=2;HaplotypeScore=21.10;MQ=76.75;MQ0=137;OQ=12977.31;QD=13.06;RankSumP=0.360080;SB=-2745.02;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.534T>C;refseq.codingCoordStr_3=c.534T>C;refseq.codonCoord_2=178;refseq.codonCoord_3=178;refseq.end_1=110003222;refseq.end_2=110003222;refseq.end_3=110003222;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=766;refseq.mrnaCoord_2=848;refseq.mrnaCoord_3=848;refseq.name2_1=GSTM4;refseq.name2_2=GSTM4;refseq.name2_3=GSTM4;refseq.name_1=NR_024538;refseq.name_2=NM_000850;refseq.name_3=NM_147148;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.F178F;refseq.proteinCoordStr_3=p.F178F;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceCodon_2=TTT;refseq.referenceCodon_3=TTT;refseq.spliceDist_1=-34;refseq.spliceDist_2=-34;refseq.spliceDist_3=-34;refseq.start_1=110003222;refseq.start_2=110003222;refseq.start_3=110003222;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantCodon_2=TTC;refseq.variantCodon_3=TTC;set=Intersection GT 1/0
|
|
chr1 110034661 . G C 88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=507;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=65.06;MQ0=193;OQ=14361.21;QD=28.33;RankSumP=1.00000;SB=-5241.52;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.519G>C;refseq.codonCoord_2=173;refseq.end_1=110037340;refseq.end_2=110034661;refseq.frame_2=2;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=597;refseq.name2_1=GSTM1;refseq.name2_2=GSTM1;refseq.name_1=NM_146421;refseq.name_2=NM_000561;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.K173N;refseq.referenceAA_2=Lys;refseq.referenceCodon_2=AAG;refseq.spliceDist_2=-49;refseq.start_1=110034522;refseq.start_2=110034661;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Asn;refseq.variantCodon_2=AAC;set=Intersection GT 1/1
|
|
chr1 110081224 . C T 314.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=308;Dels=0.00;HRun=0;HaplotypeScore=10.47;MQ=98.68;MQ0=0;OQ=5695.19;QD=18.49;RankSumP=0.135131;SB=-1164.81;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.670G>A;refseq.codonCoord_2=224;refseq.end_1=110081224;refseq.end_2=110081224;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=904;refseq.mrnaCoord_2=980;refseq.name2_1=GSTM3;refseq.name2_2=GSTM3;refseq.name_1=NR_024537;refseq.name_2=NM_000849;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V224I;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTA;refseq.spliceDist_1=91;refseq.spliceDist_2=91;refseq.start_1=110081224;refseq.start_2=110081224;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ile;refseq.variantCodon_2=ATA;set=Intersection GT 0/1
|
|
chr1 110097295 . T C 224.59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=308;Dels=0.00;HRun=1;HaplotypeScore=6.54;MQ=98.31;MQ0=0;OQ=5708.64;QD=18.53;RankSumP=0.137312;SB=-2377.54;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1167A>G;refseq.codingCoordStr_2=c.1167A>G;refseq.codingCoordStr_3=c.1170A>G;refseq.codonCoord_1=389;refseq.codonCoord_2=389;refseq.codonCoord_3=390;refseq.end_1=110097295;refseq.end_2=110097295;refseq.end_3=110097295;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1312;refseq.mrnaCoord_2=1312;refseq.mrnaCoord_3=1315;refseq.name2_1=EPS8L3;refseq.name2_2=EPS8L3;refseq.name2_3=EPS8L3;refseq.name_1=NM_024526;refseq.name_2=NM_133181;refseq.name_3=NM_139053;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S389S;refseq.proteinCoordStr_2=p.S389S;refseq.proteinCoordStr_3=p.S390S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.spliceDist_1=-34;refseq.spliceDist_2=-34;refseq.spliceDist_3=-34;refseq.start_1=110097295;refseq.start_2=110097295;refseq.start_3=110097295;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;refseq.variantCodon_3=TCG;set=Intersection GT 1/0
|
|
chr1 110101964 . G A 364.41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.36;MQ0=0;OQ=1911.89;QD=40.68;RankSumP=1.00000;SB=-592.77;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.877C>T;refseq.codingCoordStr_2=c.877C>T;refseq.codingCoordStr_3=c.880C>T;refseq.codonCoord_1=293;refseq.codonCoord_2=293;refseq.codonCoord_3=294;refseq.end_1=110101964;refseq.end_2=110101964;refseq.end_3=110101964;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1022;refseq.mrnaCoord_2=1022;refseq.mrnaCoord_3=1025;refseq.name2_1=EPS8L3;refseq.name2_2=EPS8L3;refseq.name2_3=EPS8L3;refseq.name_1=NM_024526;refseq.name_2=NM_133181;refseq.name_3=NM_139053;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.H293Y;refseq.proteinCoordStr_2=p.H293Y;refseq.proteinCoordStr_3=p.H294Y;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.referenceCodon_3=CAC;refseq.spliceDist_1=-18;refseq.spliceDist_2=-18;refseq.spliceDist_3=-18;refseq.start_1=110101964;refseq.start_2=110101964;refseq.start_3=110101964;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;refseq.variantCodon_3=TAC;set=Intersection GT 1/1
|
|
chr1 110258528 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.162+2;refseq.codingCoordStr_2=c.162+2;refseq.codingCoordStr_3=c.162+2;refseq.codingCoordStr_4=c.162+2;refseq.end_1=110258528;refseq.end_2=110258528;refseq.end_3=110258528;refseq.end_4=110258528;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.name2_1=CSF1;refseq.name2_2=CSF1;refseq.name2_3=CSF1;refseq.name2_4=CSF1;refseq.name_1=NM_000757;refseq.name_2=NM_172210;refseq.name_3=NM_172211;refseq.name_4=NM_172212;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.positionType_4=intron;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceDist_3=2;refseq.spliceDist_4=2;refseq.spliceInfo_1=splice-donor_2;refseq.spliceInfo_2=splice-donor_2;refseq.spliceInfo_3=splice-donor_2;refseq.spliceInfo_4=splice-donor_2;refseq.start_1=110258528;refseq.start_2=110258528;refseq.start_3=110258528;refseq.start_4=110258528;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;set=FilteredInAll GT 1/0
|
|
chr1 110267861 . C A 288.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=170;Dels=0.00;HRun=0;HaplotypeScore=7.04;MQ=98.48;MQ0=0;OQ=6420.87;QD=37.77;RankSumP=1.00000;SB=-2830.64;SecondBestBaseQ=28;refseq.changesAA_2=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_2=c.1095C>A;refseq.codingCoordStr_3=c.1090+5;refseq.codingCoordStr_4=c.1095C>A;refseq.codonCoord_2=365;refseq.codonCoord_4=365;refseq.end_1=110268194;refseq.end_2=110267861;refseq.end_3=110267861;refseq.end_4=110267861;refseq.frame_2=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=true;refseq.mrnaCoord_2=1508;refseq.mrnaCoord_4=1508;refseq.name2_1=CSF1;refseq.name2_2=CSF1;refseq.name2_3=CSF1;refseq.name2_4=CSF1;refseq.name_1=NM_172211;refseq.name_2=NM_000757;refseq.name_3=NM_172210;refseq.name_4=NM_172212;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=intron;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.T365T;refseq.proteinCoordStr_4=p.T365T;refseq.referenceAA_2=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_2=ACC;refseq.referenceCodon_4=ACC;refseq.spliceDist_2=-475;refseq.spliceDist_3=5;refseq.spliceDist_4=-475;refseq.spliceInfo_3=splice-donor_5;refseq.start_1=110266150;refseq.start_2=110267861;refseq.start_3=110267861;refseq.start_4=110267861;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_2=Thr;refseq.variantAA_4=Thr;refseq.variantCodon_2=ACA;refseq.variantCodon_4=ACA;set=Intersection GT 1/1
|
|
chr1 110268232 . T C 286.89 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=97.91;MQ0=0;OQ=2512.70;QD=39.26;RankSumP=1.00000;SB=-930.04;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1466T>C;refseq.codingCoordStr_2=c.1118T>C;refseq.codingCoordStr_3=c.572T>C;refseq.codingCoordStr_4=c.1466T>C;refseq.codonCoord_1=489;refseq.codonCoord_2=373;refseq.codonCoord_3=191;refseq.codonCoord_4=489;refseq.end_1=110268232;refseq.end_2=110268232;refseq.end_3=110268232;refseq.end_4=110268232;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1879;refseq.mrnaCoord_2=1531;refseq.mrnaCoord_3=985;refseq.mrnaCoord_4=1879;refseq.name2_1=CSF1;refseq.name2_2=CSF1;refseq.name2_3=CSF1;refseq.name2_4=CSF1;refseq.name_1=NM_000757;refseq.name_2=NM_172210;refseq.name_3=NM_172211;refseq.name_4=NM_172212;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.F489S;refseq.proteinCoordStr_2=p.F373S;refseq.proteinCoordStr_3=p.F191S;refseq.proteinCoordStr_4=p.F489S;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceAA_4=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.referenceCodon_3=TTC;refseq.referenceCodon_4=TTC;refseq.spliceDist_1=-104;refseq.spliceDist_2=28;refseq.spliceDist_3=28;refseq.spliceDist_4=-104;refseq.start_1=110268232;refseq.start_2=110268232;refseq.start_3=110268232;refseq.start_4=110268232;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;refseq.variantCodon_3=TCC;refseq.variantCodon_4=TCC;set=Intersection GT 1/1
|
|
chr1 110363250 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=2.37526e-09;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1372A>C;refseq.codonCoord=458;refseq.end=110363250;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1739;refseq.name=NM_006621;refseq.name2=AHCYL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T458P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-15;refseq.start=110363250;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 0/1
|
|
chr1 110456927 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.248A>C;refseq.codonCoord=83;refseq.end=110456927;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=343;refseq.name=NM_203412;refseq.name2=UBL4B;refseq.positionType=CDS;refseq.proteinCoordStr=p.H83P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=343;refseq.start=110456927;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 110511200 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.126T>G;refseq.codonCoord=42;refseq.end=110511200;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=587;refseq.name=NM_001010898;refseq.name2=SLC6A17;refseq.positionType=CDS;refseq.proteinCoordStr=p.G42G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-161;refseq.start=110511200;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 110511242 . T C 113.29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=9.25;MQ=97.44;MQ0=0;OQ=1024.53;QD=15.07;RankSumP=0.393476;SB=-475.35;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.168T>C;refseq.codonCoord=56;refseq.end=110511242;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=629;refseq.name=NM_001010898;refseq.name2=SLC6A17;refseq.positionType=CDS;refseq.proteinCoordStr=p.D56D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-119;refseq.start=110511242;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/0
|
|
chr1 110511243 . G A 118.03 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=8.45;MQ=97.46;MQ0=0;OQ=1026.80;QD=14.88;RankSumP=0.385759;SB=-528.14;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.169G>A;refseq.codonCoord=57;refseq.end=110511243;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=630;refseq.name=NM_001010898;refseq.name2=SLC6A17;refseq.positionType=CDS;refseq.proteinCoordStr=p.A57T;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-118;refseq.start=110511243;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 110539819 . G A 87.86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=253;Dels=0.00;HRun=0;HaplotypeScore=13.64;MQ=98.35;MQ0=0;OQ=6997.01;QD=27.66;RankSumP=1.00000;SB=-1517.43;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1581G>A;refseq.codonCoord=527;refseq.end=110539819;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2042;refseq.name=NM_001010898;refseq.name2=SLC6A17;refseq.positionType=CDS;refseq.proteinCoordStr=p.S527S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-72;refseq.start=110539819;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/1
|
|
chr1 110539823 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1585A>C;refseq.codonCoord=529;refseq.end=110539823;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2046;refseq.name=NM_001010898;refseq.name2=SLC6A17;refseq.positionType=CDS;refseq.proteinCoordStr=p.T529P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-68;refseq.start=110539823;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 110542556 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2151C>A;refseq.codonCoord=717;refseq.end=110542556;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2612;refseq.name=NM_001010898;refseq.name2=SLC6A17;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y717*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=336;refseq.start=110542556;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=FilteredInAll GT 1/0
|
|
chr1 110567810 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1380C>G;refseq.codingCoordStr_2=c.1380C>G;refseq.codingCoordStr_3=c.1380C>G;refseq.codonCoord_1=460;refseq.codonCoord_2=460;refseq.codonCoord_3=460;refseq.end_1=110567810;refseq.end_2=110567810;refseq.end_3=110567810;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1437;refseq.mrnaCoord_2=1437;refseq.mrnaCoord_3=1437;refseq.name2_1=KCNC4;refseq.name2_2=KCNC4;refseq.name2_3=KCNC4;refseq.name_1=NM_001039574;refseq.name_2=NM_004978;refseq.name_3=NM_153763;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.G460G;refseq.proteinCoordStr_2=p.G460G;refseq.proteinCoordStr_3=p.G460G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.referenceCodon_3=GGC;refseq.spliceDist_1=-236;refseq.spliceDist_2=-236;refseq.spliceDist_3=-419;refseq.start_1=110567810;refseq.start_2=110567810;refseq.start_3=110567810;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=FilteredInAll GT 1/0
|
|
chr1 110683967 . A G 169.91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=96.58;MQ0=0;OQ=992.32;QD=33.08;RankSumP=1.00000;SB=-382.80;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.417A>G;refseq.codonCoord=139;refseq.end=110683967;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=500;refseq.name=NM_022768;refseq.name2=RBM15;refseq.positionType=CDS;refseq.proteinCoordStr=p.E139E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=500;refseq.start=110683967;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 110751962 . C T 69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=99.00;MQ0=0;OQ=3098.23;QD=39.72;RankSumP=1.00000;SB=-1038.38;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.50G>A;refseq.codonCoord=17;refseq.end=110751962;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=108;refseq.name=NM_006402;refseq.name2=HBXIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.S17N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=108;refseq.start=110751962;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 110862192 . T C 186.26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=426;Dels=0.00;HRun=0;HaplotypeScore=16.02;MQ=98.39;MQ0=0;OQ=8599.39;QD=20.19;RankSumP=0.259520;SB=-2511.53;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.741A>G;refseq.codonCoord=247;refseq.end=110862192;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1129;refseq.name=NM_005549;refseq.name2=KCNA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.L247L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-831;refseq.start=110862192;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/0
|
|
chr1 110862585 . T C 267.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.91;MQ0=0;OQ=2035.53;QD=19.20;RankSumP=0.271304;SB=-1022.40;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.348A>G;refseq.codonCoord=116;refseq.end=110862585;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=736;refseq.name=NM_005549;refseq.name2=KCNA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.E116E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=736;refseq.start=110862585;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 111528392 . G A 244.73 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=453;Dels=0.00;HRun=0;HaplotypeScore=13.42;MQ=98.84;MQ0=0;OQ=9309.28;QD=20.55;RankSumP=0.379911;SB=-3846.17;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1188G>A;refseq.codingCoordStr_2=c.1188G>A;refseq.codonCoord_1=396;refseq.codonCoord_2=396;refseq.end_1=111528392;refseq.end_2=111528392;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1396;refseq.mrnaCoord_2=1358;refseq.name2_1=CEPT1;refseq.name2_2=CEPT1;refseq.name_1=NM_001007794;refseq.name_2=NM_006090;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A396A;refseq.proteinCoordStr_2=p.A396A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=57;refseq.spliceDist_2=57;refseq.start_1=111528392;refseq.start_2=111528392;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 1/0
|
|
chr1 111532362 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1253A>C;refseq.codonCoord=418;refseq.end=111532362;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1453;refseq.name=NM_024901;refseq.name2=DENND2D;refseq.positionType=CDS;refseq.proteinCoordStr=p.N418T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-87;refseq.start=111532362;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 111542845 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=228;Dels=0.00;HRun=1;HaplotypeScore=25.40;MQ=98.79;MQ0=0;OQ=4548.44;QD=19.95;RankSumP=0.119255;SB=-1931.49;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.286C>T;refseq.codonCoord=96;refseq.end=111542845;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=486;refseq.name=NM_024901;refseq.name2=DENND2D;refseq.positionType=CDS;refseq.proteinCoordStr=p.L96L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=43;refseq.start=111542845;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/0
|
|
chr1 111585505 . C A,T 288.13 PASS AC=1,1;AF=0.50,0.50;AN=2;BestBaseQ=32;DB;DP=379;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=98.75;MQ0=0;OQ=15341.58;QD=40.48;RankSumP=0.273839;SB=-2803.55;SecondBestBaseQ=31;set=Intersection GT 1/2
|
|
chr1 111585519 . A G 68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=327;Dels=0.00;HRun=0;HaplotypeScore=17.43;MQ=98.74;MQ0=0;OQ=13206.63;QD=40.39;RankSumP=1.00000;SB=-4617.90;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.936A>G;refseq.codingCoordStr_2=c.729A>G;refseq.codingCoordStr_3=c.966A>G;refseq.codonCoord_1=312;refseq.codonCoord_2=243;refseq.codonCoord_3=322;refseq.end_1=111585519;refseq.end_2=111585519;refseq.end_3=111585519;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1007;refseq.mrnaCoord_2=1067;refseq.mrnaCoord_3=1037;refseq.name2_1=CHI3L2;refseq.name2_2=CHI3L2;refseq.name2_3=CHI3L2;refseq.name_1=NM_001025197;refseq.name_2=NM_001025199;refseq.name_3=NM_004000;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Q312Q;refseq.proteinCoordStr_2=p.Q243Q;refseq.proteinCoordStr_3=p.Q322Q;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceCodon_1=CAA;refseq.referenceCodon_2=CAA;refseq.referenceCodon_3=CAA;refseq.spliceDist_1=48;refseq.spliceDist_2=48;refseq.spliceDist_3=48;refseq.start_1=111585519;refseq.start_2=111585519;refseq.start_3=111585519;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantAA_3=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;refseq.variantCodon_3=CAG;set=Intersection GT 1/1
|
|
chr1 111659474 . A G 185.83 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=549;Dels=0.00;HRun=0;HaplotypeScore=11.73;MQ=75.93;MQ0=10;OQ=10836.65;QD=19.74;RankSumP=0.449634;SB=-3589.38;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.50A>G;refseq.codingCoordStr_2=c.374A>G;refseq.codonCoord_1=17;refseq.codonCoord_2=125;refseq.end_1=111659474;refseq.end_2=111659474;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=206;refseq.mrnaCoord_2=477;refseq.name2_1=CHIA;refseq.name2_2=CHIA;refseq.name_1=NM_021797;refseq.name_2=NM_201653;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K17R;refseq.proteinCoordStr_2=p.K125R;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=60;refseq.spliceDist_2=60;refseq.start_1=111659474;refseq.start_2=111659474;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGA;refseq.variantCodon_2=AGA;set=Intersection GT 0/1
|
|
chr1 111663364 . A G 204.63 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=439;Dels=0.00;HRun=0;HaplotypeScore=9.54;MQ=98.74;MQ0=0;OQ=16756.57;QD=38.17;RankSumP=1.00000;SB=-8131.27;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.691A>G;refseq.codingCoordStr_2=c.1015A>G;refseq.codonCoord_1=231;refseq.codonCoord_2=339;refseq.end_1=111663364;refseq.end_2=111663364;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=847;refseq.mrnaCoord_2=1118;refseq.name2_1=CHIA;refseq.name2_2=CHIA;refseq.name_1=NM_021797;refseq.name_2=NM_201653;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I231V;refseq.proteinCoordStr_2=p.I339V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=-21;refseq.spliceDist_2=-21;refseq.start_1=111663364;refseq.start_2=111663364;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=Intersection GT 1/1
|
|
chr1 111663497 . T C 420.34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=4556.51;QD=42.19;RankSumP=1.00000;SB=-1690.02;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.737T>C;refseq.codingCoordStr_2=c.1061T>C;refseq.codonCoord_1=246;refseq.codonCoord_2=354;refseq.end_1=111663497;refseq.end_2=111663497;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=893;refseq.mrnaCoord_2=1164;refseq.name2_1=CHIA;refseq.name2_2=CHIA;refseq.name_1=NM_021797;refseq.name_2=NM_201653;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F246S;refseq.proteinCoordStr_2=p.F354S;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.spliceDist_1=26;refseq.spliceDist_2=26;refseq.start_1=111663497;refseq.start_2=111663497;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCT;refseq.variantCodon_2=TCT;set=Intersection GT 1/1
|
|
chr1 111664475 . T G 102.51 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=163;Dels=0.00;HRun=1;HaplotypeScore=12.16;MQ=98.20;MQ0=0;OQ=5115.18;QD=31.38;RankSumP=1.00000;SB=-1777.24;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.971T>G;refseq.codingCoordStr_2=c.1295T>G;refseq.codonCoord_1=324;refseq.codonCoord_2=432;refseq.end_1=111664475;refseq.end_2=111664475;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1127;refseq.mrnaCoord_2=1398;refseq.name2_1=CHIA;refseq.name2_2=CHIA;refseq.name_1=NM_021797;refseq.name_2=NM_201653;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V324G;refseq.proteinCoordStr_2=p.V432G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=118;refseq.spliceDist_2=118;refseq.start_1=111664475;refseq.start_2=111664475;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=Intersection GT 1/1
|
|
chr1 111844155 . A G 252 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=190;Dels=0.00;HRun=1;HaplotypeScore=1.94;MQ=98.95;MQ0=0;OQ=7830.18;QD=41.21;RankSumP=1.00000;SB=-2478.84;SecondBestBaseQ=0;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.897T>C;refseq.codonCoord_3=299;refseq.end_1=111847139;refseq.end_2=111907980;refseq.end_3=111844155;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=1664;refseq.name2_1=ADORA3;refseq.name2_2=ADORA3;refseq.name2_3=ADORA3;refseq.name_1=NM_020683;refseq.name_2=NM_001081976;refseq.name_3=NM_000677;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.A299A;refseq.referenceAA_3=Ala;refseq.referenceCodon_3=GCT;refseq.spliceDist_3=547;refseq.start_1=111834918;refseq.start_2=111834918;refseq.start_3=111844155;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_3=Ala;refseq.variantCodon_3=GCC;set=Intersection GT 1/1
|
|
chr1 112071395 . G A 71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=98.93;MQ0=0;OQ=1773.85;QD=42.23;RankSumP=1.00000;SB=-897.65;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.612C>T;refseq.codingCoordStr_2=c.567C>T;refseq.codonCoord_1=204;refseq.codonCoord_2=189;refseq.end_1=112071395;refseq.end_2=112071395;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=794;refseq.mrnaCoord_2=652;refseq.name2_1=C1orf183;refseq.name2_2=C1orf183;refseq.name_1=NM_019099;refseq.name_2=NM_198926;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F204F;refseq.proteinCoordStr_2=p.F189F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.spliceDist_1=555;refseq.spliceDist_2=555;refseq.start_1=112071395;refseq.start_2=112071395;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTT;refseq.variantCodon_2=TTT;set=Intersection GT 1/1
|
|
chr1 112100105 . A G 74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=21;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=6.83;MQ=95.41;MQ0=0;OQ=1776.44;QD=24.67;RankSumP=1.00000;SB=-255.70;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.36A>G;refseq.codonCoord=12;refseq.end=112100105;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=393;refseq.name=NM_007204;refseq.name2=DDX20;refseq.positionType=CDS;refseq.proteinCoordStr=p.A12A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-266;refseq.start=112100105;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 112100352 . T C 5.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=55.84;QD=27.92;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.283T>C;refseq.codonCoord=95;refseq.end=112100352;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=640;refseq.name=NM_007204;refseq.name2=DDX20;refseq.positionType=CDS;refseq.proteinCoordStr=p.L95L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-19;refseq.start=112100352;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=filterInsoap-gatk GT 1/1
|
|
chr1 112110476 . T C 330.21 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=136;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=98.67;MQ0=0;OQ=4542.78;QD=33.40;RankSumP=1.00000;SB=-1830.08;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1907T>C;refseq.codonCoord=636;refseq.end=112110476;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2264;refseq.name=NM_007204;refseq.name2=DDX20;refseq.positionType=CDS;refseq.proteinCoordStr=p.I636T;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=595;refseq.start=112110476;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 112110495 . G A 295.23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=153;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=98.77;MQ0=0;OQ=5010.12;QD=32.75;RankSumP=1.00000;SB=-926.13;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1926G>A;refseq.codonCoord=642;refseq.end=112110495;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2283;refseq.name=NM_007204;refseq.name2=DDX20;refseq.positionType=CDS;refseq.proteinCoordStr=p.V642V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=614;refseq.start=112110495;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/1
|
|
chr1 112110646 . C A 308.58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=418;Dels=0.00;HRun=0;HaplotypeScore=13.47;MQ=98.83;MQ0=0;OQ=7264.02;QD=17.38;RankSumP=0.320804;SB=-2516.47;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2077C>A;refseq.codonCoord=693;refseq.end=112110646;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2434;refseq.name=NM_007204;refseq.name2=DDX20;refseq.positionType=CDS;refseq.proteinCoordStr=p.R693S;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=765;refseq.start=112110646;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/0
|
|
chr1 112110854 . T C 352.11 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=372;Dels=0.00;HRun=0;HaplotypeScore=6.62;MQ=98.86;MQ0=0;OQ=7387.07;QD=19.86;RankSumP=0.0844817;SB=-2614.89;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2285T>C;refseq.codonCoord=762;refseq.end=112110854;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2642;refseq.name=NM_007204;refseq.name2=DDX20;refseq.positionType=CDS;refseq.proteinCoordStr=p.I762T;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=-868;refseq.start=112110854;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 112326128 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.744T>C;refseq.codingCoordStr_2=c.744T>C;refseq.codonCoord_1=248;refseq.codonCoord_2=248;refseq.end_1=112326128;refseq.end_2=112326128;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1224;refseq.mrnaCoord_2=1224;refseq.name2_1=KCND3;refseq.name2_2=KCND3;refseq.name_1=NM_004980;refseq.name_2=NM_172198;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A248A;refseq.proteinCoordStr_2=p.A248A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-365;refseq.spliceDist_2=-365;refseq.start_1=112326128;refseq.start_2=112326128;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=FilteredInAll GT 0/1
|
|
chr1 112793221 . T C 99.39 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=193;Dels=0.00;HRun=2;HaplotypeScore=1.09;MQ=98.87;MQ0=0;OQ=3927.04;QD=20.35;RankSumP=0.0668576;SB=-1474.70;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.234T>C;refseq.codonCoord=78;refseq.end=112793221;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=462;refseq.name=NM_018704;refseq.name2=CTTNBP2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.N78N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-97;refseq.start=112793221;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/0
|
|
chr1 112800750 . G A 329.41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=123;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=98.70;MQ0=0;OQ=5103.08;QD=41.49;RankSumP=1.00000;SB=-1960.41;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1113G>A;refseq.codonCoord=371;refseq.end=112800750;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1341;refseq.name=NM_018704;refseq.name2=CTTNBP2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q371Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=675;refseq.start=112800750;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/1
|
|
chr1 112801194 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1557C>A;refseq.codonCoord=519;refseq.end=112801194;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1785;refseq.name=NM_018704;refseq.name2=CTTNBP2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.I519I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=1119;refseq.start=112801194;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=FilteredInAll GT 1/0
|
|
chr1 112864648 . A G 142.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=7.35;MQ=98.48;MQ0=0;OQ=2194.40;QD=14.07;RankSumP=0.0140197;SB=-192.38;SecondBestBaseQ=26;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1113A>G;refseq.codingCoordStr_2=c.1170A>G;refseq.codonCoord_1=371;refseq.codonCoord_2=390;refseq.end_1=112864648;refseq.end_2=112864648;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1233;refseq.mrnaCoord_2=1685;refseq.name2_1=WNT2B;refseq.name2_2=WNT2B;refseq.name_1=NM_004185;refseq.name_2=NM_024494;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q371Q;refseq.proteinCoordStr_2=p.Q390Q;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAA;refseq.referenceCodon_2=CAA;refseq.spliceDist_1=224;refseq.spliceDist_2=224;refseq.start_1=112864648;refseq.start_2=112864648;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=Intersection GT 0/1
|
|
chr1 113038204 . C T 334.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=312;Dels=0.00;HRun=0;HaplotypeScore=8.19;MQ=98.73;MQ0=0;OQ=5216.68;QD=16.72;RankSumP=0.0978650;SB=-1920.22;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1182C>T;refseq.codingCoordStr_2=c.1182C>T;refseq.codonCoord_1=394;refseq.codonCoord_2=394;refseq.end_1=113038204;refseq.end_2=113038204;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1452;refseq.mrnaCoord_2=1567;refseq.name2_1=MOV10;refseq.name2_2=MOV10;refseq.name_1=NM_001130079;refseq.name_2=NM_020963;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G394G;refseq.proteinCoordStr_2=p.G394G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.start_1=113038204;refseq.start_2=113038204;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=Intersection GT 0/1
|
|
chr1 113038694 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=130;Dels=0.00;HRun=3;HaplotypeScore=1.85;MQ=98.79;MQ0=0;OQ=1917.49;QD=14.75;RankSumP=0.300493;SB=-594.84;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1392A>G;refseq.codingCoordStr_2=c.1392A>G;refseq.codonCoord_1=464;refseq.codonCoord_2=464;refseq.end_1=113038694;refseq.end_2=113038694;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1662;refseq.mrnaCoord_2=1777;refseq.name2_1=MOV10;refseq.name2_2=MOV10;refseq.name_1=NM_001130079;refseq.name_2=NM_020963;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T464T;refseq.proteinCoordStr_2=p.T464T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=-81;refseq.spliceDist_2=-81;refseq.start_1=113038694;refseq.start_2=113038694;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 0/1
|
|
chr1 113040642 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1944C>G;refseq.codingCoordStr_2=c.1944C>G;refseq.codonCoord_1=648;refseq.codonCoord_2=648;refseq.end_1=113040642;refseq.end_2=113040642;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2214;refseq.mrnaCoord_2=2329;refseq.name2_1=MOV10;refseq.name2_2=MOV10;refseq.name_1=NM_001130079;refseq.name_2=NM_020963;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G648G;refseq.proteinCoordStr_2=p.G648G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=-38;refseq.spliceDist_2=-38;refseq.start_1=113040642;refseq.start_2=113040642;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 113040905 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=6.42;MQ=96.89;MQ0=0;OQ=893.82;QD=13.54;RankSumP=0.0103829;SB=-350.32;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2112G>A;refseq.codingCoordStr_2=c.2112G>A;refseq.codonCoord_1=704;refseq.codonCoord_2=704;refseq.end_1=113040905;refseq.end_2=113040905;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2382;refseq.mrnaCoord_2=2497;refseq.name2_1=MOV10;refseq.name2_2=MOV10;refseq.name_1=NM_001130079;refseq.name_2=NM_020963;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E704E;refseq.proteinCoordStr_2=p.E704E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-87;refseq.spliceDist_2=-87;refseq.start_1=113040905;refseq.start_2=113040905;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=Intersection GT 1/0
|
|
chr1 113042575 . T C 257.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=193;Dels=0.00;HRun=1;HaplotypeScore=6.60;MQ=98.85;MQ0=0;OQ=3233.06;QD=16.75;RankSumP=0.252223;SB=-1517.50;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2460T>C;refseq.codingCoordStr_2=c.2460T>C;refseq.codonCoord_1=820;refseq.codonCoord_2=820;refseq.end_1=113042575;refseq.end_2=113042575;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2730;refseq.mrnaCoord_2=2845;refseq.name2_1=MOV10;refseq.name2_2=MOV10;refseq.name_1=NM_001130079;refseq.name_2=NM_020963;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A820A;refseq.proteinCoordStr_2=p.A820A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-49;refseq.spliceDist_2=-49;refseq.start_1=113042575;refseq.start_2=113042575;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/0
|
|
chr1 113044571 . C T 212.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=98.00;MQ0=0;OQ=1435.70;QD=14.50;RankSumP=0.00560903;SB=-680.69;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2931C>T;refseq.codingCoordStr_2=c.2931C>T;refseq.codonCoord_1=977;refseq.codonCoord_2=977;refseq.end_1=113044571;refseq.end_2=113044571;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3201;refseq.mrnaCoord_2=3316;refseq.name2_1=MOV10;refseq.name2_2=MOV10;refseq.name_1=NM_001130079;refseq.name_2=NM_020963;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S977S;refseq.proteinCoordStr_2=p.S977S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=11;refseq.spliceDist_2=11;refseq.start_1=113044571;refseq.start_2=113044571;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=filterInsoap-gatk GT 0/1
|
|
chr1 113056912 . C T 134.24 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=362;Dels=0.00;HRun=0;HaplotypeScore=16.47;MQ=98.78;MQ0=0;OQ=14373.25;QD=39.71;RankSumP=1.00000;SB=-6518.97;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.706G>A;refseq.codonCoord=236;refseq.end=113056912;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=733;refseq.name=NM_005167;refseq.name2=PPM1J;refseq.positionType=CDS;refseq.proteinCoordStr=p.V236I;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-24;refseq.start=113056912;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/1
|
|
chr1 113451788 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1363C>A;refseq.codonCoord=455;refseq.end=113451788;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1561;refseq.name=NM_014813;refseq.name2=LRIG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L455I;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=50;refseq.start=113451788;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=FilteredInAll GT 1/0
|
|
chr1 113458615 . A C 273.64 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=297;Dels=0.00;HRun=1;HaplotypeScore=7.52;MQ=98.81;MQ0=0;OQ=12090.92;QD=40.71;RankSumP=1.00000;SB=-4496.65;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2124A>C;refseq.codonCoord=708;refseq.end=113458615;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2322;refseq.name=NM_014813;refseq.name2=LRIG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T708T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=44;refseq.start=113458615;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 113468082 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3034T>C;refseq.codonCoord=1012;refseq.end=113468082;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3232;refseq.name=NM_014813;refseq.name2=LRIG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1012P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=63;refseq.start=113468082;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 113998018 . A G 166.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=147;Dels=0.00;HRun=0;HaplotypeScore=3.11;MQ=98.87;MQ0=0;OQ=1915.30;QD=13.03;RankSumP=0.414239;SB=-962.13;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2484A>G;refseq.codingCoordStr_2=c.2484A>G;refseq.codonCoord_1=828;refseq.codonCoord_2=828;refseq.end_1=113998018;refseq.end_2=113998018;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2665;refseq.mrnaCoord_2=2665;refseq.name2_1=MAGI3;refseq.name2_2=MAGI3;refseq.name_1=NM_001142782;refseq.name_2=NM_152900;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T828T;refseq.proteinCoordStr_2=p.T828T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=44;refseq.spliceDist_2=44;refseq.start_1=113998018;refseq.start_2=113998018;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 0/1
|
|
chr1 114179091 . A G 463.08 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=98.70;MQ0=0;OQ=4726.66;QD=38.74;RankSumP=1.00000;SB=-2148.73;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1858T>C;refseq.codingCoordStr_2=c.1858T>C;refseq.codonCoord_1=620;refseq.codonCoord_2=620;refseq.end_1=114179091;refseq.end_2=114179091;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1988;refseq.mrnaCoord_2=1988;refseq.name2_1=PTPN22;refseq.name2_2=PTPN22;refseq.name_1=NM_012411;refseq.name_2=NM_015967;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.W620R;refseq.proteinCoordStr_2=p.W620R;refseq.referenceAA_1=Trp;refseq.referenceAA_2=Trp;refseq.referenceCodon_1=TGG;refseq.referenceCodon_2=TGG;refseq.spliceDist_1=-37;refseq.spliceDist_2=-37;refseq.start_1=114179091;refseq.start_2=114179091;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;set=Intersection GT 1/1
|
|
chr1 114226124 . C T 283.17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=173;Dels=0.00;HRun=1;HaplotypeScore=3.75;MQ=99.00;MQ0=0;OQ=7424.01;QD=42.91;RankSumP=1.00000;SB=-1889.87;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.268G>A;refseq.codonCoord=90;refseq.end=114226124;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=440;refseq.name=NM_001010922;refseq.name2=BCL2L15;refseq.positionType=CDS;refseq.proteinCoordStr=p.D90N;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=19;refseq.start=114226124;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 114239357 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2073T>G;refseq.codonCoord=691;refseq.end=114239357;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2327;refseq.name=NM_006594;refseq.name2=AP4B1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C691W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-158;refseq.start=114239357;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 0/1
|
|
chr1 114244228 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.935G>C;refseq.codonCoord=312;refseq.end=114244228;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1189;refseq.name=NM_006594;refseq.name2=AP4B1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S312T;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-180;refseq.start=114244228;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 114284674 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=3;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.146T>C;refseq.codingCoordStr_2=c.146T>C;refseq.codonCoord_1=49;refseq.codonCoord_2=49;refseq.end_1=114284674;refseq.end_2=114284674;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=307;refseq.mrnaCoord_2=307;refseq.name2_1=HIPK1;refseq.name2_2=HIPK1;refseq.name_1=NM_152696;refseq.name_2=NM_198268;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L49P;refseq.proteinCoordStr_2=p.L49P;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.spliceDist_1=148;refseq.spliceDist_2=148;refseq.start_1=114284674;refseq.start_2=114284674;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 114317240 . G A 118.87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=9.00;MQ=97.03;MQ0=0;OQ=1550.49;QD=12.71;RankSumP=0.139989;SB=-584.59;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2034G>A;refseq.codingCoordStr_2=c.3216G>A;refseq.codingCoordStr_3=c.2094G>A;refseq.codonCoord_1=678;refseq.codonCoord_2=1072;refseq.codonCoord_3=698;refseq.end_1=114317240;refseq.end_2=114317240;refseq.end_3=114317240;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2097;refseq.mrnaCoord_2=3377;refseq.mrnaCoord_3=2288;refseq.name2_1=HIPK1;refseq.name2_2=HIPK1;refseq.name2_3=HIPK1;refseq.name_1=NM_181358;refseq.name_2=NM_198268;refseq.name_3=NM_198269;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A678A;refseq.proteinCoordStr_2=p.A1072A;refseq.proteinCoordStr_3=p.A698A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.referenceCodon_3=GCG;refseq.spliceDist_1=72;refseq.spliceDist_2=72;refseq.spliceDist_3=72;refseq.start_1=114317240;refseq.start_2=114317240;refseq.start_3=114317240;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;refseq.variantCodon_3=GCA;set=Intersection GT 1/0
|
|
chr1 114482063 . C T 240.52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=564;Dels=0.00;HRun=0;HaplotypeScore=13.78;MQ=98.89;MQ0=0;OQ=8833.13;QD=15.66;RankSumP=0.0284510;SB=-2672.78;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.393G>A;refseq.codonCoord=131;refseq.end=114482063;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=643;refseq.name=NM_205848;refseq.name2=SYT6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S131S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=136;refseq.start=114482063;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 0/1
|
|
chr1 114749804 . A G 134.05 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=548;Dels=0.00;HRun=0;HaplotypeScore=8.42;MQ=98.94;MQ0=0;OQ=21735.93;QD=39.66;RankSumP=1.00000;SB=-9743.90;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2519T>C;refseq.codingCoordStr_2=c.2519T>C;refseq.codonCoord_1=840;refseq.codonCoord_2=840;refseq.end_1=114749804;refseq.end_2=114749804;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2603;refseq.mrnaCoord_2=2603;refseq.name2_1=TRIM33;refseq.name2_2=TRIM33;refseq.name_1=NM_015906;refseq.name_2=NM_033020;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I840T;refseq.proteinCoordStr_2=p.I840T;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=101;refseq.spliceDist_2=101;refseq.start_1=114749804;refseq.start_2=114749804;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;set=Intersection GT 1/1
|
|
chr1 114969909 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.220A>C;refseq.codonCoord=74;refseq.end=114969909;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=553;refseq.name=NM_198459;refseq.name2=DENND2C;refseq.positionType=CDS;refseq.proteinCoordStr=p.T74P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=424;refseq.start=114969909;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 114970123 . A T 273.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=369;Dels=0.00;HRun=1;HaplotypeScore=4.97;MQ=98.81;MQ0=0;OQ=6405.67;QD=17.36;RankSumP=0.0880117;SB=-1413.65;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6T>A;refseq.codonCoord=2;refseq.end=114970123;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=339;refseq.name=NM_198459;refseq.name2=DENND2C;refseq.positionType=CDS;refseq.proteinCoordStr=p.D2E;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=210;refseq.start=114970123;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 115037580 . G A 177.12 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=206;Dels=0.00;HRun=0;HaplotypeScore=5.98;MQ=98.61;MQ0=0;OQ=2671.49;QD=12.97;RankSumP=0.398925;SB=-1276.55;SecondBestBaseQ=32;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.133C>T;refseq.codonCoord_2=45;refseq.end_1=115039583;refseq.end_2=115037580;refseq.frame_2=0;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=181;refseq.name2_1=AMPD1;refseq.name2_2=AMPD1;refseq.name_1=NM_001172626;refseq.name_2=NM_000036;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.Q45*;refseq.referenceAA_2=Gln;refseq.referenceCodon_2=CAA;refseq.spliceDist_2=-1;refseq.spliceInfo_2=splice-donor_-1;refseq.start_1=115032896;refseq.start_2=115037580;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Stop;refseq.variantCodon_2=TAA;set=Intersection GT 1/0
|
|
chr1 115201407 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=124;Dels=0.00;HRun=1;HaplotypeScore=12.73;MQ=98.14;MQ0=0;OQ=1440.26;QD=11.62;RankSumP=0.287617;SB=-745.31;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.225C>G;refseq.codonCoord=75;refseq.end=115201407;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=434;refseq.name=NM_003176;refseq.name2=SYCP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P75P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-13;refseq.start=115201407;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/0
|
|
chr1 115377546 . A G 226.13 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=413;Dels=0.00;HRun=0;HaplotypeScore=11.69;MQ=98.89;MQ0=0;OQ=17513.94;QD=42.41;RankSumP=1.00000;SB=-5012.69;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.40A>G;refseq.codonCoord=14;refseq.end=115377546;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=108;refseq.name=NM_000549;refseq.name2=TSHB;refseq.positionType=CDS;refseq.proteinCoordStr=p.T14A;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=41;refseq.start=115377546;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 115403051 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=848;Dels=0.00;HRun=0;HaplotypeScore=33.86;MQ=98.91;MQ0=0;OQ=19543.69;QD=23.05;RankSumP=0.248901;SB=-6517.34;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.420G>C;refseq.codonCoord=140;refseq.end=115403051;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=488;refseq.name=NM_005725;refseq.name2=TSPAN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G140G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-25;refseq.start=115403051;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/0
|
|
chr1 115406321 . C T 329.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=97.82;MQ0=0;OQ=1435.14;QD=35.00;RankSumP=1.00000;SB=-586.32;SecondBestBaseQ=21;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.228G>A;refseq.codonCoord=76;refseq.end=115406321;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=296;refseq.name=NM_005725;refseq.name2=TSPAN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G76G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-43;refseq.start=115406321;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 115630836 . G A 220.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=221;Dels=0.00;HRun=0;HaplotypeScore=5.85;MQ=98.65;MQ0=0;OQ=3138.05;QD=14.20;RankSumP=0.107573;SB=-799.18;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.104C>T;refseq.codonCoord=35;refseq.end=115630836;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=273;refseq.name=NM_002506;refseq.name2=NGF;refseq.positionType=CDS;refseq.proteinCoordStr=p.A35V;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=116;refseq.start=115630836;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 116007946 . G A 289.74 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=523;Dels=0.00;HRun=0;HaplotypeScore=8.42;MQ=98.73;MQ0=0;OQ=10623.13;QD=20.31;RankSumP=0.118275;SB=-3507.43;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.340G>A;refseq.codingCoordStr_2=c.346G>A;refseq.codingCoordStr_3=c.346G>A;refseq.codonCoord_1=114;refseq.codonCoord_2=116;refseq.codonCoord_3=116;refseq.end_1=116007946;refseq.end_2=116007946;refseq.end_3=116007946;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=611;refseq.mrnaCoord_2=561;refseq.mrnaCoord_3=617;refseq.name2_1=VANGL1;refseq.name2_2=VANGL1;refseq.name2_3=VANGL1;refseq.name_1=NM_001172411;refseq.name_2=NM_001172412;refseq.name_3=NM_138959;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A114T;refseq.proteinCoordStr_2=p.A116T;refseq.proteinCoordStr_3=p.A116T;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GCC;refseq.spliceDist_1=142;refseq.spliceDist_2=142;refseq.spliceDist_3=142;refseq.start_1=116007946;refseq.start_2=116007946;refseq.start_3=116007946;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;refseq.variantCodon_3=ACC;set=Intersection GT 1/0
|
|
chr1 116028154 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=21;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1007C>A;refseq.codingCoordStr_2=c.1013C>A;refseq.codingCoordStr_3=c.1013C>A;refseq.codonCoord_1=336;refseq.codonCoord_2=338;refseq.codonCoord_3=338;refseq.end_1=116028154;refseq.end_2=116028154;refseq.end_3=116028154;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.functionalClass_3=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1278;refseq.mrnaCoord_2=1228;refseq.mrnaCoord_3=1284;refseq.name2_1=VANGL1;refseq.name2_2=VANGL1;refseq.name2_3=VANGL1;refseq.name_1=NM_001172411;refseq.name_2=NM_001172412;refseq.name_3=NM_138959;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S336*;refseq.proteinCoordStr_2=p.S338*;refseq.proteinCoordStr_3=p.S338*;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.spliceDist_1=-67;refseq.spliceDist_2=-67;refseq.spliceDist_3=-67;refseq.start_1=116028154;refseq.start_2=116028154;refseq.start_3=116028154;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantAA_3=Stop;refseq.variantCodon_1=TAA;refseq.variantCodon_2=TAA;refseq.variantCodon_3=TAA;set=FilteredInAll GT 1/0
|
|
chr1 116045400 . G A 295.46 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=176;Dels=0.00;HRun=0;HaplotypeScore=7.60;MQ=98.75;MQ0=0;OQ=3079.21;QD=17.50;RankSumP=0.191085;SB=-796.21;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1185C>T;refseq.codonCoord=395;refseq.end=116045400;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1449;refseq.name=NM_001232;refseq.name2=CASQ2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D395D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=171;refseq.start=116045400;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/0
|
|
chr1 116049349 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=101;Dels=0.00;HRun=2;HaplotypeScore=1.43;MQ=98.58;MQ0=0;OQ=955.17;QD=9.46;RankSumP=0.338944;SB=-365.24;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.926A>G;refseq.codonCoord=309;refseq.end=116049349;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1190;refseq.name=NM_001232;refseq.name2=CASQ2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D309G;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-14;refseq.start=116049349;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/0
|
|
chr1 116112490 . T C 227.92 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=515;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=98.62;MQ0=0;OQ=9184.72;QD=17.83;RankSumP=0.493528;SB=-3053.94;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.196A>G;refseq.codonCoord=66;refseq.end=116112490;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=460;refseq.name=NM_001232;refseq.name2=CASQ2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T66A;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-39;refseq.start=116112490;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/0
|
|
chr1 116468364 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=1.08423e-07;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.344A>G;refseq.codonCoord=115;refseq.end=116468364;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=609;refseq.name=NM_152367;refseq.name2=C1orf161;refseq.positionType=CDS;refseq.proteinCoordStr=p.E115G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-138;refseq.start=116468364;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 116477328 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.908T>G;refseq.codonCoord=303;refseq.end=116477328;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1173;refseq.name=NM_152367;refseq.name2=C1orf161;refseq.positionType=CDS;refseq.proteinCoordStr=p.V303G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=53;refseq.start=116477328;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 116745305 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_3=c.2749A>C;refseq.codingCoordStr_4=c.2749A>C;refseq.codingCoordStr_5=c.2656A>C;refseq.codonCoord_3=917;refseq.codonCoord_4=917;refseq.codonCoord_5=886;refseq.end_1=116762593;refseq.end_2=116762593;refseq.end_3=116745305;refseq.end_4=116745305;refseq.end_5=116745305;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_3=3088;refseq.mrnaCoord_4=3112;refseq.mrnaCoord_5=2921;refseq.name2_1=C1orf203;refseq.name2_2=C1orf203;refseq.name2_3=ATP1A1;refseq.name2_4=ATP1A1;refseq.name2_5=ATP1A1;refseq.name_1=NR_027645;refseq.name_2=NR_027646;refseq.name_3=NM_000701;refseq.name_4=NM_001160233;refseq.name_5=NM_001160234;refseq.numMatchingRecords=5;refseq.positionType_1=non_coding_intron;refseq.positionType_2=non_coding_intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_3=p.T917P;refseq.proteinCoordStr_4=p.T917P;refseq.proteinCoordStr_5=p.T886P;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.referenceCodon_5=ACC;refseq.spliceDist_3=31;refseq.spliceDist_4=31;refseq.spliceDist_5=31;refseq.start_1=116745287;refseq.start_2=116745287;refseq.start_3=116745305;refseq.start_4=116745305;refseq.start_5=116745305;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Pro;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;refseq.variantCodon_5=CCC;set=FilteredInAll GT 0/1
|
|
chr1 116923582 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3289A>G;refseq.codingCoordStr_2=c.3349A>G;refseq.codonCoord_1=1097;refseq.codonCoord_2=1117;refseq.end_1=116923582;refseq.end_2=116923582;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3994;refseq.mrnaCoord_2=4054;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T1097A;refseq.proteinCoordStr_2=p.T1117A;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.spliceDist_1=-46;refseq.spliceDist_2=-46;refseq.start_1=116923582;refseq.start_2=116923582;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=FilteredInAll GT 1/0
|
|
chr1 116923808 . G C 25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=54;Dels=0.00;HRun=1;HaplotypeScore=9.29;MQ=95.94;MQ0=0;OQ=341.30;QD=6.32;RankSumP=0.136852;SB=-11.76;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3063C>G;refseq.codingCoordStr_2=c.3123C>G;refseq.codonCoord_1=1021;refseq.codonCoord_2=1041;refseq.end_1=116923808;refseq.end_2=116923808;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3768;refseq.mrnaCoord_2=3828;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D1021E;refseq.proteinCoordStr_2=p.D1041E;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=215;refseq.spliceDist_2=215;refseq.start_1=116923808;refseq.start_2=116923808;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 0/1
|
|
chr1 116923811 . G C 86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=8.55;MQ=95.94;MQ0=0;OQ=690.85;QD=12.79;RankSumP=0.0407959;SB=-271.39;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3060C>G;refseq.codingCoordStr_2=c.3120C>G;refseq.codonCoord_1=1020;refseq.codonCoord_2=1040;refseq.end_1=116923811;refseq.end_2=116923811;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3765;refseq.mrnaCoord_2=3825;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D1020E;refseq.proteinCoordStr_2=p.D1040E;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=212;refseq.spliceDist_2=212;refseq.start_1=116923811;refseq.start_2=116923811;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 0/1
|
|
chr1 116944136 . C T 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00663842;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1979G>A;refseq.codingCoordStr_2=c.2039G>A;refseq.codonCoord_1=660;refseq.codonCoord_2=680;refseq.end_1=116944136;refseq.end_2=116944136;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2684;refseq.mrnaCoord_2=2744;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R660Q;refseq.proteinCoordStr_2=p.R680Q;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.spliceDist_1=-51;refseq.spliceDist_2=-51;refseq.start_1=116944136;refseq.start_2=116944136;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;set=FilteredInAll GT 0/1
|
|
chr1 116944164 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.122362;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1951C>T;refseq.codingCoordStr_2=c.2011C>T;refseq.codonCoord_1=651;refseq.codonCoord_2=671;refseq.end_1=116944164;refseq.end_2=116944164;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2656;refseq.mrnaCoord_2=2716;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R651W;refseq.proteinCoordStr_2=p.R671W;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.spliceDist_1=-79;refseq.spliceDist_2=-79;refseq.start_1=116944164;refseq.start_2=116944164;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Trp;refseq.variantAA_2=Trp;refseq.variantCodon_1=TGG;refseq.variantCodon_2=TGG;set=soap GT 1/0
|
|
chr1 116944230 . G A 61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=0;RankSumP=0.493898;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1885C>T;refseq.codingCoordStr_2=c.1945C>T;refseq.codonCoord_1=629;refseq.codonCoord_2=649;refseq.end_1=116944230;refseq.end_2=116944230;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2590;refseq.mrnaCoord_2=2650;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R629C;refseq.proteinCoordStr_2=p.R649C;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.spliceDist_1=-145;refseq.spliceDist_2=-145;refseq.start_1=116944230;refseq.start_2=116944230;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=soap GT 1/0
|
|
chr1 116948029 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=18;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1364A>C;refseq.codingCoordStr_2=c.1424A>C;refseq.codonCoord_1=455;refseq.codonCoord_2=475;refseq.end_1=116948029;refseq.end_2=116948029;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2069;refseq.mrnaCoord_2=2129;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N455T;refseq.proteinCoordStr_2=p.N475T;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=142;refseq.spliceDist_2=142;refseq.start_1=116948029;refseq.start_2=116948029;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=FilteredInAll GT 1/0
|
|
chr1 116952140 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.416502;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1169T>C;refseq.codingCoordStr_2=c.1169T>C;refseq.codonCoord_1=390;refseq.codonCoord_2=390;refseq.end_1=116952140;refseq.end_2=116952140;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1874;refseq.mrnaCoord_2=1874;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I390T;refseq.proteinCoordStr_2=p.I390T;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=-54;refseq.spliceDist_2=-54;refseq.start_1=116952140;refseq.start_2=116952140;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;set=soap GT 0/1
|
|
chr1 116958077 . T C 10 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=2;RankSumP=0.000291375;SecondBestBaseQ=20;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.665A>G;refseq.codingCoordStr_2=c.665A>G;refseq.codonCoord_1=222;refseq.codonCoord_2=222;refseq.end_1=116958077;refseq.end_2=116958077;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1370;refseq.mrnaCoord_2=1370;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D222G;refseq.proteinCoordStr_2=p.D222G;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-168;refseq.spliceDist_2=-168;refseq.start_1=116958077;refseq.start_2=116958077;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=FilteredInAll GT 1/0
|
|
chr1 116960495 . A G 4 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.355556;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.151T>C;refseq.codingCoordStr_2=c.151T>C;refseq.codonCoord_1=51;refseq.codonCoord_2=51;refseq.end_1=116960495;refseq.end_2=116960495;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=856;refseq.mrnaCoord_2=856;refseq.name2_1=IGSF3;refseq.name2_2=IGSF3;refseq.name_1=NM_001007237;refseq.name_2=NM_001542;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S51P;refseq.proteinCoordStr_2=p.S51P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCT;refseq.referenceCodon_2=TCT;refseq.spliceDist_1=108;refseq.spliceDist_2=108;refseq.start_1=116960495;refseq.start_2=116960495;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;set=FilteredInAll GT 0/1
|
|
chr1 117112670 . C A 147.45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=98.67;MQ0=0;OQ=1712.02;QD=16.46;RankSumP=0.0981220;SB=-655.65;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.798C>A;refseq.codonCoord=266;refseq.end=117112670;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=827;refseq.name=NM_001767;refseq.name2=CD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.H266Q;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=62;refseq.start=117112670;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 117289233 . A G 445.34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=228;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=98.57;MQ0=0;OQ=8557.58;QD=37.53;RankSumP=1.00000;SB=-2573.13;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.828A>G;refseq.codonCoord=276;refseq.end=117289233;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=965;refseq.name=NM_020440;refseq.name2=PTGFRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.P276P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-5;refseq.spliceInfo=splice-donor_-5;refseq.start=117289233;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 117289234 . T A 174.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=222;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=98.56;MQ0=0;OQ=8206.23;QD=36.96;RankSumP=1.00000;SB=-2808.92;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.829T>A;refseq.codonCoord=277;refseq.end=117289234;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=966;refseq.name=NM_020440;refseq.name2=PTGFRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S277T;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-4;refseq.spliceInfo=splice-donor_-4;refseq.start=117289234;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 117330981 . G A 256.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=6.81;MQ=98.16;MQ0=0;OQ=2108.04;QD=15.06;RankSumP=0.308243;SB=-896.40;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2509G>A;refseq.codonCoord=837;refseq.end=117330981;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2646;refseq.name=NM_020440;refseq.name2=PTGFRN;refseq.positionType=CDS;refseq.proteinCoordStr=p.V837I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=36;refseq.start=117330981;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/0
|
|
chr1 117355944 . A G 228.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=4.21;MQ=98.62;MQ0=0;OQ=2911.17;QD=14.06;RankSumP=0.479338;SB=-1171.15;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.674A>G;refseq.codonCoord=225;refseq.end=117355944;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=732;refseq.name=NM_004258;refseq.name2=CD101;refseq.positionType=CDS;refseq.proteinCoordStr=p.N225S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-168;refseq.start=117355944;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 117361249 . A G 218.74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=448;Dels=0.00;HRun=0;HaplotypeScore=11.86;MQ=98.97;MQ0=0;OQ=17068.95;QD=38.10;RankSumP=1.00000;SB=-7223.57;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1243A>G;refseq.codonCoord=415;refseq.end=117361249;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1301;refseq.name=NM_004258;refseq.name2=CD101;refseq.positionType=CDS;refseq.proteinCoordStr=p.M415V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=15;refseq.start=117361249;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 117419228 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=165;Dels=0.01;HRun=1;HaplotypeScore=18.79;MQ=98.77;MQ0=0;OQ=4101.56;QD=24.86;RankSumP=0.490447;SB=-1410.02;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.499A>G;refseq.codonCoord=167;refseq.end=117419228;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=519;refseq.name=NM_003594;refseq.name2=TTF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K167E;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=214;refseq.start=117419228;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 117419590 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=98.27;MQ0=0;OQ=1156.95;QD=15.85;RankSumP=0.369367;SB=-505.51;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.861C>T;refseq.codonCoord=287;refseq.end=117419590;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=881;refseq.name=NM_003594;refseq.name2=TTF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N287N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-415;refseq.start=117419590;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 117445581 . A G 199.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=363;Dels=0.00;HRun=0;HaplotypeScore=14.78;MQ=98.53;MQ0=0;OQ=7415.32;QD=20.43;RankSumP=0.357980;SB=-2193.56;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3401A>G;refseq.codonCoord=1134;refseq.end=117445581;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3421;refseq.name=NM_003594;refseq.name2=TTF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1134R;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=57;refseq.start=117445581;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 0/1
|
|
chr1 117457611 . A G 245.30 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=139;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=98.44;MQ0=0;OQ=2163.35;QD=15.56;RankSumP=0.287752;SB=-854.18;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1433T>C;refseq.codingCoordStr_2=c.1487T>C;refseq.codonCoord_1=478;refseq.codonCoord_2=496;refseq.end_1=117457611;refseq.end_2=117457611;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2021;refseq.mrnaCoord_2=2075;refseq.name2_1=TRIM45;refseq.name2_2=TRIM45;refseq.name_1=NM_001145635;refseq.name_2=NM_025188;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.M478T;refseq.proteinCoordStr_2=p.M496T;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=20;refseq.spliceDist_2=20;refseq.start_1=117457611;refseq.start_2=117457611;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 0/1
|
|
chr1 117462277 . C T 177.24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.92;MQ0=0;OQ=2346.78;QD=14.85;RankSumP=0.155885;SB=-706.62;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1124G>A;refseq.codingCoordStr_2=c.1124G>A;refseq.codonCoord_1=375;refseq.codonCoord_2=375;refseq.end_1=117462277;refseq.end_2=117462277;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1712;refseq.mrnaCoord_2=1712;refseq.name2_1=TRIM45;refseq.name2_2=TRIM45;refseq.name_1=NM_001145635;refseq.name_2=NM_025188;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C375Y;refseq.proteinCoordStr_2=p.C375Y;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=-45;refseq.spliceDist_2=-99;refseq.start_1=117462277;refseq.start_2=117462277;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;set=Intersection GT 0/1
|
|
chr1 117746487 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.459C>A;refseq.codonCoord=153;refseq.end=117746487;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1180;refseq.name=NM_006699;refseq.name2=MAN1A2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N153K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-100;refseq.start=117746487;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 1/0
|
|
chr1 117967214 . C T 253.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=299;Dels=0.00;HRun=0;HaplotypeScore=8.80;MQ=98.52;MQ0=0;OQ=5273.35;QD=17.64;RankSumP=0.272755;SB=-2090.57;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.201C>T;refseq.codonCoord=67;refseq.end=117967214;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=400;refseq.name=NM_017709;refseq.name2=FAM46C;refseq.positionType=CDS;refseq.proteinCoordStr=p.H67H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=228;refseq.start=117967214;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 0/1
|
|
chr1 118303464 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2703T>G;refseq.codonCoord_2=901;refseq.end_1=118307934;refseq.end_2=118303464;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=2769;refseq.name2_1=SPAG17;refseq.name2_2=WDR3;refseq.name_1=NM_206996;refseq.name_2=NM_006784;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.G901G;refseq.referenceAA_2=Gly;refseq.referenceCodon_2=GGT;refseq.spliceDist_2=27;refseq.start_1=118298206;refseq.start_2=118303464;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 118303465 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=0;RankSumP=0.00000;SecondBestBaseQ=3;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2704C>G;refseq.codonCoord_2=902;refseq.end_1=118307934;refseq.end_2=118303465;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=2770;refseq.name2_1=SPAG17;refseq.name2_2=WDR3;refseq.name_1=NM_206996;refseq.name_2=NM_006784;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.L902V;refseq.referenceAA_2=Leu;refseq.referenceCodon_2=CTT;refseq.spliceDist_2=28;refseq.start_1=118298206;refseq.start_2=118303465;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_2=Val;refseq.variantCodon_2=GTT;set=FilteredInAll GT 1/0
|
|
chr1 118338665 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=392;Dels=0.00;HRun=0;HaplotypeScore=7.55;MQ=98.80;MQ0=0;OQ=8070.43;QD=20.59;RankSumP=0.272857;SB=-3002.23;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5065A>G;refseq.codonCoord=1689;refseq.end=118338665;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5133;refseq.name=NM_206996;refseq.name2=SPAG17;refseq.positionType=CDS;refseq.proteinCoordStr=p.I1689V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=12;refseq.start=118338665;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 118367476 . G A 387.97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=188;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=98.90;MQ0=0;OQ=7922.51;QD=42.14;RankSumP=1.00000;SB=-3569.43;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4043C>T;refseq.codonCoord=1348;refseq.end=118367476;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4111;refseq.name=NM_206996;refseq.name2=SPAG17;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1348L;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-27;refseq.start=118367476;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/1
|
|
chr1 118384931 . G A 226.91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=388;Dels=0.00;HRun=0;HaplotypeScore=8.63;MQ=98.85;MQ0=0;OQ=16423.16;QD=42.33;RankSumP=1.00000;SB=-8079.38;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3111C>T;refseq.codonCoord=1037;refseq.end=118384931;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3179;refseq.name=NM_206996;refseq.name2=SPAG17;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y1037Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-56;refseq.start=118384931;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 118445953 . A G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=685;Dels=0.00;HRun=0;HaplotypeScore=12.22;MQ=98.60;MQ0=0;OQ=25632.30;QD=37.42;RankSumP=1.00000;SB=-11247.92;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.567T>C;refseq.codonCoord=189;refseq.end=118445953;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=635;refseq.name=NM_206996;refseq.name2=SPAG17;refseq.positionType=CDS;refseq.proteinCoordStr=p.N189N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-68;refseq.start=118445953;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 119229424 . G T 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=2;RankSumP=1.15406e-05;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.945C>A;refseq.codonCoord=315;refseq.end=119229424;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1260;refseq.name=NM_152380;refseq.name2=TBX15;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y315*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=239;refseq.start=119229424;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=FilteredInAll GT 0/1
|
|
chr1 119377341 . C G 103.87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=4.35;MQ=98.73;MQ0=0;OQ=1701.71;QD=22.10;RankSumP=0.441865;SB=-831.60;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.799G>C;refseq.codingCoordStr_2=c.*165G>C;refseq.codonCoord_1=267;refseq.end_1=119377341;refseq.end_2=119377341;refseq.frame_1=0;refseq.functionalClass_1=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.mrnaCoord_1=827;refseq.mrnaCoord_2=856;refseq.name2_1=WARS2;refseq.name2_2=WARS2;refseq.name_1=NM_015836;refseq.name_2=NM_201263;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=utr3;refseq.proteinCoordStr_1=p.A267P;refseq.referenceAA_1=Ala;refseq.referenceCodon_1=GCT;refseq.spliceDist_1=165;refseq.spliceDist_2=194;refseq.start_1=119377341;refseq.start_2=119377341;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantCodon_1=CCT;set=Intersection GT 1/0
|
|
chr1 119725247 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=712;Dels=0.00;HRun=0;HaplotypeScore=9.00;MQ=98.85;MQ0=0;OQ=13942.48;QD=19.58;RankSumP=0.179133;SB=-5871.61;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.16T>C;refseq.codingCoordStr_2=c.16T>C;refseq.codonCoord_1=6;refseq.codonCoord_2=6;refseq.end_1=119725247;refseq.end_2=119725247;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=368;refseq.mrnaCoord_2=148;refseq.name2_1=HAO2;refseq.name2_2=HAO2;refseq.name_1=NM_001005783;refseq.name_2=NM_016527;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L6L;refseq.proteinCoordStr_2=p.L6L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTG;refseq.referenceCodon_2=TTG;refseq.spliceDist_1=24;refseq.spliceDist_2=24;refseq.start_1=119725247;refseq.start_2=119725247;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 1/0
|
|
chr1 119766456 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=342;Dels=0.00;HRun=2;HaplotypeScore=3.79;MQ=92.43;MQ0=6;OQ=6714.64;QD=19.63;RankSumP=0.404034;SB=-2545.99;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.809T>C;refseq.codingCoordStr_2=c.809T>C;refseq.codonCoord_1=270;refseq.codonCoord_2=270;refseq.end_1=119766456;refseq.end_2=119766456;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=981;refseq.mrnaCoord_2=1058;refseq.name2_1=HSD3B2;refseq.name2_2=HSD3B2;refseq.name_1=NM_000198;refseq.name_2=NM_001166120;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I270T;refseq.proteinCoordStr_2=p.I270T;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=502;refseq.spliceDist_2=502;refseq.start_1=119766456;refseq.start_2=119766456;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=Intersection GT 1/0
|
|
chr1 119858681 . C T 273.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=360;Dels=0.00;HRun=1;HaplotypeScore=5.15;MQ=91.46;MQ0=0;OQ=6734.84;QD=18.71;RankSumP=0.352221;SB=-1989.35;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1012C>T;refseq.codonCoord=338;refseq.end=119858681;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1157;refseq.name=NM_000862;refseq.name2=HSD3B1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L338L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-524;refseq.start=119858681;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 119858769 . C A 93.14 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=187;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=55.15;MQ0=56;OQ=4864.39;QD=26.01;RankSumP=1.00000;SB=-1427.95;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1100C>A;refseq.codonCoord=367;refseq.end=119858769;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1245;refseq.name=NM_000862;refseq.name2=HSD3B1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T367N;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-436;refseq.start=119858769;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 120087069 . G A 313.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1064.23;QD=36.70;RankSumP=1.00000;SB=-298.38;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1326G>A;refseq.codonCoord=442;refseq.end=120087069;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1553;refseq.name=NM_006623;refseq.name2=PHGDH;refseq.positionType=CDS;refseq.proteinCoordStr=p.T442T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=117;refseq.start=120087069;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 120180201 . C T 280.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=234;Dels=0.00;HRun=1;HaplotypeScore=5.00;MQ=98.85;MQ0=0;OQ=4524.39;QD=19.33;RankSumP=0.241882;SB=-1864.62;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1068G>A;refseq.codonCoord=356;refseq.end=120180201;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1689;refseq.name=NM_001047980;refseq.name2=NBPF7;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q356Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-59;refseq.start=120180201;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 0/1
|
|
chr1 120185728 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=608;Dels=0.00;HRun=1;HaplotypeScore=23.47;MQ=85.60;MQ0=4;OQ=12365.40;QD=20.34;RankSumP=0.188412;SB=-3752.36;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.357T>C;refseq.codonCoord=119;refseq.end=120185728;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=978;refseq.name=NM_001047980;refseq.name2=NBPF7;refseq.positionType=CDS;refseq.proteinCoordStr=p.V119V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=19;refseq.start=120185728;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 0/1
|
|
chr1 120238274 . T C 237.36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=392;Dels=0.00;HRun=0;HaplotypeScore=9.04;MQ=98.34;MQ0=1;OQ=8423.07;QD=21.49;RankSumP=1.93002e-08;SB=-2623.94;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2209A>G;refseq.codonCoord=737;refseq.end=120238274;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2363;refseq.name=NM_021794;refseq.name2=ADAM30;refseq.positionType=CDS;refseq.proteinCoordStr=p.T737A;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-596;refseq.start=120238274;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=filterInsoap-gatk GT 1/0
|
|
chr1 120239241 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=718;Dels=0.00;HRun=1;HaplotypeScore=13.44;MQ=98.90;MQ0=0;OQ=15383.88;QD=21.43;RankSumP=0.418089;SB=-6020.45;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1242C>T;refseq.codonCoord=414;refseq.end=120239241;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1396;refseq.name=NM_021794;refseq.name2=ADAM30;refseq.positionType=CDS;refseq.proteinCoordStr=p.D414D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=1396;refseq.start=120239241;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/0
|
|
chr1 120239407 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=648;Dels=0.00;HRun=1;HaplotypeScore=23.00;MQ=98.55;MQ0=0;OQ=12135.06;QD=18.73;RankSumP=0.216506;SB=-3865.25;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1076T>C;refseq.codonCoord=359;refseq.end=120239407;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1230;refseq.name=NM_021794;refseq.name2=ADAM30;refseq.positionType=CDS;refseq.proteinCoordStr=p.L359P;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=1230;refseq.start=120239407;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 120259527 . A T 342.45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=529;Dels=0.00;HRun=0;HaplotypeScore=10.03;MQ=98.87;MQ0=0;OQ=9469.22;QD=17.90;RankSumP=0.00169434;SB=-2536.69;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.7341T>A;refseq.codonCoord=2447;refseq.end=120259527;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=7597;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2447G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=1314;refseq.start=120259527;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=filterInsoap-gatk GT 0/1
|
|
chr1 120341360 . T C 47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.547619;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.534A>G;refseq.codonCoord=178;refseq.end=120341360;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=790;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K178K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=119;refseq.start=120341360;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=soap GT 1/0
|
|
chr1 120341439 . G A 8 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=0;RankSumP=0.214286;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.455C>T;refseq.codonCoord=152;refseq.end=120341439;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=711;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P152L;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=40;refseq.start=120341439;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=FilteredInAll GT 1/0
|
|
chr1 120341459 . C G 4 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.100000;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.435G>C;refseq.codonCoord=145;refseq.end=120341459;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=691;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T145T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=20;refseq.start=120341459;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 120374070 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.367567;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.137A>G;refseq.codonCoord=46;refseq.end=120374070;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=393;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N46S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-19;refseq.start=120374070;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=soap GT 1/0
|
|
chr1 120374095 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.0478738;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.112G>A;refseq.codonCoord=38;refseq.end=120374095;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=368;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.E38K;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=39;refseq.start=120374095;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=soap GT 0/1
|
|
chr1 120374135 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.324372;SecondBestBaseQ=33;refseq.chr=chr1;refseq.codingCoordStr=c.74-2;refseq.end=120374135;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=intron;refseq.spliceDist=-2;refseq.spliceInfo=splice-acceptor_-2;refseq.start=120374135;refseq.transcriptStrand=-;set=soap GT 1/0
|
|
chr1 120413487 . G C 42.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=3.57;MQ=47.58;MQ0=7;OQ=738.79;QD=13.68;RankSumP=0.687500;SB=-354.62;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.57C>G;refseq.codonCoord=19;refseq.end=120413487;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=313;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C19W;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-17;refseq.start=120413487;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=filterInsoap-gatk GT 0/1
|
|
chr1 120413529 . G A 24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=58.46;MQ0=3;OQ=462.83;QD=11.29;RankSumP=0.0327657;SB=-201.88;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.15C>T;refseq.codonCoord=5;refseq.end=120413529;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=271;refseq.name=NM_024408;refseq.name2=NOTCH2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R5R;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-59;refseq.start=120413529;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/0
|
|
chr1 120656051 . T C 81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=352;Dels=0.00;HRun=0;HaplotypeScore=6.79;MQ=21.11;MQ0=158;OQ=2779.71;QD=7.90;RankSumP=0.329635;SB=-1207.04;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.392T>C;refseq.codonCoord=131;refseq.end=120656051;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1221;refseq.name=NM_001100910;refseq.name2=FAM72B;refseq.positionType=CDS;refseq.proteinCoordStr=p.I131T;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=37;refseq.start=120656051;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 120728815 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.403605;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.412A>G;refseq.codingCoordStr_2=c.688A>G;refseq.codonCoord_1=138;refseq.codonCoord_2=230;refseq.end_1=120728815;refseq.end_2=120728815;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=462;refseq.mrnaCoord_2=738;refseq.name2_1=FCGR1B;refseq.name2_2=FCGR1B;refseq.name_1=NM_001004340;refseq.name_2=NM_001017986;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N138D;refseq.proteinCoordStr_2=p.N230D;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=126;refseq.spliceDist_2=126;refseq.start_1=120728815;refseq.start_2=120728815;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=soap GT 1/0
|
|
chr1 120731578 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.555556;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.270A>G;refseq.codingCoordStr_2=c.546A>G;refseq.codonCoord_1=90;refseq.codonCoord_2=182;refseq.end_1=120731578;refseq.end_2=120731578;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=320;refseq.mrnaCoord_2=596;refseq.name2_1=FCGR1B;refseq.name2_2=FCGR1B;refseq.name_1=NM_001004340;refseq.name_2=NM_001017986;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S90S;refseq.proteinCoordStr_2=p.S182S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=-17;refseq.spliceDist_2=-17;refseq.start_1=120731578;refseq.start_2=120731578;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;set=FilteredInAll GT 1/0
|
|
chr1 120731780 . A G 84 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.472527;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.68T>C;refseq.codingCoordStr_2=c.344T>C;refseq.codonCoord_1=23;refseq.codonCoord_2=115;refseq.end_1=120731780;refseq.end_2=120731780;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=118;refseq.mrnaCoord_2=394;refseq.name2_1=FCGR1B;refseq.name2_2=FCGR1B;refseq.name_1=NM_001004340;refseq.name_2=NM_001017986;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.M23T;refseq.proteinCoordStr_2=p.M115T;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=37;refseq.spliceDist_2=37;refseq.start_1=120731780;refseq.start_2=120731780;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=soap GT 0/1
|
|
chr1 120731810 . A G 59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.681041;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.38T>C;refseq.codingCoordStr_2=c.314T>C;refseq.codonCoord_1=13;refseq.codonCoord_2=105;refseq.end_1=120731810;refseq.end_2=120731810;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=88;refseq.mrnaCoord_2=364;refseq.name2_1=FCGR1B;refseq.name2_2=FCGR1B;refseq.name_1=NM_001004340;refseq.name_2=NM_001017986;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L13P;refseq.proteinCoordStr_2=p.L105P;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTA;refseq.referenceCodon_2=CTA;refseq.spliceDist_1=7;refseq.spliceDist_2=7;refseq.spliceInfo_1=splice-acceptor_7;refseq.spliceInfo_2=splice-acceptor_7;refseq.start_1=120731810;refseq.start_2=120731810;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=soap GT 0/1
|
|
chr1 120736052 . G A 25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=0;RankSumP=0.136852;SecondBestBaseQ=21;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.159C>T;refseq.codonCoord_2=53;refseq.end_1=120737376;refseq.end_2=120736052;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=209;refseq.name2_1=FCGR1B;refseq.name2_2=FCGR1B;refseq.name_1=NM_001004340;refseq.name_2=NM_001017986;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S53S;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCC;refseq.spliceDist_2=107;refseq.start_1=120731827;refseq.start_2=120736052;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ser;refseq.variantCodon_2=TCT;set=soap GT 1/0
|
|
chr1 120736096 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.114354;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.115G>A;refseq.codonCoord_2=39;refseq.end_1=120737376;refseq.end_2=120736096;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=165;refseq.name2_1=FCGR1B;refseq.name2_2=FCGR1B;refseq.name_1=NM_001004340;refseq.name_2=NM_001017986;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V39I;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTA;refseq.spliceDist_2=63;refseq.start_1=120731827;refseq.start_2=120736096;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ile;refseq.variantCodon_2=ATA;set=soap GT 0/1
|
|
chr1 142559036 . A T 66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=2036;Dels=0.00;HRun=0;HaplotypeScore=57.12;MQ=28.10;MQ0=1016;OQ=13040.32;QD=6.40;RankSumP=0.414982;SB=-3543.34;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.336T>A;refseq.codonCoord=112;refseq.end=142559036;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=369;refseq.name=NM_001123068;refseq.name2=PPIAL4G;refseq.positionType=CDS;refseq.proteinCoordStr=p.F112L;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=369;refseq.start=142559036;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=soap-filterIngatk GT 0/1
|
|
chr1 142559045 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1817;Dels=0.00;HRun=0;HaplotypeScore=26.85;MQ=25.59;MQ0=1062;OQ=9979.16;QD=5.49;RankSumP=0.112319;SB=-2692.89;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.327T>C;refseq.codonCoord=109;refseq.end=142559045;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=360;refseq.name=NM_001123068;refseq.name2=PPIAL4G;refseq.positionType=CDS;refseq.proteinCoordStr=p.G109G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=360;refseq.start=142559045;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=soap-filterIngatk GT 0/1
|
|
chr1 142559070 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1345;Dels=0.00;HRun=0;HaplotypeScore=20.88;MQ=21.02;MQ0=1133;OQ=3633.57;QD=2.70;RankSumP=0.618360;SB=-669.73;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.302C>T;refseq.codonCoord=101;refseq.end=142559070;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=335;refseq.name=NM_001123068;refseq.name2=PPIAL4G;refseq.positionType=CDS;refseq.proteinCoordStr=p.A101V;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=335;refseq.start=142559070;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/0
|
|
chr1 142559151 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.488144;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.221G>A;refseq.codonCoord=74;refseq.end=142559151;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=254;refseq.name=NM_001123068;refseq.name2=PPIAL4G;refseq.positionType=CDS;refseq.proteinCoordStr=p.G74D;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=254;refseq.start=142559151;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=soap GT 0/1
|
|
chr1 142559166 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.539430;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.206A>G;refseq.codonCoord=69;refseq.end=142559166;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=239;refseq.name=NM_001123068;refseq.name2=PPIAL4G;refseq.positionType=CDS;refseq.proteinCoordStr=p.H69R;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=239;refseq.start=142559166;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=soap GT 1/0
|
|
chr1 142559301 . T A 5 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.122895;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.71A>T;refseq.codonCoord=24;refseq.end=142559301;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=104;refseq.name=NM_001123068;refseq.name2=PPIAL4G;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q24L;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=104;refseq.start=142559301;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT 1/0
|
|
chr1 143563833 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.526926;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.7023A>G;refseq.codonCoord=2341;refseq.end=143563833;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7314;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.P2341P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=24;refseq.start=143563833;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=soap GT 1/0
|
|
chr1 143565537 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.196165;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6984A>G;refseq.codonCoord=2328;refseq.end=143565537;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7275;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2328A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-16;refseq.start=143565537;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=soap GT 1/0
|
|
chr1 143565954 . T C 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=727;Dels=0.00;HRun=1;HaplotypeScore=144.70;MQ=19.40;MQ0=618;OQ=1884.73;QD=2.59;RankSumP=0.00676588;SB=-444.08;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6873A>G;refseq.codonCoord=2291;refseq.end=143565954;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7164;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2291R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=60;refseq.start=143565954;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=FilteredInAll GT 1/0
|
|
chr1 143565955 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=713;Dels=0.00;HRun=1;HaplotypeScore=235.85;MQ=19.47;MQ0=610;OQ=1825.98;QD=2.56;RankSumP=0.404151;SB=-498.54;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6872G>A;refseq.codonCoord=2291;refseq.end=143565955;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7163;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2291Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=59;refseq.start=143565955;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap-filterIngatk GT 0/1
|
|
chr1 143565965 rs2798855 T G -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=653;Dels=0.00;HRun=2;HaplotypeScore=129.41;MQ=19.34;MQ0=601;OQ=966.62;QD=1.48;SB=-352.97;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6862A>C;refseq.codonCoord=2288;refseq.end=143565965;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7153;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.K2288Q;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=49;refseq.start=143565965;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:498,154:44:-113.20,-13.25,-55.63:99
|
|
chr1 143567169 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.712496;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6741A>G;refseq.codonCoord=2247;refseq.end=143567169;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7032;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2247S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=72;refseq.start=143567169;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=soap GT 1/0
|
|
chr1 143567223 . A G 86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.588997;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6687T>C;refseq.codonCoord=2229;refseq.end=143567223;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6978;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2229G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=18;refseq.start=143567223;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=soap GT 0/1
|
|
chr1 143568257 . C T 8 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.666667;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6585G>A;refseq.codonCoord=2195;refseq.end=143568257;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6876;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2195A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-85;refseq.start=143568257;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=FilteredInAll GT 0/1
|
|
chr1 143574677 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.448696;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6083A>G;refseq.codonCoord=2028;refseq.end=143574677;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6374;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.K2028R;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-3;refseq.spliceInfo=splice-donor_-3;refseq.start=143574677;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=soap GT 1/0
|
|
chr1 143574712 . G A 1 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.461954;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6048C>T;refseq.codonCoord=2016;refseq.end=143574712;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6339;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2016Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-38;refseq.start=143574712;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=FilteredInAll GT 1/0
|
|
chr1 143574723 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.00577938;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6037C>T;refseq.codonCoord=2013;refseq.end=143574723;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6328;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.L2013L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-49;refseq.start=143574723;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=FilteredInAll GT 1/0
|
|
chr1 143575500 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1114;Dels=0.00;HRun=0;HaplotypeScore=18.45;MQ=5.55;MQ0=1077;OQ=91.71;QD=0.08;RankSumP=0.405950;SB=-10.00;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5952C>T;refseq.codonCoord=1984;refseq.end=143575500;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6243;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1984N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=143575500;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 143575518 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.306428;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5934T>C;refseq.codonCoord=1978;refseq.end=143575518;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6225;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1978R;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-27;refseq.start=143575518;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=soap GT 0/1
|
|
chr1 143575610 . T C 56 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.167906;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5842A>G;refseq.codonCoord=1948;refseq.end=143575610;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6133;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1948E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=72;refseq.start=143575610;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=soap GT 1/0
|
|
chr1 143577207 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.456799;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5730C>A;refseq.codonCoord=1910;refseq.end=143577207;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6021;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1910E;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-41;refseq.start=143577207;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=soap GT 0/1
|
|
chr1 143578000 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.0216339;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5599C>T;refseq.codonCoord=1867;refseq.end=143578000;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5890;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1867C;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-52;refseq.start=143578000;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=soap GT 1/0
|
|
chr1 143578019 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.392900;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5580A>G;refseq.codonCoord=1860;refseq.end=143578019;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5871;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1860E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=62;refseq.start=143578019;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=soap GT 1/0
|
|
chr1 143579527 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.163709;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5269G>A;refseq.codonCoord=1757;refseq.end=143579527;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5560;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1757T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=3;refseq.spliceInfo=splice-acceptor_3;refseq.start=143579527;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap GT 0/1
|
|
chr1 143583095 . C A 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=1.25389e-05;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5224G>T;refseq.codonCoord=1742;refseq.end=143583095;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5515;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1742S;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-43;refseq.start=143583095;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=FilteredInAll GT 1/0
|
|
chr1 143583112 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.0752674;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5207T>A;refseq.codonCoord=1736;refseq.end=143583112;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5498;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1736E;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-60;refseq.start=143583112;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=soap GT 0/1
|
|
chr1 143583139 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.218775;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5180T>C;refseq.codonCoord=1727;refseq.end=143583139;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5471;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1727P;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-87;refseq.start=143583139;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=soap GT 0/1
|
|
chr1 143583186 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.196902;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5133G>A;refseq.codonCoord=1711;refseq.end=143583186;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5424;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1711L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=53;refseq.start=143583186;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=soap GT 0/1
|
|
chr1 143585244 . C T 83 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=13;DB;DP=738;Dels=0.00;HRun=1;HaplotypeScore=62.23;MQ=11.72;MQ0=723;OQ=286.39;QD=0.39;RankSumP=0.00898022;SB=-10.00;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5070G>A;refseq.codonCoord=1690;refseq.end=143585244;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5361;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1690Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-11;refseq.start=143585244;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=FilteredInAll GT 0/1
|
|
chr1 143586117 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=812;Dels=0.00;HRun=0;HaplotypeScore=12.80;MQ=1.05;MQ0=811;QD=0.01;RankSumP=0.425243;SB=-10.00;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4848A>G;refseq.codonCoord=1616;refseq.end=143586117;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5139;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1616E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-80;refseq.start=143586117;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=soap-filterIngatk GT 1/0
|
|
chr1 143586172 . T C 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.00194097;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4793A>G;refseq.codonCoord=1598;refseq.end=143586172;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5084;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1598R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=90;refseq.start=143586172;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=FilteredInAll GT 1/0
|
|
chr1 143587336 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.374172;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4701C>G;refseq.codonCoord=1567;refseq.end=143587336;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4992;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1567L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-3;refseq.spliceInfo=splice-donor_-3;refseq.start=143587336;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=soap GT 0/1
|
|
chr1 143588533 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=603;Dels=0.00;HRun=0;HaplotypeScore=13.42;MQ=34.28;MQ0=147;OQ=8221.05;QD=13.63;RankSumP=0.472546;SB=-2033.89;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4511G>A;refseq.codonCoord=1504;refseq.end=143588533;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4802;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1504Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=96;refseq.start=143588533;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 143590447 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.103610;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4360A>G;refseq.codonCoord=1454;refseq.end=143590447;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4651;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1454E;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-56;refseq.start=143590447;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=soap GT 1/0
|
|
chr1 143590732 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.379318;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4075A>G;refseq.codonCoord=1359;refseq.end=143590732;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4366;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1359E;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=189;refseq.start=143590732;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=soap GT 1/0
|
|
chr1 143590842 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.291069;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3965C>G;refseq.codonCoord=1322;refseq.end=143590842;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4256;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1322R;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=79;refseq.start=143590842;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=soap GT 0/1
|
|
chr1 143592189 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.120014;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3796A>G;refseq.codonCoord=1266;refseq.end=143592189;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4087;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1266E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=30;refseq.start=143592189;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=soap GT 1/0
|
|
chr1 143593938 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.231831;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3438T>C;refseq.codonCoord=1146;refseq.end=143593938;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3729;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.I1146I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-136;refseq.start=143593938;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=soap GT 0/1
|
|
chr1 143594180 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.307246;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3196G>A;refseq.codonCoord=1066;refseq.end=143594180;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3487;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1066T;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=59;refseq.start=143594180;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=soap GT 0/1
|
|
chr1 143597554 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.459061;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3037T>A;refseq.codonCoord=1013;refseq.end=143597554;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3328;refseq.name=NM_014644;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.F1013I;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-101;refseq.start=143597554;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=soap GT 0/1
|
|
chr1 143617865 . C T 83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2838G>A;refseq.codingCoordStr_2=c.2349G>A;refseq.codingCoordStr_3=c.2349G>A;refseq.codonCoord_1=946;refseq.codonCoord_2=783;refseq.codonCoord_3=783;refseq.end_1=143617865;refseq.end_2=143617865;refseq.end_3=143617865;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3162;refseq.mrnaCoord_2=2640;refseq.mrnaCoord_3=2640;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.M946I;refseq.proteinCoordStr_2=p.M783I;refseq.proteinCoordStr_3=p.M783I;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceAA_3=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.referenceCodon_3=ATG;refseq.spliceDist_1=30;refseq.spliceDist_2=30;refseq.spliceDist_3=30;refseq.start_1=143617865;refseq.start_2=143617865;refseq.start_3=143617865;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantCodon_1=ATA;refseq.variantCodon_2=ATA;refseq.variantCodon_3=ATA;set=soap GT 1/1
|
|
chr1 143623510 . A G 91.32 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=407;Dels=0.00;HRun=1;HaplotypeScore=10.36;MQ=97.37;MQ0=0;OQ=15654.90;QD=38.46;RankSumP=1.00000;SB=-7001.48;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2611T>C;refseq.codingCoordStr_2=c.2122T>C;refseq.codingCoordStr_3=c.2122T>C;refseq.codonCoord_1=871;refseq.codonCoord_2=708;refseq.codonCoord_3=708;refseq.end_1=143623510;refseq.end_2=143623510;refseq.end_3=143623510;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2935;refseq.mrnaCoord_2=2413;refseq.mrnaCoord_3=2413;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.C871R;refseq.proteinCoordStr_2=p.C708R;refseq.proteinCoordStr_3=p.C708R;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.referenceCodon_3=TGT;refseq.spliceDist_1=-24;refseq.spliceDist_2=-24;refseq.spliceDist_3=-24;refseq.start_1=143623510;refseq.start_2=143623510;refseq.start_3=143623510;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;refseq.variantCodon_3=CGT;set=Intersection GT 1/1
|
|
chr1 143623590 . C T 204.25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=211;Dels=0.00;HRun=0;HaplotypeScore=3.89;MQ=90.52;MQ0=3;OQ=4255.42;QD=20.17;RankSumP=0.0279132;SB=-976.98;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2531G>A;refseq.codingCoordStr_2=c.2042G>A;refseq.codingCoordStr_3=c.2042G>A;refseq.codonCoord_1=844;refseq.codonCoord_2=681;refseq.codonCoord_3=681;refseq.end_1=143623590;refseq.end_2=143623590;refseq.end_3=143623590;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2855;refseq.mrnaCoord_2=2333;refseq.mrnaCoord_3=2333;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R844H;refseq.proteinCoordStr_2=p.R681H;refseq.proteinCoordStr_3=p.R681H;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.referenceCodon_3=CGC;refseq.spliceDist_1=62;refseq.spliceDist_2=62;refseq.spliceDist_3=62;refseq.start_1=143623590;refseq.start_2=143623590;refseq.start_3=143623590;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;set=Intersection GT 0/1
|
|
chr1 143626918 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.204216;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2353C>T;refseq.codingCoordStr_2=c.1864C>T;refseq.codingCoordStr_3=c.1864C>T;refseq.codonCoord_1=785;refseq.codonCoord_2=622;refseq.codonCoord_3=622;refseq.end_1=143626918;refseq.end_2=143626918;refseq.end_3=143626918;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.functionalClass_3=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2677;refseq.mrnaCoord_2=2155;refseq.mrnaCoord_3=2155;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R785*;refseq.proteinCoordStr_2=p.R622*;refseq.proteinCoordStr_3=p.R622*;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.referenceCodon_3=CGA;refseq.spliceDist_1=79;refseq.spliceDist_2=79;refseq.spliceDist_3=79;refseq.start_1=143626918;refseq.start_2=143626918;refseq.start_3=143626918;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantAA_3=Stop;refseq.variantCodon_1=TGA;refseq.variantCodon_2=TGA;refseq.variantCodon_3=TGA;set=soap GT 1/0
|
|
chr1 143626981 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.494903;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2290C>T;refseq.codingCoordStr_2=c.1801C>T;refseq.codingCoordStr_3=c.1801C>T;refseq.codonCoord_1=764;refseq.codonCoord_2=601;refseq.codonCoord_3=601;refseq.end_1=143626981;refseq.end_2=143626981;refseq.end_3=143626981;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2614;refseq.mrnaCoord_2=2092;refseq.mrnaCoord_3=2092;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.L764L;refseq.proteinCoordStr_2=p.L601L;refseq.proteinCoordStr_3=p.L601L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.spliceDist_1=16;refseq.spliceDist_2=16;refseq.spliceDist_3=16;refseq.start_1=143626981;refseq.start_2=143626981;refseq.start_3=143626981;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=TTG;refseq.variantCodon_2=TTG;refseq.variantCodon_3=TTG;set=soap GT 1/0
|
|
chr1 143628105 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=0;RankSumP=0.0433698;SecondBestBaseQ=24;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2096G>C;refseq.codingCoordStr_2=c.1607G>C;refseq.codingCoordStr_3=c.1607G>C;refseq.codonCoord_1=699;refseq.codonCoord_2=536;refseq.codonCoord_3=536;refseq.end_1=143628105;refseq.end_2=143628105;refseq.end_3=143628105;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2420;refseq.mrnaCoord_2=1898;refseq.mrnaCoord_3=1898;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S699T;refseq.proteinCoordStr_2=p.S536T;refseq.proteinCoordStr_3=p.S536T;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=AGT;refseq.referenceCodon_2=AGT;refseq.referenceCodon_3=AGT;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceDist_3=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.spliceInfo_3=splice-acceptor_2;refseq.start_1=143628105;refseq.start_2=143628105;refseq.start_3=143628105;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=ACT;set=soap GT 1/0
|
|
chr1 143628903 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.0471696;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2047T>C;refseq.codingCoordStr_2=c.1558T>C;refseq.codingCoordStr_3=c.1558T>C;refseq.codonCoord_1=683;refseq.codonCoord_2=520;refseq.codonCoord_3=520;refseq.end_1=143628903;refseq.end_2=143628903;refseq.end_3=143628903;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2371;refseq.mrnaCoord_2=1849;refseq.mrnaCoord_3=1849;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.L683L;refseq.proteinCoordStr_2=p.L520L;refseq.proteinCoordStr_3=p.L520L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceCodon_1=TTA;refseq.referenceCodon_2=TTA;refseq.referenceCodon_3=TTA;refseq.spliceDist_1=-48;refseq.spliceDist_2=-48;refseq.spliceDist_3=-48;refseq.start_1=143628903;refseq.start_2=143628903;refseq.start_3=143628903;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;refseq.variantCodon_3=CTA;set=soap GT 0/1
|
|
chr1 143629198 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.331038;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1934A>G;refseq.codingCoordStr_2=c.1445A>G;refseq.codingCoordStr_3=c.1445A>G;refseq.codonCoord_1=645;refseq.codonCoord_2=482;refseq.codonCoord_3=482;refseq.end_1=143629198;refseq.end_2=143629198;refseq.end_3=143629198;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2258;refseq.mrnaCoord_2=1736;refseq.mrnaCoord_3=1736;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.H645R;refseq.proteinCoordStr_2=p.H482R;refseq.proteinCoordStr_3=p.H482R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.referenceCodon_3=CAT;refseq.spliceDist_1=-23;refseq.spliceDist_2=-23;refseq.spliceDist_3=-23;refseq.start_1=143629198;refseq.start_2=143629198;refseq.start_3=143629198;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;refseq.variantCodon_3=CGT;set=soap GT 1/0
|
|
chr1 143630237 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.269748;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1795A>G;refseq.codingCoordStr_2=c.1306A>G;refseq.codingCoordStr_3=c.1306A>G;refseq.codonCoord_1=599;refseq.codonCoord_2=436;refseq.codonCoord_3=436;refseq.end_1=143630237;refseq.end_2=143630237;refseq.end_3=143630237;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2119;refseq.mrnaCoord_2=1597;refseq.mrnaCoord_3=1597;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.I599V;refseq.proteinCoordStr_2=p.I436V;refseq.proteinCoordStr_3=p.I436V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.spliceDist_1=-48;refseq.spliceDist_2=-48;refseq.spliceDist_3=-48;refseq.start_1=143630237;refseq.start_2=143630237;refseq.start_3=143630237;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;refseq.variantCodon_3=GTC;set=soap GT 1/0
|
|
chr1 143630261 . C G 82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.290031;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1771G>C;refseq.codingCoordStr_2=c.1282G>C;refseq.codingCoordStr_3=c.1282G>C;refseq.codonCoord_1=591;refseq.codonCoord_2=428;refseq.codonCoord_3=428;refseq.end_1=143630261;refseq.end_2=143630261;refseq.end_3=143630261;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2095;refseq.mrnaCoord_2=1573;refseq.mrnaCoord_3=1573;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E591Q;refseq.proteinCoordStr_2=p.E428Q;refseq.proteinCoordStr_3=p.E428Q;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.spliceDist_1=-72;refseq.spliceDist_2=-72;refseq.spliceDist_3=-72;refseq.start_1=143630261;refseq.start_2=143630261;refseq.start_3=143630261;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantAA_3=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;refseq.variantCodon_3=CAG;set=soap GT 1/0
|
|
chr1 143630314 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.0857137;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1718A>T;refseq.codingCoordStr_2=c.1229A>T;refseq.codingCoordStr_3=c.1229A>T;refseq.codonCoord_1=573;refseq.codonCoord_2=410;refseq.codonCoord_3=410;refseq.end_1=143630314;refseq.end_2=143630314;refseq.end_3=143630314;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2042;refseq.mrnaCoord_2=1520;refseq.mrnaCoord_3=1520;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E573V;refseq.proteinCoordStr_2=p.E410V;refseq.proteinCoordStr_3=p.E410V;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.referenceCodon_3=GAA;refseq.spliceDist_1=35;refseq.spliceDist_2=35;refseq.spliceDist_3=35;refseq.start_1=143630314;refseq.start_2=143630314;refseq.start_3=143630314;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;refseq.variantCodon_3=GTA;set=soap GT 1/0
|
|
chr1 143633281 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.136424;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1594C>T;refseq.codingCoordStr_2=c.1105C>T;refseq.codingCoordStr_3=c.1105C>T;refseq.codonCoord_1=532;refseq.codonCoord_2=369;refseq.codonCoord_3=369;refseq.end_1=143633281;refseq.end_2=143633281;refseq.end_3=143633281;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1918;refseq.mrnaCoord_2=1396;refseq.mrnaCoord_3=1396;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.L532L;refseq.proteinCoordStr_2=p.L369L;refseq.proteinCoordStr_3=p.L369L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.spliceDist_1=-90;refseq.spliceDist_2=-90;refseq.spliceDist_3=-90;refseq.start_1=143633281;refseq.start_2=143633281;refseq.start_3=143633281;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=TTG;refseq.variantCodon_2=TTG;refseq.variantCodon_3=TTG;set=soap GT 1/0
|
|
chr1 143633940 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=545;Dels=0.00;HRun=1;HaplotypeScore=7.59;MQ=11.76;MQ0=536;OQ=63.74;QD=0.12;RankSumP=0.0503477;SB=-10.00;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1313C>T;refseq.codingCoordStr_2=c.824C>T;refseq.codingCoordStr_3=c.824C>T;refseq.codonCoord_1=438;refseq.codonCoord_2=275;refseq.codonCoord_3=275;refseq.end_1=143633940;refseq.end_2=143633940;refseq.end_3=143633940;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1637;refseq.mrnaCoord_2=1115;refseq.mrnaCoord_3=1115;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002811;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S438L;refseq.proteinCoordStr_2=p.S275L;refseq.proteinCoordStr_3=p.S275L;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCG;refseq.referenceCodon_2=TCG;refseq.referenceCodon_3=TCG;refseq.spliceDist_1=56;refseq.spliceDist_2=56;refseq.spliceDist_3=56;refseq.start_1=143633940;refseq.start_2=143633940;refseq.start_3=143633940;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=TTG;refseq.variantCodon_2=TTG;refseq.variantCodon_3=TTG;set=Intersection GT 1/0
|
|
chr1 143641953 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=116;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=99.00;MQ0=0;OQ=1307.55;QD=11.27;RankSumP=0.372107;SB=-502.94;SecondBestBaseQ=33;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.1113G>T;refseq.codonCoord_3=371;refseq.end_1=143657971;refseq.end_2=143657971;refseq.end_3=143641953;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=1437;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002812;refseq.name_2=NM_014644;refseq.name_3=NM_001002811;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.P371P;refseq.referenceAA_3=Pro;refseq.referenceCodon_3=CCG;refseq.spliceDist_3=-13;refseq.start_1=143635189;refseq.start_2=143635189;refseq.start_3=143641953;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_3=Pro;refseq.variantCodon_3=CCT;set=Intersection GT 1/0
|
|
chr1 143642297 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=659;Dels=0.00;HRun=1;HaplotypeScore=17.33;MQ=98.79;MQ0=0;OQ=13751.15;QD=20.87;RankSumP=0.423129;SB=-5402.13;SecondBestBaseQ=33;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.769A>G;refseq.codonCoord_3=257;refseq.end_1=143657971;refseq.end_2=143657971;refseq.end_3=143642297;refseq.frame_3=0;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=1093;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002812;refseq.name_2=NM_014644;refseq.name_3=NM_001002811;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.K257E;refseq.referenceAA_3=Lys;refseq.referenceCodon_3=AAA;refseq.spliceDist_3=-357;refseq.start_1=143635189;refseq.start_2=143635189;refseq.start_3=143642297;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_3=Glu;refseq.variantCodon_3=GAA;set=Intersection GT 1/0
|
|
chr1 143642687 . C T 166.99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=527;Dels=0.00;HRun=0;HaplotypeScore=6.11;MQ=98.73;MQ0=0;OQ=9705.57;QD=18.42;RankSumP=0.434530;SB=-3393.17;SecondBestBaseQ=32;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.379G>A;refseq.codonCoord_3=127;refseq.end_1=143657971;refseq.end_2=143657971;refseq.end_3=143642687;refseq.frame_3=0;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=703;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002812;refseq.name_2=NM_014644;refseq.name_3=NM_001002811;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.A127T;refseq.referenceAA_3=Ala;refseq.referenceCodon_3=GCA;refseq.spliceDist_3=703;refseq.start_1=143635189;refseq.start_2=143635189;refseq.start_3=143642687;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_3=Thr;refseq.variantCodon_3=ACA;set=Intersection GT 0/1
|
|
chr1 143642749 . G A 230.33 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=211;Dels=0.00;HRun=0;HaplotypeScore=3.59;MQ=98.69;MQ0=0;OQ=3094.93;QD=14.67;RankSumP=0.162764;SB=-757.02;SecondBestBaseQ=32;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.317C>T;refseq.codonCoord_3=106;refseq.end_1=143657971;refseq.end_2=143657971;refseq.end_3=143642749;refseq.frame_3=1;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=641;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002812;refseq.name_2=NM_014644;refseq.name_3=NM_001002811;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.A106V;refseq.referenceAA_3=Ala;refseq.referenceCodon_3=GCG;refseq.spliceDist_3=641;refseq.start_1=143635189;refseq.start_2=143635189;refseq.start_3=143642749;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_3=Val;refseq.variantCodon_3=GTG;set=Intersection GT 1/0
|
|
chr1 143642818 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=2.32;MQ=98.91;MQ0=0;OQ=573.87;QD=6.52;RankSumP=0.144918;SB=-268.47;SecondBestBaseQ=34;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.248T>A;refseq.codonCoord_3=83;refseq.end_1=143657971;refseq.end_2=143657971;refseq.end_3=143642818;refseq.frame_3=1;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=572;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name_1=NM_001002812;refseq.name_2=NM_014644;refseq.name_3=NM_001002811;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.L83Q;refseq.referenceAA_3=Leu;refseq.referenceCodon_3=CTA;refseq.spliceDist_3=572;refseq.start_1=143635189;refseq.start_2=143635189;refseq.start_3=143642818;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_3=Gln;refseq.variantCodon_3=CAA;set=Intersection GT 0/1
|
|
chr1 143663564 . C T 27 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=1017;Dels=0.00;HRun=1;HaplotypeScore=16.24;MQ=25.46;MQ0=355;OQ=6072.43;QD=5.97;RankSumP=1.00000;SB=-1397.61;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.512G>A;refseq.codingCoordStr_2=c.512G>A;refseq.codingCoordStr_3=c.512G>A;refseq.codingCoordStr_4=c.923G>A;refseq.codonCoord_1=171;refseq.codonCoord_2=171;refseq.codonCoord_3=171;refseq.codonCoord_4=308;refseq.end_1=143663564;refseq.end_2=143663564;refseq.end_3=143663564;refseq.end_4=143663564;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=803;refseq.mrnaCoord_2=803;refseq.mrnaCoord_3=803;refseq.mrnaCoord_4=1140;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name2_4=PDE4DIP;refseq.name_1=NM_001002810;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.name_4=NM_022359;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.R171K;refseq.proteinCoordStr_2=p.R171K;refseq.proteinCoordStr_3=p.R171K;refseq.proteinCoordStr_4=p.R308K;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_1=AGG;refseq.referenceCodon_2=AGG;refseq.referenceCodon_3=AGG;refseq.referenceCodon_4=AGG;refseq.spliceDist_1=170;refseq.spliceDist_2=-7;refseq.spliceDist_3=-7;refseq.spliceDist_4=170;refseq.spliceInfo_2=splice-donor_-7;refseq.spliceInfo_3=splice-donor_-7;refseq.start_1=143663564;refseq.start_2=143663564;refseq.start_3=143663564;refseq.start_4=143663564;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantAA_3=Lys;refseq.variantAA_4=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;refseq.variantCodon_3=AAG;refseq.variantCodon_4=AAG;set=Intersection GT 1/1
|
|
chr1 143663577 . C T 81 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=1025;Dels=0.00;HRun=0;HaplotypeScore=38.35;MQ=23.16;MQ0=501;OQ=6831.07;QD=6.66;RankSumP=1.00000;SB=-2494.84;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.499G>A;refseq.codingCoordStr_2=c.499G>A;refseq.codingCoordStr_3=c.499G>A;refseq.codingCoordStr_4=c.910G>A;refseq.codonCoord_1=167;refseq.codonCoord_2=167;refseq.codonCoord_3=167;refseq.codonCoord_4=304;refseq.end_1=143663577;refseq.end_2=143663577;refseq.end_3=143663577;refseq.end_4=143663577;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=790;refseq.mrnaCoord_2=790;refseq.mrnaCoord_3=790;refseq.mrnaCoord_4=1127;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name2_4=PDE4DIP;refseq.name_1=NM_001002810;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.name_4=NM_022359;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.A167T;refseq.proteinCoordStr_2=p.A167T;refseq.proteinCoordStr_3=p.A167T;refseq.proteinCoordStr_4=p.A304T;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GCC;refseq.referenceCodon_4=GCC;refseq.spliceDist_1=157;refseq.spliceDist_2=-20;refseq.spliceDist_3=-20;refseq.spliceDist_4=157;refseq.start_1=143663577;refseq.start_2=143663577;refseq.start_3=143663577;refseq.start_4=143663577;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;refseq.variantCodon_3=ACC;refseq.variantCodon_4=ACC;set=soap-filterIngatk GT 1/1
|
|
chr1 143663612 rs61805377 G C 0.12 PASS AC=1;AF=0.50;AN=2;DB;DP=796;Dels=0.00;HRun=0;HaplotypeScore=6.42;MQ=17.12;MQ0=684;OQ=678.48;QD=0.85;SB=-324.19;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.464C>G;refseq.codingCoordStr_2=c.464C>G;refseq.codingCoordStr_3=c.464C>G;refseq.codingCoordStr_4=c.875C>G;refseq.codonCoord_1=155;refseq.codonCoord_2=155;refseq.codonCoord_3=155;refseq.codonCoord_4=292;refseq.end_1=143663612;refseq.end_2=143663612;refseq.end_3=143663612;refseq.end_4=143663612;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=755;refseq.mrnaCoord_2=755;refseq.mrnaCoord_3=755;refseq.mrnaCoord_4=1092;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name2_4=PDE4DIP;refseq.name_1=NM_001002810;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.name_4=NM_022359;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.P155R;refseq.proteinCoordStr_2=p.P155R;refseq.proteinCoordStr_3=p.P155R;refseq.proteinCoordStr_4=p.P292R;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.referenceCodon_3=CCA;refseq.referenceCodon_4=CCA;refseq.spliceDist_1=122;refseq.spliceDist_2=-55;refseq.spliceDist_3=-55;refseq.spliceDist_4=122;refseq.start_1=143663612;refseq.start_2=143663612;refseq.start_3=143663612;refseq.start_4=143663612;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantCodon_1=CGA;refseq.variantCodon_2=CGA;refseq.variantCodon_3=CGA;refseq.variantCodon_4=CGA;set=gatk GT:AD:DP:GL:GQ 0/1:710,86:84:-96.43,-25.30,-284.35:99
|
|
chr1 143706015 . C A 127.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=605;Dels=0.00;HRun=0;HaplotypeScore=13.96;MQ=98.74;MQ0=0;OQ=12323.18;QD=20.37;RankSumP=0.251138;SB=-4073.01;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.74G>T;refseq.codingCoordStr_2=c.74G>T;refseq.codingCoordStr_3=c.74G>T;refseq.codingCoordStr_4=c.485G>T;refseq.codonCoord_1=25;refseq.codonCoord_2=25;refseq.codonCoord_3=25;refseq.codonCoord_4=162;refseq.end_1=143706015;refseq.end_2=143706015;refseq.end_3=143706015;refseq.end_4=143706015;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=365;refseq.mrnaCoord_2=365;refseq.mrnaCoord_3=365;refseq.mrnaCoord_4=702;refseq.name2_1=PDE4DIP;refseq.name2_2=PDE4DIP;refseq.name2_3=PDE4DIP;refseq.name2_4=PDE4DIP;refseq.name_1=NM_001002810;refseq.name_2=NM_001002812;refseq.name_3=NM_014644;refseq.name_4=NM_022359;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.R25L;refseq.proteinCoordStr_2=p.R25L;refseq.proteinCoordStr_3=p.R25L;refseq.proteinCoordStr_4=p.R162L;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.referenceCodon_3=CGC;refseq.referenceCodon_4=CGC;refseq.spliceDist_1=-68;refseq.spliceDist_2=-68;refseq.spliceDist_3=-68;refseq.spliceDist_4=44;refseq.start_1=143706015;refseq.start_2=143706015;refseq.start_3=143706015;refseq.start_4=143706015;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;set=Intersection GT 1/0
|
|
chr1 143732507 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=833;Dels=0.00;HRun=2;HaplotypeScore=26.67;MQ=98.86;MQ0=0;OQ=6638.39;QD=7.97;RankSumP=0.153599;SB=-1507.97;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.251A>G;refseq.codonCoord=84;refseq.end=143732507;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=468;refseq.name=NM_022359;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.D84G;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=18;refseq.start=143732507;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap-filterIngatk GT 1/0
|
|
chr1 143787040 . C T 78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=10.73;MQ=97.56;MQ0=0;OQ=263.70;QD=2.69;RankSumP=0.433496;SB=-83.52;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.180G>A;refseq.codonCoord=60;refseq.end=143787040;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=397;refseq.name=NM_022359;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.W60*;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=-54;refseq.start=143787040;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TGA;set=Intersection GT 0/1
|
|
chr1 143787132 . G A 97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DP=249;Dels=0.00;HRun=0;HaplotypeScore=20.63;MQ=98.47;MQ0=0;OQ=168.54;QD=0.68;RankSumP=0.419988;SB=-44.35;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.88C>T;refseq.codonCoord=30;refseq.end=143787132;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=305;refseq.name=NM_022359;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.P30S;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-146;refseq.start=143787132;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=soap-filterIngatk GT 1/0
|
|
chr1 143787211 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=133;Dels=0.00;HRun=3;HaplotypeScore=18.89;MQ=96.48;MQ0=0;OQ=2091.86;QD=15.73;RankSumP=0.313039;SB=-55.46;SecondBestBaseQ=23;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9C>G;refseq.codonCoord=3;refseq.end=143787211;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=226;refseq.name=NM_022359;refseq.name2=PDE4DIP;refseq.positionType=CDS;refseq.proteinCoordStr=p.G3G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-225;refseq.start=143787211;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 0/1
|
|
chr1 143960233 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.462881;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.20A>G;refseq.codonCoord=7;refseq.end=143960233;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=390;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.N7S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-19;refseq.start=143960233;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=soap GT 0/1
|
|
chr1 143984659 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=2256;Dels=0.00;HRun=1;HaplotypeScore=73.35;MQ=28.17;MQ0=1129;OQ=7004.45;QD=3.10;RankSumP=0.498740;SB=-1392.96;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.156A>G;refseq.codonCoord=52;refseq.end=143984659;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=526;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.R52R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=118;refseq.start=143984659;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=soap-filterIngatk GT 0/1
|
|
chr1 143984702 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=2438;Dels=0.00;HRun=1;HaplotypeScore=68.01;MQ=34.20;MQ0=270;OQ=13736.86;QD=5.63;RankSumP=0.131877;SB=-3686.37;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.199T>C;refseq.codonCoord=67;refseq.end=143984702;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=569;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.S67P;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-100;refseq.start=143984702;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=soap-filterIngatk GT 1/0
|
|
chr1 143992765 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=3099;Dels=0.00;HRun=0;HaplotypeScore=41.32;MQ=21.07;MQ0=1104;OQ=15412.32;QD=4.97;RankSumP=0.639605;SB=-3665.47;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.338C>T;refseq.codonCoord=113;refseq.end=143992765;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=708;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.P113L;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=40;refseq.start=143992765;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=soap-filterIngatk GT 0/1
|
|
chr1 143992900 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=956;Dels=0.00;HRun=0;HaplotypeScore=113.36;MQ=28.46;MQ0=360;OQ=5390.53;QD=5.64;RankSumP=0.122404;SB=-1616.84;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.473C>T;refseq.codonCoord=158;refseq.end=143992900;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=843;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.T158I;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-162;refseq.start=143992900;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=soap-filterIngatk GT 0/1
|
|
chr1 143992970 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=951;Dels=0.00;HRun=0;HaplotypeScore=46.93;MQ=41.71;MQ0=33;OQ=6630.30;QD=6.97;RankSumP=0.464216;SB=-1991.90;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.543C>A;refseq.codonCoord=181;refseq.end=143992970;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=913;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.S181R;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-92;refseq.start=143992970;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=soap-filterIngatk GT 1/0
|
|
chr1 143992990 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1089;Dels=0.00;HRun=0;HaplotypeScore=34.36;MQ=40.43;MQ0=95;OQ=6573.88;QD=6.04;RankSumP=0.449703;SB=-1723.84;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.563C>A;refseq.codonCoord=188;refseq.end=143992990;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=933;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.P188H;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-72;refseq.start=143992990;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 1/0
|
|
chr1 143993013 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=1087;Dels=0.00;HRun=0;HaplotypeScore=17.05;MQ=35.19;MQ0=240;OQ=796.17;QD=0.73;RankSumP=0.0291949;SB=-8.91;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.586A>T;refseq.codonCoord=196;refseq.end=143993013;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=956;refseq.name=NM_203458;refseq.name2=NOTCH2NL;refseq.positionType=CDS;refseq.proteinCoordStr=p.T196S;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-49;refseq.start=143993013;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 0/1
|
|
chr1 144209539 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.chr=chr1;refseq.codingCoordStr=c.771+2;refseq.end=144209539;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_153713;refseq.name2=LIX1L;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=144209539;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 144243906 . T C 281.98 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=219;Dels=0.00;HRun=0;HaplotypeScore=6.69;MQ=98.53;MQ0=0;OQ=8993.71;QD=41.07;RankSumP=1.00000;SB=-3016.88;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1002T>C;refseq.codonCoord=334;refseq.end=144243906;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1078;refseq.name=NM_003637;refseq.name2=ITGA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.F334F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=-74;refseq.start=144243906;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 144245234 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1523C>G;refseq.codonCoord=508;refseq.end=144245234;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1599;refseq.name=NM_003637;refseq.name2=ITGA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.A508G;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-65;refseq.start=144245234;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 1/0
|
|
chr1 144246346 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1892T>G;refseq.codonCoord=631;refseq.end=144246346;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1968;refseq.name=NM_003637;refseq.name2=ITGA10;refseq.positionType=CDS;refseq.proteinCoordStr=p.V631G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-31;refseq.start=144246346;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 144272473 . G A 184.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=133;Dels=0.00;HRun=1;HaplotypeScore=7.15;MQ=98.81;MQ0=0;OQ=2286.06;QD=17.19;RankSumP=0.353515;SB=-877.32;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.804G>A;refseq.codonCoord=268;refseq.end=144272473;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=912;refseq.name=NM_144698;refseq.name2=ANKRD35;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q268Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=21;refseq.start=144272473;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 144273444 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.79;MQ0=0;OQ=763.44;QD=18.62;RankSumP=0.611439;SB=-320.80;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1775G>A;refseq.codonCoord=592;refseq.end=144273444;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1883;refseq.name=NM_144698;refseq.name2=ANKRD35;refseq.positionType=CDS;refseq.proteinCoordStr=p.R592Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=992;refseq.start=144273444;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 144273650 . G C 52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=20;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=6.48;MQ=95.66;MQ0=0;OQ=1211.68;QD=26.34;RankSumP=1.00000;SB=-564.62;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1981G>C;refseq.codonCoord=661;refseq.end=144273650;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2089;refseq.name=NM_144698;refseq.name2=ANKRD35;refseq.positionType=CDS;refseq.proteinCoordStr=p.E661Q;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-807;refseq.start=144273650;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 144308902 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1039A>C;refseq.codonCoord=347;refseq.end=144308902;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1200;refseq.name=NM_006468;refseq.name2=POLR3C;refseq.positionType=CDS;refseq.proteinCoordStr=p.T347P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=30;refseq.start=144308902;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 144459917 . T C 1 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.601430;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.433T>C;refseq.codonCoord=145;refseq.end=144459917;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=530;refseq.name=NM_002614;refseq.name2=PDZK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y145H;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-28;refseq.start=144459917;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT 1/0
|
|
chr1 144472659 . T A 90 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.294942;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1115T>A;refseq.codonCoord=372;refseq.end=144472659;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1212;refseq.name=NM_002614;refseq.name2=PDZK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V372E;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-101;refseq.start=144472659;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=soap GT 1/0
|
|
chr1 144480853 . A C 70 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=11;HRun=2;RankSumP=2.03489e-06;SecondBestBaseQ=23;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1007T>G;refseq.codingCoordStr_2=c.647T>G;refseq.codonCoord_1=336;refseq.codonCoord_2=216;refseq.end_1=144480853;refseq.end_2=144480853;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1181;refseq.mrnaCoord_2=1201;refseq.name2_1=GPR89A;refseq.name2_2=GPR89A;refseq.name_1=NM_001097612;refseq.name_2=NM_001097613;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V336G;refseq.proteinCoordStr_2=p.V216G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.start_1=144480853;refseq.start_2=144480853;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 144757744 rs28626270 T C 42.28 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=582;Dels=0.00;HRun=1;HaplotypeScore=15.54;MQ=2.10;MQ0=575;QD=0.07;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1263A>G;refseq.codingCoordStr_2=c.1263A>G;refseq.codonCoord_1=421;refseq.codonCoord_2=421;refseq.end_1=144757744;refseq.end_2=144757744;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1926;refseq.mrnaCoord_2=1926;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R421R;refseq.proteinCoordStr_2=p.R421R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=AGA;refseq.referenceCodon_2=AGA;refseq.spliceDist_1=-98;refseq.spliceDist_2=-98;refseq.start_1=144757744;refseq.start_2=144757744;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:446,136:2:-7.64,-0.60,-0.00:6.02
|
|
chr1 144759594 . A G 11.45 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=1692;Dels=0.00;HRun=0;HaplotypeScore=51.65;MQ=0.66;MQ0=1691;QD=0.01;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.913T>C;refseq.codingCoordStr_2=c.913T>C;refseq.codonCoord_1=305;refseq.codonCoord_2=305;refseq.end_1=144759594;refseq.end_2=144759594;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1576;refseq.mrnaCoord_2=1576;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L305L;refseq.proteinCoordStr_2=p.L305L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTA;refseq.referenceCodon_2=TTA;refseq.spliceDist_1=47;refseq.spliceDist_2=47;refseq.start_1=144759594;refseq.start_2=144759594;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1669,19:1:-4.40,-0.30,-0.00:1.76
|
|
chr1 144762391 . C G 0.06 PASS AC=2;AF=1.00;AN=2;DP=771;Dels=0.00;HRun=0;HaplotypeScore=10.49;MQ=1.60;MQ0=768;OQ=108.98;QD=0.14;SB=-56.93;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.727G>C;refseq.codingCoordStr_2=c.727G>C;refseq.codonCoord_1=243;refseq.codonCoord_2=243;refseq.end_1=144762391;refseq.end_2=144762391;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1390;refseq.mrnaCoord_2=1390;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V243L;refseq.proteinCoordStr_2=p.V243L;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-37;refseq.spliceDist_2=-37;refseq.start_1=144762391;refseq.start_2=144762391;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=gatk GT:AD:DP:GL:GQ 1/1:680,91:3:-14.39,-0.90,-0.00:9.03
|
|
chr1 144762457 rs6675215 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=538;Dels=0.00;HRun=0;HaplotypeScore=61.87;MQ=1.91;MQ0=535;OQ=75.45;QD=0.14;SB=-45.96;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.661T>C;refseq.codingCoordStr_2=c.661T>C;refseq.codonCoord_1=221;refseq.codonCoord_2=221;refseq.end_1=144762457;refseq.end_2=144762457;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1324;refseq.mrnaCoord_2=1324;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C221R;refseq.proteinCoordStr_2=p.C221R;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=-103;refseq.spliceDist_2=-103;refseq.start_1=144762457;refseq.start_2=144762457;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:315,223:3:-11.03,-0.90,-0.00:9.03
|
|
chr1 145110204 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.06;MQ=97.00;MQ0=0;OQ=741.76;QD=16.13;RankSumP=0.632855;SB=-332.78;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.144C>T;refseq.codonCoord=48;refseq.end=145110204;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=289;refseq.name=NM_005399;refseq.name2=PRKAB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L48L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-13;refseq.start=145110204;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/0
|
|
chr1 145139530 . C T 356.67 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=271;Dels=0.00;HRun=0;HaplotypeScore=4.42;MQ=98.82;MQ0=0;OQ=5174.72;QD=19.09;RankSumP=0.00515215;SB=-1501.47;SecondBestBaseQ=31;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.1011G>A;refseq.codingCoordStr_3=c.1011G>A;refseq.codonCoord_2=337;refseq.codonCoord_3=337;refseq.end_1=145147027;refseq.end_2=145139530;refseq.end_3=145139530;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=1410;refseq.mrnaCoord_3=1400;refseq.name2_1=FMO5;refseq.name2_2=FMO5;refseq.name2_3=FMO5;refseq.name_1=NM_001144830;refseq.name_2=NM_001144829;refseq.name_3=NM_001461;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.P337P;refseq.proteinCoordStr_3=p.P337P;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_2=CCG;refseq.referenceCodon_3=CCG;refseq.spliceDist_2=-173;refseq.spliceDist_3=-173;refseq.start_1=145128463;refseq.start_2=145139530;refseq.start_3=145139530;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_2=CCA;refseq.variantCodon_3=CCA;set=filterInsoap-gatk GT 0/1
|
|
chr1 145139610 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=1;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.931G>C;refseq.codingCoordStr_3=c.931G>C;refseq.codonCoord_2=311;refseq.codonCoord_3=311;refseq.end_1=145147027;refseq.end_2=145139610;refseq.end_3=145139610;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=1330;refseq.mrnaCoord_3=1320;refseq.name2_1=FMO5;refseq.name2_2=FMO5;refseq.name2_3=FMO5;refseq.name_1=NM_001144830;refseq.name_2=NM_001144829;refseq.name_3=NM_001461;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.A311P;refseq.proteinCoordStr_3=p.A311P;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_2=GCT;refseq.referenceCodon_3=GCT;refseq.spliceDist_2=101;refseq.spliceDist_3=101;refseq.start_1=145128463;refseq.start_2=145139610;refseq.start_3=145139610;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;set=FilteredInAll GT 1/0
|
|
chr1 145181016 . G C 43.04 BadSOAPSNP;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=6;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=7.17;RankSumP=0.400000;SB=-3.98;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.39G>C;refseq.codonCoord=13;refseq.end=145181016;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=102;refseq.name=NM_004284;refseq.name2=CHD1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.A13A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-89;refseq.start=145181016;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 145181051 . G C 67 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=8;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=198.79;QD=24.85;RankSumP=0.392857;SB=-94.90;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.74G>C;refseq.codonCoord=25;refseq.end=145181051;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=137;refseq.name=NM_004284;refseq.name2=CHD1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.R25P;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-54;refseq.start=145181051;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 145218406 . A C 300.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=220;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.87;MQ0=0;OQ=8772.44;QD=39.87;RankSumP=1.00000;SB=-3656.53;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1623A>C;refseq.codonCoord=541;refseq.end=145218406;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1686;refseq.name=NM_004284;refseq.name2=CHD1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.I541I;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=-83;refseq.start=145218406;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 145225944 . C G 106.96 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=98.89;MQ0=0;OQ=2429.21;QD=22.92;RankSumP=0.304073;SB=-402.47;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2228C>G;refseq.codonCoord=743;refseq.end=145225944;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2291;refseq.name=NM_004284;refseq.name2=CHD1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.S743C;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=7;refseq.spliceInfo=splice-acceptor_7;refseq.start=145225944;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/0
|
|
chr1 145233773 . G T 333.64 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=143;Dels=0.00;HRun=1;HaplotypeScore=1.42;MQ=98.72;MQ0=0;OQ=5503.54;QD=38.49;RankSumP=1.00000;SB=-2366.12;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2653G>T;refseq.codonCoord=885;refseq.end=145233773;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2716;refseq.name=NM_004284;refseq.name2=CHD1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.A885S;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=38;refseq.start=145233773;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/1
|
|
chr1 145558596 . C T 418.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=6604.33;QD=41.80;RankSumP=1.00000;SB=-2774.19;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2011C>T;refseq.codonCoord=671;refseq.end=145558596;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2751;refseq.name=NM_004326;refseq.name2=BCL9;refseq.positionType=CDS;refseq.proteinCoordStr=p.P671S;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-892;refseq.start=145558596;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 145558976 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2391G>T;refseq.codonCoord=797;refseq.end=145558976;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3131;refseq.name=NM_004326;refseq.name2=BCL9;refseq.positionType=CDS;refseq.proteinCoordStr=p.L797F;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-512;refseq.start=145558976;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 0/1
|
|
chr1 145559070 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=4;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2485A>C;refseq.codonCoord=829;refseq.end=145559070;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3225;refseq.name=NM_004326;refseq.name2=BCL9;refseq.positionType=CDS;refseq.proteinCoordStr=p.T829P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-418;refseq.start=145559070;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 145562350 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3247A>C;refseq.codonCoord=1083;refseq.end=145562350;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3987;refseq.name=NM_004326;refseq.name2=BCL9;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1083P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=84;refseq.start=145562350;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 145585897 . G A 171.99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=486;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=98.73;MQ0=0;OQ=20640.94;QD=42.47;RankSumP=1.00000;SB=-8834.42;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1239C>T;refseq.codonCoord=413;refseq.end=145585897;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1703;refseq.name=NM_016361;refseq.name2=ACP6;refseq.positionType=CDS;refseq.proteinCoordStr=p.H413H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=96;refseq.start=145585897;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/1
|
|
chr1 145588601 . C T 421.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=164;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=98.57;MQ0=0;OQ=6765.30;QD=41.25;RankSumP=1.00000;SB=-3369.45;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.946G>A;refseq.codonCoord=316;refseq.end=145588601;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1410;refseq.name=NM_016361;refseq.name2=ACP6;refseq.positionType=CDS;refseq.proteinCoordStr=p.V316M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-32;refseq.start=145588601;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/1
|
|
chr1 145590934 . T G 345.22 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=223;Dels=0.00;HRun=0;HaplotypeScore=4.76;MQ=98.47;MQ0=0;OQ=8205.38;QD=36.80;RankSumP=1.00000;SB=-3354.36;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.823A>C;refseq.codonCoord=275;refseq.end=145590934;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1287;refseq.name=NM_016361;refseq.name2=ACP6;refseq.positionType=CDS;refseq.proteinCoordStr=p.R275R;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=43;refseq.start=145590934;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/1
|
|
chr1 146042804 . G A 11.18 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=464;Dels=0.00;HRun=0;HaplotypeScore=20.22;MQ=1.16;MQ0=463;QD=0.02;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2366C>T;refseq.codingCoordStr_2=c.2366C>T;refseq.codonCoord_1=789;refseq.codonCoord_2=789;refseq.end_1=146042804;refseq.end_2=146042804;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3029;refseq.mrnaCoord_2=3029;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A789V;refseq.proteinCoordStr_2=p.A789V;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=10;refseq.spliceDist_2=10;refseq.spliceInfo_1=splice-acceptor_10;refseq.spliceInfo_2=splice-acceptor_10;refseq.start_1=146042804;refseq.start_2=146042804;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:460,4:1:-4.37,-0.30,-0.00:1.76
|
|
chr1 146047415 rs61812001 T C 34.77 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=570;Dels=0.00;HRun=0;HaplotypeScore=41.66;MQ=3.87;MQ0=557;QD=0.06;SB=-39.67;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1777A>G;refseq.codingCoordStr_2=c.1777A>G;refseq.codonCoord_1=593;refseq.codonCoord_2=593;refseq.end_1=146047415;refseq.end_2=146047415;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2440;refseq.mrnaCoord_2=2440;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I593V;refseq.proteinCoordStr_2=p.I593V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=-25;refseq.spliceDist_2=-25;refseq.start_1=146047415;refseq.start_2=146047415;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:421,149:4:-7.97,-1.21,-7.52:63.17
|
|
chr1 146057581 rs6666178 C A 40.25 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=1482;Dels=0.00;HRun=0;HaplotypeScore=38.33;MQ=0.89;MQ0=1477;QD=0.03;SB=-41.39;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.812G>T;refseq.codingCoordStr_2=c.812G>T;refseq.codonCoord_1=271;refseq.codonCoord_2=271;refseq.end_1=146057581;refseq.end_2=146057581;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1475;refseq.mrnaCoord_2=1475;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R271L;refseq.proteinCoordStr_2=p.R271L;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.spliceDist_1=49;refseq.spliceDist_2=49;refseq.start_1=146057581;refseq.start_2=146057581;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:787,694:2:-7.43,-0.60,-0.00:6.02
|
|
chr1 146057606 rs61804562 T G 46.49 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=1294;Dels=0.00;HRun=1;HaplotypeScore=56.57;MQ=0.96;MQ0=1289;QD=0.04;SB=-48.57;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.787A>C;refseq.codingCoordStr_2=c.787A>C;refseq.codonCoord_1=263;refseq.codonCoord_2=263;refseq.end_1=146057606;refseq.end_2=146057606;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1450;refseq.mrnaCoord_2=1450;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I263L;refseq.proteinCoordStr_2=p.I263L;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATA;refseq.referenceCodon_2=ATA;refseq.spliceDist_1=24;refseq.spliceDist_2=24;refseq.start_1=146057606;refseq.start_2=146057606;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:1011,282:2:-8.06,-0.60,-0.00:6.02
|
|
chr1 146059444 . C G 0.01 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=674;Dels=0.00;HRun=0;HaplotypeScore=5.75;MQ=1.63;MQ0=672;OQ=59.85;QD=0.09;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.727G>C;refseq.codingCoordStr_2=c.727G>C;refseq.codonCoord_1=243;refseq.codonCoord_2=243;refseq.end_1=146059444;refseq.end_2=146059444;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1390;refseq.mrnaCoord_2=1390;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V243L;refseq.proteinCoordStr_2=p.V243L;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-37;refseq.spliceDist_2=-37;refseq.start_1=146059444;refseq.start_2=146059444;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:587,86:2:-9.39,-0.60,-0.00:6.02
|
|
chr1 146059510 rs6675215 A G 44.28 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=557;Dels=0.00;HRun=0;HaplotypeScore=68.72;MQ=2.07;MQ0=553;QD=0.08;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.661T>C;refseq.codingCoordStr_2=c.661T>C;refseq.codonCoord_1=221;refseq.codonCoord_2=221;refseq.end_1=146059510;refseq.end_2=146059510;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1324;refseq.mrnaCoord_2=1324;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C221R;refseq.proteinCoordStr_2=p.C221R;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=-103;refseq.spliceDist_2=-103;refseq.start_1=146059510;refseq.start_2=146059510;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:326,229:2:-7.84,-0.60,-0.00:6.02
|
|
chr1 146059514 rs6678406 T C 46.84 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=604;Dels=0.00;HRun=0;HaplotypeScore=88.76;MQ=1.98;MQ0=600;QD=0.08;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.657A>G;refseq.codingCoordStr_2=c.657A>G;refseq.codonCoord_1=219;refseq.codonCoord_2=219;refseq.end_1=146059514;refseq.end_2=146059514;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1320;refseq.mrnaCoord_2=1320;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K219K;refseq.proteinCoordStr_2=p.K219K;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=104;refseq.spliceDist_2=104;refseq.start_1=146059514;refseq.start_2=146059514;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:421,183:2:-8.09,-0.60,-0.00:6.02
|
|
chr1 146061701 . G A 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=639;Dels=0.00;HRun=0;HaplotypeScore=37.15;MQ=1.99;MQ0=636;OQ=97.13;QD=0.15;RankSumP=0.333333;SB=-10.00;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.276C>T;refseq.codingCoordStr_2=c.276C>T;refseq.codonCoord_1=92;refseq.codonCoord_2=92;refseq.end_1=146061701;refseq.end_2=146061701;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=939;refseq.mrnaCoord_2=939;refseq.name2_1=NBPF11;refseq.name2_2=LOC200030;refseq.name_1=NM_001101663;refseq.name_2=NM_183372;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D92D;refseq.proteinCoordStr_2=p.D92D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=146061701;refseq.start_2=146061701;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=FilteredInAll GT 1/0
|
|
chr1 146421585 rs28479875 G C 0.69 PASS AC=2;AF=1.00;AN=2;DB;DP=697;Dels=0.00;HRun=0;HaplotypeScore=13.49;MQ=1.43;MQ0=694;OQ=53.76;QD=0.08;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.384C>G;refseq.codonCoord=128;refseq.end=146421585;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=459;refseq.name=NM_178230;refseq.name2=PPIAL4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.A128A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-202;refseq.start=146421585;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=gatk GT:AD:DP:GL:GQ 1/1:631,66:2:-8.78,-0.60,-0.00:6.02
|
|
chr1 146421880 rs2691730 A G 10.53 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=317;Dels=0.00;HRun=1;HaplotypeScore=13.13;MQ=1.35;MQ0=316;QD=0.03;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.89T>C;refseq.codonCoord=30;refseq.end=146421880;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=164;refseq.name=NM_178230;refseq.name2=PPIAL4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.L30P;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=164;refseq.start=146421880;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:234,83:1:-4.30,-0.30,-0.00:1.76
|
|
chr1 146471172 . T C 63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.0708109;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2766A>G;refseq.codonCoord=922;refseq.end=146471172;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2783;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.*922*;refseq.referenceAA=Stop;refseq.referenceCodon=TAA;refseq.spliceDist=244;refseq.start=146471172;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAG;set=soap GT 1/0
|
|
chr1 146471249 . C A 18 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1438;Dels=0.00;HRun=1;HaplotypeScore=41.42;MQ=11.85;MQ0=1326;OQ=141.46;QD=0.10;RankSumP=0.437727;SB=-7.00;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2689G>T;refseq.codonCoord=897;refseq.end=146471249;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2706;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.V897L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=167;refseq.start=146471249;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=FilteredInAll GT 1/0
|
|
chr1 146476134 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1476;Dels=0.00;HRun=0;HaplotypeScore=329.36;MQ=79.75;MQ0=5;OQ=12395.02;QD=8.40;RankSumP=0.480867;SB=-2601.40;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1797C>T;refseq.codonCoord=599;refseq.end=146476134;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1814;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.S599S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=7;refseq.spliceInfo=splice-acceptor_7;refseq.start=146476134;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=soap-filterIngatk GT 1/0
|
|
chr1 146476141 . C A 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1346;Dels=0.00;HRun=0;HaplotypeScore=300.87;MQ=76.61;MQ0=5;OQ=11464.55;QD=8.52;RankSumP=0.00488144;SB=-1467.91;SecondBestBaseQ=31;refseq.chr=chr1;refseq.codingCoordStr=c.1791-1;refseq.end=146476141;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=false;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=intron;refseq.spliceDist=-1;refseq.spliceInfo=splice-acceptor_-1;refseq.start=146476141;refseq.transcriptStrand=-;set=FilteredInAll GT 1/0
|
|
chr1 146477535 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=6658;Dels=0.00;HRun=0;HaplotypeScore=350.17;MQ=2.95;MQ0=6428;OQ=625.59;QD=0.09;RankSumP=0.111125;SB=-0.98;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1711C>T;refseq.codonCoord=571;refseq.end=146477535;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1728;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.R571C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-28;refseq.start=146477535;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=soap-filterIngatk GT 1/0
|
|
chr1 146477539 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.427063;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1707A>G;refseq.codonCoord=569;refseq.end=146477539;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1724;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q569Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-32;refseq.start=146477539;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap GT 1/0
|
|
chr1 146477563 . T A 16 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.139009;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1683A>T;refseq.codonCoord=561;refseq.end=146477563;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1700;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.R561S;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=-56;refseq.start=146477563;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=FilteredInAll GT 1/0
|
|
chr1 146477566 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.154118;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1680C>T;refseq.codonCoord=560;refseq.end=146477566;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1697;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y560Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-59;refseq.start=146477566;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=soap GT 1/0
|
|
chr1 146477611 . T C 25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=3947;Dels=0.00;HRun=0;HaplotypeScore=183.74;MQ=5.12;MQ0=3580;OQ=59.65;QD=0.02;RankSumP=0.138333;SB=59.23;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1635A>G;refseq.codonCoord=545;refseq.end=146477611;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1652;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.S545S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=70;refseq.start=146477611;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=soap-filterIngatk GT 1/0
|
|
chr1 146477651 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.0506536;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1595G>A;refseq.codonCoord=532;refseq.end=146477651;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1612;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.G532E;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=30;refseq.start=146477651;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=FilteredInAll GT 0/1
|
|
chr1 146477661 . C G 26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.500000;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1585G>C;refseq.codonCoord=529;refseq.end=146477661;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1602;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.D529H;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=20;refseq.start=146477661;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap GT 1/0
|
|
chr1 146479193 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.833333;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1390C>T;refseq.codonCoord=464;refseq.end=146479193;refseq.frame=0;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1407;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q464*;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-67;refseq.start=146479193;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAG;set=FilteredInAll GT 1/0
|
|
chr1 146482258 . T C 1 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=2;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.997A>G;refseq.codonCoord=333;refseq.end=146482258;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1014;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.N333D;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-10;refseq.spliceInfo=splice-donor_-10;refseq.start=146482258;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT 1/1
|
|
chr1 146482275 . C T 7 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.238095;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.980G>A;refseq.codonCoord=327;refseq.end=146482275;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=997;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.R327H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-27;refseq.start=146482275;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT 0/1
|
|
chr1 146482292 . G A 37 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.963C>T;refseq.codonCoord=321;refseq.end=146482292;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=980;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y321Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-44;refseq.start=146482292;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=soap GT 1/1
|
|
chr1 146482337 . A G 0.07 PASS AC=2;AF=1.00;AN=2;DP=543;Dels=0.00;HRun=1;HaplotypeScore=10.43;MQ=2.76;MQ0=523;OQ=132.51;QD=0.24;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.918T>C;refseq.codonCoord=306;refseq.end=146482337;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=935;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.C306C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=85;refseq.start=146482337;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=gatk GT:AD:DP:GL:GQ 1/1:472,71:4:-16.78,-1.20,-0.00:12.04
|
|
chr1 146484202 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=2632;Dels=0.00;HRun=0;HaplotypeScore=66.36;MQ=13.61;MQ0=1477;OQ=1796.83;QD=0.68;RankSumP=0.420714;SB=-670.39;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.705G>A;refseq.codonCoord=235;refseq.end=146484202;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=722;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.L235L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-77;refseq.start=146484202;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=soap-filterIngatk GT 0/1
|
|
chr1 146484253 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=1457;Dels=0.00;HRun=1;HaplotypeScore=23.12;MQ=9.30;MQ0=1190;OQ=1485.73;QD=1.02;RankSumP=0.708748;SB=61.60;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.654G>A;refseq.codonCoord=218;refseq.end=146484253;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=671;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q218Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=37;refseq.start=146484253;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap-filterIngatk GT 0/1
|
|
chr1 146489659 . G T 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.457C>A;refseq.codonCoord=153;refseq.end=146489659;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=474;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q153K;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=98;refseq.start=146489659;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=FilteredInAll GT 1/1
|
|
chr1 146489664 . G C -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=2252;Dels=0.00;HRun=0;HaplotypeScore=221.19;MQ=2.92;MQ0=2224;OQ=54.95;QD=0.02;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.452C>G;refseq.codonCoord=151;refseq.end=146489664;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=469;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.S151C;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=93;refseq.start=146489664;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1965,283:6:-10.59,-1.81,-19.79:87.79
|
|
chr1 146489705 rs9437906 T C 0.09 PASS AC=1;AF=0.50;AN=2;DB;DP=1979;Dels=0.00;HRun=0;HaplotypeScore=24.28;MQ=3.19;MQ0=1950;OQ=113.94;QD=0.06;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.411A>G;refseq.codonCoord=137;refseq.end=146489705;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=428;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.E137E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=52;refseq.start=146489705;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=gatk GT:AD:DP:GL:GQ 0/1:1897,80:7:-16.79,-2.11,-13.80:99
|
|
chr1 146490279 . C G 48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.433602;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.301G>C;refseq.codonCoord=101;refseq.end=146490279;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=318;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.D101H;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=15;refseq.start=146490279;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap GT 1/0
|
|
chr1 146490283 . G A 47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.344393;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.297C>T;refseq.codonCoord=99;refseq.end=146490283;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=314;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.N99N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=11;refseq.start=146490283;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=soap GT 1/0
|
|
chr1 146492387 . G A 19 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.539001;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.69C>T;refseq.codonCoord=23;refseq.end=146492387;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=86;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.L23L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-3;refseq.spliceInfo=splice-donor_-3;refseq.start=146492387;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=FilteredInAll GT 1/0
|
|
chr1 146492457 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.583459;SecondBestBaseQ=33;refseq.chr=chr1;refseq.codingCoordStr=c.-2C>T;refseq.end=146492457;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=false;refseq.mrnaCoord=16;refseq.name=NM_015383;refseq.name2=NBPF14;refseq.positionType=utr5;refseq.spliceDist=16;refseq.start=146492457;refseq.transcriptStrand=-;set=soap GT 1/0
|
|
chr1 146846249 . T C 66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.518207;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.195T>C;refseq.codingCoordStr_2=c.195T>C;refseq.codingCoordStr_3=c.195T>C;refseq.codonCoord_1=65;refseq.codonCoord_2=65;refseq.codonCoord_3=65;refseq.end_1=146846249;refseq.end_2=146846249;refseq.end_3=146846249;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=386;refseq.mrnaCoord_2=1357;refseq.mrnaCoord_3=827;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.D65D;refseq.proteinCoordStr_2=p.D65D;refseq.proteinCoordStr_3=p.D65D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.referenceCodon_3=GAT;refseq.spliceDist_1=20;refseq.spliceDist_2=20;refseq.spliceDist_3=20;refseq.start_1=146846249;refseq.start_2=146846249;refseq.start_3=146846249;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;refseq.variantCodon_3=GAC;set=soap GT 1/0
|
|
chr1 146846260 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.512882;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.206T>C;refseq.codingCoordStr_2=c.206T>C;refseq.codingCoordStr_3=c.206T>C;refseq.codonCoord_1=69;refseq.codonCoord_2=69;refseq.codonCoord_3=69;refseq.end_1=146846260;refseq.end_2=146846260;refseq.end_3=146846260;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=397;refseq.mrnaCoord_2=1368;refseq.mrnaCoord_3=838;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.F69S;refseq.proteinCoordStr_2=p.F69S;refseq.proteinCoordStr_3=p.F69S;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.referenceCodon_3=TTT;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.spliceDist_3=31;refseq.start_1=146846260;refseq.start_2=146846260;refseq.start_3=146846260;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=TCT;refseq.variantCodon_2=TCT;refseq.variantCodon_3=TCT;set=soap GT 1/0
|
|
chr1 146846296 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.0112607;SecondBestBaseQ=27;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.242A>T;refseq.codingCoordStr_2=c.242A>T;refseq.codingCoordStr_3=c.242A>T;refseq.codonCoord_1=81;refseq.codonCoord_2=81;refseq.codonCoord_3=81;refseq.end_1=146846296;refseq.end_2=146846296;refseq.end_3=146846296;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=433;refseq.mrnaCoord_2=1404;refseq.mrnaCoord_3=874;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.K81M;refseq.proteinCoordStr_2=p.K81M;refseq.proteinCoordStr_3=p.K81M;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceAA_3=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.referenceCodon_3=AAG;refseq.spliceDist_1=-37;refseq.spliceDist_2=-37;refseq.spliceDist_3=-37;refseq.start_1=146846296;refseq.start_2=146846296;refseq.start_3=146846296;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantAA_3=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;refseq.variantCodon_3=ATG;set=soap GT 0/1
|
|
chr1 146846330 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.192278;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.276C>T;refseq.codingCoordStr_2=c.276C>T;refseq.codingCoordStr_3=c.276C>T;refseq.codonCoord_1=92;refseq.codonCoord_2=92;refseq.codonCoord_3=92;refseq.end_1=146846330;refseq.end_2=146846330;refseq.end_3=146846330;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=467;refseq.mrnaCoord_2=1438;refseq.mrnaCoord_3=908;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.L92L;refseq.proteinCoordStr_2=p.L92L;refseq.proteinCoordStr_3=p.L92L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.referenceCodon_3=CTC;refseq.spliceDist_1=-3;refseq.spliceDist_2=-3;refseq.spliceDist_3=-3;refseq.spliceInfo_1=splice-donor_-3;refseq.spliceInfo_2=splice-donor_-3;refseq.spliceInfo_3=splice-donor_-3;refseq.start_1=146846330;refseq.start_2=146846330;refseq.start_3=146846330;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;refseq.variantCodon_3=CTT;set=soap GT 0/1
|
|
chr1 146848427 . C T 177.41 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=2056;Dels=0.00;HRun=0;HaplotypeScore=243.12;MQ=1.63;MQ0=2047;QD=0.09;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.501C>T;refseq.codingCoordStr_2=c.501C>T;refseq.codingCoordStr_3=c.501C>T;refseq.codonCoord_1=167;refseq.codonCoord_2=167;refseq.codonCoord_3=167;refseq.end_1=146848427;refseq.end_2=146848427;refseq.end_3=146848427;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=692;refseq.mrnaCoord_2=1663;refseq.mrnaCoord_3=1133;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.D167D;refseq.proteinCoordStr_2=p.D167D;refseq.proteinCoordStr_3=p.D167D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.referenceCodon_3=GAC;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceDist_3=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.spliceInfo_3=splice-acceptor_8;refseq.start_1=146848427;refseq.start_2=146848427;refseq.start_3=146848427;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;refseq.variantCodon_3=GAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1992,62:8:-23.43,-2.41,-7.94:55.29
|
|
chr1 146848430 rs4661824 C T 24.21 ESPStandard;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=2189;Dels=0.00;HRun=0;HaplotypeScore=272.40;MQ=1.58;MQ0=2180;QD=0.01;SB=-10.00;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.504C>T;refseq.codingCoordStr_2=c.504C>T;refseq.codingCoordStr_3=c.504C>T;refseq.codonCoord_1=168;refseq.codonCoord_2=168;refseq.codonCoord_3=168;refseq.end_1=146848430;refseq.end_2=146848430;refseq.end_3=146848430;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=695;refseq.mrnaCoord_2=1666;refseq.mrnaCoord_3=1136;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.N168N;refseq.proteinCoordStr_2=p.N168N;refseq.proteinCoordStr_3=p.N168N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.spliceDist_1=11;refseq.spliceDist_2=11;refseq.spliceDist_3=11;refseq.start_1=146848430;refseq.start_2=146848430;refseq.start_3=146848430;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantAA_3=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;refseq.variantCodon_3=AAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1711,477:8:-8.11,-2.41,-23.21:57.03
|
|
chr1 146848434 rs4950572 G C 38.02 ESPStandard;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=2365;Dels=0.00;HRun=0;HaplotypeScore=277.81;MQ=1.52;MQ0=2356;QD=0.02;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.508G>C;refseq.codingCoordStr_2=c.508G>C;refseq.codingCoordStr_3=c.508G>C;refseq.codonCoord_1=170;refseq.codonCoord_2=170;refseq.codonCoord_3=170;refseq.end_1=146848434;refseq.end_2=146848434;refseq.end_3=146848434;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=699;refseq.mrnaCoord_2=1670;refseq.mrnaCoord_3=1140;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.D170H;refseq.proteinCoordStr_2=p.D170H;refseq.proteinCoordStr_3=p.D170H;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.referenceCodon_3=GAC;refseq.spliceDist_1=15;refseq.spliceDist_2=15;refseq.spliceDist_3=15;refseq.start_1=146848434;refseq.start_2=146848434;refseq.start_3=146848434;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1998,366:8:-9.49,-2.41,-30.55:70.86
|
|
chr1 146849049 . C G 10.99 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=637;Dels=0.00;HRun=0;HaplotypeScore=49.40;MQ=1.15;MQ0=636;QD=0.02;SB=-10.00;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.659C>G;refseq.codingCoordStr_2=c.659C>G;refseq.codingCoordStr_3=c.659C>G;refseq.codonCoord_1=220;refseq.codonCoord_2=220;refseq.codonCoord_3=220;refseq.end_1=146849049;refseq.end_2=146849049;refseq.end_3=146849049;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=850;refseq.mrnaCoord_2=1821;refseq.mrnaCoord_3=1291;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S220C;refseq.proteinCoordStr_2=p.S220C;refseq.proteinCoordStr_3=p.S220C;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCC;refseq.referenceCodon_2=TCC;refseq.referenceCodon_3=TCC;refseq.spliceDist_1=93;refseq.spliceDist_2=93;refseq.spliceDist_3=93;refseq.start_1=146849049;refseq.start_2=146849049;refseq.start_3=146849049;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantAA_3=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;refseq.variantCodon_3=TGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:615,22:1:-4.35,-0.30,-0.00:1.76
|
|
chr1 146857905 . A T 14 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=31;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1346A>T;refseq.codingCoordStr_2=c.1346A>T;refseq.codingCoordStr_3=c.1346A>T;refseq.codonCoord_1=449;refseq.codonCoord_2=449;refseq.codonCoord_3=449;refseq.end_1=146857905;refseq.end_2=146857905;refseq.end_3=146857905;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1537;refseq.mrnaCoord_2=2508;refseq.mrnaCoord_3=1978;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.D449V;refseq.proteinCoordStr_2=p.D449V;refseq.proteinCoordStr_3=p.D449V;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.referenceCodon_3=GAT;refseq.spliceDist_1=81;refseq.spliceDist_2=81;refseq.spliceDist_3=81;refseq.start_1=146857905;refseq.start_2=146857905;refseq.start_3=146857905;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;refseq.variantCodon_3=GTT;set=FilteredInAll GT 1/1
|
|
chr1 146857914 . A G 5 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1355A>G;refseq.codingCoordStr_2=c.1355A>G;refseq.codingCoordStr_3=c.1355A>G;refseq.codonCoord_1=452;refseq.codonCoord_2=452;refseq.codonCoord_3=452;refseq.end_1=146857914;refseq.end_2=146857914;refseq.end_3=146857914;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1546;refseq.mrnaCoord_2=2517;refseq.mrnaCoord_3=1987;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E452G;refseq.proteinCoordStr_2=p.E452G;refseq.proteinCoordStr_3=p.E452G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.referenceCodon_3=GAA;refseq.spliceDist_1=-84;refseq.spliceDist_2=-84;refseq.spliceDist_3=-84;refseq.start_1=146857914;refseq.start_2=146857914;refseq.start_3=146857914;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;refseq.variantCodon_3=GGA;set=FilteredInAll GT 1/1
|
|
chr1 146861030 . C T 45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.574843;SecondBestBaseQ=25;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1779C>T;refseq.codingCoordStr_2=c.1779C>T;refseq.codingCoordStr_3=c.1779C>T;refseq.codonCoord_1=593;refseq.codonCoord_2=593;refseq.codonCoord_3=593;refseq.end_1=146861030;refseq.end_2=146861030;refseq.end_3=146861030;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1970;refseq.mrnaCoord_2=2941;refseq.mrnaCoord_3=2411;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.G593G;refseq.proteinCoordStr_2=p.G593G;refseq.proteinCoordStr_3=p.G593G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.referenceCodon_3=GGC;refseq.spliceDist_1=10;refseq.spliceDist_2=10;refseq.spliceDist_3=10;refseq.spliceInfo_1=splice-acceptor_10;refseq.spliceInfo_2=splice-acceptor_10;refseq.spliceInfo_3=splice-acceptor_10;refseq.start_1=146861030;refseq.start_2=146861030;refseq.start_3=146861030;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;refseq.variantCodon_3=GGT;set=soap GT 0/1
|
|
chr1 146861104 . A T 44 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.378790;SecondBestBaseQ=25;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1853A>T;refseq.codingCoordStr_2=c.1853A>T;refseq.codingCoordStr_3=c.1853A>T;refseq.codonCoord_1=618;refseq.codonCoord_2=618;refseq.codonCoord_3=618;refseq.end_1=146861104;refseq.end_2=146861104;refseq.end_3=146861104;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2044;refseq.mrnaCoord_2=3015;refseq.mrnaCoord_3=2485;refseq.name2_1=NBPF16;refseq.name2_2=NBPF15;refseq.name2_3=NBPF15;refseq.name_1=NM_001102663;refseq.name_2=NM_001170755;refseq.name_3=NM_173638;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Y618F;refseq.proteinCoordStr_2=p.Y618F;refseq.proteinCoordStr_3=p.Y618F;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.spliceDist_1=84;refseq.spliceDist_2=84;refseq.spliceDist_3=84;refseq.start_1=146861104;refseq.start_2=146861104;refseq.start_3=146861104;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;refseq.variantCodon_3=TTC;set=soap GT 0/1
|
|
chr1 147010514 . C T 58.75 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=1849;Dels=0.00;HRun=0;HaplotypeScore=203.63;MQ=1.76;MQ0=1841;QD=0.03;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.501C>T;refseq.codonCoord=167;refseq.end=147010514;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=692;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.D167D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=147010514;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1797,51:8:-11.57,-2.41,-18.74:91.58
|
|
chr1 147010517 rs4661824 C T 145.86 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=1991;Dels=0.00;HRun=0;HaplotypeScore=240.96;MQ=1.70;MQ0=1983;QD=0.07;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.504C>T;refseq.codonCoord=168;refseq.end=147010517;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=695;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.N168N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=11;refseq.start=147010517;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1542,448:8:-20.28,-2.41,-11.41:89.97
|
|
chr1 147010521 rs4950572 G C 180.42 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=2144;Dels=0.00;HRun=0;HaplotypeScore=229.11;MQ=1.63;MQ0=2136;QD=0.08;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.508G>C;refseq.codonCoord=170;refseq.end=147010521;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=699;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.D170H;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=15;refseq.start=147010521;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1774,368:8:-23.73,-2.41,-15.38:99
|
|
chr1 147023070 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=912;Dels=0.00;HRun=0;HaplotypeScore=261.52;MQ=13.53;MQ0=720;OQ=1332.00;QD=1.46;RankSumP=0.395552;SB=-581.65;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1775A>G;refseq.codonCoord=592;refseq.end=147023070;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1966;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.N592S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=147023070;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=soap-filterIngatk GT 0/1
|
|
chr1 147023072 . G A 94 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.495005;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1777G>A;refseq.codonCoord=593;refseq.end=147023072;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1968;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.G593S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=147023072;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=soap GT 1/0
|
|
chr1 147023074 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=901;Dels=0.00;HRun=0;HaplotypeScore=263.37;MQ=13.57;MQ0=711;OQ=1361.36;QD=1.51;RankSumP=0.0766988;SB=-544.35;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1779C>T;refseq.codonCoord=593;refseq.end=147023074;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1970;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.G593G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=147023074;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap-filterIngatk GT 0/1
|
|
chr1 147023123 . A G 31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.414212;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1828A>G;refseq.codonCoord=610;refseq.end=147023123;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2019;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.R610G;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=59;refseq.start=147023123;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=soap GT 0/1
|
|
chr1 147023139 . A C 88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=410;Dels=0.00;HRun=1;HaplotypeScore=63.84;MQ=5.38;MQ0=393;OQ=369.20;QD=0.90;RankSumP=1.00000;SB=-112.34;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1844A>C;refseq.codonCoord=615;refseq.end=147023139;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2035;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q615P;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=75;refseq.start=147023139;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=soap-filterIngatk GT 1/1
|
|
chr1 147023142 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=451;Dels=0.00;HRun=1;HaplotypeScore=66.68;MQ=5.03;MQ0=435;OQ=215.74;QD=0.48;SB=2.02;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1847C>T;refseq.codonCoord=616;refseq.end=147023142;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2038;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.S616L;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=78;refseq.start=147023142;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:335,116:12:-28.47,-3.62,-19.47:99
|
|
chr1 147023148 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.565301;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1853A>T;refseq.codonCoord=618;refseq.end=147023148;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2044;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y618F;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=84;refseq.start=147023148;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=soap GT 0/1
|
|
chr1 147023207 . G C 81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=855;Dels=0.00;HRun=0;HaplotypeScore=10.95;MQ=4.89;MQ0=845;QD=0.06;RankSumP=0.737429;SB=-0.97;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1912G>C;refseq.codonCoord=638;refseq.end=147023207;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2103;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.E638Q;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=143;refseq.start=147023207;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap-filterIngatk GT 0/1
|
|
chr1 147023212 . T C 32.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=882;Dels=0.00;HRun=0;HaplotypeScore=5.79;MQ=4.74;MQ0=873;QD=0.04;RankSumP=0.670707;SB=-0.97;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1917T>C;refseq.codonCoord=639;refseq.end=147023212;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2108;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.H639H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=148;refseq.start=147023212;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 1/0
|
|
chr1 147023228 . T G 42.29 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=743;Dels=0.00;HRun=0;HaplotypeScore=10.24;MQ=3.24;MQ0=738;QD=0.06;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1933T>G;refseq.codonCoord=645;refseq.end=147023228;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2124;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y645D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=164;refseq.start=147023228;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:741,2:4:-8.72,-1.21,-6.18:49.72
|
|
chr1 147023231 . G T 8 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=31;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1936G>T;refseq.codonCoord=646;refseq.end=147023231;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2127;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.V646L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=167;refseq.start=147023231;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=FilteredInAll GT 1/1
|
|
chr1 147023272 rs1043762 C T 46.48 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=484;Dels=0.00;HRun=0;HaplotypeScore=25.77;MQ=3.00;MQ0=481;QD=0.10;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1977C>T;refseq.codonCoord=659;refseq.end=147023272;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2168;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.H659H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=208;refseq.start=147023272;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:429,54:3:-8.83,-0.90,-3.70:27.93
|
|
chr1 147023278 rs3863780 G C 10.47 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=449;Dels=0.00;HRun=0;HaplotypeScore=8.69;MQ=3.11;MQ0=446;QD=0.02;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1983G>C;refseq.codonCoord=661;refseq.end=147023278;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2174;refseq.name=NM_001102663;refseq.name2=NBPF16;refseq.positionType=CDS;refseq.proteinCoordStr=p.V661V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=214;refseq.start=147023278;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:447,2:3:-5.19,-0.90,-8.39:42.89
|
|
chr1 148028241 . T A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.00000;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.567T>A;refseq.codonCoord_2=189;refseq.end_1=148050115;refseq.end_2=148028241;refseq.frame_2=2;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=617;refseq.name2_1=HIST2H2BF;refseq.name2_2=FCGR1A;refseq.name_1=NM_001161334;refseq.name_2=NM_000566;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.F189L;refseq.referenceAA_2=Phe;refseq.referenceCodon_2=TTT;refseq.spliceDist_2=8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=148021451;refseq.start_2=148028241;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_2=Leu;refseq.variantCodon_2=TTA;set=FilteredInAll GT 1/0
|
|
chr1 148138529 . G C 110.12 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=98.75;MQ0=0;OQ=499.01;QD=13.13;RankSumP=0.161101;SB=-158.74;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.293G>C;refseq.codonCoord=98;refseq.end=148138529;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=414;refseq.name=NM_016074;refseq.name2=BOLA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G98A;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=343;refseq.start=148138529;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 148165198 . G A 51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.271680;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.400C>T;refseq.codonCoord=134;refseq.end=148165198;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=451;refseq.name=NM_005850;refseq.name2=SF3B4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R134W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=237;refseq.start=148165198;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=soap GT 1/0
|
|
chr1 148165205 . T C 56 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.477564;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.393A>G;refseq.codonCoord=131;refseq.end=148165205;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=444;refseq.name=NM_005850;refseq.name2=SF3B4;refseq.positionType=CDS;refseq.proteinCoordStr=p.K131K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=230;refseq.start=148165205;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=soap GT 1/0
|
|
chr1 148173814 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.325+2;refseq.codingCoordStr_2=c.109+2;refseq.end_1=148173814;refseq.end_2=148173814;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.name2_1=MTMR11;refseq.name2_2=MTMR11;refseq.name_1=NM_001145862;refseq.name_2=NM_181873;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-donor_2;refseq.spliceInfo_2=splice-donor_2;refseq.start_1=148173814;refseq.start_2=148173814;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;set=FilteredInAll GT 0/1
|
|
chr1 148465747 . G T 291.18 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=98.34;MQ0=0;OQ=1868.68;QD=16.83;RankSumP=0.218722;SB=-859.40;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.375C>A;refseq.codingCoordStr_2=c.354C>A;refseq.codingCoordStr_3=c.498C>A;refseq.codonCoord_1=125;refseq.codonCoord_2=118;refseq.codonCoord_3=166;refseq.end_1=148465747;refseq.end_2=148465747;refseq.end_3=148465747;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=745;refseq.mrnaCoord_2=544;refseq.mrnaCoord_3=868;refseq.name2_1=ANP32E;refseq.name2_2=ANP32E;refseq.name2_3=ANP32E;refseq.name_1=NM_001136478;refseq.name_2=NM_001136479;refseq.name_3=NM_030920;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.G125G;refseq.proteinCoordStr_2=p.G118G;refseq.proteinCoordStr_3=p.G166G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.referenceCodon_3=GGC;refseq.spliceDist_1=5;refseq.spliceDist_2=5;refseq.spliceDist_3=5;refseq.spliceInfo_1=splice-acceptor_5;refseq.spliceInfo_2=splice-acceptor_5;refseq.spliceInfo_3=splice-acceptor_5;refseq.start_1=148465747;refseq.start_2=148465747;refseq.start_3=148465747;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;refseq.variantCodon_3=GGA;set=Intersection GT 0/1
|
|
chr1 148749979 . C T 234.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=142;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=98.15;MQ0=0;OQ=2168.31;QD=15.27;RankSumP=0.0429402;SB=-814.87;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.389C>T;refseq.codingCoordStr_2=c.389C>T;refseq.codonCoord_1=130;refseq.codonCoord_2=130;refseq.end_1=148749979;refseq.end_2=148749979;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=588;refseq.mrnaCoord_2=588;refseq.name2_1=ECM1;refseq.name2_2=ECM1;refseq.name_1=NM_004425;refseq.name_2=NM_022664;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T130M;refseq.proteinCoordStr_2=p.T130M;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.spliceDist_1=4;refseq.spliceDist_2=4;refseq.spliceInfo_1=splice-acceptor_4;refseq.spliceInfo_2=splice-acceptor_4;refseq.start_1=148749979;refseq.start_2=148749979;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;set=Intersection GT 0/1
|
|
chr1 148750670 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=4;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.822T>C;refseq.codonCoord_2=274;refseq.end_1=148751441;refseq.end_2=148750670;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1021;refseq.name2_1=ECM1;refseq.name2_2=ECM1;refseq.name_1=NM_022664;refseq.name_2=NM_004425;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A274A;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCT;refseq.spliceDist_2=114;refseq.start_1=148750309;refseq.start_2=148750670;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ala;refseq.variantCodon_2=GCC;set=FilteredInAll GT 1/0
|
|
chr1 148751611 . G A 327.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=334;Dels=0.00;HRun=0;HaplotypeScore=10.36;MQ=98.82;MQ0=0;OQ=7187.83;QD=21.52;RankSumP=0.495255;SB=-2731.83;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1243G>A;refseq.codingCoordStr_2=c.868G>A;refseq.codonCoord_1=415;refseq.codonCoord_2=290;refseq.end_1=148751611;refseq.end_2=148751611;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1442;refseq.mrnaCoord_2=1067;refseq.name2_1=ECM1;refseq.name2_2=ECM1;refseq.name_1=NM_004425;refseq.name_2=NM_022664;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G415S;refseq.proteinCoordStr_2=p.G290S;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=-62;refseq.spliceDist_2=-62;refseq.start_1=148751611;refseq.start_2=148751611;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 1/0
|
|
chr1 148791410 . T G 21 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;HRun=2;RankSumP=0.319444;SecondBestBaseQ=14;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.20+2;refseq.codingCoordStr_2=c.20+2;refseq.end_1=148791410;refseq.end_2=148791410;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.name2_1=ADAMTSL4;refseq.name2_2=ADAMTSL4;refseq.name_1=NM_019032;refseq.name_2=NM_025008;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-donor_2;refseq.spliceInfo_2=splice-donor_2;refseq.start_1=148791410;refseq.start_2=148791410;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;set=soap GT 1/0
|
|
chr1 148792668 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=197;Dels=0.00;HRun=1;HaplotypeScore=9.15;MQ=98.68;MQ0=0;OQ=4587.99;QD=23.29;RankSumP=0.288593;SB=-1863.55;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.577G>C;refseq.codingCoordStr_2=c.577G>C;refseq.codonCoord_1=193;refseq.codonCoord_2=193;refseq.end_1=148792668;refseq.end_2=148792668;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=813;refseq.mrnaCoord_2=813;refseq.name2_1=ADAMTSL4;refseq.name2_2=ADAMTSL4;refseq.name_1=NM_019032;refseq.name_2=NM_025008;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A193P;refseq.proteinCoordStr_2=p.A193P;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=143;refseq.spliceDist_2=143;refseq.start_1=148792668;refseq.start_2=148792668;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;set=Intersection GT 0/1
|
|
chr1 148793030 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=379.13;QD=23.70;RankSumP=0.665118;SB=-77.06;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.939C>T;refseq.codingCoordStr_2=c.939C>T;refseq.codonCoord_1=313;refseq.codonCoord_2=313;refseq.end_1=148793030;refseq.end_2=148793030;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1175;refseq.mrnaCoord_2=1175;refseq.name2_1=ADAMTSL4;refseq.name2_2=ADAMTSL4;refseq.name_1=NM_019032;refseq.name_2=NM_025008;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G313G;refseq.proteinCoordStr_2=p.G313G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=-193;refseq.spliceDist_2=-193;refseq.start_1=148793030;refseq.start_2=148793030;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=Intersection GT 0/1
|
|
chr1 148797632 . T C 221.72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=3.59;MQ=96.85;MQ0=0;OQ=3090.84;QD=30.91;RankSumP=1.00000;SB=-1161.59;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2442T>C;refseq.codingCoordStr_2=c.2442T>C;refseq.codonCoord_1=814;refseq.codonCoord_2=814;refseq.end_1=148797632;refseq.end_2=148797632;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2678;refseq.mrnaCoord_2=2678;refseq.name2_1=ADAMTSL4;refseq.name2_2=ADAMTSL4;refseq.name_1=NM_019032;refseq.name_2=NM_025008;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N814N;refseq.proteinCoordStr_2=p.N814N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=60;refseq.spliceDist_2=60;refseq.start_1=148797632;refseq.start_2=148797632;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=Intersection GT 1/1
|
|
chr1 148797674 . G A 349.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=148;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=95.67;MQ0=0;OQ=5575.29;QD=37.67;RankSumP=1.00000;SB=-2422.23;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2484G>A;refseq.codingCoordStr_2=c.2484G>A;refseq.codonCoord_1=828;refseq.codonCoord_2=828;refseq.end_1=148797674;refseq.end_2=148797674;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2720;refseq.mrnaCoord_2=2720;refseq.name2_1=ADAMTSL4;refseq.name2_2=ADAMTSL4;refseq.name_1=NM_019032;refseq.name_2=NM_025008;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P828P;refseq.proteinCoordStr_2=p.P828P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=-76;refseq.spliceDist_2=102;refseq.start_1=148797674;refseq.start_2=148797674;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=Intersection GT 1/1
|
|
chr1 148797761 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=101;Dels=0.00;HRun=5;HaplotypeScore=24.47;MQ=95.28;MQ0=0;OQ=58.62;QD=0.58;RankSumP=0.00000;SB=125.43;SecondBestBaseQ=10;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2571A>C;refseq.codonCoord_2=857;refseq.end_1=148798051;refseq.end_2=148797761;refseq.frame_2=2;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=2807;refseq.name2_1=ADAMTSL4;refseq.name2_2=ADAMTSL4;refseq.name_1=NM_019032;refseq.name_2=NM_025008;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.E857D;refseq.referenceAA_2=Glu;refseq.referenceCodon_2=GAA;refseq.spliceDist_2=-87;refseq.start_1=148797760;refseq.start_2=148797761;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Asp;refseq.variantCodon_2=GAC;set=FilteredInAll GT 0/1
|
|
chr1 148797794 . C T 190.05 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=3.35;MQ=96.11;MQ0=0;OQ=3412.43;QD=42.66;RankSumP=1.00000;SB=-939.21;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2604C>T;refseq.codonCoord_2=868;refseq.end_1=148798051;refseq.end_2=148797794;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=2840;refseq.name2_1=ADAMTSL4;refseq.name2_2=ADAMTSL4;refseq.name_1=NM_019032;refseq.name_2=NM_025008;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.H868H;refseq.referenceAA_2=His;refseq.referenceCodon_2=CAC;refseq.spliceDist_2=-54;refseq.start_1=148797760;refseq.start_2=148797794;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=His;refseq.variantCodon_2=CAT;set=Intersection GT 1/1
|
|
chr1 148799000 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=98.01;MQ0=0;OQ=1225.68;QD=13.47;RankSumP=0.0209327;SB=-586.34;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3083G>A;refseq.codonCoord=1028;refseq.end=148799000;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3319;refseq.name=NM_019032;refseq.name2=ADAMTSL4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1028H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-6;refseq.spliceInfo=splice-donor_-6;refseq.start=148799000;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/0
|
|
chr1 148945657 . G A 140.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=216;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=98.96;MQ0=0;OQ=2861.98;QD=13.25;RankSumP=0.201666;SB=-1105.41;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.800C>T;refseq.codonCoord=267;refseq.end=148945657;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=906;refseq.name=NM_032132;refseq.name2=HORMAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T267I;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-5;refseq.spliceInfo=splice-donor_-5;refseq.start=148945657;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/0
|
|
chr1 148994163 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=836;Dels=0.00;HRun=1;HaplotypeScore=32.86;MQ=98.85;MQ0=0;OQ=17919.78;QD=21.44;RankSumP=0.279379;SB=-6858.47;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.337C>T;refseq.codonCoord=113;refseq.end=148994163;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=470;refseq.name=NM_004079;refseq.name2=CTSS;refseq.positionType=CDS;refseq.proteinCoordStr=p.R113W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-63;refseq.start=148994163;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/0
|
|
chr1 149038327 . T C 98 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=487;Dels=0.00;HRun=1;HaplotypeScore=2.63;MQ=98.83;MQ0=0;OQ=19052.72;QD=39.12;RankSumP=1.00000;SB=-9385.97;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.831A>G;refseq.codonCoord=277;refseq.end=149038327;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=955;refseq.name=NM_000396;refseq.name2=CTSK;refseq.positionType=CDS;refseq.proteinCoordStr=p.A277A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=47;refseq.start=149038327;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 149052311 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.2241A>C;refseq.codingCoordStr_3=c.2196A>C;refseq.codonCoord_2=747;refseq.codonCoord_3=732;refseq.end_1=149069043;refseq.end_2=149052311;refseq.end_3=149052311;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=2384;refseq.mrnaCoord_3=2339;refseq.name2_1=ARNT;refseq.name2_2=ARNT;refseq.name2_3=ARNT;refseq.name_1=NM_178426;refseq.name_2=NM_001668;refseq.name_3=NM_178427;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.Q747H;refseq.proteinCoordStr_3=p.Q732H;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceCodon_2=CAA;refseq.referenceCodon_3=CAA;refseq.spliceDist_2=-40;refseq.spliceDist_3=-40;refseq.start_1=149052297;refseq.start_2=149052311;refseq.start_3=149052311;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;set=FilteredInAll GT 1/0
|
|
chr1 149052359 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=3;RankSumP=9.33456e-08;SecondBestBaseQ=4;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.2193C>G;refseq.codingCoordStr_3=c.2148C>G;refseq.codonCoord_2=731;refseq.codonCoord_3=716;refseq.end_1=149069043;refseq.end_2=149052359;refseq.end_3=149052359;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=2336;refseq.mrnaCoord_3=2291;refseq.name2_1=ARNT;refseq.name2_2=ARNT;refseq.name2_3=ARNT;refseq.name_1=NM_178426;refseq.name_2=NM_001668;refseq.name_3=NM_178427;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.G731G;refseq.proteinCoordStr_3=p.G716G;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_2=GGC;refseq.referenceCodon_3=GGC;refseq.spliceDist_2=80;refseq.spliceDist_3=80;refseq.start_1=149052297;refseq.start_2=149052359;refseq.start_3=149052359;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=FilteredInAll GT 0/1
|
|
chr1 149075513 . C G 107.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=14.11;MQ=98.90;MQ0=0;OQ=2686.92;QD=12.98;RankSumP=0.292052;SB=-869.63;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.567G>C;refseq.codingCoordStr_2=c.567G>C;refseq.codingCoordStr_3=c.522G>C;refseq.codonCoord_1=189;refseq.codonCoord_2=189;refseq.codonCoord_3=174;refseq.end_1=149075513;refseq.end_2=149075513;refseq.end_3=149075513;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=710;refseq.mrnaCoord_2=710;refseq.mrnaCoord_3=665;refseq.name2_1=ARNT;refseq.name2_2=ARNT;refseq.name2_3=ARNT;refseq.name_1=NM_001668;refseq.name_2=NM_178426;refseq.name_3=NM_178427;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V189V;refseq.proteinCoordStr_2=p.V189V;refseq.proteinCoordStr_3=p.V174V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.spliceDist_1=81;refseq.spliceDist_2=81;refseq.spliceDist_3=81;refseq.start_1=149075513;refseq.start_2=149075513;refseq.start_3=149075513;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;refseq.variantCodon_3=GTC;set=Intersection GT 1/0
|
|
chr1 149184050 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.982T>C;refseq.codingCoordStr_3=c.982T>C;refseq.codonCoord_2=328;refseq.codonCoord_3=328;refseq.end_1=149184050;refseq.end_2=149184050;refseq.end_3=149184050;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1108;refseq.mrnaCoord_2=1172;refseq.mrnaCoord_3=1172;refseq.name2_1=SETDB1;refseq.name2_2=SETDB1;refseq.name2_3=SETDB1;refseq.name_1=NR_026977;refseq.name_2=NM_001145415;refseq.name_3=NM_012432;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.S328P;refseq.proteinCoordStr_3=p.S328P;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_2=TCC;refseq.referenceCodon_3=TCC;refseq.spliceDist_1=33;refseq.spliceDist_2=33;refseq.spliceDist_3=33;refseq.start_1=149184050;refseq.start_2=149184050;refseq.start_3=149184050;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;set=FilteredInAll GT 1/0
|
|
chr1 149189927 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1950T>G;refseq.codingCoordStr_2=c.1950T>G;refseq.codonCoord_1=650;refseq.codonCoord_2=650;refseq.end_1=149189927;refseq.end_2=149189927;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2140;refseq.mrnaCoord_2=2140;refseq.name2_1=SETDB1;refseq.name2_2=SETDB1;refseq.name_1=NM_001145415;refseq.name_2=NM_012432;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C650W;refseq.proteinCoordStr_2=p.C650W;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=-264;refseq.spliceDist_2=-264;refseq.start_1=149189927;refseq.start_2=149189927;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Trp;refseq.variantAA_2=Trp;refseq.variantCodon_1=TGG;refseq.variantCodon_2=TGG;set=FilteredInAll GT 1/0
|
|
chr1 149226974 . A C 132.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=282;Dels=0.00;HRun=1;HaplotypeScore=5.49;MQ=98.87;MQ0=0;OQ=4221.46;QD=14.97;RankSumP=0.149061;SB=-494.55;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.615A>C;refseq.codonCoord=205;refseq.end=149226974;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1085;refseq.name=NM_003568;refseq.name2=ANXA9;refseq.positionType=CDS;refseq.proteinCoordStr=p.A205A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=3;refseq.spliceInfo=splice-acceptor_3;refseq.start=149226974;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 149237201 . G T 72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=159;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=98.36;MQ0=0;OQ=5943.10;QD=37.38;RankSumP=1.00000;SB=-2290.54;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.728C>A;refseq.codingCoordStr_2=c.1298C>A;refseq.codingCoordStr_3=c.869C>A;refseq.codingCoordStr_4=c.728C>A;refseq.codingCoordStr_5=c.1154C>A;refseq.codonCoord_1=243;refseq.codonCoord_2=433;refseq.codonCoord_3=290;refseq.codonCoord_4=243;refseq.codonCoord_5=385;refseq.end_1=149237201;refseq.end_2=149237201;refseq.end_3=149237201;refseq.end_4=149237201;refseq.end_5=149237201;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=1458;refseq.mrnaCoord_2=1521;refseq.mrnaCoord_3=1423;refseq.mrnaCoord_4=1334;refseq.mrnaCoord_5=2122;refseq.name2_1=FAM63A;refseq.name2_2=FAM63A;refseq.name2_3=FAM63A;refseq.name2_4=FAM63A;refseq.name2_5=FAM63A;refseq.name_1=NM_001040217;refseq.name_2=NM_001163258;refseq.name_3=NM_001163259;refseq.name_4=NM_001163260;refseq.name_5=NM_018379;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.T243K;refseq.proteinCoordStr_2=p.T433K;refseq.proteinCoordStr_3=p.T290K;refseq.proteinCoordStr_4=p.T243K;refseq.proteinCoordStr_5=p.T385K;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.referenceCodon_3=ACG;refseq.referenceCodon_4=ACG;refseq.referenceCodon_5=ACG;refseq.spliceDist_1=-20;refseq.spliceDist_2=-20;refseq.spliceDist_3=-20;refseq.spliceDist_4=-20;refseq.spliceDist_5=-20;refseq.start_1=149237201;refseq.start_2=149237201;refseq.start_3=149237201;refseq.start_4=149237201;refseq.start_5=149237201;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantAA_3=Lys;refseq.variantAA_4=Lys;refseq.variantAA_5=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;refseq.variantCodon_3=AAG;refseq.variantCodon_4=AAG;refseq.variantCodon_5=AAG;set=Intersection GT 1/1
|
|
chr1 149273163 . C A 349.15 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.39;MQ0=0;OQ=2123.91;QD=36.00;RankSumP=1.00000;SB=-1060.56;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1191C>A;refseq.codonCoord=397;refseq.end=149273163;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1327;refseq.name=NM_021222;refseq.name2=PRUNE;refseq.positionType=CDS;refseq.proteinCoordStr=p.G397G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=258;refseq.start=149273163;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 149337025 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.545C>G;refseq.codonCoord=182;refseq.end=149337025;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=876;refseq.name=NM_144618;refseq.name2=GABPB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A182G;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=74;refseq.start=149337025;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 149372448 . C G 80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=1.59;MQ=98.09;MQ0=0;OQ=389.42;QD=20.50;RankSumP=0.0345479;SB=-186.83;SecondBestBaseQ=17;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1929G>C;refseq.codonCoord=643;refseq.end=149372448;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2229;refseq.name=NM_030913;refseq.name2=SEMA6C;refseq.positionType=CDS;refseq.proteinCoordStr=p.P643P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=170;refseq.start=149372448;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/0
|
|
chr1 149374761 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=99;Dels=0.00;HRun=4;HaplotypeScore=3.06;MQ=98.83;MQ0=0;OQ=1199.68;QD=12.12;RankSumP=0.391423;SB=-373.01;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1363A>C;refseq.codonCoord=455;refseq.end=149374761;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1663;refseq.name=NM_030913;refseq.name2=SEMA6C;refseq.positionType=CDS;refseq.proteinCoordStr=p.T455P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-71;refseq.start=149374761;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/0
|
|
chr1 149374825 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1299T>G;refseq.codonCoord=433;refseq.end=149374825;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1599;refseq.name=NM_030913;refseq.name2=SEMA6C;refseq.positionType=CDS;refseq.proteinCoordStr=p.G433G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=40;refseq.start=149374825;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 149377456 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=194;Dels=0.00;HRun=0;HaplotypeScore=8.46;MQ=98.70;MQ0=0;OQ=2992.46;QD=15.43;RankSumP=0.448662;SB=-1442.17;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.507C>T;refseq.codonCoord=169;refseq.end=149377456;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=807;refseq.name=NM_030913;refseq.name2=SEMA6C;refseq.positionType=CDS;refseq.proteinCoordStr=p.C169C;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-41;refseq.start=149377456;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/0
|
|
chr1 149398088 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=3;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.291T>G;refseq.codonCoord=97;refseq.end=149398088;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=417;refseq.name=NM_024575;refseq.name2=TNFAIP8L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G97G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=323;refseq.start=149398088;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 149475687 . C T 258.37 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=84.81;MQ0=19;OQ=4594.51;QD=35.89;RankSumP=1.00000;SB=-1906.43;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.933C>T;refseq.codingCoordStr_2=c.930C>T;refseq.codingCoordStr_3=c.969C>T;refseq.codingCoordStr_4=c.930C>T;refseq.codonCoord_1=311;refseq.codonCoord_2=310;refseq.codonCoord_3=323;refseq.codonCoord_4=310;refseq.end_1=149475687;refseq.end_2=149475687;refseq.end_3=149475687;refseq.end_4=149475687;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1385;refseq.mrnaCoord_2=1382;refseq.mrnaCoord_3=1421;refseq.mrnaCoord_4=1382;refseq.name2_1=PIP5K1A;refseq.name2_2=PIP5K1A;refseq.name2_3=PIP5K1A;refseq.name2_4=PIP5K1A;refseq.name_1=NM_001135636;refseq.name_2=NM_001135637;refseq.name_3=NM_001135638;refseq.name_4=NM_003557;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.Y311Y;refseq.proteinCoordStr_2=p.Y310Y;refseq.proteinCoordStr_3=p.Y323Y;refseq.proteinCoordStr_4=p.Y310Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceAA_4=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.referenceCodon_4=TAC;refseq.spliceDist_1=30;refseq.spliceDist_2=30;refseq.spliceDist_3=30;refseq.spliceDist_4=30;refseq.start_1=149475687;refseq.start_2=149475687;refseq.start_3=149475687;refseq.start_4=149475687;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantAA_4=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;refseq.variantCodon_3=TAT;refseq.variantCodon_4=TAT;set=Intersection GT 1/1
|
|
chr1 149505144 . A G 20 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=1.87444e-06;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.695A>G;refseq.codonCoord=232;refseq.end=149505144;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=757;refseq.name=NM_002810;refseq.name2=PSMD4;refseq.positionType=CDS;refseq.proteinCoordStr=p.E232G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=41;refseq.start=149505144;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 149505675 . T C 114.19 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=114;Dels=0.00;HRun=1;HaplotypeScore=1.44;MQ=98.81;MQ0=0;OQ=3891.62;QD=34.14;RankSumP=1.00000;SB=-1484.23;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.951T>C;refseq.codonCoord=317;refseq.end=149505675;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1013;refseq.name=NM_002810;refseq.name2=PSMD4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S317S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-13;refseq.start=149505675;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 149530021 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=17;HRun=2;RankSumP=9.80065e-08;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3426G>T;refseq.codonCoord=1142;refseq.end=149530021;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3524;refseq.name=NM_020832;refseq.name2=ZNF687;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1142F;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=207;refseq.start=149530021;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 0/1
|
|
chr1 149554796 . G A 394.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=175;Dels=0.00;HRun=0;HaplotypeScore=3.73;MQ=98.91;MQ0=0;OQ=6648.53;QD=37.99;RankSumP=1.00000;SB=-1510.66;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.822C>T;refseq.codonCoord=274;refseq.end=149554796;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=891;refseq.name=NM_002651;refseq.name2=PI4KB;refseq.positionType=CDS;refseq.proteinCoordStr=p.D274D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-124;refseq.start=149554796;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 149555015 . A G 291.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=247;Dels=0.00;HRun=0;HaplotypeScore=6.27;MQ=98.77;MQ0=0;OQ=8955.53;QD=36.26;RankSumP=1.00000;SB=-3584.02;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.603T>C;refseq.codonCoord=201;refseq.end=149555015;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=672;refseq.name=NM_002651;refseq.name2=PI4KB;refseq.positionType=CDS;refseq.proteinCoordStr=p.D201D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-343;refseq.start=149555015;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 149582785 . G A 168.19 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.47;MQ0=0;OQ=1605.19;QD=39.15;RankSumP=1.00000;SB=-524.66;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.753C>T;refseq.codingCoordStr_2=c.753C>T;refseq.codonCoord_1=251;refseq.codonCoord_2=251;refseq.end_1=149582785;refseq.end_2=149582785;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=974;refseq.mrnaCoord_2=967;refseq.name2_1=RFX5;refseq.name2_2=RFX5;refseq.name_1=NM_000449;refseq.name_2=NM_001025603;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L251L;refseq.proteinCoordStr_2=p.L251L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.spliceDist_1=-5;refseq.spliceDist_2=-5;refseq.spliceInfo_1=splice-donor_-5;refseq.spliceInfo_2=splice-donor_-5;refseq.start_1=149582785;refseq.start_2=149582785;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;set=Intersection GT 1/1
|
|
chr1 149604327 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=97;Dels=0.00;HRun=1;HaplotypeScore=2.99;MQ=99.00;MQ0=0;OQ=2195.15;QD=22.63;RankSumP=0.443955;SB=-914.61;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1099G>A;refseq.codonCoord=367;refseq.end=149604327;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1146;refseq.name=NM_003944;refseq.name2=SELENBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E367K;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-39;refseq.start=149604327;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 0/1
|
|
chr1 149607368 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.412A>C;refseq.codonCoord=138;refseq.end=149607368;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=459;refseq.name=NM_003944;refseq.name2=SELENBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T138P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=52;refseq.start=149607368;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 149638762 . G A 276.97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=168;Dels=0.00;HRun=0;HaplotypeScore=8.20;MQ=97.66;MQ0=0;OQ=6260.94;QD=37.27;RankSumP=1.00000;SB=-2946.09;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.75G>A;refseq.codonCoord=25;refseq.end=149638762;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=98;refseq.name=NM_002796;refseq.name2=PSMB4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P25P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-66;refseq.start=149638762;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 149644538 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3597C>A;refseq.codingCoordStr_2=c.3438C>A;refseq.codonCoord_1=1199;refseq.codonCoord_2=1146;refseq.end_1=149644538;refseq.end_2=149644538;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3903;refseq.mrnaCoord_2=3744;refseq.name2_1=POGZ;refseq.name2_2=POGZ;refseq.name_1=NM_015100;refseq.name_2=NM_207171;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y1199*;refseq.proteinCoordStr_2=p.Y1146*;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=1027;refseq.spliceDist_2=1027;refseq.start_1=149644538;refseq.start_2=149644538;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantCodon_1=TAA;refseq.variantCodon_2=TAA;set=FilteredInAll GT 0/1
|
|
chr1 149645538 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=0;RankSumP=0.169963;SecondBestBaseQ=19;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2597A>G;refseq.codingCoordStr_2=c.2438A>G;refseq.codonCoord_1=866;refseq.codonCoord_2=813;refseq.end_1=149645538;refseq.end_2=149645538;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2903;refseq.mrnaCoord_2=2744;refseq.name2_1=POGZ;refseq.name2_2=POGZ;refseq.name_1=NM_015100;refseq.name_2=NM_207171;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H866R;refseq.proteinCoordStr_2=p.H813R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=27;refseq.spliceDist_2=27;refseq.start_1=149645538;refseq.start_2=149645538;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=FilteredInAll GT 1/0
|
|
chr1 149759737 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1086T>G;refseq.codonCoord=362;refseq.end=149759737;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1230;refseq.name=NM_020770;refseq.name2=CGN;refseq.positionType=CDS;refseq.proteinCoordStr=p.G362G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=42;refseq.start=149759737;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 150086922 . G C 355.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=191;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=98.72;MQ0=0;OQ=8618.21;QD=45.12;RankSumP=1.00000;SB=-2476.10;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.616C>G;refseq.codonCoord=206;refseq.end=150086922;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=748;refseq.name=NM_182578;refseq.name2=THEM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.L206V;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=41;refseq.start=150086922;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 150086948 . T C 66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=226;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=98.75;MQ0=0;OQ=9123.03;QD=40.37;RankSumP=1.00000;SB=-3990.37;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.590A>G;refseq.codonCoord=197;refseq.end=150086948;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=722;refseq.name=NM_182578;refseq.name2=THEM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.D197G;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=15;refseq.start=150086948;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 150087378 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=0;RankSumP=0.0326771;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.479G>T;refseq.codonCoord=160;refseq.end=150087378;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=611;refseq.name=NM_182578;refseq.name2=THEM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.G160V;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=15;refseq.start=150087378;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT 1/0
|
|
chr1 150092615 . G T 234.78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=5.22;MQ=98.98;MQ0=0;OQ=4064.53;QD=32.26;RankSumP=1.00000;SB=-1681.54;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.51C>A;refseq.codonCoord=17;refseq.end=150092615;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=183;refseq.name=NM_182578;refseq.name2=THEM5;refseq.positionType=CDS;refseq.proteinCoordStr=p.G17G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-73;refseq.start=150092615;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 150134184 . G A 96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=304;Dels=0.00;HRun=0;HaplotypeScore=16.43;MQ=70.42;MQ0=92;OQ=8598.10;QD=28.28;RankSumP=1.00000;SB=-3298.81;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.210C>T;refseq.codonCoord=70;refseq.end=150134184;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=389;refseq.name=NM_053055;refseq.name2=THEM4;refseq.positionType=CDS;refseq.proteinCoordStr=p.D70D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-77;refseq.start=150134184;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 150324101 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2681T>G;refseq.codonCoord=894;refseq.end=150324101;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2746;refseq.name=NM_001008536;refseq.name2=TCHHL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V894G;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-858;refseq.start=150324101;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=FilteredInAll GT 0/1
|
|
chr1 150325670 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1112A>C;refseq.codonCoord=371;refseq.end=150325670;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1177;refseq.name=NM_001008536;refseq.name2=TCHHL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D371A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=974;refseq.start=150325670;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 150346613 . T G 310.38 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=280;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=98.87;MQ0=0;OQ=5833.16;QD=20.83;RankSumP=0.480328;SB=-1419.51;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5704A>C;refseq.codonCoord=1902;refseq.end=150346613;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5704;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1902Q;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-1197;refseq.start=150346613;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 150346951 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5366G>C;refseq.codonCoord=1789;refseq.end=150346951;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5366;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1789P;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-1535;refseq.start=150346951;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 150348545 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=234;Dels=0.00;HRun=1;HaplotypeScore=3.27;MQ=98.86;MQ0=0;OQ=6046.41;QD=25.84;RankSumP=0.444528;SB=-1847.20;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3772C>G;refseq.codonCoord=1258;refseq.end=150348545;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3772;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1258V;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-3129;refseq.start=150348545;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 0/1
|
|
chr1 150349949 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=90.83;MQ0=0;OQ=184.61;QD=5.96;RankSumP=0.265884;SB=-42.96;SecondBestBaseQ=22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2368T>A;refseq.codonCoord=790;refseq.end=150349949;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2368;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.L790M;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=2230;refseq.start=150349949;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 150349996 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=3.71011e-08;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2321A>G;refseq.codonCoord=774;refseq.end=150349996;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2321;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.E774G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=2183;refseq.start=150349996;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 150349999 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.500035;SecondBestBaseQ=19;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2318C>G;refseq.codonCoord=773;refseq.end=150349999;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2318;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.A773G;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=2180;refseq.start=150349999;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=soap GT 0/1
|
|
chr1 150350663 . G T 343.34 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=263;Dels=0.00;HRun=0;HaplotypeScore=6.51;MQ=98.55;MQ0=0;OQ=4487.38;QD=17.06;RankSumP=0.364743;SB=-1882.78;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1654C>A;refseq.codonCoord=552;refseq.end=150350663;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1654;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.R552S;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=1516;refseq.start=150350663;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 150352129 . A C 255.06 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=153;Dels=0.00;HRun=0;HaplotypeScore=10.00;MQ=98.81;MQ0=0;OQ=5843.39;QD=38.19;RankSumP=1.00000;SB=-2678.30;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.188T>G;refseq.codonCoord=63;refseq.end=150352129;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=188;refseq.name=NM_007113;refseq.name2=TCHH;refseq.positionType=CDS;refseq.proteinCoordStr=p.L63R;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=50;refseq.start=150352129;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/1
|
|
chr1 150394745 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=2376;Dels=0.00;HRun=2;HaplotypeScore=67.91;MQ=96.50;MQ0=0;OQ=46929.39;QD=19.75;RankSumP=0.159516;SB=-18097.18;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1454C>T;refseq.codonCoord=485;refseq.end=150394745;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1519;refseq.name=NM_001122965;refseq.name2=RPTN;refseq.positionType=CDS;refseq.proteinCoordStr=p.S485F;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=1316;refseq.start=150394745;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=soap-filterIngatk GT 1/0
|
|
chr1 150452374 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=373;Dels=0.00;HRun=0;HaplotypeScore=10.46;MQ=94.38;MQ0=0;OQ=9774.96;QD=26.21;RankSumP=0.178408;SB=-4049.27;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8355C>T;refseq.codonCoord=2785;refseq.end=150452374;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=8431;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2785Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-1193;refseq.start=150452374;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/0
|
|
chr1 150452386 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=329;Dels=0.00;HRun=0;HaplotypeScore=7.63;MQ=93.15;MQ0=0;OQ=3139.13;QD=9.54;RankSumP=0.413260;SB=-1222.74;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8343G>C;refseq.codonCoord=2781;refseq.end=150452386;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8419;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q2781H;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-1205;refseq.start=150452386;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/0
|
|
chr1 150452392 . T G 52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=315;Dels=0.00;HRun=1;HaplotypeScore=11.42;MQ=92.66;MQ0=0;OQ=1517.25;QD=4.82;RankSumP=0.478717;SB=-337.54;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8337A>C;refseq.codonCoord=2779;refseq.end=150452392;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=8413;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2779S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-1211;refseq.start=150452392;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/0
|
|
chr1 150452398 rs61814932 A G 0.42 PASS AC=1;AF=0.50;AN=2;DB;DP=311;Dels=0.00;HRun=1;HaplotypeScore=13.10;MQ=91.84;MQ0=0;OQ=449.81;QD=1.45;SB=-4.79;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8331T>C;refseq.codonCoord=2777;refseq.end=150452398;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=8407;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2777S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-1217;refseq.start=150452398;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=gatk GT:AD:DP:GL:GQ 0/1:260,50:280:-132.60,-84.33,-1038.67:99
|
|
chr1 150452723 . C T 9 BadSOAPSNP;FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;BestBaseQ=34;DP=764;Dels=0.00;HRun=0;HaplotypeScore=138.70;MQ=9.80;MQ0=666;OQ=3167.19;QD=4.15;RankSumP=1.00000;SB=-318.28;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8006G>A;refseq.codonCoord=2669;refseq.end=150452723;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8082;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2669D;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-1542;refseq.start=150452723;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT 1/1
|
|
chr1 150452744 . A G 35.93 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=954;Dels=0.00;HRun=0;HaplotypeScore=73.48;MQ=4.46;MQ0=929;QD=0.04;SB=11.07;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7985T>C;refseq.codonCoord=2662;refseq.end=150452744;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=8061;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.L2662S;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-1563;refseq.start=150452744;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:771,155:10:-9.89,-3.01,-28.19:68.76
|
|
chr1 150452768 . C T 6 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7961G>A;refseq.codonCoord=2654;refseq.end=150452768;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8037;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2654N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-1587;refseq.start=150452768;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 1/1
|
|
chr1 150452820 . G A 14 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=30;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7909C>T;refseq.codonCoord=2637;refseq.end=150452820;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=7985;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2637C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-1639;refseq.start=150452820;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=FilteredInAll GT 1/1
|
|
chr1 150452846 . T C 26.72 BadSOAPSNP;ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;BestBaseQ=18;DB;DP=1038;Dels=0.00;HRun=0;HaplotypeScore=77.69;MQ=7.96;MQ0=974;QD=0.03;RankSumP=1.00000;SB=20.09;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7883A>G;refseq.codonCoord=2628;refseq.end=150452846;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7959;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2628R;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-1665;refseq.start=150452846;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=FilteredInAll GT 1/1
|
|
chr1 150453076 . G A 44.02 ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=1901;Dels=0.00;HRun=0;HaplotypeScore=213.19;MQ=0.83;MQ0=1899;QD=0.02;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.7653C>T;refseq.codonCoord=2551;refseq.end=150453076;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=7729;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2551Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-1895;refseq.start=150453076;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:1726,173:2:-7.81,-0.60,-0.00:6.02
|
|
chr1 150453215 . C G 19.14 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=5014;Dels=0.00;HRun=1;HaplotypeScore=119.01;MQ=0.35;MQ0=5013;QD=0.00;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7514G>C;refseq.codonCoord=2505;refseq.end=150453215;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7590;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2505T;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-2034;refseq.start=150453215;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:4998,10:1:-5.19,-0.30,-0.00:1.76
|
|
chr1 150453323 . T A 12 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=28;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7406A>T;refseq.codonCoord=2469;refseq.end=150453323;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7482;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q2469L;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-2142;refseq.start=150453323;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT 1/1
|
|
chr1 150453390 . G A 25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=4335;Dels=0.00;HRun=0;HaplotypeScore=125.48;MQ=8.73;MQ0=3590;OQ=8990.43;QD=2.07;RankSumP=1.00000;SB=-3295.80;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7339C>T;refseq.codonCoord=2447;refseq.end=150453390;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=7415;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2447C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-2209;refseq.start=150453390;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=soap-filterIngatk GT 1/1
|
|
chr1 150453921 rs12116427 T A -0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=5525;Dels=0.00;HRun=0;HaplotypeScore=205.78;MQ=1.16;MQ0=5519;OQ=152.36;QD=0.03;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6808A>T;refseq.codonCoord=2270;refseq.end=150453921;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6884;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.T2270S;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-2740;refseq.start=150453921;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:5427,70:5:-18.80,-1.51,-0.00:15.05
|
|
chr1 150454178 . C T -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1401;Dels=0.00;HRun=1;HaplotypeScore=129.42;MQ=15.31;MQ0=888;OQ=649.91;QD=0.46;SB=-76.43;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6551G>A;refseq.codonCoord=2184;refseq.end=150454178;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6627;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2184N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-2997;refseq.start=150454178;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1092,270:178:-121.88,-53.61,-589.06:99
|
|
chr1 150454186 . A C 39 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=1371;Dels=0.00;HRun=0;HaplotypeScore=143.51;MQ=14.17;MQ0=1019;OQ=2996.80;QD=2.19;RankSumP=1.00000;SB=-1062.39;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6543T>G;refseq.codonCoord=2181;refseq.end=150454186;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6619;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2181Q;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-3005;refseq.start=150454186;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap-filterIngatk GT 1/1
|
|
chr1 150454212 . C T -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=2951;Dels=0.00;HRun=0;HaplotypeScore=440.48;MQ=18.46;MQ0=1260;OQ=1264.00;QD=0.43;SB=-350.49;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6517G>A;refseq.codonCoord=2173;refseq.end=150454212;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6593;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2173S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-3031;refseq.start=150454212;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:2653,282:1055:-447.48,-317.80,-3503.03:99
|
|
chr1 150454213 . G A 23 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=3016;Dels=0.00;HRun=0;HaplotypeScore=433.85;MQ=18.56;MQ0=1251;OQ=6871.21;QD=2.28;RankSumP=0.000205513;SB=-814.14;SecondBestBaseQ=15;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6516C>T;refseq.codonCoord=2172;refseq.end=150454213;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6592;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2172H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-3032;refseq.start=150454213;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT 1/0
|
|
chr1 150454230 . G A -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=4381;Dels=0.00;HRun=0;HaplotypeScore=203.08;MQ=20.43;MQ0=1159;OQ=93.45;QD=0.02;SB=-8.30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6499C>T;refseq.codonCoord=2167;refseq.end=150454230;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6575;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2167C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-3049;refseq.start=150454230;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:4073,302:2526:-773.44,-760.81,-8982.21:99
|
|
chr1 150454252 . A G 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=6241;Dels=0.00;HRun=0;HaplotypeScore=203.80;MQ=20.52;MQ0=1437;OQ=20080.46;QD=3.22;RankSumP=0.00436852;SB=-3907.89;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6477T>C;refseq.codonCoord=2159;refseq.end=150454252;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6553;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2159Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-3071;refseq.start=150454252;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=FilteredInAll GT 0/1
|
|
chr1 150454434 . G A 16 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DP=411;Dels=0.00;HRun=0;HaplotypeScore=19.68;MQ=6.38;MQ0=349;OQ=841.19;QD=2.05;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6295C>T;refseq.codonCoord=2099;refseq.end=150454434;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6371;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.P2099S;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-3253;refseq.start=150454434;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=filterInsoap-gatk GT 1/1
|
|
chr1 150454559 . C T 56 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DP=1703;Dels=0.00;HRun=1;HaplotypeScore=48.58;MQ=6.78;MQ0=1643;QD=0.01;RankSumP=1.00000;SB=14.07;SecondBestBaseQ=21;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6170G>A;refseq.codonCoord=2057;refseq.end=150454559;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6246;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2057Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-3378;refseq.start=150454559;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap-filterIngatk GT 1/1
|
|
chr1 150454569 . C T 57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DP=2127;Dels=0.00;HRun=0;HaplotypeScore=84.69;MQ=4.85;MQ0=2074;QD=0.01;RankSumP=1.00000;SB=11.06;SecondBestBaseQ=22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6160G>A;refseq.codonCoord=2054;refseq.end=150454569;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6236;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2054S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-3388;refseq.start=150454569;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=soap-filterIngatk GT 1/1
|
|
chr1 150454686 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=4464;Dels=0.00;HRun=0;HaplotypeScore=86.08;MQ=17.96;MQ0=2031;OQ=20092.83;QD=4.50;RankSumP=0.200621;SB=-5216.38;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6043A>G;refseq.codonCoord=2015;refseq.end=150454686;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6119;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.T2015A;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-3505;refseq.start=150454686;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=soap-filterIngatk GT 1/0
|
|
chr1 150454733 . T A 48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=5107;Dels=0.00;HRun=0;HaplotypeScore=354.27;MQ=7.79;MQ0=4701;OQ=11751.74;QD=2.30;RankSumP=1.00000;SB=-172.94;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5996A>T;refseq.codonCoord=1999;refseq.end=150454733;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6072;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1999L;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-3552;refseq.start=150454733;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=soap-filterIngatk GT 1/1
|
|
chr1 150454800 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.220588;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5929C>T;refseq.codonCoord=1977;refseq.end=150454800;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6005;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1977C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-3619;refseq.start=150454800;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=FilteredInAll GT 1/0
|
|
chr1 150454836 . C T 29 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=3.98529e-05;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5893G>A;refseq.codonCoord=1965;refseq.end=150454836;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5969;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1965S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-3655;refseq.start=150454836;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT 0/1
|
|
chr1 150455037 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DP=5849;Dels=0.00;HRun=2;HaplotypeScore=120.40;MQ=15.44;MQ0=3461;OQ=10212.14;QD=1.75;RankSumP=0.538744;SB=-1990.65;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5692G>A;refseq.codonCoord=1898;refseq.end=150455037;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5768;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1898K;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-3856;refseq.start=150455037;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=soap-filterIngatk GT 0/1
|
|
chr1 150455087 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=4982;Dels=0.00;HRun=1;HaplotypeScore=103.75;MQ=19.01;MQ0=2090;OQ=12669.05;QD=2.54;RankSumP=0.227932;SB=-2098.40;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5642C>T;refseq.codonCoord=1881;refseq.end=150455087;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5718;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1881F;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-3906;refseq.start=150455087;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=soap-filterIngatk GT 1/0
|
|
chr1 150455486 . G A 26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.750000;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5243C>T;refseq.codonCoord=1748;refseq.end=150455486;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5319;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1748L;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-4305;refseq.start=150455486;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=soap GT 1/0
|
|
chr1 150455544 . C T -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1683;Dels=0.00;HRun=0;HaplotypeScore=177.45;MQ=2.30;MQ0=1679;OQ=78.79;QD=0.05;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5185G>A;refseq.codonCoord=1729;refseq.end=150455544;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5261;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1729S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-4363;refseq.start=150455544;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1387,288:4:-12.37,-1.20,-4.27:30.64
|
|
chr1 150455564 . A G 42 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=1542;Dels=0.00;HRun=0;HaplotypeScore=92.89;MQ=2.89;MQ0=1533;OQ=128.02;QD=0.08;RankSumP=0.400000;SB=-10.00;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5165T>C;refseq.codonCoord=1722;refseq.end=150455564;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5241;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1722S;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-4383;refseq.start=150455564;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=soap-filterIngatk GT 0/1
|
|
chr1 150455585 . C T 43 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DP=1910;Dels=0.00;HRun=0;HaplotypeScore=225.12;MQ=9.04;MQ0=1768;QD=0.01;RankSumP=0.316413;SB=-36.74;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5144G>A;refseq.codonCoord=1715;refseq.end=150455585;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5220;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1715H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-4404;refseq.start=150455585;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150455588 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DP=1982;Dels=0.00;HRun=1;HaplotypeScore=223.83;MQ=9.14;MQ0=1831;OQ=157.73;QD=0.08;RankSumP=0.130874;SB=-83.55;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5141G>A;refseq.codonCoord=1714;refseq.end=150455588;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5217;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1714N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-4407;refseq.start=150455588;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150455622 . C T 50 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=2066;Dels=0.00;HRun=0;HaplotypeScore=311.46;MQ=10.77;MQ0=1691;OQ=332.21;QD=0.16;RankSumP=0.127032;SB=59.41;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5107G>A;refseq.codonCoord=1703;refseq.end=150455622;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5183;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1703S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-4441;refseq.start=150455622;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=soap-filterIngatk GT 0/1
|
|
chr1 150455623 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=2052;Dels=0.00;HRun=0;HaplotypeScore=309.60;MQ=10.80;MQ0=1677;OQ=286.34;QD=0.14;RankSumP=0.427788;SB=-44.97;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5106C>T;refseq.codonCoord=1702;refseq.end=150455623;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5182;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1702H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-4442;refseq.start=150455623;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap-filterIngatk GT 1/0
|
|
chr1 150455640 . G A 49 BadSOAPSNP;ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=1857;Dels=0.00;HRun=0;HaplotypeScore=117.49;MQ=11.48;MQ0=1483;QD=0.01;RankSumP=0.00885839;SB=37.71;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5089C>T;refseq.codonCoord=1697;refseq.end=150455640;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5165;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1697C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-4459;refseq.start=150455640;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=FilteredInAll GT 1/0
|
|
chr1 150455662 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=1371;Dels=0.00;HRun=0;HaplotypeScore=57.30;MQ=13.47;MQ0=999;OQ=217.14;QD=0.16;RankSumP=0.375827;SB=-71.80;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5067T>C;refseq.codonCoord=1689;refseq.end=150455662;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5143;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y1689Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-4481;refseq.start=150455662;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150455679 . G C 54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DP=650;Dels=0.00;HRun=1;HaplotypeScore=24.62;MQ=7.44;MQ0=616;OQ=213.03;QD=0.33;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5050C>G;refseq.codonCoord=1684;refseq.end=150455679;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5126;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1684G;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-4498;refseq.start=150455679;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap-filterIngatk GT 1/1
|
|
chr1 150455896 . G A -0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=1964;Dels=0.00;HRun=0;HaplotypeScore=197.38;MQ=1.47;MQ0=1957;OQ=244.10;QD=0.12;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4833C>T;refseq.codonCoord=1611;refseq.end=150455896;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4909;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y1611Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=4695;refseq.start=150455896;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:1805,152:7:-27.99,-2.11,-0.00:21.07
|
|
chr1 150456210 . G A 0.05 PASS AC=2;AF=1.00;AN=2;DP=427;Dels=0.00;HRun=0;HaplotypeScore=9.34;MQ=1.65;MQ0=424;OQ=55.14;QD=0.13;SB=-54.56;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4519C>T;refseq.codonCoord=1507;refseq.end=150456210;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4595;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1507C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=4381;refseq.start=150456210;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=gatk GT:AD:DP:GL:GQ 1/1:299,128:2:-8.92,-0.60,-0.00:6.02
|
|
chr1 150457032 . C T 11.18 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=0;HaplotypeScore=14.78;MQ=10.63;MQ0=122;QD=0.09;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3697G>A;refseq.codonCoord=1233;refseq.end=150457032;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3773;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1233S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=3559;refseq.start=150457032;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:120,5:1:-4.37,-0.30,-0.00:1.76
|
|
chr1 150457306 . G A -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1932;Dels=0.00;HRun=0;HaplotypeScore=187.10;MQ=1.37;MQ0=1926;OQ=102.32;QD=0.05;SB=-3.98;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3423C>T;refseq.codonCoord=1141;refseq.end=150457306;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3499;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y1141Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=3285;refseq.start=150457306;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1755,173:6:-15.32,-1.81,-7.29:54.86
|
|
chr1 150457459 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=2435;Dels=0.00;HRun=0;HaplotypeScore=57.03;MQ=15.87;MQ0=1507;OQ=17092.47;QD=7.02;RankSumP=0.0141103;SB=-6436.36;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3270C>T;refseq.codonCoord=1090;refseq.end=150457459;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3346;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1090G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=3132;refseq.start=150457459;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap-filterIngatk GT 1/0
|
|
chr1 150457569 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=2537;Dels=0.00;HRun=1;HaplotypeScore=111.57;MQ=20.28;MQ0=2159;OQ=5912.57;QD=2.33;RankSumP=0.0730815;SB=-2397.23;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3160G>A;refseq.codonCoord=1054;refseq.end=150457569;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3236;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1054K;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=3022;refseq.start=150457569;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=soap-filterIngatk GT 0/1
|
|
chr1 150458333 . C G 184.07 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=239;Dels=0.00;HRun=0;HaplotypeScore=15.54;MQ=98.73;MQ0=0;OQ=5365.31;QD=22.45;RankSumP=0.455301;SB=-1629.15;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2396G>C;refseq.codonCoord=799;refseq.end=150458333;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2472;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S799T;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=2258;refseq.start=150458333;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/0
|
|
chr1 150458503 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=767;Dels=0.00;HRun=0;HaplotypeScore=14.43;MQ=97.43;MQ0=0;OQ=15175.72;QD=19.79;RankSumP=0.487114;SB=-5819.59;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2226C>T;refseq.codonCoord=742;refseq.end=150458503;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2302;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H742H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=2088;refseq.start=150458503;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 150458738 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=863;Dels=0.00;HRun=1;HaplotypeScore=22.91;MQ=73.87;MQ0=151;OQ=14049.96;QD=16.28;RankSumP=0.0918279;SB=-4635.39;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1991G>A;refseq.codonCoord=664;refseq.end=150458738;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2067;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R664Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=1853;refseq.start=150458738;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 0/1
|
|
chr1 150458917 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1691;Dels=0.00;HRun=0;HaplotypeScore=58.18;MQ=41.36;MQ0=522;OQ=11608.47;QD=6.86;RankSumP=0.440828;SB=-3940.45;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1812G>A;refseq.codonCoord=604;refseq.end=150458917;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1888;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S604S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=1674;refseq.start=150458917;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=soap-filterIngatk GT 0/1
|
|
chr1 150459179 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=1165;Dels=0.00;HRun=0;HaplotypeScore=20.89;MQ=96.48;MQ0=1;OQ=21698.70;QD=18.63;RankSumP=0.405837;SB=-9190.52;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1550A>G;refseq.codonCoord=517;refseq.end=150459179;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1626;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y517C;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=1412;refseq.start=150459179;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/0
|
|
chr1 150459255 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1491;Dels=0.00;HRun=0;HaplotypeScore=41.75;MQ=96.83;MQ0=2;OQ=30192.97;QD=20.25;RankSumP=0.0976942;SB=-12894.39;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1474G>A;refseq.codonCoord=492;refseq.end=150459255;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1550;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G492R;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=1336;refseq.start=150459255;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=soap-filterIngatk GT 0/1
|
|
chr1 150459311 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=1184;Dels=0.00;HRun=1;HaplotypeScore=28.46;MQ=97.23;MQ0=1;OQ=47734.57;QD=40.32;RankSumP=1.00000;SB=-18236.95;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1418A>G;refseq.codonCoord=473;refseq.end=150459311;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1494;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.E473G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=1280;refseq.start=150459311;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=soap-filterIngatk GT 1/1
|
|
chr1 150459449 . C T 257.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=261;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=98.10;MQ0=0;OQ=5131.17;QD=19.66;RankSumP=0.358124;SB=-1709.25;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1280G>A;refseq.codonCoord=427;refseq.end=150459449;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1356;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G427D;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=1142;refseq.start=150459449;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 0/1
|
|
chr1 150459602 . T C 83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=655;Dels=0.00;HRun=0;HaplotypeScore=11.59;MQ=98.37;MQ0=0;OQ=25063.06;QD=38.26;RankSumP=1.00000;SB=-10609.19;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1127A>G;refseq.codonCoord=376;refseq.end=150459602;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1203;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q376R;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=989;refseq.start=150459602;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/1
|
|
chr1 150459676 . A G 145.94 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=614;Dels=0.00;HRun=0;HaplotypeScore=5.24;MQ=98.50;MQ0=0;OQ=22892.54;QD=37.28;RankSumP=1.00000;SB=-8642.37;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1053T>C;refseq.codonCoord=351;refseq.end=150459676;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1129;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H351H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=915;refseq.start=150459676;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 150459745 . G T 260.39 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=368;Dels=0.00;HRun=0;HaplotypeScore=6.04;MQ=97.65;MQ0=0;OQ=5621.13;QD=15.27;RankSumP=0.00729458;SB=-2142.20;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.984C>A;refseq.codonCoord=328;refseq.end=150459745;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1060;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G328G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=846;refseq.start=150459745;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=filterInsoap-gatk GT 0/1
|
|
chr1 150459771 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.958T>C;refseq.codonCoord=320;refseq.end=150459771;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1034;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S320P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=820;refseq.start=150459771;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 150459910 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1478;Dels=0.00;HRun=1;HaplotypeScore=58.08;MQ=82.41;MQ0=3;OQ=25029.45;QD=16.93;RankSumP=0.250946;SB=-8600.98;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.819C>A;refseq.codonCoord=273;refseq.end=150459910;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=895;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H273Q;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=681;refseq.start=150459910;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap-filterIngatk GT 0/1
|
|
chr1 150459915 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1498;Dels=0.00;HRun=2;HaplotypeScore=56.14;MQ=81.95;MQ0=3;OQ=26175.85;QD=17.47;RankSumP=0.185241;SB=-8884.09;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.814C>A;refseq.codonCoord=272;refseq.end=150459915;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=890;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R272R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=676;refseq.start=150459915;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=soap-filterIngatk GT 0/1
|
|
chr1 150460168 . A G 146.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=215;Dels=0.00;HRun=1;HaplotypeScore=3.17;MQ=98.44;MQ0=0;OQ=3937.93;QD=18.32;RankSumP=0.304793;SB=-1075.20;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.561T>C;refseq.codonCoord=187;refseq.end=150460168;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=637;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.H187H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=423;refseq.start=150460168;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 0/1
|
|
chr1 150460171 . G A 266.84 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=4.68;MQ=98.26;MQ0=0;OQ=8179.38;QD=39.51;RankSumP=1.00000;SB=-2473.35;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.558C>T;refseq.codonCoord=186;refseq.end=150460171;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=634;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S186S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=420;refseq.start=150460171;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 150460475 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=98.90;MQ0=0;OQ=1483.24;QD=12.90;RankSumP=0.448535;SB=-131.46;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.254G>A;refseq.codonCoord=85;refseq.end=150460475;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=330;refseq.name=NM_001009931;refseq.name2=HRNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R85H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=116;refseq.start=150460475;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 0/1
|
|
chr1 150542773 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=1441;Dels=0.00;HRun=0;HaplotypeScore=58.30;MQ=78.02;MQ0=201;OQ=22649.27;QD=15.72;RankSumP=0.491064;SB=-7407.77;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.11213G>A;refseq.codonCoord=3738;refseq.end=150542773;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=11249;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R3738H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-1499;refseq.start=150542773;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150543001 . C G 29 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10985G>C;refseq.codonCoord=3662;refseq.end=150543001;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=11021;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S3662T;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-1727;refseq.start=150543001;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=soap GT 1/1
|
|
chr1 150543083 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=4014;Dels=0.00;HRun=1;HaplotypeScore=95.66;MQ=16.26;MQ0=1986;OQ=19172.07;QD=4.78;RankSumP=0.207962;SB=-5706.63;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10903G>A;refseq.codonCoord=3635;refseq.end=150543083;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10939;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.D3635N;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-1809;refseq.start=150543083;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150543207 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.312921;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10779G>C;refseq.codonCoord=3593;refseq.end=150543207;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10815;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.E3593D;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-1933;refseq.start=150543207;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=soap GT 1/0
|
|
chr1 150543222 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.0324707;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10764C>T;refseq.codonCoord=3588;refseq.end=150543222;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=10800;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H3588H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-1948;refseq.start=150543222;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap GT 1/0
|
|
chr1 150543250 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.311804;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10736C>G;refseq.codonCoord=3579;refseq.end=150543250;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=10772;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.T3579R;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-1976;refseq.start=150543250;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=soap GT 0/1
|
|
chr1 150543295 rs7518080 C T 33.26 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=845;Dels=0.00;HRun=0;HaplotypeScore=34.59;MQ=40.44;MQ0=180;QD=0.04;SB=775.42;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10691G>A;refseq.codonCoord=3564;refseq.end=150543295;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10727;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R3564H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-2021;refseq.start=150543295;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:786,59:559:-174.97,-168.36,-1976.30:66.10
|
|
chr1 150543323 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=893;Dels=0.00;HRun=0;HaplotypeScore=31.88;MQ=47.63;MQ0=300;OQ=1120.59;QD=1.25;RankSumP=0.340804;SB=-515.26;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10663T>C;refseq.codonCoord=3555;refseq.end=150543323;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10699;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.W3555R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=-2049;refseq.start=150543323;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=soap-filterIngatk GT 0/1
|
|
chr1 150543396 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=923;Dels=0.00;HRun=0;HaplotypeScore=38.64;MQ=86.94;MQ0=82;OQ=13692.62;QD=14.83;RankSumP=0.489830;SB=-4947.32;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10590G>T;refseq.codonCoord=3530;refseq.end=150543396;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10626;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R3530S;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-2122;refseq.start=150543396;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/0
|
|
chr1 150543495 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=1155;Dels=0.00;HRun=0;HaplotypeScore=20.10;MQ=93.14;MQ0=4;OQ=18420.30;QD=15.95;RankSumP=0.324922;SB=-6806.20;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10491T>C;refseq.codonCoord=3497;refseq.end=150543495;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10527;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.D3497D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-2221;refseq.start=150543495;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 0/1
|
|
chr1 150543513 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=1370;Dels=0.00;HRun=0;HaplotypeScore=37.64;MQ=92.00;MQ0=3;OQ=23168.78;QD=16.91;RankSumP=0.304032;SB=-7498.21;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10473T>C;refseq.codonCoord=3491;refseq.end=150543513;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10509;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.N3491N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-2239;refseq.start=150543513;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 0/1
|
|
chr1 150543679 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=2169;Dels=0.00;HRun=0;HaplotypeScore=58.78;MQ=45.35;MQ0=364;OQ=33215.07;QD=15.31;RankSumP=0.346483;SB=-13918.03;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10307G>C;refseq.codonCoord=3436;refseq.end=150543679;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10343;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.G3436A;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-2405;refseq.start=150543679;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=soap-filterIngatk GT 1/0
|
|
chr1 150543792 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1027;Dels=0.00;HRun=1;HaplotypeScore=37.20;MQ=25.76;MQ0=490;OQ=7100.13;QD=6.91;RankSumP=0.462429;SB=-2534.42;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10194T>C;refseq.codonCoord=3398;refseq.end=150543792;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10230;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S3398S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-2518;refseq.start=150543792;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=soap-filterIngatk GT 0/1
|
|
chr1 150543969 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=2177;Dels=0.00;HRun=1;HaplotypeScore=70.84;MQ=56.58;MQ0=6;OQ=37113.55;QD=17.05;RankSumP=0.250765;SB=-15059.89;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10017G>A;refseq.codonCoord=3339;refseq.end=150543969;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10053;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q3339Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-2695;refseq.start=150543969;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap-filterIngatk GT 0/1
|
|
chr1 150544020 . T C 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=2339;Dels=0.00;HRun=1;HaplotypeScore=60.09;MQ=70.28;MQ0=10;OQ=38438.08;QD=16.43;RankSumP=1.94858e-05;SB=-14408.53;SecondBestBaseQ=23;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9966A>G;refseq.codonCoord=3322;refseq.end=150544020;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=10002;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q3322Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-2746;refseq.start=150544020;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=FilteredInAll GT 1/0
|
|
chr1 150544341 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1225;Dels=0.00;HRun=1;HaplotypeScore=24.91;MQ=13.30;MQ0=1156;OQ=89.28;QD=0.07;RankSumP=0.231974;SB=44.17;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9645G>T;refseq.codonCoord=3215;refseq.end=150544341;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=9681;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.V3215V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-3067;refseq.start=150544341;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=soap-filterIngatk GT 1/0
|
|
chr1 150544446 . T C 58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=0;RankSumP=0.377137;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9540A>G;refseq.codonCoord=3180;refseq.end=150544446;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=9576;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S3180S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-3172;refseq.start=150544446;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=soap GT 1/0
|
|
chr1 150544450 . A C 34 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.463134;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.9536T>G;refseq.codonCoord=3179;refseq.end=150544450;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=9572;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.V3179G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-3176;refseq.start=150544450;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=soap GT 0/1
|
|
chr1 150545066 . C G -0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=3638;Dels=0.00;HRun=1;HaplotypeScore=161.23;MQ=0.86;MQ0=3635;OQ=102.53;QD=0.03;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8920G>C;refseq.codonCoord=2974;refseq.end=150545066;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8956;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2974P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-3792;refseq.start=150545066;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:3554,83:3:-13.74,-0.90,-0.00:9.03
|
|
chr1 150545313 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1842;Dels=0.00;HRun=1;HaplotypeScore=52.38;MQ=9.12;MQ0=1744;OQ=1079.12;QD=0.59;RankSumP=0.208747;SB=-220.91;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8673G>T;refseq.codonCoord=2891;refseq.end=150545313;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8709;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.V2891V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-4039;refseq.start=150545313;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=soap-filterIngatk GT 1/0
|
|
chr1 150545438 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=3319;Dels=0.00;HRun=0;HaplotypeScore=85.90;MQ=32.17;MQ0=563;OQ=14713.37;QD=4.43;SB=-3779.79;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8548G>A;refseq.codonCoord=2850;refseq.end=150545438;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8584;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2850S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-4164;refseq.start=150545438;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:2644,673:2343:-1470.34,-705.69,-7648.29:99
|
|
chr1 150545480 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=3593;Dels=0.00;HRun=0;HaplotypeScore=89.07;MQ=21.01;MQ0=2435;OQ=11069.65;QD=3.08;RankSumP=0.380833;SB=-2945.33;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8506A>C;refseq.codonCoord=2836;refseq.end=150545480;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=8542;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2836R;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-4206;refseq.start=150545480;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=soap-filterIngatk GT 1/0
|
|
chr1 150545643 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=3854;Dels=0.00;HRun=0;HaplotypeScore=78.23;MQ=22.17;MQ0=972;OQ=24041.79;QD=6.24;RankSumP=0.352745;SB=-7175.91;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8343C>T;refseq.codonCoord=2781;refseq.end=150545643;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=8379;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.D2781D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-4369;refseq.start=150545643;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=soap-filterIngatk GT 1/0
|
|
chr1 150545908 . C G 19.14 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=3296;Dels=0.00;HRun=0;HaplotypeScore=172.19;MQ=0.52;MQ0=3295;QD=0.01;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8078G>C;refseq.codonCoord=2693;refseq.end=150545908;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8114;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2693T;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-4634;refseq.start=150545908;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:3245,47:1:-5.19,-0.30,-0.00:1.76
|
|
chr1 150546030 . T G 23.13 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=3778;Dels=0.00;HRun=0;HaplotypeScore=179.86;MQ=3.08;MQ0=3771;QD=0.01;SB=-3.98;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7956A>C;refseq.codonCoord=2652;refseq.end=150546030;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7992;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.E2652D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-4756;refseq.start=150546030;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:3131,645:7:-7.70,-2.11,-20.06:55.94
|
|
chr1 150546038 . C G 31.02 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=3685;Dels=0.00;HRun=1;HaplotypeScore=161.03;MQ=3.44;MQ0=3677;QD=0.01;SB=8.06;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7948G>C;refseq.codonCoord=2650;refseq.end=150546038;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7984;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2650P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-4764;refseq.start=150546038;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:3594,88:8:-8.79,-2.41,-27.98:63.85
|
|
chr1 150546353 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=1170;Dels=0.00;HRun=0;HaplotypeScore=32.06;MQ=81.80;MQ0=115;OQ=18878.83;QD=16.14;RankSumP=0.416816;SB=-6253.70;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7633G>A;refseq.codonCoord=2545;refseq.end=150546353;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7669;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.G2545R;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-5079;refseq.start=150546353;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 0/1
|
|
chr1 150546465 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1830;Dels=0.00;HRun=0;HaplotypeScore=43.73;MQ=74.59;MQ0=290;OQ=29979.30;QD=16.38;RankSumP=0.380842;SB=-11656.65;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7521C>G;refseq.codonCoord=2507;refseq.end=150546465;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=7557;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2507Q;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-5191;refseq.start=150546465;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap-filterIngatk GT 0/1
|
|
chr1 150546544 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=1797;Dels=0.00;HRun=0;HaplotypeScore=51.81;MQ=80.99;MQ0=69;OQ=27916.80;QD=15.54;RankSumP=0.457742;SB=-9838.81;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7442T>C;refseq.codonCoord=2481;refseq.end=150546544;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=7478;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.L2481S;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-5270;refseq.start=150546544;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=soap-filterIngatk GT 0/1
|
|
chr1 150546656 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=1508;Dels=0.00;HRun=0;HaplotypeScore=34.56;MQ=77.82;MQ0=94;OQ=22488.52;QD=14.91;RankSumP=0.206893;SB=-7211.81;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7330A>G;refseq.codonCoord=2444;refseq.end=150546656;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7366;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.K2444E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-5382;refseq.start=150546656;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 150546794 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DP=1585;Dels=0.00;HRun=0;HaplotypeScore=58.74;MQ=24.91;MQ0=1417;OQ=2437.52;QD=1.54;RankSumP=0.0932996;SB=-55.92;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7192G>C;refseq.codonCoord=2398;refseq.end=150546794;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7228;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.E2398Q;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-5520;refseq.start=150546794;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap-filterIngatk GT 1/0
|
|
chr1 150546889 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=2353;Dels=0.00;HRun=0;HaplotypeScore=97.10;MQ=8.19;MQ0=2325;OQ=267.67;QD=0.11;SB=-6.99;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7097G>C;refseq.codonCoord=2366;refseq.end=150546889;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7133;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2366T;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-5615;refseq.start=150546889;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1867,485:23:-36.98,-6.93,-73.54:99
|
|
chr1 150546971 . C T 52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.254012;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7015G>A;refseq.codonCoord=2339;refseq.end=150546971;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7051;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.D2339N;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-5697;refseq.start=150546971;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=soap GT 0/1
|
|
chr1 150546996 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.0710377;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6990C>T;refseq.codonCoord=2330;refseq.end=150546996;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=7026;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2330H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-5722;refseq.start=150546996;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap GT 1/0
|
|
chr1 150547095 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=1964;Dels=0.00;HRun=0;HaplotypeScore=46.97;MQ=30.88;MQ0=658;OQ=15188.54;QD=7.73;RankSumP=0.201871;SB=-5305.45;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6891G>C;refseq.codonCoord=2297;refseq.end=150547095;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6927;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.E2297D;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-5821;refseq.start=150547095;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=soap-filterIngatk GT 1/0
|
|
chr1 150547183 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.180540;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6803A>G;refseq.codonCoord=2268;refseq.end=150547183;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6839;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2268R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-5909;refseq.start=150547183;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=soap GT 1/0
|
|
chr1 150547197 . C A 71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.416584;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6789G>T;refseq.codonCoord=2263;refseq.end=150547197;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6825;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2263A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-5923;refseq.start=150547197;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=soap GT 1/0
|
|
chr1 150547360 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1877;Dels=0.00;HRun=0;HaplotypeScore=38.78;MQ=94.65;MQ0=0;OQ=13822.09;QD=7.36;SB=-2185.57;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6626A>G;refseq.codonCoord=2209;refseq.end=150547360;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6662;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2209R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-6086;refseq.start=150547360;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1496,379:1802:-1381.21,-542.79,-5953.86:99
|
|
chr1 150547383 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=2148;Dels=0.00;HRun=0;HaplotypeScore=55.06;MQ=93.87;MQ0=0;OQ=21480.81;QD=10.00;SB=-6498.65;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6603T>C;refseq.codonCoord=2201;refseq.end=150547383;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6639;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.D2201D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-6109;refseq.start=150547383;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1538,602:2052:-2147.08,-618.09,-6188.54:99
|
|
chr1 150547406 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=2462;Dels=0.00;HRun=0;HaplotypeScore=883.65;MQ=91.80;MQ0=51;OQ=61964.49;QD=25.17;RankSumP=0.0231591;SB=-21244.68;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6580T>C;refseq.codonCoord=2194;refseq.end=150547406;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6616;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2194H;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-6132;refseq.start=150547406;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap-filterIngatk GT 0/1
|
|
chr1 150547412 . T G -0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=2496;Dels=0.00;HRun=0;HaplotypeScore=767.14;MQ=90.40;MQ0=110;OQ=28546.61;QD=11.44;SB=-9251.39;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6574A>C;refseq.codonCoord=2192;refseq.end=150547412;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6610;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.K2192Q;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-6138;refseq.start=150547412;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1762,733:2314:-2853.66,-696.75,-6531.62:99
|
|
chr1 150547488 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=19;DP=2194;Dels=0.00;HRun=1;HaplotypeScore=154.05;MQ=77.87;MQ0=309;OQ=32980.11;QD=15.03;RankSumP=0.111941;SB=-8985.70;SecondBestBaseQ=22;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6498T>C;refseq.codonCoord=2166;refseq.end=150547488;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6534;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2166S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-6214;refseq.start=150547488;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=soap-filterIngatk GT 0/1
|
|
chr1 150547524 . T G 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=27;DP=2132;Dels=0.00;HRun=0;HaplotypeScore=68.15;MQ=85.26;MQ0=146;OQ=19985.19;QD=9.37;RankSumP=0.000117034;SB=-6382.13;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6462A>C;refseq.codonCoord=2154;refseq.end=150547524;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6498;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q2154H;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-6250;refseq.start=150547524;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=FilteredInAll GT 1/0
|
|
chr1 150547631 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=1655;Dels=0.00;HRun=0;HaplotypeScore=42.30;MQ=93.89;MQ0=34;OQ=22446.78;QD=13.56;RankSumP=0.0994103;SB=-7638.53;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6355T>C;refseq.codonCoord=2119;refseq.end=150547631;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6391;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2119H;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=6217;refseq.start=150547631;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap-filterIngatk GT 0/1
|
|
chr1 150547632 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=1638;Dels=0.00;HRun=0;HaplotypeScore=46.11;MQ=93.98;MQ0=34;OQ=21978.74;QD=13.42;RankSumP=0.0674316;SB=-7385.59;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6354T>C;refseq.codonCoord=2118;refseq.end=150547632;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6390;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2118H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=6216;refseq.start=150547632;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150547663 . G A 0.15 PASS AC=1;AF=0.50;AN=2;DP=1232;Dels=0.00;HRun=0;HaplotypeScore=27.30;MQ=96.88;MQ0=0;OQ=18295.16;QD=14.85;SB=-6484.36;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6323C>T;refseq.codonCoord=2108;refseq.end=150547663;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6359;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2108V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=6185;refseq.start=150547663;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=gatk GT:AD:DP:GL:GQ 0/1:780,450:1198:-1828.52,-360.78,-2979.13:99
|
|
chr1 150547852 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=3142;Dels=0.00;HRun=0;HaplotypeScore=112.97;MQ=64.08;MQ0=447;OQ=19981.63;QD=6.36;RankSumP=0.395972;SB=-6306.10;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6134G>C;refseq.codonCoord=2045;refseq.end=150547852;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6170;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2045T;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=5996;refseq.start=150547852;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=soap-filterIngatk GT 1/0
|
|
chr1 150547914 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=3762;Dels=0.00;HRun=0;HaplotypeScore=72.56;MQ=51.06;MQ0=523;OQ=16084.02;QD=4.28;RankSumP=0.319419;SB=-2812.41;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6072T>C;refseq.codonCoord=2024;refseq.end=150547914;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6108;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H2024H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=5934;refseq.start=150547914;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150547928 . A C 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=3800;Dels=0.00;HRun=0;HaplotypeScore=71.21;MQ=52.05;MQ0=414;OQ=21611.40;QD=5.69;RankSumP=0.00545957;SB=-4730.48;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6058T>G;refseq.codonCoord=2020;refseq.end=150547928;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6094;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2020A;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=5920;refseq.start=150547928;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=FilteredInAll GT 0/1
|
|
chr1 150548103 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=1664;Dels=0.00;HRun=1;HaplotypeScore=44.33;MQ=77.55;MQ0=29;OQ=36133.49;QD=21.71;RankSumP=0.242800;SB=-12424.89;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5883C>A;refseq.codonCoord=1961;refseq.end=150548103;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5919;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1961Q;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=5745;refseq.start=150548103;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap-filterIngatk GT 0/1
|
|
chr1 150548147 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=1231;Dels=0.00;HRun=3;HaplotypeScore=20.15;MQ=82.19;MQ0=96;OQ=9108.79;QD=7.40;RankSumP=0.473364;SB=-1611.22;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5839T>G;refseq.codonCoord=1947;refseq.end=150548147;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5875;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.W1947G;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=5701;refseq.start=150548147;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 0/1
|
|
chr1 150548158 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1190;Dels=0.00;HRun=0;HaplotypeScore=34.81;MQ=78.17;MQ0=163;OQ=7161.06;QD=6.02;SB=-713.92;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5828T>A;refseq.codonCoord=1943;refseq.end=150548158;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5864;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1943H;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=5690;refseq.start=150548158;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:910,276:961:-715.11,-289.38,-3234.77:99
|
|
chr1 150548314 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=1518;Dels=0.00;HRun=0;HaplotypeScore=51.03;MQ=87.09;MQ0=26;OQ=30611.31;QD=20.17;RankSumP=0.0147022;SB=-12653.81;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5672G>A;refseq.codonCoord=1891;refseq.end=150548314;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5708;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1891Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=5534;refseq.start=150548314;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=soap-filterIngatk GT 0/1
|
|
chr1 150548572 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1911;Dels=0.00;HRun=0;HaplotypeScore=63.45;MQ=74.64;MQ0=164;OQ=32592.18;QD=17.06;RankSumP=0.0700357;SB=-13193.80;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5414C>T;refseq.codonCoord=1805;refseq.end=150548572;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5450;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1805V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=5276;refseq.start=150548572;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=soap-filterIngatk GT 1/0
|
|
chr1 150548891 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=1378;Dels=0.00;HRun=0;HaplotypeScore=33.38;MQ=98.04;MQ0=0;OQ=27812.30;QD=20.18;RankSumP=0.496857;SB=-9382.72;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5095C>T;refseq.codonCoord=1699;refseq.end=150548891;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5131;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1699C;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=4957;refseq.start=150548891;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 1/0
|
|
chr1 150548935 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=1736;Dels=0.00;HRun=0;HaplotypeScore=47.80;MQ=96.00;MQ0=0;OQ=33810.07;QD=19.48;RankSumP=0.415645;SB=-14227.65;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5051G>A;refseq.codonCoord=1684;refseq.end=150548935;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5087;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1684H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=4913;refseq.start=150548935;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150549541 . G T 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=1867;Dels=0.00;HRun=0;HaplotypeScore=39.07;MQ=87.98;MQ0=66;OQ=34226.14;QD=18.33;RankSumP=0.00900027;SB=-11679.20;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4445C>A;refseq.codonCoord=1482;refseq.end=150549541;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4481;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1482Y;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=4307;refseq.start=150549541;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=FilteredInAll GT 0/1
|
|
chr1 150549860 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=2066;Dels=0.00;HRun=1;HaplotypeScore=47.09;MQ=53.90;MQ0=489;OQ=11136.71;QD=5.39;RankSumP=0.455999;SB=-2202.45;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4126A>G;refseq.codonCoord=1376;refseq.end=150549860;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4162;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1376G;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=3988;refseq.start=150549860;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=soap-filterIngatk GT 1/0
|
|
chr1 150549907 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=2031;Dels=0.00;HRun=0;HaplotypeScore=101.28;MQ=64.72;MQ0=248;OQ=21348.30;QD=10.51;RankSumP=0.0981165;SB=-6865.34;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4079G>A;refseq.codonCoord=1360;refseq.end=150549907;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4115;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1360H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=3941;refseq.start=150549907;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150550402 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3584A>C;refseq.codonCoord=1195;refseq.end=150550402;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3620;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1195P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=3446;refseq.start=150550402;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 150550486 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=2084;Dels=0.00;HRun=1;HaplotypeScore=32.25;MQ=65.11;MQ0=447;OQ=23260.38;QD=11.16;RankSumP=0.445632;SB=-6750.48;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3500C>G;refseq.codonCoord=1167;refseq.end=150550486;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3536;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1167G;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=3362;refseq.start=150550486;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=soap-filterIngatk GT 0/1
|
|
chr1 150550599 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=961;Dels=0.00;HRun=1;HaplotypeScore=28.00;MQ=31.13;MQ0=454;OQ=6795.77;QD=7.07;RankSumP=0.204599;SB=-1935.55;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3387T>C;refseq.codonCoord=1129;refseq.end=150550599;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3423;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1129S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=3249;refseq.start=150550599;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=soap-filterIngatk GT 0/1
|
|
chr1 150551430 . C T 56 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=0;RankSumP=0.00304953;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2556G>A;refseq.codonCoord=852;refseq.end=150551430;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2592;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.R852R;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=2418;refseq.start=150551430;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=FilteredInAll GT 0/1
|
|
chr1 150551478 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=1984;Dels=0.00;HRun=0;HaplotypeScore=39.54;MQ=81.52;MQ0=115;OQ=31428.63;QD=15.84;RankSumP=0.0185071;SB=-13060.18;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2508T>C;refseq.codonCoord=836;refseq.end=150551478;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2544;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.D836D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=2370;refseq.start=150551478;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=soap-filterIngatk GT 0/1
|
|
chr1 150551723 . C T 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=2179;Dels=0.00;HRun=2;HaplotypeScore=45.62;MQ=75.96;MQ0=100;OQ=39968.78;QD=18.34;RankSumP=0.00169390;SB=-16955.79;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2263G>A;refseq.codonCoord=755;refseq.end=150551723;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2299;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.E755K;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=2125;refseq.start=150551723;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 0/1
|
|
chr1 150552349 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1637A>C;refseq.codonCoord=546;refseq.end=150552349;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1673;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.H546P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=1499;refseq.start=150552349;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 150552554 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=940;Dels=0.00;HRun=0;HaplotypeScore=19.61;MQ=93.54;MQ0=2;OQ=20360.76;QD=21.66;RankSumP=0.237774;SB=-8757.83;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1432C>T;refseq.codonCoord=478;refseq.end=150552554;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1468;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.P478S;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=1294;refseq.start=150552554;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/0
|
|
chr1 150552626 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=983;Dels=0.00;HRun=0;HaplotypeScore=32.25;MQ=96.99;MQ0=2;OQ=16663.46;QD=16.95;RankSumP=0.110958;SB=-6207.63;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1360A>G;refseq.codonCoord=454;refseq.end=150552626;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1396;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.T454A;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=1222;refseq.start=150552626;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 150552656 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=977;Dels=0.00;HRun=0;HaplotypeScore=29.33;MQ=98.33;MQ0=0;OQ=17307.40;QD=17.71;RankSumP=0.0335347;SB=-6941.11;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1330G>A;refseq.codonCoord=444;refseq.end=150552656;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1366;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.G444R;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=1192;refseq.start=150552656;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 0/1
|
|
chr1 150552991 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=782;Dels=0.00;HRun=0;HaplotypeScore=12.97;MQ=98.10;MQ0=0;OQ=14528.13;QD=18.58;RankSumP=0.426484;SB=-4298.34;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.995G>T;refseq.codonCoord=332;refseq.end=150552991;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1031;refseq.name=NM_002016;refseq.name2=FLG;refseq.positionType=CDS;refseq.proteinCoordStr=p.G332V;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=857;refseq.start=150552991;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 150589756 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=422;Dels=0.00;HRun=1;HaplotypeScore=17.11;MQ=98.83;MQ0=0;OQ=7508.77;QD=17.79;RankSumP=0.218105;SB=-1871.68;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7130C>A;refseq.codonCoord=2377;refseq.end=150589756;refseq.frame=1;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=7203;refseq.name=NM_001014342;refseq.name2=FLG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2377*;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-1920;refseq.start=150589756;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=Intersection GT 0/1
|
|
chr1 150592356 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1470;Dels=0.00;HRun=1;HaplotypeScore=35.33;MQ=93.31;MQ0=11;OQ=31311.26;QD=21.30;RankSumP=0.237335;SB=-11512.48;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4530C>T;refseq.codonCoord=1510;refseq.end=150592356;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4603;refseq.name=NM_001014342;refseq.name2=FLG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1510H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=4392;refseq.start=150592356;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap-filterIngatk GT 1/0
|
|
chr1 150594093 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1339;Dels=0.00;HRun=1;HaplotypeScore=31.58;MQ=86.17;MQ0=42;OQ=18005.81;QD=13.45;RankSumP=0.0613222;SB=-5765.30;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2793G>A;refseq.codonCoord=931;refseq.end=150594093;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2866;refseq.name=NM_001014342;refseq.name2=FLG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q931Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=2655;refseq.start=150594093;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 0/1
|
|
chr1 150594126 . A G 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=943;Dels=0.00;HRun=1;HaplotypeScore=40.16;MQ=84.48;MQ0=21;OQ=1654.23;QD=1.75;RankSumP=0.00609028;SB=-134.81;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2760T>C;refseq.codonCoord=920;refseq.end=150594126;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2833;refseq.name=NM_001014342;refseq.name2=FLG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S920S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=2622;refseq.start=150594126;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 0/1
|
|
chr1 150595035 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=929;Dels=0.00;HRun=0;HaplotypeScore=2.27;MQ=48.76;MQ0=170;OQ=6355.68;QD=6.84;RankSumP=0.322052;SB=61.56;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1851T>C;refseq.codonCoord=617;refseq.end=150595035;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1924;refseq.name=NM_001014342;refseq.name2=FLG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S617S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=1713;refseq.start=150595035;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 150596059 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=618;Dels=0.00;HRun=2;HaplotypeScore=15.76;MQ=98.75;MQ0=0;OQ=14032.03;QD=22.71;RankSumP=0.0791536;SB=-3472.83;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.827G>A;refseq.codonCoord=276;refseq.end=150596059;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=900;refseq.name=NM_001014342;refseq.name2=FLG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R276Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=689;refseq.start=150596059;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 0/1
|
|
chr1 150597864 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.79;MQ=98.77;MQ0=0;OQ=1336.47;QD=21.21;RankSumP=0.148818;SB=-380.40;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.121C>T;refseq.codonCoord=41;refseq.end=150597864;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=194;refseq.name=NM_001014342;refseq.name2=FLG2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L41F;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=-18;refseq.start=150597864;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/0
|
|
chr1 150648744 . C T 182.22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=342;Dels=0.00;HRun=1;HaplotypeScore=3.79;MQ=98.88;MQ0=0;OQ=5648.60;QD=16.52;RankSumP=0.485755;SB=-2248.99;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1438G>A;refseq.codonCoord=480;refseq.end=150648744;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1512;refseq.name=NM_016190;refseq.name2=CRNN;refseq.positionType=CDS;refseq.proteinCoordStr=p.G480S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-402;refseq.start=150648744;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 150750753 . G A 377.34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=97.43;MQ0=0;OQ=2232.49;QD=36.01;RankSumP=1.00000;SB=-848.97;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.119G>A;refseq.codonCoord=40;refseq.end=150750753;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=295;refseq.name=NM_178438;refseq.name2=LCE5A;refseq.positionType=CDS;refseq.proteinCoordStr=p.C40Y;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=140;refseq.start=150750753;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 150754603 . C T 62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=98.68;MQ0=0;OQ=810.35;QD=30.01;RankSumP=1.00000;SB=-228.35;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.120C>T;refseq.codonCoord=40;refseq.end=150754603;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=193;refseq.name=NM_019060;refseq.name2=CRCT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C40C;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=142;refseq.start=150754603;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/1
|
|
chr1 150754687 . C T 68.08 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=96.57;MQ0=0;OQ=679.29;QD=22.64;RankSumP=1.00000;SB=-85.11;SecondBestBaseQ=4;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.204C>T;refseq.codonCoord=68;refseq.end=150754687;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=277;refseq.name=NM_019060;refseq.name2=CRCT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R68R;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=226;refseq.start=150754687;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/1
|
|
chr1 150818909 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=3.98;MQ=54.92;MQ0=50;OQ=1022.35;QD=9.47;RankSumP=0.393591;SB=-525.91;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.128G>T;refseq.codonCoord=43;refseq.end=150818909;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=185;refseq.name=NM_032563;refseq.name2=LCE3D;refseq.positionType=CDS;refseq.proteinCoordStr=p.G43V;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=149;refseq.start=150818909;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 150839987 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=3.65876e-07;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.156C>G;refseq.codonCoord=52;refseq.end=150839987;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=226;refseq.name=NM_178434;refseq.name2=LCE3C;refseq.positionType=CDS;refseq.proteinCoordStr=p.C52W;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-200;refseq.start=150839987;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 1/0
|
|
chr1 150853144 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.234T>G;refseq.codonCoord=78;refseq.end=150853144;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=234;refseq.name=NM_178433;refseq.name2=LCE3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.S78R;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-55;refseq.start=150853144;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=FilteredInAll GT 1/0
|
|
chr1 150903467 . A T 113.10 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=11.16;MQ=68.92;MQ0=3;OQ=1771.29;QD=14.40;RankSumP=0.0341016;SB=-898.84;SecondBestBaseQ=24;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.262A>T;refseq.codonCoord=88;refseq.end=150903467;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=317;refseq.name=NM_178430;refseq.name2=LCE2D;refseq.positionType=CDS;refseq.proteinCoordStr=p.S88C;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=283;refseq.start=150903467;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 0/1
|
|
chr1 150948319 . T C 88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=0;RankSumP=0.619519;SecondBestBaseQ=19;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.144T>C;refseq.codonCoord=48;refseq.end=150948319;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=173;refseq.name=NM_178356;refseq.name2=LCE4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.C48C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=173;refseq.start=150948319;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=soap GT 1/0
|
|
chr1 150948320 . G T 41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.543454;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.145G>T;refseq.codonCoord=49;refseq.end=150948320;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=174;refseq.name=NM_178356;refseq.name2=LCE4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G49C;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=174;refseq.start=150948320;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=soap GT 0/1
|
|
chr1 150998717 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=1.10651e-08;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.29G>C;refseq.codonCoord=10;refseq.end=150998717;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=87;refseq.name=NM_001025231;refseq.name2=KPRP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R10P;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=57;refseq.start=150998717;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 150999060 . G C 78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=2506.49;QD=47.29;RankSumP=1.00000;SB=-826.97;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.372G>C;refseq.codonCoord=124;refseq.end=150999060;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=430;refseq.name=NM_001025231;refseq.name2=KPRP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A124A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=400;refseq.start=150999060;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 150999925 . T A 317.25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=236;Dels=0.00;HRun=1;HaplotypeScore=5.62;MQ=98.58;MQ0=0;OQ=9518.18;QD=40.33;RankSumP=1.00000;SB=-4502.68;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1237T>A;refseq.codonCoord=413;refseq.end=150999925;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1295;refseq.name=NM_001025231;refseq.name2=KPRP;refseq.positionType=CDS;refseq.proteinCoordStr=p.C413S;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-1229;refseq.start=150999925;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 151026574 . A G 10.85 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=6.54;MQ=56.39;MQ0=21;OQ=529.51;QD=10.59;RankSumP=1.00000;SB=-67.19;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.175A>G;refseq.codonCoord=59;refseq.end=151026574;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=228;refseq.name=NM_178353;refseq.name2=LCE1E;refseq.positionType=CDS;refseq.proteinCoordStr=p.S59G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=197;refseq.start=151026574;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=filterInsoap-gatk GT 1/1
|
|
chr1 151044492 . A G 78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=51;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=66.86;MQ0=4;OQ=1885.41;QD=36.97;RankSumP=1.00000;SB=-746.30;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.87T>C;refseq.codonCoord=29;refseq.end=151044492;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=138;refseq.name=NM_178351;refseq.name2=LCE1C;refseq.positionType=CDS;refseq.proteinCoordStr=p.C29C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=107;refseq.start=151044492;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=soap-filterIngatk GT 1/1
|
|
chr1 151051794 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=51.17;MQ0=20;OQ=672.83;QD=9.89;RankSumP=0.622546;SB=-294.19;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.248G>A;refseq.codonCoord=83;refseq.end=151051794;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=724;refseq.name=NM_178349;refseq.name2=LCE1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.R83H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-416;refseq.start=151051794;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 151150156 . T G 16 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=2;RankSumP=0.0178571;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1259T>G;refseq.codonCoord=420;refseq.end=151150156;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1305;refseq.name=NM_005547;refseq.name2=IVL;refseq.positionType=CDS;refseq.proteinCoordStr=p.V420G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-831;refseq.start=151150156;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 151150159 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.0571429;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1262A>G;refseq.codonCoord=421;refseq.end=151150159;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1308;refseq.name=NM_005547;refseq.name2=IVL;refseq.positionType=CDS;refseq.proteinCoordStr=p.E421G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-828;refseq.start=151150159;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 151211218 . C T 190.81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=196;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=98.85;MQ0=0;OQ=2944.34;QD=15.02;RankSumP=0.309177;SB=-507.93;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.228C>T;refseq.codonCoord=76;refseq.end=151211218;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=291;refseq.name=NM_173080;refseq.name2=SPRR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S76S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=248;refseq.start=151211218;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 151224456 . C A 99.19 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=145;Dels=0.00;HRun=1;HaplotypeScore=5.55;MQ=62.84;MQ0=18;OQ=1730.02;QD=11.93;RankSumP=0.265598;SB=-790.13;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.126C>A;refseq.codonCoord=42;refseq.end=151224456;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=190;refseq.name=NM_005987;refseq.name2=SPRR1A;refseq.positionType=CDS;refseq.proteinCoordStr=p.H42Q;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=145;refseq.start=151224456;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 151224511 . G A 289.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=127;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=85.34;MQ0=2;OQ=2226.43;QD=17.53;RankSumP=0.0149564;SB=-934.45;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.181G>A;refseq.codonCoord=61;refseq.end=151224511;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=245;refseq.name=NM_005987;refseq.name2=SPRR1A;refseq.positionType=CDS;refseq.proteinCoordStr=p.V61I;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=200;refseq.start=151224511;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 151242119 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=296;Dels=0.00;HRun=2;HaplotypeScore=3.07;MQ=98.59;MQ0=0;OQ=5042.44;QD=17.04;RankSumP=0.456455;SB=-1409.25;SecondBestBaseQ=32;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.-2G>A;refseq.codingCoordStr_2=c.-2G>A;refseq.end_1=151242119;refseq.end_2=151242119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.mrnaCoord_1=65;refseq.mrnaCoord_2=149;refseq.name2_1=SPRR3;refseq.name2_2=SPRR3;refseq.name_1=NM_001097589;refseq.name_2=NM_005416;refseq.numMatchingRecords=2;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.spliceDist_1=18;refseq.spliceDist_2=18;refseq.start_1=151242119;refseq.start_2=151242119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;set=Intersection GT 1/0
|
|
chr1 151242339 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=222;Dels=0.00;HRun=1;HaplotypeScore=33.79;MQ=46.82;MQ0=38;OQ=372.23;QD=1.68;RankSumP=0.677214;SB=-133.81;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.219C>T;refseq.codingCoordStr_2=c.219C>T;refseq.codonCoord_1=73;refseq.codonCoord_2=73;refseq.end_1=151242339;refseq.end_2=151242339;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=285;refseq.mrnaCoord_2=369;refseq.name2_1=SPRR3;refseq.name2_2=SPRR3;refseq.name_1=NM_001097589;refseq.name_2=NM_005416;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G73G;refseq.proteinCoordStr_2=p.G73G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=238;refseq.spliceDist_2=238;refseq.start_1=151242339;refseq.start_2=151242339;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=soap-filterIngatk GT 0/1
|
|
chr1 151242387 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=329;Dels=0.00;HRun=0;HaplotypeScore=10.75;MQ=46.39;MQ0=84;OQ=4132.25;QD=12.56;RankSumP=0.488556;SB=-1670.77;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.267C>A;refseq.codingCoordStr_2=c.267C>A;refseq.codonCoord_1=89;refseq.codonCoord_2=89;refseq.end_1=151242387;refseq.end_2=151242387;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=333;refseq.mrnaCoord_2=417;refseq.name2_1=SPRR3;refseq.name2_2=SPRR3;refseq.name_1=NM_001097589;refseq.name_2=NM_005416;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G89G;refseq.proteinCoordStr_2=p.G89G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=286;refseq.spliceDist_2=286;refseq.start_1=151242387;refseq.start_2=151242387;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;set=Intersection GT 1/0
|
|
chr1 151242453 . A G 239.29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=328;Dels=0.00;HRun=0;HaplotypeScore=3.76;MQ=91.73;MQ0=4;OQ=6261.42;QD=19.09;RankSumP=0.0193783;SB=-2307.19;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.333A>G;refseq.codingCoordStr_2=c.333A>G;refseq.codonCoord_1=111;refseq.codonCoord_2=111;refseq.end_1=151242453;refseq.end_2=151242453;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=399;refseq.mrnaCoord_2=483;refseq.name2_1=SPRR3;refseq.name2_2=SPRR3;refseq.name_1=NM_001097589;refseq.name_2=NM_005416;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E111E;refseq.proteinCoordStr_2=p.E111E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=352;refseq.spliceDist_2=352;refseq.start_1=151242453;refseq.start_2=151242453;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 0/1
|
|
chr1 151242565 . C G 266.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=172;Dels=0.00;HRun=1;HaplotypeScore=3.33;MQ=98.57;MQ0=0;OQ=3209.03;QD=18.66;RankSumP=0.439278;SB=-1371.14;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.445C>G;refseq.codingCoordStr_2=c.445C>G;refseq.codonCoord_1=149;refseq.codonCoord_2=149;refseq.end_1=151242565;refseq.end_2=151242565;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=511;refseq.mrnaCoord_2=595;refseq.name2_1=SPRR3;refseq.name2_2=SPRR3;refseq.name_1=NM_001097589;refseq.name_2=NM_005416;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L149V;refseq.proteinCoordStr_2=p.L149V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTA;refseq.referenceCodon_2=CTA;refseq.spliceDist_1=-392;refseq.spliceDist_2=-392;refseq.start_1=151242565;refseq.start_2=151242565;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=Intersection GT 1/0
|
|
chr1 151271472 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=154;Dels=0.00;HRun=2;HaplotypeScore=9.54;MQ=94.30;MQ0=0;OQ=1705.83;QD=11.08;RankSumP=0.0912653;SB=-563.90;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.27T>C;refseq.codonCoord=9;refseq.end=151271472;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=91;refseq.name=NM_003125;refseq.name2=SPRR1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P9P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=46;refseq.start=151271472;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/0
|
|
chr1 151271477 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=153;Dels=0.00;HRun=0;HaplotypeScore=10.02;MQ=93.26;MQ0=0;OQ=1724.28;QD=11.27;RankSumP=0.0169401;SB=-368.25;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.32C>T;refseq.codonCoord=11;refseq.end=151271477;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=96;refseq.name=NM_003125;refseq.name2=SPRR1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T11I;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=51;refseq.start=151271477;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 0/1
|
|
chr1 151271607 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=154;Dels=0.00;HRun=0;HaplotypeScore=11.40;MQ=64.95;MQ0=38;OQ=1659.68;QD=10.78;RankSumP=0.418701;SB=-766.63;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.162C>T;refseq.codonCoord=54;refseq.end=151271607;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=226;refseq.name=NM_003125;refseq.name2=SPRR1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P54P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=181;refseq.start=151271607;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 151295653 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=4;RankSumP=0.00000;SecondBestBaseQ=16;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.183A>C;refseq.codonCoord=61;refseq.end=151295653;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=244;refseq.name=NM_005988;refseq.name2=SPRR2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.P61P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=202;refseq.start=151295653;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 151295761 . C T 81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=516;Dels=0.00;HRun=1;HaplotypeScore=7.84;MQ=27.94;MQ0=464;OQ=1204.95;QD=2.34;RankSumP=0.619048;SB=-40.54;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.75G>A;refseq.codonCoord=25;refseq.end=151295761;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=136;refseq.name=NM_005988;refseq.name2=SPRR2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.E25E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=94;refseq.start=151295761;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 151309757 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=4;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.183A>C;refseq.codonCoord=61;refseq.end=151309757;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=246;refseq.name=NM_001017418;refseq.name2=SPRR2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P61P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=199;refseq.start=151309757;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 151351651 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=4;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.183A>C;refseq.codonCoord=61;refseq.end=151351651;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=242;refseq.name=NM_001014450;refseq.name2=SPRR2F;refseq.positionType=CDS;refseq.proteinCoordStr=p.P61P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=202;refseq.start=151351651;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 151500134 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=1.39;MQ=96.01;MQ0=0;OQ=247.11;QD=10.30;RankSumP=0.532638;SB=-10.00;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.85A>G;refseq.codonCoord=29;refseq.end=151500134;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=139;refseq.name=NM_000427;refseq.name2=LOR;refseq.positionType=CDS;refseq.proteinCoordStr=p.S29G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=108;refseq.start=151500134;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 151542996 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.490A>C;refseq.codonCoord=164;refseq.end=151542996;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=543;refseq.name=NM_052891;refseq.name2=PGLYRP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T164P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-40;refseq.start=151542996;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 151544047 . C T 173.15 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=189;Dels=0.00;HRun=1;HaplotypeScore=2.31;MQ=98.61;MQ0=0;OQ=2812.10;QD=14.88;RankSumP=0.424055;SB=-823.16;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.376G>A;refseq.codonCoord=126;refseq.end=151544047;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=429;refseq.name=NM_052891;refseq.name2=PGLYRP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.G126S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-1;refseq.spliceInfo=splice-donor_-1;refseq.start=151544047;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 151546320 . C T 133.63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=8.07;MQ=97.87;MQ0=0;OQ=1271.60;QD=17.42;RankSumP=0.245424;SB=-271.79;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.103G>A;refseq.codonCoord=35;refseq.end=151546320;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=156;refseq.name=NM_052891;refseq.name2=PGLYRP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A35T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=48;refseq.start=151546320;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 151579668 . C T 125.09 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=149;Dels=0.00;HRun=0;HaplotypeScore=11.31;MQ=98.87;MQ0=0;OQ=2001.92;QD=13.44;RankSumP=0.147130;SB=-511.96;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.637G>A;refseq.codonCoord=213;refseq.end=151579668;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=702;refseq.name=NM_020393;refseq.name2=PGLYRP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V213I;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=12;refseq.start=151579668;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 151580777 . C A 281.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=177;Dels=0.00;HRun=0;HaplotypeScore=3.32;MQ=98.14;MQ0=0;OQ=2748.88;QD=15.53;RankSumP=0.131710;SB=-1268.34;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.575G>T;refseq.codonCoord=192;refseq.end=151580777;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=640;refseq.name=NM_020393;refseq.name2=PGLYRP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G192V;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-51;refseq.start=151580777;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 151582203 . A G 328.77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=164;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.45;MQ0=0;OQ=6039.76;QD=36.83;RankSumP=1.00000;SB=-442.51;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.459T>C;refseq.codonCoord=153;refseq.end=151582203;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=524;refseq.name=NM_020393;refseq.name2=PGLYRP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.F153F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=-14;refseq.start=151582203;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 151586996 . T G 166.44 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=6.26;MQ=98.64;MQ0=0;OQ=1545.55;QD=13.44;RankSumP=0.326671;SB=-559.93;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.37A>C;refseq.codonCoord=13;refseq.end=151586996;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=102;refseq.name=NM_020393;refseq.name2=PGLYRP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.I13L;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-13;refseq.start=151586996;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/0
|
|
chr1 151587025 . G A 186.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=139;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=98.47;MQ0=0;OQ=3018.57;QD=21.72;RankSumP=0.162146;SB=-1487.81;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8C>T;refseq.codonCoord=3;refseq.end=151587025;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=73;refseq.name=NM_020393;refseq.name2=PGLYRP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P3L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-42;refseq.start=151587025;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/0
|
|
chr1 151657250 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=756;Dels=0.00;HRun=0;HaplotypeScore=18.90;MQ=76.82;MQ0=40;OQ=14508.61;QD=19.19;RankSumP=0.216945;SB=-5404.52;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.68G>A;refseq.codonCoord=23;refseq.end=151657250;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=125;refseq.name=NM_176823;refseq.name2=S100A7A;refseq.positionType=CDS;refseq.proteinCoordStr=p.R23H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-74;refseq.start=151657250;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 151698030 . C G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=915;Dels=0.00;HRun=0;HaplotypeScore=22.18;MQ=89.22;MQ0=15;OQ=37299.09;QD=40.76;RankSumP=1.00000;SB=-16388.27;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.84G>C;refseq.codonCoord=28;refseq.end=151698030;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=155;refseq.name=NM_002963;refseq.name2=S100A7;refseq.positionType=CDS;refseq.proteinCoordStr=p.E28D;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-58;refseq.start=151698030;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 151698059 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DP=890;Dels=0.00;HRun=1;HaplotypeScore=23.68;MQ=81.69;MQ0=76;OQ=14886.71;QD=16.73;RankSumP=0.0620996;SB=-3638.49;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.55A>C;refseq.codonCoord=19;refseq.end=151698059;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=126;refseq.name=NM_002963;refseq.name2=S100A7;refseq.positionType=CDS;refseq.proteinCoordStr=p.K19Q;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=72;refseq.start=151698059;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 151776514 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=533;Dels=0.00;HRun=1;HaplotypeScore=13.78;MQ=98.85;MQ0=0;OQ=9854.34;QD=18.49;RankSumP=0.201487;SB=-3807.14;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.215A>G;refseq.codonCoord=72;refseq.end=151776514;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=443;refseq.name=NM_002962;refseq.name2=S100A5;refseq.positionType=CDS;refseq.proteinCoordStr=p.D72G;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=23;refseq.start=151776514;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/0
|
|
chr1 151986156 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.418A>C;refseq.codonCoord=140;refseq.end=151986156;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=962;refseq.name=NM_023015;refseq.name2=INTS3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T140P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-15;refseq.start=151986156;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 151998677 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1201T>G;refseq.codonCoord=401;refseq.end=151998677;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1745;refseq.name=NM_023015;refseq.name2=INTS3;refseq.positionType=CDS;refseq.proteinCoordStr=p.F401V;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-37;refseq.start=151998677;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=FilteredInAll GT 1/0
|
|
chr1 151999450 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=4;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1277A>C;refseq.codonCoord=426;refseq.end=151999450;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1821;refseq.name=NM_023015;refseq.name2=INTS3;refseq.positionType=CDS;refseq.proteinCoordStr=p.H426P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=40;refseq.start=151999450;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 152014861 . G C 70 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=1;RankSumP=1.06503e-05;SecondBestBaseQ=10;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.405G>C;refseq.codonCoord=135;refseq.end=152014861;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=470;refseq.name=NM_024330;refseq.name2=SLC27A3;refseq.positionType=CDS;refseq.proteinCoordStr=p.S135S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-404;refseq.start=152014861;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 0/1
|
|
chr1 152191317 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.798A>C;refseq.codonCoord=266;refseq.end=152191317;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=868;refseq.name=NM_181715;refseq.name2=CRTC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P266P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=46;refseq.start=152191317;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 152192702 . T C 175.87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=150;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=99.00;MQ0=0;OQ=2423.05;QD=16.15;RankSumP=0.170254;SB=-865.57;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.439A>G;refseq.codonCoord=147;refseq.end=152192702;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=509;refseq.name=NM_181715;refseq.name2=CRTC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.M147V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=5;refseq.spliceInfo=splice-acceptor_5;refseq.start=152192702;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 152199485 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.688T>G;refseq.codonCoord=230;refseq.end=152199485;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1154;refseq.name=NM_014437;refseq.name2=SLC39A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L230V;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=370;refseq.start=152199485;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT 0/1
|
|
chr1 152208138 . C T 276.63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=434;Dels=0.00;HRun=0;HaplotypeScore=6.67;MQ=98.82;MQ0=0;OQ=7531.67;QD=17.35;RankSumP=0.0120434;SB=-3041.12;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.283C>T;refseq.codonCoord=95;refseq.end=152208138;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=551;refseq.name=NM_130898;refseq.name2=CREB3L4;refseq.positionType=CDS;refseq.proteinCoordStr=p.P95S;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=109;refseq.start=152208138;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 0/1
|
|
chr1 152261271 . C T 152.87 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.48;MQ=99.00;MQ0=0;OQ=1028.24;QD=14.90;RankSumP=0.470616;SB=-192.27;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4471G>A;refseq.codingCoordStr_2=c.4471G>A;refseq.codonCoord_1=1491;refseq.codonCoord_2=1491;refseq.end_1=152261271;refseq.end_2=152261271;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4543;refseq.mrnaCoord_2=4543;refseq.name2_1=NUP210L;refseq.name2_2=NUP210L;refseq.name_1=NM_001159484;refseq.name_2=NM_207308;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V1491I;refseq.proteinCoordStr_2=p.V1491I;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=-46;refseq.spliceDist_2=-46;refseq.start_1=152261271;refseq.start_2=152261271;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;set=Intersection GT 0/1
|
|
chr1 152328606 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2276A>C;refseq.codingCoordStr_2=c.2276A>C;refseq.codonCoord_1=759;refseq.codonCoord_2=759;refseq.end_1=152328606;refseq.end_2=152328606;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2348;refseq.mrnaCoord_2=2348;refseq.name2_1=NUP210L;refseq.name2_2=NUP210L;refseq.name_1=NM_001159484;refseq.name_2=NM_207308;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H759P;refseq.proteinCoordStr_2=p.H759P;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=-86;refseq.spliceDist_2=-86;refseq.start_1=152328606;refseq.start_2=152328606;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 152375011 . G A 291.15 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=301;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=98.85;MQ0=0;OQ=12331.36;QD=40.97;RankSumP=1.00000;SB=-4788.46;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.912C>T;refseq.codingCoordStr_2=c.912C>T;refseq.codonCoord_1=304;refseq.codonCoord_2=304;refseq.end_1=152375011;refseq.end_2=152375011;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=984;refseq.mrnaCoord_2=984;refseq.name2_1=NUP210L;refseq.name2_2=NUP210L;refseq.name_1=NM_001159484;refseq.name_2=NM_207308;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N304N;refseq.proteinCoordStr_2=p.N304N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=62;refseq.spliceDist_2=62;refseq.start_1=152375011;refseq.start_2=152375011;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 1/1
|
|
chr1 152496513 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2421A>C;refseq.codingCoordStr_2=c.2421A>C;refseq.codonCoord_1=807;refseq.codonCoord_2=807;refseq.end_1=152496513;refseq.end_2=152496513;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2527;refseq.mrnaCoord_2=2588;refseq.name2_1=UBAP2L;refseq.name2_2=UBAP2L;refseq.name_1=NM_001127320;refseq.name_2=NM_014847;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P807P;refseq.proteinCoordStr_2=p.P807P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=-22;refseq.spliceDist_2=-22;refseq.start_1=152496513;refseq.start_2=152496513;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 152563398 . T G 36 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=3.70414e-08;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.724T>G;refseq.codonCoord=242;refseq.end=152563398;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=764;refseq.name=NM_080429;refseq.name2=AQP10;refseq.positionType=CDS;refseq.proteinCoordStr=p.W242G;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=17;refseq.start=152563398;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 152576672 . C G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=731;Dels=0.00;HRun=0;HaplotypeScore=18.52;MQ=98.83;MQ0=0;OQ=34583.86;QD=47.31;RankSumP=1.00000;SB=-9763.65;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1062C>G;refseq.codonCoord_2=354;refseq.end_1=152579943;refseq.end_2=152576672;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1242;refseq.name2_1=ATP8B2;refseq.name2_2=ATP8B2;refseq.name_1=NM_020452;refseq.name_2=NM_001005855;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.L354L;refseq.referenceAA_2=Leu;refseq.referenceCodon_2=CTC;refseq.spliceDist_2=225;refseq.start_1=152576655;refseq.start_2=152576672;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Leu;refseq.variantCodon_2=CTG;set=Intersection GT 1/1
|
|
chr1 152583777 . C T 351.24 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=315;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=98.63;MQ0=0;OQ=13237.75;QD=42.02;RankSumP=1.00000;SB=-4255.30;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2277C>T;refseq.codonCoord=759;refseq.end=152583777;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2277;refseq.name=NM_020452;refseq.name2=ATP8B2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S759S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=37;refseq.start=152583777;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 152668303 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=253;Dels=0.00;HRun=1;HaplotypeScore=38.07;MQ=98.63;MQ0=0;OQ=4221.90;QD=16.69;RankSumP=0.433014;SB=-1513.73;SecondBestBaseQ=24;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.93G>A;refseq.codingCoordStr_2=c.93G>A;refseq.codonCoord_1=31;refseq.codonCoord_2=31;refseq.end_1=152668303;refseq.end_2=152668303;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=530;refseq.mrnaCoord_2=530;refseq.name2_1=IL6R;refseq.name2_2=IL6R;refseq.name_1=NM_000565;refseq.name_2=NM_181359;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A31A;refseq.proteinCoordStr_2=p.A31A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=152668303;refseq.start_2=152668303;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 1/0
|
|
chr1 152693594 . A C 127.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.59;MQ0=0;OQ=1304.93;QD=17.63;RankSumP=0.476053;SB=-360.86;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.1073A>C;refseq.codonCoord_2=358;refseq.end_1=152704223;refseq.end_2=152693594;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1510;refseq.name2_1=IL6R;refseq.name2_2=IL6R;refseq.name_1=NM_181359;refseq.name_2=NM_000565;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.D358A;refseq.referenceAA_2=Asp;refseq.referenceCodon_2=GAT;refseq.spliceDist_2=7;refseq.spliceInfo_2=splice-acceptor_7;refseq.start_1=152689091;refseq.start_2=152693594;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ala;refseq.variantCodon_2=GCT;set=Intersection GT 0/1
|
|
chr1 152740755 . C G 247.65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=3.85;MQ=97.13;MQ0=0;OQ=1593.58;QD=19.20;RankSumP=0.0656493;SB=-450.76;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.372G>C;refseq.codonCoord=124;refseq.end=152740755;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=459;refseq.name=NM_001010846;refseq.name2=SHE;refseq.positionType=CDS;refseq.proteinCoordStr=p.R124R;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-220;refseq.start=152740755;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/0
|
|
chr1 152781160 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.406A>C;refseq.codingCoordStr_2=c.406A>C;refseq.codonCoord_1=136;refseq.codonCoord_2=136;refseq.end_1=152781160;refseq.end_2=152781160;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1244;refseq.mrnaCoord_2=1244;refseq.name2_1=TDRD10;refseq.name2_2=TDRD10;refseq.name_1=NM_001098475;refseq.name_2=NM_182499;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T136P;refseq.proteinCoordStr_2=p.T136P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-7;refseq.spliceDist_2=-7;refseq.spliceInfo_1=splice-donor_-7;refseq.spliceInfo_2=splice-donor_-7;refseq.start_1=152781160;refseq.start_2=152781160;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 152783101 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=840;Dels=0.00;HRun=1;HaplotypeScore=13.87;MQ=98.69;MQ0=0;OQ=16493.64;QD=19.64;RankSumP=0.489171;SB=-5074.72;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.542G>A;refseq.codingCoordStr_2=c.542G>A;refseq.codonCoord_1=181;refseq.codonCoord_2=181;refseq.end_1=152783101;refseq.end_2=152783101;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1380;refseq.mrnaCoord_2=1380;refseq.name2_1=TDRD10;refseq.name2_2=TDRD10;refseq.name_1=NM_001098475;refseq.name_2=NM_182499;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R181Q;refseq.proteinCoordStr_2=p.R181Q;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.spliceDist_1=39;refseq.spliceDist_2=39;refseq.start_1=152783101;refseq.start_2=152783101;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;set=Intersection GT 1/0
|
|
chr1 152783195 . T C 296.61 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=223;Dels=0.00;HRun=1;HaplotypeScore=5.94;MQ=98.71;MQ0=0;OQ=8648.65;QD=38.78;RankSumP=1.00000;SB=-1944.43;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.636T>C;refseq.codingCoordStr_2=c.636T>C;refseq.codonCoord_1=212;refseq.codonCoord_2=212;refseq.end_1=152783195;refseq.end_2=152783195;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1474;refseq.mrnaCoord_2=1474;refseq.name2_1=TDRD10;refseq.name2_2=TDRD10;refseq.name_1=NM_001098475;refseq.name_2=NM_182499;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A212A;refseq.proteinCoordStr_2=p.A212A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-16;refseq.spliceDist_2=-16;refseq.start_1=152783195;refseq.start_2=152783195;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/1
|
|
chr1 152794985 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.407T>G;refseq.codonCoord=136;refseq.end=152794985;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=498;refseq.name=NM_017582;refseq.name2=UBE2Q1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V136G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-26;refseq.start=152794985;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 152808595 . T G 30.49 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=134;Dels=0.00;HRun=2;HaplotypeScore=11.63;MQ=98.55;MQ0=0;QD=0.23;RankSumP=0.00000;SB=179.54;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.98T>G;refseq.codonCoord=33;refseq.end=152808595;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=362;refseq.name=NM_000748;refseq.name2=CHRNB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V33G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=34;refseq.start=152808595;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 152840591 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=895;Dels=0.00;HRun=0;HaplotypeScore=8.93;MQ=98.61;MQ0=0;OQ=37294.36;QD=41.67;RankSumP=1.00000;SB=-18127.08;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.266A>G;refseq.codingCoordStr_2=c.1151A>G;refseq.codingCoordStr_3=c.1151A>G;refseq.codingCoordStr_4=c.1151A>G;refseq.codonCoord_1=89;refseq.codonCoord_2=384;refseq.codonCoord_3=384;refseq.codonCoord_4=384;refseq.end_1=152840591;refseq.end_2=152840591;refseq.end_3=152840591;refseq.end_4=152840591;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1243;refseq.mrnaCoord_2=1351;refseq.mrnaCoord_3=1351;refseq.mrnaCoord_4=1351;refseq.name2_1=ADAR;refseq.name2_2=ADAR;refseq.name2_3=ADAR;refseq.name2_4=ADAR;refseq.name_1=NM_001025107;refseq.name_2=NM_001111;refseq.name_3=NM_015840;refseq.name_4=NM_015841;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.K89R;refseq.proteinCoordStr_2=p.K384R;refseq.proteinCoordStr_3=p.K384R;refseq.proteinCoordStr_4=p.K384R;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceAA_3=Lys;refseq.referenceAA_4=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.referenceCodon_3=AAA;refseq.referenceCodon_4=AAA;refseq.spliceDist_1=-451;refseq.spliceDist_2=-451;refseq.spliceDist_3=-451;refseq.spliceDist_4=-451;refseq.start_1=152840591;refseq.start_2=152840591;refseq.start_3=152840591;refseq.start_4=152840591;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantCodon_1=AGA;refseq.variantCodon_2=AGA;refseq.variantCodon_3=AGA;refseq.variantCodon_4=AGA;set=soap-filterIngatk GT 1/1
|
|
chr1 152841444 . T C 157.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=346;Dels=0.00;HRun=1;HaplotypeScore=8.29;MQ=98.83;MQ0=0;OQ=12115.29;QD=35.02;RankSumP=1.00000;SB=-4474.11;SecondBestBaseQ=34;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.-588A>G;refseq.codingCoordStr_2=c.298A>G;refseq.codingCoordStr_3=c.298A>G;refseq.codingCoordStr_4=c.298A>G;refseq.codonCoord_2=100;refseq.codonCoord_3=100;refseq.codonCoord_4=100;refseq.end_1=152841444;refseq.end_2=152841444;refseq.end_3=152841444;refseq.end_4=152841444;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=390;refseq.mrnaCoord_2=498;refseq.mrnaCoord_3=498;refseq.mrnaCoord_4=498;refseq.name2_1=ADAR;refseq.name2_2=ADAR;refseq.name2_3=ADAR;refseq.name2_4=ADAR;refseq.name_1=NM_001025107;refseq.name_2=NM_001111;refseq.name_3=NM_015840;refseq.name_4=NM_015841;refseq.numMatchingRecords=4;refseq.positionType_1=utr5;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.R100G;refseq.proteinCoordStr_3=p.R100G;refseq.proteinCoordStr_4=p.R100G;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_2=AGA;refseq.referenceCodon_3=AGA;refseq.referenceCodon_4=AGA;refseq.spliceDist_1=283;refseq.spliceDist_2=283;refseq.spliceDist_3=283;refseq.spliceDist_4=283;refseq.start_1=152841444;refseq.start_2=152841444;refseq.start_3=152841444;refseq.start_4=152841444;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_2=GGA;refseq.variantCodon_3=GGA;refseq.variantCodon_4=GGA;set=Intersection GT 1/1
|
|
chr1 152841664 . C T 418.50 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=3227.04;QD=39.84;RankSumP=1.00000;SB=-1300.05;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.-808G>A;refseq.codingCoordStr_2=c.78G>A;refseq.codingCoordStr_3=c.78G>A;refseq.codingCoordStr_4=c.78G>A;refseq.codonCoord_2=26;refseq.codonCoord_3=26;refseq.codonCoord_4=26;refseq.end_1=152841664;refseq.end_2=152841664;refseq.end_3=152841664;refseq.end_4=152841664;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=170;refseq.mrnaCoord_2=278;refseq.mrnaCoord_3=278;refseq.mrnaCoord_4=278;refseq.name2_1=ADAR;refseq.name2_2=ADAR;refseq.name2_3=ADAR;refseq.name2_4=ADAR;refseq.name_1=NM_001025107;refseq.name_2=NM_001111;refseq.name_3=NM_015840;refseq.name_4=NM_015841;refseq.numMatchingRecords=4;refseq.positionType_1=utr5;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_2=p.R26R;refseq.proteinCoordStr_3=p.R26R;refseq.proteinCoordStr_4=p.R26R;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_2=AGG;refseq.referenceCodon_3=AGG;refseq.referenceCodon_4=AGG;refseq.spliceDist_1=63;refseq.spliceDist_2=63;refseq.spliceDist_3=63;refseq.spliceDist_4=63;refseq.start_1=152841664;refseq.start_2=152841664;refseq.start_3=152841664;refseq.start_4=152841664;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantCodon_2=AGA;refseq.variantCodon_3=AGA;refseq.variantCodon_4=AGA;set=Intersection GT 1/1
|
|
chr1 152972243 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1450T>G;refseq.codingCoordStr_2=c.535T>G;refseq.codonCoord_1=484;refseq.codonCoord_2=179;refseq.end_1=152972243;refseq.end_2=152972243;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1764;refseq.mrnaCoord_2=685;refseq.name2_1=KCNN3;refseq.name2_2=KCNN3;refseq.name_1=NM_002249;refseq.name_2=NM_170782;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y484D;refseq.proteinCoordStr_2=p.Y179D;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.start_1=152972243;refseq.start_2=152972243;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=FilteredInAll GT 0/1
|
|
chr1 153011431 . C G 297.97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=147;Dels=0.00;HRun=0;HaplotypeScore=9.42;MQ=98.04;MQ0=0;OQ=2471.45;QD=16.81;RankSumP=0.237466;SB=-1037.55;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1092G>C;refseq.codingCoordStr_2=c.177G>C;refseq.codonCoord_1=364;refseq.codonCoord_2=59;refseq.end_1=153011431;refseq.end_2=153011431;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1406;refseq.mrnaCoord_2=327;refseq.name2_1=KCNN3;refseq.name2_2=KCNN3;refseq.name_1=NM_002249;refseq.name_2=NM_170782;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L364L;refseq.proteinCoordStr_2=p.L59L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=63;refseq.spliceDist_2=63;refseq.start_1=153011431;refseq.start_2=153011431;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;set=Intersection GT 1/0
|
|
chr1 153011476 . A G 103.74 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=177;Dels=0.00;HRun=0;HaplotypeScore=7.81;MQ=98.53;MQ0=0;OQ=2105.34;QD=11.89;RankSumP=0.334551;SB=-770.05;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1047T>C;refseq.codingCoordStr_2=c.132T>C;refseq.codonCoord_1=349;refseq.codonCoord_2=44;refseq.end_1=153011476;refseq.end_2=153011476;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1361;refseq.mrnaCoord_2=282;refseq.name2_1=KCNN3;refseq.name2_2=KCNN3;refseq.name_1=NM_002249;refseq.name_2=NM_170782;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N349N;refseq.proteinCoordStr_2=p.N44N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=18;refseq.spliceDist_2=18;refseq.start_1=153011476;refseq.start_2=153011476;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=Intersection GT 0/1
|
|
chr1 153185704 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=97.86;MQ0=0;OQ=724.92;QD=12.50;RankSumP=0.00343892;SB=-127.09;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1070G>A;refseq.codonCoord=357;refseq.end=153185704;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1129;refseq.name=NM_020524;refseq.name2=PBXIP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G357D;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=200;refseq.start=153185704;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=filterInsoap-gatk GT 0/1
|
|
chr1 153204859 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=98.52;MQ0=0;OQ=1092.84;QD=13.33;RankSumP=0.299543;SB=-536.11;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1410C>G;refseq.codingCoordStr_2=c.1077C>G;refseq.codingCoordStr_3=c.1080C>G;refseq.codingCoordStr_4=c.1407C>G;refseq.codonCoord_1=470;refseq.codonCoord_2=359;refseq.codonCoord_3=360;refseq.codonCoord_4=469;refseq.end_1=153204859;refseq.end_2=153204859;refseq.end_3=153204859;refseq.end_4=153204859;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1631;refseq.mrnaCoord_2=1316;refseq.mrnaCoord_3=1319;refseq.mrnaCoord_4=1628;refseq.name2_1=SHC1;refseq.name2_2=SHC1;refseq.name2_3=SHC1;refseq.name2_4=SHC1;refseq.name_1=NM_001130040;refseq.name_2=NM_001130041;refseq.name_3=NM_003029;refseq.name_4=NM_183001;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.R470R;refseq.proteinCoordStr_2=p.R359R;refseq.proteinCoordStr_3=p.R360R;refseq.proteinCoordStr_4=p.R469R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.referenceCodon_3=CGC;refseq.referenceCodon_4=CGC;refseq.spliceDist_1=23;refseq.spliceDist_2=23;refseq.spliceDist_3=23;refseq.spliceDist_4=23;refseq.start_1=153204859;refseq.start_2=153204859;refseq.start_3=153204859;refseq.start_4=153204859;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;refseq.variantCodon_4=CGG;set=Intersection GT 0/1
|
|
chr1 153205286 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=176;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=98.70;MQ0=0;OQ=1972.73;QD=11.21;RankSumP=0.0131940;SB=-367.75;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1228A>G;refseq.codingCoordStr_2=c.898A>G;refseq.codingCoordStr_3=c.898A>G;refseq.codingCoordStr_4=c.1228A>G;refseq.codonCoord_1=410;refseq.codonCoord_2=300;refseq.codonCoord_3=300;refseq.codonCoord_4=410;refseq.end_1=153205286;refseq.end_2=153205286;refseq.end_3=153205286;refseq.end_4=153205286;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1449;refseq.mrnaCoord_2=1137;refseq.mrnaCoord_3=1137;refseq.mrnaCoord_4=1449;refseq.name2_1=SHC1;refseq.name2_2=SHC1;refseq.name2_3=SHC1;refseq.name2_4=SHC1;refseq.name_1=NM_001130040;refseq.name_2=NM_001130041;refseq.name_3=NM_003029;refseq.name_4=NM_183001;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.M410V;refseq.proteinCoordStr_2=p.M300V;refseq.proteinCoordStr_3=p.M300V;refseq.proteinCoordStr_4=p.M410V;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceAA_3=Met;refseq.referenceAA_4=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.referenceCodon_3=ATG;refseq.referenceCodon_4=ATG;refseq.spliceDist_1=-25;refseq.spliceDist_2=-25;refseq.spliceDist_3=-25;refseq.spliceDist_4=-25;refseq.start_1=153205286;refseq.start_2=153205286;refseq.start_3=153205286;refseq.start_4=153205286;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;refseq.variantCodon_3=GTG;refseq.variantCodon_4=GTG;set=Intersection GT 1/0
|
|
chr1 153253924 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.164G>T;refseq.codonCoord=55;refseq.end=153253924;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=322;refseq.name=NM_015872;refseq.name2=ZBTB7B;refseq.positionType=CDS;refseq.proteinCoordStr=p.C55F;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=170;refseq.start=153253924;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 0/1
|
|
chr1 153254150 . C T 272.46 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=229;Dels=0.00;HRun=1;HaplotypeScore=3.86;MQ=98.45;MQ0=0;OQ=3979.85;QD=17.38;RankSumP=0.0559707;SB=-1583.78;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.390C>T;refseq.codonCoord=130;refseq.end=153254150;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=548;refseq.name=NM_015872;refseq.name2=ZBTB7B;refseq.positionType=CDS;refseq.proteinCoordStr=p.I130I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=396;refseq.start=153254150;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 153255581 . A G 70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=8.43;MQ=98.21;MQ0=0;OQ=2082.24;QD=24.50;RankSumP=1.00000;SB=-694.93;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1416A>G;refseq.codonCoord=472;refseq.end=153255581;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1574;refseq.name=NM_015872;refseq.name2=ZBTB7B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P472P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=262;refseq.start=153255581;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 153262544 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=99.00;MQ0=0;OQ=695.30;QD=15.80;RankSumP=0.199840;SB=-148.57;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1884C>T;refseq.codonCoord=628;refseq.end=153262544;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1964;refseq.name=NM_144622;refseq.name2=DCST2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L628L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=14;refseq.start=153262544;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/0
|
|
chr1 153270838 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.575T>C;refseq.codonCoord=192;refseq.end=153270838;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=655;refseq.name=NM_144622;refseq.name2=DCST2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L192P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=34;refseq.start=153270838;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=FilteredInAll GT 0/1
|
|
chr1 153272715 . A G 269.73 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=169;Dels=0.00;HRun=0;HaplotypeScore=6.62;MQ=98.90;MQ0=0;OQ=3077.63;QD=18.21;RankSumP=0.143718;SB=-542.63;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.87T>C;refseq.codonCoord=29;refseq.end=153272715;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=167;refseq.name=NM_144622;refseq.name2=DCST2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G29G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=167;refseq.start=153272715;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 153273623 . C T 114.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.98;MQ=97.40;MQ0=0;OQ=828.64;QD=17.26;RankSumP=0.145686;SB=-369.36;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.150C>T;refseq.codingCoordStr_2=c.150C>T;refseq.codonCoord_1=50;refseq.codonCoord_2=50;refseq.end_1=153273623;refseq.end_2=153273623;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=246;refseq.mrnaCoord_2=246;refseq.name2_1=DCST1;refseq.name2_2=DCST1;refseq.name_1=NM_001143687;refseq.name_2=NM_152494;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L50L;refseq.proteinCoordStr_2=p.L50L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.spliceDist_1=-38;refseq.spliceDist_2=-38;refseq.start_1=153273623;refseq.start_2=153273623;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;set=Intersection GT 0/1
|
|
chr1 153286334 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=282;Dels=0.00;HRun=2;HaplotypeScore=1.63;MQ=98.81;MQ0=0;OQ=4735.42;QD=16.79;RankSumP=0.0817218;SB=-973.77;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1459A>C;refseq.codingCoordStr_2=c.1534A>C;refseq.codonCoord_1=487;refseq.codonCoord_2=512;refseq.end_1=153286334;refseq.end_2=153286334;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1555;refseq.mrnaCoord_2=1630;refseq.name2_1=DCST1;refseq.name2_2=DCST1;refseq.name_1=NM_001143687;refseq.name_2=NM_152494;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.M487L;refseq.proteinCoordStr_2=p.M512L;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=39;refseq.spliceDist_2=39;refseq.start_1=153286334;refseq.start_2=153286334;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 0/1
|
|
chr1 153293566 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=2.27;MQ=98.56;MQ0=0;OQ=1769.80;QD=11.34;RankSumP=0.105118;SB=-802.49;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.572A>C;refseq.codingCoordStr_2=c.572A>C;refseq.codingCoordStr_3=c.572A>C;refseq.codingCoordStr_4=c.572A>C;refseq.codingCoordStr_5=c.572A>C;refseq.codingCoordStr_6=c.572A>C;refseq.codonCoord_1=191;refseq.codonCoord_2=191;refseq.codonCoord_3=191;refseq.codonCoord_4=191;refseq.codonCoord_5=191;refseq.codonCoord_6=191;refseq.end_1=153293566;refseq.end_2=153293566;refseq.end_3=153293566;refseq.end_4=153293566;refseq.end_5=153293566;refseq.end_6=153293566;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=673;refseq.mrnaCoord_2=673;refseq.mrnaCoord_3=673;refseq.mrnaCoord_4=673;refseq.mrnaCoord_5=673;refseq.mrnaCoord_6=673;refseq.name2_1=ADAM15;refseq.name2_2=ADAM15;refseq.name2_3=ADAM15;refseq.name2_4=ADAM15;refseq.name2_5=ADAM15;refseq.name2_6=ADAM15;refseq.name_1=NM_003815;refseq.name_2=NM_207191;refseq.name_3=NM_207194;refseq.name_4=NM_207195;refseq.name_5=NM_207196;refseq.name_6=NM_207197;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.K191T;refseq.proteinCoordStr_2=p.K191T;refseq.proteinCoordStr_3=p.K191T;refseq.proteinCoordStr_4=p.K191T;refseq.proteinCoordStr_5=p.K191T;refseq.proteinCoordStr_6=p.K191T;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceAA_3=Lys;refseq.referenceAA_4=Lys;refseq.referenceAA_5=Lys;refseq.referenceAA_6=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.referenceCodon_3=AAG;refseq.referenceCodon_4=AAG;refseq.referenceCodon_5=AAG;refseq.referenceCodon_6=AAG;refseq.spliceDist_1=-41;refseq.spliceDist_2=-41;refseq.spliceDist_3=-41;refseq.spliceDist_4=-41;refseq.spliceDist_5=-41;refseq.spliceDist_6=-41;refseq.start_1=153293566;refseq.start_2=153293566;refseq.start_3=153293566;refseq.start_4=153293566;refseq.start_5=153293566;refseq.start_6=153293566;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantAA_5=Thr;refseq.variantAA_6=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;refseq.variantCodon_3=ACG;refseq.variantCodon_4=ACG;refseq.variantCodon_5=ACG;refseq.variantCodon_6=ACG;set=Intersection GT 0/1
|
|
chr1 153299430 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=216;Dels=0.00;HRun=3;HaplotypeScore=22.58;MQ=98.01;MQ0=0;OQ=128.78;QD=0.60;RankSumP=0.00000;SB=333.08;SecondBestBaseQ=16;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.2194A>C;refseq.codingCoordStr_2=c.2194A>C;refseq.codingCoordStr_3=c.2194A>C;refseq.codingCoordStr_4=c.2194A>C;refseq.codingCoordStr_5=c.2194A>C;refseq.codingCoordStr_6=c.2194A>C;refseq.codonCoord_1=732;refseq.codonCoord_2=732;refseq.codonCoord_3=732;refseq.codonCoord_4=732;refseq.codonCoord_5=732;refseq.codonCoord_6=732;refseq.end_1=153299430;refseq.end_2=153299430;refseq.end_3=153299430;refseq.end_4=153299430;refseq.end_5=153299430;refseq.end_6=153299430;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=2295;refseq.mrnaCoord_2=2295;refseq.mrnaCoord_3=2295;refseq.mrnaCoord_4=2295;refseq.mrnaCoord_5=2295;refseq.mrnaCoord_6=2295;refseq.name2_1=ADAM15;refseq.name2_2=ADAM15;refseq.name2_3=ADAM15;refseq.name2_4=ADAM15;refseq.name2_5=ADAM15;refseq.name2_6=ADAM15;refseq.name_1=NM_003815;refseq.name_2=NM_207191;refseq.name_3=NM_207194;refseq.name_4=NM_207195;refseq.name_5=NM_207196;refseq.name_6=NM_207197;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.T732P;refseq.proteinCoordStr_2=p.T732P;refseq.proteinCoordStr_3=p.T732P;refseq.proteinCoordStr_4=p.T732P;refseq.proteinCoordStr_5=p.T732P;refseq.proteinCoordStr_6=p.T732P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceAA_6=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.referenceCodon_5=ACC;refseq.referenceCodon_6=ACC;refseq.spliceDist_1=-14;refseq.spliceDist_2=-14;refseq.spliceDist_3=-14;refseq.spliceDist_4=-14;refseq.spliceDist_5=-14;refseq.spliceDist_6=-14;refseq.start_1=153299430;refseq.start_2=153299430;refseq.start_3=153299430;refseq.start_4=153299430;refseq.start_5=153299430;refseq.start_6=153299430;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Pro;refseq.variantAA_6=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;refseq.variantCodon_5=CCC;refseq.variantCodon_6=CCC;set=FilteredInAll GT 0/1
|
|
chr1 153299932 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=99.00;MQ0=0;OQ=601.41;QD=18.79;RankSumP=0.252811;SB=-43.63;SecondBestBaseQ=31;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_2=c.2277G>A;refseq.codingCoordStr_3=c.2277G>A;refseq.codingCoordStr_4=c.2277G>A;refseq.codingCoordStr_5=c.2277G>A;refseq.codingCoordStr_6=c.2277G>A;refseq.codonCoord_2=759;refseq.codonCoord_3=759;refseq.codonCoord_4=759;refseq.codonCoord_5=759;refseq.codonCoord_6=759;refseq.end_1=153301334;refseq.end_2=153299932;refseq.end_3=153299932;refseq.end_4=153299932;refseq.end_5=153299932;refseq.end_6=153299932;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeAlternate_5=A;refseq.haplotypeAlternate_6=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_2=2378;refseq.mrnaCoord_3=2378;refseq.mrnaCoord_4=2378;refseq.mrnaCoord_5=2378;refseq.mrnaCoord_6=2378;refseq.name2_1=ADAM15;refseq.name2_2=ADAM15;refseq.name2_3=ADAM15;refseq.name2_4=ADAM15;refseq.name2_5=ADAM15;refseq.name2_6=ADAM15;refseq.name_1=NM_207191;refseq.name_2=NM_003815;refseq.name_3=NM_207194;refseq.name_4=NM_207195;refseq.name_5=NM_207196;refseq.name_6=NM_207197;refseq.numMatchingRecords=6;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_2=p.K759K;refseq.proteinCoordStr_3=p.K759K;refseq.proteinCoordStr_4=p.K759K;refseq.proteinCoordStr_5=p.K759K;refseq.proteinCoordStr_6=p.K759K;refseq.referenceAA_2=Lys;refseq.referenceAA_3=Lys;refseq.referenceAA_4=Lys;refseq.referenceAA_5=Lys;refseq.referenceAA_6=Lys;refseq.referenceCodon_2=AAG;refseq.referenceCodon_3=AAG;refseq.referenceCodon_4=AAG;refseq.referenceCodon_5=AAG;refseq.referenceCodon_6=AAG;refseq.spliceDist_2=-1;refseq.spliceDist_3=-1;refseq.spliceDist_4=-1;refseq.spliceDist_5=-1;refseq.spliceDist_6=-1;refseq.spliceInfo_2=splice-donor_-1;refseq.spliceInfo_3=splice-donor_-1;refseq.spliceInfo_4=splice-donor_-1;refseq.spliceInfo_5=splice-donor_-1;refseq.spliceInfo_6=splice-donor_-1;refseq.start_1=153299454;refseq.start_2=153299932;refseq.start_3=153299932;refseq.start_4=153299932;refseq.start_5=153299932;refseq.start_6=153299932;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_2=Lys;refseq.variantAA_3=Lys;refseq.variantAA_4=Lys;refseq.variantAA_5=Lys;refseq.variantAA_6=Lys;refseq.variantCodon_2=AAA;refseq.variantCodon_3=AAA;refseq.variantCodon_4=AAA;refseq.variantCodon_5=AAA;refseq.variantCodon_6=AAA;set=Intersection GT 1/0
|
|
chr1 153301404 . C A 17 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=24;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=95.94;MQ0=0;QD=1.11;RankSumP=0.592657;SB=-27.32;SecondBestBaseQ=22;refseq.changesAA_1=false;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.2337C>A;refseq.codingCoordStr_2=c.2267C>A;refseq.codingCoordStr_3=c.2412C>A;refseq.codingCoordStr_4=c.2409C>A;refseq.codingCoordStr_5=c.2481C>A;refseq.codingCoordStr_6=c.2484C>A;refseq.codonCoord_1=779;refseq.codonCoord_2=756;refseq.codonCoord_3=804;refseq.codonCoord_4=803;refseq.codonCoord_5=827;refseq.codonCoord_6=828;refseq.end_1=153301404;refseq.end_2=153301404;refseq.end_3=153301404;refseq.end_4=153301404;refseq.end_5=153301404;refseq.end_6=153301404;refseq.frame_1=2;refseq.frame_2=1;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeAlternate_5=A;refseq.haplotypeAlternate_6=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=2438;refseq.mrnaCoord_2=2368;refseq.mrnaCoord_3=2513;refseq.mrnaCoord_4=2510;refseq.mrnaCoord_5=2582;refseq.mrnaCoord_6=2585;refseq.name2_1=ADAM15;refseq.name2_2=ADAM15;refseq.name2_3=ADAM15;refseq.name2_4=ADAM15;refseq.name2_5=ADAM15;refseq.name2_6=ADAM15;refseq.name_1=NM_003815;refseq.name_2=NM_207191;refseq.name_3=NM_207194;refseq.name_4=NM_207195;refseq.name_5=NM_207196;refseq.name_6=NM_207197;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.G779G;refseq.proteinCoordStr_2=p.A756D;refseq.proteinCoordStr_3=p.G804G;refseq.proteinCoordStr_4=p.G803G;refseq.proteinCoordStr_5=p.G827G;refseq.proteinCoordStr_6=p.G828G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Gly;refseq.referenceAA_4=Gly;refseq.referenceAA_5=Gly;refseq.referenceAA_6=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GGC;refseq.referenceCodon_4=GGC;refseq.referenceCodon_5=GGC;refseq.referenceCodon_6=GGC;refseq.spliceDist_1=60;refseq.spliceDist_2=60;refseq.spliceDist_3=60;refseq.spliceDist_4=60;refseq.spliceDist_5=60;refseq.spliceDist_6=60;refseq.start_1=153301404;refseq.start_2=153301404;refseq.start_3=153301404;refseq.start_4=153301404;refseq.start_5=153301404;refseq.start_6=153301404;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Asp;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantAA_5=Gly;refseq.variantAA_6=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GAC;refseq.variantCodon_3=GGA;refseq.variantCodon_4=GGA;refseq.variantCodon_5=GGA;refseq.variantCodon_6=GGA;set=FilteredInAll GT 1/0
|
|
chr1 153372851 . A T 288.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=314;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=98.45;MQ0=0;OQ=5182.20;QD=16.50;RankSumP=0.0632070;SB=-2081.28;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.476A>T;refseq.codingCoordStr_2=c.410A>T;refseq.codonCoord_1=159;refseq.codonCoord_2=137;refseq.end_1=153372851;refseq.end_2=153372851;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=581;refseq.mrnaCoord_2=515;refseq.name2_1=EFNA1;refseq.name2_2=EFNA1;refseq.name_1=NM_004428;refseq.name_2=NM_182685;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D159V;refseq.proteinCoordStr_2=p.D137V;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.start_1=153372851;refseq.start_2=153372851;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=Intersection GT 0/1
|
|
chr1 153376720 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.177C>A;refseq.codingCoordStr_3=c.342C>A;refseq.codonCoord_2=59;refseq.codonCoord_3=114;refseq.end_1=153377068;refseq.end_2=153376720;refseq.end_3=153376720;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=nonsense;refseq.functionalClass_3=nonsense;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=318;refseq.mrnaCoord_3=442;refseq.name2_1=RAG1AP1;refseq.name2_2=RAG1AP1;refseq.name2_3=RAG1AP1;refseq.name_1=NM_001122839;refseq.name_2=NM_001122837;refseq.name_3=NM_018845;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.Y59*;refseq.proteinCoordStr_3=p.Y114*;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.spliceDist_2=60;refseq.spliceDist_3=60;refseq.start_1=153376062;refseq.start_2=153376720;refseq.start_3=153376720;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Stop;refseq.variantAA_3=Stop;refseq.variantCodon_2=TAA;refseq.variantCodon_3=TAA;set=FilteredInAll GT 1/0
|
|
chr1 153416342 . G A 239.03 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=1417.25;QD=18.65;RankSumP=0.0856543;SB=-591.75;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.861G>A;refseq.codonCoord=287;refseq.end=153416342;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=944;refseq.name=NM_025058;refseq.name2=TRIM46;refseq.positionType=CDS;refseq.proteinCoordStr=p.T287T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=48;refseq.start=153416342;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 153426387 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=4;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.codingCoordStr_1=c.658A>C;refseq.codingCoordStr_2=c.631A>C;refseq.codingCoordStr_3=c.475A>C;refseq.codingCoordStr_4=c.316A>C;refseq.codingCoordStr_5=c.343A>C;refseq.codingCoordStr_6=c.443A>C;refseq.codingCoordStr_7=c.685A>C;refseq.codonCoord_1=220;refseq.codonCoord_2=211;refseq.codonCoord_3=159;refseq.codonCoord_4=106;refseq.codonCoord_5=115;refseq.codonCoord_6=148;refseq.codonCoord_7=229;refseq.end_1=153426387;refseq.end_2=153426387;refseq.end_3=153426387;refseq.end_4=153426387;refseq.end_5=153426387;refseq.end_6=153426387;refseq.end_7=153426387;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=1;refseq.frame_7=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.haplotypeReference_7=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.mrnaCoord_1=724;refseq.mrnaCoord_2=697;refseq.mrnaCoord_3=541;refseq.mrnaCoord_4=382;refseq.mrnaCoord_5=409;refseq.mrnaCoord_6=509;refseq.mrnaCoord_7=751;refseq.name2_1=MUC1;refseq.name2_2=MUC1;refseq.name2_3=MUC1;refseq.name2_4=MUC1;refseq.name2_5=MUC1;refseq.name2_6=MUC1;refseq.name2_7=MUC1;refseq.name_1=NM_001018016;refseq.name_2=NM_001018017;refseq.name_3=NM_001044390;refseq.name_4=NM_001044391;refseq.name_5=NM_001044392;refseq.name_6=NM_001044393;refseq.name_7=NM_002456;refseq.numMatchingRecords=7;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.proteinCoordStr_1=p.T220P;refseq.proteinCoordStr_2=p.T211P;refseq.proteinCoordStr_3=p.T159P;refseq.proteinCoordStr_4=p.T106P;refseq.proteinCoordStr_5=p.T115P;refseq.proteinCoordStr_6=p.H148P;refseq.proteinCoordStr_7=p.T229P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceAA_6=His;refseq.referenceAA_7=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.referenceCodon_5=ACC;refseq.referenceCodon_6=CAC;refseq.referenceCodon_7=ACC;refseq.spliceDist_1=-63;refseq.spliceDist_2=-63;refseq.spliceDist_3=-63;refseq.spliceDist_4=-63;refseq.spliceDist_5=-63;refseq.spliceDist_6=-63;refseq.spliceDist_7=-63;refseq.start_1=153426387;refseq.start_2=153426387;refseq.start_3=153426387;refseq.start_4=153426387;refseq.start_5=153426387;refseq.start_6=153426387;refseq.start_7=153426387;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.transcriptStrand_7=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Pro;refseq.variantAA_6=Pro;refseq.variantAA_7=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;refseq.variantCodon_5=CCC;refseq.variantCodon_6=CCC;refseq.variantCodon_7=CCC;set=FilteredInAll GT 1/0
|
|
chr1 153428691 . C T 309.71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=187;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=98.44;MQ0=0;OQ=3983.58;QD=21.30;RankSumP=0.239337;SB=-1576.27;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.changesAA_7=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.codingCoordStr_1=c.93G>A;refseq.codingCoordStr_2=c.66G>A;refseq.codingCoordStr_3=c.66G>A;refseq.codingCoordStr_4=c.66G>A;refseq.codingCoordStr_5=c.93G>A;refseq.codingCoordStr_6=c.66G>A;refseq.codingCoordStr_7=c.66G>A;refseq.codonCoord_1=31;refseq.codonCoord_2=22;refseq.codonCoord_3=22;refseq.codonCoord_4=22;refseq.codonCoord_5=31;refseq.codonCoord_6=22;refseq.codonCoord_7=22;refseq.end_1=153428691;refseq.end_2=153428691;refseq.end_3=153428691;refseq.end_4=153428691;refseq.end_5=153428691;refseq.end_6=153428691;refseq.end_7=153428691;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.frame_7=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.functionalClass_7=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeAlternate_6=T;refseq.haplotypeAlternate_7=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.mrnaCoord_1=159;refseq.mrnaCoord_2=132;refseq.mrnaCoord_3=132;refseq.mrnaCoord_4=132;refseq.mrnaCoord_5=159;refseq.mrnaCoord_6=132;refseq.mrnaCoord_7=132;refseq.name2_1=MUC1;refseq.name2_2=MUC1;refseq.name2_3=MUC1;refseq.name2_4=MUC1;refseq.name2_5=MUC1;refseq.name2_6=MUC1;refseq.name2_7=MUC1;refseq.name_1=NM_001018016;refseq.name_2=NM_001018017;refseq.name_3=NM_001044390;refseq.name_4=NM_001044391;refseq.name_5=NM_001044392;refseq.name_6=NM_001044393;refseq.name_7=NM_002456;refseq.numMatchingRecords=7;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.proteinCoordStr_1=p.T31T;refseq.proteinCoordStr_2=p.T22T;refseq.proteinCoordStr_3=p.T22T;refseq.proteinCoordStr_4=p.T22T;refseq.proteinCoordStr_5=p.T31T;refseq.proteinCoordStr_6=p.T22T;refseq.proteinCoordStr_7=p.T22T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceAA_6=Thr;refseq.referenceAA_7=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.referenceCodon_3=ACG;refseq.referenceCodon_4=ACG;refseq.referenceCodon_5=ACG;refseq.referenceCodon_6=ACG;refseq.referenceCodon_7=ACG;refseq.spliceDist_1=35;refseq.spliceDist_2=8;refseq.spliceDist_3=8;refseq.spliceDist_4=8;refseq.spliceDist_5=35;refseq.spliceDist_6=8;refseq.spliceDist_7=8;refseq.spliceInfo_2=splice-acceptor_8;refseq.spliceInfo_3=splice-acceptor_8;refseq.spliceInfo_4=splice-acceptor_8;refseq.spliceInfo_6=splice-acceptor_8;refseq.spliceInfo_7=splice-acceptor_8;refseq.start_1=153428691;refseq.start_2=153428691;refseq.start_3=153428691;refseq.start_4=153428691;refseq.start_5=153428691;refseq.start_6=153428691;refseq.start_7=153428691;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.transcriptStrand_7=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantAA_5=Thr;refseq.variantAA_6=Thr;refseq.variantAA_7=Thr;refseq.variantCodon_1=ACA;refseq.variantCodon_2=ACA;refseq.variantCodon_3=ACA;refseq.variantCodon_4=ACA;refseq.variantCodon_5=ACA;refseq.variantCodon_6=ACA;refseq.variantCodon_7=ACA;set=Intersection GT 0/1
|
|
chr1 153445406 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.81;MQ0=0;OQ=192.20;QD=6.20;RankSumP=0.500000;SB=-17.32;SecondBestBaseQ=25;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.187A>T;refseq.codingCoordStr_2=c.187A>T;refseq.codonCoord_1=63;refseq.codonCoord_2=63;refseq.end_1=153445406;refseq.end_2=153445406;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=293;refseq.mrnaCoord_2=293;refseq.name2_1=MTX1;refseq.name2_2=MTX1;refseq.name_1=NM_002455;refseq.name_2=NM_198883;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T63S;refseq.proteinCoordStr_2=p.T63S;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=293;refseq.spliceDist_2=293;refseq.start_1=153445406;refseq.start_2=153445406;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCT;refseq.variantCodon_2=TCT;set=Intersection GT 0/1
|
|
chr1 153493199 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=2.66410e-08;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.787A>G;refseq.codingCoordStr_2=c.709A>G;refseq.codonCoord_1=263;refseq.codonCoord_2=237;refseq.end_1=153493199;refseq.end_2=153493199;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1040;refseq.mrnaCoord_2=962;refseq.name2_1=SCAMP3;refseq.name2_2=SCAMP3;refseq.name_1=NM_005698;refseq.name_2=NM_052837;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I263V;refseq.proteinCoordStr_2=p.I237V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=153493199;refseq.start_2=153493199;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=FilteredInAll GT 1/0
|
|
chr1 153496755 . C T 186.88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=383;Dels=0.00;HRun=0;HaplotypeScore=6.37;MQ=98.47;MQ0=0;OQ=6210.92;QD=16.22;RankSumP=0.0241548;SB=-2471.01;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.378G>A;refseq.codingCoordStr_2=c.300G>A;refseq.codonCoord_1=126;refseq.codonCoord_2=100;refseq.end_1=153496755;refseq.end_2=153496755;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=631;refseq.mrnaCoord_2=553;refseq.name2_1=SCAMP3;refseq.name2_2=SCAMP3;refseq.name_1=NM_005698;refseq.name_2=NM_052837;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G126G;refseq.proteinCoordStr_2=p.G100G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=-11;refseq.spliceDist_2=-11;refseq.start_1=153496755;refseq.start_2=153496755;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;set=Intersection GT 0/1
|
|
chr1 153527007 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=192;Dels=0.00;HRun=0;HaplotypeScore=14.50;MQ=98.36;MQ0=0;OQ=2287.10;QD=11.91;RankSumP=0.155190;SB=-380.10;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1705C>A;refseq.codingCoordStr_2=c.1612C>A;refseq.codonCoord_1=569;refseq.codonCoord_2=538;refseq.end_1=153527007;refseq.end_2=153527007;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1744;refseq.mrnaCoord_2=1726;refseq.name2_1=PKLR;refseq.name2_2=PKLR;refseq.name_1=NM_000298;refseq.name_2=NM_181871;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R569R;refseq.proteinCoordStr_2=p.R538R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.spliceDist_1=87;refseq.spliceDist_2=87;refseq.start_1=153527007;refseq.start_2=153527007;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=Intersection GT 0/1
|
|
chr1 153560898 . A G 104.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.48;MQ=98.31;MQ0=0;OQ=1992.20;QD=31.62;RankSumP=1.00000;SB=-88.92;SecondBestBaseQ=2;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_3=c.66A>G;refseq.codingCoordStr_4=c.-155A>G;refseq.codonCoord_3=22;refseq.end_1=153561249;refseq.end_2=153561249;refseq.end_3=153560898;refseq.end_4=153560898;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=false;refseq.mrnaCoord_3=547;refseq.mrnaCoord_4=57;refseq.name2_1=RUSC1;refseq.name2_2=RUSC1;refseq.name2_3=RUSC1;refseq.name2_4=RUSC1;refseq.name_1=NM_001105203;refseq.name_2=NM_001105204;refseq.name_3=NM_001105205;refseq.name_4=NM_014328;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=utr5;refseq.proteinCoordStr_3=p.L22L;refseq.referenceAA_3=Leu;refseq.referenceCodon_3=CTA;refseq.spliceDist_3=-62;refseq.spliceDist_4=57;refseq.start_1=153559556;refseq.start_2=153559556;refseq.start_3=153560898;refseq.start_4=153560898;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_3=Leu;refseq.variantCodon_3=CTG;set=Intersection GT 1/1
|
|
chr1 153589180 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7307G>C;refseq.codonCoord=2436;refseq.end=153589180;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7787;refseq.name=NM_018489;refseq.name2=ASH1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2436P;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-60;refseq.start=153589180;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=FilteredInAll GT 1/0
|
|
chr1 153674783 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=1.74381e-09;SecondBestBaseQ=11;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5787G>A;refseq.codonCoord=1929;refseq.end=153674783;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6267;refseq.name=NM_018489;refseq.name2=ASH1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1929Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-42;refseq.start=153674783;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=FilteredInAll GT 0/1
|
|
chr1 153675259 . T C 302.20 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=252;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=98.62;MQ0=0;OQ=9447.50;QD=37.49;RankSumP=1.00000;SB=-4720.66;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5311A>G;refseq.codonCoord=1771;refseq.end=153675259;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5791;refseq.name=NM_018489;refseq.name2=ASH1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1771A;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=225;refseq.start=153675259;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 153757608 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.327A>C;refseq.codonCoord=109;refseq.end=153757608;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=807;refseq.name=NM_018489;refseq.name2=ASH1L;refseq.positionType=CDS;refseq.proteinCoordStr=p.R109R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-94;refseq.start=153757608;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=FilteredInAll GT 1/0
|
|
chr1 153850561 rs3844257 A G 0.42 PASS AC=1;AF=0.50;AN=2;DB;DP=594;Dels=0.00;HRun=0;HaplotypeScore=16.55;MQ=18.35;MQ0=570;OQ=349.47;QD=0.59;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1586A>G;refseq.codonCoord=529;refseq.end=153850561;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1619;refseq.name=NM_018116;refseq.name2=MSTO1;refseq.positionType=CDS;refseq.proteinCoordStr=p.K529R;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=88;refseq.start=153850561;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=gatk GT:AD:DP:GL:GQ 0/1:459,134:21:-44.55,-6.32,-41.16:99
|
|
chr1 153896696 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1767A>C;refseq.codingCoordStr_2=c.1629A>C;refseq.codonCoord_1=589;refseq.codonCoord_2=543;refseq.end_1=153896696;refseq.end_2=153896696;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1791;refseq.mrnaCoord_2=1896;refseq.name2_1=YY1AP1;refseq.name2_2=YY1AP1;refseq.name_1=NM_139118;refseq.name_2=NM_139119;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K589N;refseq.proteinCoordStr_2=p.K543N;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=633;refseq.spliceDist_2=633;refseq.start_1=153896696;refseq.start_2=153896696;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=FilteredInAll GT 1/0
|
|
chr1 154001636 . T C 303.65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=305;Dels=0.00;HRun=0;HaplotypeScore=8.36;MQ=98.80;MQ0=0;OQ=5946.86;QD=19.50;RankSumP=0.349631;SB=-954.20;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4252A>G;refseq.codingCoordStr_2=c.4252A>G;refseq.codonCoord_1=1418;refseq.codonCoord_2=1418;refseq.end_1=154001636;refseq.end_2=154001636;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4301;refseq.mrnaCoord_2=4301;refseq.name2_1=GON4L;refseq.name2_2=GON4L;refseq.name_1=NM_001037533;refseq.name_2=NM_032292;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.M1418V;refseq.proteinCoordStr_2=p.M1418V;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=-222;refseq.spliceDist_2=-437;refseq.start_1=154001636;refseq.start_2=154001636;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=Intersection GT 1/0
|
|
chr1 154104489 . G C 90.57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=116;Dels=0.00;HRun=0;HaplotypeScore=6.83;MQ=98.65;MQ0=0;OQ=5433.89;QD=46.84;RankSumP=1.00000;SB=-2476.10;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.144G>C;refseq.codonCoord=48;refseq.end=154104489;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=407;refseq.name=NM_152280;refseq.name2=SYT11;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q48H;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=110;refseq.start=154104489;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 154104891 . T C 165.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=303;Dels=0.00;HRun=0;HaplotypeScore=7.94;MQ=98.58;MQ0=0;OQ=10866.85;QD=35.86;RankSumP=1.00000;SB=-2774.34;SecondBestBaseQ=15;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.546T>C;refseq.codonCoord=182;refseq.end=154104891;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=809;refseq.name=NM_152280;refseq.name2=SYT11;refseq.positionType=CDS;refseq.proteinCoordStr=p.H182H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-316;refseq.start=154104891;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 154105148 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=4;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.803T>G;refseq.codonCoord=268;refseq.end=154105148;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1066;refseq.name=NM_152280;refseq.name2=SYT11;refseq.positionType=CDS;refseq.proteinCoordStr=p.V268G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-59;refseq.start=154105148;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 154179110 . T C 96.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=5.75;MQ=98.76;MQ0=0;OQ=2485.51;QD=29.24;RankSumP=1.00000;SB=-677.58;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.986T>C;refseq.codonCoord=329;refseq.end=154179110;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1007;refseq.name=NM_181885;refseq.name2=RXFP4;refseq.positionType=CDS;refseq.proteinCoordStr=p.L329S;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-140;refseq.start=154179110;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/1
|
|
chr1 154370916 . G A 178.53 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=226;Dels=0.00;HRun=0;HaplotypeScore=16.09;MQ=98.33;MQ0=0;OQ=4454.42;QD=19.71;RankSumP=0.450168;SB=-912.88;SecondBestBaseQ=27;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.612G>A;refseq.codingCoordStr_2=c.612G>A;refseq.codingCoordStr_3=c.612G>A;refseq.codonCoord_1=204;refseq.codonCoord_2=204;refseq.codonCoord_3=204;refseq.end_1=154370916;refseq.end_2=154370916;refseq.end_3=154370916;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=861;refseq.mrnaCoord_2=861;refseq.mrnaCoord_3=861;refseq.name2_1=LMNA;refseq.name2_2=LMNA;refseq.name2_3=LMNA;refseq.name_1=NM_005572;refseq.name_2=NM_170707;refseq.name_3=NM_170708;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.L204L;refseq.proteinCoordStr_2=p.L204L;refseq.proteinCoordStr_3=p.L204L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.spliceDist_3=-28;refseq.start_1=154370916;refseq.start_2=154370916;refseq.start_3=154370916;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;refseq.variantCodon_3=CTA;set=Intersection GT 1/0
|
|
chr1 154374158 . C T 59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=93.45;MQ0=0;OQ=136.04;QD=9.07;RankSumP=0.570596;SB=-81.31;SecondBestBaseQ=23;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.1698C>T;refseq.codingCoordStr_3=c.1698C>T;refseq.codonCoord_2=566;refseq.codonCoord_3=566;refseq.end_1=154374892;refseq.end_2=154374158;refseq.end_3=154374158;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=1947;refseq.mrnaCoord_3=1947;refseq.name2_1=LMNA;refseq.name2_2=LMNA;refseq.name2_3=LMNA;refseq.name_1=NM_170708;refseq.name_2=NM_005572;refseq.name_3=NM_170707;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.H566H;refseq.proteinCoordStr_3=p.H566H;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceCodon_2=CAC;refseq.referenceCodon_3=CAC;refseq.spliceDist_2=90;refseq.spliceDist_3=-1;refseq.spliceInfo_3=splice-donor_-1;refseq.start_1=154373658;refseq.start_2=154374158;refseq.start_3=154374158;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantCodon_2=CAT;refseq.variantCodon_3=CAT;set=Intersection GT 0/1
|
|
chr1 154394844 . T C 239.29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=421;Dels=0.00;HRun=0;HaplotypeScore=5.70;MQ=98.53;MQ0=0;OQ=8298.70;QD=19.71;RankSumP=0.259108;SB=-2720.94;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.405T>C;refseq.codonCoord=135;refseq.end=154394844;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=602;refseq.name=NM_022367;refseq.name2=SEMA4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.N135N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=42;refseq.start=154394844;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/0
|
|
chr1 154412842 . C T 241.75 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=3.81;MQ=98.35;MQ0=0;OQ=1536.40;QD=17.66;RankSumP=0.0923241;SB=-365.06;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1716C>T;refseq.codonCoord=572;refseq.end=154412842;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1913;refseq.name=NM_022367;refseq.name2=SEMA4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.P572P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=23;refseq.start=154412842;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 154468797 . A G 307.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=243;Dels=0.00;HRun=0;HaplotypeScore=7.72;MQ=98.81;MQ0=0;OQ=9581.30;QD=39.43;RankSumP=1.00000;SB=-4030.65;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.224A>G;refseq.codonCoord=75;refseq.end=154468797;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=247;refseq.name=NM_007221;refseq.name2=PMF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q75R;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-44;refseq.start=154468797;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/1
|
|
chr1 154472745 . G A 289.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=201;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=98.91;MQ0=0;OQ=3124.70;QD=15.55;RankSumP=0.0667862;SB=-1543.46;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.411G>A;refseq.codonCoord=137;refseq.end=154472745;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=434;refseq.name=NM_007221;refseq.name2=PMF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M137I;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=43;refseq.start=154472745;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/0
|
|
chr1 154482369 . G C 5 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=2;HRun=3;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.-106C>G;refseq.codingCoordStr_2=c.213C>G;refseq.codonCoord_2=71;refseq.end_1=154482369;refseq.end_2=154482369;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=511;refseq.mrnaCoord_2=283;refseq.name2_1=PAQR6;refseq.name2_2=PAQR6;refseq.name_1=NM_024897;refseq.name_2=NM_198406;refseq.numMatchingRecords=2;refseq.positionType_1=utr5;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.G71G;refseq.referenceAA_2=Gly;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=-173;refseq.spliceDist_2=34;refseq.start_1=154482369;refseq.start_2=154482369;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/1
|
|
chr1 154531272 . C T 238.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=98.73;MQ0=0;OQ=1328.30;QD=17.48;RankSumP=0.467971;SB=-485.49;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.280G>A;refseq.codonCoord=94;refseq.end=154531272;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=293;refseq.name=NM_144580;refseq.name2=C1orf85;refseq.positionType=CDS;refseq.proteinCoordStr=p.V94I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-99;refseq.start=154531272;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 0/1
|
|
chr1 154581080 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=382;Dels=0.00;HRun=4;HaplotypeScore=14.26;MQ=98.78;MQ0=0;OQ=209.88;QD=0.55;RankSumP=0.00000;SB=756.79;SecondBestBaseQ=20;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.120A>C;refseq.codonCoord=40;refseq.end=154581080;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=480;refseq.name=NM_144627;refseq.name2=C1orf182;refseq.positionType=CDS;refseq.proteinCoordStr=p.P40P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-44;refseq.start=154581080;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 154581121 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=488;Dels=0.00;HRun=1;HaplotypeScore=6.27;MQ=98.92;MQ0=0;OQ=9580.40;QD=19.63;RankSumP=0.241863;SB=-3918.65;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.161C>T;refseq.codonCoord=54;refseq.end=154581121;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=521;refseq.name=NM_144627;refseq.name2=C1orf182;refseq.positionType=CDS;refseq.proteinCoordStr=p.S54L;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-3;refseq.spliceInfo=splice-donor_-3;refseq.start=154581121;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 154613755 . G A 253.83 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=6.56;MQ=98.65;MQ0=0;OQ=1270.37;QD=16.50;RankSumP=0.278077;SB=-521.56;SecondBestBaseQ=32;refseq.chr=chr1;refseq.end=154613755;refseq.haplotypeAlternate=*;refseq.haplotypeReference=*;refseq.mrnaCoord=388;refseq.name=NR_026549;refseq.name2=RHBG;refseq.positionType=non_coding_exon;refseq.spliceDist=40;refseq.start=154613755;refseq.transcriptStrand=+;set=Intersection GT 1/0
|
|
chr1 154618323 . G A 346.91 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=231;Dels=0.00;HRun=0;HaplotypeScore=6.33;MQ=98.73;MQ0=0;OQ=3970.67;QD=17.19;RankSumP=0.246698;SB=-1547.63;SecondBestBaseQ=30;refseq.chr=chr1;refseq.end=154618323;refseq.haplotypeAlternate=*;refseq.haplotypeReference=*;refseq.mrnaCoord=1104;refseq.name=NR_026549;refseq.name2=RHBG;refseq.positionType=non_coding_exon;refseq.spliceDist=-36;refseq.start=154618323;refseq.transcriptStrand=+;set=Intersection GT 1/0
|
|
chr1 154618587 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.chr=chr1;refseq.end=154618587;refseq.haplotypeAlternate=*;refseq.haplotypeReference=*;refseq.mrnaCoord=1244;refseq.name=NR_026549;refseq.name2=RHBG;refseq.positionType=non_coding_exon;refseq.spliceDist=-30;refseq.start=154618587;refseq.transcriptStrand=+;set=FilteredInAll GT 0/1
|
|
chr1 154620991 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=232;Dels=0.00;HRun=0;HaplotypeScore=8.37;MQ=95.43;MQ0=0;OQ=2174.83;QD=9.37;RankSumP=0.490456;SB=-796.85;SecondBestBaseQ=33;refseq.chr=chr1;refseq.end=154620991;refseq.haplotypeAlternate=*;refseq.haplotypeReference=*;refseq.mrnaCoord=1445;refseq.name=NR_026549;refseq.name2=RHBG;refseq.positionType=non_coding_exon;refseq.spliceDist=-26;refseq.start=154620991;refseq.transcriptStrand=+;set=Intersection GT 0/1
|
|
chr1 154621018 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.chr=chr1;refseq.end=154621018;refseq.haplotypeAlternate=*;refseq.haplotypeReference=*;refseq.name=NR_026549;refseq.name2=RHBG;refseq.positionType=non_coding_intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=154621018;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 154713527 . T C 97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=202;Dels=0.00;HRun=0;HaplotypeScore=20.82;MQ=98.30;MQ0=0;OQ=5768.45;QD=28.56;RankSumP=1.00000;SB=-678.56;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.756A>G;refseq.codonCoord=252;refseq.end=154713527;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1146;refseq.name=NM_005920;refseq.name2=MEF2D;refseq.positionType=CDS;refseq.proteinCoordStr=p.P252P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=92;refseq.start=154713527;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 154717364 . G A 141.20 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=251;Dels=0.00;HRun=0;HaplotypeScore=15.84;MQ=97.67;MQ0=0;OQ=8830.58;QD=35.18;RankSumP=1.00000;SB=-3846.61;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.282C>T;refseq.codonCoord=94;refseq.end=154717364;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=672;refseq.name=NM_005920;refseq.name2=MEF2D;refseq.positionType=CDS;refseq.proteinCoordStr=p.N94N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=24;refseq.start=154717364;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/1
|
|
chr1 154762981 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4817T>G;refseq.codonCoord=1606;refseq.end=154762981;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4892;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1606G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=35;refseq.start=154762981;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 0/1
|
|
chr1 154765380 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4523A>C;refseq.codonCoord=1508;refseq.end=154765380;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4598;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y1508S;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-49;refseq.start=154765380;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 1/0
|
|
chr1 154766593 . T C 84.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=5.40;MQ=97.68;MQ0=0;OQ=1821.70;QD=28.46;RankSumP=1.00000;SB=-643.42;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4332A>G;refseq.codonCoord=1444;refseq.end=154766593;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4407;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1444L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-73;refseq.start=154766593;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 154766636 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4289T>C;refseq.codonCoord=1430;refseq.end=154766636;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4364;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1430P;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=98;refseq.start=154766636;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 154780465 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=3.89204e-15;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2462T>G;refseq.codonCoord=821;refseq.end=154780465;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2537;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V821G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=154780465;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 154780874 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=4;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2319T>G;refseq.codonCoord=773;refseq.end=154780874;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2394;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.G773G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=15;refseq.start=154780874;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 154785003 . G A 176.19 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=295;Dels=0.00;HRun=0;HaplotypeScore=11.20;MQ=98.46;MQ0=0;OQ=9725.09;QD=32.97;RankSumP=1.00000;SB=-3767.60;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1987C>T;refseq.codonCoord=663;refseq.end=154785003;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2062;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R663C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=154785003;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/1
|
|
chr1 154790713 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=2;RankSumP=1.26441e-09;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1386C>T;refseq.codonCoord=462;refseq.end=154790713;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1461;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.F462F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-63;refseq.start=154790713;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 1/0
|
|
chr1 154793068 . T C 90 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=204;Dels=0.00;HRun=2;HaplotypeScore=23.06;MQ=97.79;MQ0=0;OQ=6110.09;QD=29.95;RankSumP=1.00000;SB=-1986.19;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1171A>G;refseq.codonCoord=391;refseq.end=154793068;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1246;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R391G;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=42;refseq.start=154793068;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 154797356 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=19;HRun=2;RankSumP=2.72344e-09;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1123C>A;refseq.codonCoord=375;refseq.end=154797356;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1198;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q375K;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=154797356;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 0/1
|
|
chr1 154799601 . T C 108.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=176;Dels=0.00;HRun=1;HaplotypeScore=11.50;MQ=98.66;MQ0=0;OQ=6468.35;QD=36.75;RankSumP=1.00000;SB=-2076.17;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.747A>G;refseq.codonCoord=249;refseq.end=154799601;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=822;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q249Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-52;refseq.start=154799601;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 154802845 . G C 376.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=136;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.42;MQ0=0;OQ=6040.79;QD=44.42;RankSumP=1.00000;SB=-2894.97;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.243C>G;refseq.codonCoord=81;refseq.end=154802845;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=318;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P81P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-40;refseq.start=154802845;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 154802875 . T C 86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=132;Dels=0.00;HRun=2;HaplotypeScore=2.31;MQ=98.62;MQ0=0;OQ=5208.91;QD=39.46;RankSumP=1.00000;SB=-2539.71;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.213A>G;refseq.codonCoord=71;refseq.end=154802875;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=288;refseq.name=NM_178229;refseq.name2=IQGAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.L71L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-70;refseq.start=154802875;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 154828275 . G C 40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=3.02;MQ=96.63;MQ0=0;OQ=719.90;QD=25.71;RankSumP=1.00000;SB=-196.69;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.55G>C;refseq.codonCoord=19;refseq.end=154828275;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=94;refseq.name=NM_144772;refseq.name2=APOA1BP;refseq.positionType=CDS;refseq.proteinCoordStr=p.V19L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=94;refseq.start=154828275;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 154830350 . A C 347.35 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.79;MQ0=0;OQ=3583.82;QD=39.38;RankSumP=1.00000;SB=-1455.20;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.717A>C;refseq.codonCoord=239;refseq.end=154830350;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=756;refseq.name=NM_144772;refseq.name2=APOA1BP;refseq.positionType=CDS;refseq.proteinCoordStr=p.I239I;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=53;refseq.start=154830350;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 154830437 . G A 103.74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=97;Dels=0.00;HRun=2;HaplotypeScore=2.48;MQ=98.18;MQ0=0;OQ=3506.84;QD=36.15;RankSumP=1.00000;SB=-1388.29;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.804G>A;refseq.codonCoord=268;refseq.end=154830437;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=843;refseq.name=NM_144772;refseq.name2=APOA1BP;refseq.positionType=CDS;refseq.proteinCoordStr=p.E268E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=140;refseq.start=154830437;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 154830476 . C T 317.43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=97.73;MQ0=0;OQ=3635.65;QD=40.85;RankSumP=1.00000;SB=-1273.10;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.843C>T;refseq.codonCoord=281;refseq.end=154830476;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=882;refseq.name=NM_144772;refseq.name2=APOA1BP;refseq.positionType=CDS;refseq.proteinCoordStr=p.T281T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=179;refseq.start=154830476;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 154831673 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.153740;SecondBestBaseQ=27;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1084T>G;refseq.codingCoordStr_2=c.1069T>G;refseq.codonCoord_1=362;refseq.codonCoord_2=357;refseq.end_1=154831673;refseq.end_2=154831673;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1123;refseq.mrnaCoord_2=1197;refseq.name2_1=GPATCH4;refseq.name2_2=GPATCH4;refseq.name_1=NM_015590;refseq.name_2=NM_182679;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F362V;refseq.proteinCoordStr_2=p.F357V;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.spliceDist_1=593;refseq.spliceDist_2=593;refseq.start_1=154831673;refseq.start_2=154831673;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=soap GT 0/1
|
|
chr1 154831675 . G C 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.00280674;SecondBestBaseQ=28;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1082C>G;refseq.codingCoordStr_2=c.1067C>G;refseq.codonCoord_1=361;refseq.codonCoord_2=356;refseq.end_1=154831675;refseq.end_2=154831675;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1121;refseq.mrnaCoord_2=1195;refseq.name2_1=GPATCH4;refseq.name2_2=GPATCH4;refseq.name_1=NM_015590;refseq.name_2=NM_182679;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T361S;refseq.proteinCoordStr_2=p.T356S;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=591;refseq.spliceDist_2=591;refseq.start_1=154831675;refseq.start_2=154831675;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=FilteredInAll GT 0/1
|
|
chr1 154831676 . T A 91 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=0;RankSumP=0.508168;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1081A>T;refseq.codingCoordStr_2=c.1066A>T;refseq.codonCoord_1=361;refseq.codonCoord_2=356;refseq.end_1=154831676;refseq.end_2=154831676;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1120;refseq.mrnaCoord_2=1194;refseq.name2_1=GPATCH4;refseq.name2_2=GPATCH4;refseq.name_1=NM_015590;refseq.name_2=NM_182679;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T361S;refseq.proteinCoordStr_2=p.T356S;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=590;refseq.spliceDist_2=590;refseq.start_1=154831676;refseq.start_2=154831676;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCT;refseq.variantCodon_2=TCT;set=soap GT 1/0
|
|
chr1 154888876 . G A 217.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=986.95;QD=36.55;RankSumP=1.00000;SB=-479.11;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1510G>A;refseq.codingCoordStr_2=c.1510G>A;refseq.codonCoord_1=504;refseq.codonCoord_2=504;refseq.end_1=154888876;refseq.end_2=154888876;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1846;refseq.mrnaCoord_2=1846;refseq.name2_1=BCAN;refseq.name2_2=BCAN;refseq.name_1=NM_021948;refseq.name_2=NM_198427;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E504K;refseq.proteinCoordStr_2=p.E504K;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=213;refseq.spliceDist_2=213;refseq.start_1=154888876;refseq.start_2=154888876;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/1
|
|
chr1 154906167 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4437T>G;refseq.codonCoord=1479;refseq.end=154906167;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4570;refseq.name=NM_006617;refseq.name2=NES;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1479G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-988;refseq.start=154906167;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 154908161 . C T 366.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=181;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=98.83;MQ0=0;OQ=7784.70;QD=43.01;RankSumP=1.00000;SB=-3592.62;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2443G>A;refseq.codonCoord=815;refseq.end=154908161;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2576;refseq.name=NM_006617;refseq.name2=NES;refseq.positionType=CDS;refseq.proteinCoordStr=p.V815I;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=1461;refseq.start=154908161;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/1
|
|
chr1 154913292 . A G 42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=98.20;MQ0=0;OQ=598.67;QD=28.51;RankSumP=1.00000;SB=-250.69;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.389T>C;refseq.codonCoord=130;refseq.end=154913292;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=522;refseq.name=NM_006617;refseq.name2=NES;refseq.positionType=CDS;refseq.proteinCoordStr=p.V130A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-395;refseq.start=154913292;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 154972217 . G C 309.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=207;Dels=0.00;HRun=1;HaplotypeScore=4.20;MQ=98.06;MQ0=0;OQ=8818.56;QD=42.60;RankSumP=1.00000;SB=-2510.12;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.713G>C;refseq.codingCoordStr_2=c.1198G>C;refseq.codonCoord_1=238;refseq.codonCoord_2=400;refseq.end_1=154972217;refseq.end_2=154972217;refseq.frame_1=1;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1347;refseq.mrnaCoord_2=1832;refseq.name2_1=C1orf66;refseq.name2_2=C1orf66;refseq.name_1=NM_001142560;refseq.name_2=NM_015997;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R238P;refseq.proteinCoordStr_2=p.V400L;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Val;refseq.referenceCodon_1=CGT;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=77;refseq.spliceDist_2=77;refseq.start_1=154972217;refseq.start_2=154972217;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Leu;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CTG;set=Intersection GT 1/1
|
|
chr1 154980136 . C T 229.79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=97.97;MQ0=0;OQ=723.72;QD=38.09;RankSumP=1.00000;SB=-186.22;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.696G>A;refseq.codingCoordStr_2=c.627G>A;refseq.codingCoordStr_3=c.648G>A;refseq.codonCoord_1=232;refseq.codonCoord_2=209;refseq.codonCoord_3=216;refseq.end_1=154980136;refseq.end_2=154980136;refseq.end_3=154980136;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=781;refseq.mrnaCoord_2=756;refseq.mrnaCoord_3=970;refseq.name2_1=HDGF;refseq.name2_2=HDGF;refseq.name2_3=HDGF;refseq.name_1=NM_001126050;refseq.name_2=NM_001126051;refseq.name_3=NM_004494;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E232E;refseq.proteinCoordStr_2=p.E209E;refseq.proteinCoordStr_3=p.E216E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.spliceDist_1=-69;refseq.spliceDist_2=-69;refseq.spliceDist_3=-69;refseq.start_1=154980136;refseq.start_2=154980136;refseq.start_3=154980136;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;refseq.variantCodon_3=GAA;set=Intersection GT 1/1
|
|
chr1 154980182 . G A 110.36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=98.27;MQ0=0;OQ=507.09;QD=18.78;RankSumP=0.524316;SB=-233.26;SecondBestBaseQ=34;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.650C>T;refseq.codingCoordStr_2=c.581C>T;refseq.codingCoordStr_3=c.602C>T;refseq.codonCoord_1=217;refseq.codonCoord_2=194;refseq.codonCoord_3=201;refseq.end_1=154980182;refseq.end_2=154980182;refseq.end_3=154980182;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=735;refseq.mrnaCoord_2=710;refseq.mrnaCoord_3=924;refseq.name2_1=HDGF;refseq.name2_2=HDGF;refseq.name2_3=HDGF;refseq.name_1=NM_001126050;refseq.name_2=NM_001126051;refseq.name_3=NM_004494;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P217L;refseq.proteinCoordStr_2=p.P194L;refseq.proteinCoordStr_3=p.P201L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.spliceDist_1=113;refseq.spliceDist_2=113;refseq.spliceDist_3=113;refseq.start_1=154980182;refseq.start_2=154980182;refseq.start_3=154980182;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;refseq.variantCodon_3=CTC;set=Intersection GT 1/0
|
|
chr1 155051606 . T C 272.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=99.00;MQ0=0;OQ=1046.64;QD=33.76;RankSumP=1.00000;SB=-447.56;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.155A>G;refseq.codingCoordStr_2=c.101A>G;refseq.codingCoordStr_3=c.71A>G;refseq.codingCoordStr_4=c.155A>G;refseq.codingCoordStr_5=c.155A>G;refseq.codonCoord_1=52;refseq.codonCoord_2=34;refseq.codonCoord_3=24;refseq.codonCoord_4=52;refseq.codonCoord_5=52;refseq.end_1=155051606;refseq.end_2=155051606;refseq.end_3=155051606;refseq.end_4=155051606;refseq.end_5=155051606;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=295;refseq.mrnaCoord_2=264;refseq.mrnaCoord_3=174;refseq.mrnaCoord_4=295;refseq.mrnaCoord_5=295;refseq.name2_1=SH2D2A;refseq.name2_2=SH2D2A;refseq.name2_3=SH2D2A;refseq.name2_4=SH2D2A;refseq.name2_5=SH2D2A;refseq.name_1=NM_001161441;refseq.name_2=NM_001161442;refseq.name_3=NM_001161443;refseq.name_4=NM_001161444;refseq.name_5=NM_003975;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.N52S;refseq.proteinCoordStr_2=p.N34S;refseq.proteinCoordStr_3=p.N24S;refseq.proteinCoordStr_4=p.N52S;refseq.proteinCoordStr_5=p.N52S;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceAA_4=Asn;refseq.referenceAA_5=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.referenceCodon_4=AAC;refseq.referenceCodon_5=AAC;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.spliceDist_3=32;refseq.spliceDist_4=32;refseq.spliceDist_5=32;refseq.start_1=155051606;refseq.start_2=155051606;refseq.start_3=155051606;refseq.start_4=155051606;refseq.start_5=155051606;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantAA_5=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;refseq.variantCodon_3=AGC;refseq.variantCodon_4=AGC;refseq.variantCodon_5=AGC;set=Intersection GT 1/1
|
|
chr1 155112857 . G A 231.86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=215;Dels=0.00;HRun=1;HaplotypeScore=8.05;MQ=98.97;MQ0=0;OQ=4006.66;QD=18.64;RankSumP=0.112603;SB=-1466.40;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1566G>A;refseq.codingCoordStr_2=c.1656G>A;refseq.codingCoordStr_3=c.1674G>A;refseq.codonCoord_1=522;refseq.codonCoord_2=552;refseq.codonCoord_3=558;refseq.end_1=155112857;refseq.end_2=155112857;refseq.end_3=155112857;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1646;refseq.mrnaCoord_2=1712;refseq.mrnaCoord_3=1730;refseq.name2_1=NTRK1;refseq.name2_2=NTRK1;refseq.name2_3=NTRK1;refseq.name_1=NM_001007792;refseq.name_2=NM_001012331;refseq.name_3=NM_002529;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Q522Q;refseq.proteinCoordStr_2=p.Q552Q;refseq.proteinCoordStr_3=p.Q558Q;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.referenceCodon_3=CAG;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.spliceDist_3=42;refseq.start_1=155112857;refseq.start_2=155112857;refseq.start_3=155112857;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantAA_3=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;refseq.variantCodon_3=CAA;set=Intersection GT 1/0
|
|
chr1 155115619 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=98.76;MQ0=0;OQ=370.80;QD=9.27;RankSumP=0.00666331;SB=-3.46;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1779C>T;refseq.codingCoordStr_2=c.1869C>T;refseq.codingCoordStr_3=c.1887C>T;refseq.codonCoord_1=593;refseq.codonCoord_2=623;refseq.codonCoord_3=629;refseq.end_1=155115619;refseq.end_2=155115619;refseq.end_3=155115619;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1859;refseq.mrnaCoord_2=1925;refseq.mrnaCoord_3=1943;refseq.name2_1=NTRK1;refseq.name2_2=NTRK1;refseq.name2_3=NTRK1;refseq.name_1=NM_001007792;refseq.name_2=NM_001012331;refseq.name_3=NM_002529;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A593A;refseq.proteinCoordStr_2=p.A623A;refseq.proteinCoordStr_3=p.A629A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.referenceCodon_3=GCC;refseq.spliceDist_1=82;refseq.spliceDist_2=82;refseq.spliceDist_3=82;refseq.start_1=155115619;refseq.start_2=155115619;refseq.start_3=155115619;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;refseq.variantCodon_3=GCT;set=filterInsoap-gatk GT 0/1
|
|
chr1 155116416 . T G 24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=3;RankSumP=0.500012;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1940T>G;refseq.codingCoordStr_2=c.2030T>G;refseq.codingCoordStr_3=c.2048T>G;refseq.codonCoord_1=647;refseq.codonCoord_2=677;refseq.codonCoord_3=683;refseq.end_1=155116416;refseq.end_2=155116416;refseq.end_3=155116416;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2020;refseq.mrnaCoord_2=2086;refseq.mrnaCoord_3=2104;refseq.name2_1=NTRK1;refseq.name2_2=NTRK1;refseq.name2_3=NTRK1;refseq.name_1=NM_001007792;refseq.name_2=NM_001012331;refseq.name_3=NM_002529;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V647G;refseq.proteinCoordStr_2=p.V677G;refseq.proteinCoordStr_3=p.V683G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceDist_3=2;refseq.spliceInfo_1=splice-acceptor_2;refseq.spliceInfo_2=splice-acceptor_2;refseq.spliceInfo_3=splice-acceptor_2;refseq.start_1=155116416;refseq.start_2=155116416;refseq.start_3=155116416;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=soap GT 1/0
|
|
chr1 155140351 . G A 154.70 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=220;Dels=0.00;HRun=0;HaplotypeScore=10.84;MQ=98.73;MQ0=0;OQ=3140.01;QD=14.27;RankSumP=0.0684033;SB=-449.40;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9G>A;refseq.codonCoord=3;refseq.end=155140351;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=125;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P3P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=18;refseq.start=155140351;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/0
|
|
chr1 155144081 . T C 275.10 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=177;Dels=0.00;HRun=1;HaplotypeScore=7.22;MQ=98.70;MQ0=0;OQ=6830.92;QD=38.59;RankSumP=1.00000;SB=-2516.68;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.700T>C;refseq.codonCoord=234;refseq.end=155144081;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=816;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S234P;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=56;refseq.start=155144081;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 155144421 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=93.76;MQ0=0;OQ=350.73;QD=15.94;RankSumP=0.695329;SB=-105.12;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.856C>A;refseq.codonCoord=286;refseq.end=155144421;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=972;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R286R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-47;refseq.start=155144421;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/0
|
|
chr1 155145155 . T C 11 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=96.39;MQ0=0;OQ=56.11;QD=5.61;RankSumP=0.428571;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1200T>C;refseq.codonCoord=400;refseq.end=155145155;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1316;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H400H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=85;refseq.start=155145155;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=filterInsoap-gatk GT 1/0
|
|
chr1 155145361 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=395;Dels=0.00;HRun=2;HaplotypeScore=7.16;MQ=98.63;MQ0=0;OQ=6981.45;QD=17.67;RankSumP=0.287081;SB=-2616.84;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1320T>C;refseq.codonCoord=440;refseq.end=155145361;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1436;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P440P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=30;refseq.start=155145361;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/0
|
|
chr1 155146204 . C T 206.15 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=6.66;MQ=98.01;MQ0=0;OQ=1692.24;QD=14.10;RankSumP=0.365698;SB=-718.24;SecondBestBaseQ=24;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1449C>T;refseq.codonCoord=483;refseq.end=155146204;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1565;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P483P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=38;refseq.start=155146204;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 155149620 . G C 40.61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=473;Dels=0.00;HRun=2;HaplotypeScore=18.13;MQ=98.82;MQ0=0;OQ=9493.69;QD=20.07;RankSumP=0.00000;SB=-2437.63;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2433G>C;refseq.codonCoord=811;refseq.end=155149620;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2549;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P811P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=11;refseq.start=155149620;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=filterInsoap-gatk GT 0/1
|
|
chr1 155149839 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=5.98;MQ=99.00;MQ0=0;OQ=397.16;QD=8.63;RankSumP=0.507665;SB=-155.80;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2544C>A;refseq.codonCoord=848;refseq.end=155149839;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2660;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N848K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=33;refseq.start=155149839;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/0
|
|
chr1 155151135 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3035A>C;refseq.codonCoord=1012;refseq.end=155151135;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3151;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1012T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=73;refseq.start=155151135;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 0/1
|
|
chr1 155151208 . C T 174.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=146;Dels=0.00;HRun=0;HaplotypeScore=5.05;MQ=98.38;MQ0=0;OQ=2301.28;QD=15.76;RankSumP=0.0325081;SB=-764.25;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3108C>T;refseq.codonCoord=1036;refseq.end=155151208;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3224;refseq.name=NM_001080471;refseq.name2=PEAR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1036D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=146;refseq.start=155151208;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 155173705 . T C 184.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.41;MQ0=0;OQ=2050.17;QD=14.64;RankSumP=0.135353;SB=-985.23;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4280A>G;refseq.codingCoordStr_2=c.4400A>G;refseq.codonCoord_1=1427;refseq.codonCoord_2=1467;refseq.end_1=155173705;refseq.end_2=155173705;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=5320;refseq.mrnaCoord_2=5440;refseq.name2_1=ARHGEF11;refseq.name2_2=ARHGEF11;refseq.name_1=NM_014784;refseq.name_2=NM_198236;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H1427R;refseq.proteinCoordStr_2=p.H1467R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=-41;refseq.spliceDist_2=-41;refseq.start_1=155173705;refseq.start_2=155173705;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=Intersection GT 1/0
|
|
chr1 155176319 . G A 191.53 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=182;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=98.02;MQ0=0;OQ=2510.66;QD=13.79;RankSumP=0.475792;SB=-1178.25;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3621C>T;refseq.codingCoordStr_2=c.3741C>T;refseq.codonCoord_1=1207;refseq.codonCoord_2=1247;refseq.end_1=155176319;refseq.end_2=155176319;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4661;refseq.mrnaCoord_2=4781;refseq.name2_1=ARHGEF11;refseq.name2_2=ARHGEF11;refseq.name_1=NM_014784;refseq.name_2=NM_198236;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N1207N;refseq.proteinCoordStr_2=p.N1247N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=155176319;refseq.start_2=155176319;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 1/0
|
|
chr1 155329320 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=687.57;QD=14.63;RankSumP=0.750000;SB=-224.48;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.831C>A;refseq.codonCoord=277;refseq.end=155329320;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1116;refseq.name=NM_001004341;refseq.name2=ETV3L;refseq.positionType=CDS;refseq.proteinCoordStr=p.L277L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=224;refseq.start=155329320;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 0/1
|
|
chr1 155335157 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=103;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=98.86;MQ0=0;OQ=1174.51;QD=11.40;RankSumP=0.368815;SB=-237.67;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.451C>T;refseq.codonCoord=151;refseq.end=155335157;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=736;refseq.name=NM_001004341;refseq.name2=ETV3L;refseq.positionType=CDS;refseq.proteinCoordStr=p.R151W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-36;refseq.start=155335157;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/0
|
|
chr1 155775506 . C T 291.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=95.91;MQ0=0;OQ=4131.73;QD=33.59;RankSumP=1.00000;SB=-1785.65;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1396G>A;refseq.codonCoord=466;refseq.end=155775506;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1554;refseq.name=NM_031281;refseq.name2=FCRL5;refseq.positionType=CDS;refseq.proteinCoordStr=p.V466I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-7;refseq.spliceInfo=splice-donor_-7;refseq.start=155775506;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 155775649 . C T 304.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=249;Dels=0.00;HRun=0;HaplotypeScore=6.47;MQ=98.31;MQ0=0;OQ=10398.04;QD=41.76;RankSumP=1.00000;SB=-4858.37;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1253G>A;refseq.codonCoord=418;refseq.end=155775649;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1411;refseq.name=NM_031281;refseq.name2=FCRL5;refseq.positionType=CDS;refseq.proteinCoordStr=p.G418D;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=130;refseq.start=155775649;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 155780721 . A G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=601;Dels=0.00;HRun=0;HaplotypeScore=13.31;MQ=98.78;MQ0=0;OQ=25259.80;QD=42.03;RankSumP=1.00000;SB=-10580.80;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.799T>C;refseq.codonCoord=267;refseq.end=155780721;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=957;refseq.name=NM_031281;refseq.name2=FCRL5;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y267H;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-46;refseq.start=155780721;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 155824325 . G A 389.61 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.69;MQ0=0;OQ=2311.08;QD=42.02;RankSumP=1.00000;SB=-1065.87;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.516C>T;refseq.codonCoord=172;refseq.end=155824325;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=652;refseq.name=NM_031282;refseq.name2=FCRL4;refseq.positionType=CDS;refseq.proteinCoordStr=p.D172D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-47;refseq.start=155824325;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 155825746 . C T 361.01 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=222;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=98.40;MQ0=0;OQ=9443.49;QD=42.54;RankSumP=1.00000;SB=-3839.28;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.179G>A;refseq.codonCoord=60;refseq.end=155825746;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=315;refseq.name=NM_031282;refseq.name2=FCRL4;refseq.positionType=CDS;refseq.proteinCoordStr=p.R60Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=127;refseq.start=155825746;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 156004025 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.chr=chr1;refseq.end=156004817;refseq.haplotypeReference=*;refseq.inCodingRegion=false;refseq.name=NM_030764;refseq.name2=FCRL2;refseq.positionType=intron;refseq.start=156003934;refseq.transcriptStrand=-;set=FilteredInAll GT 1/0
|
|
chr1 156038504 . C T 322.82 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=167;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=98.55;MQ0=0;OQ=6664.53;QD=39.91;RankSumP=1.00000;SB=-3287.32;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.711G>A;refseq.codingCoordStr_2=c.711G>A;refseq.codingCoordStr_3=c.711G>A;refseq.codonCoord_1=237;refseq.codonCoord_2=237;refseq.codonCoord_3=237;refseq.end_1=156038504;refseq.end_2=156038504;refseq.end_3=156038504;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=824;refseq.mrnaCoord_2=824;refseq.mrnaCoord_3=824;refseq.name2_1=FCRL1;refseq.name2_2=FCRL1;refseq.name2_3=FCRL1;refseq.name_1=NM_001159397;refseq.name_2=NM_001159398;refseq.name_3=NM_052938;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P237P;refseq.proteinCoordStr_2=p.P237P;refseq.proteinCoordStr_3=p.P237P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.referenceCodon_3=CCG;refseq.spliceDist_1=104;refseq.spliceDist_2=104;refseq.spliceDist_3=104;refseq.start_1=156038504;refseq.start_2=156038504;refseq.start_3=156038504;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;refseq.variantCodon_3=CCA;set=Intersection GT 1/1
|
|
chr1 156039006 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.392T>G;refseq.codingCoordStr_2=c.392T>G;refseq.codingCoordStr_3=c.392T>G;refseq.codonCoord_1=131;refseq.codonCoord_2=131;refseq.codonCoord_3=131;refseq.end_1=156039006;refseq.end_2=156039006;refseq.end_3=156039006;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=505;refseq.mrnaCoord_2=505;refseq.mrnaCoord_3=505;refseq.name2_1=FCRL1;refseq.name2_2=FCRL1;refseq.name2_3=FCRL1;refseq.name_1=NM_001159397;refseq.name_2=NM_001159398;refseq.name_3=NM_052938;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V131G;refseq.proteinCoordStr_2=p.V131G;refseq.proteinCoordStr_3=p.V131G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.referenceCodon_3=GTC;refseq.spliceDist_1=73;refseq.spliceDist_2=73;refseq.spliceDist_3=73;refseq.start_1=156039006;refseq.start_2=156039006;refseq.start_3=156039006;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;refseq.variantCodon_3=GGC;set=FilteredInAll GT 0/1
|
|
chr1 156043523 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.45A>C;refseq.codingCoordStr_2=c.45A>C;refseq.codingCoordStr_3=c.45A>C;refseq.codonCoord_1=15;refseq.codonCoord_2=15;refseq.codonCoord_3=15;refseq.end_1=156043523;refseq.end_2=156043523;refseq.end_3=156043523;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=158;refseq.mrnaCoord_2=158;refseq.mrnaCoord_3=158;refseq.name2_1=FCRL1;refseq.name2_2=FCRL1;refseq.name2_3=FCRL1;refseq.name_1=NM_001159397;refseq.name_2=NM_001159398;refseq.name_3=NM_052938;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E15D;refseq.proteinCoordStr_2=p.E15D;refseq.proteinCoordStr_3=p.E15D;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.referenceCodon_3=GAA;refseq.spliceDist_1=-8;refseq.spliceDist_2=-8;refseq.spliceDist_3=-8;refseq.spliceInfo_1=splice-donor_-8;refseq.spliceInfo_2=splice-donor_-8;refseq.spliceInfo_3=splice-donor_-8;refseq.start_1=156043523;refseq.start_2=156043523;refseq.start_3=156043523;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;refseq.variantCodon_3=GAC;set=FilteredInAll GT 1/0
|
|
chr1 156324234 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.727A>C;refseq.codonCoord=243;refseq.end=156324234;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1131;refseq.name=NM_018240;refseq.name2=KIRREL;refseq.positionType=CDS;refseq.proteinCoordStr=p.T243P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-41;refseq.start=156324234;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 156331454 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=126;Dels=0.00;HRun=2;HaplotypeScore=16.31;MQ=98.52;MQ0=0;OQ=60.37;QD=0.48;RankSumP=0.00000;SB=179.59;SecondBestBaseQ=17;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2194A>C;refseq.codonCoord=732;refseq.end=156331454;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2598;refseq.name=NM_018240;refseq.name2=KIRREL;refseq.positionType=CDS;refseq.proteinCoordStr=p.T732P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=397;refseq.start=156331454;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 0/1
|
|
chr1 156656841 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.440C>G;refseq.codonCoord=147;refseq.end=156656841;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=440;refseq.name=NM_001004476;refseq.name2=OR10K2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A147G;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=440;refseq.start=156656841;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 156702415 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.440C>G;refseq.codonCoord=147;refseq.end=156702415;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=440;refseq.name=NM_001004473;refseq.name2=OR10K1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A147G;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=440;refseq.start=156702415;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 156717172 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.881T>G;refseq.codonCoord=294;refseq.end=156717172;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=881;refseq.name=NM_001004472;refseq.name2=OR10R2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V294G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-128;refseq.start=156717172;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 156784135 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.385G>T;refseq.codonCoord=129;refseq.end=156784135;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=385;refseq.name=NM_001005189;refseq.name2=OR6Y1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V129L;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=385;refseq.start=156784135;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=FilteredInAll GT 1/0
|
|
chr1 156815412 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=468;Dels=0.00;HRun=1;HaplotypeScore=15.72;MQ=98.97;MQ0=0;OQ=9724.04;QD=20.78;RankSumP=0.479571;SB=-2628.89;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.902T>C;refseq.codonCoord=301;refseq.end=156815412;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=902;refseq.name=NM_001004477;refseq.name2=OR10X1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I301T;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-80;refseq.start=156815412;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 156843791 rs2427808 A T 20.39 PASS AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=95.51;MQ0=0;OQ=151.97;QD=12.66;SB=-6.99;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.939A>T;refseq.codonCoord=313;refseq.end=156843791;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=939;refseq.name=NM_001004478;refseq.name2=OR10Z1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G313G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-4;refseq.spliceInfo=splice-donor_-4;refseq.start=156843791;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=gatk GT:AD:DP:GL:GQ 0/1:7,5:12:-22.09,-3.61,-27.63:99
|
|
chr1 156886352 . A C 298.15 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.12;MQ0=0;OQ=4039.77;QD=41.22;RankSumP=1.00000;SB=-1039.26;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3487T>G;refseq.codonCoord=1163;refseq.end=156886352;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3686;refseq.name=NM_003126;refseq.name2=SPTA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1163A;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=156886352;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 156910990 . A C 0.01 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=148;Dels=0.00;HRun=2;HaplotypeScore=9.94;MQ=98.61;MQ0=0;OQ=143.21;QD=0.97;RankSumP=0.00000;SB=203.67;SecondBestBaseQ=22;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1212T>G;refseq.codonCoord=404;refseq.end=156910990;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1411;refseq.name=NM_003126;refseq.name2=SPTA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G404G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-37;refseq.start=156910990;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 156914119 . A T 434.74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=131;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.90;MQ0=0;OQ=5321.44;QD=40.62;RankSumP=1.00000;SB=-1816.34;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.942T>A;refseq.codonCoord=314;refseq.end=156914119;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1141;refseq.name=NM_003126;refseq.name2=SPTA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A314A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-16;refseq.start=156914119;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 156921660 . G A 232.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=275;Dels=0.00;HRun=1;HaplotypeScore=3.32;MQ=98.77;MQ0=0;OQ=11799.69;QD=42.91;RankSumP=1.00000;SB=-3483.92;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.126C>T;refseq.codonCoord=42;refseq.end=156921660;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=325;refseq.name=NM_003126;refseq.name2=SPTA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V42V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=102;refseq.start=156921660;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/1
|
|
chr1 156936844 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=2.53638e-08;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.223A>C;refseq.codonCoord=75;refseq.end=156936844;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=223;refseq.name=NM_001005279;refseq.name2=OR6K2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T75P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=223;refseq.start=156936844;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 157002219 . C T 332.28 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=98.69;MQ0=0;OQ=11604.05;QD=41.74;RankSumP=1.00000;SB=-4566.00;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.878G>A;refseq.codonCoord=293;refseq.end=157002219;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=878;refseq.name=NM_001005185;refseq.name2=OR6N1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R293H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-62;refseq.start=157002219;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 157002315 . T C 300.23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=116;Dels=0.00;HRun=1;HaplotypeScore=1.27;MQ=98.24;MQ0=0;OQ=4317.40;QD=37.22;RankSumP=1.00000;SB=-1704.03;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.782A>G;refseq.codonCoord=261;refseq.end=157002315;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=782;refseq.name=NM_001005185;refseq.name2=OR6N1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q261R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-158;refseq.start=157002315;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/1
|
|
chr1 157002364 . A G 325.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=98.68;MQ0=0;OQ=3850.34;QD=41.40;RankSumP=1.00000;SB=-1773.40;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.733T>C;refseq.codonCoord=245;refseq.end=157002364;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=733;refseq.name=NM_001005185;refseq.name2=OR6N1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F245L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-207;refseq.start=157002364;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/1
|
|
chr1 157002516 . A G 382.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1537.03;QD=39.41;RankSumP=1.00000;SB=-756.62;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.581T>C;refseq.codonCoord=194;refseq.end=157002516;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=581;refseq.name=NM_001005185;refseq.name2=OR6N1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I194T;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=-359;refseq.start=157002516;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 157002839 . G A 297.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=250;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.96;MQ0=0;OQ=10519.70;QD=42.08;RankSumP=1.00000;SB=-3837.37;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.258C>T;refseq.codonCoord=86;refseq.end=157002839;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=258;refseq.name=NM_001005185;refseq.name2=OR6N1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L86L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=258;refseq.start=157002839;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/1
|
|
chr1 157003069 . C T 136.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=92;Dels=0.00;HRun=1;HaplotypeScore=6.93;MQ=98.72;MQ0=0;OQ=3942.90;QD=42.86;RankSumP=1.00000;SB=-1131.98;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.28G>A;refseq.codonCoord=10;refseq.end=157003069;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=28;refseq.name=NM_001005185;refseq.name2=OR6N1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A10T;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=28;refseq.start=157003069;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 157080443 . A G 83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=105;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=98.20;MQ0=0;OQ=3894.96;QD=37.09;RankSumP=1.00000;SB=-1321.51;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.477A>G;refseq.codonCoord=159;refseq.end=157080443;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=677;refseq.name=NM_002432;refseq.name2=MNDA;refseq.positionType=CDS;refseq.proteinCoordStr=p.P159P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=75;refseq.start=157080443;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 157082029 . T G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=247;Dels=0.00;HRun=2;HaplotypeScore=19.39;MQ=98.53;MQ0=0;OQ=118.91;QD=0.48;RankSumP=0.00000;SB=263.87;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.599T>G;refseq.codonCoord=200;refseq.end=157082029;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=799;refseq.name=NM_002432;refseq.name2=MNDA;refseq.positionType=CDS;refseq.proteinCoordStr=p.V200G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=29;refseq.start=157082029;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 157178545 . C A 22.13 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=27;DP=194;Dels=0.00;HRun=1;HaplotypeScore=11.20;MQ=97.93;MQ0=0;QD=0.11;RankSumP=0.00000;SB=293.87;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.734C>A;refseq.codingCoordStr_2=c.707C>A;refseq.codingCoordStr_3=c.734C>A;refseq.codingCoordStr_4=c.707C>A;refseq.codonCoord_1=245;refseq.codonCoord_2=236;refseq.codonCoord_3=245;refseq.codonCoord_4=236;refseq.end_1=157178545;refseq.end_2=157178545;refseq.end_3=157178545;refseq.end_4=157178545;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=979;refseq.mrnaCoord_2=952;refseq.mrnaCoord_3=979;refseq.mrnaCoord_4=952;refseq.name2_1=PYHIN1;refseq.name2_2=PYHIN1;refseq.name2_3=PYHIN1;refseq.name2_4=PYHIN1;refseq.name_1=NM_152501;refseq.name_2=NM_198928;refseq.name_3=NM_198929;refseq.name_4=NM_198930;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T245K;refseq.proteinCoordStr_2=p.T236K;refseq.proteinCoordStr_3=p.T245K;refseq.proteinCoordStr_4=p.T236K;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.referenceCodon_3=ACG;refseq.referenceCodon_4=ACG;refseq.spliceDist_1=155;refseq.spliceDist_2=155;refseq.spliceDist_3=155;refseq.spliceDist_4=155;refseq.start_1=157178545;refseq.start_2=157178545;refseq.start_3=157178545;refseq.start_4=157178545;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantAA_3=Lys;refseq.variantAA_4=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;refseq.variantCodon_3=AAG;refseq.variantCodon_4=AAG;set=FilteredInAll GT 1/0
|
|
chr1 157253101 . G C 178.16 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=431;Dels=0.00;HRun=0;HaplotypeScore=5.91;MQ=98.78;MQ0=0;OQ=10388.32;QD=24.10;RankSumP=0.212251;SB=-3669.13;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.536G>C;refseq.codonCoord=179;refseq.end=157253101;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=826;refseq.name=NM_005531;refseq.name2=IFI16;refseq.positionType=CDS;refseq.proteinCoordStr=p.S179T;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-14;refseq.start=157253101;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 0/1
|
|
chr1 157254894 . T C 133.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=146;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=98.98;MQ0=0;OQ=2221.90;QD=15.22;RankSumP=0.229671;SB=-911.23;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.801T>C;refseq.codonCoord=267;refseq.end=157254894;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1091;refseq.name=NM_005531;refseq.name2=IFI16;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y267Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-172;refseq.start=157254894;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/0
|
|
chr1 157269001 . C A 280.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=236;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=98.52;MQ0=0;OQ=3973.32;QD=16.84;RankSumP=0.00745220;SB=-1074.90;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1225C>A;refseq.codonCoord=409;refseq.end=157269001;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1515;refseq.name=NM_005531;refseq.name2=IFI16;refseq.positionType=CDS;refseq.proteinCoordStr=p.R409S;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=64;refseq.start=157269001;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=filterInsoap-gatk GT 1/0
|
|
chr1 157269013 . T A 233.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=277;Dels=0.00;HRun=1;HaplotypeScore=6.26;MQ=98.52;MQ0=0;OQ=4776.52;QD=17.24;RankSumP=0.305142;SB=-1094.44;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1237T>A;refseq.codonCoord=413;refseq.end=157269013;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1527;refseq.name=NM_005531;refseq.name2=IFI16;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y413N;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=76;refseq.start=157269013;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 157288130 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=85;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=98.74;MQ0=0;OQ=1531.33;QD=18.02;RankSumP=0.300915;SB=-238.89;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1535C>T;refseq.codonCoord=512;refseq.end=157288130;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1825;refseq.name=NM_005531;refseq.name2=IFI16;refseq.positionType=CDS;refseq.proteinCoordStr=p.S512F;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=38;refseq.start=157288130;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 0/1
|
|
chr1 157428390 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.129T>G;refseq.codingCoordStr_2=c.231T>G;refseq.codonCoord_1=43;refseq.codonCoord_2=77;refseq.end_1=157428390;refseq.end_2=157428390;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=271;refseq.mrnaCoord_2=410;refseq.name2_1=CADM3;refseq.name2_2=CADM3;refseq.name_1=NM_001127173;refseq.name_2=NM_021189;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G43G;refseq.proteinCoordStr_2=p.G77G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=41;refseq.spliceDist_2=41;refseq.start_1=157428390;refseq.start_2=157428390;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 157436265 . T C 158.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=205;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=98.96;MQ0=0;OQ=2764.01;QD=13.48;RankSumP=0.380602;SB=-435.58;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1053T>C;refseq.codingCoordStr_2=c.1155T>C;refseq.codonCoord_1=351;refseq.codonCoord_2=385;refseq.end_1=157436265;refseq.end_2=157436265;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1195;refseq.mrnaCoord_2=1334;refseq.name2_1=CADM3;refseq.name2_2=CADM3;refseq.name_1=NM_001127173;refseq.name_2=NM_021189;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L351L;refseq.proteinCoordStr_2=p.L385L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTT;refseq.referenceCodon_2=CTT;refseq.spliceDist_1=-26;refseq.spliceDist_2=-26;refseq.start_1=157436265;refseq.start_2=157436265;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;set=Intersection GT 1/0
|
|
chr1 157441978 . G A 296.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=210;Dels=0.00;HRun=0;HaplotypeScore=11.21;MQ=98.82;MQ0=0;OQ=3839.13;QD=18.28;RankSumP=0.257551;SB=-1064.14;SecondBestBaseQ=27;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.131G>A;refseq.codingCoordStr_2=c.125G>A;refseq.codonCoord_1=44;refseq.codonCoord_2=42;refseq.end_1=157441978;refseq.end_2=157441978;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=154;refseq.mrnaCoord_2=365;refseq.name2_1=DARC;refseq.name2_2=DARC;refseq.name_1=NM_001122951;refseq.name_2=NM_002036;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G44D;refseq.proteinCoordStr_2=p.G42D;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=154;refseq.spliceDist_2=104;refseq.start_1=157441978;refseq.start_2=157441978;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 1/0
|
|
chr1 157544185 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=9.41725e-07;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.613C>A;refseq.codonCoord=205;refseq.end=157544185;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=712;refseq.name=NM_002001;refseq.name2=FCER1A;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q205K;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=24;refseq.start=157544185;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 1/0
|
|
chr1 157676358 . G T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=611;Dels=0.00;HRun=1;HaplotypeScore=18.95;MQ=98.87;MQ0=0;OQ=23408.70;QD=38.31;RankSumP=1.00000;SB=-8420.98;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.186G>T;refseq.codonCoord=62;refseq.end=157676358;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=223;refseq.name=NM_012351;refseq.name2=OR10J1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M62I;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=223;refseq.start=157676358;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/1
|
|
chr1 157676481 . A G 315.14 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=260;Dels=0.00;HRun=0;HaplotypeScore=12.58;MQ=98.41;MQ0=0;OQ=4518.18;QD=17.38;RankSumP=0.158016;SB=-1680.71;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.309A>G;refseq.codonCoord=103;refseq.end=157676481;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=346;refseq.name=NM_012351;refseq.name2=OR10J1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I103M;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=346;refseq.start=157676481;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 157676494 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.322T>G;refseq.codonCoord=108;refseq.end=157676494;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=359;refseq.name=NM_012351;refseq.name2=OR10J1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C108G;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=359;refseq.start=157676494;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 157676964 . T A 329.61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=406;Dels=0.00;HRun=0;HaplotypeScore=3.66;MQ=98.90;MQ0=0;OQ=8037.67;QD=19.80;RankSumP=0.115983;SB=-2490.39;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.792T>A;refseq.codonCoord=264;refseq.end=157676964;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=829;refseq.name=NM_012351;refseq.name2=OR10J1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C264*;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-260;refseq.start=157676964;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TGA;set=Intersection GT 1/0
|
|
chr1 157771725 . G A 243.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=304;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=98.84;MQ0=0;OQ=6039.13;QD=19.87;RankSumP=0.336942;SB=-1963.65;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.697C>T;refseq.codonCoord=233;refseq.end=157771725;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=697;refseq.name=NM_001004469;refseq.name2=OR10J5;refseq.positionType=CDS;refseq.proteinCoordStr=p.R233W;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-234;refseq.start=157771725;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/0
|
|
chr1 157771921 . C T 302.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=481;Dels=0.00;HRun=0;HaplotypeScore=11.87;MQ=98.85;MQ0=0;OQ=7937.72;QD=16.50;RankSumP=0.439443;SB=-2367.02;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.501G>A;refseq.codonCoord=167;refseq.end=157771921;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=501;refseq.name=NM_001004469;refseq.name2=OR10J5;refseq.positionType=CDS;refseq.proteinCoordStr=p.P167P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-430;refseq.start=157771921;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 157825040 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.590T>C;refseq.codonCoord=197;refseq.end=157825040;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=686;refseq.name=NM_001639;refseq.name2=APCS;refseq.positionType=CDS;refseq.proteinCoordStr=p.L197P;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-245;refseq.start=157825040;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 157950869 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.31A>C;refseq.codonCoord=11;refseq.end=157950869;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=135;refseq.name=NM_000567;refseq.name2=CRP;refseq.positionType=CDS;refseq.proteinCoordStr=p.T11P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-31;refseq.start=157950869;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 158044651 . C T 65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.486122;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.112C>T;refseq.codonCoord=38;refseq.end=158044651;refseq.frame=0;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=154;refseq.name=NM_001004310;refseq.name2=FCRL6;refseq.positionType=CDS;refseq.proteinCoordStr=p.R38*;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=60;refseq.start=158044651;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TGA;set=soap GT 0/1
|
|
chr1 158045534 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=135;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=91.69;MQ0=0;OQ=2399.18;QD=17.77;RankSumP=0.0525050;SB=-1046.61;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.479G>A;refseq.codonCoord=160;refseq.end=158045534;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=521;refseq.name=NM_001004310;refseq.name2=FCRL6;refseq.positionType=CDS;refseq.proteinCoordStr=p.G160D;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-126;refseq.start=158045534;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/0
|
|
chr1 158045607 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=2.69;MQ=91.67;MQ0=4;OQ=457.17;QD=9.14;RankSumP=0.622011;SB=-240.59;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.552T>C;refseq.codonCoord=184;refseq.end=158045607;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=594;refseq.name=NM_001004310;refseq.name2=FCRL6;refseq.positionType=CDS;refseq.proteinCoordStr=p.P184P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-53;refseq.start=158045607;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=soap-filterIngatk GT 1/0
|
|
chr1 158052037 . C T 189.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=209;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=98.90;MQ0=0;OQ=4282.89;QD=20.49;RankSumP=0.368540;SB=-1285.17;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1267C>T;refseq.codonCoord=423;refseq.end=158052037;refseq.frame=0;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1309;refseq.name=NM_001004310;refseq.name2=FCRL6;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q423*;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=88;refseq.start=158052037;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=Intersection GT 0/1
|
|
chr1 158052049 . A G 243.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=200;Dels=0.00;HRun=1;HaplotypeScore=3.26;MQ=98.76;MQ0=0;OQ=3212.69;QD=16.06;RankSumP=0.495406;SB=-1392.83;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1279A>G;refseq.codonCoord=427;refseq.end=158052049;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1321;refseq.name=NM_001004310;refseq.name2=FCRL6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S427G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=100;refseq.start=158052049;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 158109547 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=1.08517e-07;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1388A>G;refseq.codonCoord=463;refseq.end=158109547;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1406;refseq.name=NM_012337;refseq.name2=CCDC19;refseq.positionType=CDS;refseq.proteinCoordStr=p.E463G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=36;refseq.start=158109547;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 158120875 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=592;Dels=0.00;HRun=2;HaplotypeScore=7.89;MQ=98.91;MQ0=0;OQ=11661.96;QD=19.70;RankSumP=0.171101;SB=-3937.10;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.872A>G;refseq.codonCoord=291;refseq.end=158120875;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=890;refseq.name=NM_012337;refseq.name2=CCDC19;refseq.positionType=CDS;refseq.proteinCoordStr=p.E291G;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-26;refseq.start=158120875;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 158164724 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=96.65;MQ0=0;OQ=556.05;QD=14.63;RankSumP=0.196972;SB=-237.62;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3078T>C;refseq.codingCoordStr_2=c.3030T>C;refseq.codonCoord_1=1026;refseq.codonCoord_2=1010;refseq.end_1=158164724;refseq.end_2=158164724;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3276;refseq.mrnaCoord_2=3228;refseq.name2_1=IGSF9;refseq.name2_2=IGSF9;refseq.name_1=NM_001135050;refseq.name_2=NM_020789;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S1026S;refseq.proteinCoordStr_2=p.S1010S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGT;refseq.referenceCodon_2=AGT;refseq.spliceDist_1=-153;refseq.spliceDist_2=-153;refseq.start_1=158164724;refseq.start_2=158164724;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;set=Intersection GT 0/1
|
|
chr1 158172873 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.613A>C;refseq.codingCoordStr_2=c.613A>C;refseq.codonCoord_1=205;refseq.codonCoord_2=205;refseq.end_1=158172873;refseq.end_2=158172873;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=811;refseq.mrnaCoord_2=811;refseq.name2_1=IGSF9;refseq.name2_2=IGSF9;refseq.name_1=NM_001135050;refseq.name_2=NM_020789;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T205P;refseq.proteinCoordStr_2=p.T205P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=58;refseq.spliceDist_2=58;refseq.start_1=158172873;refseq.start_2=158172873;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 158189735 . T G 252.66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=450;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=98.89;MQ0=0;OQ=18312.47;QD=40.69;RankSumP=1.00000;SB=-5978.36;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.379A>C;refseq.codingCoordStr_3=c.379A>C;refseq.codonCoord_2=127;refseq.codonCoord_3=127;refseq.end_1=158189848;refseq.end_2=158189735;refseq.end_3=158189735;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=496;refseq.mrnaCoord_3=496;refseq.name2_1=SLAMF9;refseq.name2_2=SLAMF9;refseq.name2_3=SLAMF9;refseq.name_1=NM_001146173;refseq.name_2=NM_001146172;refseq.name_3=NM_033438;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.I127L;refseq.proteinCoordStr_3=p.I127L;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceCodon_2=ATA;refseq.referenceCodon_3=ATA;refseq.spliceDist_2=-13;refseq.spliceDist_3=-13;refseq.start_1=158188291;refseq.start_2=158189735;refseq.start_3=158189735;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_2=CTA;refseq.variantCodon_3=CTA;set=Intersection GT 1/1
|
|
chr1 158267059 . A T 109.33 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=237;Dels=0.00;HRun=1;HaplotypeScore=13.56;MQ=98.57;MQ0=0;OQ=4247.36;QD=17.92;RankSumP=0.187427;SB=-1762.70;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1095T>A;refseq.codonCoord=365;refseq.end=158267059;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1349;refseq.name=NM_145167;refseq.name2=PIGM;refseq.positionType=CDS;refseq.proteinCoordStr=p.F365L;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=1349;refseq.start=158267059;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=Intersection GT 0/1
|
|
chr1 158267753 . T G 8 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=5;RankSumP=9.59083e-05;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.401A>C;refseq.codonCoord=134;refseq.end=158267753;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=655;refseq.name=NM_145167;refseq.name2=PIGM;refseq.positionType=CDS;refseq.proteinCoordStr=p.N134T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=655;refseq.start=158267753;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 158328964 . G A 144.65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.70;MQ=96.06;MQ0=0;OQ=670.56;QD=18.63;RankSumP=0.436856;SB=-337.88;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1458C>T;refseq.codonCoord=486;refseq.end=158328964;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1604;refseq.name=NM_052868;refseq.name2=IGSF8;refseq.positionType=CDS;refseq.proteinCoordStr=p.D486D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=146;refseq.start=158328964;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/0
|
|
chr1 158329096 . C T 258.74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=139;Dels=0.00;HRun=1;HaplotypeScore=2.06;MQ=98.15;MQ0=0;OQ=5624.14;QD=40.46;RankSumP=1.00000;SB=-2752.51;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1326G>A;refseq.codonCoord=442;refseq.end=158329096;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1472;refseq.name=NM_052868;refseq.name2=IGSF8;refseq.positionType=CDS;refseq.proteinCoordStr=p.E442E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=14;refseq.start=158329096;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 158329351 . A G 371.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=97.55;MQ0=0;OQ=2225.62;QD=35.33;RankSumP=1.00000;SB=-1139.69;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1299T>C;refseq.codonCoord=433;refseq.end=158329351;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1445;refseq.name=NM_052868;refseq.name2=IGSF8;refseq.positionType=CDS;refseq.proteinCoordStr=p.H433H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-14;refseq.start=158329351;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 158371711 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.chr=chr1;refseq.codingCoordStr=c.2115+2;refseq.end=158371711;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_000702;refseq.name2=ATP1A2;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=158371711;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 158391499 . G A 119.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=157;Dels=0.00;HRun=0;HaplotypeScore=0.42;MQ=98.67;MQ0=0;OQ=2053.51;QD=13.08;RankSumP=0.283986;SB=-736.05;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.248G>A;refseq.codonCoord=83;refseq.end=158391499;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=727;refseq.name=NM_144699;refseq.name2=ATP1A4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G83D;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=41;refseq.start=158391499;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/0
|
|
chr1 158400829 . C T 361.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=97.63;MQ0=0;OQ=1535.02;QD=39.36;RankSumP=1.00000;SB=-519.16;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1038C>T;refseq.codonCoord=346;refseq.end=158400829;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1517;refseq.name=NM_144699;refseq.name2=ATP1A4;refseq.positionType=CDS;refseq.proteinCoordStr=p.A346A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-10;refseq.spliceInfo=splice-donor_-10;refseq.start=158400829;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 158402974 . G A 263.14 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=327;Dels=0.00;HRun=0;HaplotypeScore=12.40;MQ=86.15;MQ0=35;OQ=5073.55;QD=15.52;RankSumP=0.0293198;SB=-1546.52;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1080G>A;refseq.codonCoord=360;refseq.end=158402974;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1559;refseq.name=NM_144699;refseq.name2=ATP1A4;refseq.positionType=CDS;refseq.proteinCoordStr=p.A360A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=33;refseq.start=158402974;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 158407820 . C T 72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=211;Dels=0.00;HRun=2;HaplotypeScore=5.62;MQ=98.90;MQ0=0;OQ=9161.40;QD=43.42;RankSumP=1.00000;SB=-4573.20;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1647C>T;refseq.codonCoord=549;refseq.end=158407820;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2126;refseq.name=NM_144699;refseq.name2=ATP1A4;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y549Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-35;refseq.start=158407820;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 158412606 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=4;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2412A>C;refseq.codonCoord=804;refseq.end=158412606;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2891;refseq.name=NM_144699;refseq.name2=ATP1A4;refseq.positionType=CDS;refseq.proteinCoordStr=p.I804I;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=-55;refseq.start=158412606;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=FilteredInAll GT 0/1
|
|
chr1 158437732 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1133A>G;refseq.codonCoord=378;refseq.end=158437732;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1390;refseq.name=NM_001231;refseq.name2=CASQ1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E378G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=74;refseq.start=158437732;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 158437755 . A T 22 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=0;RankSumP=0.00701145;SecondBestBaseQ=17;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1156A>T;refseq.codonCoord=386;refseq.end=158437755;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1413;refseq.name=NM_001231;refseq.name2=CASQ1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N386Y;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=97;refseq.start=158437755;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=FilteredInAll GT 0/1
|
|
chr1 158476159 . C G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=22;DP=158;Dels=0.00;HRun=1;HaplotypeScore=61.93;MQ=92.61;MQ0=0;OQ=163.01;QD=1.03;RankSumP=0.00000;SB=98.36;SecondBestBaseQ=7;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_5=c.675G>C;refseq.codonCoord_5=225;refseq.end_1=158476159;refseq.end_2=158476159;refseq.end_3=158476159;refseq.end_4=158476159;refseq.end_5=158476159;refseq.frame_5=2;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=*;refseq.haplotypeAlternate_3=*;refseq.haplotypeAlternate_4=*;refseq.haplotypeAlternate_5=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=C;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=1187;refseq.mrnaCoord_2=1113;refseq.mrnaCoord_3=1187;refseq.mrnaCoord_4=954;refseq.mrnaCoord_5=887;refseq.name2_1=DCAF8;refseq.name2_2=DCAF8;refseq.name2_3=DCAF8;refseq.name2_4=DCAF8;refseq.name2_5=DCAF8;refseq.name_1=NR_028103;refseq.name_2=NR_028104;refseq.name_3=NR_028105;refseq.name_4=NR_028106;refseq.name_5=NM_015726;refseq.numMatchingRecords=5;refseq.positionType_1=non_coding_exon;refseq.positionType_2=non_coding_exon;refseq.positionType_3=non_coding_exon;refseq.positionType_4=non_coding_exon;refseq.positionType_5=CDS;refseq.proteinCoordStr_5=p.R225R;refseq.referenceAA_5=Arg;refseq.referenceCodon_5=CGG;refseq.spliceDist_1=-49;refseq.spliceDist_2=-49;refseq.spliceDist_3=-523;refseq.spliceDist_4=-523;refseq.spliceDist_5=-49;refseq.start_1=158476159;refseq.start_2=158476159;refseq.start_3=158476159;refseq.start_4=158476159;refseq.start_5=158476159;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_5=Arg;refseq.variantCodon_5=CGC;set=FilteredInAll GT 1/0
|
|
chr1 158570040 . G A 176.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=203;Dels=0.00;HRun=1;HaplotypeScore=8.87;MQ=99.00;MQ0=0;OQ=8712.42;QD=42.92;RankSumP=1.00000;SB=-3776.90;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.363C>T;refseq.codingCoordStr_2=c.363C>T;refseq.codonCoord_1=121;refseq.codonCoord_2=121;refseq.end_1=158570040;refseq.end_2=158570040;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=757;refseq.mrnaCoord_2=757;refseq.name2_1=COPA;refseq.name2_2=COPA;refseq.name_1=NM_001098398;refseq.name_2=NM_004371;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N121N;refseq.proteinCoordStr_2=p.N121N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-24;refseq.spliceDist_2=-24;refseq.start_1=158570040;refseq.start_2=158570040;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 1/1
|
|
chr1 158579828 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=5;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.-244A>C;refseq.codingCoordStr_2=c.-244A>C;refseq.codingCoordStr_3=c.18T>G;refseq.codonCoord_3=6;refseq.end_1=158579828;refseq.end_2=158579828;refseq.end_3=158579828;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=151;refseq.mrnaCoord_2=151;refseq.mrnaCoord_3=142;refseq.name2_1=COPA;refseq.name2_2=COPA;refseq.name2_3=NCSTN;refseq.name_1=NM_001098398;refseq.name_2=NM_004371;refseq.name_3=NM_015331;refseq.numMatchingRecords=3;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.G6G;refseq.referenceAA_3=Gly;refseq.referenceCodon_3=GGT;refseq.spliceDist_1=151;refseq.spliceDist_2=151;refseq.spliceDist_3=-68;refseq.start_1=158579828;refseq.start_2=158579828;refseq.start_3=158579828;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=+;refseq.variantAA_3=Gly;refseq.variantCodon_3=GGG;set=FilteredInAll GT 1/0
|
|
chr1 158660529 . A G 122.15 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=97.92;MQ0=0;OQ=517.80;QD=21.57;RankSumP=0.424996;SB=-88.35;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1137A>G;refseq.codonCoord=379;refseq.end=158660529;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1620;refseq.name=NM_020335;refseq.name2=VANGL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K379K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=64;refseq.start=158660529;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 0/1
|
|
chr1 158661561 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=301;Dels=0.00;HRun=2;HaplotypeScore=17.75;MQ=98.84;MQ0=0;OQ=4364.94;QD=14.50;RankSumP=8.32250e-06;SB=-1783.15;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1335A>C;refseq.codonCoord=445;refseq.end=158661561;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1818;refseq.name=NM_020335;refseq.name2=VANGL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G445G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=30;refseq.start=158661561;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=filterInsoap-gatk GT 0/1
|
|
chr1 158661627 . G A 247.01 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=6.31;MQ=98.71;MQ0=0;OQ=3884.48;QD=18.77;RankSumP=0.276451;SB=-1246.68;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1401G>A;refseq.codonCoord=467;refseq.end=158661627;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1884;refseq.name=NM_020335;refseq.name2=VANGL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P467P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=96;refseq.start=158661627;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/0
|
|
chr1 158759594 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.13T>G;refseq.codonCoord=5;refseq.end=158759594;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=73;refseq.name=NM_052931;refseq.name2=SLAMF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.F5V;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-37;refseq.start=158759594;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=FilteredInAll GT 0/1
|
|
chr1 158975724 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9T>G;refseq.codonCoord=3;refseq.end=158975724;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=24;refseq.name=NM_021181;refseq.name2=SLAMF7;refseq.positionType=CDS;refseq.proteinCoordStr=p.G3G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=24;refseq.start=158975724;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 159050245 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.650A>C;refseq.codonCoord=217;refseq.end=159050245;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=700;refseq.name=NM_002348;refseq.name2=LY9;refseq.positionType=CDS;refseq.proteinCoordStr=p.D217A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-81;refseq.start=159050245;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 159050899 . A C 13.67 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=136;Dels=0.00;HRun=3;HaplotypeScore=17.52;MQ=97.90;MQ0=0;QD=0.10;RankSumP=0.00000;SB=164.52;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.796A>C;refseq.codonCoord=266;refseq.end=159050899;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=846;refseq.name=NM_002348;refseq.name2=LY9;refseq.positionType=CDS;refseq.proteinCoordStr=p.T266P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=66;refseq.start=159050899;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 159060066 . A G 232.25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=258;Dels=0.00;HRun=0;HaplotypeScore=12.99;MQ=99.00;MQ0=0;OQ=10045.32;QD=38.94;RankSumP=1.00000;SB=-4214.30;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1686A>G;refseq.codonCoord=562;refseq.end=159060066;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1736;refseq.name=NM_002348;refseq.name2=LY9;refseq.positionType=CDS;refseq.proteinCoordStr=p.V562V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-145;refseq.start=159060066;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 159060184 . A G 324.07 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1416.79;QD=38.29;RankSumP=1.00000;SB=-200.80;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1804A>G;refseq.codonCoord=602;refseq.end=159060184;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1854;refseq.name=NM_002348;refseq.name2=LY9;refseq.positionType=CDS;refseq.proteinCoordStr=p.M602V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-27;refseq.start=159060184;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 159118450 . A T 351.19 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=233;Dels=0.00;HRun=0;HaplotypeScore=10.72;MQ=68.06;MQ0=4;OQ=4332.00;QD=18.59;RankSumP=0.0441705;SB=-1797.29;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.326T>A;refseq.codonCoord=109;refseq.end=159118450;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=442;refseq.name=NM_017625;refseq.name2=ITLN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V109D;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-80;refseq.start=159118450;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 0/1
|
|
chr1 159118518 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=231;Dels=0.00;HRun=0;HaplotypeScore=18.03;MQ=68.93;MQ0=11;OQ=2872.03;QD=12.43;RankSumP=0.183798;SB=-1297.38;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.258C>T;refseq.codonCoord=86;refseq.end=159118518;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=374;refseq.name=NM_017625;refseq.name2=ITLN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H86H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=101;refseq.start=159118518;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 159186534 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.647G>C;refseq.codonCoord=216;refseq.end=159186534;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=705;refseq.name=NM_080878;refseq.name2=ITLN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G216A;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=47;refseq.start=159186534;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 159187590 . C T 236.30 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=236;Dels=0.00;HRun=0;HaplotypeScore=9.35;MQ=77.92;MQ0=28;OQ=4052.78;QD=17.17;RankSumP=0.418590;SB=-1520.70;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.308G>A;refseq.codonCoord=103;refseq.end=159187590;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=366;refseq.name=NM_080878;refseq.name2=ITLN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R103H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=115;refseq.start=159187590;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 0/1
|
|
chr1 159236713 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=84;Dels=0.00;HRun=2;HaplotypeScore=1.92;MQ=98.96;MQ0=0;OQ=1708.62;QD=20.34;RankSumP=0.254804;SB=-518.01;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.438G>A;refseq.codonCoord=146;refseq.end=159236713;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=708;refseq.name=NM_016946;refseq.name2=F11R;refseq.positionType=CDS;refseq.proteinCoordStr=p.G146G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=50;refseq.start=159236713;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 0/1
|
|
chr1 159278555 . T G 63 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=24;DP=99;Dels=0.00;HRun=3;HaplotypeScore=14.68;MQ=96.62;MQ0=0;OQ=163.84;QD=1.65;RankSumP=4.21977e-08;SB=41.14;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.251A>C;refseq.codingCoordStr_2=c.74A>C;refseq.codonCoord_1=84;refseq.codonCoord_2=25;refseq.end_1=159278555;refseq.end_2=159278555;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=446;refseq.mrnaCoord_2=415;refseq.name2_1=USF1;refseq.name2_2=USF1;refseq.name_1=NM_007122;refseq.name_2=NM_207005;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y84S;refseq.proteinCoordStr_2=p.Y25S;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-26;refseq.spliceDist_2=-26;refseq.start_1=159278555;refseq.start_2=159278555;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=FilteredInAll GT 1/0
|
|
chr1 159279072 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=17;HRun=1;RankSumP=2.37734e-05;SecondBestBaseQ=5;refseq.changesAA_1=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.71C>A;refseq.codingCoordStr_2=c.-76C>A;refseq.codonCoord_1=24;refseq.end_1=159279072;refseq.end_2=159279072;refseq.frame_1=1;refseq.functionalClass_1=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.mrnaCoord_1=266;refseq.mrnaCoord_2=266;refseq.name2_1=USF1;refseq.name2_2=USF1;refseq.name_1=NM_007122;refseq.name_2=NM_207005;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=utr5;refseq.proteinCoordStr_1=p.T24N;refseq.referenceAA_1=Thr;refseq.referenceCodon_1=ACT;refseq.spliceDist_1=13;refseq.spliceDist_2=13;refseq.start_1=159279072;refseq.start_2=159279072;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.uorfChange_2=+1;refseq.variantAA_1=Asn;refseq.variantCodon_1=AAT;set=FilteredInAll GT 0/1
|
|
chr1 159285664 . G C 291.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.77;MQ0=0;OQ=1646.25;QD=44.49;RankSumP=1.00000;SB=-678.81;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1771C>G;refseq.codingCoordStr_2=c.1771C>G;refseq.codonCoord_1=591;refseq.codonCoord_2=591;refseq.end_1=159285664;refseq.end_2=159285664;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2117;refseq.mrnaCoord_2=2117;refseq.name2_1=ARHGAP30;refseq.name2_2=ARHGAP30;refseq.name_1=NM_001025598;refseq.name_2=NM_181720;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L591V;refseq.proteinCoordStr_2=p.L591V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=85;refseq.spliceDist_2=85;refseq.start_1=159285664;refseq.start_2=159285664;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=Intersection GT 1/1
|
|
chr1 159335460 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=78;Dels=0.00;HRun=4;HaplotypeScore=3.47;MQ=99.00;MQ0=0;OQ=1136.70;QD=14.57;RankSumP=0.273258;SB=-593.84;SecondBestBaseQ=32;refseq.changesAA_3=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_3=c.511A>C;refseq.codingCoordStr_4=c.-204A>C;refseq.codingCoordStr_5=c.511A>C;refseq.codonCoord_3=171;refseq.codonCoord_5=171;refseq.end_1=159335460;refseq.end_2=159335460;refseq.end_3=159335460;refseq.end_4=159335460;refseq.end_5=159335460;refseq.frame_3=0;refseq.frame_5=0;refseq.functionalClass_3=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=*;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=425;refseq.mrnaCoord_2=425;refseq.mrnaCoord_3=656;refseq.mrnaCoord_4=422;refseq.mrnaCoord_5=656;refseq.name2_1=KLHDC9;refseq.name2_2=KLHDC9;refseq.name2_3=KLHDC9;refseq.name2_4=KLHDC9;refseq.name2_5=KLHDC9;refseq.name_1=NR_033385;refseq.name_2=NR_033386;refseq.name_3=NM_001007255;refseq.name_4=NM_001007256;refseq.name_5=NM_152366;refseq.numMatchingRecords=5;refseq.positionType_1=non_coding_exon;refseq.positionType_2=non_coding_exon;refseq.positionType_3=CDS;refseq.positionType_4=utr5;refseq.positionType_5=CDS;refseq.proteinCoordStr_3=p.S171R;refseq.proteinCoordStr_5=p.S171R;refseq.referenceAA_3=Ser;refseq.referenceAA_5=Ser;refseq.referenceCodon_3=AGC;refseq.referenceCodon_5=AGC;refseq.spliceDist_1=-17;refseq.spliceDist_2=-17;refseq.spliceDist_3=-17;refseq.spliceDist_4=-17;refseq.spliceDist_5=-17;refseq.start_1=159335460;refseq.start_2=159335460;refseq.start_3=159335460;refseq.start_4=159335460;refseq.start_5=159335460;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_3=Arg;refseq.variantAA_5=Arg;refseq.variantCodon_3=CGC;refseq.variantCodon_5=CGC;set=Intersection GT 0/1
|
|
chr1 159397325 . C T 193.01 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=172;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=98.75;MQ0=0;OQ=2693.25;QD=15.66;RankSumP=0.252870;SB=-1327.81;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.271C>T;refseq.codingCoordStr_2=c.271C>T;refseq.codonCoord_1=91;refseq.codonCoord_2=91;refseq.end_1=159397325;refseq.end_2=159397325;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=648;refseq.mrnaCoord_2=507;refseq.name2_1=USP21;refseq.name2_2=USP21;refseq.name_1=NM_001014443;refseq.name_2=NM_012475;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P91S;refseq.proteinCoordStr_2=p.P91S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.spliceDist_1=292;refseq.spliceDist_2=292;refseq.start_1=159397325;refseq.start_2=159397325;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCT;refseq.variantCodon_2=TCT;set=Intersection GT 0/1
|
|
chr1 159429661 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=33;Dels=0.00;HRun=2;HaplotypeScore=4.00;MQ=99.00;MQ0=0;OQ=354.67;QD=10.75;RankSumP=0.306434;SB=-198.95;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1877A>G;refseq.codonCoord=626;refseq.end=159429661;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2305;refseq.name=NM_005099;refseq.name2=ADAMTS4;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q626R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-35;refseq.start=159429661;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/0
|
|
chr1 159434628 . C T 187.56 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=198;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=98.83;MQ0=0;OQ=3044.28;QD=15.38;RankSumP=0.414099;SB=-1409.62;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.414G>A;refseq.codonCoord=138;refseq.end=159434628;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=842;refseq.name=NM_005099;refseq.name2=ADAMTS4;refseq.positionType=CDS;refseq.proteinCoordStr=p.S138S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-220;refseq.start=159434628;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 0/1
|
|
chr1 159464358 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.439A>C;refseq.codonCoord=147;refseq.end=159464358;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=668;refseq.name=NM_032174;refseq.name2=TOMM40L;refseq.positionType=CDS;refseq.proteinCoordStr=p.T147P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-46;refseq.start=159464358;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 0/1
|
|
chr1 159464645 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.530T>G;refseq.codonCoord=177;refseq.end=159464645;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=759;refseq.name=NM_032174;refseq.name2=TOMM40L;refseq.positionType=CDS;refseq.proteinCoordStr=p.V177G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=46;refseq.start=159464645;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 159464713 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.598A>G;refseq.codonCoord=200;refseq.end=159464713;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=827;refseq.name=NM_032174;refseq.name2=TOMM40L;refseq.positionType=CDS;refseq.proteinCoordStr=p.K200E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-10;refseq.spliceInfo=splice-donor_-10;refseq.start=159464713;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=FilteredInAll GT 0/1
|
|
chr1 159469229 . G A 252.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=437;Dels=0.00;HRun=0;HaplotypeScore=14.27;MQ=98.80;MQ0=0;OQ=9255.31;QD=21.18;RankSumP=0.346304;SB=-3618.74;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_10=false;refseq.changesAA_11=false;refseq.changesAA_12=false;refseq.changesAA_13=false;refseq.changesAA_14=false;refseq.changesAA_15=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.changesAA_7=false;refseq.changesAA_8=false;refseq.changesAA_9=false;refseq.chr_1=chr1;refseq.chr_10=chr1;refseq.chr_11=chr1;refseq.chr_12=chr1;refseq.chr_13=chr1;refseq.chr_14=chr1;refseq.chr_15=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.chr_8=chr1;refseq.chr_9=chr1;refseq.codingCoordStr_1=c.540C>T;refseq.codingCoordStr_10=c.540C>T;refseq.codingCoordStr_11=c.453C>T;refseq.codingCoordStr_12=c.540C>T;refseq.codingCoordStr_13=c.540C>T;refseq.codingCoordStr_14=c.540C>T;refseq.codingCoordStr_15=c.540C>T;refseq.codingCoordStr_2=c.453C>T;refseq.codingCoordStr_3=c.540C>T;refseq.codingCoordStr_4=c.453C>T;refseq.codingCoordStr_5=c.453C>T;refseq.codingCoordStr_6=c.540C>T;refseq.codingCoordStr_7=c.453C>T;refseq.codingCoordStr_8=c.453C>T;refseq.codingCoordStr_9=c.453C>T;refseq.codonCoord_1=180;refseq.codonCoord_10=180;refseq.codonCoord_11=151;refseq.codonCoord_12=180;refseq.codonCoord_13=180;refseq.codonCoord_14=180;refseq.codonCoord_15=180;refseq.codonCoord_2=151;refseq.codonCoord_3=180;refseq.codonCoord_4=151;refseq.codonCoord_5=151;refseq.codonCoord_6=180;refseq.codonCoord_7=151;refseq.codonCoord_8=151;refseq.codonCoord_9=151;refseq.end_1=159469229;refseq.end_10=159469229;refseq.end_11=159469229;refseq.end_12=159469229;refseq.end_13=159469229;refseq.end_14=159469229;refseq.end_15=159469229;refseq.end_2=159469229;refseq.end_3=159469229;refseq.end_4=159469229;refseq.end_5=159469229;refseq.end_6=159469229;refseq.end_7=159469229;refseq.end_8=159469229;refseq.end_9=159469229;refseq.frame_1=2;refseq.frame_10=2;refseq.frame_11=2;refseq.frame_12=2;refseq.frame_13=2;refseq.frame_14=2;refseq.frame_15=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.frame_7=2;refseq.frame_8=2;refseq.frame_9=2;refseq.functionalClass_1=silent;refseq.functionalClass_10=silent;refseq.functionalClass_11=silent;refseq.functionalClass_12=silent;refseq.functionalClass_13=silent;refseq.functionalClass_14=silent;refseq.functionalClass_15=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.functionalClass_7=silent;refseq.functionalClass_8=silent;refseq.functionalClass_9=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_10=A;refseq.haplotypeAlternate_11=A;refseq.haplotypeAlternate_12=A;refseq.haplotypeAlternate_13=A;refseq.haplotypeAlternate_14=A;refseq.haplotypeAlternate_15=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeAlternate_5=A;refseq.haplotypeAlternate_6=A;refseq.haplotypeAlternate_7=A;refseq.haplotypeAlternate_8=A;refseq.haplotypeAlternate_9=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_10=G;refseq.haplotypeReference_11=G;refseq.haplotypeReference_12=G;refseq.haplotypeReference_13=G;refseq.haplotypeReference_14=G;refseq.haplotypeReference_15=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.haplotypeReference_9=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_10=true;refseq.inCodingRegion_11=true;refseq.inCodingRegion_12=true;refseq.inCodingRegion_13=true;refseq.inCodingRegion_14=true;refseq.inCodingRegion_15=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.inCodingRegion_9=true;refseq.mrnaCoord_1=743;refseq.mrnaCoord_10=743;refseq.mrnaCoord_11=603;refseq.mrnaCoord_12=743;refseq.mrnaCoord_13=743;refseq.mrnaCoord_14=743;refseq.mrnaCoord_15=743;refseq.mrnaCoord_2=603;refseq.mrnaCoord_3=743;refseq.mrnaCoord_4=603;refseq.mrnaCoord_5=603;refseq.mrnaCoord_6=743;refseq.mrnaCoord_7=603;refseq.mrnaCoord_8=603;refseq.mrnaCoord_9=603;refseq.name2_1=NR1I3;refseq.name2_10=NR1I3;refseq.name2_11=NR1I3;refseq.name2_12=NR1I3;refseq.name2_13=NR1I3;refseq.name2_14=NR1I3;refseq.name2_15=NR1I3;refseq.name2_2=NR1I3;refseq.name2_3=NR1I3;refseq.name2_4=NR1I3;refseq.name2_5=NR1I3;refseq.name2_6=NR1I3;refseq.name2_7=NR1I3;refseq.name2_8=NR1I3;refseq.name2_9=NR1I3;refseq.name_1=NM_001077469;refseq.name_10=NM_001077478;refseq.name_11=NM_001077479;refseq.name_12=NM_001077480;refseq.name_13=NM_001077481;refseq.name_14=NM_001077482;refseq.name_15=NM_005122;refseq.name_2=NM_001077470;refseq.name_3=NM_001077471;refseq.name_4=NM_001077472;refseq.name_5=NM_001077473;refseq.name_6=NM_001077474;refseq.name_7=NM_001077475;refseq.name_8=NM_001077476;refseq.name_9=NM_001077477;refseq.numMatchingRecords=15;refseq.positionType_1=CDS;refseq.positionType_10=CDS;refseq.positionType_11=CDS;refseq.positionType_12=CDS;refseq.positionType_13=CDS;refseq.positionType_14=CDS;refseq.positionType_15=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.positionType_9=CDS;refseq.proteinCoordStr_1=p.P180P;refseq.proteinCoordStr_10=p.P180P;refseq.proteinCoordStr_11=p.P151P;refseq.proteinCoordStr_12=p.P180P;refseq.proteinCoordStr_13=p.P180P;refseq.proteinCoordStr_14=p.P180P;refseq.proteinCoordStr_15=p.P180P;refseq.proteinCoordStr_2=p.P151P;refseq.proteinCoordStr_3=p.P180P;refseq.proteinCoordStr_4=p.P151P;refseq.proteinCoordStr_5=p.P151P;refseq.proteinCoordStr_6=p.P180P;refseq.proteinCoordStr_7=p.P151P;refseq.proteinCoordStr_8=p.P151P;refseq.proteinCoordStr_9=p.P151P;refseq.referenceAA_1=Pro;refseq.referenceAA_10=Pro;refseq.referenceAA_11=Pro;refseq.referenceAA_12=Pro;refseq.referenceAA_13=Pro;refseq.referenceAA_14=Pro;refseq.referenceAA_15=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceAA_9=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_10=CCC;refseq.referenceCodon_11=CCC;refseq.referenceCodon_12=CCC;refseq.referenceCodon_13=CCC;refseq.referenceCodon_14=CCC;refseq.referenceCodon_15=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.referenceCodon_4=CCC;refseq.referenceCodon_5=CCC;refseq.referenceCodon_6=CCC;refseq.referenceCodon_7=CCC;refseq.referenceCodon_8=CCC;refseq.referenceCodon_9=CCC;refseq.spliceDist_1=-9;refseq.spliceDist_10=-9;refseq.spliceDist_11=-9;refseq.spliceDist_12=-9;refseq.spliceDist_13=-9;refseq.spliceDist_14=-9;refseq.spliceDist_15=-9;refseq.spliceDist_2=-9;refseq.spliceDist_3=-9;refseq.spliceDist_4=-9;refseq.spliceDist_5=-9;refseq.spliceDist_6=-9;refseq.spliceDist_7=-9;refseq.spliceDist_8=-9;refseq.spliceDist_9=-9;refseq.spliceInfo_1=splice-donor_-9;refseq.spliceInfo_10=splice-donor_-9;refseq.spliceInfo_11=splice-donor_-9;refseq.spliceInfo_12=splice-donor_-9;refseq.spliceInfo_13=splice-donor_-9;refseq.spliceInfo_14=splice-donor_-9;refseq.spliceInfo_15=splice-donor_-9;refseq.spliceInfo_2=splice-donor_-9;refseq.spliceInfo_3=splice-donor_-9;refseq.spliceInfo_4=splice-donor_-9;refseq.spliceInfo_5=splice-donor_-9;refseq.spliceInfo_6=splice-donor_-9;refseq.spliceInfo_7=splice-donor_-9;refseq.spliceInfo_8=splice-donor_-9;refseq.spliceInfo_9=splice-donor_-9;refseq.start_1=159469229;refseq.start_10=159469229;refseq.start_11=159469229;refseq.start_12=159469229;refseq.start_13=159469229;refseq.start_14=159469229;refseq.start_15=159469229;refseq.start_2=159469229;refseq.start_3=159469229;refseq.start_4=159469229;refseq.start_5=159469229;refseq.start_6=159469229;refseq.start_7=159469229;refseq.start_8=159469229;refseq.start_9=159469229;refseq.transcriptStrand_1=-;refseq.transcriptStrand_10=-;refseq.transcriptStrand_11=-;refseq.transcriptStrand_12=-;refseq.transcriptStrand_13=-;refseq.transcriptStrand_14=-;refseq.transcriptStrand_15=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.transcriptStrand_7=-;refseq.transcriptStrand_8=-;refseq.transcriptStrand_9=-;refseq.variantAA_1=Pro;refseq.variantAA_10=Pro;refseq.variantAA_11=Pro;refseq.variantAA_12=Pro;refseq.variantAA_13=Pro;refseq.variantAA_14=Pro;refseq.variantAA_15=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Pro;refseq.variantAA_6=Pro;refseq.variantAA_7=Pro;refseq.variantAA_8=Pro;refseq.variantAA_9=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_10=CCT;refseq.variantCodon_11=CCT;refseq.variantCodon_12=CCT;refseq.variantCodon_13=CCT;refseq.variantCodon_14=CCT;refseq.variantCodon_15=CCT;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=CCT;refseq.variantCodon_6=CCT;refseq.variantCodon_7=CCT;refseq.variantCodon_8=CCT;refseq.variantCodon_9=CCT;set=Intersection GT 1/0
|
|
chr1 159742828 . C T 110.51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=209;Dels=0.00;HRun=0;HaplotypeScore=15.01;MQ=81.87;MQ0=11;OQ=2693.24;QD=12.89;RankSumP=0.0613690;SB=-1247.04;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.187C>T;refseq.codingCoordStr_2=c.184C>T;refseq.codonCoord_1=63;refseq.codonCoord_2=62;refseq.end_1=159742828;refseq.end_2=159742828;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=240;refseq.mrnaCoord_2=237;refseq.name2_1=FCGR2A;refseq.name2_2=FCGR2A;refseq.name_1=NM_001136219;refseq.name_2=NM_021642;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q63*;refseq.proteinCoordStr_2=p.Q62*;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=81;refseq.spliceDist_2=78;refseq.start_1=159742828;refseq.start_2=159742828;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantCodon_1=TAG;refseq.variantCodon_2=TAG;set=Intersection GT 0/1
|
|
chr1 159742829 . A G 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=209;Dels=0.00;HRun=5;HaplotypeScore=14.85;MQ=80.73;MQ0=14;OQ=2605.87;QD=12.47;RankSumP=0.00182228;SB=-1248.85;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.188A>G;refseq.codingCoordStr_2=c.185A>G;refseq.codonCoord_1=63;refseq.codonCoord_2=62;refseq.end_1=159742829;refseq.end_2=159742829;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=241;refseq.mrnaCoord_2=238;refseq.name2_1=FCGR2A;refseq.name2_2=FCGR2A;refseq.name_1=NM_001136219;refseq.name_2=NM_021642;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q63R;refseq.proteinCoordStr_2=p.Q62R;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=82;refseq.spliceDist_2=79;refseq.start_1=159742829;refseq.start_2=159742829;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;set=FilteredInAll GT 0/1
|
|
chr1 159746369 . A G 352.15 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=277;Dels=0.00;HRun=0;HaplotypeScore=3.91;MQ=92.42;MQ0=0;OQ=5058.03;QD=18.26;RankSumP=0.00580338;SB=-1726.80;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.500A>G;refseq.codingCoordStr_2=c.497A>G;refseq.codonCoord_1=167;refseq.codonCoord_2=166;refseq.end_1=159746369;refseq.end_2=159746369;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=553;refseq.mrnaCoord_2=550;refseq.name2_1=FCGR2A;refseq.name2_2=FCGR2A;refseq.name_1=NM_001136219;refseq.name_2=NM_021642;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H167R;refseq.proteinCoordStr_2=p.H166R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=-120;refseq.spliceDist_2=-120;refseq.start_1=159746369;refseq.start_2=159746369;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=filterInsoap-gatk GT 0/1
|
|
chr1 159747273 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=544;Dels=0.00;HRun=0;HaplotypeScore=42.57;MQ=94.67;MQ0=0;OQ=8690.51;QD=15.98;RankSumP=0.253162;SB=-1180.97;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.645A>G;refseq.codingCoordStr_2=c.642A>G;refseq.codonCoord_1=215;refseq.codonCoord_2=214;refseq.end_1=159747273;refseq.end_2=159747273;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=698;refseq.mrnaCoord_2=695;refseq.name2_1=FCGR2A;refseq.name2_2=FCGR2A;refseq.name_1=NM_001136219;refseq.name_2=NM_021642;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P215P;refseq.proteinCoordStr_2=p.P214P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=26;refseq.spliceDist_2=26;refseq.start_1=159747273;refseq.start_2=159747273;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCG;refseq.variantCodon_2=CCG;set=Intersection GT 0/1
|
|
chr1 159747293 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=20;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.665T>G;refseq.codingCoordStr_2=c.662T>G;refseq.codonCoord_1=222;refseq.codonCoord_2=221;refseq.end_1=159747293;refseq.end_2=159747293;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=718;refseq.mrnaCoord_2=715;refseq.name2_1=FCGR2A;refseq.name2_2=FCGR2A;refseq.name_1=NM_001136219;refseq.name_2=NM_021642;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V222G;refseq.proteinCoordStr_2=p.V221G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=46;refseq.spliceDist_2=46;refseq.start_1=159747293;refseq.start_2=159747293;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 159762101 . A T 277.22 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=85.49;MQ0=5;OQ=4346.77;QD=35.34;RankSumP=1.00000;SB=-2129.34;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1029A>T;refseq.codonCoord=343;refseq.end=159762101;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1442;refseq.name=NM_002155;refseq.name2=HSPA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.T343T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-1211;refseq.start=159762101;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 159762509 . T C 70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=248;Dels=0.00;HRun=1;HaplotypeScore=8.65;MQ=62.64;MQ0=36;OQ=7020.99;QD=28.31;RankSumP=1.00000;SB=-2555.54;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1437T>C;refseq.codonCoord=479;refseq.end=159762509;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1850;refseq.name=NM_002155;refseq.name2=HSPA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.T479T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-803;refseq.start=159762509;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 159781166 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=198;Dels=0.00;HRun=0;HaplotypeScore=6.58;MQ=28.28;MQ0=61;OQ=128.11;QD=0.65;RankSumP=0.589490;SB=-30.46;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.634T>G;refseq.codingCoordStr_2=c.631T>G;refseq.codingCoordStr_3=c.526T>G;refseq.codingCoordStr_4=c.526T>G;refseq.codingCoordStr_5=c.523T>G;refseq.codonCoord_1=212;refseq.codonCoord_2=211;refseq.codonCoord_3=176;refseq.codonCoord_4=176;refseq.codonCoord_5=175;refseq.end_1=159781166;refseq.end_2=159781166;refseq.end_3=159781166;refseq.end_4=159781166;refseq.end_5=159781166;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=818;refseq.mrnaCoord_2=815;refseq.mrnaCoord_3=681;refseq.mrnaCoord_4=663;refseq.mrnaCoord_5=660;refseq.name2_1=FCGR3A;refseq.name2_2=FCGR3A;refseq.name2_3=FCGR3A;refseq.name2_4=FCGR3A;refseq.name2_5=FCGR3A;refseq.name_1=NM_000569;refseq.name_2=NM_001127592;refseq.name_3=NM_001127593;refseq.name_4=NM_001127595;refseq.name_5=NM_001127596;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.F212V;refseq.proteinCoordStr_2=p.F211V;refseq.proteinCoordStr_3=p.F176V;refseq.proteinCoordStr_4=p.F176V;refseq.proteinCoordStr_5=p.F175V;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceAA_4=Phe;refseq.referenceAA_5=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.referenceCodon_3=TTT;refseq.referenceCodon_4=TTT;refseq.referenceCodon_5=TTT;refseq.spliceDist_1=-52;refseq.spliceDist_2=-52;refseq.spliceDist_3=-52;refseq.spliceDist_4=-52;refseq.spliceDist_5=-52;refseq.start_1=159781166;refseq.start_2=159781166;refseq.start_3=159781166;refseq.start_4=159781166;refseq.start_5=159781166;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantAA_5=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;refseq.variantCodon_3=GTT;refseq.variantCodon_4=GTT;refseq.variantCodon_5=GTT;set=Intersection GT 0/1
|
|
chr1 159784957 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=1081;Dels=0.00;HRun=0;HaplotypeScore=39.78;MQ=26.72;MQ0=159;OQ=9567.74;QD=8.85;RankSumP=0.0573919;SB=-1751.50;SecondBestBaseQ=28;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.305T>A;refseq.codingCoordStr_2=c.302T>A;refseq.codingCoordStr_3=c.197T>A;refseq.codingCoordStr_4=c.197T>A;refseq.codingCoordStr_5=c.194T>A;refseq.codonCoord_1=102;refseq.codonCoord_2=101;refseq.codonCoord_3=66;refseq.codonCoord_4=66;refseq.codonCoord_5=65;refseq.end_1=159784957;refseq.end_2=159784957;refseq.end_3=159784957;refseq.end_4=159784957;refseq.end_5=159784957;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=489;refseq.mrnaCoord_2=486;refseq.mrnaCoord_3=352;refseq.mrnaCoord_4=334;refseq.mrnaCoord_5=331;refseq.name2_1=FCGR3A;refseq.name2_2=FCGR3A;refseq.name2_3=FCGR3A;refseq.name2_4=FCGR3A;refseq.name2_5=FCGR3A;refseq.name_1=NM_000569;refseq.name_2=NM_001127592;refseq.name_3=NM_001127593;refseq.name_4=NM_001127595;refseq.name_5=NM_001127596;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.L102H;refseq.proteinCoordStr_2=p.L101H;refseq.proteinCoordStr_3=p.L66H;refseq.proteinCoordStr_4=p.L66H;refseq.proteinCoordStr_5=p.L65H;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceAA_4=Leu;refseq.referenceAA_5=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.referenceCodon_3=CTC;refseq.referenceCodon_4=CTC;refseq.referenceCodon_5=CTC;refseq.spliceDist_1=-123;refseq.spliceDist_2=-123;refseq.spliceDist_3=-123;refseq.spliceDist_4=-123;refseq.spliceDist_5=-123;refseq.start_1=159784957;refseq.start_2=159784957;refseq.start_3=159784957;refseq.start_4=159784957;refseq.start_5=159784957;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantAA_4=His;refseq.variantAA_5=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;refseq.variantCodon_4=CAC;refseq.variantCodon_5=CAC;set=Intersection GT 0/1
|
|
chr1 159866317 . T C 7.50 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=286;Dels=0.00;HRun=0;HaplotypeScore=17.41;MQ=15.10;MQ0=221;OQ=1126.33;QD=3.94;RankSumP=0.00000;SB=-226.08;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.194A>G;refseq.codonCoord=65;refseq.end=159866317;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=468;refseq.name=NM_000570;refseq.name2=FCGR3B;refseq.positionType=CDS;refseq.proteinCoordStr=p.N65S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-126;refseq.start=159866317;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=filterInsoap-gatk GT 1/0
|
|
chr1 159909398 . T G 21 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=34;DP=65;Dels=0.00;HRun=2;HaplotypeScore=4.60;MQ=61.05;MQ0=14;OQ=69.85;QD=1.07;RankSumP=0.00396825;SB=65.23;SecondBestBaseQ=26;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.398T>G;refseq.codingCoordStr_2=c.401T>G;refseq.codingCoordStr_3=c.398T>G;refseq.codingCoordStr_4=c.401T>G;refseq.codonCoord_1=133;refseq.codonCoord_2=134;refseq.codonCoord_3=133;refseq.codonCoord_4=134;refseq.end_1=159909398;refseq.end_2=159909398;refseq.end_3=159909398;refseq.end_4=159909398;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=490;refseq.mrnaCoord_2=493;refseq.mrnaCoord_3=490;refseq.mrnaCoord_4=493;refseq.name2_1=FCGR2B;refseq.name2_2=FCGR2B;refseq.name2_3=FCGR2B;refseq.name2_4=FCGR2B;refseq.name_1=NM_001002273;refseq.name_2=NM_001002274;refseq.name_3=NM_001002275;refseq.name_4=NM_004001;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.V133G;refseq.proteinCoordStr_2=p.V134G;refseq.proteinCoordStr_3=p.V133G;refseq.proteinCoordStr_4=p.V134G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceAA_4=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.referenceCodon_4=GTG;refseq.spliceDist_1=10;refseq.spliceDist_2=10;refseq.spliceDist_3=10;refseq.spliceDist_4=10;refseq.spliceInfo_1=splice-acceptor_10;refseq.spliceInfo_2=splice-acceptor_10;refseq.spliceInfo_3=splice-acceptor_10;refseq.spliceInfo_4=splice-acceptor_10;refseq.start_1=159909398;refseq.start_2=159909398;refseq.start_3=159909398;refseq.start_4=159909398;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;set=FilteredInAll GT 1/0
|
|
chr1 159948404 . A G 199.32 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=117;Dels=0.00;HRun=1;HaplotypeScore=4.72;MQ=98.83;MQ0=0;OQ=1869.08;QD=15.98;RankSumP=0.382123;SB=-793.68;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.607A>G;refseq.codonCoord=203;refseq.end=159948404;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=849;refseq.name=NM_032738;refseq.name2=FCRLA;refseq.positionType=CDS;refseq.proteinCoordStr=p.S203G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=57;refseq.start=159948404;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 0/1
|
|
chr1 159949760 . G A 211.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=98.84;MQ0=0;OQ=1866.68;QD=14.58;RankSumP=0.486889;SB=-742.50;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1097G>A;refseq.codonCoord=366;refseq.end=159949760;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1339;refseq.name=NM_032738;refseq.name2=FCRLA;refseq.positionType=CDS;refseq.proteinCoordStr=p.R366Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=262;refseq.start=159949760;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 159962263 . G T 208.43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=98.94;MQ0=0;OQ=3032.35;QD=31.59;RankSumP=1.00000;SB=-356.82;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.336G>T;refseq.codonCoord=112;refseq.end=159962263;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=342;refseq.name=NM_001002901;refseq.name2=FCRLB;refseq.positionType=CDS;refseq.proteinCoordStr=p.A112A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=29;refseq.start=159962263;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 159963406 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=1.90;MQ=97.47;MQ0=0;OQ=418.38;QD=11.62;RankSumP=0.600890;SB=-114.34;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.864G>C;refseq.codonCoord=288;refseq.end=159963406;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=870;refseq.name=NM_001002901;refseq.name2=FCRLB;refseq.positionType=CDS;refseq.proteinCoordStr=p.P288P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-2;refseq.spliceInfo=splice-donor_-2;refseq.start=159963406;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 0/1
|
|
chr1 159963696 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=102;Dels=0.00;HRun=1;HaplotypeScore=7.42;MQ=98.38;MQ0=0;OQ=1604.08;QD=15.73;RankSumP=0.202243;SB=-778.14;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.901G>C;refseq.codonCoord=301;refseq.end=159963696;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=907;refseq.name=NM_001002901;refseq.name2=FCRLB;refseq.positionType=CDS;refseq.proteinCoordStr=p.A301P;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=36;refseq.start=159963696;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 159963773 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=3.62;MQ=98.14;MQ0=0;OQ=825.37;QD=16.51;RankSumP=0.182648;SB=-308.32;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.978G>T;refseq.codonCoord=326;refseq.end=159963773;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=984;refseq.name=NM_001002901;refseq.name2=FCRLB;refseq.positionType=CDS;refseq.proteinCoordStr=p.P326P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=113;refseq.start=159963773;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 160018365 . A G 186.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=169;Dels=0.00;HRun=1;HaplotypeScore=7.31;MQ=98.81;MQ0=0;OQ=2502.08;QD=14.81;RankSumP=0.149895;SB=-1059.46;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.199A>G;refseq.codonCoord=67;refseq.end=160018365;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=266;refseq.name=NM_007348;refseq.name2=ATF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.M67V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=40;refseq.start=160018365;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 0/1
|
|
chr1 160194951 . A G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=485;Dels=0.00;HRun=1;HaplotypeScore=19.45;MQ=98.71;MQ0=0;OQ=17353.97;QD=35.78;RankSumP=1.00000;SB=-8081.76;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1896A>G;refseq.codonCoord=632;refseq.end=160194951;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1963;refseq.name=NM_007348;refseq.name2=ATF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S632S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=92;refseq.start=160194951;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/1
|
|
chr1 160234305 . A G 106.62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=98.17;MQ0=0;OQ=830.96;QD=13.62;RankSumP=0.0442612;SB=-278.96;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1408T>C;refseq.codonCoord=470;refseq.end=160234305;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1832;refseq.name=NM_015441;refseq.name2=OLFML2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.W470R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=-67;refseq.start=160234305;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 0/1
|
|
chr1 160242858 . A G 407.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=217;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=94.59;MQ0=0;OQ=8077.68;QD=37.22;RankSumP=1.00000;SB=-3181.67;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.576T>C;refseq.codonCoord=192;refseq.end=160242858;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1000;refseq.name=NM_015441;refseq.name2=OLFML2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.N192N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=30;refseq.start=160242858;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 160580359 . C T 141.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=239;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=98.86;MQ0=0;OQ=4990.62;QD=20.88;RankSumP=0.141110;SB=-744.73;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.549C>T;refseq.codingCoordStr_2=c.564C>T;refseq.codonCoord_1=183;refseq.codonCoord_2=188;refseq.end_1=160580359;refseq.end_2=160580359;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=936;refseq.mrnaCoord_2=951;refseq.name2_1=NOS1AP;refseq.name2_2=NOS1AP;refseq.name_1=NM_001164757;refseq.name_2=NM_014697;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S183S;refseq.proteinCoordStr_2=p.S188S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=-32;refseq.spliceDist_2=-32;refseq.start_1=160580359;refseq.start_2=160580359;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 0/1
|
|
chr1 160601880 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=270;Dels=0.00;HRun=0;HaplotypeScore=45.09;MQ=98.06;MQ0=0;OQ=4222.96;QD=15.64;RankSumP=0.443902;SB=-538.08;SecondBestBaseQ=22;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.117C>T;refseq.codingCoordStr_2=c.987C>T;refseq.codingCoordStr_3=c.1002C>T;refseq.codonCoord_1=39;refseq.codonCoord_2=329;refseq.codonCoord_3=334;refseq.end_1=160601880;refseq.end_2=160601880;refseq.end_3=160601880;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2484;refseq.mrnaCoord_2=1374;refseq.mrnaCoord_3=1389;refseq.name2_1=NOS1AP;refseq.name2_2=NOS1AP;refseq.name2_3=NOS1AP;refseq.name_1=NM_001126060;refseq.name_2=NM_001164757;refseq.name_3=NM_014697;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R39R;refseq.proteinCoordStr_2=p.R329R;refseq.proteinCoordStr_3=p.R334R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGC;refseq.referenceCodon_2=CGC;refseq.referenceCodon_3=CGC;refseq.spliceDist_1=-104;refseq.spliceDist_2=63;refseq.spliceDist_3=63;refseq.start_1=160601880;refseq.start_2=160601880;refseq.start_3=160601880;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;refseq.variantCodon_3=CGT;set=Intersection GT 0/1
|
|
chr1 160610726 . C T 235.97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=5.81;MQ=98.38;MQ0=0;OQ=1633.11;QD=14.58;RankSumP=0.398437;SB=-813.79;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.522G>A;refseq.codonCoord=174;refseq.end=160610726;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=586;refseq.name=NM_182581;refseq.name2=C1orf111;refseq.positionType=CDS;refseq.proteinCoordStr=p.R174R;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=305;refseq.start=160610726;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 0/1
|
|
chr1 160611014 . A G 444.52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=98.96;MQ0=0;OQ=4592.24;QD=39.93;RankSumP=1.00000;SB=-1359.80;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.234T>C;refseq.codonCoord=78;refseq.end=160611014;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=298;refseq.name=NM_182581;refseq.name2=C1orf111;refseq.positionType=CDS;refseq.proteinCoordStr=p.D78D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=17;refseq.start=160611014;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 160611715 . G A 422.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.53;MQ0=0;OQ=6588.41;QD=41.70;RankSumP=1.00000;SB=-1589.61;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.206C>T;refseq.codonCoord=69;refseq.end=160611715;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=270;refseq.name=NM_182581;refseq.name2=C1orf111;refseq.positionType=CDS;refseq.proteinCoordStr=p.A69V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-12;refseq.start=160611715;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 160633695 . C T 87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=295;Dels=0.00;HRun=2;HaplotypeScore=4.42;MQ=98.68;MQ0=0;OQ=11962.09;QD=40.55;RankSumP=1.00000;SB=-5675.11;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.398G>A;refseq.codonCoord=133;refseq.end=160633695;refseq.frame=1;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=520;refseq.name=NM_053282;refseq.name2=SH2D1B;refseq.positionType=CDS;refseq.proteinCoordStr=p.*133*;refseq.referenceAA=Stop;refseq.referenceCodon=TGA;refseq.spliceDist=35;refseq.start=160633695;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=Intersection GT 1/1
|
|
chr1 160758909 . C A 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=29;DP=278;Dels=0.00;HRun=1;HaplotypeScore=16.84;MQ=98.57;MQ0=0;OQ=76.45;QD=0.27;RankSumP=0.00000;SB=459.52;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1205C>A;refseq.codonCoord=402;refseq.end=160758909;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1341;refseq.name=NM_175866;refseq.name2=UHMK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T402K;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=92;refseq.start=160758909;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 1/0
|
|
chr1 161008597 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1664T>G;refseq.codingCoordStr_2=c.1664T>G;refseq.codonCoord_1=555;refseq.codonCoord_2=555;refseq.end_1=161008597;refseq.end_2=161008597;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2129;refseq.mrnaCoord_2=2049;refseq.name2_1=DDR2;refseq.name2_2=DDR2;refseq.name_1=NM_001014796;refseq.name_2=NM_006182;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V555G;refseq.proteinCoordStr_2=p.V555G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-65;refseq.spliceDist_2=-65;refseq.start_1=161008597;refseq.start_2=161008597;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 161012576 . C A 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=21;DP=566;Dels=0.00;HRun=1;HaplotypeScore=155.07;MQ=98.31;MQ0=0;OQ=338.34;QD=0.60;RankSumP=0.00000;SB=594.94;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2075C>A;refseq.codingCoordStr_2=c.2075C>A;refseq.codonCoord_1=692;refseq.codonCoord_2=692;refseq.end_1=161012576;refseq.end_2=161012576;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2540;refseq.mrnaCoord_2=2460;refseq.name2_1=DDR2;refseq.name2_2=DDR2;refseq.name_1=NM_001014796;refseq.name_2=NM_006182;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T692N;refseq.proteinCoordStr_2=p.T692N;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=27;refseq.spliceDist_2=27;refseq.start_1=161012576;refseq.start_2=161012576;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=FilteredInAll GT 1/0
|
|
chr1 161041891 . C T 26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=256;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=15.89;MQ0=163;OQ=981.34;QD=3.83;RankSumP=0.750000;SB=-194.13;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.888C>T;refseq.codonCoord=296;refseq.end=161041891;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=983;refseq.name=NM_016371;refseq.name2=HSD17B7;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y296Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-16;refseq.start=161041891;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=soap-filterIngatk GT 0/1
|
|
chr1 161048720 . A G 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=25;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.912A>G;refseq.codonCoord=304;refseq.end=161048720;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1007;refseq.name=NM_016371;refseq.name2=HSD17B7;refseq.positionType=CDS;refseq.proteinCoordStr=p.L304L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=9;refseq.spliceInfo=splice-acceptor_9;refseq.start=161048720;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT 1/1
|
|
chr1 163439840 . A G 325.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=161;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=98.81;MQ0=0;OQ=6401.89;QD=39.76;RankSumP=1.00000;SB=-3119.52;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.204T>C;refseq.codingCoordStr_2=c.1050T>C;refseq.codingCoordStr_3=c.1050T>C;refseq.codingCoordStr_4=c.303T>C;refseq.codonCoord_1=68;refseq.codonCoord_2=350;refseq.codonCoord_3=350;refseq.codonCoord_4=101;refseq.end_1=163439840;refseq.end_2=163439840;refseq.end_3=163439840;refseq.end_4=163439840;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=679;refseq.mrnaCoord_2=1244;refseq.mrnaCoord_3=1433;refseq.mrnaCoord_4=546;refseq.name2_1=LMX1A;refseq.name2_2=LMX1A;refseq.name2_3=LMX1A;refseq.name2_4=LMX1A;refseq.name_1=NM_001033507;refseq.name_2=NM_001174069;refseq.name_3=NM_177398;refseq.name_4=NM_177399;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.D68D;refseq.proteinCoordStr_2=p.D350D;refseq.proteinCoordStr_3=p.D350D;refseq.proteinCoordStr_4=p.D101D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.referenceCodon_3=GAT;refseq.referenceCodon_4=GAT;refseq.spliceDist_1=62;refseq.spliceDist_2=62;refseq.spliceDist_3=62;refseq.spliceDist_4=62;refseq.start_1=163439840;refseq.start_2=163439840;refseq.start_3=163439840;refseq.start_4=163439840;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantAA_4=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;refseq.variantCodon_3=GAC;refseq.variantCodon_4=GAC;set=Intersection GT 1/1
|
|
chr1 163485303 . C T 277.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=314;Dels=0.00;HRun=0;HaplotypeScore=11.93;MQ=98.76;MQ0=0;OQ=5019.59;QD=15.99;RankSumP=0.0365001;SB=-1397.24;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.462G>A;refseq.codingCoordStr_2=c.462G>A;refseq.codonCoord_1=154;refseq.codonCoord_2=154;refseq.end_1=163485303;refseq.end_2=163485303;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=656;refseq.mrnaCoord_2=845;refseq.name2_1=LMX1A;refseq.name2_2=LMX1A;refseq.name_1=NM_001174069;refseq.name_2=NM_177398;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L154L;refseq.proteinCoordStr_2=p.L154L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=-35;refseq.spliceDist_2=-35;refseq.start_1=163485303;refseq.start_2=163485303;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=Intersection GT 0/1
|
|
chr1 163644176 . G A 220.45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=313;Dels=0.00;HRun=1;HaplotypeScore=7.47;MQ=98.73;MQ0=0;OQ=6593.75;QD=21.07;RankSumP=0.341172;SB=-1683.53;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1050C>T;refseq.codonCoord=350;refseq.end=163644176;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1350;refseq.name=NM_006917;refseq.name2=RXRG;refseq.positionType=CDS;refseq.proteinCoordStr=p.V350V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=4;refseq.spliceInfo=splice-acceptor_4;refseq.start=163644176;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/0
|
|
chr1 163664739 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=98.25;MQ0=0;OQ=1081.24;QD=15.23;RankSumP=0.104875;SB=-424.15;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.138A>G;refseq.codonCoord=46;refseq.end=163664739;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=438;refseq.name=NM_006917;refseq.name2=RXRG;refseq.positionType=CDS;refseq.proteinCoordStr=p.T46T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=89;refseq.start=163664739;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/0
|
|
chr1 163915333 . C T 176.62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=210;Dels=0.00;HRun=0;HaplotypeScore=3.87;MQ=98.75;MQ0=0;OQ=3187.76;QD=15.18;RankSumP=0.0401292;SB=-1135.06;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.900G>A;refseq.codonCoord=300;refseq.end=163915333;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1005;refseq.name=NM_000696;refseq.name2=ALDH9A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A300A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-31;refseq.start=163915333;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 163918897 . A G 357.84 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=375;Dels=0.00;HRun=0;HaplotypeScore=4.46;MQ=98.96;MQ0=0;OQ=7467.80;QD=19.91;RankSumP=0.479468;SB=-2055.58;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.402T>C;refseq.codonCoord=134;refseq.end=163918897;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=507;refseq.name=NM_000696;refseq.name2=ALDH9A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I134I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-56;refseq.start=163918897;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 0/1
|
|
chr1 164306522 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=408;Dels=0.00;HRun=0;HaplotypeScore=11.40;MQ=98.60;MQ0=0;OQ=10062.84;QD=24.66;RankSumP=0.450001;SB=-3639.45;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.366G>C;refseq.codonCoord=122;refseq.end=164306522;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=839;refseq.name=NM_001017961;refseq.name2=FAM78B;refseq.positionType=CDS;refseq.proteinCoordStr=p.V122V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=103;refseq.start=164306522;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 165096097 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=4;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.642G>C;refseq.codonCoord=214;refseq.end=165096097;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=826;refseq.name=NM_053053;refseq.name2=TADA1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P214P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-51;refseq.start=165096097;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 165156924 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.750000;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1528C>G;refseq.codonCoord=510;refseq.end=165156924;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1584;refseq.name=NM_199351;refseq.name2=ILDR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L510V;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=317;refseq.start=165156924;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT 0/1
|
|
chr1 165361787 . G C 162.98 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=148;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=98.44;MQ0=0;OQ=1944.92;QD=13.14;RankSumP=0.300731;SB=-745.36;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.795G>C;refseq.codonCoord=265;refseq.end=165361787;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=795;refseq.name=NM_001080426;refseq.name2=DUSP27;refseq.positionType=CDS;refseq.proteinCoordStr=p.E265D;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=140;refseq.start=165361787;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 0/1
|
|
chr1 165362389 . G A 120.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=580.69;QD=21.51;RankSumP=0.523619;SB=-180.67;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1397G>A;refseq.codonCoord=466;refseq.end=165362389;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1397;refseq.name=NM_001080426;refseq.name2=DUSP27;refseq.positionType=CDS;refseq.proteinCoordStr=p.R466H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=742;refseq.start=165362389;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/0
|
|
chr1 165362505 . G A 202.10 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=98.80;MQ0=0;OQ=841.98;QD=17.54;RankSumP=0.361356;SB=-298.18;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1513G>A;refseq.codonCoord=505;refseq.end=165362505;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1513;refseq.name=NM_001080426;refseq.name2=DUSP27;refseq.positionType=CDS;refseq.proteinCoordStr=p.A505T;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=858;refseq.start=165362505;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 165363118 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2126A>C;refseq.codonCoord=709;refseq.end=165363118;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2126;refseq.name=NM_001080426;refseq.name2=DUSP27;refseq.positionType=CDS;refseq.proteinCoordStr=p.N709T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=1471;refseq.start=165363118;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 0/1
|
|
chr1 165364363 . C A 164.58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=114;Dels=0.00;HRun=1;HaplotypeScore=4.74;MQ=98.67;MQ0=0;OQ=1585.53;QD=13.91;RankSumP=0.228489;SB=-805.11;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3371C>A;refseq.codonCoord=1124;refseq.end=165364363;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3371;refseq.name=NM_001080426;refseq.name2=DUSP27;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1124N;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-664;refseq.start=165364363;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 165610059 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=5.60595e-05;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.424G>C;refseq.codonCoord=142;refseq.end=165610059;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=586;refseq.name=NM_002697;refseq.name2=POU2F1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A142P;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=91;refseq.start=165610059;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 165782074 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.547T>C;refseq.codonCoord=183;refseq.end=165782074;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=625;refseq.name=NM_003851;refseq.name2=CREG1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S183P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=73;refseq.start=165782074;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 166058980 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=155;Dels=0.00;HRun=0;HaplotypeScore=6.91;MQ=98.30;MQ0=0;OQ=2424.24;QD=15.64;RankSumP=0.0965660;SB=-756.95;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3599C>T;refseq.codingCoordStr_2=c.4058C>T;refseq.codonCoord_1=1200;refseq.codonCoord_2=1353;refseq.end_1=166058980;refseq.end_2=166058980;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3901;refseq.mrnaCoord_2=4356;refseq.name2_1=ADCY10;refseq.name2_2=ADCY10;refseq.name_1=NM_001167749;refseq.name_2=NM_018417;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P1200L;refseq.proteinCoordStr_2=p.P1353L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=6;refseq.spliceDist_2=6;refseq.spliceInfo_1=splice-acceptor_6;refseq.spliceInfo_2=splice-acceptor_6;refseq.start_1=166058980;refseq.start_2=166058980;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 1/0
|
|
chr1 166081654 . A G 161.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=298;Dels=0.00;HRun=1;HaplotypeScore=3.16;MQ=98.81;MQ0=0;OQ=6398.23;QD=21.47;RankSumP=0.408015;SB=-2717.84;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2319T>C;refseq.codingCoordStr_2=c.2778T>C;refseq.codonCoord_1=773;refseq.codonCoord_2=926;refseq.end_1=166081654;refseq.end_2=166081654;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2621;refseq.mrnaCoord_2=3076;refseq.name2_1=ADCY10;refseq.name2_2=ADCY10;refseq.name_1=NM_001167749;refseq.name_2=NM_018417;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I773I;refseq.proteinCoordStr_2=p.I926I;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=62;refseq.spliceDist_2=62;refseq.start_1=166081654;refseq.start_2=166081654;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;set=Intersection GT 0/1
|
|
chr1 166084263 . A G 391.57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=228;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.82;MQ0=0;OQ=8830.90;QD=38.73;RankSumP=1.00000;SB=-2900.84;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1938T>C;refseq.codingCoordStr_2=c.2397T>C;refseq.codonCoord_1=646;refseq.codonCoord_2=799;refseq.end_1=166084263;refseq.end_2=166084263;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2240;refseq.mrnaCoord_2=2695;refseq.name2_1=ADCY10;refseq.name2_2=ADCY10;refseq.name_1=NM_001167749;refseq.name_2=NM_018417;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G646G;refseq.proteinCoordStr_2=p.G799G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=-41;refseq.spliceDist_2=-41;refseq.start_1=166084263;refseq.start_2=166084263;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=Intersection GT 1/1
|
|
chr1 166092109 . T C 90 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=534;Dels=0.00;HRun=0;HaplotypeScore=34.42;MQ=98.90;MQ0=0;OQ=19954.65;QD=37.37;RankSumP=1.00000;SB=-5261.48;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1630A>G;refseq.codingCoordStr_2=c.2089A>G;refseq.codonCoord_1=544;refseq.codonCoord_2=697;refseq.end_1=166092109;refseq.end_2=166092109;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1932;refseq.mrnaCoord_2=2387;refseq.name2_1=ADCY10;refseq.name2_2=ADCY10;refseq.name_1=NM_001167749;refseq.name_2=NM_018417;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I544V;refseq.proteinCoordStr_2=p.I697V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=-83;refseq.spliceDist_2=-83;refseq.start_1=166092109;refseq.start_2=166092109;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=Intersection GT 1/1
|
|
chr1 166092230 . A G 185.86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.62;MQ0=0;OQ=1275.44;QD=14.83;RankSumP=0.347361;SB=-559.09;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1509T>C;refseq.codingCoordStr_2=c.1968T>C;refseq.codonCoord_1=503;refseq.codonCoord_2=656;refseq.end_1=166092230;refseq.end_2=166092230;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1811;refseq.mrnaCoord_2=2266;refseq.name2_1=ADCY10;refseq.name2_2=ADCY10;refseq.name_1=NM_001167749;refseq.name_2=NM_018417;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F503F;refseq.proteinCoordStr_2=p.F656F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.spliceDist_1=72;refseq.spliceDist_2=72;refseq.start_1=166092230;refseq.start_2=166092230;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;set=Intersection GT 0/1
|
|
chr1 166106202 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=141;Dels=0.00;HRun=2;HaplotypeScore=6.26;MQ=98.87;MQ0=0;OQ=2597.32;QD=18.42;RankSumP=0.390564;SB=-741.34;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1074C>T;refseq.codingCoordStr_2=c.1533C>T;refseq.codonCoord_1=358;refseq.codonCoord_2=511;refseq.end_1=166106202;refseq.end_2=166106202;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1376;refseq.mrnaCoord_2=1831;refseq.name2_1=ADCY10;refseq.name2_2=ADCY10;refseq.name_1=NM_001167749;refseq.name_2=NM_018417;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V358V;refseq.proteinCoordStr_2=p.V511V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.spliceDist_1=71;refseq.spliceDist_2=71;refseq.start_1=166106202;refseq.start_2=166106202;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=Intersection GT 1/0
|
|
chr1 166116038 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=195;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=98.68;MQ0=0;OQ=1778.35;QD=9.12;RankSumP=0.309732;SB=-618.39;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.696T>C;refseq.codingCoordStr_2=c.1155T>C;refseq.codonCoord_1=232;refseq.codonCoord_2=385;refseq.end_1=166116038;refseq.end_2=166116038;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=998;refseq.mrnaCoord_2=1453;refseq.name2_1=ADCY10;refseq.name2_2=ADCY10;refseq.name_1=NM_001167749;refseq.name_2=NM_018417;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G232G;refseq.proteinCoordStr_2=p.G385G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=16;refseq.spliceDist_2=16;refseq.start_1=166116038;refseq.start_2=166116038;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=Intersection GT 0/1
|
|
chr1 166160383 . G A 98 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=48;Dels=0.00;HRun=4;HaplotypeScore=0.32;MQ=98.13;MQ0=0;OQ=540.37;QD=11.26;RankSumP=0.550027;SB=-265.47;SecondBestBaseQ=34;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.126C>T;refseq.codingCoordStr_3=c.126C>T;refseq.codonCoord_2=42;refseq.codonCoord_3=42;refseq.end_1=166160383;refseq.end_2=166160383;refseq.end_3=166160383;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=427;refseq.mrnaCoord_2=285;refseq.mrnaCoord_3=280;refseq.name2_1=BRP44;refseq.name2_2=BRP44;refseq.name2_3=BRP44;refseq.name_1=NR_026550;refseq.name_2=NM_001143674;refseq.name_3=NM_015415;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.F42F;refseq.proteinCoordStr_3=p.F42F;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceCodon_2=TTC;refseq.referenceCodon_3=TTC;refseq.spliceDist_1=17;refseq.spliceDist_2=17;refseq.spliceDist_3=17;refseq.start_1=166160383;refseq.start_2=166160383;refseq.start_3=166160383;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantCodon_2=TTT;refseq.variantCodon_3=TTT;set=Intersection GT 1/0
|
|
chr1 166172863 . A C 94.06 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=98.20;MQ0=0;OQ=1417.57;QD=30.82;RankSumP=1.00000;SB=-476.28;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.90A>C;refseq.codingCoordStr_2=c.-120T>G;refseq.codingCoordStr_3=c.90A>C;refseq.codonCoord_1=30;refseq.codonCoord_3=30;refseq.end_1=166172863;refseq.end_2=166172863;refseq.end_3=166172863;refseq.frame_1=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=332;refseq.mrnaCoord_2=40;refseq.mrnaCoord_3=332;refseq.name2_1=DCAF6;refseq.name2_2=BRP44;refseq.name2_3=DCAF6;refseq.name_1=NM_001017977;refseq.name_2=NM_001143674;refseq.name_3=NM_018442;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=utr5;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R30R;refseq.proteinCoordStr_3=p.R30R;refseq.referenceAA_1=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_3=CGA;refseq.spliceDist_1=-8;refseq.spliceDist_2=40;refseq.spliceDist_3=-8;refseq.spliceInfo_1=splice-donor_-8;refseq.spliceInfo_3=splice-donor_-8;refseq.start_1=166172863;refseq.start_2=166172863;refseq.start_3=166172863;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=+;refseq.variantAA_1=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_3=CGC;set=Intersection GT 1/1
|
|
chr1 166240600 . C T 173.24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=480;Dels=0.00;HRun=0;HaplotypeScore=5.14;MQ=98.52;MQ0=0;OQ=7239.49;QD=15.08;RankSumP=0.441194;SB=-2871.90;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1323C>T;refseq.codingCoordStr_2=c.1323C>T;refseq.codonCoord_1=441;refseq.codonCoord_2=441;refseq.end_1=166240600;refseq.end_2=166240600;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1565;refseq.mrnaCoord_2=1565;refseq.name2_1=DCAF6;refseq.name2_2=DCAF6;refseq.name_1=NM_001017977;refseq.name_2=NM_018442;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D441D;refseq.proteinCoordStr_2=p.D441D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-56;refseq.spliceDist_2=-56;refseq.start_1=166240600;refseq.start_2=166240600;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 0/1
|
|
chr1 166280474 . T C 263.52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=160;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=98.69;MQ0=0;OQ=2533.81;QD=15.84;RankSumP=0.263119;SB=-941.11;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1640T>C;refseq.codingCoordStr_2=c.1700T>C;refseq.codonCoord_1=547;refseq.codonCoord_2=567;refseq.end_1=166280474;refseq.end_2=166280474;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1882;refseq.mrnaCoord_2=1942;refseq.name2_1=DCAF6;refseq.name2_2=DCAF6;refseq.name_1=NM_001017977;refseq.name_2=NM_018442;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V547A;refseq.proteinCoordStr_2=p.V567A;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.start_1=166280474;refseq.start_2=166280474;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/0
|
|
chr1 166326490 . A G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=35.79;MQ=97.65;MQ0=0;OQ=470.86;QD=4.36;RankSumP=0.105427;SB=-10.60;SecondBestBaseQ=13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1140T>C;refseq.codonCoord=380;refseq.end=166326490;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1454;refseq.name=NM_153832;refseq.name2=GPR161;refseq.positionType=CDS;refseq.proteinCoordStr=p.G380G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=41;refseq.start=166326490;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 0/1
|
|
chr1 166517157 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.chr=chr1;refseq.codingCoordStr=c.203+2;refseq.end=166517157;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_005149;refseq.name2=TBX19;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=166517157;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 166776826 . G A 5 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.575851;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.333C>T;refseq.codonCoord=111;refseq.end=166776826;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=366;refseq.name=NM_003175;refseq.name2=XCL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T111T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=157;refseq.start=166776826;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=FilteredInAll GT 1/0
|
|
chr1 166950100 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=20;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=13.17;MQ=98.15;MQ0=0;OQ=1025.74;QD=9.68;RankSumP=0.405580;SB=-207.28;SecondBestBaseQ=20;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.414G>A;refseq.codonCoord=138;refseq.end=166950100;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=430;refseq.name=NM_001937;refseq.name2=DPT;refseq.positionType=CDS;refseq.proteinCoordStr=p.R138R;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-18;refseq.start=166950100;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 0/1
|
|
chr1 166950126 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.388T>G;refseq.codonCoord=130;refseq.end=166950126;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=404;refseq.name=NM_001937;refseq.name2=DPT;refseq.positionType=CDS;refseq.proteinCoordStr=p.F130V;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=-44;refseq.start=166950126;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=FilteredInAll GT 0/1
|
|
chr1 166964797 . C T 181.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=666;Dels=0.00;HRun=0;HaplotypeScore=9.52;MQ=98.89;MQ0=0;OQ=11563.86;QD=17.36;RankSumP=0.000112106;SB=-3952.26;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.240G>A;refseq.codonCoord=80;refseq.end=166964797;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=256;refseq.name=NM_001937;refseq.name2=DPT;refseq.positionType=CDS;refseq.proteinCoordStr=p.T80T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-66;refseq.start=166964797;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=filterInsoap-gatk GT 0/1
|
|
chr1 167363210 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=3;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.507C>A;refseq.codingCoordStr_2=c.507C>A;refseq.codonCoord_1=169;refseq.codonCoord_2=169;refseq.end_1=167363210;refseq.end_2=167363210;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=628;refseq.mrnaCoord_2=628;refseq.name2_1=ATP1B1;refseq.name2_2=ATP1B1;refseq.name_1=NM_001001787;refseq.name_2=NM_001677;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y169*;refseq.proteinCoordStr_2=p.Y169*;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-61;refseq.spliceDist_2=-61;refseq.start_1=167363210;refseq.start_2=167363210;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantCodon_1=TAA;refseq.variantCodon_2=TAA;set=FilteredInAll GT 1/0
|
|
chr1 167657778 . A G 257.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.83;MQ0=0;OQ=2652.35;QD=21.05;RankSumP=0.0908461;SB=-1253.30;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.515T>C;refseq.codonCoord=172;refseq.end=167657778;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=683;refseq.name=NM_021179;refseq.name2=C1orf114;refseq.positionType=CDS;refseq.proteinCoordStr=p.F172S;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=398;refseq.start=167657778;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 0/1
|
|
chr1 167713421 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.403A>C;refseq.codonCoord=135;refseq.end=167713421;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=607;refseq.name=NM_006996;refseq.name2=SLC19A2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T135P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=199;refseq.start=167713421;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 167750185 . T C 117.74 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=266;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=98.86;MQ0=0;OQ=6218.32;QD=23.38;RankSumP=0.179577;SB=-2575.52;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6665A>G;refseq.codonCoord=2222;refseq.end=167750185;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6810;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.D2222G;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=137;refseq.start=167750185;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 1/0
|
|
chr1 167751374 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6460A>C;refseq.codonCoord=2154;refseq.end=167751374;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6605;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.T2154P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-69;refseq.start=167751374;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 167765599 . T C 142.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=485;Dels=0.00;HRun=0;HaplotypeScore=9.58;MQ=98.70;MQ0=0;OQ=19964.52;QD=41.16;RankSumP=1.00000;SB=-9673.57;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5290A>G;refseq.codonCoord=1764;refseq.end=167765599;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5435;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.M1764V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=82;refseq.start=167765599;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 167776972 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=1048;Dels=0.00;HRun=0;HaplotypeScore=31.93;MQ=64.84;MQ0=165;OQ=14808.64;QD=14.13;RankSumP=0.221295;SB=-5019.28;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3980A>G;refseq.codonCoord=1327;refseq.end=167776972;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4125;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1327R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-817;refseq.start=167776972;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/0
|
|
chr1 167777004 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=1167;Dels=0.00;HRun=1;HaplotypeScore=25.86;MQ=77.92;MQ0=130;OQ=19161.62;QD=16.42;RankSumP=0.0247608;SB=-7505.45;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3948C>T;refseq.codonCoord=1316;refseq.end=167777004;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4093;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1316L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-849;refseq.start=167777004;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/0
|
|
chr1 167777148 . A G 90 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=826;Dels=0.00;HRun=2;HaplotypeScore=29.14;MQ=54.16;MQ0=291;OQ=17563.39;QD=21.26;RankSumP=1.00000;SB=-7524.17;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3804T>C;refseq.codonCoord=1268;refseq.end=167777148;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3949;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1268S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-993;refseq.start=167777148;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 167778179 . T C 112.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=430;Dels=0.00;HRun=2;HaplotypeScore=9.34;MQ=98.53;MQ0=0;OQ=8772.59;QD=20.40;RankSumP=0.359369;SB=-2496.84;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2773A>G;refseq.codonCoord=925;refseq.end=167778179;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2918;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.K925E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=798;refseq.start=167778179;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 167778358 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=734;Dels=0.00;HRun=0;HaplotypeScore=8.65;MQ=98.81;MQ0=0;OQ=14624.56;QD=19.92;RankSumP=0.179489;SB=-5803.08;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2594A>G;refseq.codonCoord=865;refseq.end=167778358;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2739;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.H865R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=619;refseq.start=167778358;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/0
|
|
chr1 167778379 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=718;Dels=0.00;HRun=0;HaplotypeScore=15.70;MQ=98.84;MQ0=0;OQ=15873.70;QD=22.11;RankSumP=0.245030;SB=-6530.61;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2573A>G;refseq.codonCoord=858;refseq.end=167778379;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2718;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.K858R;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=598;refseq.start=167778379;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/0
|
|
chr1 167778502 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=545;Dels=0.00;HRun=1;HaplotypeScore=36.57;MQ=98.70;MQ0=0;OQ=10947.56;QD=20.09;RankSumP=0.168871;SB=-4297.40;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2450A>C;refseq.codonCoord=817;refseq.end=167778502;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2595;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.N817T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=475;refseq.start=167778502;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/0
|
|
chr1 167778651 . T C 323.12 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=549;Dels=0.00;HRun=0;HaplotypeScore=6.63;MQ=98.68;MQ0=0;OQ=9537.71;QD=17.37;RankSumP=0.381820;SB=-2508.70;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2301A>G;refseq.codonCoord=767;refseq.end=167778651;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2446;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.S767S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=326;refseq.start=167778651;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/0
|
|
chr1 167778663 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=610;Dels=0.00;HRun=0;HaplotypeScore=22.55;MQ=98.67;MQ0=0;OQ=13947.75;QD=22.87;RankSumP=0.331445;SB=-4776.01;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2289A>G;refseq.codonCoord=763;refseq.end=167778663;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2434;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.E763E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=314;refseq.start=167778663;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 167778717 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=773;Dels=0.00;HRun=1;HaplotypeScore=6.11;MQ=98.77;MQ0=0;OQ=13150.87;QD=17.01;RankSumP=0.102401;SB=-4090.78;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2235T>C;refseq.codonCoord=745;refseq.end=167778717;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2380;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.N745N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=260;refseq.start=167778717;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 0/1
|
|
chr1 167778744 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=797;Dels=0.00;HRun=1;HaplotypeScore=40.94;MQ=98.87;MQ0=0;OQ=12777.56;QD=16.03;RankSumP=0.266079;SB=-3956.41;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2208C>T;refseq.codonCoord=736;refseq.end=167778744;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2353;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.I736I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=233;refseq.start=167778744;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 167780207 . G T 183.55 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=335;Dels=0.00;HRun=0;HaplotypeScore=2.03;MQ=98.96;MQ0=0;OQ=6085.40;QD=18.17;RankSumP=0.0392713;SB=-2504.54;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1926C>A;refseq.codonCoord=642;refseq.end=167780207;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2071;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.T642T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-50;refseq.start=167780207;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 167782350 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=366;Dels=0.00;HRun=1;HaplotypeScore=16.98;MQ=98.77;MQ0=0;OQ=7798.06;QD=21.31;RankSumP=0.338692;SB=-2235.00;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1716G>A;refseq.codonCoord=572;refseq.end=167782350;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1861;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.E572E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-47;refseq.start=167782350;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 167785673 . T C 414.39 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=137;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=97.96;MQ0=0;OQ=5248.96;QD=38.31;RankSumP=1.00000;SB=-1153.80;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1601A>G;refseq.codonCoord=534;refseq.end=167785673;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1746;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q534R;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-11;refseq.start=167785673;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/1
|
|
chr1 167786518 . G A 148.07 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=303;Dels=0.00;HRun=1;HaplotypeScore=10.28;MQ=98.83;MQ0=0;OQ=6440.32;QD=21.26;RankSumP=0.276639;SB=-1690.13;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1380C>T;refseq.codonCoord=460;refseq.end=167786518;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1525;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.N460N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-17;refseq.start=167786518;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 167788477 . A G 317.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=180;Dels=0.00;HRun=0;HaplotypeScore=4.01;MQ=99.00;MQ0=0;OQ=3082.13;QD=17.12;RankSumP=0.370619;SB=-1047.13;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1238T>C;refseq.codonCoord=413;refseq.end=167788477;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1383;refseq.name=NM_000130;refseq.name2=F5;refseq.positionType=CDS;refseq.proteinCoordStr=p.M413T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-59;refseq.start=167788477;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 0/1
|
|
chr1 167832955 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1789A>C;refseq.codonCoord=597;refseq.end=167832955;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1854;refseq.name=NM_003005;refseq.name2=SELP;refseq.positionType=CDS;refseq.proteinCoordStr=p.T597P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=84;refseq.start=167832955;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 167852905 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=574;Dels=0.00;HRun=0;HaplotypeScore=5.94;MQ=98.69;MQ0=0;OQ=10613.73;QD=18.49;RankSumP=0.135223;SB=-3576.57;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.466G>A;refseq.codonCoord=156;refseq.end=167852905;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=531;refseq.name=NM_003005;refseq.name2=SELP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A156T;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-16;refseq.start=167852905;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 167965118 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.923G>C;refseq.codonCoord=308;refseq.end=167965118;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1080;refseq.name=NM_000450;refseq.name2=SELE;refseq.positionType=CDS;refseq.proteinCoordStr=p.R308P;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=22;refseq.start=167965118;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 168100172 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.917T>G;refseq.codingCoordStr_2=c.917T>G;refseq.codonCoord_1=306;refseq.codonCoord_2=306;refseq.end_1=168100172;refseq.end_2=168100172;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1115;refseq.mrnaCoord_2=1115;refseq.name2_1=SCYL3;refseq.name2_2=SCYL3;refseq.name_1=NM_020423;refseq.name_2=NM_181093;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V306G;refseq.proteinCoordStr_2=p.V306G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTT;refseq.referenceCodon_2=GTT;refseq.spliceDist_1=-39;refseq.spliceDist_2=-39;refseq.start_1=168100172;refseq.start_2=168100172;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 0/1
|
|
chr1 168218621 . C T 156.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=7.99;MQ=98.74;MQ0=0;OQ=2158.52;QD=17.99;RankSumP=0.436119;SB=-435.90;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1518G>A;refseq.codonCoord=506;refseq.end=168218621;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1789;refseq.name=NM_014970;refseq.name2=KIFAP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.G506G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=12;refseq.start=168218621;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 0/1
|
|
chr1 168768009 . A C 423.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=98.88;MQ0=0;OQ=4266.59;QD=36.16;RankSumP=1.00000;SB=-1802.26;SecondBestBaseQ=2;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.96A>C;refseq.codingCoordStr_3=c.96A>C;refseq.codonCoord_2=32;refseq.codonCoord_3=32;refseq.end_1=168768009;refseq.end_2=168768009;refseq.end_3=168768009;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=123;refseq.mrnaCoord_2=123;refseq.mrnaCoord_3=123;refseq.name2_1=GORAB;refseq.name2_2=GORAB;refseq.name2_3=GORAB;refseq.name_1=NR_027397;refseq.name_2=NM_001146039;refseq.name_3=NM_152281;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.G32G;refseq.proteinCoordStr_3=p.G32G;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_2=GGA;refseq.referenceCodon_3=GGA;refseq.spliceDist_1=-41;refseq.spliceDist_2=-41;refseq.spliceDist_3=-41;refseq.start_1=168768009;refseq.start_2=168768009;refseq.start_3=168768009;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_2=GGC;refseq.variantCodon_3=GGC;set=Intersection GT 1/1
|
|
chr1 168788000 . G A 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=196;Dels=0.00;HRun=2;HaplotypeScore=8.99;MQ=98.85;MQ0=0;OQ=8338.54;QD=42.54;RankSumP=1.00000;SB=-3329.71;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.958G>A;refseq.codonCoord_2=320;refseq.end_1=168788000;refseq.end_2=168788000;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=989;refseq.mrnaCoord_2=985;refseq.name2_1=GORAB;refseq.name2_2=GORAB;refseq.name_1=NR_027397;refseq.name_2=NM_152281;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.E320K;refseq.referenceAA_2=Glu;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=221;refseq.spliceDist_2=221;refseq.start_1=168788000;refseq.start_2=168788000;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Lys;refseq.variantCodon_2=AAA;set=Intersection GT 1/1
|
|
chr1 169194239 . A G 164.99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=97.64;MQ0=0;OQ=2112.98;QD=13.54;RankSumP=0.288334;SB=-504.53;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.86A>G;refseq.codingCoordStr_2=c.86A>G;refseq.codonCoord_1=29;refseq.codonCoord_2=29;refseq.end_1=169194239;refseq.end_2=169194239;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=240;refseq.mrnaCoord_2=216;refseq.name2_1=C1orf129;refseq.name2_2=C1orf129;refseq.name_1=NM_001163629;refseq.name_2=NM_025063;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N29S;refseq.proteinCoordStr_2=p.N29S;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=14;refseq.spliceDist_2=14;refseq.start_1=169194239;refseq.start_2=169194239;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;set=Intersection GT 0/1
|
|
chr1 169225653 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=583;Dels=0.00;HRun=1;HaplotypeScore=7.10;MQ=98.89;MQ0=0;OQ=11030.51;QD=18.92;RankSumP=0.409050;SB=-4178.48;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.913C>T;refseq.codingCoordStr_2=c.913C>T;refseq.codonCoord_1=305;refseq.codonCoord_2=305;refseq.end_1=169225653;refseq.end_2=169225653;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1067;refseq.mrnaCoord_2=1043;refseq.name2_1=C1orf129;refseq.name2_2=C1orf129;refseq.name_1=NM_001163629;refseq.name_2=NM_025063;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L305L;refseq.proteinCoordStr_2=p.L305L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=34;refseq.spliceDist_2=34;refseq.start_1=169225653;refseq.start_2=169225653;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=TTG;refseq.variantCodon_2=TTG;set=Intersection GT 0/1
|
|
chr1 169225712 . C T 233.22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=262;Dels=0.00;HRun=0;HaplotypeScore=4.89;MQ=99.00;MQ0=0;OQ=4857.42;QD=18.54;RankSumP=0.0714558;SB=-1070.03;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.972C>T;refseq.codingCoordStr_2=c.972C>T;refseq.codonCoord_1=324;refseq.codonCoord_2=324;refseq.end_1=169225712;refseq.end_2=169225712;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1126;refseq.mrnaCoord_2=1102;refseq.name2_1=C1orf129;refseq.name2_2=C1orf129;refseq.name_1=NM_001163629;refseq.name_2=NM_025063;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C324C;refseq.proteinCoordStr_2=p.C324C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=-57;refseq.spliceDist_2=-57;refseq.start_1=169225712;refseq.start_2=169225712;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;set=Intersection GT 0/1
|
|
chr1 169232305 . T C 247.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=344;Dels=0.00;HRun=0;HaplotypeScore=5.58;MQ=98.89;MQ0=0;OQ=7001.15;QD=20.35;RankSumP=0.232366;SB=-2537.05;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1371T>C;refseq.codingCoordStr_2=c.1371T>C;refseq.codonCoord_1=457;refseq.codonCoord_2=457;refseq.end_1=169232305;refseq.end_2=169232305;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1525;refseq.mrnaCoord_2=1501;refseq.name2_1=C1orf129;refseq.name2_2=C1orf129;refseq.name_1=NM_001163629;refseq.name_2=NM_025063;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N457N;refseq.proteinCoordStr_2=p.N457N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=34;refseq.spliceDist_2=34;refseq.start_1=169232305;refseq.start_2=169232305;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=Intersection GT 1/0
|
|
chr1 169343590 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=509;Dels=0.00;HRun=4;HaplotypeScore=13.34;MQ=98.73;MQ0=0;OQ=10712.66;QD=21.05;RankSumP=0.0397563;SB=-4084.97;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.472G>A;refseq.codingCoordStr_2=c.472G>A;refseq.codonCoord_1=158;refseq.codonCoord_2=158;refseq.end_1=169343590;refseq.end_2=169343590;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=583;refseq.mrnaCoord_2=566;refseq.name2_1=FMO3;refseq.name2_2=FMO3;refseq.name_1=NM_001002294;refseq.name_2=NM_006894;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E158K;refseq.proteinCoordStr_2=p.E158K;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=-13;refseq.spliceDist_2=-13;refseq.start_1=169343590;refseq.start_2=169343590;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/0
|
|
chr1 169435208 . C T 226.39 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=429;Dels=0.00;HRun=1;HaplotypeScore=5.00;MQ=98.91;MQ0=0;OQ=8748.62;QD=20.39;RankSumP=0.130036;SB=-2458.68;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.584C>T;refseq.codonCoord=195;refseq.end=169435208;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=701;refseq.name=NM_001460;refseq.name2=FMO2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S195L;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-44;refseq.start=169435208;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=Intersection GT 0/1
|
|
chr1 169435209 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=430;Dels=0.00;HRun=2;HaplotypeScore=4.00;MQ=98.91;MQ0=0;OQ=8681.33;QD=20.19;RankSumP=0.0246750;SB=-2299.63;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.585A>G;refseq.codonCoord=195;refseq.end=169435209;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=702;refseq.name=NM_001460;refseq.name2=FMO2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S195S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-43;refseq.start=169435209;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 0/1
|
|
chr1 169441155 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=252;Dels=0.00;HRun=2;HaplotypeScore=11.91;MQ=98.89;MQ0=0;OQ=4991.50;QD=19.81;RankSumP=0.148319;SB=-1600.29;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.941A>G;refseq.codonCoord=314;refseq.end=169441155;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1058;refseq.name=NM_001460;refseq.name2=FMO2;refseq.positionType=CDS;refseq.proteinCoordStr=p.E314G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=114;refseq.start=169441155;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 0/1
|
|
chr1 169570460 . G A 205.61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=277;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=98.85;MQ0=0;OQ=6137.30;QD=22.16;RankSumP=0.312327;SB=-2307.16;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1114G>A;refseq.codonCoord=372;refseq.end=169570460;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1331;refseq.name=NM_002022;refseq.name2=FMO4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G372S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-67;refseq.start=169570460;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/0
|
|
chr1 169872010 . T C 209.08 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=337;Dels=0.00;HRun=0;HaplotypeScore=14.94;MQ=98.98;MQ0=0;OQ=6575.82;QD=19.51;RankSumP=0.378597;SB=-2275.72;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1193A>G;refseq.codonCoord=398;refseq.end=169872010;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1215;refseq.name=NM_000261;refseq.name2=MYOC;refseq.positionType=CDS;refseq.proteinCoordStr=p.K398R;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=463;refseq.start=169872010;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/0
|
|
chr1 170017859 . T C 342.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=317;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=98.70;MQ0=0;OQ=6586.89;QD=20.78;RankSumP=0.489499;SB=-2612.02;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.129T>C;refseq.codingCoordStr_3=c.129T>C;refseq.codonCoord_2=43;refseq.codonCoord_3=43;refseq.end_1=170019492;refseq.end_2=170017859;refseq.end_3=170017859;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=476;refseq.mrnaCoord_3=476;refseq.name2_1=METTL13;refseq.name2_2=METTL13;refseq.name2_3=METTL13;refseq.name_1=NM_014955;refseq.name_2=NM_001007239;refseq.name_3=NM_015935;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.H43H;refseq.proteinCoordStr_3=p.H43H;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceCodon_2=CAT;refseq.referenceCodon_3=CAT;refseq.spliceDist_2=-25;refseq.spliceDist_3=-25;refseq.start_1=170017569;refseq.start_2=170017859;refseq.start_3=170017859;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;set=Intersection GT 1/0
|
|
chr1 170021805 . G A 224.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=137;Dels=0.00;HRun=0;HaplotypeScore=4.11;MQ=98.97;MQ0=0;OQ=1961.68;QD=14.32;RankSumP=0.0777742;SB=-808.43;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.609G>A;refseq.codingCoordStr_2=c.819G>A;refseq.codingCoordStr_3=c.1077G>A;refseq.codonCoord_1=203;refseq.codonCoord_2=273;refseq.codonCoord_3=359;refseq.end_1=170021805;refseq.end_2=170021805;refseq.end_3=170021805;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=956;refseq.mrnaCoord_2=1099;refseq.mrnaCoord_3=1424;refseq.name2_1=METTL13;refseq.name2_2=METTL13;refseq.name2_3=METTL13;refseq.name_1=NM_001007239;refseq.name_2=NM_014955;refseq.name_3=NM_015935;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.M203I;refseq.proteinCoordStr_2=p.M273I;refseq.proteinCoordStr_3=p.M359I;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceAA_3=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.referenceCodon_3=ATG;refseq.spliceDist_1=-37;refseq.spliceDist_2=-37;refseq.spliceDist_3=-37;refseq.start_1=170021805;refseq.start_2=170021805;refseq.start_3=170021805;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantCodon_1=ATA;refseq.variantCodon_2=ATA;refseq.variantCodon_3=ATA;set=Intersection GT 1/0
|
|
chr1 170030172 . C T 326.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=180;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=99.00;MQ0=0;OQ=3148.55;QD=17.49;RankSumP=0.434926;SB=-1268.01;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1239C>T;refseq.codingCoordStr_2=c.1449C>T;refseq.codingCoordStr_3=c.1707C>T;refseq.codonCoord_1=413;refseq.codonCoord_2=483;refseq.codonCoord_3=569;refseq.end_1=170030172;refseq.end_2=170030172;refseq.end_3=170030172;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1586;refseq.mrnaCoord_2=1729;refseq.mrnaCoord_3=2054;refseq.name2_1=METTL13;refseq.name2_2=METTL13;refseq.name2_3=METTL13;refseq.name_1=NM_001007239;refseq.name_2=NM_014955;refseq.name_3=NM_015935;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Y413Y;refseq.proteinCoordStr_2=p.Y483Y;refseq.proteinCoordStr_3=p.Y569Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.spliceDist_1=14;refseq.spliceDist_2=14;refseq.spliceDist_3=14;refseq.start_1=170030172;refseq.start_2=170030172;refseq.start_3=170030172;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;refseq.variantCodon_3=TAT;set=Intersection GT 0/1
|
|
chr1 170677590 . G A 183.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=239;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.84;MQ0=0;OQ=4903.23;QD=20.52;RankSumP=0.440151;SB=-1822.19;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.796C>T;refseq.codingCoordStr_3=c.796C>T;refseq.codonCoord_2=266;refseq.codonCoord_3=266;refseq.end_1=170680825;refseq.end_2=170677590;refseq.end_3=170677590;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=1130;refseq.mrnaCoord_3=1107;refseq.name2_1=C1orf105;refseq.name2_2=PIGC;refseq.name2_3=PIGC;refseq.name_1=NM_139240;refseq.name_2=NM_002642;refseq.name_3=NM_153747;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.P266S;refseq.proteinCoordStr_3=p.P266S;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_2=CCA;refseq.referenceCodon_3=CCA;refseq.spliceDist_2=-371;refseq.spliceDist_3=-371;refseq.start_1=170656680;refseq.start_2=170677590;refseq.start_3=170677590;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_2=TCA;refseq.variantCodon_3=TCA;set=Intersection GT 1/0
|
|
chr1 170678119 . A G 156.36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=130;Dels=0.00;HRun=1;HaplotypeScore=1.89;MQ=88.09;MQ0=0;OQ=1927.61;QD=14.83;RankSumP=0.0571277;SB=-739.56;SecondBestBaseQ=32;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.267T>C;refseq.codingCoordStr_3=c.267T>C;refseq.codonCoord_2=89;refseq.codonCoord_3=89;refseq.end_1=170680825;refseq.end_2=170678119;refseq.end_3=170678119;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=601;refseq.mrnaCoord_3=578;refseq.name2_1=C1orf105;refseq.name2_2=PIGC;refseq.name2_3=PIGC;refseq.name_1=NM_139240;refseq.name_2=NM_002642;refseq.name_3=NM_153747;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.G89G;refseq.proteinCoordStr_3=p.G89G;refseq.referenceAA_2=Gly;refseq.referenceAA_3=Gly;refseq.referenceCodon_2=GGT;refseq.referenceCodon_3=GGT;refseq.spliceDist_2=498;refseq.spliceDist_3=475;refseq.start_1=170656680;refseq.start_2=170678119;refseq.start_3=170678119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_2=GGC;refseq.variantCodon_3=GGC;set=Intersection GT 0/1
|
|
chr1 170704215 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=549;Dels=0.00;HRun=3;HaplotypeScore=28.83;MQ=98.84;MQ0=0;OQ=10877.24;QD=19.81;RankSumP=0.386207;SB=-2816.16;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.410G>A;refseq.codonCoord=137;refseq.end=170704215;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=608;refseq.name=NM_139240;refseq.name2=C1orf105;refseq.positionType=CDS;refseq.proteinCoordStr=p.S137N;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=4;refseq.spliceInfo=splice-acceptor_4;refseq.start=170704215;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/0
|
|
chr1 170814088 . A G 205.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=265;Dels=0.00;HRun=0;HaplotypeScore=14.52;MQ=98.71;MQ0=0;OQ=5913.43;QD=22.31;RankSumP=0.435278;SB=-1569.83;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1368A>G;refseq.codingCoordStr_2=c.1236A>G;refseq.codonCoord_1=456;refseq.codonCoord_2=412;refseq.end_1=170814088;refseq.end_2=170814088;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1684;refseq.mrnaCoord_2=1495;refseq.name2_1=C1orf9;refseq.name2_2=C1orf9;refseq.name_1=NM_014283;refseq.name_2=NM_016227;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E456E;refseq.proteinCoordStr_2=p.E412E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=28;refseq.spliceDist_2=28;refseq.start_1=170814088;refseq.start_2=170814088;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 0/1
|
|
chr1 171739088 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=100;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.72;MQ0=0;OQ=1525.97;QD=15.26;RankSumP=0.490438;SB=-654.98;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3311C>T;refseq.codonCoord=1104;refseq.end=171739088;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3734;refseq.name=NM_178527;refseq.name2=SLC9A11;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1104V;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=1;refseq.spliceInfo=splice-acceptor_1;refseq.start=171739088;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 172039203 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.622T>G;refseq.codingCoordStr_2=c.484T>G;refseq.codingCoordStr_3=c.484T>G;refseq.codonCoord_1=208;refseq.codonCoord_2=162;refseq.codonCoord_3=162;refseq.end_1=172039203;refseq.end_2=172039203;refseq.end_3=172039203;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1225;refseq.mrnaCoord_2=698;refseq.mrnaCoord_3=1087;refseq.name2_1=CENPL;refseq.name2_2=CENPL;refseq.name2_3=CENPL;refseq.name_1=NM_001127181;refseq.name_2=NM_001171182;refseq.name_3=NM_033319;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.F208V;refseq.proteinCoordStr_2=p.F162V;refseq.proteinCoordStr_3=p.F162V;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.referenceCodon_3=TTC;refseq.spliceDist_1=64;refseq.spliceDist_2=64;refseq.spliceDist_3=64;refseq.start_1=172039203;refseq.start_2=172039203;refseq.start_3=172039203;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;refseq.variantCodon_3=GTC;set=FilteredInAll GT 0/1
|
|
chr1 172145455 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=806;Dels=0.00;HRun=1;HaplotypeScore=29.28;MQ=98.20;MQ0=0;OQ=15477.12;QD=19.20;RankSumP=0.205044;SB=-5867.11;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1011A>G;refseq.codonCoord=337;refseq.end=172145455;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1130;refseq.name=NM_000488;refseq.name2=SERPINC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q337Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-143;refseq.start=172145455;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 172145485 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=642;Dels=0.00;HRun=1;HaplotypeScore=15.61;MQ=98.50;MQ0=0;OQ=12636.13;QD=19.68;RankSumP=0.355909;SB=-3704.00;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.981A>G;refseq.codonCoord=327;refseq.end=172145485;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1100;refseq.name=NM_000488;refseq.name2=SERPINC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V327V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-173;refseq.start=172145485;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 173313412 . A G 76 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=150;Dels=0.00;HRun=3;HaplotypeScore=2.70;MQ=98.74;MQ0=0;OQ=4841.44;QD=32.28;RankSumP=1.00000;SB=-2157.49;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.235A>G;refseq.codonCoord=79;refseq.end=173313412;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=348;refseq.name=NM_022093;refseq.name2=TNN;refseq.positionType=CDS;refseq.proteinCoordStr=p.R79G;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-175;refseq.start=173313412;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 1/1
|
|
chr1 173321171 . C T 315.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=98.12;MQ0=0;OQ=1846.00;QD=34.83;RankSumP=1.00000;SB=-359.35;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1242C>T;refseq.codonCoord=414;refseq.end=173321171;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1355;refseq.name=NM_022093;refseq.name2=TNN;refseq.positionType=CDS;refseq.proteinCoordStr=p.H414H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=173321171;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/1
|
|
chr1 173354352 . T C 87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=329;Dels=0.00;HRun=1;HaplotypeScore=21.79;MQ=92.68;MQ0=0;OQ=8513.13;QD=25.88;RankSumP=1.00000;SB=-1600.48;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2419T>C;refseq.codonCoord=807;refseq.end=173354352;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2532;refseq.name=NM_022093;refseq.name2=TNN;refseq.positionType=CDS;refseq.proteinCoordStr=p.W807R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=33;refseq.start=173354352;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/1
|
|
chr1 173359297 . C T 281.74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=409;Dels=0.00;HRun=0;HaplotypeScore=6.25;MQ=98.45;MQ0=0;OQ=16486.80;QD=40.31;RankSumP=1.00000;SB=-6918.01;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2789C>T;refseq.codonCoord=930;refseq.end=173359297;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2902;refseq.name=NM_022093;refseq.name2=TNN;refseq.positionType=CDS;refseq.proteinCoordStr=p.P930L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-126;refseq.start=173359297;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 173359330 . C T 344.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=383;Dels=0.00;HRun=0;HaplotypeScore=10.28;MQ=98.12;MQ0=0;OQ=7537.06;QD=19.68;RankSumP=0.234226;SB=-2850.86;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2822C>T;refseq.codonCoord=941;refseq.end=173359330;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2935;refseq.name=NM_022093;refseq.name2=TNN;refseq.positionType=CDS;refseq.proteinCoordStr=p.T941M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-93;refseq.start=173359330;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 173380201 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=555;Dels=0.00;HRun=0;HaplotypeScore=9.81;MQ=98.71;MQ0=0;OQ=19272.63;QD=34.73;RankSumP=1.00000;SB=-9455.45;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3651T>C;refseq.codonCoord=1217;refseq.end=173380201;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3764;refseq.name=NM_022093;refseq.name2=TNN;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1217N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=56;refseq.start=173380201;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 173565924 . T C 144.33 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=217;Dels=0.00;HRun=1;HaplotypeScore=3.48;MQ=98.79;MQ0=0;OQ=2878.22;QD=13.26;RankSumP=0.263604;SB=-852.46;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3702A>G;refseq.codonCoord=1234;refseq.end=173565924;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4257;refseq.name=NM_003285;refseq.name2=TNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1234Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=71;refseq.start=173565924;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 173591274 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=275;Dels=0.00;HRun=0;HaplotypeScore=8.68;MQ=98.00;MQ0=0;OQ=3090.93;QD=11.24;RankSumP=0.164011;SB=-551.18;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3237T>C;refseq.codonCoord=1079;refseq.end=173591274;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3792;refseq.name=NM_003285;refseq.name2=TNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1079D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-13;refseq.start=173591274;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 0/1
|
|
chr1 173615346 . C T 178.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=284;Dels=0.00;HRun=1;HaplotypeScore=9.02;MQ=98.68;MQ0=0;OQ=12058.94;QD=42.46;RankSumP=1.00000;SB=-5425.60;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1928G>A;refseq.codonCoord=643;refseq.end=173615346;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2483;refseq.name=NM_003285;refseq.name2=TNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.R643K;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-36;refseq.start=173615346;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 173622014 . A G 239.53 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=7.31;MQ=98.61;MQ0=0;OQ=4095.49;QD=36.57;RankSumP=1.00000;SB=-1988.66;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1554T>C;refseq.codonCoord=518;refseq.end=173622014;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2109;refseq.name=NM_003285;refseq.name2=TNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.T518T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=47;refseq.start=173622014;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 173642092 . C A 101.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=432;Dels=0.00;HRun=1;HaplotypeScore=11.15;MQ=98.49;MQ0=0;OQ=6966.85;QD=16.13;RankSumP=0.00126640;SB=-2370.92;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.382G>T;refseq.codonCoord=128;refseq.end=173642092;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=937;refseq.name=NM_003285;refseq.name2=TNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.A128S;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-118;refseq.start=173642092;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=filterInsoap-gatk GT 1/0
|
|
chr1 173642306 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=738;Dels=0.00;HRun=0;HaplotypeScore=14.84;MQ=98.82;MQ0=0;OQ=25338.35;QD=34.33;RankSumP=1.00000;SB=-10052.63;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.168A>G;refseq.codonCoord=56;refseq.end=173642306;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=723;refseq.name=NM_003285;refseq.name2=TNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.T56T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=231;refseq.start=173642306;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 173642425 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=622;Dels=0.00;HRun=0;HaplotypeScore=9.69;MQ=98.76;MQ0=0;OQ=23360.39;QD=37.56;RankSumP=1.00000;SB=-9889.27;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.49A>G;refseq.codonCoord=17;refseq.end=173642425;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=604;refseq.name=NM_003285;refseq.name2=TNR;refseq.positionType=CDS;refseq.proteinCoordStr=p.I17V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=112;refseq.start=173642425;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 174204163 . C T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=500;Dels=0.00;HRun=0;HaplotypeScore=19.36;MQ=98.65;MQ0=0;OQ=17837.22;QD=35.67;RankSumP=1.00000;SB=-8563.46;SecondBestBaseQ=0;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.end_1=174222691;refseq.end_2=174222691;refseq.end_3=174204163;refseq.haplotypeAlternate_3=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.mrnaCoord_3=137;refseq.name2_1=RFWD2;refseq.name2_2=RFWD2;refseq.name2_3=SCARNA3;refseq.name_1=NM_001001740;refseq.name_2=NM_022457;refseq.name_3=NR_002998;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=non_coding_exon;refseq.spliceDist_3=-8;refseq.spliceInfo_3=splice-donor_-8;refseq.start_1=174183009;refseq.start_2=174183009;refseq.start_3=174204163;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;set=Intersection GT 1/1
|
|
chr1 174926086 . C T 292.45 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=240;Dels=0.00;HRun=0;HaplotypeScore=7.25;MQ=98.61;MQ0=0;OQ=9274.22;QD=38.64;RankSumP=1.00000;SB=-3007.05;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2328C>T;refseq.codingCoordStr_2=c.2328C>T;refseq.codonCoord_1=776;refseq.codonCoord_2=776;refseq.end_1=174926086;refseq.end_2=174926086;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3492;refseq.mrnaCoord_2=3492;refseq.name2_1=PAPPA2;refseq.name2_2=PAPPA2;refseq.name_1=NM_020318;refseq.name_2=NM_021936;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P776P;refseq.proteinCoordStr_2=p.P776P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=-104;refseq.spliceDist_2=191;refseq.start_1=174926086;refseq.start_2=174926086;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;set=Intersection GT 1/1
|
|
chr1 175075991 . C T 336.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=303;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=98.23;MQ0=0;OQ=11718.80;QD=38.68;RankSumP=1.00000;SB=-4433.71;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5262C>T;refseq.codonCoord=1754;refseq.end=175075991;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6426;refseq.name=NM_020318;refseq.name2=PAPPA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1754D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-40;refseq.start=175075991;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 175130459 . G C 307 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=5.44;MQ=98.77;MQ0=0;OQ=3819.80;QD=38.98;RankSumP=1.00000;SB=-1827.81;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2802C>G;refseq.codingCoordStr_2=c.2802C>G;refseq.codonCoord_1=934;refseq.codonCoord_2=934;refseq.end_1=175130459;refseq.end_2=175130459;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3014;refseq.mrnaCoord_2=3014;refseq.name2_1=ASTN1;refseq.name2_2=ASTN1;refseq.name_1=NM_004319;refseq.name_2=NM_207108;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H934Q;refseq.proteinCoordStr_2=p.H934Q;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=131;refseq.spliceDist_2=131;refseq.start_1=175130459;refseq.start_2=175130459;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=Intersection GT 1/1
|
|
chr1 175130490 . T C 289.19 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=98.54;MQ0=0;OQ=2550.31;QD=33.56;RankSumP=1.00000;SB=-1170.61;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2771A>G;refseq.codingCoordStr_2=c.2771A>G;refseq.codonCoord_1=924;refseq.codonCoord_2=924;refseq.end_1=175130490;refseq.end_2=175130490;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2983;refseq.mrnaCoord_2=2983;refseq.name2_1=ASTN1;refseq.name2_2=ASTN1;refseq.name_1=NM_004319;refseq.name_2=NM_207108;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H924R;refseq.proteinCoordStr_2=p.H924R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=100;refseq.spliceDist_2=100;refseq.start_1=175130490;refseq.start_2=175130490;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=Intersection GT 1/1
|
|
chr1 175259176 . A G 165.53 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=97.75;MQ0=0;OQ=1131.73;QD=31.44;RankSumP=1.00000;SB=-418.49;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1425T>C;refseq.codingCoordStr_2=c.1425T>C;refseq.codonCoord_1=475;refseq.codonCoord_2=475;refseq.end_1=175259176;refseq.end_2=175259176;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1637;refseq.mrnaCoord_2=1637;refseq.name2_1=ASTN1;refseq.name2_2=ASTN1;refseq.name_1=NM_004319;refseq.name_2=NM_207108;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C475C;refseq.proteinCoordStr_2=p.C475C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=-14;refseq.spliceDist_2=-14;refseq.start_1=175259176;refseq.start_2=175259176;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;set=Intersection GT 1/1
|
|
chr1 175259299 . C T 357.28 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=200;Dels=0.00;HRun=1;HaplotypeScore=2.48;MQ=98.23;MQ0=0;OQ=7932.73;QD=39.66;RankSumP=1.00000;SB=-2975.81;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1302G>A;refseq.codingCoordStr_2=c.1302G>A;refseq.codonCoord_1=434;refseq.codonCoord_2=434;refseq.end_1=175259299;refseq.end_2=175259299;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1514;refseq.mrnaCoord_2=1514;refseq.name2_1=ASTN1;refseq.name2_2=ASTN1;refseq.name_1=NM_004319;refseq.name_2=NM_207108;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Q434Q;refseq.proteinCoordStr_2=p.Q434Q;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceCodon_1=CAG;refseq.referenceCodon_2=CAG;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.start_1=175259299;refseq.start_2=175259299;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;set=Intersection GT 1/1
|
|
chr1 175296967 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.341A>G;refseq.codingCoordStr_2=c.341A>G;refseq.codonCoord_1=114;refseq.codonCoord_2=114;refseq.end_1=175296967;refseq.end_2=175296967;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=553;refseq.mrnaCoord_2=553;refseq.name2_1=ASTN1;refseq.name2_2=ASTN1;refseq.name_1=NM_004319;refseq.name_2=NM_207108;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E114G;refseq.proteinCoordStr_2=p.E114G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=58;refseq.spliceDist_2=58;refseq.start_1=175296967;refseq.start_2=175296967;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 175514477 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=99.00;MQ0=0;OQ=890.48;QD=12.37;RankSumP=0.0934631;SB=-324.94;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1168C>G;refseq.codonCoord=390;refseq.end=175514477;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1480;refseq.name=NM_021165;refseq.name2=FAM5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.L390V;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-68;refseq.start=175514477;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/0
|
|
chr1 175516719 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1784G>C;refseq.codonCoord=595;refseq.end=175516719;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2096;refseq.name=NM_021165;refseq.name2=FAM5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.G595A;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=549;refseq.start=175516719;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 176756601 . T G 100.37 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=88;Dels=0.00;HRun=2;HaplotypeScore=1.75;MQ=98.75;MQ0=0;OQ=3212.38;QD=36.50;RankSumP=1.00000;SB=-1390.14;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.536T>G;refseq.codingCoordStr_2=c.512T>G;refseq.codingCoordStr_3=c.512T>G;refseq.codingCoordStr_4=c.512T>G;refseq.codonCoord_1=179;refseq.codonCoord_2=171;refseq.codonCoord_3=171;refseq.codonCoord_4=171;refseq.end_1=176756601;refseq.end_2=176756601;refseq.end_3=176756601;refseq.end_4=176756601;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=648;refseq.mrnaCoord_2=624;refseq.mrnaCoord_3=624;refseq.mrnaCoord_4=624;refseq.name2_1=C1orf49;refseq.name2_2=C1orf49;refseq.name2_3=C1orf49;refseq.name2_4=C1orf49;refseq.name_1=NM_001170722;refseq.name_2=NM_001170723;refseq.name_3=NM_001170724;refseq.name_4=NM_032126;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.L179R;refseq.proteinCoordStr_2=p.L171R;refseq.proteinCoordStr_3=p.L171R;refseq.proteinCoordStr_4=p.L171R;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceAA_4=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.referenceCodon_4=CTG;refseq.spliceDist_1=-32;refseq.spliceDist_2=-32;refseq.spliceDist_3=-32;refseq.spliceDist_4=-32;refseq.start_1=176756601;refseq.start_2=176756601;refseq.start_3=176756601;refseq.start_4=176756601;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;refseq.variantCodon_4=CGG;set=Intersection GT 1/1
|
|
chr1 176781245 . C T 72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=97.30;MQ0=0;OQ=604.96;QD=28.81;RankSumP=0.222265;SB=-52.66;SecondBestBaseQ=34;refseq.chr=chr1;refseq.end=176781245;refseq.haplotypeAlternate=*;refseq.haplotypeReference=*;refseq.mrnaCoord=365;refseq.name=NR_033186;refseq.name2=C1orf220;refseq.positionType=non_coding_exon;refseq.spliceDist=275;refseq.start=176781245;refseq.transcriptStrand=+;set=Intersection GT 0/1
|
|
chr1 177012570 . T G 140.86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=225;Dels=0.00;HRun=1;HaplotypeScore=8.09;MQ=98.49;MQ0=0;OQ=8843.61;QD=39.30;RankSumP=1.00000;SB=-2183.22;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.48T>G;refseq.codonCoord=16;refseq.end=177012570;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=386;refseq.name=NM_152663;refseq.name2=RALGPS2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T16T;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-10;refseq.spliceInfo=splice-donor_-10;refseq.start=177012570;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 177047112 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.0494869;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.337A>G;refseq.codonCoord=113;refseq.end=177047112;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=675;refseq.name=NM_152663;refseq.name2=RALGPS2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T113A;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=40;refseq.start=177047112;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=FilteredInAll GT 0/1
|
|
chr1 177317923 . T C 104.35 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.05;MQ0=0;OQ=310.42;QD=31.04;RankSumP=1.00000;SB=-171.85;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.37T>C;refseq.codonCoord=13;refseq.end=177317923;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=189;refseq.name=NM_022371;refseq.name2=TOR3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.F13L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=189;refseq.start=177317923;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/1
|
|
chr1 177318703 . C G 58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.514668;SecondBestBaseQ=17;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.265C>G;refseq.codonCoord=89;refseq.end=177318703;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=417;refseq.name=NM_022371;refseq.name2=TOR3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.R89G;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=177318703;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=soap GT 1/0
|
|
chr1 177321643 . C T 245.09 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=202;Dels=0.00;HRun=1;HaplotypeScore=6.73;MQ=98.77;MQ0=0;OQ=4035.99;QD=19.98;RankSumP=0.319356;SB=-1507.91;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.631C>T;refseq.codonCoord=211;refseq.end=177321643;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=783;refseq.name=NM_022371;refseq.name2=TOR3A;refseq.positionType=CDS;refseq.proteinCoordStr=p.L211L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=177321643;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 177344720 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.codingCoordStr_5=c.2242A>C;refseq.codingCoordStr_6=c.2260A>C;refseq.codingCoordStr_7=c.2305A>C;refseq.codonCoord_5=748;refseq.codonCoord_6=754;refseq.codonCoord_7=769;refseq.end_1=177344955;refseq.end_2=177344955;refseq.end_3=177344955;refseq.end_4=177344955;refseq.end_5=177344720;refseq.end_6=177344720;refseq.end_7=177344720;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.haplotypeReference_7=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.mrnaCoord_5=2529;refseq.mrnaCoord_6=2305;refseq.mrnaCoord_7=2592;refseq.name2_1=ABL2;refseq.name2_2=ABL2;refseq.name2_3=ABL2;refseq.name2_4=ABL2;refseq.name2_5=ABL2;refseq.name2_6=ABL2;refseq.name2_7=ABL2;refseq.name_1=NM_001136000;refseq.name_2=NM_001168237;refseq.name_3=NM_001168238;refseq.name_4=NM_001168239;refseq.name_5=NM_001168236;refseq.name_6=NM_005158;refseq.name_7=NM_007314;refseq.numMatchingRecords=7;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.positionType_4=intron;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.proteinCoordStr_5=p.T748P;refseq.proteinCoordStr_6=p.T754P;refseq.proteinCoordStr_7=p.T769P;refseq.referenceAA_5=Thr;refseq.referenceAA_6=Thr;refseq.referenceAA_7=Thr;refseq.referenceCodon_5=ACA;refseq.referenceCodon_6=ACA;refseq.referenceCodon_7=ACA;refseq.spliceDist_5=480;refseq.spliceDist_6=480;refseq.spliceDist_7=480;refseq.start_1=177344667;refseq.start_2=177344667;refseq.start_3=177344667;refseq.start_4=177344667;refseq.start_5=177344720;refseq.start_6=177344720;refseq.start_7=177344720;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.transcriptStrand_7=-;refseq.variantAA_5=Pro;refseq.variantAA_6=Pro;refseq.variantAA_7=Pro;refseq.variantCodon_5=CCA;refseq.variantCodon_6=CCA;refseq.variantCodon_7=CCA;set=FilteredInAll GT 1/0
|
|
chr1 177576885 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=486;Dels=0.00;HRun=1;HaplotypeScore=17.89;MQ=98.91;MQ0=0;OQ=8552.10;QD=17.60;RankSumP=0.0136148;SB=-1648.45;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.597C>T;refseq.codonCoord=199;refseq.end=177576885;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=660;refseq.name=NM_003101;refseq.name2=SOAT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P199P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=100;refseq.start=177576885;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 177614455 . T C 321.09 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=383;Dels=0.00;HRun=0;HaplotypeScore=13.57;MQ=98.78;MQ0=0;OQ=6908.04;QD=18.04;RankSumP=0.109288;SB=-2464.89;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.435T>C;refseq.codonCoord=145;refseq.end=177614455;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=822;refseq.name=NM_144696;refseq.name2=C1orf125;refseq.positionType=CDS;refseq.proteinCoordStr=p.V145V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-61;refseq.start=177614455;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 177770660 . G C 25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=0;RankSumP=0.145993;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2971G>C;refseq.codonCoord=991;refseq.end=177770660;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3358;refseq.name=NM_144696;refseq.name2=C1orf125;refseq.positionType=CDS;refseq.proteinCoordStr=p.E991Q;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-61;refseq.start=177770660;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap GT 0/1
|
|
chr1 177770666 rs6658180 C G 206.96 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=97.96;MQ0=0;OQ=1413.89;QD=16.07;SB=-603.61;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2977C>G;refseq.codonCoord=993;refseq.end=177770666;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3364;refseq.name=NM_144696;refseq.name2=C1orf125;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q993E;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-55;refseq.start=177770666;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=gatk GT:AD:DP:GL:GQ 0/1:52,36:83:-169.66,-24.99,-239.48:99
|
|
chr1 177787129 . G A 161.43 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=368;Dels=0.00;HRun=0;HaplotypeScore=15.41;MQ=98.53;MQ0=0;OQ=14901.91;QD=40.49;RankSumP=1.00000;SB=-5975.92;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.954C>T;refseq.codonCoord_2=318;refseq.end_1=177790259;refseq.end_2=177787129;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1039;refseq.name2_1=C1orf125;refseq.name2_2=NPHS2;refseq.name_1=NM_144696;refseq.name_2=NM_014625;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A318A;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCC;refseq.spliceDist_2=81;refseq.start_1=177770731;refseq.start_2=177787129;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ala;refseq.variantCodon_2=GCT;set=Intersection GT 1/1
|
|
chr1 177788395 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.839T>G;refseq.codonCoord_2=280;refseq.end_1=177790259;refseq.end_2=177788395;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=924;refseq.name2_1=C1orf125;refseq.name2_2=NPHS2;refseq.name_1=NM_144696;refseq.name_2=NM_014625;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V280G;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTG;refseq.spliceDist_2=-35;refseq.start_1=177770731;refseq.start_2=177788395;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 177811521 . T C 46.28 BadSOAPSNP;LowQual AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=2;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=23.14;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.102A>G;refseq.codonCoord=34;refseq.end=177811521;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=187;refseq.name=NM_014625;refseq.name2=NPHS2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G34G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-173;refseq.start=177811521;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/1
|
|
chr1 177866624 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=386;Dels=0.00;HRun=2;HaplotypeScore=18.79;MQ=98.74;MQ0=0;OQ=7510.31;QD=19.46;RankSumP=0.396392;SB=-2275.62;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1072A>G;refseq.codonCoord=358;refseq.end=177866624;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1322;refseq.name=NM_173533;refseq.name2=TDRD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.K358E;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-55;refseq.start=177866624;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 177866665 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=430;Dels=0.00;HRun=2;HaplotypeScore=5.57;MQ=98.49;MQ0=0;OQ=8449.74;QD=19.65;RankSumP=0.421012;SB=-3421.93;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1113G>A;refseq.codonCoord=371;refseq.end=177866665;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1363;refseq.name=NM_173533;refseq.name2=TDRD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.K371K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-14;refseq.start=177866665;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 1/0
|
|
chr1 177871487 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=204;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=98.86;MQ0=0;OQ=2133.36;QD=10.46;RankSumP=0.405313;SB=-967.32;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1362C>T;refseq.codonCoord=454;refseq.end=177871487;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1612;refseq.name=NM_173533;refseq.name2=TDRD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.D454D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=63;refseq.start=177871487;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 177887847 . G A 350.24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=312;Dels=0.00;HRun=0;HaplotypeScore=7.88;MQ=98.92;MQ0=0;OQ=5493.58;QD=17.61;RankSumP=0.0414356;SB=-2204.96;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2052G>A;refseq.codonCoord=684;refseq.end=177887847;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2302;refseq.name=NM_173533;refseq.name2=TDRD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.G684G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=51;refseq.start=177887847;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 177897865 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=536;Dels=0.00;HRun=1;HaplotypeScore=20.53;MQ=98.93;MQ0=0;OQ=10582.56;QD=19.74;RankSumP=0.255168;SB=-2877.14;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2164G>A;refseq.codonCoord=722;refseq.end=177897865;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2414;refseq.name=NM_173533;refseq.name2=TDRD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.E722K;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=4;refseq.spliceInfo=splice-acceptor_4;refseq.start=177897865;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/0
|
|
chr1 177899159 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=309;Dels=0.00;HRun=2;HaplotypeScore=15.29;MQ=98.97;MQ0=0;OQ=5151.51;QD=16.67;RankSumP=0.344531;SB=-1449.85;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2397A>G;refseq.codonCoord=799;refseq.end=177899159;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2647;refseq.name=NM_173533;refseq.name2=TDRD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.S799S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=54;refseq.start=177899159;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 0/1
|
|
chr1 178049718 . C G 23 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=1.10646e-06;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.275C>G;refseq.codonCoord=92;refseq.end=178049718;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=671;refseq.name=NM_173509;refseq.name2=FAM163A;refseq.positionType=CDS;refseq.proteinCoordStr=p.A92G;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=182;refseq.start=178049718;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 178082553 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=5.75443e-08;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.689T>G;refseq.codonCoord=230;refseq.end=178082553;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1084;refseq.name=NM_145034;refseq.name2=TOR1AIP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V230G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=34;refseq.start=178082553;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 178118697 . T C 174.44 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=6.35;MQ=98.83;MQ0=0;OQ=1313.91;QD=13.98;RankSumP=0.230017;SB=-442.69;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.437T>C;refseq.codonCoord=146;refseq.end=178118697;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=655;refseq.name=NM_015602;refseq.name2=TOR1AIP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M146T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-39;refseq.start=178118697;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/0
|
|
chr1 178143611 . C G 182.90 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=188;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=98.45;MQ0=0;OQ=4642.07;QD=24.69;RankSumP=0.237471;SB=-1767.85;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.827C>G;refseq.codonCoord=276;refseq.end=178143611;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1045;refseq.name=NM_015602;refseq.name2=TOR1AIP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P276R;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-12;refseq.start=178143611;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/0
|
|
chr1 178153748 . G A 241.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=361;Dels=0.00;HRun=0;HaplotypeScore=6.02;MQ=98.78;MQ0=0;OQ=15560.02;QD=43.10;RankSumP=1.00000;SB=-7745.38;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1503G>A;refseq.codonCoord=501;refseq.end=178153748;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1721;refseq.name=NM_015602;refseq.name2=TOR1AIP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A501A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=539;refseq.start=178153748;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 178411696 . T G 71 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=12;HRun=2;RankSumP=0.000737901;SecondBestBaseQ=24;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.420T>G;refseq.codingCoordStr_2=c.420T>G;refseq.codonCoord_1=140;refseq.codonCoord_2=140;refseq.end_1=178411696;refseq.end_2=178411696;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=495;refseq.mrnaCoord_2=495;refseq.name2_1=QSOX1;refseq.name2_2=QSOX1;refseq.name_1=NM_001004128;refseq.name_2=NM_002826;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G140G;refseq.proteinCoordStr_2=p.G140G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=178411696;refseq.start_2=178411696;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 178411711 . A G 178.05 PASS AC=2;AF=1.00;AN=2;BestBaseQ=13;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=12.06;MQ=92.93;MQ0=0;OQ=884.10;QD=14.49;RankSumP=1.00000;SB=-252.70;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.435A>G;refseq.codingCoordStr_2=c.435A>G;refseq.codonCoord_1=145;refseq.codonCoord_2=145;refseq.end_1=178411711;refseq.end_2=178411711;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=510;refseq.mrnaCoord_2=510;refseq.name2_1=QSOX1;refseq.name2_2=QSOX1;refseq.name_1=NM_001004128;refseq.name_2=NM_002826;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T145T;refseq.proteinCoordStr_2=p.T145T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=23;refseq.spliceDist_2=23;refseq.start_1=178411711;refseq.start_2=178411711;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 1/1
|
|
chr1 178414557 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.521A>G;refseq.codingCoordStr_2=c.521A>G;refseq.codonCoord_1=174;refseq.codonCoord_2=174;refseq.end_1=178414557;refseq.end_2=178414557;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=596;refseq.mrnaCoord_2=596;refseq.name2_1=QSOX1;refseq.name2_2=QSOX1;refseq.name_1=NM_001004128;refseq.name_2=NM_002826;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E174G;refseq.proteinCoordStr_2=p.E174G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=6;refseq.spliceDist_2=6;refseq.spliceInfo_1=splice-acceptor_6;refseq.spliceInfo_2=splice-acceptor_6;refseq.start_1=178414557;refseq.start_2=178414557;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 178432322 . A C 138.04 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=97.82;MQ0=0;OQ=1586.69;QD=13.45;RankSumP=0.0264504;SB=-698.96;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1771A>C;refseq.codingCoordStr_2=c.1771A>C;refseq.codonCoord_1=591;refseq.codonCoord_2=591;refseq.end_1=178432322;refseq.end_2=178432322;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1846;refseq.mrnaCoord_2=1846;refseq.name2_1=QSOX1;refseq.name2_2=QSOX1;refseq.name_1=NM_001004128;refseq.name_2=NM_002826;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N591H;refseq.proteinCoordStr_2=p.N591H;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-36;refseq.spliceDist_2=303;refseq.start_1=178432322;refseq.start_2=178432322;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;set=Intersection GT 0/1
|
|
chr1 178502351 . C T 188.97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.23;MQ0=0;OQ=1185.54;QD=16.94;RankSumP=0.140108;SB=-207.17;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.450C>T;refseq.codonCoord=150;refseq.end=178502351;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=673;refseq.name=NM_033343;refseq.name2=LHX4;refseq.positionType=CDS;refseq.proteinCoordStr=p.N150N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-2;refseq.spliceInfo=splice-donor_-2;refseq.start=178502351;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 178507594 . T G 16 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=1.39878e-08;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.608T>G;refseq.codonCoord=203;refseq.end=178507594;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=831;refseq.name=NM_033343;refseq.name2=LHX4;refseq.positionType=CDS;refseq.proteinCoordStr=p.V203G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=178507594;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 1/0
|
|
chr1 178510147 . A G 299.58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=183;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=98.57;MQ0=0;OQ=3834.58;QD=20.95;RankSumP=0.261261;SB=-1265.99;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.983A>G;refseq.codonCoord=328;refseq.end=178510147;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1206;refseq.name=NM_033343;refseq.name2=LHX4;refseq.positionType=CDS;refseq.proteinCoordStr=p.N328S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=205;refseq.start=178510147;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 179152053 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=89;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=98.80;MQ0=0;OQ=3194.44;QD=35.89;RankSumP=1.00000;SB=-1102.75;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.191T>C;refseq.codonCoord=64;refseq.end=179152053;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=258;refseq.name=NM_020950;refseq.name2=KIAA1614;refseq.positionType=CDS;refseq.proteinCoordStr=p.L64P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=141;refseq.start=179152053;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 179171975 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=247;Dels=0.00;HRun=0;HaplotypeScore=13.20;MQ=98.80;MQ0=0;OQ=3112.36;QD=12.60;RankSumP=0.274554;SB=-680.83;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2307C>T;refseq.codonCoord=769;refseq.end=179171975;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2374;refseq.name=NM_020950;refseq.name2=KIAA1614;refseq.positionType=CDS;refseq.proteinCoordStr=p.S769S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-455;refseq.start=179171975;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 179172071 . G T 133.21 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=273;Dels=0.00;HRun=2;HaplotypeScore=5.76;MQ=98.50;MQ0=0;OQ=4626.61;QD=16.95;RankSumP=0.367036;SB=-1223.42;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2403G>T;refseq.codonCoord=801;refseq.end=179172071;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2470;refseq.name=NM_020950;refseq.name2=KIAA1614;refseq.positionType=CDS;refseq.proteinCoordStr=p.L801F;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-359;refseq.start=179172071;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 0/1
|
|
chr1 179180220 . A G 73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=195;Dels=0.00;HRun=4;HaplotypeScore=13.40;MQ=98.59;MQ0=0;OQ=6227.26;QD=31.93;RankSumP=1.00000;SB=-3087.15;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3232A>G;refseq.codonCoord=1078;refseq.end=179180220;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3299;refseq.name=NM_020950;refseq.name2=KIAA1614;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1078D;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-56;refseq.start=179180220;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 179220476 . A G 307.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=205;Dels=0.00;HRun=0;HaplotypeScore=5.49;MQ=98.96;MQ0=0;OQ=7362.78;QD=35.92;RankSumP=1.00000;SB=-3307.63;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.651T>C;refseq.codonCoord=217;refseq.end=179220476;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=888;refseq.name=NM_005819;refseq.name2=STX6;refseq.positionType=CDS;refseq.proteinCoordStr=p.N217N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-41;refseq.start=179220476;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 179284859 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=179;Dels=0.00;HRun=0;HaplotypeScore=13.95;MQ=33.31;MQ0=96;OQ=1239.56;QD=6.92;RankSumP=0.379991;SB=-425.95;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.116A>G;refseq.codonCoord=39;refseq.end=179284859;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=121;refseq.name=NM_001531;refseq.name2=MR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H39R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=49;refseq.start=179284859;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 0/1
|
|
chr1 179288106 . C T 238.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=6.32;MQ=98.99;MQ0=0;OQ=3051.80;QD=17.85;RankSumP=0.196068;SB=-1153.67;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.717C>T;refseq.codonCoord=239;refseq.end=179288106;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=722;refseq.name=NM_001531;refseq.name2=MR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N239N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=113;refseq.start=179288106;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 179324936 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=97.79;MQ0=0;OQ=353.33;QD=17.67;RankSumP=0.257393;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.275G>A;refseq.codonCoord=92;refseq.end=179324936;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=676;refseq.name=NM_016545;refseq.name2=IER5;refseq.positionType=CDS;refseq.proteinCoordStr=p.R92H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=676;refseq.start=179324936;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 180293436 . G C 111.97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=149;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.90;MQ0=0;OQ=2979.29;QD=20.00;RankSumP=0.217836;SB=-738.01;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.333C>G;refseq.codonCoord=111;refseq.end=180293436;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=541;refseq.name=NM_001009992;refseq.name2=ZNF648;refseq.positionType=CDS;refseq.proteinCoordStr=p.N111K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=396;refseq.start=180293436;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 0/1
|
|
chr1 180293645 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=461;Dels=0.00;HRun=1;HaplotypeScore=22.36;MQ=98.62;MQ0=0;OQ=9347.99;QD=20.28;RankSumP=0.00277705;SB=-3856.30;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.124G>A;refseq.codonCoord=42;refseq.end=180293645;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=332;refseq.name=NM_001009992;refseq.name2=ZNF648;refseq.positionType=CDS;refseq.proteinCoordStr=p.E42K;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=187;refseq.start=180293645;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=filterInsoap-gatk GT 0/1
|
|
chr1 180811204 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=169;Dels=0.00;HRun=2;HaplotypeScore=2.10;MQ=98.63;MQ0=0;OQ=2903.70;QD=17.18;RankSumP=5.64839e-06;SB=-1374.42;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2172G>A;refseq.codonCoord=724;refseq.end=180811204;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2339;refseq.name=NM_021133;refseq.name2=RNASEL;refseq.positionType=CDS;refseq.proteinCoordStr=p.K724K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=133;refseq.start=180811204;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=filterInsoap-gatk GT 0/1
|
|
chr1 180817960 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.62;MQ0=0;OQ=565.24;QD=12.56;RankSumP=0.622449;SB=-240.33;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1623T>G;refseq.codonCoord=541;refseq.end=180817960;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1790;refseq.name=NM_021133;refseq.name2=RNASEL;refseq.positionType=CDS;refseq.proteinCoordStr=p.D541E;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=57;refseq.start=180817960;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 0/1
|
|
chr1 180821180 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=248;Dels=0.00;HRun=3;HaplotypeScore=4.90;MQ=98.68;MQ0=0;OQ=5351.06;QD=21.58;RankSumP=0.411710;SB=-2149.01;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1385G>A;refseq.codonCoord=462;refseq.end=180821180;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1552;refseq.name=NM_021133;refseq.name2=RNASEL;refseq.positionType=CDS;refseq.proteinCoordStr=p.R462Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-96;refseq.start=180821180;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 0/1
|
|
chr1 180822187 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=2;RankSumP=3.53557e-09;SecondBestBaseQ=6;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.378C>T;refseq.codonCoord=126;refseq.end=180822187;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=545;refseq.name=NM_021133;refseq.name2=RNASEL;refseq.positionType=CDS;refseq.proteinCoordStr=p.F126F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=545;refseq.start=180822187;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 1/0
|
|
chr1 180836249 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=361;Dels=0.00;HRun=0;HaplotypeScore=18.34;MQ=98.66;MQ0=0;OQ=11024.13;QD=30.54;RankSumP=1.00000;SB=-2480.53;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.410A>G;refseq.codonCoord=137;refseq.end=180836249;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=564;refseq.name=NM_002928;refseq.name2=RGS16;refseq.positionType=CDS;refseq.proteinCoordStr=p.H137R;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=23;refseq.start=180836249;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/1
|
|
chr1 180837878 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.233C>G;refseq.codonCoord=78;refseq.end=180837878;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=387;refseq.name=NM_002928;refseq.name2=RGS16;refseq.positionType=CDS;refseq.proteinCoordStr=p.A78G;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=13;refseq.start=180837878;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 0/1
|
|
chr1 181052505 . C G 38.75 PASS AC=1;AF=0.50;AN=2;BestBaseQ=4;DP=190;Dels=0.00;HRun=1;HaplotypeScore=48.25;MQ=96.96;MQ0=0;QD=0.20;RankSumP=0.272879;SB=8.06;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.398C>G;refseq.codonCoord=133;refseq.end=181052505;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=442;refseq.name=NM_030769;refseq.name2=NPL;refseq.positionType=CDS;refseq.proteinCoordStr=p.A133G;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=34;refseq.start=181052505;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap-filterIngatk GT 1/0
|
|
chr1 181117350 . T C 340.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=183;Dels=0.00;HRun=1;HaplotypeScore=4.73;MQ=98.86;MQ0=0;OQ=7551.09;QD=41.26;RankSumP=1.00000;SB=-3088.89;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.2859T>C;refseq.codonCoord_2=953;refseq.end_1=181117350;refseq.end_2=181117350;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3171;refseq.mrnaCoord_2=3034;refseq.name2_1=DHX9;refseq.name2_2=DHX9;refseq.name_1=NR_033302;refseq.name_2=NM_001357;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.T953T;refseq.referenceAA_2=Thr;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=-56;refseq.spliceDist_2=-56;refseq.start_1=181117350;refseq.start_2=181117350;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Thr;refseq.variantCodon_2=ACC;set=Intersection GT 1/1
|
|
chr1 181122940 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.3561T>G;refseq.codonCoord_2=1187;refseq.end_1=181122940;refseq.end_2=181122940;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3873;refseq.mrnaCoord_2=3736;refseq.name2_1=DHX9;refseq.name2_2=DHX9;refseq.name_1=NR_033302;refseq.name_2=NM_001357;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.G1187G;refseq.referenceAA_2=Gly;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=100;refseq.spliceDist_2=100;refseq.start_1=181122940;refseq.start_2=181122940;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 181259648 . C T 111.51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=134;Dels=0.00;HRun=2;HaplotypeScore=2.86;MQ=98.21;MQ0=0;OQ=2284.76;QD=17.05;RankSumP=0.230116;SB=-1150.09;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.174C>T;refseq.codonCoord=58;refseq.end=181259648;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=431;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A58A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-245;refseq.start=181259648;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 0/1
|
|
chr1 181339213 . T C 295.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=160;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=98.09;MQ0=0;OQ=2555.45;QD=15.97;RankSumP=0.322148;SB=-1183.68;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.546T>C;refseq.codonCoord=182;refseq.end=181339213;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=803;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C182C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=128;refseq.start=181339213;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 1/0
|
|
chr1 181352378 . A G 135.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=523;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=98.78;MQ0=0;OQ=11071.18;QD=21.17;RankSumP=0.377019;SB=-4369.25;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1372A>G;refseq.codonCoord=458;refseq.end=181352378;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1629;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I458V;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=44;refseq.start=181352378;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 0/1
|
|
chr1 181353380 . A C 142.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=424;Dels=0.00;HRun=1;HaplotypeScore=3.62;MQ=98.76;MQ0=0;OQ=7217.97;QD=17.02;RankSumP=0.0164235;SB=-2523.48;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1776A>C;refseq.codonCoord=592;refseq.end=181353380;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2033;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A592A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=89;refseq.start=181353380;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 181357852 . C G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=296;Dels=0.00;HRun=2;HaplotypeScore=33.56;MQ=97.89;MQ0=0;OQ=141.18;QD=0.48;RankSumP=0.00000;SB=306.07;SecondBestBaseQ=10;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2244C>G;refseq.codonCoord=748;refseq.end=181357852;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2501;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G748G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=32;refseq.start=181357852;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 181360498 . T C 218.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=225;Dels=0.00;HRun=0;HaplotypeScore=4.19;MQ=98.99;MQ0=0;OQ=4130.25;QD=18.36;RankSumP=0.203038;SB=-929.57;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2511T>C;refseq.codonCoord=837;refseq.end=181360498;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2768;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N837N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=110;refseq.start=181360498;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/0
|
|
chr1 181361170 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=575;Dels=0.00;HRun=1;HaplotypeScore=13.19;MQ=98.52;MQ0=0;OQ=10167.48;QD=17.68;RankSumP=0.466708;SB=-3134.40;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2663T>C;refseq.codonCoord=888;refseq.end=181361170;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2920;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L888P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=16;refseq.start=181361170;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/0
|
|
chr1 181363152 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3113T>G;refseq.codonCoord=1038;refseq.end=181363152;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3370;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1038G;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=-11;refseq.start=181363152;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=FilteredInAll GT 1/0
|
|
chr1 181366183 . G A 272.73 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=249;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=98.68;MQ0=0;OQ=5641.40;QD=22.66;RankSumP=0.352795;SB=-1659.54;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3362G>A;refseq.codonCoord=1121;refseq.end=181366183;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3619;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1121Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=82;refseq.start=181366183;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 181372157 . T C 161.86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=309;Dels=0.00;HRun=0;HaplotypeScore=11.11;MQ=98.72;MQ0=0;OQ=5030.47;QD=16.28;RankSumP=0.202418;SB=-861.91;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4128T>C;refseq.codonCoord=1376;refseq.end=181372157;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4385;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1376R;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=14;refseq.start=181372157;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/0
|
|
chr1 181372328 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=99.00;MQ0=0;OQ=513.86;QD=11.68;RankSumP=0.348558;SB=-80.28;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4299G>A;refseq.codonCoord=1433;refseq.end=181372328;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4556;refseq.name=NM_002293;refseq.name2=LAMC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1433A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-16;refseq.start=181372328;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 181464275 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1612T>G;refseq.codingCoordStr_2=c.1612T>G;refseq.codonCoord_1=538;refseq.codonCoord_2=538;refseq.end_1=181464275;refseq.end_2=181464275;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1926;refseq.mrnaCoord_2=1926;refseq.name2_1=LAMC2;refseq.name2_2=LAMC2;refseq.name_1=NM_005562;refseq.name_2=NM_018891;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C538G;refseq.proteinCoordStr_2=p.C538G;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=-103;refseq.spliceDist_2=-103;refseq.start_1=181464275;refseq.start_2=181464275;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 1/0
|
|
chr1 181475163 . G A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2911G>A;refseq.codingCoordStr_2=c.2911G>A;refseq.codonCoord_1=971;refseq.codonCoord_2=971;refseq.end_1=181475163;refseq.end_2=181475163;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3225;refseq.mrnaCoord_2=3225;refseq.name2_1=LAMC2;refseq.name2_2=LAMC2;refseq.name_1=NM_005562;refseq.name_2=NM_018891;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E971K;refseq.proteinCoordStr_2=p.E971K;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=42;refseq.spliceDist_2=42;refseq.start_1=181475163;refseq.start_2=181475163;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=FilteredInAll GT 1/0
|
|
chr1 181522487 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.381A>C;refseq.codingCoordStr_2=c.366A>C;refseq.codonCoord_1=127;refseq.codonCoord_2=122;refseq.end_1=181522487;refseq.end_2=181522487;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=716;refseq.mrnaCoord_2=501;refseq.name2_1=NMNAT2;refseq.name2_2=NMNAT2;refseq.name_1=NM_015039;refseq.name_2=NM_170706;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G127G;refseq.proteinCoordStr_2=p.G122G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=60;refseq.spliceDist_2=60;refseq.start_1=181522487;refseq.start_2=181522487;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGC;refseq.variantCodon_2=GGC;set=FilteredInAll GT 1/0
|
|
chr1 181753482 . G A 100.05 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=517;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=98.93;MQ0=0;OQ=21297.81;QD=41.19;RankSumP=1.00000;SB=-9836.47;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.90G>A;refseq.codingCoordStr_2=c.216G>A;refseq.codingCoordStr_3=c.216G>A;refseq.codingCoordStr_4=c.216G>A;refseq.codonCoord_1=30;refseq.codonCoord_2=72;refseq.codonCoord_3=72;refseq.codonCoord_4=72;refseq.end_1=181753482;refseq.end_2=181753482;refseq.end_3=181753482;refseq.end_4=181753482;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=434;refseq.mrnaCoord_2=466;refseq.mrnaCoord_3=466;refseq.mrnaCoord_4=466;refseq.name2_1=SMG7;refseq.name2_2=SMG7;refseq.name2_3=SMG7;refseq.name2_4=SMG7;refseq.name_1=NM_001174061;refseq.name_2=NM_173156;refseq.name_3=NM_201568;refseq.name_4=NM_201569;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.L30L;refseq.proteinCoordStr_2=p.L72L;refseq.proteinCoordStr_3=p.L72L;refseq.proteinCoordStr_4=p.L72L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceAA_4=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.referenceCodon_4=CTG;refseq.spliceDist_1=37;refseq.spliceDist_2=37;refseq.spliceDist_3=37;refseq.spliceDist_4=37;refseq.start_1=181753482;refseq.start_2=181753482;refseq.start_3=181753482;refseq.start_4=181753482;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;refseq.variantCodon_3=CTA;refseq.variantCodon_4=CTA;set=Intersection GT 1/1
|
|
chr1 181753569 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.177C>T;refseq.codingCoordStr_2=c.303C>T;refseq.codingCoordStr_3=c.303C>T;refseq.codingCoordStr_4=c.303C>T;refseq.codonCoord_1=59;refseq.codonCoord_2=101;refseq.codonCoord_3=101;refseq.codonCoord_4=101;refseq.end_1=181753569;refseq.end_2=181753569;refseq.end_3=181753569;refseq.end_4=181753569;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=521;refseq.mrnaCoord_2=553;refseq.mrnaCoord_3=553;refseq.mrnaCoord_4=553;refseq.name2_1=SMG7;refseq.name2_2=SMG7;refseq.name2_3=SMG7;refseq.name2_4=SMG7;refseq.name_1=NM_001174061;refseq.name_2=NM_173156;refseq.name_3=NM_201568;refseq.name_4=NM_201569;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.F59F;refseq.proteinCoordStr_2=p.F101F;refseq.proteinCoordStr_3=p.F101F;refseq.proteinCoordStr_4=p.F101F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceAA_4=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.referenceCodon_3=TTC;refseq.referenceCodon_4=TTC;refseq.spliceDist_1=-10;refseq.spliceDist_2=-10;refseq.spliceDist_3=-10;refseq.spliceDist_4=-10;refseq.spliceInfo_1=splice-donor_-10;refseq.spliceInfo_2=splice-donor_-10;refseq.spliceInfo_3=splice-donor_-10;refseq.spliceInfo_4=splice-donor_-10;refseq.start_1=181753569;refseq.start_2=181753569;refseq.start_3=181753569;refseq.start_4=181753569;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantAA_4=Phe;refseq.variantCodon_1=TTT;refseq.variantCodon_2=TTT;refseq.variantCodon_3=TTT;refseq.variantCodon_4=TTT;set=FilteredInAll GT 0/1
|
|
chr1 181883549 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=575;Dels=0.00;HRun=0;HaplotypeScore=14.08;MQ=98.85;MQ0=0;OQ=22019.83;QD=38.30;RankSumP=1.00000;SB=-9355.41;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.991A>G;refseq.codonCoord_2=331;refseq.end_1=181977873;refseq.end_2=181883549;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1263;refseq.name2_1=RGL1;refseq.name2_2=APOBEC4;refseq.name_1=NM_015149;refseq.name_2=NM_203454;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.K331E;refseq.referenceAA_2=Lys;refseq.referenceCodon_2=AAG;refseq.spliceDist_2=1021;refseq.start_1=181872270;refseq.start_2=181883549;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.variantAA_2=Glu;refseq.variantCodon_2=GAG;set=Intersection GT 1/1
|
|
chr1 181883728 . A G 299.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=283;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=98.89;MQ0=0;OQ=11672.62;QD=41.25;RankSumP=1.00000;SB=-4776.58;SecondBestBaseQ=9;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.812T>C;refseq.codonCoord_2=271;refseq.end_1=181977873;refseq.end_2=181883728;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1084;refseq.name2_1=RGL1;refseq.name2_2=APOBEC4;refseq.name_1=NM_015149;refseq.name_2=NM_203454;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.F271S;refseq.referenceAA_2=Phe;refseq.referenceCodon_2=TTT;refseq.spliceDist_2=842;refseq.start_1=181872270;refseq.start_2=181883728;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ser;refseq.variantCodon_2=TCT;set=Intersection GT 1/1
|
|
chr1 181978004 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.89T>G;refseq.codonCoord=30;refseq.end=181978004;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=550;refseq.name=NM_015149;refseq.name2=RGL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V30G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-44;refseq.start=181978004;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 182290152 . A C 288.45 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=476;Dels=0.00;HRun=0;HaplotypeScore=4.59;MQ=98.81;MQ0=0;OQ=18747.96;QD=39.39;RankSumP=1.00000;SB=-6123.67;SecondBestBaseQ=2;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.177A>C;refseq.codingCoordStr_3=c.177A>C;refseq.codonCoord_2=59;refseq.codonCoord_3=59;refseq.end_1=182290152;refseq.end_2=182290152;refseq.end_3=182290152;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=256;refseq.mrnaCoord_2=256;refseq.mrnaCoord_3=256;refseq.name2_1=TSEN15;refseq.name2_2=TSEN15;refseq.name2_3=TSEN15;refseq.name_1=NR_023349;refseq.name_2=NM_001127394;refseq.name_3=NM_052965;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.Q59H;refseq.proteinCoordStr_3=p.Q59H;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceCodon_2=CAA;refseq.referenceCodon_3=CAA;refseq.spliceDist_1=-41;refseq.spliceDist_2=-41;refseq.spliceDist_3=-41;refseq.start_1=182290152;refseq.start_2=182290152;refseq.start_3=182290152;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_2=His;refseq.variantAA_3=His;refseq.variantCodon_2=CAC;refseq.variantCodon_3=CAC;set=Intersection GT 1/1
|
|
chr1 182930160 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=98.26;MQ0=0;OQ=1097.04;QD=11.55;RankSumP=0.389693;SB=-565.59;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2459T>G;refseq.codonCoord=820;refseq.end=182930160;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2720;refseq.name=NM_025191;refseq.name2=EDEM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.I820S;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=70;refseq.start=182930160;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 182930204 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=96.89;MQ0=0;OQ=1343.42;QD=13.99;RankSumP=0.116881;SB=-666.58;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2415A>G;refseq.codonCoord=805;refseq.end=182930204;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2676;refseq.name=NM_025191;refseq.name2=EDEM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q805Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=26;refseq.start=182930204;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 182942437 . G A 180.70 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=422;Dels=0.00;HRun=0;HaplotypeScore=5.76;MQ=98.63;MQ0=0;OQ=7132.09;QD=16.90;RankSumP=0.0170652;SB=-2789.06;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2166C>T;refseq.codonCoord=722;refseq.end=182942437;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2427;refseq.name=NM_025191;refseq.name2=EDEM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.N722N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-38;refseq.start=182942437;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 182944087 . G A 273.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=269;Dels=0.00;HRun=1;HaplotypeScore=3.22;MQ=98.50;MQ0=0;OQ=5052.89;QD=18.78;RankSumP=0.314919;SB=-1592.76;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1860C>T;refseq.codonCoord=620;refseq.end=182944087;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2121;refseq.name=NM_025191;refseq.name2=EDEM3;refseq.positionType=CDS;refseq.proteinCoordStr=p.I620I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=15;refseq.start=182944087;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 183031130 . C G 61 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=1.25127e-07;SecondBestBaseQ=17;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2391G>C;refseq.codonCoord=797;refseq.end=183031130;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2585;refseq.name=NM_052966;refseq.name2=FAM129A;refseq.positionType=CDS;refseq.proteinCoordStr=p.P797P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=725;refseq.start=183031130;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 183031133 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2388T>C;refseq.codonCoord=796;refseq.end=183031133;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2582;refseq.name=NM_052966;refseq.name2=FAM129A;refseq.positionType=CDS;refseq.proteinCoordStr=p.S796S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=722;refseq.start=183031133;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 0/1
|
|
chr1 183335697 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.889A>C;refseq.codonCoord=297;refseq.end=183335697;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1122;refseq.name=NM_007212;refseq.name2=RNF2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T297P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-21;refseq.start=183335697;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 0/1
|
|
chr1 183386232 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=3.56691e-07;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.362G>T;refseq.codonCoord=121;refseq.end=183386232;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=634;refseq.name=NM_030934;refseq.name2=C1orf25;refseq.positionType=CDS;refseq.proteinCoordStr=p.C121F;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=16;refseq.start=183386232;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=FilteredInAll GT 1/0
|
|
chr1 183410344 . A G 277.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=182;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=98.72;MQ0=0;OQ=2874.29;QD=15.79;RankSumP=0.363402;SB=-1273.88;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.442A>G;refseq.codingCoordStr_2=c.442A>G;refseq.codonCoord_1=148;refseq.codonCoord_2=148;refseq.end_1=183410344;refseq.end_2=183410344;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=556;refseq.mrnaCoord_2=607;refseq.name2_1=C1orf26;refseq.name2_2=C1orf26;refseq.name_1=NM_001105518;refseq.name_2=NM_017673;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I148V;refseq.proteinCoordStr_2=p.I148V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=218;refseq.spliceDist_2=218;refseq.start_1=183410344;refseq.start_2=183410344;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=Intersection GT 0/1
|
|
chr1 183438492 . A G 352.63 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=232;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=98.90;MQ0=0;OQ=4233.30;QD=18.25;RankSumP=0.0549740;SB=-1375.26;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1607A>G;refseq.codingCoordStr_2=c.1607A>G;refseq.codonCoord_1=536;refseq.codonCoord_2=536;refseq.end_1=183438492;refseq.end_2=183438492;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1721;refseq.mrnaCoord_2=1772;refseq.name2_1=C1orf26;refseq.name2_2=C1orf26;refseq.name_1=NM_001105518;refseq.name_2=NM_017673;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H536R;refseq.proteinCoordStr_2=p.H536R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=-63;refseq.spliceDist_2=-63;refseq.start_1=183438492;refseq.start_2=183438492;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=Intersection GT 0/1
|
|
chr1 183507097 . A G 262.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=121;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.96;MQ0=0;OQ=2414.68;QD=19.96;RankSumP=0.255153;SB=-1053.68;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2461A>G;refseq.codingCoordStr_2=c.2461A>G;refseq.codonCoord_1=821;refseq.codonCoord_2=821;refseq.end_1=183507097;refseq.end_2=183507097;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2575;refseq.mrnaCoord_2=2626;refseq.name2_1=C1orf26;refseq.name2_2=C1orf26;refseq.name_1=NM_001105518;refseq.name_2=NM_017673;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N821D;refseq.proteinCoordStr_2=p.N821D;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=20;refseq.spliceDist_2=20;refseq.start_1=183507097;refseq.start_2=183507097;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 0/1
|
|
chr1 184293097 . T C 261.78 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=349;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=98.85;MQ0=0;OQ=14474.57;QD=41.47;RankSumP=1.00000;SB=-6448.33;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7253T>C;refseq.codonCoord=2418;refseq.end=184293097;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7482;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I2418T;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=-60;refseq.start=184293097;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 184297664 . C T 196.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=344;Dels=0.00;HRun=0;HaplotypeScore=4.39;MQ=98.44;MQ0=0;OQ=12442.90;QD=36.17;RankSumP=1.00000;SB=-4366.89;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.7371C>T;refseq.codonCoord=2457;refseq.end=184297664;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7600;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C2457C;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-56;refseq.start=184297664;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/1
|
|
chr1 184312239 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=4.12801e-09;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8347A>G;refseq.codonCoord=2783;refseq.end=184312239;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=8576;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N2783D;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=57;refseq.start=184312239;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 0/1
|
|
chr1 184317040 . A G 339.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=148;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=98.57;MQ0=0;OQ=6052.79;QD=40.90;RankSumP=1.00000;SB=-1895.44;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8678A>G;refseq.codonCoord=2893;refseq.end=184317040;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=8907;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E2893G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=79;refseq.start=184317040;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 1/1
|
|
chr1 184318653 . T G 0.01 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=159;Dels=0.00;HRun=2;HaplotypeScore=12.94;MQ=98.29;MQ0=0;OQ=50.46;QD=0.32;RankSumP=0.00000;SB=170.57;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8821T>G;refseq.codonCoord=2941;refseq.end=184318653;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=9050;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2941D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=34;refseq.start=184318653;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 1/0
|
|
chr1 184329301 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10073C>A;refseq.codonCoord=3358;refseq.end=184329301;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=10302;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T3358N;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=61;refseq.start=184329301;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=FilteredInAll GT 1/0
|
|
chr1 184368162 . A G 191.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.62;MQ0=0;OQ=1178.92;QD=17.34;RankSumP=0.407069;SB=-307.50;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.13310A>G;refseq.codonCoord=4437;refseq.end=184368162;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=13539;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q4437R;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=-3;refseq.spliceInfo=splice-donor_-3;refseq.start=184368162;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 0/1
|
|
chr1 184381192 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=4;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.14301A>G;refseq.codonCoord=4767;refseq.end=184381192;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=14530;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G4767G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=35;refseq.start=184381192;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 184402592 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.15469A>C;refseq.codonCoord=5157;refseq.end=184402592;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=15698;refseq.name=NM_031935;refseq.name2=HMCN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T5157P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=30;refseq.start=184402592;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 184542723 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.000277132;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.1126A>C;refseq.codingCoordStr_2=c.970A>C;refseq.codingCoordStr_3=c.847A>C;refseq.codingCoordStr_4=c.1249A>C;refseq.codonCoord_1=376;refseq.codonCoord_2=324;refseq.codonCoord_3=283;refseq.codonCoord_4=417;refseq.end_1=184542723;refseq.end_2=184542723;refseq.end_3=184542723;refseq.end_4=184542723;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1177;refseq.mrnaCoord_2=1021;refseq.mrnaCoord_3=898;refseq.mrnaCoord_4=1300;refseq.name2_1=PRG4;refseq.name2_2=PRG4;refseq.name2_3=PRG4;refseq.name2_4=PRG4;refseq.name_1=NM_001127708;refseq.name_2=NM_001127709;refseq.name_3=NM_001127710;refseq.name_4=NM_005807;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.T376P;refseq.proteinCoordStr_2=p.T324P;refseq.proteinCoordStr_3=p.T283P;refseq.proteinCoordStr_4=p.T417P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.spliceDist_1=651;refseq.spliceDist_2=651;refseq.spliceDist_3=651;refseq.spliceDist_4=651;refseq.start_1=184542723;refseq.start_2=184542723;refseq.start_3=184542723;refseq.start_4=184542723;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;set=FilteredInAll GT 0/1
|
|
chr1 184543711 . G C 75.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DP=229;Dels=0.00;HRun=0;HaplotypeScore=6.84;MQ=80.89;MQ0=21;OQ=9248.44;QD=40.39;RankSumP=1.00000;SB=-3773.45;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.2114G>C;refseq.codingCoordStr_2=c.1958G>C;refseq.codingCoordStr_3=c.1835G>C;refseq.codingCoordStr_4=c.2237G>C;refseq.codonCoord_1=705;refseq.codonCoord_2=653;refseq.codonCoord_3=612;refseq.codonCoord_4=746;refseq.end_1=184543711;refseq.end_2=184543711;refseq.end_3=184543711;refseq.end_4=184543711;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=2165;refseq.mrnaCoord_2=2009;refseq.mrnaCoord_3=1886;refseq.mrnaCoord_4=2288;refseq.name2_1=PRG4;refseq.name2_2=PRG4;refseq.name2_3=PRG4;refseq.name2_4=PRG4;refseq.name_1=NM_001127708;refseq.name_2=NM_001127709;refseq.name_3=NM_001127710;refseq.name_4=NM_005807;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.C705S;refseq.proteinCoordStr_2=p.C653S;refseq.proteinCoordStr_3=p.C612S;refseq.proteinCoordStr_4=p.C746S;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.referenceCodon_3=TGT;refseq.referenceCodon_4=TGT;refseq.spliceDist_1=-1185;refseq.spliceDist_2=-1185;refseq.spliceDist_3=-1185;refseq.spliceDist_4=-1185;refseq.start_1=184543711;refseq.start_2=184543711;refseq.start_3=184543711;refseq.start_4=184543711;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_1=TCT;refseq.variantCodon_2=TCT;refseq.variantCodon_3=TCT;refseq.variantCodon_4=TCT;set=Intersection GT 1/1
|
|
chr1 184570198 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5064A>G;refseq.codonCoord=1688;refseq.end=184570198;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5361;refseq.name=NM_003292;refseq.name2=TPR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1688G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=91;refseq.start=184570198;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 184570266 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4996A>C;refseq.codonCoord=1666;refseq.end=184570266;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5293;refseq.name=NM_003292;refseq.name2=TPR;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1666P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=23;refseq.start=184570266;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 184914107 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=4;RankSumP=5.77296e-09;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.366C>A;refseq.codonCoord=122;refseq.end=184914107;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=503;refseq.name=NM_000963;refseq.name2=PTGS2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y122*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=53;refseq.start=184914107;refseq.transcriptStrand=-;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=FilteredInAll GT 0/1
|
|
chr1 185201248 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1664A>C;refseq.codonCoord=555;refseq.end=185201248;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1869;refseq.name=NM_024420;refseq.name2=PLA2G4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.N555T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=85;refseq.start=185201248;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 0/1
|
|
chr1 185213492 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=514;Dels=0.00;HRun=0;HaplotypeScore=17.86;MQ=98.89;MQ0=0;OQ=8109.46;QD=15.78;RankSumP=0.232347;SB=-3155.46;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1909A>G;refseq.codonCoord=637;refseq.end=185213492;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2114;refseq.name=NM_024420;refseq.name2=PLA2G4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.I637V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-52;refseq.start=185213492;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 0/1
|
|
chr1 185213535 . G A 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=384;Dels=0.00;HRun=1;HaplotypeScore=13.85;MQ=98.83;MQ0=0;OQ=16535.82;QD=43.06;RankSumP=1.00000;SB=-4644.53;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1952G>A;refseq.codonCoord=651;refseq.end=185213535;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2157;refseq.name=NM_024420;refseq.name2=PLA2G4A;refseq.positionType=CDS;refseq.proteinCoordStr=p.R651K;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=185213535;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 190883735 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=4;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.122C>A;refseq.codingCoordStr_2=c.122C>A;refseq.codonCoord_1=41;refseq.codonCoord_2=41;refseq.end_1=190883735;refseq.end_2=190883735;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=403;refseq.mrnaCoord_2=363;refseq.name2_1=RGS13;refseq.name2_2=RGS13;refseq.name_1=NM_002927;refseq.name_2=NM_144766;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T41K;refseq.proteinCoordStr_2=p.T41K;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=-6;refseq.spliceDist_2=-6;refseq.spliceInfo_1=splice-donor_-6;refseq.spliceInfo_2=splice-donor_-6;refseq.start_1=190883735;refseq.start_2=190883735;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=FilteredInAll GT 1/0
|
|
chr1 191341274 . T A 208.37 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.42;MQ0=0;OQ=1063.73;QD=39.40;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.118A>T;refseq.codonCoord=40;refseq.end=191341274;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=594;refseq.name=NM_016066;refseq.name2=GLRX2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R40W;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-5;refseq.spliceInfo=splice-donor_-5;refseq.start=191341274;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=Intersection GT 1/1
|
|
chr1 191416842 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=256;Dels=0.00;HRun=1;HaplotypeScore=19.23;MQ=98.65;MQ0=0;OQ=4688.27;QD=18.31;RankSumP=0.364200;SB=-1515.09;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.474T>C;refseq.codonCoord_2=158;refseq.end_1=191439537;refseq.end_2=191416842;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=1189;refseq.name2_1=CDC73;refseq.name2_2=B3GALT2;refseq.name_1=NM_024529;refseq.name_2=NM_003783;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A158A;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCT;refseq.spliceDist_2=594;refseq.start_1=191388208;refseq.start_2=191416842;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=-;refseq.variantAA_2=Ala;refseq.variantCodon_2=GCC;set=Intersection GT 0/1
|
|
chr1 194494149 . A G 82 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=388;Dels=0.00;HRun=1;HaplotypeScore=24.64;MQ=98.79;MQ0=0;OQ=15881.98;QD=40.93;RankSumP=1.00000;SB=-4513.82;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3009T>C;refseq.codonCoord=1003;refseq.end=194494149;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3069;refseq.name=NM_198503;refseq.name2=KCNT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1003D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=99;refseq.start=194494149;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 194908856 . G A 213.22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=312;Dels=0.00;HRun=0;HaplotypeScore=17.72;MQ=98.81;MQ0=0;OQ=5099.00;QD=16.34;RankSumP=0.434715;SB=-2043.83;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.184G>A;refseq.codingCoordStr_2=c.184G>A;refseq.codonCoord_1=62;refseq.codonCoord_2=62;refseq.end_1=194908856;refseq.end_2=194908856;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=424;refseq.mrnaCoord_2=424;refseq.name2_1=CFH;refseq.name2_2=CFH;refseq.name_1=NM_000186;refseq.name_2=NM_001014975;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V62I;refseq.proteinCoordStr_2=p.V62I;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTA;refseq.referenceCodon_2=GTA;refseq.spliceDist_1=-61;refseq.spliceDist_2=-61;refseq.start_1=194908856;refseq.start_2=194908856;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantCodon_1=ATA;refseq.variantCodon_2=ATA;set=Intersection GT 1/0
|
|
chr1 194920947 . A C 131.39 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=249;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.47;MQ0=0;OQ=8912.14;QD=35.79;RankSumP=1.00000;SB=-4273.63;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.921A>C;refseq.codingCoordStr_2=c.921A>C;refseq.codonCoord_1=307;refseq.codonCoord_2=307;refseq.end_1=194920947;refseq.end_2=194920947;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1161;refseq.mrnaCoord_2=1161;refseq.name2_1=CFH;refseq.name2_2=CFH;refseq.name_1=NM_000186;refseq.name_2=NM_001014975;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A307A;refseq.proteinCoordStr_2=p.A307A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=-44;refseq.spliceDist_2=-44;refseq.start_1=194920947;refseq.start_2=194920947;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/1
|
|
chr1 194925860 . C T 295.01 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=102;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=92.37;MQ0=5;OQ=3974.02;QD=38.96;RankSumP=1.00000;SB=-1248.38;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1204C>T;refseq.codingCoordStr_2=c.1204C>T;refseq.codonCoord_1=402;refseq.codonCoord_2=402;refseq.end_1=194925860;refseq.end_2=194925860;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1444;refseq.mrnaCoord_2=1444;refseq.name2_1=CFH;refseq.name2_2=CFH;refseq.name_1=NM_000186;refseq.name_2=NM_001014975;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H402Y;refseq.proteinCoordStr_2=p.H402Y;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=45;refseq.spliceDist_2=45;refseq.start_1=194925860;refseq.start_2=194925860;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;set=Intersection GT 1/1
|
|
chr1 194925965 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1309T>G;refseq.codingCoordStr_2=c.1309T>G;refseq.codonCoord_1=437;refseq.codonCoord_2=437;refseq.end_1=194925965;refseq.end_2=194925965;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1549;refseq.mrnaCoord_2=1549;refseq.name2_1=CFH;refseq.name2_2=CFH;refseq.name_1=NM_000186;refseq.name_2=NM_001014975;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S437A;refseq.proteinCoordStr_2=p.S437A;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCT;refseq.referenceCodon_2=TCT;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.start_1=194925965;refseq.start_2=194925965;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=FilteredInAll GT 1/0
|
|
chr1 194949570 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=176;Dels=0.00;HRun=3;HaplotypeScore=11.96;MQ=98.70;MQ0=0;OQ=3162.40;QD=17.97;RankSumP=0.418742;SB=-412.87;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1419G>A;refseq.codonCoord=473;refseq.end=194949570;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1659;refseq.name=NM_000186;refseq.name2=CFH;refseq.positionType=CDS;refseq.proteinCoordStr=p.A473A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=83;refseq.start=194949570;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 194979209 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=310;Dels=0.00;HRun=1;HaplotypeScore=8.31;MQ=77.17;MQ0=22;OQ=226.78;QD=0.73;RankSumP=0.489422;SB=73.16;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3138C>T;refseq.codonCoord=1046;refseq.end=194979209;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3378;refseq.name=NM_000186;refseq.name2=CFH;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1046T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=5;refseq.spliceInfo=splice-acceptor_5;refseq.start=194979209;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 0/1
|
|
chr1 195024015 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=67.00;MQ0=5;OQ=446.22;QD=12.06;RankSumP=0.750000;SB=-109.57;SecondBestBaseQ=34;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.477C>T;refseq.codonCoord_2=159;refseq.end_1=195025787;refseq.end_2=195024015;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=564;refseq.name2_1=CFHR3;refseq.name2_2=CFHR3;refseq.name_1=NM_001166624;refseq.name_2=NM_021023;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S159S;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCC;refseq.spliceDist_2=47;refseq.start_1=195015737;refseq.start_2=195024015;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ser;refseq.variantCodon_2=TCT;set=Intersection GT 0/1
|
|
chr1 195024093 . T C 13 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.266667;SecondBestBaseQ=34;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.555T>C;refseq.codonCoord_2=185;refseq.end_1=195025787;refseq.end_2=195024093;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=642;refseq.name2_1=CFHR3;refseq.name2_2=CFHR3;refseq.name_1=NM_001166624;refseq.name_2=NM_021023;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.N185N;refseq.referenceAA_2=Asn;refseq.referenceCodon_2=AAT;refseq.spliceDist_2=-59;refseq.start_1=195015737;refseq.start_2=195024093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Asn;refseq.variantCodon_2=AAC;set=FilteredInAll GT 1/0
|
|
chr1 195024130 . T C 12 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=0.190476;SecondBestBaseQ=34;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.592T>C;refseq.codonCoord_2=198;refseq.end_1=195025787;refseq.end_2=195024130;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=679;refseq.name2_1=CFHR3;refseq.name2_2=CFHR3;refseq.name_1=NM_001166624;refseq.name_2=NM_021023;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S198P;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCA;refseq.spliceDist_2=-22;refseq.start_1=195015737;refseq.start_2=195024130;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCA;set=FilteredInAll GT 1/0
|
|
chr1 195063861 . C T 1 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=188;Dels=0.00;HRun=1;HaplotypeScore=10.63;MQ=72.37;MQ0=20;OQ=193.69;QD=1.03;RankSumP=0.298510;SB=161.73;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.469C>T;refseq.codonCoord=157;refseq.end=195063861;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=583;refseq.name=NM_002113;refseq.name2=CFHR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H157Y;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=39;refseq.start=195063861;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=filterInsoap-gatk GT 0/1
|
|
chr1 195063867 rs410232 C G 0.14 PASS AC=1;AF=0.50;AN=2;DB;DP=193;Dels=0.00;HRun=0;HaplotypeScore=18.78;MQ=70.96;MQ0=20;OQ=73.98;QD=0.38;SB=262.79;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.475C>G;refseq.codonCoord=159;refseq.end=195063867;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=589;refseq.name=NM_002113;refseq.name2=CFHR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L159V;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=45;refseq.start=195063867;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=gatk GT:AD:DP:GL:GQ 0/1:166,24:165:-68.06,-57.38,-744.29:99
|
|
chr1 195067665 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=429;Dels=0.00;HRun=0;HaplotypeScore=10.63;MQ=37.49;MQ0=132;OQ=5007.44;QD=11.67;RankSumP=0.0821169;SB=-1292.96;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.906G>T;refseq.codonCoord=302;refseq.end=195067665;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1020;refseq.name=NM_002113;refseq.name2=CFHR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R302R;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=116;refseq.start=195067665;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 0/1
|
|
chr1 195067701 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=400;Dels=0.00;HRun=0;HaplotypeScore=14.80;MQ=33.96;MQ0=263;OQ=1765.27;QD=4.41;RankSumP=0.142670;SB=-644.70;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.942A>T;refseq.codonCoord=314;refseq.end=195067701;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1056;refseq.name=NM_002113;refseq.name2=CFHR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R314R;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=152;refseq.start=195067701;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 0/1
|
|
chr1 195148657 . G C 1 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=26;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.421G>C;refseq.codonCoord=141;refseq.end=195148657;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=490;refseq.name=NM_006684;refseq.name2=CFHR4;refseq.positionType=CDS;refseq.proteinCoordStr=p.A141P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-19;refseq.start=195148657;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/1
|
|
chr1 195186771 . C T 290.39 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=338;Dels=0.00;HRun=0;HaplotypeScore=6.79;MQ=91.69;MQ0=11;OQ=5317.78;QD=15.73;RankSumP=0.0421756;SB=-1073.33;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.420C>T;refseq.codonCoord=140;refseq.end=195186771;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=497;refseq.name=NM_005666;refseq.name2=CFHR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C140C;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-11;refseq.start=195186771;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 0/1
|
|
chr1 195276421 . A G 229.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.63;MQ0=0;OQ=1395.68;QD=17.02;RankSumP=0.484859;SB=-692.96;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1806T>C;refseq.codonCoord=602;refseq.end=195276421;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1850;refseq.name=NM_001994;refseq.name2=F13B;refseq.positionType=CDS;refseq.proteinCoordStr=p.N602N;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=68;refseq.start=195276421;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 0/1
|
|
chr1 195296824 . T C 245.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1908.03;QD=34.69;RankSumP=1.00000;SB=-135.05;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.456A>G;refseq.codonCoord=152;refseq.end=195296824;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=500;refseq.name=NM_001994;refseq.name2=F13B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T152T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=5;refseq.spliceInfo=splice-acceptor_5;refseq.start=195296824;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 195297644 . C T 307.41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=4.57;MQ=98.89;MQ0=0;OQ=7223.21;QD=42.24;RankSumP=1.00000;SB=-2095.73;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.344G>A;refseq.codonCoord=115;refseq.end=195297644;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=388;refseq.name=NM_001994;refseq.name2=F13B;refseq.positionType=CDS;refseq.proteinCoordStr=p.R115H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=79;refseq.start=195297644;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/1
|
|
chr1 195337065 . G T 137.01 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=127;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=99.00;MQ0=0;OQ=1594.97;QD=12.56;RankSumP=0.268629;SB=-739.27;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7939C>A;refseq.codonCoord=2647;refseq.end=195337065;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=8196;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.L2647I;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=-882;refseq.start=195337065;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 195337320 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=130;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=98.99;MQ0=0;OQ=2513.65;QD=19.34;RankSumP=0.227422;SB=-961.53;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7684A>G;refseq.codonCoord=2562;refseq.end=195337320;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7941;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2562G;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-1137;refseq.start=195337320;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/0
|
|
chr1 195337330 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=148;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=98.99;MQ0=0;OQ=2867.80;QD=19.38;RankSumP=0.483934;SB=-1000.45;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.7674C>T;refseq.codonCoord=2558;refseq.end=195337330;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=7931;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.I2558I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-1147;refseq.start=195337330;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 195337399 . C T 305.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=308;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=98.64;MQ0=0;OQ=5255.94;QD=17.06;RankSumP=0.432455;SB=-1866.05;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.7605G>A;refseq.codonCoord=2535;refseq.end=195337399;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7862;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.V2535V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-1216;refseq.start=195337399;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 0/1
|
|
chr1 195337438 . T C 292.53 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=274;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=98.76;MQ0=0;OQ=11641.51;QD=42.49;RankSumP=1.00000;SB=-5337.82;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.7566A>G;refseq.codonCoord=2522;refseq.end=195337438;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=7823;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.L2522L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=-1255;refseq.start=195337438;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/1
|
|
chr1 195337524 . A G 279.49 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=358;Dels=0.00;HRun=0;HaplotypeScore=3.95;MQ=98.96;MQ0=0;OQ=15348.44;QD=42.87;RankSumP=1.00000;SB=-5973.39;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7480T>C;refseq.codonCoord=2494;refseq.end=195337524;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=7737;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y2494H;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-1341;refseq.start=195337524;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 195339043 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=539;Dels=0.00;HRun=0;HaplotypeScore=29.40;MQ=98.91;MQ0=0;OQ=10971.50;QD=20.36;RankSumP=0.430240;SB=-1913.86;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5961A>G;refseq.codonCoord=1987;refseq.end=195339043;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6218;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1987Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=1896;refseq.start=195339043;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 195340555 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=570.22;QD=11.88;RankSumP=0.494732;SB=-279.44;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4449A>G;refseq.codonCoord=1483;refseq.end=195340555;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4706;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1483K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=384;refseq.start=195340555;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/0
|
|
chr1 195358160 . A T 393.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=244;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.71;MQ0=0;OQ=9471.47;QD=38.82;RankSumP=1.00000;SB=-3471.76;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3579T>A;refseq.codonCoord=1193;refseq.end=195358160;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3836;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.S1193S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-20;refseq.start=195358160;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/1
|
|
chr1 195379156 . G A 260.31 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=220;Dels=0.00;HRun=0;HaplotypeScore=7.54;MQ=98.73;MQ0=0;OQ=9496.24;QD=43.16;RankSumP=1.00000;SB=-4098.09;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.849C>T;refseq.codonCoord=283;refseq.end=195379156;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1106;refseq.name=NM_018136;refseq.name2=ASPM;refseq.positionType=CDS;refseq.proteinCoordStr=p.S283S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=408;refseq.start=195379156;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 195395319 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2523A>C;refseq.codonCoord=841;refseq.end=195395319;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2592;refseq.name=NM_194314;refseq.name2=ZBTB41;refseq.positionType=CDS;refseq.proteinCoordStr=p.P841P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=449;refseq.start=195395319;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 195395349 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=295;Dels=0.00;HRun=1;HaplotypeScore=32.37;MQ=98.65;MQ0=0;OQ=4087.96;QD=13.86;RankSumP=0.000821283;SB=-468.37;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2493C>T;refseq.codonCoord=831;refseq.end=195395349;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2562;refseq.name=NM_194314;refseq.name2=ZBTB41;refseq.positionType=CDS;refseq.proteinCoordStr=p.L831L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=419;refseq.start=195395349;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=filterInsoap-gatk GT 1/0
|
|
chr1 195592632 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=4;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1037A>C;refseq.codonCoord=346;refseq.end=195592632;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1172;refseq.name=NM_201253;refseq.name2=CRB1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N346T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=49;refseq.start=195592632;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 0/1
|
|
chr1 195656991 . A G 352.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=221;Dels=0.00;HRun=0;HaplotypeScore=3.47;MQ=98.75;MQ0=0;OQ=8757.98;QD=39.63;RankSumP=1.00000;SB=-4262.68;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1410A>G;refseq.codonCoord=470;refseq.end=195656991;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1545;refseq.name=NM_201253;refseq.name2=CRB1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L470L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=239;refseq.start=195656991;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 196148314 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.chr=chr1;refseq.codingCoordStr=c.28+2;refseq.end=196148314;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_001014434;refseq.name2=LHX9;refseq.positionType=intron;refseq.spliceDist=2;refseq.spliceInfo=splice-donor_2;refseq.start=196148314;refseq.transcriptStrand=+;set=FilteredInAll GT 1/0
|
|
chr1 196163351 . T C 114.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1398.66;QD=22.93;RankSumP=0.452939;SB=-524.12;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.714T>C;refseq.codingCoordStr_2=c.741T>C;refseq.codonCoord_1=238;refseq.codonCoord_2=247;refseq.end_1=196163351;refseq.end_2=196163351;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=741;refseq.mrnaCoord_2=1178;refseq.name2_1=LHX9;refseq.name2_2=LHX9;refseq.name_1=NM_001014434;refseq.name_2=NM_020204;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N238N;refseq.proteinCoordStr_2=p.N247N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAT;refseq.referenceCodon_2=AAT;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.start_1=196163351;refseq.start_2=196163351;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAC;refseq.variantCodon_2=AAC;set=Intersection GT 1/0
|
|
chr1 196776399 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5C>A;refseq.codingCoordStr_2=c.5C>A;refseq.codonCoord_1=2;refseq.codonCoord_2=2;refseq.end_1=196776399;refseq.end_2=196776399;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=111;refseq.mrnaCoord_2=111;refseq.name2_1=ATP6V1G3;refseq.name2_2=ATP6V1G3;refseq.name_1=NM_133262;refseq.name_2=NM_133326;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T2K;refseq.proteinCoordStr_2=p.T2K;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=40;refseq.spliceDist_2=40;refseq.start_1=196776399;refseq.start_2=196776399;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=FilteredInAll GT 0/1
|
|
chr1 198409904 . C T 191.56 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=150;Dels=0.00;HRun=0;HaplotypeScore=6.00;MQ=99.00;MQ0=0;OQ=2017.16;QD=13.45;RankSumP=0.359819;SB=-853.40;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1431C>T;refseq.codingCoordStr_2=c.1569C>T;refseq.codonCoord_1=477;refseq.codonCoord_2=523;refseq.end_1=198409904;refseq.end_2=198409904;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1637;refseq.mrnaCoord_2=1775;refseq.name2_1=NR5A2;refseq.name2_2=NR5A2;refseq.name_1=NM_003822;refseq.name_2=NM_205860;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N477N;refseq.proteinCoordStr_2=p.N523N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=191;refseq.spliceDist_2=191;refseq.start_1=198409904;refseq.start_2=198409904;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 0/1
|
|
chr1 198643318 . C T 186.68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=333;Dels=0.00;HRun=0;HaplotypeScore=3.89;MQ=98.57;MQ0=0;OQ=13691.71;QD=41.12;RankSumP=1.00000;SB=-6432.62;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2139G>A;refseq.codonCoord=713;refseq.end=198643318;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2246;refseq.name=NM_012482;refseq.name2=ZNF281;refseq.positionType=CDS;refseq.proteinCoordStr=p.T713T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-1276;refseq.start=198643318;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 198789189 . G C 165.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=98.92;MQ0=0;OQ=831.78;QD=13.86;RankSumP=0.717665;SB=-374.97;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4897C>G;refseq.codonCoord=1633;refseq.end=198789189;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5336;refseq.name=NM_014875;refseq.name2=KIF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1633A;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=330;refseq.start=198789189;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 198800871 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=165;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.88;MQ0=0;OQ=2048.34;QD=12.41;RankSumP=0.481299;SB=-995.29;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4020G>A;refseq.codonCoord=1340;refseq.end=198800871;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4459;refseq.name=NM_014875;refseq.name2=KIF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1340E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-52;refseq.start=198800871;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 0/1
|
|
chr1 198824986 . T C 232.95 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.80;MQ0=0;OQ=1567.13;QD=16.50;RankSumP=0.468773;SB=-800.17;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3096A>G;refseq.codonCoord=1032;refseq.end=198824986;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3535;refseq.name=NM_014875;refseq.name2=KIF14;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1032E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-19;refseq.start=198824986;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 198884861 . T C 347.25 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=274;Dels=0.00;HRun=1;HaplotypeScore=4.20;MQ=98.67;MQ0=0;OQ=10714.80;QD=39.11;RankSumP=1.00000;SB=-3554.12;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1431A>G;refseq.codonCoord=477;refseq.end=198884861;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1674;refseq.name=NM_001031725;refseq.name2=DDX59;refseq.positionType=CDS;refseq.proteinCoordStr=p.S477S;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-37;refseq.start=198884861;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 1/1
|
|
chr1 199108964 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DP=42;Dels=0.00;HRun=0;HaplotypeScore=4.07;MQ=96.84;MQ0=0;OQ=481.16;QD=11.46;RankSumP=0.591706;SB=-130.64;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.176T>C;refseq.codonCoord=59;refseq.end=199108964;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=176;refseq.name=NM_005298;refseq.name2=GPR25;refseq.positionType=CDS;refseq.proteinCoordStr=p.F59S;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=176;refseq.start=199108964;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/0
|
|
chr1 199134115 . C G 331.04 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=215;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=98.85;MQ0=0;OQ=4596.46;QD=21.38;RankSumP=0.0777179;SB=-1859.28;SecondBestBaseQ=32;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.-37C>G;refseq.codingCoordStr_2=c.219C>G;refseq.codonCoord_2=73;refseq.end_1=199134115;refseq.end_2=199134115;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=275;refseq.mrnaCoord_2=249;refseq.name2_1=C1orf106;refseq.name2_2=C1orf106;refseq.name_1=NM_001142569;refseq.name_2=NM_018265;refseq.numMatchingRecords=2;refseq.positionType_1=utr5;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.P73P;refseq.referenceAA_2=Pro;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=58;refseq.spliceDist_2=58;refseq.start_1=199134115;refseq.start_2=199134115;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCG;set=Intersection GT 1/0
|
|
chr1 199147334 . G C 88 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=1.16092e-09;SecondBestBaseQ=15;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1090G>C;refseq.codingCoordStr_2=c.1345G>C;refseq.codonCoord_1=364;refseq.codonCoord_2=449;refseq.end_1=199147334;refseq.end_2=199147334;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1401;refseq.mrnaCoord_2=1375;refseq.name2_1=C1orf106;refseq.name2_2=C1orf106;refseq.name_1=NM_001142569;refseq.name_2=NM_018265;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A364P;refseq.proteinCoordStr_2=p.A449P;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=131;refseq.spliceDist_2=131;refseq.start_1=199147334;refseq.start_2=199147334;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 199224073 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3382A>C;refseq.codonCoord=1128;refseq.end=199224073;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3699;refseq.name=NM_017596;refseq.name2=KIF21B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1128P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-27;refseq.start=199224073;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 199235188 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1797T>G;refseq.codonCoord=599;refseq.end=199235188;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2114;refseq.name=NM_017596;refseq.name2=KIF21B;refseq.positionType=CDS;refseq.proteinCoordStr=p.C599W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=30;refseq.start=199235188;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 0/1
|
|
chr1 199239408 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1141A>C;refseq.codonCoord=381;refseq.end=199239408;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1458;refseq.name=NM_017596;refseq.name2=KIF21B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T381P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-72;refseq.start=199239408;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 199284428 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=3;RankSumP=0.00000;SecondBestBaseQ=19;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4346T>G;refseq.codonCoord=1449;refseq.end=199284428;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4573;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1449G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=199284428;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 199305310 . A G 128.19 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=582.07;QD=20.79;RankSumP=0.290808;SB=-90.91;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2403T>C;refseq.codonCoord=801;refseq.end=199305310;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2630;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.F801F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=43;refseq.start=199305310;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 0/1
|
|
chr1 199313685 . G A 125.86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=194;Dels=0.00;HRun=1;HaplotypeScore=4.74;MQ=98.95;MQ0=0;OQ=4736.79;QD=24.42;RankSumP=0.00741987;SB=-1542.14;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1564C>T;refseq.codonCoord=522;refseq.end=199313685;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1791;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.L522L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-56;refseq.start=199313685;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=filterInsoap-gatk GT 1/0
|
|
chr1 199313698 . A G 363.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=206;Dels=0.00;HRun=0;HaplotypeScore=4.52;MQ=98.95;MQ0=0;OQ=7420.74;QD=36.02;RankSumP=1.00000;SB=-2539.68;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1551T>C;refseq.codonCoord=517;refseq.end=199313698;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1778;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.G517G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-69;refseq.start=199313698;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 199313734 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=316;Dels=0.00;HRun=0;HaplotypeScore=24.44;MQ=98.63;MQ0=0;OQ=5815.70;QD=18.40;RankSumP=0.266019;SB=-1255.03;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1515T>C;refseq.codonCoord=505;refseq.end=199313734;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1742;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.C505C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-105;refseq.start=199313734;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 0/1
|
|
chr1 199318933 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=237;Dels=0.00;HRun=0;HaplotypeScore=27.80;MQ=97.23;MQ0=0;OQ=2628.28;QD=11.09;RankSumP=0.171754;SB=-749.23;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1373T>A;refseq.codonCoord=458;refseq.end=199318933;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1600;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.L458H;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-21;refseq.start=199318933;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 0/1
|
|
chr1 199318935 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=246;Dels=0.00;HRun=0;HaplotypeScore=32.40;MQ=97.16;MQ0=0;OQ=2943.58;QD=11.97;RankSumP=0.386159;SB=-590.50;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1371T>G;refseq.codonCoord=457;refseq.end=199318935;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1598;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.P457P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-23;refseq.start=199318935;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 0/1
|
|
chr1 199318993 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1313T>G;refseq.codonCoord=438;refseq.end=199318993;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1540;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.V438G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=81;refseq.start=199318993;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 199327488 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.80;MQ0=0;OQ=548.77;QD=14.07;RankSumP=0.602082;SB=-190.26;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.597C>T;refseq.codonCoord=199;refseq.end=199327488;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=824;refseq.name=NM_000069;refseq.name2=CACNA1S;refseq.positionType=CDS;refseq.proteinCoordStr=p.I199I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=56;refseq.start=199327488;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 199371489 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.477T>G;refseq.codonCoord=159;refseq.end=199371489;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=573;refseq.name=NM_016456;refseq.name2=TMEM9;refseq.positionType=CDS;refseq.proteinCoordStr=p.G159G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=78;refseq.start=199371489;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 199379604 . A G 353.71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=253;Dels=0.00;HRun=0;HaplotypeScore=8.03;MQ=98.84;MQ0=0;OQ=4433.57;QD=17.52;RankSumP=0.0774041;SB=-1741.03;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.366T>C;refseq.codonCoord=122;refseq.end=199379604;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=462;refseq.name=NM_016456;refseq.name2=TMEM9;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y122Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-34;refseq.start=199379604;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 0/1
|
|
chr1 199449986 . C T 200.46 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=98.87;MQ0=0;OQ=1141.83;QD=15.22;RankSumP=0.388609;SB=-346.86;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8787C>T;refseq.codonCoord=2929;refseq.end=199449986;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=8917;refseq.name=NM_001164586;refseq.name2=IGFN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2929A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=59;refseq.start=199449986;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 0/1
|
|
chr1 199450025 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=135;Dels=0.00;HRun=2;HaplotypeScore=6.62;MQ=98.76;MQ0=0;OQ=1479.15;QD=10.96;RankSumP=0.473283;SB=-551.13;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8826T>C;refseq.codonCoord=2942;refseq.end=199450025;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=8956;refseq.name=NM_001164586;refseq.name2=IGFN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P2942P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-28;refseq.start=199450025;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/0
|
|
chr1 199450898 . C T 280.96 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=173;Dels=0.00;HRun=0;HaplotypeScore=6.31;MQ=98.69;MQ0=0;OQ=2968.62;QD=17.16;RankSumP=0.322092;SB=-658.63;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8988C>T;refseq.codonCoord=2996;refseq.end=199450898;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=9118;refseq.name=NM_001164586;refseq.name2=IGFN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T2996T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-8;refseq.spliceInfo=splice-donor_-8;refseq.start=199450898;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 0/1
|
|
chr1 199454387 . T C 79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=136;Dels=0.00;HRun=1;HaplotypeScore=14.77;MQ=98.40;MQ0=0;OQ=3964.05;QD=29.15;RankSumP=1.00000;SB=-1858.95;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.9876T>C;refseq.codonCoord=3292;refseq.end=199454387;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=10006;refseq.name=NM_001164586;refseq.name2=IGFN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A3292A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-23;refseq.start=199454387;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 199457355 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=9.79;MQ=97.07;MQ0=0;OQ=523.11;QD=8.58;RankSumP=0.554700;SB=-268.19;SecondBestBaseQ=17;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.10059G>A;refseq.codonCoord=3353;refseq.end=199457355;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=10189;refseq.name=NM_001164586;refseq.name2=IGFN1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V3353V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-143;refseq.start=199457355;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/0
|
|
chr1 199519489 . C T 261.36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=139;Dels=0.00;HRun=0;HaplotypeScore=5.55;MQ=98.77;MQ0=0;OQ=2102.93;QD=15.13;RankSumP=0.129091;SB=-886.54;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.36C>T;refseq.codingCoordStr_2=c.36C>T;refseq.codonCoord_1=12;refseq.codonCoord_2=12;refseq.end_1=199519489;refseq.end_2=199519489;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=287;refseq.mrnaCoord_2=287;refseq.name2_1=PKP1;refseq.name2_2=PKP1;refseq.name_1=NM_000299;refseq.name_2=NM_001005337;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y12Y;refseq.proteinCoordStr_2=p.Y12Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-167;refseq.spliceDist_2=-167;refseq.start_1=199519489;refseq.start_2=199519489;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;set=Intersection GT 0/1
|
|
chr1 199549196 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=99.00;MQ0=0;OQ=609.14;QD=14.86;RankSumP=0.393237;SB=-111.99;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.586A>G;refseq.codingCoordStr_2=c.586A>G;refseq.codonCoord_1=196;refseq.codonCoord_2=196;refseq.end_1=199549196;refseq.end_2=199549196;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=837;refseq.mrnaCoord_2=837;refseq.name2_1=PKP1;refseq.name2_2=PKP1;refseq.name_1=NM_000299;refseq.name_2=NM_001005337;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I196V;refseq.proteinCoordStr_2=p.I196V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATA;refseq.referenceCodon_2=ATA;refseq.spliceDist_1=-116;refseq.spliceDist_2=-116;refseq.start_1=199549196;refseq.start_2=199549196;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=Intersection GT 0/1
|
|
chr1 199552382 . A G 401.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=138;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=98.71;MQ0=0;OQ=5454.08;QD=39.52;RankSumP=1.00000;SB=-2404.60;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.780A>G;refseq.codingCoordStr_2=c.780A>G;refseq.codonCoord_1=260;refseq.codonCoord_2=260;refseq.end_1=199552382;refseq.end_2=199552382;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1031;refseq.mrnaCoord_2=1031;refseq.name2_1=PKP1;refseq.name2_2=PKP1;refseq.name_1=NM_000299;refseq.name_2=NM_001005337;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K260K;refseq.proteinCoordStr_2=p.K260K;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAA;refseq.referenceCodon_2=AAA;refseq.spliceDist_1=-67;refseq.spliceDist_2=-67;refseq.start_1=199552382;refseq.start_2=199552382;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/1
|
|
chr1 199597691 . A G 223.79 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=485;Dels=0.00;HRun=0;HaplotypeScore=10.69;MQ=98.79;MQ0=0;OQ=8101.69;QD=16.70;RankSumP=0.0129418;SB=-2115.00;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.683T>C;refseq.codingCoordStr_2=c.662T>C;refseq.codingCoordStr_3=c.653T>C;refseq.codingCoordStr_4=c.644T>C;refseq.codonCoord_1=228;refseq.codonCoord_2=221;refseq.codonCoord_3=218;refseq.codonCoord_4=215;refseq.end_1=199597691;refseq.end_2=199597691;refseq.end_3=199597691;refseq.end_4=199597691;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=752;refseq.mrnaCoord_2=731;refseq.mrnaCoord_3=722;refseq.mrnaCoord_4=713;refseq.name2_1=TNNT2;refseq.name2_2=TNNT2;refseq.name2_3=TNNT2;refseq.name2_4=TNNT2;refseq.name_1=NM_000364;refseq.name_2=NM_001001430;refseq.name_3=NM_001001431;refseq.name_4=NM_001001432;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.I228T;refseq.proteinCoordStr_2=p.I221T;refseq.proteinCoordStr_3=p.I218T;refseq.proteinCoordStr_4=p.I215T;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.referenceCodon_3=ATT;refseq.referenceCodon_4=ATT;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.spliceDist_3=-28;refseq.spliceDist_4=-28;refseq.start_1=199597691;refseq.start_2=199597691;refseq.start_3=199597691;refseq.start_4=199597691;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=ACT;refseq.variantCodon_4=ACT;set=Intersection GT 0/1
|
|
chr1 199601005 . G A 216.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=128;Dels=0.00;HRun=1;HaplotypeScore=7.92;MQ=98.00;MQ0=0;OQ=5156.72;QD=40.29;RankSumP=1.00000;SB=-1973.01;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.348C>T;refseq.codingCoordStr_2=c.318C>T;refseq.codingCoordStr_3=c.318C>T;refseq.codingCoordStr_4=c.303C>T;refseq.codonCoord_1=116;refseq.codonCoord_2=106;refseq.codonCoord_3=106;refseq.codonCoord_4=101;refseq.end_1=199601005;refseq.end_2=199601005;refseq.end_3=199601005;refseq.end_4=199601005;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=417;refseq.mrnaCoord_2=387;refseq.mrnaCoord_3=387;refseq.mrnaCoord_4=372;refseq.name2_1=TNNT2;refseq.name2_2=TNNT2;refseq.name2_3=TNNT2;refseq.name2_4=TNNT2;refseq.name_1=NM_000364;refseq.name_2=NM_001001430;refseq.name_3=NM_001001431;refseq.name_4=NM_001001432;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.I116I;refseq.proteinCoordStr_2=p.I106I;refseq.proteinCoordStr_3=p.I106I;refseq.proteinCoordStr_4=p.I101I;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.spliceDist_1=54;refseq.spliceDist_2=54;refseq.spliceDist_3=54;refseq.spliceDist_4=54;refseq.start_1=199601005;refseq.start_2=199601005;refseq.start_3=199601005;refseq.start_4=199601005;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Ile;refseq.variantAA_4=Ile;refseq.variantCodon_1=ATT;refseq.variantCodon_2=ATT;refseq.variantCodon_3=ATT;refseq.variantCodon_4=ATT;set=Intersection GT 1/1
|
|
chr1 199601418 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=130;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1628.97;QD=12.53;RankSumP=0.230000;SB=-608.48;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.237G>A;refseq.codingCoordStr_2=c.207G>A;refseq.codingCoordStr_3=c.207G>A;refseq.codingCoordStr_4=c.192G>A;refseq.codonCoord_1=79;refseq.codonCoord_2=69;refseq.codonCoord_3=69;refseq.codonCoord_4=64;refseq.end_1=199601418;refseq.end_2=199601418;refseq.end_3=199601418;refseq.end_4=199601418;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=306;refseq.mrnaCoord_2=276;refseq.mrnaCoord_3=276;refseq.mrnaCoord_4=261;refseq.name2_1=TNNT2;refseq.name2_2=TNNT2;refseq.name2_3=TNNT2;refseq.name2_4=TNNT2;refseq.name_1=NM_000364;refseq.name_2=NM_001001430;refseq.name_3=NM_001001431;refseq.name_4=NM_001001432;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.S79S;refseq.proteinCoordStr_2=p.S69S;refseq.proteinCoordStr_3=p.S69S;refseq.proteinCoordStr_4=p.S64S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_1=TCG;refseq.referenceCodon_2=TCG;refseq.referenceCodon_3=TCG;refseq.referenceCodon_4=TCG;refseq.spliceDist_1=4;refseq.spliceDist_2=4;refseq.spliceDist_3=4;refseq.spliceDist_4=4;refseq.spliceInfo_1=splice-acceptor_4;refseq.spliceInfo_2=splice-acceptor_4;refseq.spliceInfo_3=splice-acceptor_4;refseq.spliceInfo_4=splice-acceptor_4;refseq.start_1=199601418;refseq.start_2=199601418;refseq.start_3=199601418;refseq.start_4=199601418;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_1=TCA;refseq.variantCodon_2=TCA;refseq.variantCodon_3=TCA;refseq.variantCodon_4=TCA;set=Intersection GT 0/1
|
|
chr1 199622145 . T C 35 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=98.93;MQ0=0;OQ=75.78;QD=5.41;RankSumP=0.619048;SB=-6.99;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.967A>G;refseq.codonCoord=323;refseq.end=199622145;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1202;refseq.name=NM_005558;refseq.name2=LAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.K323E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-60;refseq.start=199622145;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 199622292 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=96.57;MQ0=0;OQ=493.15;QD=12.64;RankSumP=0.342152;SB=-128.62;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.820A>G;refseq.codonCoord=274;refseq.end=199622292;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1055;refseq.name=NM_005558;refseq.name2=LAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T274A;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-207;refseq.start=199622292;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/0
|
|
chr1 199622566 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=98.85;MQ0=0;OQ=703.64;QD=12.57;RankSumP=0.741357;SB=-318.80;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.546G>A;refseq.codonCoord=182;refseq.end=199622566;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=781;refseq.name=NM_005558;refseq.name2=LAD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.K182K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=364;refseq.start=199622566;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 0/1
|
|
chr1 200018109 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.673A>C;refseq.codingCoordStr_2=c.1846A>C;refseq.codonCoord_1=225;refseq.codonCoord_2=616;refseq.end_1=200018109;refseq.end_2=200018109;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=862;refseq.mrnaCoord_2=2193;refseq.name2_1=NAV1;refseq.name2_2=NAV1;refseq.name_1=NM_001167738;refseq.name_2=NM_020443;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T225P;refseq.proteinCoordStr_2=p.T616P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=183;refseq.spliceDist_2=183;refseq.start_1=200018109;refseq.start_2=200018109;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=FilteredInAll GT 0/1
|
|
chr1 200094246 . G C 52 PASS AC=1;AF=0.50;AN=2;BestBaseQ=11;HRun=1;RankSumP=0.0625707;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1270G>C;refseq.codonCoord=424;refseq.end=200094246;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1320;refseq.name=NM_018085;refseq.name2=IPO9;refseq.positionType=CDS;refseq.proteinCoordStr=p.A424P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=49;refseq.start=200094246;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=soap GT 0/1
|
|
chr1 200127249 . A G 84 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=269;Dels=0.00;HRun=0;HaplotypeScore=18.11;MQ=98.37;MQ0=0;OQ=9844.14;QD=36.60;RankSumP=1.00000;SB=-2868.00;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.477A>G;refseq.codonCoord_2=159;refseq.end_1=200127249;refseq.end_2=200127249;refseq.frame_2=2;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=517;refseq.mrnaCoord_2=795;refseq.name2_1=SHISA4;refseq.name2_2=SHISA4;refseq.name_1=NR_030775;refseq.name_2=NM_198149;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.I159M;refseq.referenceAA_2=Ile;refseq.referenceCodon_2=ATA;refseq.spliceDist_1=-71;refseq.spliceDist_2=-71;refseq.start_1=200127249;refseq.start_2=200127249;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Met;refseq.variantCodon_2=ATG;set=Intersection GT 1/1
|
|
chr1 200201201 . G A 187.32 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=322;Dels=0.00;HRun=0;HaplotypeScore=5.37;MQ=98.65;MQ0=0;OQ=5043.87;QD=15.66;RankSumP=0.185885;SB=-957.72;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.337G>A;refseq.codonCoord=113;refseq.end=200201201;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=373;refseq.name=NM_006335;refseq.name2=TIMM17A;refseq.positionType=CDS;refseq.proteinCoordStr=p.V113I;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=18;refseq.start=200201201;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 200218692 . C G 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=2;HRun=2;RankSumP=0.750000;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.275C>G;refseq.codonCoord=92;refseq.end=200218692;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=304;refseq.name=NM_020216;refseq.name2=RNPEP;refseq.positionType=CDS;refseq.proteinCoordStr=p.A92G;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-173;refseq.start=200218692;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 200218697 . C G 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=2;HRun=2;RankSumP=0.750000;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.280C>G;refseq.codonCoord=94;refseq.end=200218697;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=309;refseq.name=NM_020216;refseq.name2=RNPEP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R94G;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-168;refseq.start=200218697;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 200218706 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=2;HRun=2;RankSumP=0.750000;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.289C>G;refseq.codonCoord=97;refseq.end=200218706;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=318;refseq.name=NM_020216;refseq.name2=RNPEP;refseq.positionType=CDS;refseq.proteinCoordStr=p.R97G;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-159;refseq.start=200218706;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 200233071 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=6.16138e-08;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.856T>G;refseq.codonCoord=286;refseq.end=200233071;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=885;refseq.name=NM_020216;refseq.name2=RNPEP;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y286D;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=200233071;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 1/0
|
|
chr1 200235705 . G A 237.85 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=203;Dels=0.00;HRun=1;HaplotypeScore=4.60;MQ=98.77;MQ0=0;OQ=7859.35;QD=38.72;RankSumP=1.00000;SB=-3783.08;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1143G>A;refseq.codonCoord=381;refseq.end=200235705;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1172;refseq.name=NM_020216;refseq.name2=RNPEP;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q381Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=53;refseq.start=200235705;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/1
|
|
chr1 200237185 . T C 271.12 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=321;Dels=0.00;HRun=0;HaplotypeScore=3.06;MQ=98.80;MQ0=0;OQ=13310.09;QD=41.46;RankSumP=1.00000;SB=-6412.92;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1263T>C;refseq.codonCoord=421;refseq.end=200237185;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1292;refseq.name=NM_020216;refseq.name2=RNPEP;refseq.positionType=CDS;refseq.proteinCoordStr=p.V421V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-55;refseq.start=200237185;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 200247841 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=2.28;MQ=98.82;MQ0=0;OQ=1490.08;QD=19.10;RankSumP=0.105945;SB=-689.52;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.297C>G;refseq.codingCoordStr_2=c.297C>G;refseq.codonCoord_1=99;refseq.codonCoord_2=99;refseq.end_1=200247841;refseq.end_2=200247841;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=564;refseq.mrnaCoord_2=450;refseq.name2_1=ELF3;refseq.name2_2=ELF3;refseq.name_1=NM_001114309;refseq.name_2=NM_004433;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G99G;refseq.proteinCoordStr_2=p.G99G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=-89;refseq.spliceDist_2=-89;refseq.start_1=200247841;refseq.start_2=200247841;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=Intersection GT 1/0
|
|
chr1 200248485 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=70;Dels=0.00;HRun=4;HaplotypeScore=2.22;MQ=97.97;MQ0=0;OQ=770.38;QD=11.01;RankSumP=0.216128;SB=-118.67;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.573T>C;refseq.codingCoordStr_2=c.573T>C;refseq.codonCoord_1=191;refseq.codonCoord_2=191;refseq.end_1=200248485;refseq.end_2=200248485;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=840;refseq.mrnaCoord_2=726;refseq.name2_1=ELF3;refseq.name2_2=ELF3;refseq.name_1=NM_001114309;refseq.name_2=NM_004433;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P191P;refseq.proteinCoordStr_2=p.P191P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.spliceDist_1=-26;refseq.spliceDist_2=-26;refseq.start_1=200248485;refseq.start_2=200248485;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=soap-filterIngatk GT 1/0
|
|
chr1 200358983 . G A 326.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=99.00;MQ0=0;OQ=3043.46;QD=39.02;RankSumP=1.00000;SB=-535.21;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.269G>A;refseq.codonCoord=90;refseq.end=200358983;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=332;refseq.name=NM_004767;refseq.name2=GPR37L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G90D;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=332;refseq.start=200358983;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 200359038 . A G 95.71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=194;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=98.76;MQ0=0;OQ=7714.12;QD=39.76;RankSumP=1.00000;SB=-1729.32;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.324A>G;refseq.codonCoord=108;refseq.end=200359038;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=387;refseq.name=NM_004767;refseq.name2=GPR37L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G108G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-307;refseq.start=200359038;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 1/1
|
|
chr1 200359203 . T C 397.21 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.73;MQ0=0;OQ=3507.49;QD=37.31;RankSumP=1.00000;SB=-1622.18;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.489T>C;refseq.codonCoord=163;refseq.end=200359203;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=552;refseq.name=NM_004767;refseq.name2=GPR37L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S163S;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-142;refseq.start=200359203;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 200449931 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=98.44;MQ0=0;OQ=789.78;QD=21.94;RankSumP=0.395005;SB=-392.14;SecondBestBaseQ=32;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_3=c.26C>T;refseq.codonCoord_3=9;refseq.end_1=200461163;refseq.end_2=200461163;refseq.end_3=200449931;refseq.frame_3=1;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=26;refseq.name2_1=LGR6;refseq.name2_2=LGR6;refseq.name2_3=LGR6;refseq.name_1=NM_001017403;refseq.name_2=NM_021636;refseq.name_3=NM_001017404;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.S9L;refseq.referenceAA_3=Ser;refseq.referenceCodon_3=TCA;refseq.spliceDist_3=26;refseq.start_1=200429963;refseq.start_2=200439637;refseq.start_3=200449931;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Leu;refseq.variantCodon_3=TTA;set=Intersection GT 0/1
|
|
chr1 200543117 . C T 133.15 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=497;Dels=0.00;HRun=0;HaplotypeScore=6.97;MQ=98.81;MQ0=0;OQ=20482.73;QD=41.21;RankSumP=1.00000;SB=-9944.50;SecondBestBaseQ=6;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1245C>T;refseq.codingCoordStr_2=c.828C>T;refseq.codingCoordStr_3=c.1089C>T;refseq.codonCoord_1=415;refseq.codonCoord_2=276;refseq.codonCoord_3=363;refseq.end_1=200543117;refseq.end_2=200543117;refseq.end_3=200543117;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1245;refseq.mrnaCoord_2=828;refseq.mrnaCoord_3=1132;refseq.name2_1=LGR6;refseq.name2_2=LGR6;refseq.name2_3=LGR6;refseq.name_1=NM_001017403;refseq.name_2=NM_001017404;refseq.name_3=NM_021636;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P415P;refseq.proteinCoordStr_2=p.P276P;refseq.proteinCoordStr_3=p.P363P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.referenceCodon_3=CCC;refseq.spliceDist_1=-36;refseq.spliceDist_2=-36;refseq.spliceDist_3=-36;refseq.start_1=200543117;refseq.start_2=200543117;refseq.start_3=200543117;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;refseq.variantCodon_3=CCT;set=Intersection GT 1/1
|
|
chr1 200553829 . T C 91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=59;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=98.39;MQ0=0;OQ=2106.57;QD=35.70;RankSumP=1.00000;SB=-298.09;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1775T>C;refseq.codingCoordStr_2=c.1358T>C;refseq.codingCoordStr_3=c.1619T>C;refseq.codonCoord_1=592;refseq.codonCoord_2=453;refseq.codonCoord_3=540;refseq.end_1=200553829;refseq.end_2=200553829;refseq.end_3=200553829;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1775;refseq.mrnaCoord_2=1358;refseq.mrnaCoord_3=1662;refseq.name2_1=LGR6;refseq.name2_2=LGR6;refseq.name2_3=LGR6;refseq.name_1=NM_001017403;refseq.name_2=NM_001017404;refseq.name_3=NM_021636;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V592A;refseq.proteinCoordStr_2=p.V453A;refseq.proteinCoordStr_3=p.V540A;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTC;refseq.referenceCodon_2=GTC;refseq.referenceCodon_3=GTC;refseq.spliceDist_1=127;refseq.spliceDist_2=127;refseq.spliceDist_3=127;refseq.start_1=200553829;refseq.start_2=200553829;refseq.start_3=200553829;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;refseq.variantCodon_3=GCC;set=soap-filterIngatk GT 1/1
|
|
chr1 200554160 . G A 116.35 PASS AC=2;AF=1.00;AN=2;BestBaseQ=20;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=96.94;MQ0=0;OQ=467.80;QD=21.26;RankSumP=1.00000;SB=-166.67;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2106G>A;refseq.codingCoordStr_2=c.1689G>A;refseq.codingCoordStr_3=c.1950G>A;refseq.codonCoord_1=702;refseq.codonCoord_2=563;refseq.codonCoord_3=650;refseq.end_1=200554160;refseq.end_2=200554160;refseq.end_3=200554160;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2106;refseq.mrnaCoord_2=1689;refseq.mrnaCoord_3=1993;refseq.name2_1=LGR6;refseq.name2_2=LGR6;refseq.name2_3=LGR6;refseq.name_1=NM_001017403;refseq.name_2=NM_001017404;refseq.name_3=NM_021636;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A702A;refseq.proteinCoordStr_2=p.A563A;refseq.proteinCoordStr_3=p.A650A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.referenceCodon_3=GCG;refseq.spliceDist_1=458;refseq.spliceDist_2=458;refseq.spliceDist_3=458;refseq.start_1=200554160;refseq.start_2=200554160;refseq.start_3=200554160;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;refseq.variantCodon_3=GCA;set=Intersection GT 1/1
|
|
chr1 200554436 . T C 426.12 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=98.95;MQ0=0;OQ=4040.47;QD=36.08;RankSumP=1.00000;SB=-2018.78;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2382T>C;refseq.codingCoordStr_2=c.1965T>C;refseq.codingCoordStr_3=c.2226T>C;refseq.codonCoord_1=794;refseq.codonCoord_2=655;refseq.codonCoord_3=742;refseq.end_1=200554436;refseq.end_2=200554436;refseq.end_3=200554436;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2382;refseq.mrnaCoord_2=1965;refseq.mrnaCoord_3=2269;refseq.name2_1=LGR6;refseq.name2_2=LGR6;refseq.name2_3=LGR6;refseq.name_1=NM_001017403;refseq.name_2=NM_001017404;refseq.name_3=NM_021636;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.F794F;refseq.proteinCoordStr_2=p.F655F;refseq.proteinCoordStr_3=p.F742F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.referenceCodon_3=TTT;refseq.spliceDist_1=734;refseq.spliceDist_2=734;refseq.spliceDist_3=734;refseq.start_1=200554436;refseq.start_2=200554436;refseq.start_3=200554436;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantAA_3=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;refseq.variantCodon_3=TTC;set=Intersection GT 1/1
|
|
chr1 200841407 . G A 238.50 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=5.17;MQ=90.44;MQ0=0;OQ=8217.83;QD=39.70;RankSumP=1.00000;SB=-3800.59;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.117C>T;refseq.codingCoordStr_2=c.117C>T;refseq.codonCoord_1=39;refseq.codonCoord_2=39;refseq.end_1=200841407;refseq.end_2=200841407;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=310;refseq.mrnaCoord_2=300;refseq.name2_1=SYT2;refseq.name2_2=SYT2;refseq.name_1=NM_001136504;refseq.name_2=NM_177402;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S39S;refseq.proteinCoordStr_2=p.S39S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.spliceDist_1=-62;refseq.spliceDist_2=-62;refseq.start_1=200841407;refseq.start_2=200841407;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;set=Intersection GT 1/1
|
|
chr1 200972078 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=267;Dels=0.00;HRun=1;HaplotypeScore=12.09;MQ=98.49;MQ0=0;OQ=6091.61;QD=22.82;RankSumP=0.137342;SB=-2376.17;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3150C>G;refseq.codonCoord=1050;refseq.end=200972078;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3266;refseq.name=NM_006618;refseq.name2=KDM5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1050P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=66;refseq.start=200972078;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 0/1
|
|
chr1 200981907 . G A 337.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=303;Dels=0.00;HRun=0;HaplotypeScore=8.12;MQ=98.05;MQ0=0;OQ=5158.47;QD=17.02;RankSumP=0.282285;SB=-1485.29;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2184C>T;refseq.codonCoord=728;refseq.end=200981907;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2300;refseq.name=NM_006618;refseq.name2=KDM5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y728Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-15;refseq.start=200981907;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/0
|
|
chr1 200984825 . G A 349.74 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=284;Dels=0.00;HRun=0;HaplotypeScore=8.00;MQ=98.87;MQ0=0;OQ=5520.83;QD=19.44;RankSumP=0.160558;SB=-1426.60;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1887C>T;refseq.codonCoord=629;refseq.end=200984825;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2003;refseq.name=NM_006618;refseq.name2=KDM5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.H629H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=66;refseq.start=200984825;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 200991182 . T C 35.18 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=127;Dels=0.00;HRun=2;HaplotypeScore=19.09;MQ=98.88;MQ0=0;QD=0.28;RankSumP=0.00000;SB=107.39;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1378A>G;refseq.codonCoord=460;refseq.end=200991182;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1494;refseq.name=NM_006618;refseq.name2=KDM5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.N460D;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=22;refseq.start=200991182;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=FilteredInAll GT 1/0
|
|
chr1 200999861 . C T 315.83 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=178;Dels=0.00;HRun=0;HaplotypeScore=5.76;MQ=98.50;MQ0=0;OQ=2998.58;QD=16.85;RankSumP=0.473793;SB=-1029.39;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.747G>A;refseq.codonCoord=249;refseq.end=200999861;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=863;refseq.name=NM_006618;refseq.name2=KDM5B;refseq.positionType=CDS;refseq.proteinCoordStr=p.T249T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=36;refseq.start=200999861;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 201116889 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.212T>G;refseq.codonCoord=71;refseq.end=201116889;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=249;refseq.name=NM_002871;refseq.name2=RABIF;refseq.positionType=CDS;refseq.proteinCoordStr=p.V71G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=86;refseq.start=201116889;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 201186777 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.45T>C;refseq.codingCoordStr_2=c.45T>C;refseq.codonCoord_1=15;refseq.codonCoord_2=15;refseq.end_1=201186777;refseq.end_2=201186777;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=304;refseq.mrnaCoord_2=312;refseq.name2_1=ADIPOR1;refseq.name2_2=ADIPOR1;refseq.name_1=NM_001127687;refseq.name_2=NM_015999;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A15A;refseq.proteinCoordStr_2=p.A15A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-97;refseq.spliceDist_2=-97;refseq.start_1=201186777;refseq.start_2=201186777;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=FilteredInAll GT 0/1
|
|
chr1 201411123 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=4;RankSumP=0.00000;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.295A>G;refseq.codonCoord=99;refseq.end=201411123;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=354;refseq.name=NM_004997;refseq.name2=MYBPH;refseq.positionType=CDS;refseq.proteinCoordStr=p.R99G;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-46;refseq.start=201411123;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 201411332 . T G 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=2.46149e-06;SecondBestBaseQ=16;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.175A>C;refseq.codonCoord=59;refseq.end=201411332;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=234;refseq.name=NM_004997;refseq.name2=MYBPH;refseq.positionType=CDS;refseq.proteinCoordStr=p.T59P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-31;refseq.start=201411332;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 201411335 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=1.26667e-09;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.172T>C;refseq.codonCoord=58;refseq.end=201411335;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=231;refseq.name=NM_004997;refseq.name2=MYBPH;refseq.positionType=CDS;refseq.proteinCoordStr=p.S58P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-34;refseq.start=201411335;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 201415256 . A G 226.23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1440.92;QD=36.95;RankSumP=1.00000;SB=-356.64;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1092T>C;refseq.codonCoord=364;refseq.end=201415256;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1263;refseq.name=NM_001276;refseq.name2=CHI3L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.C364C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=81;refseq.start=201415256;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 1/1
|
|
chr1 201419424 . T C 72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=182;Dels=0.00;HRun=2;HaplotypeScore=8.74;MQ=98.85;MQ0=0;OQ=7324.16;QD=40.24;RankSumP=1.00000;SB=-2819.44;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.433A>G;refseq.codonCoord=145;refseq.end=201419424;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=604;refseq.name=NM_001276;refseq.name2=CHI3L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R145G;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=-33;refseq.start=201419424;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 201583785 . C T 241.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=765.37;QD=40.28;RankSumP=1.00000;SB=-273.02;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.237G>A;refseq.codonCoord=79;refseq.end=201583785;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=373;refseq.name=NM_002023;refseq.name2=FMOD;refseq.positionType=CDS;refseq.proteinCoordStr=p.E79E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=244;refseq.start=201583785;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 201719032 . G A 162.86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=98.51;MQ0=0;OQ=1255.92;QD=19.32;RankSumP=0.598317;SB=-642.10;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.97G>A;refseq.codingCoordStr_2=c.97G>A;refseq.codonCoord_1=33;refseq.codonCoord_2=33;refseq.end_1=201719032;refseq.end_2=201719032;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=297;refseq.mrnaCoord_2=287;refseq.name2_1=PRELP;refseq.name2_2=PRELP;refseq.name_1=NM_002725;refseq.name_2=NM_201348;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G33R;refseq.proteinCoordStr_2=p.G33R;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=113;refseq.spliceDist_2=113;refseq.start_1=201719032;refseq.start_2=201719032;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=AGG;refseq.variantCodon_2=AGG;set=Intersection GT 1/0
|
|
chr1 201719343 . C T 169.16 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=176;Dels=0.00;HRun=0;HaplotypeScore=7.10;MQ=98.87;MQ0=0;OQ=2637.40;QD=14.99;RankSumP=0.0324030;SB=-1054.54;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.408C>T;refseq.codingCoordStr_2=c.408C>T;refseq.codonCoord_1=136;refseq.codonCoord_2=136;refseq.end_1=201719343;refseq.end_2=201719343;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=608;refseq.mrnaCoord_2=598;refseq.name2_1=PRELP;refseq.name2_2=PRELP;refseq.name_1=NM_002725;refseq.name_2=NM_201348;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N136N;refseq.proteinCoordStr_2=p.N136N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=424;refseq.spliceDist_2=424;refseq.start_1=201719343;refseq.start_2=201719343;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 0/1
|
|
chr1 201738742 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=218;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=98.74;MQ0=0;OQ=4926.95;QD=22.60;RankSumP=0.205395;SB=-1874.55;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.810G>A;refseq.codonCoord=270;refseq.end=201738742;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=926;refseq.name=NM_014359;refseq.name2=OPTC;refseq.positionType=CDS;refseq.proteinCoordStr=p.L270L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-19;refseq.start=201738742;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/0
|
|
chr1 201919067 . A G 360.59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=271;Dels=0.00;HRun=0;HaplotypeScore=7.63;MQ=98.65;MQ0=0;OQ=4865.74;QD=17.95;RankSumP=0.163054;SB=-1700.61;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.111A>G;refseq.codingCoordStr_2=c.111A>G;refseq.codonCoord_1=37;refseq.codonCoord_2=37;refseq.end_1=201919067;refseq.end_2=201919067;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=995;refseq.mrnaCoord_2=995;refseq.name2_1=ATP2B4;refseq.name2_2=ATP2B4;refseq.name_1=NM_001001396;refseq.name_2=NM_001684;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S37S;refseq.proteinCoordStr_2=p.S37S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=-83;refseq.spliceDist_2=-83;refseq.start_1=201919067;refseq.start_2=201919067;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;set=Intersection GT 0/1
|
|
chr1 201934032 . T C 191.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=501;Dels=0.00;HRun=0;HaplotypeScore=5.57;MQ=98.82;MQ0=0;OQ=10372.84;QD=20.70;RankSumP=0.463760;SB=-4061.73;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.318T>C;refseq.codingCoordStr_2=c.318T>C;refseq.codonCoord_1=106;refseq.codonCoord_2=106;refseq.end_1=201934032;refseq.end_2=201934032;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1202;refseq.mrnaCoord_2=1202;refseq.name2_1=ATP2B4;refseq.name2_2=ATP2B4;refseq.name_1=NM_001001396;refseq.name_2=NM_001684;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L106L;refseq.proteinCoordStr_2=p.L106L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTT;refseq.referenceCodon_2=CTT;refseq.spliceDist_1=-74;refseq.spliceDist_2=-74;refseq.start_1=201934032;refseq.start_2=201934032;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;set=Intersection GT 1/0
|
|
chr1 201939433 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.968T>C;refseq.codingCoordStr_2=c.968T>C;refseq.codonCoord_1=323;refseq.codonCoord_2=323;refseq.end_1=201939433;refseq.end_2=201939433;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1852;refseq.mrnaCoord_2=1852;refseq.name2_1=ATP2B4;refseq.name2_2=ATP2B4;refseq.name_1=NM_001001396;refseq.name_2=NM_001684;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I323T;refseq.proteinCoordStr_2=p.I323T;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.start_1=201939433;refseq.start_2=201939433;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=FilteredInAll GT 1/0
|
|
chr1 201959698 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3091T>G;refseq.codingCoordStr_2=c.3091T>G;refseq.codonCoord_1=1031;refseq.codonCoord_2=1031;refseq.end_1=201959698;refseq.end_2=201959698;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3975;refseq.mrnaCoord_2=3975;refseq.name2_1=ATP2B4;refseq.name2_2=ATP2B4;refseq.name_1=NM_001001396;refseq.name_2=NM_001684;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.W1031G;refseq.proteinCoordStr_2=p.W1031G;refseq.referenceAA_1=Trp;refseq.referenceAA_2=Trp;refseq.referenceCodon_1=TGG;refseq.referenceCodon_2=TGG;refseq.spliceDist_1=-42;refseq.spliceDist_2=-42;refseq.start_1=201959698;refseq.start_2=201959698;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 202054323 . T C 274.50 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=305;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.29;MQ0=0;OQ=12008.00;QD=39.37;RankSumP=1.00000;SB=-4515.19;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.57T>C;refseq.codonCoord=19;refseq.end=202054323;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=673;refseq.name=NM_014827;refseq.name2=ZC3H11A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G19G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=3;refseq.spliceInfo=splice-acceptor_3;refseq.start=202054323;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 202397809 . T G 275.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=98.80;MQ0=0;OQ=2528.35;QD=37.18;RankSumP=1.00000;SB=-874.97;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.204A>C;refseq.codonCoord=68;refseq.end=202397809;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=248;refseq.name=NM_000537;refseq.name2=REN;refseq.positionType=CDS;refseq.proteinCoordStr=p.T68T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-46;refseq.start=202397809;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 1/1
|
|
chr1 202426410 . G C 89.61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=99.00;MQ0=0;OQ=152.33;QD=19.04;RankSumP=0.598214;SB=-85.81;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.242C>G;refseq.codonCoord=81;refseq.end=202426410;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=396;refseq.name=NM_002256;refseq.name2=KISS1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P81R;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=139;refseq.start=202426410;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 0/1
|
|
chr1 202428570 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=98.08;MQ0=0;OQ=497.68;QD=7.66;RankSumP=0.0735621;SB=-175.73;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.58G>A;refseq.codonCoord=20;refseq.end=202428570;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=212;refseq.name=NM_002256;refseq.name2=KISS1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E20K;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-46;refseq.start=202428570;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 0/1
|
|
chr1 202438683 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1106.66;QD=22.58;RankSumP=0.708725;SB=-378.98;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.81C>G;refseq.codonCoord=27;refseq.end=202438683;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=267;refseq.name=NM_198447;refseq.name2=GOLT1A;refseq.positionType=CDS;refseq.proteinCoordStr=p.L27L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=-37;refseq.start=202438683;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 0/1
|
|
chr1 202438719 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.58;MQ0=0;OQ=548.10;QD=13.37;RankSumP=0.569119;SB=-147.55;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.45C>T;refseq.codonCoord=15;refseq.end=202438719;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=231;refseq.name=NM_198447;refseq.name2=GOLT1A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T15T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=20;refseq.start=202438719;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/0
|
|
chr1 202464832 . A G 317.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=147;Dels=0.00;HRun=0;HaplotypeScore=5.26;MQ=98.39;MQ0=0;OQ=5211.72;QD=35.45;RankSumP=1.00000;SB=-2216.48;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2607T>C;refseq.codonCoord=869;refseq.end=202464832;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2924;refseq.name=NM_014935;refseq.name2=PLEKHA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.H869H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=24;refseq.start=202464832;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 202466237 . C T 34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=1.90;MQ=99.00;MQ0=0;OQ=495.69;QD=29.16;RankSumP=1.00000;SB=-141.01;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2510G>A;refseq.codonCoord=837;refseq.end=202466237;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2827;refseq.name=NM_014935;refseq.name2=PLEKHA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.R837K;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-74;refseq.start=202466237;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 202484957 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=204;Dels=0.00;HRun=2;HaplotypeScore=25.89;MQ=97.95;MQ0=0;OQ=60.86;QD=0.30;RankSumP=0.00000;SB=351.11;SecondBestBaseQ=17;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1652T>G;refseq.codonCoord=551;refseq.end=202484957;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1969;refseq.name=NM_014935;refseq.name2=PLEKHA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.V551G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-23;refseq.start=202484957;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 202504039 . C T 442.44 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.19;MQ0=0;OQ=4818.95;QD=40.16;RankSumP=1.00000;SB=-1369.28;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.127G>A;refseq.codonCoord=43;refseq.end=202504039;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=444;refseq.name=NM_014935;refseq.name2=PLEKHA6;refseq.positionType=CDS;refseq.proteinCoordStr=p.V43I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=25;refseq.start=202504039;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 202646240 . T C 314.54 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=99.00;MQ0=0;OQ=2657.63;QD=35.91;RankSumP=1.00000;SB=-435.55;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.923A>G;refseq.codonCoord=308;refseq.end=202646240;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1328;refseq.name=NM_032833;refseq.name2=PPP1R15B;refseq.positionType=CDS;refseq.proteinCoordStr=p.N308S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-998;refseq.start=202646240;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 202660638 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4870T>G;refseq.codonCoord=1624;refseq.end=202660638;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5349;refseq.name=NM_002646;refseq.name2=PIK3C2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.F1624V;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=154;refseq.start=202660638;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=FilteredInAll GT 0/1
|
|
chr1 202668127 . C A 21.69 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=164;Dels=0.00;HRun=1;HaplotypeScore=13.02;MQ=98.19;MQ0=0;QD=0.13;RankSumP=0.00000;SB=309.05;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3979G>T;refseq.codonCoord=1327;refseq.end=202668127;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4458;refseq.name=NM_002646;refseq.name2=PIK3C2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1327L;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=26;refseq.start=202668127;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=FilteredInAll GT 1/0
|
|
chr1 202704957 . C T 350.72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=98.77;MQ0=0;OQ=3797.46;QD=42.19;RankSumP=1.00000;SB=-1193.06;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.597G>A;refseq.codonCoord=199;refseq.end=202704957;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1076;refseq.name=NM_002646;refseq.name2=PIK3C2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.P199P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-337;refseq.start=202704957;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/1
|
|
chr1 202705266 . G T 242.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=221;Dels=0.00;HRun=0;HaplotypeScore=5.87;MQ=98.54;MQ0=0;OQ=7539.11;QD=34.11;RankSumP=1.00000;SB=-3760.02;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.288C>A;refseq.codonCoord=96;refseq.end=202705266;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=767;refseq.name=NM_002646;refseq.name2=PIK3C2B;refseq.positionType=CDS;refseq.proteinCoordStr=p.L96L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=372;refseq.start=202705266;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/1
|
|
chr1 202853670 . G A 257.07 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=143;Dels=0.00;HRun=1;HaplotypeScore=4.33;MQ=98.38;MQ0=0;OQ=2588.05;QD=18.10;RankSumP=0.494200;SB=-1186.15;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2074C>T;refseq.codingCoordStr_2=c.2074C>T;refseq.codonCoord_1=692;refseq.codonCoord_2=692;refseq.end_1=202853670;refseq.end_2=202853670;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2462;refseq.mrnaCoord_2=2450;refseq.name2_1=LRRN2;refseq.name2_2=LRRN2;refseq.name_1=NM_006338;refseq.name_2=NM_201630;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P692S;refseq.proteinCoordStr_2=p.P692S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=-745;refseq.spliceDist_2=-745;refseq.start_1=202853670;refseq.start_2=202853670;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCA;refseq.variantCodon_2=TCA;set=Intersection GT 1/0
|
|
chr1 202853863 . G A 152.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=98.83;MQ0=0;OQ=501.08;QD=14.32;RankSumP=0.440815;SB=-240.73;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1881C>T;refseq.codingCoordStr_2=c.1881C>T;refseq.codonCoord_1=627;refseq.codonCoord_2=627;refseq.end_1=202853863;refseq.end_2=202853863;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2269;refseq.mrnaCoord_2=2257;refseq.name2_1=LRRN2;refseq.name2_2=LRRN2;refseq.name_1=NM_006338;refseq.name_2=NM_201630;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D627D;refseq.proteinCoordStr_2=p.D627D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.spliceDist_1=-938;refseq.spliceDist_2=-938;refseq.start_1=202853863;refseq.start_2=202853863;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;set=Intersection GT 1/0
|
|
chr1 202854192 . G C 179.03 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=4.24;MQ=98.54;MQ0=0;OQ=1810.26;QD=18.86;RankSumP=0.333467;SB=-598.79;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1552C>G;refseq.codingCoordStr_2=c.1552C>G;refseq.codonCoord_1=518;refseq.codonCoord_2=518;refseq.end_1=202854192;refseq.end_2=202854192;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1940;refseq.mrnaCoord_2=1928;refseq.name2_1=LRRN2;refseq.name2_2=LRRN2;refseq.name_1=NM_006338;refseq.name_2=NM_201630;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L518V;refseq.proteinCoordStr_2=p.L518V;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.spliceDist_1=-1267;refseq.spliceDist_2=-1267;refseq.start_1=202854192;refseq.start_2=202854192;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTC;refseq.variantCodon_2=GTC;set=Intersection GT 0/1
|
|
chr1 202854763 . G A 233.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=98.57;MQ0=0;OQ=1810.87;QD=18.67;RankSumP=0.232877;SB=-444.50;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.981C>T;refseq.codingCoordStr_2=c.981C>T;refseq.codonCoord_1=327;refseq.codonCoord_2=327;refseq.end_1=202854763;refseq.end_2=202854763;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1369;refseq.mrnaCoord_2=1357;refseq.name2_1=LRRN2;refseq.name2_2=LRRN2;refseq.name_1=NM_006338;refseq.name_2=NM_201630;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H327H;refseq.proteinCoordStr_2=p.H327H;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=1207;refseq.spliceDist_2=1207;refseq.start_1=202854763;refseq.start_2=202854763;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAT;refseq.variantCodon_2=CAT;set=Intersection GT 1/0
|
|
chr1 202855323 . C G 98 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.000159858;SecondBestBaseQ=22;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.421G>C;refseq.codingCoordStr_2=c.421G>C;refseq.codonCoord_1=141;refseq.codonCoord_2=141;refseq.end_1=202855323;refseq.end_2=202855323;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=809;refseq.mrnaCoord_2=797;refseq.name2_1=LRRN2;refseq.name2_2=LRRN2;refseq.name_1=NM_006338;refseq.name_2=NM_201630;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A141P;refseq.proteinCoordStr_2=p.A141P;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=647;refseq.spliceDist_2=647;refseq.start_1=202855323;refseq.start_2=202855323;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 202855324 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.420G>C;refseq.codingCoordStr_2=c.420G>C;refseq.codonCoord_1=140;refseq.codonCoord_2=140;refseq.end_1=202855324;refseq.end_2=202855324;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=808;refseq.mrnaCoord_2=796;refseq.name2_1=LRRN2;refseq.name2_2=LRRN2;refseq.name_1=NM_006338;refseq.name_2=NM_201630;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L140L;refseq.proteinCoordStr_2=p.L140L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=646;refseq.spliceDist_2=646;refseq.start_1=202855324;refseq.start_2=202855324;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;set=FilteredInAll GT 1/0
|
|
chr1 202855724 . G A 186.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.19;MQ0=0;OQ=1017.93;QD=16.97;RankSumP=0.643174;SB=-202.87;SecondBestBaseQ=27;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.20C>T;refseq.codingCoordStr_2=c.20C>T;refseq.codonCoord_1=7;refseq.codonCoord_2=7;refseq.end_1=202855724;refseq.end_2=202855724;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=408;refseq.mrnaCoord_2=396;refseq.name2_1=LRRN2;refseq.name2_2=LRRN2;refseq.name_1=NM_006338;refseq.name_2=NM_201630;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P7L;refseq.proteinCoordStr_2=p.P7L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=246;refseq.spliceDist_2=246;refseq.start_1=202855724;refseq.start_2=202855724;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=Intersection GT 1/0
|
|
chr1 203190643 . C T 299.05 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=98.51;MQ0=0;OQ=1918.80;QD=18.27;RankSumP=0.423900;SB=-803.84;SecondBestBaseQ=30;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.476C>T;refseq.codingCoordStr_2=c.476C>T;refseq.codingCoordStr_3=c.458C>T;refseq.codingCoordStr_4=c.458C>T;refseq.codingCoordStr_5=c.458C>T;refseq.codingCoordStr_6=c.458C>T;refseq.codonCoord_1=159;refseq.codonCoord_2=159;refseq.codonCoord_3=153;refseq.codonCoord_4=153;refseq.codonCoord_5=153;refseq.codonCoord_6=153;refseq.end_1=203190643;refseq.end_2=203190643;refseq.end_3=203190643;refseq.end_4=203190643;refseq.end_5=203190643;refseq.end_6=203190643;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeAlternate_6=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=804;refseq.mrnaCoord_2=804;refseq.mrnaCoord_3=548;refseq.mrnaCoord_4=786;refseq.mrnaCoord_5=786;refseq.mrnaCoord_6=786;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name2_5=NFASC;refseq.name2_6=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001005389;refseq.name_3=NM_001160331;refseq.name_4=NM_001160332;refseq.name_5=NM_001160333;refseq.name_6=NM_015090;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.T159M;refseq.proteinCoordStr_2=p.T159M;refseq.proteinCoordStr_3=p.T153M;refseq.proteinCoordStr_4=p.T153M;refseq.proteinCoordStr_5=p.T153M;refseq.proteinCoordStr_6=p.T153M;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceAA_6=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.referenceCodon_3=ACG;refseq.referenceCodon_4=ACG;refseq.referenceCodon_5=ACG;refseq.referenceCodon_6=ACG;refseq.spliceDist_1=-60;refseq.spliceDist_2=-60;refseq.spliceDist_3=-60;refseq.spliceDist_4=-60;refseq.spliceDist_5=-60;refseq.spliceDist_6=-60;refseq.start_1=203190643;refseq.start_2=203190643;refseq.start_3=203190643;refseq.start_4=203190643;refseq.start_5=203190643;refseq.start_6=203190643;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantAA_3=Met;refseq.variantAA_4=Met;refseq.variantAA_5=Met;refseq.variantAA_6=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;refseq.variantCodon_3=ATG;refseq.variantCodon_4=ATG;refseq.variantCodon_5=ATG;refseq.variantCodon_6=ATG;set=Intersection GT 0/1
|
|
chr1 203206478 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.1115T>G;refseq.codingCoordStr_2=c.1115T>G;refseq.codingCoordStr_3=c.1148T>G;refseq.codingCoordStr_4=c.1148T>G;refseq.codingCoordStr_5=c.1097T>G;refseq.codingCoordStr_6=c.1148T>G;refseq.codonCoord_1=372;refseq.codonCoord_2=372;refseq.codonCoord_3=383;refseq.codonCoord_4=383;refseq.codonCoord_5=366;refseq.codonCoord_6=383;refseq.end_1=203206478;refseq.end_2=203206478;refseq.end_3=203206478;refseq.end_4=203206478;refseq.end_5=203206478;refseq.end_6=203206478;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1443;refseq.mrnaCoord_2=1443;refseq.mrnaCoord_3=1238;refseq.mrnaCoord_4=1476;refseq.mrnaCoord_5=1425;refseq.mrnaCoord_6=1476;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name2_5=NFASC;refseq.name2_6=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001005389;refseq.name_3=NM_001160331;refseq.name_4=NM_001160332;refseq.name_5=NM_001160333;refseq.name_6=NM_015090;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.V372G;refseq.proteinCoordStr_2=p.V372G;refseq.proteinCoordStr_3=p.V383G;refseq.proteinCoordStr_4=p.V383G;refseq.proteinCoordStr_5=p.V366G;refseq.proteinCoordStr_6=p.V383G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceAA_4=Val;refseq.referenceAA_5=Val;refseq.referenceAA_6=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.referenceCodon_4=GTG;refseq.referenceCodon_5=GTG;refseq.referenceCodon_6=GTG;refseq.spliceDist_1=-21;refseq.spliceDist_2=-21;refseq.spliceDist_3=-21;refseq.spliceDist_4=-21;refseq.spliceDist_5=-21;refseq.spliceDist_6=-21;refseq.start_1=203206478;refseq.start_2=203206478;refseq.start_3=203206478;refseq.start_4=203206478;refseq.start_5=203206478;refseq.start_6=203206478;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantAA_5=Gly;refseq.variantAA_6=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;refseq.variantCodon_5=GGG;refseq.variantCodon_6=GGG;set=FilteredInAll GT 1/0
|
|
chr1 203211064 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=123;Dels=0.00;HRun=2;HaplotypeScore=4.89;MQ=97.63;MQ0=0;OQ=2252.09;QD=18.31;RankSumP=0.303398;SB=-1058.16;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.1601G>A;refseq.codingCoordStr_2=c.1601G>A;refseq.codingCoordStr_3=c.1634G>A;refseq.codingCoordStr_4=c.1634G>A;refseq.codingCoordStr_5=c.1583G>A;refseq.codingCoordStr_6=c.1634G>A;refseq.codonCoord_1=534;refseq.codonCoord_2=534;refseq.codonCoord_3=545;refseq.codonCoord_4=545;refseq.codonCoord_5=528;refseq.codonCoord_6=545;refseq.end_1=203211064;refseq.end_2=203211064;refseq.end_3=203211064;refseq.end_4=203211064;refseq.end_5=203211064;refseq.end_6=203211064;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeAlternate_5=A;refseq.haplotypeAlternate_6=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1929;refseq.mrnaCoord_2=1929;refseq.mrnaCoord_3=1724;refseq.mrnaCoord_4=1962;refseq.mrnaCoord_5=1911;refseq.mrnaCoord_6=1962;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name2_5=NFASC;refseq.name2_6=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001005389;refseq.name_3=NM_001160331;refseq.name_4=NM_001160332;refseq.name_5=NM_001160333;refseq.name_6=NM_015090;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.R534K;refseq.proteinCoordStr_2=p.R534K;refseq.proteinCoordStr_3=p.R545K;refseq.proteinCoordStr_4=p.R545K;refseq.proteinCoordStr_5=p.R528K;refseq.proteinCoordStr_6=p.R545K;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceAA_5=Arg;refseq.referenceAA_6=Arg;refseq.referenceCodon_1=AGA;refseq.referenceCodon_2=AGA;refseq.referenceCodon_3=AGA;refseq.referenceCodon_4=AGA;refseq.referenceCodon_5=AGA;refseq.referenceCodon_6=AGA;refseq.spliceDist_1=43;refseq.spliceDist_2=43;refseq.spliceDist_3=43;refseq.spliceDist_4=43;refseq.spliceDist_5=43;refseq.spliceDist_6=43;refseq.start_1=203211064;refseq.start_2=203211064;refseq.start_3=203211064;refseq.start_4=203211064;refseq.start_5=203211064;refseq.start_6=203211064;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantAA_3=Lys;refseq.variantAA_4=Lys;refseq.variantAA_5=Lys;refseq.variantAA_6=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;refseq.variantCodon_3=AAA;refseq.variantCodon_4=AAA;refseq.variantCodon_5=AAA;refseq.variantCodon_6=AAA;set=Intersection GT 1/0
|
|
chr1 203211077 . G A 221.09 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=97.79;MQ0=0;OQ=2241.04;QD=18.83;RankSumP=0.208695;SB=-988.57;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.1614G>A;refseq.codingCoordStr_2=c.1614G>A;refseq.codingCoordStr_3=c.1647G>A;refseq.codingCoordStr_4=c.1647G>A;refseq.codingCoordStr_5=c.1596G>A;refseq.codingCoordStr_6=c.1647G>A;refseq.codonCoord_1=538;refseq.codonCoord_2=538;refseq.codonCoord_3=549;refseq.codonCoord_4=549;refseq.codonCoord_5=532;refseq.codonCoord_6=549;refseq.end_1=203211077;refseq.end_2=203211077;refseq.end_3=203211077;refseq.end_4=203211077;refseq.end_5=203211077;refseq.end_6=203211077;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeAlternate_5=A;refseq.haplotypeAlternate_6=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1942;refseq.mrnaCoord_2=1942;refseq.mrnaCoord_3=1737;refseq.mrnaCoord_4=1975;refseq.mrnaCoord_5=1924;refseq.mrnaCoord_6=1975;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name2_5=NFASC;refseq.name2_6=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001005389;refseq.name_3=NM_001160331;refseq.name_4=NM_001160332;refseq.name_5=NM_001160333;refseq.name_6=NM_015090;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.T538T;refseq.proteinCoordStr_2=p.T538T;refseq.proteinCoordStr_3=p.T549T;refseq.proteinCoordStr_4=p.T549T;refseq.proteinCoordStr_5=p.T532T;refseq.proteinCoordStr_6=p.T549T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceAA_6=Thr;refseq.referenceCodon_1=ACG;refseq.referenceCodon_2=ACG;refseq.referenceCodon_3=ACG;refseq.referenceCodon_4=ACG;refseq.referenceCodon_5=ACG;refseq.referenceCodon_6=ACG;refseq.spliceDist_1=56;refseq.spliceDist_2=56;refseq.spliceDist_3=56;refseq.spliceDist_4=56;refseq.spliceDist_5=56;refseq.spliceDist_6=56;refseq.start_1=203211077;refseq.start_2=203211077;refseq.start_3=203211077;refseq.start_4=203211077;refseq.start_5=203211077;refseq.start_6=203211077;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Thr;refseq.variantAA_4=Thr;refseq.variantAA_5=Thr;refseq.variantAA_6=Thr;refseq.variantCodon_1=ACA;refseq.variantCodon_2=ACA;refseq.variantCodon_3=ACA;refseq.variantCodon_4=ACA;refseq.variantCodon_5=ACA;refseq.variantCodon_6=ACA;set=Intersection GT 1/0
|
|
chr1 203211097 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=3;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.1634T>G;refseq.codingCoordStr_2=c.1634T>G;refseq.codingCoordStr_3=c.1667T>G;refseq.codingCoordStr_4=c.1667T>G;refseq.codingCoordStr_5=c.1616T>G;refseq.codingCoordStr_6=c.1667T>G;refseq.codonCoord_1=545;refseq.codonCoord_2=545;refseq.codonCoord_3=556;refseq.codonCoord_4=556;refseq.codonCoord_5=539;refseq.codonCoord_6=556;refseq.end_1=203211097;refseq.end_2=203211097;refseq.end_3=203211097;refseq.end_4=203211097;refseq.end_5=203211097;refseq.end_6=203211097;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1962;refseq.mrnaCoord_2=1962;refseq.mrnaCoord_3=1757;refseq.mrnaCoord_4=1995;refseq.mrnaCoord_5=1944;refseq.mrnaCoord_6=1995;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name2_5=NFASC;refseq.name2_6=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001005389;refseq.name_3=NM_001160331;refseq.name_4=NM_001160332;refseq.name_5=NM_001160333;refseq.name_6=NM_015090;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.V545G;refseq.proteinCoordStr_2=p.V545G;refseq.proteinCoordStr_3=p.V556G;refseq.proteinCoordStr_4=p.V556G;refseq.proteinCoordStr_5=p.V539G;refseq.proteinCoordStr_6=p.V556G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceAA_4=Val;refseq.referenceAA_5=Val;refseq.referenceAA_6=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.referenceCodon_4=GTG;refseq.referenceCodon_5=GTG;refseq.referenceCodon_6=GTG;refseq.spliceDist_1=-73;refseq.spliceDist_2=-73;refseq.spliceDist_3=-73;refseq.spliceDist_4=-73;refseq.spliceDist_5=-73;refseq.spliceDist_6=-73;refseq.start_1=203211097;refseq.start_2=203211097;refseq.start_3=203211097;refseq.start_4=203211097;refseq.start_5=203211097;refseq.start_6=203211097;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantAA_5=Gly;refseq.variantAA_6=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;refseq.variantCodon_5=GGG;refseq.variantCodon_6=GGG;set=FilteredInAll GT 1/0
|
|
chr1 203211159 . A G 194.65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=97.64;MQ0=0;OQ=1951.99;QD=18.07;RankSumP=0.0428477;SB=-765.89;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.1696A>G;refseq.codingCoordStr_2=c.1696A>G;refseq.codingCoordStr_3=c.1729A>G;refseq.codingCoordStr_4=c.1729A>G;refseq.codingCoordStr_5=c.1678A>G;refseq.codingCoordStr_6=c.1729A>G;refseq.codonCoord_1=566;refseq.codonCoord_2=566;refseq.codonCoord_3=577;refseq.codonCoord_4=577;refseq.codonCoord_5=560;refseq.codonCoord_6=577;refseq.end_1=203211159;refseq.end_2=203211159;refseq.end_3=203211159;refseq.end_4=203211159;refseq.end_5=203211159;refseq.end_6=203211159;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=2024;refseq.mrnaCoord_2=2024;refseq.mrnaCoord_3=1819;refseq.mrnaCoord_4=2057;refseq.mrnaCoord_5=2006;refseq.mrnaCoord_6=2057;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name2_5=NFASC;refseq.name2_6=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001005389;refseq.name_3=NM_001160331;refseq.name_4=NM_001160332;refseq.name_5=NM_001160333;refseq.name_6=NM_015090;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.I566V;refseq.proteinCoordStr_2=p.I566V;refseq.proteinCoordStr_3=p.I577V;refseq.proteinCoordStr_4=p.I577V;refseq.proteinCoordStr_5=p.I560V;refseq.proteinCoordStr_6=p.I577V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.referenceCodon_3=ATT;refseq.referenceCodon_4=ATT;refseq.referenceCodon_5=ATT;refseq.referenceCodon_6=ATT;refseq.spliceDist_1=-11;refseq.spliceDist_2=-11;refseq.spliceDist_3=-11;refseq.spliceDist_4=-11;refseq.spliceDist_5=-11;refseq.spliceDist_6=-11;refseq.start_1=203211159;refseq.start_2=203211159;refseq.start_3=203211159;refseq.start_4=203211159;refseq.start_5=203211159;refseq.start_6=203211159;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;refseq.variantCodon_3=GTT;refseq.variantCodon_4=GTT;refseq.variantCodon_5=GTT;refseq.variantCodon_6=GTT;set=Intersection GT 0/1
|
|
chr1 203212437 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=5.11;MQ=98.77;MQ0=0;OQ=1130.15;QD=13.78;RankSumP=0.365760;SB=-275.12;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.1722C>T;refseq.codingCoordStr_2=c.1722C>T;refseq.codingCoordStr_3=c.1755C>T;refseq.codingCoordStr_4=c.1755C>T;refseq.codingCoordStr_5=c.1704C>T;refseq.codingCoordStr_6=c.1755C>T;refseq.codonCoord_1=574;refseq.codonCoord_2=574;refseq.codonCoord_3=585;refseq.codonCoord_4=585;refseq.codonCoord_5=568;refseq.codonCoord_6=585;refseq.end_1=203212437;refseq.end_2=203212437;refseq.end_3=203212437;refseq.end_4=203212437;refseq.end_5=203212437;refseq.end_6=203212437;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeAlternate_6=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=2050;refseq.mrnaCoord_2=2050;refseq.mrnaCoord_3=1845;refseq.mrnaCoord_4=2083;refseq.mrnaCoord_5=2032;refseq.mrnaCoord_6=2083;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name2_5=NFASC;refseq.name2_6=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001005389;refseq.name_3=NM_001160331;refseq.name_4=NM_001160332;refseq.name_5=NM_001160333;refseq.name_6=NM_015090;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.D574D;refseq.proteinCoordStr_2=p.D574D;refseq.proteinCoordStr_3=p.D585D;refseq.proteinCoordStr_4=p.D585D;refseq.proteinCoordStr_5=p.D568D;refseq.proteinCoordStr_6=p.D585D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceAA_3=Asp;refseq.referenceAA_4=Asp;refseq.referenceAA_5=Asp;refseq.referenceAA_6=Asp;refseq.referenceCodon_1=GAC;refseq.referenceCodon_2=GAC;refseq.referenceCodon_3=GAC;refseq.referenceCodon_4=GAC;refseq.referenceCodon_5=GAC;refseq.referenceCodon_6=GAC;refseq.spliceDist_1=16;refseq.spliceDist_2=16;refseq.spliceDist_3=16;refseq.spliceDist_4=16;refseq.spliceDist_5=16;refseq.spliceDist_6=16;refseq.start_1=203212437;refseq.start_2=203212437;refseq.start_3=203212437;refseq.start_4=203212437;refseq.start_5=203212437;refseq.start_6=203212437;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantAA_3=Asp;refseq.variantAA_4=Asp;refseq.variantAA_5=Asp;refseq.variantAA_6=Asp;refseq.variantCodon_1=GAT;refseq.variantCodon_2=GAT;refseq.variantCodon_3=GAT;refseq.variantCodon_4=GAT;refseq.variantCodon_5=GAT;refseq.variantCodon_6=GAT;set=Intersection GT 0/1
|
|
chr1 203215282 . A G 93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=795;Dels=0.00;HRun=0;HaplotypeScore=29.53;MQ=98.38;MQ0=0;OQ=26848.32;QD=33.77;RankSumP=1.00000;SB=-10863.92;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.2148A>G;refseq.codingCoordStr_2=c.2181A>G;refseq.codingCoordStr_3=c.2136A>G;refseq.codingCoordStr_4=c.2136A>G;refseq.codonCoord_1=716;refseq.codonCoord_2=727;refseq.codonCoord_3=712;refseq.codonCoord_4=712;refseq.end_1=203215282;refseq.end_2=203215282;refseq.end_3=203215282;refseq.end_4=203215282;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=2476;refseq.mrnaCoord_2=2271;refseq.mrnaCoord_3=2464;refseq.mrnaCoord_4=2464;refseq.name2_1=NFASC;refseq.name2_2=NFASC;refseq.name2_3=NFASC;refseq.name2_4=NFASC;refseq.name_1=NM_001005388;refseq.name_2=NM_001160331;refseq.name_3=NM_001160332;refseq.name_4=NM_015090;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.P716P;refseq.proteinCoordStr_2=p.P727P;refseq.proteinCoordStr_3=p.P712P;refseq.proteinCoordStr_4=p.P712P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.referenceCodon_3=CCA;refseq.referenceCodon_4=CCA;refseq.spliceDist_1=-29;refseq.spliceDist_2=-29;refseq.spliceDist_3=-29;refseq.spliceDist_4=-29;refseq.start_1=203215282;refseq.start_2=203215282;refseq.start_3=203215282;refseq.start_4=203215282;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCG;refseq.variantCodon_2=CCG;refseq.variantCodon_3=CCG;refseq.variantCodon_4=CCG;set=Intersection GT 1/1
|
|
chr1 203294360 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=0.26;MQ=98.85;MQ0=0;OQ=830.34;QD=12.97;RankSumP=0.0677120;SB=-386.85;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.433G>A;refseq.codonCoord=145;refseq.end=203294360;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=702;refseq.name=NM_005076;refseq.name2=CNTN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A145T;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=42;refseq.start=203294360;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/0
|
|
chr1 203294975 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.628A>C;refseq.codonCoord=210;refseq.end=203294975;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=897;refseq.name=NM_005076;refseq.name2=CNTN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T210P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-70;refseq.start=203294975;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 203297739 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=6.17;MQ=98.72;MQ0=0;OQ=323.28;QD=11.55;RankSumP=0.0254778;SB=-105.60;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1097C>T;refseq.codonCoord=366;refseq.end=203297739;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1366;refseq.name=NM_005076;refseq.name2=CNTN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P366L;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-14;refseq.start=203297739;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 0/1
|
|
chr1 203305271 . G T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.0611381;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2155G>T;refseq.codonCoord=719;refseq.end=203305271;refseq.frame=0;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2424;refseq.name=NM_005076;refseq.name2=CNTN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G719*;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=30;refseq.start=203305271;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TGA;set=FilteredInAll GT 0/1
|
|
chr1 203305619 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=1;RankSumP=5.15999e-09;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2238C>A;refseq.codonCoord=746;refseq.end=203305619;refseq.frame=2;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2507;refseq.name=NM_005076;refseq.name2=CNTN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y746*;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=42;refseq.start=203305619;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TAA;set=FilteredInAll GT 1/0
|
|
chr1 203319562 . G A 351.21 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=98.40;MQ0=0;OQ=4478.64;QD=39.99;RankSumP=1.00000;SB=-2206.10;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.510C>T;refseq.codonCoord=170;refseq.end=203319562;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=650;refseq.name=NM_203376;refseq.name2=TMEM81;refseq.positionType=CDS;refseq.proteinCoordStr=p.L170L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=650;refseq.start=203319562;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=Intersection GT 1/1
|
|
chr1 203319842 . C T 210.06 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=360;Dels=0.00;HRun=0;HaplotypeScore=12.05;MQ=98.98;MQ0=0;OQ=15274.52;QD=42.43;RankSumP=1.00000;SB=-6878.65;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.230G>A;refseq.codonCoord=77;refseq.end=203319842;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=370;refseq.name=NM_203376;refseq.name2=TMEM81;refseq.positionType=CDS;refseq.proteinCoordStr=p.R77Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=370;refseq.start=203319842;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 203337388 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.595A>C;refseq.codonCoord=199;refseq.end=203337388;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=725;refseq.name=NM_005057;refseq.name2=RBBP5;refseq.positionType=CDS;refseq.proteinCoordStr=p.T199P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-38;refseq.start=203337388;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 203397036 . A G 242.22 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=224;Dels=0.00;HRun=1;HaplotypeScore=7.79;MQ=98.87;MQ0=0;OQ=8216.26;QD=36.68;RankSumP=1.00000;SB=-3450.07;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1921T>C;refseq.codingCoordStr_2=c.1921T>C;refseq.codonCoord_1=641;refseq.codonCoord_2=641;refseq.end_1=203397036;refseq.end_2=203397036;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1985;refseq.mrnaCoord_2=1985;refseq.name2_1=DSTYK;refseq.name2_2=DSTYK;refseq.name_1=NM_015375;refseq.name_2=NM_199462;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C641R;refseq.proteinCoordStr_2=p.C641R;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.start_1=203397036;refseq.start_2=203397036;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=Intersection GT 1/1
|
|
chr1 203397785 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1818+2;refseq.codingCoordStr_2=c.1818+2;refseq.end_1=203397785;refseq.end_2=203397785;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.name2_1=DSTYK;refseq.name2_2=DSTYK;refseq.name_1=NM_015375;refseq.name_2=NM_199462;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceInfo_1=splice-donor_2;refseq.spliceInfo_2=splice-donor_2;refseq.start_1=203397785;refseq.start_2=203397785;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;set=FilteredInAll GT 0/1
|
|
chr1 203397934 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1671A>C;refseq.codingCoordStr_2=c.1671A>C;refseq.codonCoord_1=557;refseq.codonCoord_2=557;refseq.end_1=203397934;refseq.end_2=203397934;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1735;refseq.mrnaCoord_2=1735;refseq.name2_1=DSTYK;refseq.name2_2=DSTYK;refseq.name_1=NM_015375;refseq.name_2=NM_199462;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P557P;refseq.proteinCoordStr_2=p.P557P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCA;refseq.referenceCodon_2=CCA;refseq.spliceDist_1=30;refseq.spliceDist_2=30;refseq.start_1=203397934;refseq.start_2=203397934;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 1/0
|
|
chr1 203477450 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=108;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=97.83;MQ0=0;OQ=1350.04;QD=12.50;RankSumP=0.0415729;SB=-625.19;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.402C>T;refseq.codonCoord=134;refseq.end=203477450;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1057;refseq.name=NM_014858;refseq.name2=TMCC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y134Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=195;refseq.start=203477450;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 0/1
|
|
chr1 203504898 . A G 199.62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=158;Dels=0.00;HRun=1;HaplotypeScore=8.82;MQ=98.41;MQ0=0;OQ=5890.42;QD=37.28;RankSumP=1.00000;SB=-2166.63;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.945A>G;refseq.codonCoord=315;refseq.end=203504898;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1600;refseq.name=NM_014858;refseq.name2=TMCC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A315A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=198;refseq.start=203504898;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 203505153 . C T 78.42 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=95.31;MQ0=0;OQ=1052.40;QD=28.44;RankSumP=1.00000;SB=-314.69;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1200C>T;refseq.codonCoord=400;refseq.end=203505153;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1855;refseq.name=NM_014858;refseq.name2=TMCC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G400G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=453;refseq.start=203505153;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 1/1
|
|
chr1 203506874 . C T 391.55 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=99.00;MQ0=0;OQ=3584.36;QD=35.14;RankSumP=1.00000;SB=-1333.72;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1686C>T;refseq.codonCoord=562;refseq.end=203506874;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2341;refseq.name=NM_014858;refseq.name2=TMCC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y562Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=4;refseq.spliceInfo=splice-acceptor_4;refseq.start=203506874;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 203539549 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=4.38;MQ=98.76;MQ0=0;OQ=915.29;QD=11.73;RankSumP=0.277787;SB=-88.84;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1539G>A;refseq.codonCoord=513;refseq.end=203539549;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1666;refseq.name=NM_030952;refseq.name2=NUAK2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L513L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=716;refseq.start=203539549;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=Intersection GT 0/1
|
|
chr1 203539606 . C G 196.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=142;Dels=0.00;HRun=1;HaplotypeScore=1.86;MQ=98.59;MQ0=0;OQ=2781.38;QD=19.59;RankSumP=0.498485;SB=-1016.08;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1482G>C;refseq.codonCoord=494;refseq.end=203539606;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1609;refseq.name=NM_030952;refseq.name2=NUAK2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L494L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=659;refseq.start=203539606;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/0
|
|
chr1 203542044 . A G 65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=441;Dels=0.00;HRun=1;HaplotypeScore=9.00;MQ=98.82;MQ0=0;OQ=18130.49;QD=41.11;RankSumP=1.00000;SB=-8791.51;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.585T>C;refseq.codonCoord=195;refseq.end=203542044;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=712;refseq.name=NM_030952;refseq.name2=NUAK2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G195G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=15;refseq.start=203542044;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 203574958 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=182;Dels=0.00;HRun=2;HaplotypeScore=6.34;MQ=98.53;MQ0=0;OQ=3799.29;QD=20.88;RankSumP=0.00167256;SB=-754.81;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.744C>T;refseq.codonCoord=248;refseq.end=203574958;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1312;refseq.name=NM_018203;refseq.name2=KLHDC8A;refseq.positionType=CDS;refseq.proteinCoordStr=p.F248F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-14;refseq.start=203574958;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=filterInsoap-gatk GT 1/0
|
|
chr1 203574991 . C T 242.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=228;Dels=0.00;HRun=0;HaplotypeScore=5.34;MQ=98.49;MQ0=0;OQ=4869.99;QD=21.36;RankSumP=0.0685433;SB=-1949.79;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.711G>A;refseq.codonCoord=237;refseq.end=203574991;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1279;refseq.name=NM_018203;refseq.name2=KLHDC8A;refseq.positionType=CDS;refseq.proteinCoordStr=p.R237R;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-47;refseq.start=203574991;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 0/1
|
|
chr1 203575537 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=3;RankSumP=0.00000;SecondBestBaseQ=15;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.399C>G;refseq.codonCoord=133;refseq.end=203575537;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=967;refseq.name=NM_018203;refseq.name2=KLHDC8A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G133G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=23;refseq.start=203575537;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 203656276 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=402;Dels=0.00;HRun=2;HaplotypeScore=3.89;MQ=98.83;MQ0=0;OQ=8388.15;QD=20.87;RankSumP=0.486451;SB=-2520.79;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.12G>A;refseq.codonCoord=4;refseq.end=203656276;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=114;refseq.name=NM_001001552;refseq.name2=LEMD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V4V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=50;refseq.start=203656276;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 0/1
|
|
chr1 203759379 . A G 24.49 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=17;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=97.53;MQ0=0;QD=3.06;RankSumP=0.428571;SB=-10.00;SecondBestBaseQ=21;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.273+3;refseq.codingCoordStr_2=c.273+3;refseq.codingCoordStr_3=c.276A>G;refseq.codonCoord_3=92;refseq.end_1=203759379;refseq.end_2=203759379;refseq.end_3=203759379;refseq.frame_3=2;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.mrnaCoord_3=538;refseq.name2_1=CDK18;refseq.name2_2=CDK18;refseq.name2_3=CDK18;refseq.name_1=NM_002596;refseq.name_2=NM_212502;refseq.name_3=NM_212503;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.proteinCoordStr_3=p.V92V;refseq.referenceAA_3=Val;refseq.referenceCodon_3=GTA;refseq.spliceDist_1=3;refseq.spliceDist_2=3;refseq.spliceDist_3=-88;refseq.spliceInfo_1=splice-donor_3;refseq.spliceInfo_2=splice-donor_3;refseq.start_1=203759379;refseq.start_2=203759379;refseq.start_3=203759379;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_3=Val;refseq.variantCodon_3=GTG;set=FilteredInAll GT 0/1
|
|
chr1 203856197 . C T 243.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=174;Dels=0.00;HRun=0;HaplotypeScore=6.67;MQ=98.86;MQ0=0;OQ=2563.38;QD=14.73;RankSumP=0.0424082;SB=-874.76;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.600G>A;refseq.codingCoordStr_2=c.600G>A;refseq.codonCoord_1=200;refseq.codonCoord_2=200;refseq.end_1=203856197;refseq.end_2=203856197;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1850;refseq.mrnaCoord_2=1850;refseq.name2_1=ELK4;refseq.name2_2=ELK4;refseq.name_1=NM_001973;refseq.name_2=NM_021795;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P200P;refseq.proteinCoordStr_2=p.P200P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCG;refseq.referenceCodon_2=CCG;refseq.spliceDist_1=393;refseq.spliceDist_2=393;refseq.start_1=203856197;refseq.start_2=203856197;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=Intersection GT 0/1
|
|
chr1 203897799 . A C 15.75 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=84;Dels=0.00;HRun=2;HaplotypeScore=9.85;MQ=97.28;MQ0=0;QD=0.19;RankSumP=0.00000;SB=110.37;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1037T>G;refseq.codonCoord=346;refseq.end=203897799;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1376;refseq.name=NM_033102;refseq.name2=SLC45A3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V346G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=79;refseq.start=203897799;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 204034508 . G A 220.22 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=228;Dels=0.00;HRun=0;HaplotypeScore=7.62;MQ=98.51;MQ0=0;OQ=7761.91;QD=34.04;RankSumP=1.00000;SB=-2712.04;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.756C>T;refseq.codonCoord=252;refseq.end=204034508;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1628;refseq.name=NM_173854;refseq.name2=SLC41A1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N252N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=59;refseq.start=204034508;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/1
|
|
chr1 204068495 . A G 191.37 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=362;Dels=0.00;HRun=0;HaplotypeScore=14.19;MQ=98.61;MQ0=0;OQ=14682.33;QD=40.56;RankSumP=1.00000;SB=-4693.93;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1139T>C;refseq.codonCoord=380;refseq.end=204068495;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1215;refseq.name=NM_152491;refseq.name2=PM20D1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I380T;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=23;refseq.start=204068495;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 204081120 . T C 427.58 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.86;MQ0=0;OQ=4925.41;QD=38.48;RankSumP=1.00000;SB=-1907.99;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.445A>G;refseq.codonCoord=149;refseq.end=204081120;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=521;refseq.name=NM_152491;refseq.name2=PM20D1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I149V;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-45;refseq.start=204081120;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/1
|
|
chr1 204312091 . G T 29 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.245G>T;refseq.codonCoord=82;refseq.end=204312091;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=639;refseq.name=NM_001123168;refseq.name2=FAM72A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G82V;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=15;refseq.start=204312091;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTT;set=soap GT 1/1
|
|
chr1 204312141 . G A 14 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.295G>A;refseq.codonCoord=99;refseq.end=204312141;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=689;refseq.name=NM_001123168;refseq.name2=FAM72A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G99R;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-61;refseq.start=204312141;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=FilteredInAll GT 1/1
|
|
chr1 204320597 . T C 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.514286;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.373T>C;refseq.codonCoord=125;refseq.end=204320597;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=767;refseq.name=NM_001123168;refseq.name2=FAM72A;refseq.positionType=CDS;refseq.proteinCoordStr=p.W125R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=18;refseq.start=204320597;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=FilteredInAll GT 1/0
|
|
chr1 204406026 . C T 229.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=259;Dels=0.00;HRun=0;HaplotypeScore=8.86;MQ=98.79;MQ0=0;OQ=4717.38;QD=18.21;RankSumP=0.344131;SB=-1165.62;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.495G>A;refseq.codonCoord=165;refseq.end=204406026;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1134;refseq.name=NM_001007544;refseq.name2=C1orf186;refseq.positionType=CDS;refseq.proteinCoordStr=p.A165A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=177;refseq.start=204406026;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 204406038 . C T 231.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=294;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=98.81;MQ0=0;OQ=5121.67;QD=17.42;RankSumP=0.429843;SB=-1595.53;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.483G>A;refseq.codonCoord=161;refseq.end=204406038;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1122;refseq.name=NM_001007544;refseq.name2=C1orf186;refseq.positionType=CDS;refseq.proteinCoordStr=p.L161L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=165;refseq.start=204406038;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 0/1
|
|
chr1 204406197 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.72;MQ0=0;OQ=1010.62;QD=16.57;RankSumP=0.721489;SB=-234.01;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.324A>G;refseq.codonCoord=108;refseq.end=204406197;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=963;refseq.name=NM_001007544;refseq.name2=C1orf186;refseq.positionType=CDS;refseq.proteinCoordStr=p.T108T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=204406197;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/0
|
|
chr1 204494133 . T C 211.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=178;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=98.84;MQ0=0;OQ=3233.06;QD=18.16;RankSumP=0.448730;SB=-1562.13;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.699T>C;refseq.codingCoordStr_2=c.699T>C;refseq.codonCoord_1=233;refseq.codonCoord_2=233;refseq.end_1=204494133;refseq.end_2=204494133;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=817;refseq.mrnaCoord_2=817;refseq.name2_1=CTSE;refseq.name2_2=CTSE;refseq.name_1=NM_001910;refseq.name_2=NM_148964;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F233F;refseq.proteinCoordStr_2=p.F233F;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.spliceDist_1=37;refseq.spliceDist_2=37;refseq.start_1=204494133;refseq.start_2=204494133;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Phe;refseq.variantAA_2=Phe;refseq.variantCodon_1=TTC;refseq.variantCodon_2=TTC;set=Intersection GT 1/0
|
|
chr1 204495426 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=166;Dels=0.00;HRun=3;HaplotypeScore=4.40;MQ=98.89;MQ0=0;OQ=2782.83;QD=16.76;RankSumP=0.00838916;SB=-772.88;SecondBestBaseQ=32;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.870T>C;refseq.codonCoord_2=290;refseq.end_1=204495574;refseq.end_2=204495426;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=988;refseq.name2_1=CTSE;refseq.name2_2=CTSE;refseq.name_1=NM_148964;refseq.name_2=NM_001910;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.P290P;refseq.referenceAA_2=Pro;refseq.referenceCodon_2=CCT;refseq.spliceDist_2=-58;refseq.start_1=204494230;refseq.start_2=204495426;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCC;set=filterInsoap-gatk GT 1/0
|
|
chr1 204714365 . A G 172.49 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=102;Dels=0.00;HRun=1;HaplotypeScore=2.86;MQ=98.32;MQ0=0;OQ=3634.26;QD=35.63;RankSumP=1.00000;SB=-1468.56;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.156A>G;refseq.codonCoord=52;refseq.end=204714365;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=524;refseq.name=NM_014002;refseq.name2=IKBKE;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q52Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=69;refseq.start=204714365;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/1
|
|
chr1 204714410 . T C 418.01 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=97.97;MQ0=0;OQ=3503.15;QD=37.27;RankSumP=1.00000;SB=-1654.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.201T>C;refseq.codonCoord=67;refseq.end=204714410;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=569;refseq.name=NM_014002;refseq.name2=IKBKE;refseq.positionType=CDS;refseq.proteinCoordStr=p.I67I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-28;refseq.start=204714410;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 204716688 . A G 141.74 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=216;Dels=0.00;HRun=0;HaplotypeScore=8.77;MQ=98.82;MQ0=0;OQ=3156.18;QD=14.61;RankSumP=0.410159;SB=-965.82;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.585A>G;refseq.codonCoord=195;refseq.end=204716688;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=953;refseq.name=NM_014002;refseq.name2=IKBKE;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q195Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=45;refseq.start=204716688;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 204717730 . G A 153.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=155.09;QD=19.39;RankSumP=0.773810;SB=-83.31;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.717G>A;refseq.codonCoord=239;refseq.end=204717730;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1085;refseq.name=NM_014002;refseq.name2=IKBKE;refseq.positionType=CDS;refseq.proteinCoordStr=p.T239T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=16;refseq.start=204717730;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/0
|
|
chr1 204747606 . A C 23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=92.73;MQ0=0;OQ=290.45;QD=26.40;RankSumP=1.00000;SB=-157.27;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.48A>C;refseq.codingCoordStr_2=c.48A>C;refseq.codonCoord_1=16;refseq.codonCoord_2=16;refseq.end_1=204747606;refseq.end_2=204747606;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=105;refseq.mrnaCoord_2=105;refseq.name2_1=RASSF5;refseq.name2_2=RASSF5;refseq.name_1=NM_182663;refseq.name_2=NM_182664;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L16L;refseq.proteinCoordStr_2=p.L16L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTA;refseq.referenceCodon_2=CTA;refseq.spliceDist_1=105;refseq.spliceDist_2=105;refseq.start_1=204747606;refseq.start_2=204747606;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTC;refseq.variantCodon_2=CTC;set=Intersection GT 1/1
|
|
chr1 204840282 . A G 79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=478;Dels=0.00;HRun=3;HaplotypeScore=4.74;MQ=98.72;MQ0=0;OQ=18492.37;QD=38.69;RankSumP=1.00000;SB=-7982.30;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.906T>C;refseq.codonCoord=302;refseq.end=204840282;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1115;refseq.name=NM_006893;refseq.name2=LGTN;refseq.positionType=CDS;refseq.proteinCoordStr=p.P302P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=4;refseq.spliceInfo=splice-acceptor_4;refseq.start=204840282;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 204970018 . A C 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=584;Dels=0.00;HRun=2;HaplotypeScore=46.78;MQ=98.49;MQ0=0;OQ=516.09;QD=0.88;RankSumP=0.00000;SB=998.21;SecondBestBaseQ=18;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.643A>C;refseq.codingCoordStr_2=c.643A>C;refseq.codonCoord_1=215;refseq.codonCoord_2=215;refseq.end_1=204970018;refseq.end_2=204970018;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=929;refseq.mrnaCoord_2=929;refseq.name2_1=MAPKAPK2;refseq.name2_2=MAPKAPK2;refseq.name_1=NM_004759;refseq.name_2=NM_032960;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T215P;refseq.proteinCoordStr_2=p.T215P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.spliceDist_1=-49;refseq.spliceDist_2=-49;refseq.start_1=204970018;refseq.start_2=204970018;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 205082580 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=98.44;MQ0=0;OQ=557.88;QD=13.28;RankSumP=0.593971;SB=-284.31;SecondBestBaseQ=31;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.524T>C;refseq.codingCoordStr_2=c.638T>C;refseq.codonCoord_1=175;refseq.codonCoord_2=213;refseq.end_1=205082580;refseq.end_2=205082580;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1463;refseq.mrnaCoord_2=663;refseq.name2_1=IL19;refseq.name2_2=IL19;refseq.name_1=NM_013371;refseq.name_2=NM_153758;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.F175S;refseq.proteinCoordStr_2=p.F213S;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceCodon_1=TTC;refseq.referenceCodon_2=TTC;refseq.spliceDist_1=86;refseq.spliceDist_2=86;refseq.start_1=205082580;refseq.start_2=205082580;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=Intersection GT 1/0
|
|
chr1 205141528 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=304;Dels=0.00;HRun=1;HaplotypeScore=17.01;MQ=98.90;MQ0=0;OQ=6042.56;QD=19.88;RankSumP=0.362278;SB=-1952.96;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.370T>C;refseq.codingCoordStr_2=c.-105T>C;refseq.codonCoord_1=124;refseq.end_1=205141528;refseq.end_2=205141528;refseq.frame_1=0;refseq.functionalClass_1=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=false;refseq.mrnaCoord_1=644;refseq.mrnaCoord_2=302;refseq.name2_1=IL24;refseq.name2_2=IL24;refseq.name_1=NM_006850;refseq.name_2=NM_181339;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=utr5;refseq.proteinCoordStr_1=p.Y124H;refseq.referenceAA_1=Tyr;refseq.referenceCodon_1=TAC;refseq.spliceDist_1=67;refseq.spliceDist_2=67;refseq.start_1=205141528;refseq.start_2=205141528;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=His;refseq.variantCodon_1=CAC;set=Intersection GT 1/0
|
|
chr1 205154058 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.47;MQ0=0;OQ=1085.23;QD=19.04;RankSumP=0.726954;SB=-158.14;SecondBestBaseQ=31;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.42G>A;refseq.codingCoordStr_3=c.42G>A;refseq.codonCoord_2=14;refseq.codonCoord_3=14;refseq.end_1=205161775;refseq.end_2=205154058;refseq.end_3=205154058;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_2=179;refseq.mrnaCoord_3=221;refseq.name2_1=FAIM3;refseq.name2_2=FAIM3;refseq.name2_3=FAIM3;refseq.name_1=NM_001142473;refseq.name_2=NM_001142472;refseq.name_3=NM_005449;refseq.numMatchingRecords=3;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.S14S;refseq.proteinCoordStr_3=p.S14S;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_2=TCG;refseq.referenceCodon_3=TCG;refseq.spliceDist_2=5;refseq.spliceDist_3=5;refseq.spliceInfo_2=splice-acceptor_5;refseq.spliceInfo_3=splice-acceptor_5;refseq.start_1=205153021;refseq.start_2=205154058;refseq.start_3=205154058;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_2=TCA;refseq.variantCodon_3=TCA;set=Intersection GT 0/1
|
|
chr1 205175739 . C T 142.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=300;Dels=0.00;HRun=1;HaplotypeScore=10.91;MQ=98.72;MQ0=0;OQ=6194.97;QD=20.65;RankSumP=0.0984792;SB=-2334.81;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1093G>A;refseq.codonCoord=365;refseq.end=205175739;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1277;refseq.name=NM_002644;refseq.name2=PIGR;refseq.positionType=CDS;refseq.proteinCoordStr=p.G365S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=48;refseq.start=205175739;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 205177559 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.88;MQ0=0;OQ=1071.91;QD=16.49;RankSumP=0.184229;SB=-176.27;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.549A>G;refseq.codonCoord=183;refseq.end=205177559;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=733;refseq.name=NM_002644;refseq.name2=PIGR;refseq.positionType=CDS;refseq.proteinCoordStr=p.V183V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=161;refseq.start=205177559;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 205262402 . A G 341.10 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=160;Dels=0.00;HRun=1;HaplotypeScore=2.70;MQ=98.72;MQ0=0;OQ=6110.32;QD=38.19;RankSumP=1.00000;SB=-2516.74;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.592T>C;refseq.codingCoordStr_2=c.1330T>C;refseq.codonCoord_1=198;refseq.codonCoord_2=444;refseq.end_1=205262402;refseq.end_2=205262402;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1403;refseq.mrnaCoord_2=1589;refseq.name2_1=C1orf116;refseq.name2_2=C1orf116;refseq.name_1=NM_001083924;refseq.name_2=NM_023938;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S198P;refseq.proteinCoordStr_2=p.S444P;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCT;refseq.referenceCodon_2=TCT;refseq.spliceDist_1=1047;refseq.spliceDist_2=1047;refseq.start_1=205262402;refseq.start_2=205262402;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;set=Intersection GT 1/1
|
|
chr1 205290873 . C A 11.71 BadSOAPSNP;ESPStandard;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=27;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=94.87;MQ0=0;QD=1.30;RankSumP=0.355556;SB=-24.87;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.126G>T;refseq.codonCoord=42;refseq.end=205290873;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=173;refseq.name=NM_018566;refseq.name2=YOD1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R42R;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=173;refseq.start=205290873;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=FilteredInAll GT 1/0
|
|
chr1 205305042 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=114;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=99.00;MQ0=0;OQ=1831.35;QD=16.06;RankSumP=0.115945;SB=-284.15;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.546C>T;refseq.codingCoordStr_2=c.546C>T;refseq.codonCoord_1=182;refseq.codonCoord_2=182;refseq.end_1=205305042;refseq.end_2=205305042;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=655;refseq.mrnaCoord_2=655;refseq.name2_1=PFKFB2;refseq.name2_2=PFKFB2;refseq.name_1=NM_001018053;refseq.name_2=NM_006212;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N182N;refseq.proteinCoordStr_2=p.N182N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=39;refseq.spliceDist_2=39;refseq.start_1=205305042;refseq.start_2=205305042;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 0/1
|
|
chr1 205310276 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1121A>G;refseq.codingCoordStr_2=c.1121A>G;refseq.codonCoord_1=374;refseq.codonCoord_2=374;refseq.end_1=205310276;refseq.end_2=205310276;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1230;refseq.mrnaCoord_2=1230;refseq.name2_1=PFKFB2;refseq.name2_2=PFKFB2;refseq.name_1=NM_001018053;refseq.name_2=NM_006212;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E374G;refseq.proteinCoordStr_2=p.E374G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.spliceDist_1=29;refseq.spliceDist_2=29;refseq.start_1=205310276;refseq.start_2=205310276;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 205318944 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=18;HRun=1;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1373T>G;refseq.codonCoord=458;refseq.end=205318944;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1482;refseq.name=NM_001018053;refseq.name2=PFKFB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V458G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=23;refseq.start=205318944;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 205336542 . C T 102.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=269;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=98.97;MQ0=0;OQ=4935.18;QD=18.35;RankSumP=0.0164235;SB=-1746.52;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.462C>T;refseq.codingCoordStr_2=c.459C>T;refseq.codingCoordStr_3=c.462C>T;refseq.codingCoordStr_4=c.459C>T;refseq.codingCoordStr_5=c.462C>T;refseq.codonCoord_1=154;refseq.codonCoord_2=153;refseq.codonCoord_3=154;refseq.codonCoord_4=153;refseq.codonCoord_5=154;refseq.end_1=205336542;refseq.end_2=205336542;refseq.end_3=205336542;refseq.end_4=205336542;refseq.end_5=205336542;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=755;refseq.mrnaCoord_2=752;refseq.mrnaCoord_3=592;refseq.mrnaCoord_4=589;refseq.mrnaCoord_5=591;refseq.name2_1=C4BPB;refseq.name2_2=C4BPB;refseq.name2_3=C4BPB;refseq.name2_4=C4BPB;refseq.name2_5=C4BPB;refseq.name_1=NM_000716;refseq.name_2=NM_001017364;refseq.name_3=NM_001017365;refseq.name_4=NM_001017366;refseq.name_5=NM_001017367;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.N154N;refseq.proteinCoordStr_2=p.N153N;refseq.proteinCoordStr_3=p.N154N;refseq.proteinCoordStr_4=p.N153N;refseq.proteinCoordStr_5=p.N154N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceAA_4=Asn;refseq.referenceAA_5=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.referenceCodon_4=AAC;refseq.referenceCodon_5=AAC;refseq.spliceDist_1=-42;refseq.spliceDist_2=-42;refseq.spliceDist_3=-42;refseq.spliceDist_4=-42;refseq.spliceDist_5=-42;refseq.start_1=205336542;refseq.start_2=205336542;refseq.start_3=205336542;refseq.start_4=205336542;refseq.start_5=205336542;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantAA_3=Asn;refseq.variantAA_4=Asn;refseq.variantAA_5=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;refseq.variantCodon_3=AAT;refseq.variantCodon_4=AAT;refseq.variantCodon_5=AAT;set=Intersection GT 0/1
|
|
chr1 205353004 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=144;Dels=0.00;HRun=5;HaplotypeScore=5.81;MQ=98.62;MQ0=0;OQ=1803.23;QD=12.52;RankSumP=0.467734;SB=-922.06;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.11C>A;refseq.codonCoord=4;refseq.end=205353004;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=205;refseq.name=NM_000715;refseq.name2=C4BPA;refseq.positionType=CDS;refseq.proteinCoordStr=p.P4Q;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=36;refseq.start=205353004;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap-filterIngatk GT 1/0
|
|
chr1 205364303 . T C 383.45 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=217;Dels=0.00;HRun=0;HaplotypeScore=2.27;MQ=98.59;MQ0=0;OQ=8251.02;QD=38.02;RankSumP=1.00000;SB=-3719.50;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.675T>C;refseq.codonCoord=225;refseq.end=205364303;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=869;refseq.name=NM_000715;refseq.name2=C4BPA;refseq.positionType=CDS;refseq.proteinCoordStr=p.G225G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=-32;refseq.start=205364303;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 205366693 . G A 246.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=305;Dels=0.00;HRun=0;HaplotypeScore=4.18;MQ=98.72;MQ0=0;OQ=5394.81;QD=17.69;RankSumP=0.371802;SB=-1496.30;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.719G>A;refseq.codonCoord=240;refseq.end=205366693;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=913;refseq.name=NM_000715;refseq.name2=C4BPA;refseq.positionType=CDS;refseq.proteinCoordStr=p.R240H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=13;refseq.start=205366693;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/0
|
|
chr1 205371523 . T C 298.88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=155;Dels=0.00;HRun=0;HaplotypeScore=6.38;MQ=98.73;MQ0=0;OQ=2635.41;QD=17.00;RankSumP=0.308819;SB=-833.72;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.899T>C;refseq.codonCoord=300;refseq.end=205371523;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1093;refseq.name=NM_000715;refseq.name2=C4BPA;refseq.positionType=CDS;refseq.proteinCoordStr=p.I300T;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=205371523;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/0
|
|
chr1 205719987 . A G 275.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=282;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=98.98;MQ0=0;OQ=5067.99;QD=17.97;RankSumP=0.308343;SB=-2032.15;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3154A>G;refseq.codingCoordStr_2=c.2977A>G;refseq.codonCoord_1=1052;refseq.codonCoord_2=993;refseq.end_1=205719987;refseq.end_2=205719987;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3273;refseq.mrnaCoord_2=3096;refseq.name2_1=CR2;refseq.name2_2=CR2;refseq.name_1=NM_001006658;refseq.name_2=NM_001877;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.I1052V;refseq.proteinCoordStr_2=p.I993V;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceCodon_1=ATT;refseq.referenceCodon_2=ATT;refseq.spliceDist_1=-35;refseq.spliceDist_2=-35;refseq.start_1=205719987;refseq.start_2=205719987;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=Intersection GT 0/1
|
|
chr1 205720018 . C A 193.77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=214;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=98.93;MQ0=0;OQ=4441.67;QD=20.76;RankSumP=0.214968;SB=-1301.32;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3185C>A;refseq.codingCoordStr_2=c.3008C>A;refseq.codonCoord_1=1062;refseq.codonCoord_2=1003;refseq.end_1=205720018;refseq.end_2=205720018;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3304;refseq.mrnaCoord_2=3127;refseq.name2_1=CR2;refseq.name2_2=CR2;refseq.name_1=NM_001006658;refseq.name_2=NM_001877;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A1062E;refseq.proteinCoordStr_2=p.A1003E;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=-4;refseq.spliceDist_2=-4;refseq.spliceInfo_1=splice-donor_-4;refseq.spliceInfo_2=splice-donor_-4;refseq.start_1=205720018;refseq.start_2=205720018;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAA;refseq.variantCodon_2=GAA;set=Intersection GT 1/0
|
|
chr1 206274462 . G A 438.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=208;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=98.75;MQ0=0;OQ=8501.64;QD=40.87;RankSumP=1.00000;SB=-2223.39;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4863C>T;refseq.codonCoord=1621;refseq.end=206274462;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5621;refseq.name=NM_025179;refseq.name2=PLXNA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y1621Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=-2;refseq.spliceInfo=splice-donor_-2;refseq.start=206274462;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/1
|
|
chr1 206285161 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=3;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3513T>C;refseq.codonCoord=1171;refseq.end=206285161;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4271;refseq.name=NM_025179;refseq.name2=PLXNA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1171P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=18;refseq.start=206285161;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 206319269 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2545T>C;refseq.codonCoord=849;refseq.end=206319269;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3303;refseq.name=NM_025179;refseq.name2=PLXNA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S849P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-42;refseq.start=206319269;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 206319338 . A C 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=11;HRun=2;RankSumP=0.00807340;SecondBestBaseQ=21;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2476T>G;refseq.codonCoord=826;refseq.end=206319338;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3234;refseq.name=NM_025179;refseq.name2=PLXNA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C826G;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=81;refseq.start=206319338;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 0/1
|
|
chr1 206338936 . A C 98 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=8.52252e-08;SecondBestBaseQ=19;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1609T>G;refseq.codonCoord=537;refseq.end=206338936;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2367;refseq.name=NM_025179;refseq.name2=PLXNA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C537G;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=206338936;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=FilteredInAll GT 0/1
|
|
chr1 206343131 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1591T>G;refseq.codonCoord=531;refseq.end=206343131;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2349;refseq.name=NM_025179;refseq.name2=PLXNA2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C531G;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-17;refseq.start=206343131;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 207851829 . G A 295.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=138;Dels=0.00;HRun=0;HaplotypeScore=5.31;MQ=98.65;MQ0=0;OQ=2328.17;QD=16.87;RankSumP=0.00209589;SB=-807.34;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.985G>A;refseq.codonCoord=329;refseq.end=207851829;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1087;refseq.name=NM_020439;refseq.name2=CAMK1G;refseq.positionType=CDS;refseq.proteinCoordStr=p.V329I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=70;refseq.start=207851829;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=filterInsoap-gatk GT 1/0
|
|
chr1 207851963 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1119A>C;refseq.codonCoord=373;refseq.end=207851963;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1221;refseq.name=NM_020439;refseq.name2=CAMK1G;refseq.positionType=CDS;refseq.proteinCoordStr=p.L373F;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=204;refseq.start=207851963;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=FilteredInAll GT 0/1
|
|
chr1 207855326 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=133;Dels=0.00;HRun=1;HaplotypeScore=2.11;MQ=98.97;MQ0=0;OQ=1778.27;QD=13.37;RankSumP=0.121622;SB=-643.63;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.3432A>G;refseq.codingCoordStr_2=c.3432A>G;refseq.codingCoordStr_3=c.3432A>G;refseq.codonCoord_1=1144;refseq.codonCoord_2=1144;refseq.codonCoord_3=1144;refseq.end_1=207855326;refseq.end_2=207855326;refseq.end_3=207855326;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3576;refseq.mrnaCoord_2=3822;refseq.mrnaCoord_3=3550;refseq.name2_1=LAMB3;refseq.name2_2=LAMB3;refseq.name2_3=LAMB3;refseq.name_1=NM_000228;refseq.name_2=NM_001017402;refseq.name_3=NM_001127641;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S1144S;refseq.proteinCoordStr_2=p.S1144S;refseq.proteinCoordStr_3=p.S1144S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.spliceDist_1=50;refseq.spliceDist_2=50;refseq.spliceDist_3=50;refseq.start_1=207855326;refseq.start_2=207855326;refseq.start_3=207855326;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;refseq.variantCodon_3=TCG;set=Intersection GT 1/0
|
|
chr1 207857916 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.3010A>C;refseq.codingCoordStr_2=c.3010A>C;refseq.codingCoordStr_3=c.3010A>C;refseq.codonCoord_1=1004;refseq.codonCoord_2=1004;refseq.codonCoord_3=1004;refseq.end_1=207857916;refseq.end_2=207857916;refseq.end_3=207857916;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=3154;refseq.mrnaCoord_2=3400;refseq.mrnaCoord_3=3128;refseq.name2_1=LAMB3;refseq.name2_2=LAMB3;refseq.name2_3=LAMB3;refseq.name_1=NM_000228;refseq.name_2=NM_001017402;refseq.name_3=NM_001127641;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.T1004P;refseq.proteinCoordStr_2=p.T1004P;refseq.proteinCoordStr_3=p.T1004P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.spliceDist_1=-42;refseq.spliceDist_2=-42;refseq.spliceDist_3=-42;refseq.start_1=207857916;refseq.start_2=207857916;refseq.start_3=207857916;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;set=FilteredInAll GT 1/0
|
|
chr1 207863571 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=18;HRun=2;RankSumP=6.06466e-06;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2260C>G;refseq.codingCoordStr_2=c.2260C>G;refseq.codingCoordStr_3=c.2260C>G;refseq.codonCoord_1=754;refseq.codonCoord_2=754;refseq.codonCoord_3=754;refseq.end_1=207863571;refseq.end_2=207863571;refseq.end_3=207863571;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2404;refseq.mrnaCoord_2=2650;refseq.mrnaCoord_3=2378;refseq.name2_1=LAMB3;refseq.name2_2=LAMB3;refseq.name2_3=LAMB3;refseq.name_1=NM_000228;refseq.name_2=NM_001017402;refseq.name_3=NM_001127641;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R754G;refseq.proteinCoordStr_2=p.R754G;refseq.proteinCoordStr_3=p.R754G;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.referenceCodon_3=CGG;refseq.spliceDist_1=-99;refseq.spliceDist_2=-99;refseq.spliceDist_3=-99;refseq.start_1=207863571;refseq.start_2=207863571;refseq.start_3=207863571;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=FilteredInAll GT 0/1
|
|
chr1 207863573 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=17;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2258T>G;refseq.codingCoordStr_2=c.2258T>G;refseq.codingCoordStr_3=c.2258T>G;refseq.codonCoord_1=753;refseq.codonCoord_2=753;refseq.codonCoord_3=753;refseq.end_1=207863573;refseq.end_2=207863573;refseq.end_3=207863573;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2402;refseq.mrnaCoord_2=2648;refseq.mrnaCoord_3=2376;refseq.name2_1=LAMB3;refseq.name2_2=LAMB3;refseq.name2_3=LAMB3;refseq.name_1=NM_000228;refseq.name_2=NM_001017402;refseq.name_3=NM_001127641;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V753G;refseq.proteinCoordStr_2=p.V753G;refseq.proteinCoordStr_3=p.V753G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.spliceDist_1=-101;refseq.spliceDist_2=-101;refseq.spliceDist_3=-101;refseq.start_1=207863573;refseq.start_2=207863573;refseq.start_3=207863573;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=FilteredInAll GT 0/1
|
|
chr1 207865876 . A G 232.28 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=98.48;MQ0=0;OQ=920.95;QD=18.42;RankSumP=0.562302;SB=-347.65;SecondBestBaseQ=26;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1716T>C;refseq.codingCoordStr_2=c.1716T>C;refseq.codingCoordStr_3=c.1716T>C;refseq.codonCoord_1=572;refseq.codonCoord_2=572;refseq.codonCoord_3=572;refseq.end_1=207865876;refseq.end_2=207865876;refseq.end_3=207865876;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1860;refseq.mrnaCoord_2=2106;refseq.mrnaCoord_3=1834;refseq.name2_1=LAMB3;refseq.name2_2=LAMB3;refseq.name2_3=LAMB3;refseq.name_1=NM_000228;refseq.name_2=NM_001017402;refseq.name_3=NM_001127641;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.C572C;refseq.proteinCoordStr_2=p.C572C;refseq.proteinCoordStr_3=p.C572C;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceCodon_1=TGT;refseq.referenceCodon_2=TGT;refseq.referenceCodon_3=TGT;refseq.spliceDist_1=119;refseq.spliceDist_2=119;refseq.spliceDist_3=119;refseq.start_1=207865876;refseq.start_2=207865876;refseq.start_3=207865876;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantAA_3=Cys;refseq.variantCodon_1=TGC;refseq.variantCodon_2=TGC;refseq.variantCodon_3=TGC;set=Intersection GT 0/1
|
|
chr1 207878509 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=154;Dels=0.00;HRun=1;HaplotypeScore=10.21;MQ=97.51;MQ0=0;OQ=2148.64;QD=13.95;RankSumP=0.488232;SB=-441.15;SecondBestBaseQ=28;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.291A>C;refseq.codingCoordStr_2=c.291A>C;refseq.codingCoordStr_3=c.291A>C;refseq.codonCoord_1=97;refseq.codonCoord_2=97;refseq.codonCoord_3=97;refseq.end_1=207878509;refseq.end_2=207878509;refseq.end_3=207878509;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=435;refseq.mrnaCoord_2=681;refseq.mrnaCoord_3=409;refseq.name2_1=LAMB3;refseq.name2_2=LAMB3;refseq.name2_3=LAMB3;refseq.name_1=NM_000228;refseq.name_2=NM_001017402;refseq.name_3=NM_001127641;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.S97S;refseq.proteinCoordStr_2=p.S97S;refseq.proteinCoordStr_3=p.S97S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.referenceCodon_3=TCA;refseq.spliceDist_1=-8;refseq.spliceDist_2=-8;refseq.spliceDist_3=-8;refseq.spliceInfo_1=splice-donor_-8;refseq.spliceInfo_2=splice-donor_-8;refseq.spliceInfo_3=splice-donor_-8;refseq.start_1=207878509;refseq.start_2=207878509;refseq.start_3=207878509;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;refseq.variantCodon_3=TCC;set=Intersection GT 1/0
|
|
chr1 208017383 . C G 172.13 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=144;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=98.93;MQ0=0;OQ=6760.36;QD=46.95;RankSumP=1.00000;SB=-3142.68;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1057C>G;refseq.codonCoord=353;refseq.end=208017383;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1347;refseq.name=NM_025228;refseq.name2=TRAF3IP3;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q353E;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=64;refseq.start=208017383;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 208028593 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1199G>C;refseq.codonCoord=400;refseq.end=208028593;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1462;refseq.name=NM_006147;refseq.name2=IRF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.R400P;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=20;refseq.start=208028593;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=FilteredInAll GT 1/0
|
|
chr1 208035307 . C A 285.19 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=482;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=98.78;MQ0=0;OQ=19256.16;QD=39.95;RankSumP=1.00000;SB=-5648.61;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.459G>T;refseq.codonCoord=153;refseq.end=208035307;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=722;refseq.name=NM_006147;refseq.name2=IRF6;refseq.positionType=CDS;refseq.proteinCoordStr=p.S153S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-50;refseq.start=208035307;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/1
|
|
chr1 208070822 . C G 93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=11.84;MQ=98.36;MQ0=0;OQ=10223.96;QD=49.39;RankSumP=1.00000;SB=-3591.68;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.199C>G;refseq.codonCoord=67;refseq.end=208070822;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=275;refseq.name=NM_014388;refseq.name2=C1orf107;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q67E;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=52;refseq.start=208070822;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 208073226 . C T 262.91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=224;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=98.85;MQ0=0;OQ=9424.09;QD=42.07;RankSumP=1.00000;SB=-2968.13;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.462C>T;refseq.codonCoord=154;refseq.end=208073226;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=538;refseq.name=NM_014388;refseq.name2=C1orf107;refseq.positionType=CDS;refseq.proteinCoordStr=p.P154P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=74;refseq.start=208073226;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 208082552 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1670T>G;refseq.codonCoord=557;refseq.end=208082552;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1746;refseq.name=NM_014388;refseq.name2=C1orf107;refseq.positionType=CDS;refseq.proteinCoordStr=p.V557G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=208082552;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 208400704 . T C 209.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=110;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=98.11;MQ0=0;OQ=1955.33;QD=17.78;RankSumP=0.405497;SB=-236.59;SecondBestBaseQ=33;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_3=c.1554T>C;refseq.codingCoordStr_4=c.1419T>C;refseq.codingCoordStr_5=c.1497T>C;refseq.codingCoordStr_6=c.1362T>C;refseq.codonCoord_3=518;refseq.codonCoord_4=473;refseq.codonCoord_5=499;refseq.codonCoord_6=454;refseq.end_1=208400704;refseq.end_2=208400704;refseq.end_3=208400704;refseq.end_4=208400704;refseq.end_5=208400704;refseq.end_6=208400704;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=*;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=1639;refseq.mrnaCoord_2=1368;refseq.mrnaCoord_3=1612;refseq.mrnaCoord_4=1491;refseq.mrnaCoord_5=1555;refseq.mrnaCoord_6=1434;refseq.name2_1=SYT14;refseq.name2_2=SYT14;refseq.name2_3=SYT14;refseq.name2_4=SYT14;refseq.name2_5=SYT14;refseq.name2_6=SYT14;refseq.name_1=NR_027458;refseq.name_2=NR_027459;refseq.name_3=NM_001146261;refseq.name_4=NM_001146262;refseq.name_5=NM_001146264;refseq.name_6=NM_153262;refseq.numMatchingRecords=6;refseq.positionType_1=non_coding_exon;refseq.positionType_2=non_coding_exon;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_3=p.Y518Y;refseq.proteinCoordStr_4=p.Y473Y;refseq.proteinCoordStr_5=p.Y499Y;refseq.proteinCoordStr_6=p.Y454Y;refseq.referenceAA_3=Tyr;refseq.referenceAA_4=Tyr;refseq.referenceAA_5=Tyr;refseq.referenceAA_6=Tyr;refseq.referenceCodon_3=TAT;refseq.referenceCodon_4=TAT;refseq.referenceCodon_5=TAT;refseq.referenceCodon_6=TAT;refseq.spliceDist_1=8;refseq.spliceDist_2=8;refseq.spliceDist_3=8;refseq.spliceDist_4=8;refseq.spliceDist_5=8;refseq.spliceDist_6=8;refseq.spliceInfo_1=splice-acceptor_8;refseq.spliceInfo_2=splice-acceptor_8;refseq.spliceInfo_3=splice-acceptor_8;refseq.spliceInfo_4=splice-acceptor_8;refseq.spliceInfo_5=splice-acceptor_8;refseq.spliceInfo_6=splice-acceptor_8;refseq.start_1=208400704;refseq.start_2=208400704;refseq.start_3=208400704;refseq.start_4=208400704;refseq.start_5=208400704;refseq.start_6=208400704;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_3=Tyr;refseq.variantAA_4=Tyr;refseq.variantAA_5=Tyr;refseq.variantAA_6=Tyr;refseq.variantCodon_3=TAC;refseq.variantCodon_4=TAC;refseq.variantCodon_5=TAC;refseq.variantCodon_6=TAC;set=Intersection GT 1/0
|
|
chr1 208627490 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=25;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.215T>G;refseq.codingCoordStr_2=c.215T>G;refseq.codingCoordStr_3=c.215T>G;refseq.codingCoordStr_4=c.218T>G;refseq.codingCoordStr_5=c.215T>G;refseq.codingCoordStr_6=c.215T>G;refseq.codonCoord_1=72;refseq.codonCoord_2=72;refseq.codonCoord_3=72;refseq.codonCoord_4=73;refseq.codonCoord_5=72;refseq.codonCoord_6=72;refseq.end_1=208627490;refseq.end_2=208627490;refseq.end_3=208627490;refseq.end_4=208627490;refseq.end_5=208627490;refseq.end_6=208627490;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.frame_5=1;refseq.frame_6=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=391;refseq.mrnaCoord_2=391;refseq.mrnaCoord_3=446;refseq.mrnaCoord_4=323;refseq.mrnaCoord_5=457;refseq.mrnaCoord_6=457;refseq.name2_1=HHAT;refseq.name2_2=HHAT;refseq.name2_3=HHAT;refseq.name2_4=HHAT;refseq.name2_5=HHAT;refseq.name2_6=HHAT;refseq.name_1=NM_001122834;refseq.name_2=NM_001170564;refseq.name_3=NM_001170580;refseq.name_4=NM_001170587;refseq.name_5=NM_001170588;refseq.name_6=NM_018194;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.V72G;refseq.proteinCoordStr_2=p.V72G;refseq.proteinCoordStr_3=p.V72G;refseq.proteinCoordStr_4=p.V73G;refseq.proteinCoordStr_5=p.V72G;refseq.proteinCoordStr_6=p.V72G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceAA_4=Val;refseq.referenceAA_5=Val;refseq.referenceAA_6=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.referenceCodon_4=GTG;refseq.referenceCodon_5=GTG;refseq.referenceCodon_6=GTG;refseq.spliceDist_1=56;refseq.spliceDist_2=56;refseq.spliceDist_3=56;refseq.spliceDist_4=56;refseq.spliceDist_5=56;refseq.spliceDist_6=56;refseq.start_1=208627490;refseq.start_2=208627490;refseq.start_3=208627490;refseq.start_4=208627490;refseq.start_5=208627490;refseq.start_6=208627490;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantAA_5=Gly;refseq.variantAA_6=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;refseq.variantCodon_5=GGG;refseq.variantCodon_6=GGG;set=FilteredInAll GT 1/0
|
|
chr1 208627492 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_1=c.217T>G;refseq.codingCoordStr_2=c.217T>G;refseq.codingCoordStr_3=c.217T>G;refseq.codingCoordStr_4=c.220T>G;refseq.codingCoordStr_5=c.217T>G;refseq.codingCoordStr_6=c.217T>G;refseq.codonCoord_1=73;refseq.codonCoord_2=73;refseq.codonCoord_3=73;refseq.codonCoord_4=74;refseq.codonCoord_5=73;refseq.codonCoord_6=73;refseq.end_1=208627492;refseq.end_2=208627492;refseq.end_3=208627492;refseq.end_4=208627492;refseq.end_5=208627492;refseq.end_6=208627492;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_1=393;refseq.mrnaCoord_2=393;refseq.mrnaCoord_3=448;refseq.mrnaCoord_4=325;refseq.mrnaCoord_5=459;refseq.mrnaCoord_6=459;refseq.name2_1=HHAT;refseq.name2_2=HHAT;refseq.name2_3=HHAT;refseq.name2_4=HHAT;refseq.name2_5=HHAT;refseq.name2_6=HHAT;refseq.name_1=NM_001122834;refseq.name_2=NM_001170564;refseq.name_3=NM_001170580;refseq.name_4=NM_001170587;refseq.name_5=NM_001170588;refseq.name_6=NM_018194;refseq.numMatchingRecords=6;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_1=p.W73G;refseq.proteinCoordStr_2=p.W73G;refseq.proteinCoordStr_3=p.W73G;refseq.proteinCoordStr_4=p.W74G;refseq.proteinCoordStr_5=p.W73G;refseq.proteinCoordStr_6=p.W73G;refseq.referenceAA_1=Trp;refseq.referenceAA_2=Trp;refseq.referenceAA_3=Trp;refseq.referenceAA_4=Trp;refseq.referenceAA_5=Trp;refseq.referenceAA_6=Trp;refseq.referenceCodon_1=TGG;refseq.referenceCodon_2=TGG;refseq.referenceCodon_3=TGG;refseq.referenceCodon_4=TGG;refseq.referenceCodon_5=TGG;refseq.referenceCodon_6=TGG;refseq.spliceDist_1=-57;refseq.spliceDist_2=-57;refseq.spliceDist_3=-57;refseq.spliceDist_4=-57;refseq.spliceDist_5=-57;refseq.spliceDist_6=-57;refseq.start_1=208627492;refseq.start_2=208627492;refseq.start_3=208627492;refseq.start_4=208627492;refseq.start_5=208627492;refseq.start_6=208627492;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantAA_4=Gly;refseq.variantAA_5=Gly;refseq.variantAA_6=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;refseq.variantCodon_4=GGG;refseq.variantCodon_5=GGG;refseq.variantCodon_6=GGG;set=FilteredInAll GT 1/0
|
|
chr1 208644454 . C T 109.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=98.36;MQ0=0;OQ=1906.27;QD=14.33;RankSumP=0.496684;SB=-571.37;SecondBestBaseQ=31;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_2=c.492C>T;refseq.codingCoordStr_3=c.492C>T;refseq.codingCoordStr_4=c.495C>T;refseq.codingCoordStr_5=c.297C>T;refseq.codingCoordStr_6=c.492C>T;refseq.codonCoord_2=164;refseq.codonCoord_3=164;refseq.codonCoord_4=165;refseq.codonCoord_5=99;refseq.codonCoord_6=164;refseq.end_1=208658110;refseq.end_2=208644454;refseq.end_3=208644454;refseq.end_4=208644454;refseq.end_5=208644454;refseq.end_6=208644454;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeAlternate_6=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_2=668;refseq.mrnaCoord_3=723;refseq.mrnaCoord_4=600;refseq.mrnaCoord_5=539;refseq.mrnaCoord_6=734;refseq.name2_1=HHAT;refseq.name2_2=HHAT;refseq.name2_3=HHAT;refseq.name2_4=HHAT;refseq.name2_5=HHAT;refseq.name2_6=HHAT;refseq.name_1=NM_001170564;refseq.name_2=NM_001122834;refseq.name_3=NM_001170580;refseq.name_4=NM_001170587;refseq.name_5=NM_001170588;refseq.name_6=NM_018194;refseq.numMatchingRecords=6;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_2=p.N164N;refseq.proteinCoordStr_3=p.N164N;refseq.proteinCoordStr_4=p.N165N;refseq.proteinCoordStr_5=p.N99N;refseq.proteinCoordStr_6=p.N164N;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceAA_4=Asn;refseq.referenceAA_5=Asn;refseq.referenceAA_6=Asn;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.referenceCodon_4=AAC;refseq.referenceCodon_5=AAC;refseq.referenceCodon_6=AAC;refseq.spliceDist_2=24;refseq.spliceDist_3=24;refseq.spliceDist_4=24;refseq.spliceDist_5=24;refseq.spliceDist_6=24;refseq.start_1=208627559;refseq.start_2=208644454;refseq.start_3=208644454;refseq.start_4=208644454;refseq.start_5=208644454;refseq.start_6=208644454;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_2=Asn;refseq.variantAA_3=Asn;refseq.variantAA_4=Asn;refseq.variantAA_5=Asn;refseq.variantAA_6=Asn;refseq.variantCodon_2=AAT;refseq.variantCodon_3=AAT;refseq.variantCodon_4=AAT;refseq.variantCodon_5=AAT;refseq.variantCodon_6=AAT;set=Intersection GT 0/1
|
|
chr1 208644496 . G C 326.98 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=4.48;MQ=98.47;MQ0=0;OQ=7266.23;QD=42.49;RankSumP=1.00000;SB=-2900.42;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.changesAA_6=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_2=c.534G>C;refseq.codingCoordStr_3=c.534G>C;refseq.codingCoordStr_4=c.537G>C;refseq.codingCoordStr_5=c.339G>C;refseq.codingCoordStr_6=c.534G>C;refseq.codonCoord_2=178;refseq.codonCoord_3=178;refseq.codonCoord_4=179;refseq.codonCoord_5=113;refseq.codonCoord_6=178;refseq.end_1=208658110;refseq.end_2=208644496;refseq.end_3=208644496;refseq.end_4=208644496;refseq.end_5=208644496;refseq.end_6=208644496;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.frame_6=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.functionalClass_6=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_2=710;refseq.mrnaCoord_3=765;refseq.mrnaCoord_4=642;refseq.mrnaCoord_5=581;refseq.mrnaCoord_6=776;refseq.name2_1=HHAT;refseq.name2_2=HHAT;refseq.name2_3=HHAT;refseq.name2_4=HHAT;refseq.name2_5=HHAT;refseq.name2_6=HHAT;refseq.name_1=NM_001170564;refseq.name_2=NM_001122834;refseq.name_3=NM_001170580;refseq.name_4=NM_001170587;refseq.name_5=NM_001170588;refseq.name_6=NM_018194;refseq.numMatchingRecords=6;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_2=p.L178L;refseq.proteinCoordStr_3=p.L178L;refseq.proteinCoordStr_4=p.L179L;refseq.proteinCoordStr_5=p.L113L;refseq.proteinCoordStr_6=p.L178L;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceAA_4=Leu;refseq.referenceAA_5=Leu;refseq.referenceAA_6=Leu;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.referenceCodon_4=CTG;refseq.referenceCodon_5=CTG;refseq.referenceCodon_6=CTG;refseq.spliceDist_2=66;refseq.spliceDist_3=66;refseq.spliceDist_4=66;refseq.spliceDist_5=66;refseq.spliceDist_6=66;refseq.start_1=208627559;refseq.start_2=208644496;refseq.start_3=208644496;refseq.start_4=208644496;refseq.start_5=208644496;refseq.start_6=208644496;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Leu;refseq.variantAA_6=Leu;refseq.variantCodon_2=CTC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=CTC;refseq.variantCodon_6=CTC;set=Intersection GT 1/1
|
|
chr1 208644524 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=160;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=98.72;MQ0=0;OQ=2034.30;QD=12.71;RankSumP=0.297336;SB=-999.62;SecondBestBaseQ=31;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.codingCoordStr_2=c.562T>C;refseq.codingCoordStr_3=c.562T>C;refseq.codingCoordStr_4=c.565T>C;refseq.codingCoordStr_5=c.367T>C;refseq.codingCoordStr_6=c.562T>C;refseq.codonCoord_2=188;refseq.codonCoord_3=188;refseq.codonCoord_4=189;refseq.codonCoord_5=123;refseq.codonCoord_6=188;refseq.end_1=208658110;refseq.end_2=208644524;refseq.end_3=208644524;refseq.end_4=208644524;refseq.end_5=208644524;refseq.end_6=208644524;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeAlternate_6=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.mrnaCoord_2=738;refseq.mrnaCoord_3=793;refseq.mrnaCoord_4=670;refseq.mrnaCoord_5=609;refseq.mrnaCoord_6=804;refseq.name2_1=HHAT;refseq.name2_2=HHAT;refseq.name2_3=HHAT;refseq.name2_4=HHAT;refseq.name2_5=HHAT;refseq.name2_6=HHAT;refseq.name_1=NM_001170564;refseq.name_2=NM_001122834;refseq.name_3=NM_001170580;refseq.name_4=NM_001170587;refseq.name_5=NM_001170588;refseq.name_6=NM_018194;refseq.numMatchingRecords=6;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.proteinCoordStr_2=p.C188R;refseq.proteinCoordStr_3=p.C188R;refseq.proteinCoordStr_4=p.C189R;refseq.proteinCoordStr_5=p.C123R;refseq.proteinCoordStr_6=p.C188R;refseq.referenceAA_2=Cys;refseq.referenceAA_3=Cys;refseq.referenceAA_4=Cys;refseq.referenceAA_5=Cys;refseq.referenceAA_6=Cys;refseq.referenceCodon_2=TGC;refseq.referenceCodon_3=TGC;refseq.referenceCodon_4=TGC;refseq.referenceCodon_5=TGC;refseq.referenceCodon_6=TGC;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.start_1=208627559;refseq.start_2=208644524;refseq.start_3=208644524;refseq.start_4=208644524;refseq.start_5=208644524;refseq.start_6=208644524;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantAA_5=Arg;refseq.variantAA_6=Arg;refseq.variantCodon_2=CGC;refseq.variantCodon_3=CGC;refseq.variantCodon_4=CGC;refseq.variantCodon_5=CGC;refseq.variantCodon_6=CGC;set=Intersection GT 1/0
|
|
chr1 208923884 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=42;Dels=0.00;HRun=0;HaplotypeScore=5.27;MQ=98.59;MQ0=0;OQ=535.17;QD=12.74;RankSumP=0.603669;SB=-290.80;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2251G>A;refseq.codingCoordStr_2=c.2332G>A;refseq.codonCoord_1=751;refseq.codonCoord_2=778;refseq.end_1=208923884;refseq.end_2=208923884;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2421;refseq.mrnaCoord_2=2502;refseq.name2_1=KCNH1;refseq.name2_2=KCNH1;refseq.name_1=NM_002238;refseq.name_2=NM_172362;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A751T;refseq.proteinCoordStr_2=p.A778T;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCC;refseq.referenceCodon_2=GCC;refseq.spliceDist_1=220;refseq.spliceDist_2=220;refseq.start_1=208923884;refseq.start_2=208923884;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=Intersection GT 0/1
|
|
chr1 209612296 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=4.71105e-09;SecondBestBaseQ=12;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1303A>C;refseq.codingCoordStr_2=c.1303A>C;refseq.codingCoordStr_3=c.1303A>C;refseq.codonCoord_1=435;refseq.codonCoord_2=435;refseq.codonCoord_3=435;refseq.end_1=209612296;refseq.end_2=209612296;refseq.end_3=209612296;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1388;refseq.mrnaCoord_2=1363;refseq.mrnaCoord_3=1363;refseq.name2_1=TRAF5;refseq.name2_2=TRAF5;refseq.name2_3=TRAF5;refseq.name_1=NM_001033910;refseq.name_2=NM_004619;refseq.name_3=NM_145759;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.T435P;refseq.proteinCoordStr_2=p.T435P;refseq.proteinCoordStr_3=p.T435P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.spliceDist_1=204;refseq.spliceDist_2=204;refseq.spliceDist_3=204;refseq.start_1=209612296;refseq.start_2=209612296;refseq.start_3=209612296;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;set=FilteredInAll GT 0/1
|
|
chr1 209612313 . C A 19 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=24;DP=118;Dels=0.00;HRun=1;HaplotypeScore=25.54;MQ=97.61;MQ0=0;OQ=129.87;QD=1.10;RankSumP=8.68793e-09;SB=101.32;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1320C>A;refseq.codingCoordStr_2=c.1320C>A;refseq.codingCoordStr_3=c.1320C>A;refseq.codonCoord_1=440;refseq.codonCoord_2=440;refseq.codonCoord_3=440;refseq.end_1=209612313;refseq.end_2=209612313;refseq.end_3=209612313;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=nonsense;refseq.functionalClass_2=nonsense;refseq.functionalClass_3=nonsense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1405;refseq.mrnaCoord_2=1380;refseq.mrnaCoord_3=1380;refseq.name2_1=TRAF5;refseq.name2_2=TRAF5;refseq.name2_3=TRAF5;refseq.name_1=NM_001033910;refseq.name_2=NM_004619;refseq.name_3=NM_145759;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Y440*;refseq.proteinCoordStr_2=p.Y440*;refseq.proteinCoordStr_3=p.Y440*;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.referenceCodon_3=TAC;refseq.spliceDist_1=221;refseq.spliceDist_2=221;refseq.spliceDist_3=221;refseq.start_1=209612313;refseq.start_2=209612313;refseq.start_3=209612313;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Stop;refseq.variantAA_2=Stop;refseq.variantAA_3=Stop;refseq.variantCodon_1=TAA;refseq.variantCodon_2=TAA;refseq.variantCodon_3=TAA;set=FilteredInAll GT 1/0
|
|
chr1 209913499 . A G 341.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=384;Dels=0.00;HRun=0;HaplotypeScore=12.47;MQ=96.52;MQ0=2;OQ=7264.38;QD=18.92;RankSumP=0.389627;SB=-2456.21;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.504T>C;refseq.codonCoord=168;refseq.end=209913499;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=650;refseq.name=NM_002497;refseq.name2=NEK2;refseq.positionType=CDS;refseq.proteinCoordStr=p.H168H;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-52;refseq.start=209913499;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 0/1
|
|
chr1 210181837 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2841G>C;refseq.codonCoord=947;refseq.end=210181837;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2946;refseq.name=NM_015434;refseq.name2=INTS7;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q947H;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=240;refseq.start=210181837;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=FilteredInAll GT 1/0
|
|
chr1 210340229 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=210;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=98.86;MQ0=0;OQ=3885.39;QD=18.50;RankSumP=0.116370;SB=-513.94;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1274G>A;refseq.codonCoord=425;refseq.end=210340229;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1588;refseq.name=NM_016448;refseq.name2=DTL;refseq.positionType=CDS;refseq.proteinCoordStr=p.S425N;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=13;refseq.start=210340229;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 210340262 . C T 214.02 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=298;Dels=0.00;HRun=0;HaplotypeScore=5.86;MQ=98.83;MQ0=0;OQ=11246.23;QD=37.74;RankSumP=1.00000;SB=-4310.92;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1307C>T;refseq.codonCoord=436;refseq.end=210340262;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1621;refseq.name=NM_016448;refseq.name2=DTL;refseq.positionType=CDS;refseq.proteinCoordStr=p.A436V;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=46;refseq.start=210340262;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/1
|
|
chr1 210341036 . A C 389.64 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=117;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=4751.06;QD=40.61;RankSumP=1.00000;SB=-869.42;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2081A>C;refseq.codonCoord=694;refseq.end=210341036;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2395;refseq.name=NM_016448;refseq.name2=DTL;refseq.positionType=CDS;refseq.proteinCoordStr=p.K694T;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=-14;refseq.start=210341036;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 1/1
|
|
chr1 210592911 . C T 269.36 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=536;Dels=0.00;HRun=0;HaplotypeScore=15.60;MQ=98.85;MQ0=0;OQ=11291.71;QD=21.07;RankSumP=0.400748;SB=-2296.61;SecondBestBaseQ=33;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.end_1=210596580;refseq.end_2=210592911;refseq.haplotypeAlternate_2=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.inCodingRegion_1=false;refseq.mrnaCoord_2=129;refseq.name2_1=PPP2R5A;refseq.name2_2=SNORA16B;refseq.name_1=NM_006243;refseq.name_2=NR_004389;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=non_coding_exon;refseq.spliceDist_2=-5;refseq.spliceInfo_2=splice-donor_-5;refseq.start_1=210589218;refseq.start_2=210592911;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;set=Intersection GT 0/1
|
|
chr1 210626950 . A G 49.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=163;Dels=0.00;HRun=1;HaplotypeScore=8.25;MQ=98.51;MQ0=0;OQ=4018.06;QD=24.65;RankSumP=1.00000;SB=-902.56;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.249T>C;refseq.codonCoord=83;refseq.end=210626950;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=417;refseq.name=NM_018252;refseq.name2=TMEM206;refseq.positionType=CDS;refseq.proteinCoordStr=p.F83F;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=-95;refseq.start=210626950;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 210865600 . A G 135.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=97.32;MQ0=0;OQ=432.71;QD=14.92;RankSumP=0.709304;SB=-206.93;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.758A>G;refseq.codonCoord=253;refseq.end=210865600;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1189;refseq.name=NM_153606;refseq.name2=FAM71A;refseq.positionType=CDS;refseq.proteinCoordStr=p.N253S;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-1144;refseq.start=210865600;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 210866493 . A G 252.30 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=98.51;MQ0=0;OQ=4298.84;QD=38.38;RankSumP=1.00000;SB=-474.20;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1651A>G;refseq.codonCoord=551;refseq.end=210866493;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2082;refseq.name=NM_153606;refseq.name2=FAM71A;refseq.positionType=CDS;refseq.proteinCoordStr=p.N551D;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-251;refseq.start=210866493;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 210866572 . C T 288.50 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=385;Dels=0.00;HRun=0;HaplotypeScore=15.18;MQ=98.81;MQ0=0;OQ=6701.28;QD=17.41;RankSumP=0.172700;SB=-2375.08;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1730C>T;refseq.codonCoord=577;refseq.end=210866572;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2161;refseq.name=NM_153606;refseq.name2=FAM71A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T577M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-172;refseq.start=210866572;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 210978459 . T C 300.70 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=439;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=98.96;MQ0=0;OQ=8779.74;QD=20.00;RankSumP=0.341858;SB=-2789.67;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.*203A>G;refseq.codingCoordStr_2=c.760A>G;refseq.codonCoord_2=254;refseq.end_1=210978459;refseq.end_2=210978459;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=879;refseq.mrnaCoord_2=794;refseq.name2_1=NSL1;refseq.name2_2=NSL1;refseq.name_1=NM_001042549;refseq.name_2=NM_015471;refseq.numMatchingRecords=2;refseq.positionType_1=utr3;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.M254V;refseq.referenceAA_2=Met;refseq.referenceCodon_2=ATG;refseq.spliceDist_1=193;refseq.spliceDist_2=193;refseq.start_1=210978459;refseq.start_2=210978459;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Val;refseq.variantCodon_2=GTG;set=Intersection GT 1/0
|
|
chr1 211076092 . A G 296.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=427;Dels=0.00;HRun=0;HaplotypeScore=7.06;MQ=98.95;MQ0=0;OQ=8591.72;QD=20.12;RankSumP=0.240007;SB=-3358.21;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.23T>C;refseq.codonCoord=8;refseq.end=211076092;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=131;refseq.name=NM_001024601;refseq.name2=C1orf227;refseq.positionType=CDS;refseq.proteinCoordStr=p.I8T;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=61;refseq.start=211076092;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 0/1
|
|
chr1 211125343 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1178A>G;refseq.codonCoord=393;refseq.end=211125343;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1376;refseq.name=NM_014053;refseq.name2=FLVCR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D393G;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=-19;refseq.start=211125343;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 212558909 . G A 199.40 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=417;Dels=0.00;HRun=1;HaplotypeScore=2.98;MQ=98.95;MQ0=0;OQ=17868.09;QD=42.85;RankSumP=1.00000;SB=-6268.95;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.494G>A;refseq.codonCoord=165;refseq.end=212558909;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=527;refseq.name=NM_020197;refseq.name2=SMYD2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G165E;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-41;refseq.start=212558909;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 212624175 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1646G>C;refseq.codonCoord=549;refseq.end=212624175;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1917;refseq.name=NM_005401;refseq.name2=PTPN14;refseq.positionType=CDS;refseq.proteinCoordStr=p.G549A;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=580;refseq.start=212624175;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 212853753 . G A 267.18 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.77;MQ0=0;OQ=2501.80;QD=20.18;RankSumP=0.0763390;SB=-938.94;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.33G>A;refseq.codonCoord=11;refseq.end=212853753;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=207;refseq.name=NM_016343;refseq.name2=CENPF;refseq.positionType=CDS;refseq.proteinCoordStr=p.G11G;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=74;refseq.start=212853753;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 212881194 . C T 96 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.94;MQ0=0;OQ=474.15;QD=13.17;RankSumP=0.198031;SB=-167.13;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2890C>T;refseq.codonCoord=964;refseq.end=212881194;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3064;refseq.name=NM_016343;refseq.name2=CENPF;refseq.positionType=CDS;refseq.proteinCoordStr=p.L964L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=1308;refseq.start=212881194;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=Intersection GT 0/1
|
|
chr1 212886722 . A G 135.19 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=97.59;MQ0=0;OQ=427.16;QD=14.73;RankSumP=0.720028;SB=-182.69;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7186A>G;refseq.codonCoord=2396;refseq.end=212886722;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=7360;refseq.name=NM_016343;refseq.name2=CENPF;refseq.positionType=CDS;refseq.proteinCoordStr=p.N2396D;refseq.referenceAA=Asn;refseq.referenceCodon=AAT;refseq.spliceDist=-645;refseq.start=212886722;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 212892819 . G A 182.29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=98.64;MQ0=0;OQ=1711.41;QD=16.46;RankSumP=0.210479;SB=-721.15;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8186G>A;refseq.codonCoord=2729;refseq.end=212892819;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=8360;refseq.name=NM_016343;refseq.name2=CENPF;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2729Q;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=26;refseq.start=212892819;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 212897215 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=159;Dels=0.00;HRun=1;HaplotypeScore=4.18;MQ=98.99;MQ0=0;OQ=2735.46;QD=17.20;RankSumP=0.246745;SB=-1378.54;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.8802A>G;refseq.codonCoord=2934;refseq.end=212897215;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=8976;refseq.name=NM_016343;refseq.name2=CENPF;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2934R;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=-161;refseq.start=212897215;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 0/1
|
|
chr1 212897240 . A G 189.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=137;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=98.99;MQ0=0;OQ=2429.78;QD=17.74;RankSumP=0.144086;SB=-1201.56;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8827A>G;refseq.codonCoord=2943;refseq.end=212897240;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=9001;refseq.name=NM_016343;refseq.name2=CENPF;refseq.positionType=CDS;refseq.proteinCoordStr=p.R2943G;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=-136;refseq.start=212897240;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 0/1
|
|
chr1 212903733 . C G 113.71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=155;Dels=0.00;HRun=2;HaplotypeScore=2.60;MQ=98.56;MQ0=0;OQ=2594.33;QD=16.74;RankSumP=0.251201;SB=-1295.12;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.9318C>G;refseq.codonCoord=3106;refseq.end=212903733;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=9492;refseq.name=NM_016343;refseq.name2=CENPF;refseq.positionType=CDS;refseq.proteinCoordStr=p.N3106K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=177;refseq.start=212903733;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/0
|
|
chr1 213860457 . G A 293.96 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=320;Dels=0.00;HRun=0;HaplotypeScore=7.89;MQ=98.85;MQ0=0;OQ=7246.91;QD=22.65;RankSumP=0.353655;SB=-2925.44;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2322G>A;refseq.codonCoord=774;refseq.end=213860457;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2616;refseq.name=NM_016121;refseq.name2=KCTD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A774A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=436;refseq.start=213860457;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 213910996 . C T 175.99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=438;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=98.92;MQ0=0;OQ=8561.63;QD=19.55;RankSumP=0.303602;SB=-3548.56;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.14074G>A;refseq.codonCoord=4692;refseq.end=213910996;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=14461;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.G4692R;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-60;refseq.start=213910996;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 0/1
|
|
chr1 213915210 . T C 240.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=259;Dels=0.00;HRun=0;HaplotypeScore=15.33;MQ=98.67;MQ0=0;OQ=4162.91;QD=16.07;RankSumP=0.333314;SB=-1591.81;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.12666A>G;refseq.codonCoord=4222;refseq.end=213915210;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=13053;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T4222T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=372;refseq.start=213915210;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/0
|
|
chr1 213915264 . T C 265.03 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=327;Dels=0.00;HRun=0;HaplotypeScore=11.74;MQ=98.90;MQ0=0;OQ=12700.41;QD=38.84;RankSumP=1.00000;SB=-5142.47;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.12612A>G;refseq.codonCoord=4204;refseq.end=213915264;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=12999;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T4204T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=318;refseq.start=213915264;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 213981449 . T C 226.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=217;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=98.91;MQ0=0;OQ=4087.46;QD=18.84;RankSumP=0.455642;SB=-1246.91;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.11602A>G;refseq.codonCoord=3868;refseq.end=213981449;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=11989;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.M3868V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=54;refseq.start=213981449;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 213983186 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=417;Dels=0.00;HRun=1;HaplotypeScore=12.14;MQ=98.91;MQ0=0;OQ=7779.77;QD=18.66;RankSumP=0.322961;SB=-3186.21;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.11504C>T;refseq.codonCoord=3835;refseq.end=213983186;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=11891;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T3835I;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-45;refseq.start=213983186;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/0
|
|
chr1 214026761 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10261A>C;refseq.codonCoord=3421;refseq.end=214026761;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=10648;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.T3421P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=79;refseq.start=214026761;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 214026774 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=17;HRun=1;RankSumP=1.93738e-07;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10248T>G;refseq.codonCoord=3416;refseq.end=214026774;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10635;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.C3416W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=66;refseq.start=214026774;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 0/1
|
|
chr1 214026776 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;DP=161;Dels=0.00;HRun=2;HaplotypeScore=26.08;MQ=95.57;MQ0=0;OQ=106.70;QD=0.66;RankSumP=0.430670;SB=98.27;SecondBestBaseQ=17;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10246T>G;refseq.codonCoord=3416;refseq.end=214026776;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=10633;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.C3416G;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=64;refseq.start=214026776;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=soap-filterIngatk GT 0/1
|
|
chr1 214026790 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=165;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=96.47;MQ0=0;OQ=1687.10;QD=10.22;RankSumP=0.108375;SB=-572.73;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.10232A>C;refseq.codonCoord=3411;refseq.end=214026790;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=10619;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.E3411A;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=50;refseq.start=214026790;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 214210616 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.0869557;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6931G>A;refseq.codonCoord=2311;refseq.end=214210616;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=7318;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.A2311T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-27;refseq.start=214210616;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 0/1
|
|
chr1 214239003 . A G 297.92 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=194;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=98.83;MQ0=0;OQ=3155.25;QD=16.26;RankSumP=0.279655;SB=-1536.65;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6506T>C;refseq.codonCoord=2169;refseq.end=214239003;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6893;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.I2169T;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=21;refseq.start=214239003;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 214286404 . A G 278.01 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=257;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=98.94;MQ0=0;OQ=5884.07;QD=22.90;RankSumP=0.351848;SB=-1758.19;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6317T>C;refseq.codonCoord=2106;refseq.end=214286404;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=6704;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.I2106T;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=214286404;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 214318143 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5483A>C;refseq.codonCoord=1828;refseq.end=214318143;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5870;refseq.name=NM_206933;refseq.name2=USH2A;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1828A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-90;refseq.start=214318143;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 214415387 . C T 303.22 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=185;Dels=0.00;HRun=1;HaplotypeScore=4.00;MQ=98.90;MQ0=0;OQ=8069.97;QD=43.62;RankSumP=1.00000;SB=-3957.71;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4457G>A;refseq.codingCoordStr_2=c.4457G>A;refseq.codonCoord_1=1486;refseq.codonCoord_2=1486;refseq.end_1=214415387;refseq.end_2=214415387;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4844;refseq.mrnaCoord_2=4844;refseq.name2_1=USH2A;refseq.name2_2=USH2A;refseq.name_1=NM_007123;refseq.name_2=NM_206933;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R1486K;refseq.proteinCoordStr_2=p.R1486K;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=AGG;refseq.referenceCodon_2=AGG;refseq.spliceDist_1=61;refseq.spliceDist_2=61;refseq.start_1=214415387;refseq.start_2=214415387;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAG;refseq.variantCodon_2=AAG;set=Intersection GT 1/1
|
|
chr1 214438323 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4038A>G;refseq.codingCoordStr_2=c.4038A>G;refseq.codonCoord_1=1346;refseq.codonCoord_2=1346;refseq.end_1=214438323;refseq.end_2=214438323;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=4425;refseq.mrnaCoord_2=4425;refseq.name2_1=USH2A;refseq.name2_2=USH2A;refseq.name_1=NM_007123;refseq.name_2=NM_206933;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G1346G;refseq.proteinCoordStr_2=p.G1346G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=-44;refseq.spliceDist_2=-44;refseq.start_1=214438323;refseq.start_2=214438323;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 214658626 . T C 79.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=367;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=98.82;MQ0=0;OQ=14152.37;QD=38.56;RankSumP=1.00000;SB=-6530.96;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.504A>G;refseq.codingCoordStr_2=c.504A>G;refseq.codonCoord_1=168;refseq.codonCoord_2=168;refseq.end_1=214658626;refseq.end_2=214658626;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=891;refseq.mrnaCoord_2=891;refseq.name2_1=USH2A;refseq.name2_2=USH2A;refseq.name_1=NM_007123;refseq.name_2=NM_206933;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T168T;refseq.proteinCoordStr_2=p.T168T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=19;refseq.spliceDist_2=19;refseq.start_1=214658626;refseq.start_2=214658626;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=Intersection GT 1/1
|
|
chr1 214661929 . C T 309.02 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=193;Dels=0.00;HRun=0;HaplotypeScore=6.16;MQ=98.40;MQ0=0;OQ=7911.92;QD=40.99;RankSumP=1.00000;SB=-3956.81;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.373G>A;refseq.codingCoordStr_2=c.373G>A;refseq.codonCoord_1=125;refseq.codonCoord_2=125;refseq.end_1=214661929;refseq.end_2=214661929;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=760;refseq.mrnaCoord_2=760;refseq.name2_1=USH2A;refseq.name2_2=USH2A;refseq.name_1=NM_007123;refseq.name_2=NM_206933;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A125T;refseq.proteinCoordStr_2=p.A125T;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=-113;refseq.spliceDist_2=-113;refseq.start_1=214661929;refseq.start_2=214661929;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACA;refseq.variantCodon_2=ACA;set=Intersection GT 1/1
|
|
chr1 214759292 . C T 341.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=3.86;MQ=99.00;MQ0=0;OQ=2733.40;QD=19.52;RankSumP=0.451323;SB=-1314.78;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_2=c.888G>A;refseq.codingCoordStr_3=c.957G>A;refseq.codingCoordStr_4=c.888G>A;refseq.codingCoordStr_5=c.888G>A;refseq.codonCoord_2=296;refseq.codonCoord_3=319;refseq.codonCoord_4=296;refseq.codonCoord_5=296;refseq.end_1=214759292;refseq.end_2=214759292;refseq.end_3=214759292;refseq.end_4=214759292;refseq.end_5=214759292;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeAlternate_5=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=1406;refseq.mrnaCoord_2=1206;refseq.mrnaCoord_3=1123;refseq.mrnaCoord_4=1239;refseq.mrnaCoord_5=1121;refseq.name2_1=ESRRG;refseq.name2_2=ESRRG;refseq.name2_3=ESRRG;refseq.name2_4=ESRRG;refseq.name2_5=ESRRG;refseq.name_1=NR_024099;refseq.name_2=NM_001134285;refseq.name_3=NM_001438;refseq.name_4=NM_206594;refseq.name_5=NM_206595;refseq.numMatchingRecords=5;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_2=p.S296S;refseq.proteinCoordStr_3=p.S319S;refseq.proteinCoordStr_4=p.S296S;refseq.proteinCoordStr_5=p.S296S;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceAA_5=Ser;refseq.referenceCodon_2=TCG;refseq.referenceCodon_3=TCG;refseq.referenceCodon_4=TCG;refseq.referenceCodon_5=TCG;refseq.spliceDist_1=95;refseq.spliceDist_2=95;refseq.spliceDist_3=95;refseq.spliceDist_4=95;refseq.spliceDist_5=95;refseq.start_1=214759292;refseq.start_2=214759292;refseq.start_3=214759292;refseq.start_4=214759292;refseq.start_5=214759292;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantAA_5=Ser;refseq.variantCodon_2=TCA;refseq.variantCodon_3=TCA;refseq.variantCodon_4=TCA;refseq.variantCodon_5=TCA;set=Intersection GT 0/1
|
|
chr1 216014361 . G A 86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=165;Dels=0.00;HRun=2;HaplotypeScore=1.73;MQ=98.63;MQ0=0;OQ=7062.82;QD=42.80;RankSumP=1.00000;SB=-2971.51;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.582G>A;refseq.codonCoord=194;refseq.end=216014361;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=608;refseq.name=NM_138796;refseq.name2=SPATA17;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q194Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=63;refseq.start=216014361;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/1
|
|
chr1 217450528 . A G 279.12 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=347;Dels=0.00;HRun=0;HaplotypeScore=8.04;MQ=97.35;MQ0=0;OQ=14855.58;QD=42.81;RankSumP=1.00000;SB=-5434.49;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.393A>G;refseq.codonCoord=131;refseq.end=217450528;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=434;refseq.name=NM_138794;refseq.name2=LYPLAL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I131M;refseq.referenceAA=Ile;refseq.referenceCodon=ATA;refseq.spliceDist=32;refseq.start=217450528;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/1
|
|
chr1 217450564 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.429A>G;refseq.codonCoord=143;refseq.end=217450564;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=470;refseq.name=NM_138794;refseq.name2=LYPLAL1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G143G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-49;refseq.start=217450564;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 218223316 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3138T>G;refseq.codonCoord=1046;refseq.end=218223316;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3408;refseq.name=NM_004446;refseq.name2=EPRS;refseq.positionType=CDS;refseq.proteinCoordStr=p.C1046W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=48;refseq.start=218223316;refseq.transcriptStrand=-;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 0/1
|
|
chr1 218237213 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2276T>G;refseq.codonCoord=759;refseq.end=218237213;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2546;refseq.name=NM_004446;refseq.name2=EPRS;refseq.positionType=CDS;refseq.proteinCoordStr=p.V759G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=95;refseq.start=218237213;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 218241120 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2164G>A;refseq.codonCoord=722;refseq.end=218241120;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2434;refseq.name=NM_004446;refseq.name2=EPRS;refseq.positionType=CDS;refseq.proteinCoordStr=p.E722K;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-18;refseq.start=218241120;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 0/1
|
|
chr1 218264248 . G T 328.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=148;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=98.65;MQ0=0;OQ=5871.19;QD=39.67;RankSumP=1.00000;SB=-1526.73;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.924C>A;refseq.codonCoord=308;refseq.end=218264248;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1194;refseq.name=NM_004446;refseq.name2=EPRS;refseq.positionType=CDS;refseq.proteinCoordStr=p.D308E;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-20;refseq.start=218264248;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/1
|
|
chr1 218307289 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.452A>C;refseq.codonCoord=151;refseq.end=218307289;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=624;refseq.name=NM_006085;refseq.name2=BPNT1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N151T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-23;refseq.start=218307289;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/0
|
|
chr1 218391242 . C T 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4156G>A;refseq.codonCoord=1386;refseq.end=218391242;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4320;refseq.name=NM_012414;refseq.name2=RAB3GAP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1386K;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=130;refseq.start=218391242;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 0/1
|
|
chr1 218436281 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.894A>C;refseq.codonCoord=298;refseq.end=218436281;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1058;refseq.name=NM_012414;refseq.name2=RAB3GAP2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P298P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-67;refseq.start=218436281;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 218872247 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1091C>A;refseq.codonCoord=364;refseq.end=218872247;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1688;refseq.name=NM_018650;refseq.name2=MARK1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T364N;refseq.referenceAA=Thr;refseq.referenceCodon=ACT;refseq.spliceDist=-32;refseq.start=218872247;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=FilteredInAll GT 1/0
|
|
chr1 219003000 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.735T>G;refseq.codonCoord=245;refseq.end=219003000;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=933;refseq.name=NM_017898;refseq.name2=MOSC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C245W;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-16;refseq.start=219003000;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=FilteredInAll GT 1/0
|
|
chr1 219021862 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1004T>G;refseq.codonCoord=335;refseq.end=219021862;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1202;refseq.name=NM_017898;refseq.name2=MOSC2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V335G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-36;refseq.start=219021862;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 219031457 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.277T>G;refseq.codonCoord=93;refseq.end=219031457;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=525;refseq.name=NM_022746;refseq.name2=MOSC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F93V;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=219031457;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTT;set=FilteredInAll GT 1/0
|
|
chr1 219036651 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=170;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=98.86;MQ0=0;OQ=1898.89;QD=11.17;RankSumP=0.0500497;SB=-871.03;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.493A>G;refseq.codonCoord=165;refseq.end=219036651;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=741;refseq.name=NM_022746;refseq.name2=MOSC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T165A;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=44;refseq.start=219036651;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 219120168 . T C 71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=16;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=11.95;MQ=92.61;MQ0=0;OQ=184.15;QD=4.38;RankSumP=0.532149;SB=-64.31;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.346T>C;refseq.codonCoord=116;refseq.end=219120168;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=803;refseq.name=NM_021958;refseq.name2=HLX;refseq.positionType=CDS;refseq.proteinCoordStr=p.S116P;refseq.referenceAA=Ser;refseq.referenceCodon=TCA;refseq.spliceDist=-247;refseq.start=219120168;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/0
|
|
chr1 219122130 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.774T>G;refseq.codonCoord=258;refseq.end=219122130;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1231;refseq.name=NM_021958;refseq.name2=HLX;refseq.positionType=CDS;refseq.proteinCoordStr=p.G258G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=219122130;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 219124269 . C T 101.34 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=6.03;MQ=97.24;MQ0=0;OQ=995.68;QD=12.00;RankSumP=0.161463;SB=-490.05;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1067C>T;refseq.codonCoord=356;refseq.end=219124269;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1524;refseq.name=NM_021958;refseq.name2=HLX;refseq.positionType=CDS;refseq.proteinCoordStr=p.P356L;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=110;refseq.start=219124269;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 0/1
|
|
chr1 219124285 . G A 81 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=6.67;MQ=97.32;MQ0=0;OQ=590.37;QD=7.29;RankSumP=0.00505112;SB=-305.83;SecondBestBaseQ=15;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1083G>A;refseq.codonCoord=361;refseq.end=219124285;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1540;refseq.name=NM_021958;refseq.name2=HLX;refseq.positionType=CDS;refseq.proteinCoordStr=p.E361E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=126;refseq.start=219124285;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=filterInsoap-gatk GT 1/0
|
|
chr1 219978965 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.745T>C;refseq.codonCoord_2=249;refseq.end_1=219981935;refseq.end_2=219978965;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=927;refseq.name2_1=DUSP10;refseq.name2_2=DUSP10;refseq.name_1=NM_144729;refseq.name_2=NM_007207;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S249P;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=TCC;refseq.spliceDist_2=-67;refseq.start_1=219946442;refseq.start_2=219978965;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Pro;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 219978984 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=23;DB;DP=675;Dels=0.00;HRun=0;HaplotypeScore=43.37;MQ=98.13;MQ0=0;OQ=9845.21;QD=14.59;RankSumP=0.0233296;SB=-228.91;SecondBestBaseQ=28;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.726A>G;refseq.codonCoord_2=242;refseq.end_1=219981935;refseq.end_2=219978984;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=908;refseq.name2_1=DUSP10;refseq.name2_2=DUSP10;refseq.name_1=NM_144729;refseq.name_2=NM_007207;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.E242E;refseq.referenceAA_2=Glu;refseq.referenceCodon_2=GAA;refseq.spliceDist_2=-86;refseq.start_1=219946442;refseq.start_2=219978984;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Glu;refseq.variantCodon_2=GAG;set=Intersection GT 1/0
|
|
chr1 219979431 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=17;DB;DP=217;Dels=0.00;HRun=0;HaplotypeScore=26.58;MQ=98.29;MQ0=0;OQ=1696.94;QD=7.82;RankSumP=0.273859;SB=-427.09;SecondBestBaseQ=19;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.279A>G;refseq.codonCoord_2=93;refseq.end_1=219981935;refseq.end_2=219979431;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=461;refseq.name2_1=DUSP10;refseq.name2_2=DUSP10;refseq.name_1=NM_144729;refseq.name_2=NM_007207;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.Q93Q;refseq.referenceAA_2=Gln;refseq.referenceCodon_2=CAA;refseq.spliceDist_2=322;refseq.start_1=219946442;refseq.start_2=219979431;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_2=Gln;refseq.variantCodon_2=CAG;set=Intersection GT 1/0
|
|
chr1 220780126 . C G 147.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=230;Dels=0.00;HRun=1;HaplotypeScore=2.43;MQ=98.91;MQ0=0;OQ=4850.84;QD=21.09;RankSumP=0.00920360;SB=-1752.01;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1299G>C;refseq.codonCoord=433;refseq.end=220780126;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1357;refseq.name=NM_024746;refseq.name2=HHIPL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T433T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=-152;refseq.start=220780126;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=filterInsoap-gatk GT 1/0
|
|
chr1 220780254 . G C 191.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=160;Dels=0.00;HRun=0;HaplotypeScore=5.79;MQ=98.83;MQ0=0;OQ=2640.75;QD=16.50;RankSumP=0.127491;SB=-791.78;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1171C>G;refseq.codonCoord=391;refseq.end=220780254;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1229;refseq.name=NM_024746;refseq.name2=HHIPL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.H391D;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=53;refseq.start=220780254;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 0/1
|
|
chr1 220787911 . C T 341.65 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.64;MQ0=0;OQ=1990.24;QD=36.86;RankSumP=1.00000;SB=-590.75;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.99G>A;refseq.codonCoord=33;refseq.end=220787911;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=157;refseq.name=NM_024746;refseq.name2=HHIPL2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L33L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=157;refseq.start=220787911;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTA;set=Intersection GT 1/1
|
|
chr1 220801345 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.00000;SecondBestBaseQ=16;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1224T>G;refseq.codingCoordStr_2=c.882T>G;refseq.codonCoord_1=408;refseq.codonCoord_2=294;refseq.end_1=220801345;refseq.end_2=220801345;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1413;refseq.mrnaCoord_2=1243;refseq.name2_1=TAF1A;refseq.name2_2=TAF1A;refseq.name_1=NM_005681;refseq.name_2=NM_139352;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G408G;refseq.proteinCoordStr_2=p.G294G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=-17;refseq.spliceDist_2=-17;refseq.start_1=220801345;refseq.start_2=220801345;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 220801426 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=178;Dels=0.00;HRun=2;HaplotypeScore=5.16;MQ=98.83;MQ0=0;OQ=3215.74;QD=18.07;RankSumP=0.256439;SB=-1224.41;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1143C>G;refseq.codingCoordStr_2=c.801C>G;refseq.codonCoord_1=381;refseq.codonCoord_2=267;refseq.end_1=220801426;refseq.end_2=220801426;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1332;refseq.mrnaCoord_2=1162;refseq.name2_1=TAF1A;refseq.name2_2=TAF1A;refseq.name_1=NM_005681;refseq.name_2=NM_139352;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G381G;refseq.proteinCoordStr_2=p.G267G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGC;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=58;refseq.spliceDist_2=58;refseq.start_1=220801426;refseq.start_2=220801426;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=Intersection GT 0/1
|
|
chr1 220868629 . A G 262.83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1048.23;QD=40.32;RankSumP=1.00000;SB=-537.54;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1444A>G;refseq.codonCoord=482;refseq.end=220868629;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1453;refseq.name=NM_198551;refseq.name2=MIA3;refseq.positionType=CDS;refseq.proteinCoordStr=p.K482E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=1090;refseq.start=220868629;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 220869426 . T G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=153;Dels=0.00;HRun=3;HaplotypeScore=1.03;MQ=99.00;MQ0=0;OQ=5423.59;QD=35.45;RankSumP=1.00000;SB=-1710.84;SecondBestBaseQ=5;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2241T>G;refseq.codonCoord=747;refseq.end=220869426;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2250;refseq.name=NM_198551;refseq.name2=MIA3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P747P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-929;refseq.start=220869426;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/1
|
|
chr1 220869549 . C T 297.82 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=198;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.96;MQ0=0;OQ=8063.73;QD=40.73;RankSumP=1.00000;SB=-3625.82;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2364C>T;refseq.codonCoord=788;refseq.end=220869549;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2373;refseq.name=NM_198551;refseq.name2=MIA3;refseq.positionType=CDS;refseq.proteinCoordStr=p.S788S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-806;refseq.start=220869549;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/1
|
|
chr1 220900161 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=326;Dels=0.00;HRun=2;HaplotypeScore=5.81;MQ=98.82;MQ0=0;OQ=7517.44;QD=23.06;RankSumP=0.485058;SB=-2485.59;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4995C>G;refseq.codonCoord=1665;refseq.end=220900161;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5004;refseq.name=NM_198551;refseq.name2=MIA3;refseq.positionType=CDS;refseq.proteinCoordStr=p.G1665G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=20;refseq.start=220900161;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 1/0
|
|
chr1 220900224 . T C 94 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=253;Dels=0.00;HRun=2;HaplotypeScore=6.27;MQ=98.78;MQ0=0;OQ=9409.82;QD=37.19;RankSumP=1.00000;SB=-4624.49;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5058T>C;refseq.codonCoord=1686;refseq.end=220900224;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5067;refseq.name=NM_198551;refseq.name2=MIA3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1686P;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-56;refseq.start=220900224;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 220905340 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5480A>C;refseq.codonCoord=1827;refseq.end=220905340;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5489;refseq.name=NM_198551;refseq.name2=MIA3;refseq.positionType=CDS;refseq.proteinCoordStr=p.D1827A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=67;refseq.start=220905340;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 0/1
|
|
chr1 220905527 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5667A>C;refseq.codonCoord=1889;refseq.end=220905527;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5676;refseq.name=NM_198551;refseq.name2=MIA3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1889P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=254;refseq.start=220905527;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 220962471 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.393A>G;refseq.codonCoord=131;refseq.end=220962471;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=788;refseq.name=NM_144695;refseq.name2=C1orf58;refseq.positionType=CDS;refseq.proteinCoordStr=p.G131G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=220962471;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 220986518 . T G 458.51 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=98.70;MQ0=0;OQ=6793.40;QD=39.73;RankSumP=1.00000;SB=-1824.53;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8T>G;refseq.codonCoord=3;refseq.end=220986518;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=274;refseq.name=NM_207468;refseq.name2=FAM177B;refseq.positionType=CDS;refseq.proteinCoordStr=p.I3S;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=23;refseq.start=220986518;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 1/1
|
|
chr1 220989974 . A G 353.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=247;Dels=0.00;HRun=0;HaplotypeScore=4.49;MQ=98.76;MQ0=0;OQ=8815.23;QD=35.69;RankSumP=1.00000;SB=-2810.47;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.428A>G;refseq.codonCoord=143;refseq.end=220989974;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=694;refseq.name=NM_207468;refseq.name2=FAM177B;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q143R;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=89;refseq.start=220989974;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGA;set=Intersection GT 1/1
|
|
chr1 221245184 . A C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=659;Dels=0.00;HRun=3;HaplotypeScore=15.16;MQ=98.79;MQ0=0;OQ=24217.73;QD=36.75;RankSumP=1.00000;SB=-11513.13;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3822A>C;refseq.codonCoord=1274;refseq.end=221245184;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3969;refseq.name=NM_032890;refseq.name2=DISP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1274P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-775;refseq.start=221245184;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=soap-filterIngatk GT 1/1
|
|
chr1 221350533 . A G 318.33 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=175;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=98.87;MQ0=0;OQ=7314.69;QD=41.80;RankSumP=1.00000;SB=-3387.03;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2464T>C;refseq.codonCoord=822;refseq.end=221350533;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3105;refseq.name=NM_003268;refseq.name2=TLR5;refseq.positionType=CDS;refseq.proteinCoordStr=p.F822L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-1163;refseq.start=221350533;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/1
|
|
chr1 221351151 . A G 255.96 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=221;Dels=0.00;HRun=0;HaplotypeScore=3.82;MQ=98.83;MQ0=0;OQ=4335.58;QD=19.62;RankSumP=0.349548;SB=-1812.01;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1846T>C;refseq.codonCoord=616;refseq.end=221351151;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2487;refseq.name=NM_003268;refseq.name2=TLR5;refseq.positionType=CDS;refseq.proteinCoordStr=p.F616L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=-1781;refseq.start=221351151;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 0/1
|
|
chr1 221469216 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.862A>C;refseq.codonCoord=288;refseq.end=221469216;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1043;refseq.name=NM_017982;refseq.name2=SUSD4;refseq.positionType=CDS;refseq.proteinCoordStr=p.T288P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-55;refseq.start=221469216;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 221634454 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=18;HRun=2;RankSumP=0.777778;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1014C>A;refseq.codonCoord=338;refseq.end=221634454;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1117;refseq.name=NM_152610;refseq.name2=C1orf65;refseq.positionType=CDS;refseq.proteinCoordStr=p.N338K;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-982;refseq.start=221634454;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=FilteredInAll GT 1/0
|
|
chr1 221967031 . C G 178.71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=6.38;MQ=98.30;MQ0=0;OQ=2157.01;QD=35.95;RankSumP=1.00000;SB=-383.75;SecondBestBaseQ=2;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.66C>G;refseq.codonCoord_2=22;refseq.end_1=221972076;refseq.end_2=221967031;refseq.frame_2=2;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=290;refseq.name2_1=CAPN2;refseq.name2_2=CAPN2;refseq.name_1=NM_001146068;refseq.name_2=NM_001748;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.D22E;refseq.referenceAA_2=Asp;refseq.referenceCodon_2=GAC;refseq.spliceDist_2=-172;refseq.start_1=221956167;refseq.start_2=221967031;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Glu;refseq.variantCodon_2=GAG;set=Intersection GT 1/1
|
|
chr1 221972155 . G A 214.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=98.47;MQ0=0;OQ=1673.40;QD=15.08;RankSumP=0.378558;SB=-502.63;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.72G>A;refseq.codingCoordStr_2=c.306G>A;refseq.codonCoord_1=24;refseq.codonCoord_2=102;refseq.end_1=221972155;refseq.end_2=221972155;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=308;refseq.mrnaCoord_2=530;refseq.name2_1=CAPN2;refseq.name2_2=CAPN2;refseq.name_1=NM_001146068;refseq.name_2=NM_001748;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L24L;refseq.proteinCoordStr_2=p.L102L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=-2;refseq.spliceDist_2=-2;refseq.spliceInfo_1=splice-donor_-2;refseq.spliceInfo_2=splice-donor_-2;refseq.start_1=221972155;refseq.start_2=221972155;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=Intersection GT 1/0
|
|
chr1 222001343 . G A 334.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=116;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=98.77;MQ0=0;OQ=4366.15;QD=37.64;RankSumP=1.00000;SB=-1395.83;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.348G>A;refseq.codingCoordStr_2=c.582G>A;refseq.codonCoord_1=116;refseq.codonCoord_2=194;refseq.end_1=222001343;refseq.end_2=222001343;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=584;refseq.mrnaCoord_2=806;refseq.name2_1=CAPN2;refseq.name2_2=CAPN2;refseq.name_1=NM_001146068;refseq.name_2=NM_001748;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A116A;refseq.proteinCoordStr_2=p.A194A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=22;refseq.spliceDist_2=22;refseq.start_1=222001343;refseq.start_2=222001343;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=Intersection GT 1/1
|
|
chr1 222015937 . G C 144.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=448;Dels=0.00;HRun=0;HaplotypeScore=12.09;MQ=98.86;MQ0=0;OQ=10413.72;QD=23.24;RankSumP=0.448974;SB=-3380.09;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1327G>C;refseq.codingCoordStr_2=c.1561G>C;refseq.codonCoord_1=443;refseq.codonCoord_2=521;refseq.end_1=222015937;refseq.end_2=222015937;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1563;refseq.mrnaCoord_2=1785;refseq.name2_1=CAPN2;refseq.name2_2=CAPN2;refseq.name_1=NM_001146068;refseq.name_2=NM_001748;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E443Q;refseq.proteinCoordStr_2=p.E521Q;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=-6;refseq.spliceDist_2=-6;refseq.spliceInfo_1=splice-donor_-6;refseq.spliceInfo_2=splice-donor_-6;refseq.start_1=222015937;refseq.start_2=222015937;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAA;refseq.variantCodon_2=CAA;set=Intersection GT 0/1
|
|
chr1 222020703 . A C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=284;Dels=0.00;HRun=1;HaplotypeScore=11.78;MQ=98.93;MQ0=0;OQ=5124.88;QD=18.05;RankSumP=0.408585;SB=-1871.10;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1468A>C;refseq.codingCoordStr_2=c.1702A>C;refseq.codonCoord_1=490;refseq.codonCoord_2=568;refseq.end_1=222020703;refseq.end_2=222020703;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1704;refseq.mrnaCoord_2=1926;refseq.name2_1=CAPN2;refseq.name2_2=CAPN2;refseq.name_1=NM_001146068;refseq.name_2=NM_001748;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K490Q;refseq.proteinCoordStr_2=p.K568Q;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.start_1=222020703;refseq.start_2=222020703;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gln;refseq.variantAA_2=Gln;refseq.variantCodon_1=CAG;refseq.variantCodon_2=CAG;set=Intersection GT 0/1
|
|
chr1 222046830 . G C 247.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=275;Dels=0.00;HRun=0;HaplotypeScore=13.53;MQ=98.76;MQ0=0;OQ=6294.36;QD=22.89;RankSumP=0.122208;SB=-2444.76;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2880C>G;refseq.codingCoordStr_2=c.2493C>G;refseq.codonCoord_1=960;refseq.codonCoord_2=831;refseq.end_1=222046830;refseq.end_2=222046830;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3172;refseq.mrnaCoord_2=3304;refseq.name2_1=TP53BP2;refseq.name2_2=TP53BP2;refseq.name_1=NM_001031685;refseq.name_2=NM_005426;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L960L;refseq.proteinCoordStr_2=p.L831L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.spliceDist_1=18;refseq.spliceDist_2=18;refseq.start_1=222046830;refseq.start_2=222046830;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTG;refseq.variantCodon_2=CTG;set=Intersection GT 0/1
|
|
chr1 222056589 . C T 238.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=402;Dels=0.00;HRun=0;HaplotypeScore=11.52;MQ=98.58;MQ0=0;OQ=5898.42;QD=14.67;RankSumP=0.111794;SB=-1836.01;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1077G>A;refseq.codingCoordStr_2=c.690G>A;refseq.codonCoord_1=359;refseq.codonCoord_2=230;refseq.end_1=222056589;refseq.end_2=222056589;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1369;refseq.mrnaCoord_2=1501;refseq.name2_1=TP53BP2;refseq.name2_2=TP53BP2;refseq.name_1=NM_001031685;refseq.name_2=NM_005426;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S359S;refseq.proteinCoordStr_2=p.S230S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCG;refseq.referenceCodon_2=TCG;refseq.spliceDist_1=81;refseq.spliceDist_2=81;refseq.start_1=222056589;refseq.start_2=222056589;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCA;refseq.variantCodon_2=TCA;set=Intersection GT 0/1
|
|
chr1 222522377 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=1;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2164G>C;refseq.codingCoordStr_2=c.1846G>C;refseq.codonCoord_1=722;refseq.codonCoord_2=616;refseq.end_1=222522377;refseq.end_2=222522377;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2207;refseq.mrnaCoord_2=2133;refseq.name2_1=NVL;refseq.name2_2=NVL;refseq.name_1=NM_002533;refseq.name_2=NM_206840;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A722P;refseq.proteinCoordStr_2=p.A616P;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=-19;refseq.spliceDist_2=-19;refseq.start_1=222522377;refseq.start_2=222522377;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCA;refseq.variantCodon_2=CCA;set=FilteredInAll GT 1/0
|
|
chr1 222548718 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=1;RankSumP=9.90201e-10;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1199C>G;refseq.codingCoordStr_2=c.881C>G;refseq.codonCoord_1=400;refseq.codonCoord_2=294;refseq.end_1=222548718;refseq.end_2=222548718;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1242;refseq.mrnaCoord_2=1168;refseq.name2_1=NVL;refseq.name2_2=NVL;refseq.name_1=NM_002533;refseq.name_2=NM_206840;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A400G;refseq.proteinCoordStr_2=p.A294G;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=19;refseq.spliceDist_2=19;refseq.start_1=222548718;refseq.start_2=222548718;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGT;refseq.variantCodon_2=GGT;set=FilteredInAll GT 0/1
|
|
chr1 222559369 . C T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=831;Dels=0.00;HRun=0;HaplotypeScore=15.13;MQ=98.76;MQ0=0;OQ=34341.76;QD=41.33;RankSumP=1.00000;SB=-14543.36;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.738G>A;refseq.codingCoordStr_2=c.420G>A;refseq.codonCoord_1=246;refseq.codonCoord_2=140;refseq.end_1=222559369;refseq.end_2=222559369;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=781;refseq.mrnaCoord_2=707;refseq.name2_1=NVL;refseq.name2_2=NVL;refseq.name_1=NM_002533;refseq.name_2=NM_206840;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L246L;refseq.proteinCoordStr_2=p.L140L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=-11;refseq.spliceDist_2=-11;refseq.start_1=222559369;refseq.start_2=222559369;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;set=Intersection GT 1/1
|
|
chr1 222562475 . C T 92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=495;Dels=0.00;HRun=1;HaplotypeScore=20.95;MQ=98.79;MQ0=0;OQ=21125.57;QD=42.68;RankSumP=1.00000;SB=-7876.97;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.456G>A;refseq.codingCoordStr_2=c.138G>A;refseq.codonCoord_1=152;refseq.codonCoord_2=46;refseq.end_1=222562475;refseq.end_2=222562475;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=499;refseq.mrnaCoord_2=425;refseq.name2_1=NVL;refseq.name2_2=NVL;refseq.name_1=NM_002533;refseq.name_2=NM_206840;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R152R;refseq.proteinCoordStr_2=p.R46R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.spliceDist_1=114;refseq.spliceDist_2=114;refseq.start_1=222562475;refseq.start_2=222562475;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGA;refseq.variantCodon_2=CGA;set=Intersection GT 1/1
|
|
chr1 222672678 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.878T>G;refseq.codingCoordStr_2=c.926T>G;refseq.codonCoord_1=293;refseq.codonCoord_2=309;refseq.end_1=222672678;refseq.end_2=222672678;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1072;refseq.mrnaCoord_2=1120;refseq.name2_1=WDR26;refseq.name2_2=WDR26;refseq.name_1=NM_001115113;refseq.name_2=NM_025160;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V293G;refseq.proteinCoordStr_2=p.V309G;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=64;refseq.spliceDist_2=64;refseq.start_1=222672678;refseq.start_2=222672678;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 223673767 . C T 245.74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=110;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.87;MQ0=0;OQ=4807.17;QD=43.70;RankSumP=1.00000;SB=-1331.19;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.461G>A;refseq.codingCoordStr_2=c.461G>A;refseq.codonCoord_1=154;refseq.codonCoord_2=154;refseq.end_1=223673767;refseq.end_2=223673767;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=604;refseq.mrnaCoord_2=587;refseq.name2_1=LBR;refseq.name2_2=LBR;refseq.name_1=NM_002296;refseq.name_2=NM_194442;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S154N;refseq.proteinCoordStr_2=p.S154N;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=AGT;refseq.referenceCodon_2=AGT;refseq.spliceDist_1=11;refseq.spliceDist_2=11;refseq.start_1=223673767;refseq.start_2=223673767;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 1/1
|
|
chr1 223676507 . A G 59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=22;DB;DP=297;Dels=0.00;HRun=4;HaplotypeScore=58.84;MQ=97.99;MQ0=0;OQ=7780.52;QD=26.20;RankSumP=1.00000;SB=-767.00;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.261T>C;refseq.codingCoordStr_2=c.261T>C;refseq.codonCoord_1=87;refseq.codonCoord_2=87;refseq.end_1=223676507;refseq.end_2=223676507;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=404;refseq.mrnaCoord_2=387;refseq.name2_1=LBR;refseq.name2_2=LBR;refseq.name_1=NM_002296;refseq.name_2=NM_194442;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P87P;refseq.proteinCoordStr_2=p.P87P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.spliceDist_1=96;refseq.spliceDist_2=96;refseq.start_1=223676507;refseq.start_2=223676507;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=soap-filterIngatk GT 1/1
|
|
chr1 223678284 . C T 83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=126;Dels=0.00;HRun=2;HaplotypeScore=1.79;MQ=98.68;MQ0=0;OQ=5301.56;QD=42.08;RankSumP=1.00000;SB=-2430.74;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.117G>A;refseq.codingCoordStr_2=c.117G>A;refseq.codonCoord_1=39;refseq.codonCoord_2=39;refseq.end_1=223678284;refseq.end_2=223678284;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=260;refseq.mrnaCoord_2=243;refseq.name2_1=LBR;refseq.name2_2=LBR;refseq.name_1=NM_002296;refseq.name_2=NM_194442;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V39V;refseq.proteinCoordStr_2=p.V39V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.spliceDist_1=-49;refseq.spliceDist_2=-49;refseq.start_1=223678284;refseq.start_2=223678284;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTA;refseq.variantCodon_2=GTA;set=Intersection GT 1/1
|
|
chr1 224086256 . T C 326.12 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=233;Dels=0.00;HRun=0;HaplotypeScore=11.13;MQ=98.86;MQ0=0;OQ=4447.36;QD=19.09;RankSumP=0.112400;SB=-1417.47;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.337T>C;refseq.codingCoordStr_2=c.337T>C;refseq.codonCoord_1=113;refseq.codonCoord_2=113;refseq.end_1=224086256;refseq.end_2=224086256;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=586;refseq.mrnaCoord_2=417;refseq.name2_1=EPHX1;refseq.name2_2=EPHX1;refseq.name_1=NM_000120;refseq.name_2=NM_001136018;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.Y113H;refseq.proteinCoordStr_2=p.Y113H;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceCodon_1=TAC;refseq.referenceCodon_2=TAC;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.start_1=224086256;refseq.start_2=224086256;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAC;refseq.variantCodon_2=CAC;set=Intersection GT 1/0
|
|
chr1 224093029 . A G 127.25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=117;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=98.49;MQ0=0;OQ=1531.45;QD=13.09;RankSumP=0.149119;SB=-318.54;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.416A>G;refseq.codingCoordStr_2=c.416A>G;refseq.codonCoord_1=139;refseq.codonCoord_2=139;refseq.end_1=224093029;refseq.end_2=224093029;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=665;refseq.mrnaCoord_2=496;refseq.name2_1=EPHX1;refseq.name2_2=EPHX1;refseq.name_1=NM_000120;refseq.name_2=NM_001136018;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H139R;refseq.proteinCoordStr_2=p.H139R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.spliceDist_1=52;refseq.spliceDist_2=52;refseq.start_1=224093029;refseq.start_2=224093029;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;set=Intersection GT 0/1
|
|
chr1 224098852 . C T 180.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=186;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=98.95;MQ0=0;OQ=2611.96;QD=14.04;RankSumP=0.190704;SB=-1089.47;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1071C>T;refseq.codingCoordStr_2=c.1071C>T;refseq.codonCoord_1=357;refseq.codonCoord_2=357;refseq.end_1=224098852;refseq.end_2=224098852;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1320;refseq.mrnaCoord_2=1151;refseq.name2_1=EPHX1;refseq.name2_2=EPHX1;refseq.name_1=NM_000120;refseq.name_2=NM_001136018;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N357N;refseq.proteinCoordStr_2=p.N357N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.start_1=224098852;refseq.start_2=224098852;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 0/1
|
|
chr1 224101532 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.64;MQ0=0;OQ=761.51;QD=16.55;RankSumP=0.707399;SB=-181.23;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2256C>T;refseq.codonCoord=752;refseq.end=224101532;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=2878;refseq.name=NM_014698;refseq.name2=TMEM63A;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y752Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=224101532;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAT;set=Intersection GT 1/0
|
|
chr1 224116673 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.953A>G;refseq.codonCoord=318;refseq.end=224116673;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1575;refseq.name=NM_014698;refseq.name2=TMEM63A;refseq.positionType=CDS;refseq.proteinCoordStr=p.E318G;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=224116673;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=FilteredInAll GT 1/0
|
|
chr1 224122218 . G A 116.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=251;Dels=0.00;HRun=2;HaplotypeScore=9.04;MQ=98.72;MQ0=0;OQ=5431.40;QD=21.64;RankSumP=0.423583;SB=-1887.38;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.507C>T;refseq.codonCoord=169;refseq.end=224122218;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1129;refseq.name=NM_014698;refseq.name2=TMEM63A;refseq.positionType=CDS;refseq.proteinCoordStr=p.D169D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-8;refseq.spliceInfo=splice-donor_-8;refseq.start=224122218;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/0
|
|
chr1 224131814 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=159;Dels=0.00;HRun=0;HaplotypeScore=6.33;MQ=98.96;MQ0=0;OQ=3111.68;QD=19.57;RankSumP=0.357531;SB=-1488.09;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.90C>G;refseq.codonCoord=30;refseq.end=224131814;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=712;refseq.name=NM_014698;refseq.name2=TMEM63A;refseq.positionType=CDS;refseq.proteinCoordStr=p.S30S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-97;refseq.start=224131814;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=Intersection GT 0/1
|
|
chr1 224141060 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1091T>C;refseq.codonCoord=364;refseq.end=224141060;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1161;refseq.name=NM_020997;refseq.name2=LEFTY1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L364P;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=354;refseq.start=224141060;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 224141186 . T G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=151;Dels=0.00;HRun=1;HaplotypeScore=2.86;MQ=78.90;MQ0=24;OQ=1392.18;QD=9.22;RankSumP=0.233237;SB=-517.73;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.965A>C;refseq.codonCoord=322;refseq.end=224141186;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1035;refseq.name=NM_020997;refseq.name2=LEFTY1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D322A;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=228;refseq.start=224141186;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/0
|
|
chr1 224176193 . G C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=1.13883e-07;SecondBestBaseQ=14;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.528C>G;refseq.codonCoord=176;refseq.end=224176193;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=683;refseq.name=NM_013328;refseq.name2=PYCR2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S176R;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-13;refseq.start=224176193;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=FilteredInAll GT 0/1
|
|
chr1 224191774 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.989T>C;refseq.codingCoordStr_2=c.1091T>C;refseq.codonCoord_1=330;refseq.codonCoord_2=364;refseq.end_1=224191774;refseq.end_2=224191774;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1232;refseq.mrnaCoord_2=1334;refseq.name2_1=LEFTY2;refseq.name2_2=LEFTY2;refseq.name_1=NM_001172425;refseq.name_2=NM_003240;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L330P;refseq.proteinCoordStr_2=p.L364P;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTC;refseq.referenceCodon_2=CTC;refseq.spliceDist_1=354;refseq.spliceDist_2=354;refseq.start_1=224191774;refseq.start_2=224191774;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;set=FilteredInAll GT 0/1
|
|
chr1 224193839 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=19;HRun=1;RankSumP=0.00145626;SecondBestBaseQ=8;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.480G>C;refseq.codingCoordStr_2=c.582G>C;refseq.codonCoord_1=160;refseq.codonCoord_2=194;refseq.end_1=224193839;refseq.end_2=224193839;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=723;refseq.mrnaCoord_2=825;refseq.name2_1=LEFTY2;refseq.name2_2=LEFTY2;refseq.name_1=NM_001172425;refseq.name_2=NM_003240;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R160R;refseq.proteinCoordStr_2=p.R194R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGG;refseq.referenceCodon_2=CGG;refseq.spliceDist_1=85;refseq.spliceDist_2=85;refseq.start_1=224193839;refseq.start_2=224193839;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=FilteredInAll GT 1/0
|
|
chr1 224193895 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.424A>G;refseq.codingCoordStr_2=c.526A>G;refseq.codonCoord_1=142;refseq.codonCoord_2=176;refseq.end_1=224193895;refseq.end_2=224193895;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=667;refseq.mrnaCoord_2=769;refseq.name2_1=LEFTY2;refseq.name2_2=LEFTY2;refseq.name_1=NM_001172425;refseq.name_2=NM_003240;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.K142E;refseq.proteinCoordStr_2=p.K176E;refseq.referenceAA_1=Lys;refseq.referenceAA_2=Lys;refseq.referenceCodon_1=AAG;refseq.referenceCodon_2=AAG;refseq.spliceDist_1=29;refseq.spliceDist_2=29;refseq.start_1=224193895;refseq.start_2=224193895;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=FilteredInAll GT 1/0
|
|
chr1 224246829 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=2;RankSumP=1.21143e-08;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.413A>G;refseq.codonCoord=138;refseq.end=224246829;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=466;refseq.name=NM_152608;refseq.name2=C1orf55;refseq.positionType=CDS;refseq.proteinCoordStr=p.E138G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=63;refseq.start=224246829;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 224409118 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=3;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.943T>G;refseq.codonCoord=315;refseq.end=224409118;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=990;refseq.name=NM_022735;refseq.name2=ACBD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.S315A;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=40;refseq.start=224409118;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=FilteredInAll GT 0/1
|
|
chr1 224419121 . T G 288.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=286;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=98.38;MQ0=0;OQ=11147.98;QD=38.98;RankSumP=1.00000;SB=-4993.77;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.561A>C;refseq.codonCoord=187;refseq.end=224419121;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=608;refseq.name=NM_022735;refseq.name2=ACBD3;refseq.positionType=CDS;refseq.proteinCoordStr=p.E187D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=224419121;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 224540755 . G A 68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=1780.05;QD=42.38;RankSumP=1.00000;SB=-629.37;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.474C>T;refseq.codonCoord=158;refseq.end=224540755;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=784;refseq.name=NM_173083;refseq.name2=LIN9;refseq.positionType=CDS;refseq.proteinCoordStr=p.F158F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=28;refseq.start=224540755;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/1
|
|
chr1 224621925 . A G 280.71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=262;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=98.81;MQ0=0;OQ=9881.22;QD=37.71;RankSumP=1.00000;SB=-4620.95;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2285T>C;refseq.codonCoord=762;refseq.end=224621925;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2456;refseq.name=NM_001618;refseq.name2=PARP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V762A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=224621925;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 224635469 . A C 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=249;Dels=0.00;HRun=1;HaplotypeScore=2.70;MQ=98.94;MQ0=0;OQ=178.84;QD=0.72;RankSumP=2.16088e-07;SB=420.37;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1223T>G;refseq.codonCoord=408;refseq.end=224635469;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1394;refseq.name=NM_001618;refseq.name2=PARP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V408G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=64;refseq.start=224635469;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 224637390 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.54;MQ=98.41;MQ0=0;OQ=691.57;QD=15.03;RankSumP=0.653273;SB=-190.71;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1129C>T;refseq.codonCoord=377;refseq.end=224637390;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1300;refseq.name=NM_001618;refseq.name2=PARP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P377S;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=-31;refseq.start=224637390;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/0
|
|
chr1 224639987 . A G 62 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=537;Dels=0.00;HRun=1;HaplotypeScore=29.95;MQ=98.35;MQ0=0;OQ=18913.35;QD=35.22;RankSumP=1.00000;SB=-7361.90;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.852T>C;refseq.codonCoord=284;refseq.end=224639987;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1023;refseq.name=NM_001618;refseq.name2=PARP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A284A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=18;refseq.start=224639987;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 224656581 . G A 295.59 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=339;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=98.79;MQ0=0;OQ=13815.10;QD=40.75;RankSumP=1.00000;SB=-6453.91;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.243C>T;refseq.codonCoord=81;refseq.end=224656581;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=414;refseq.name=NM_001618;refseq.name2=PARP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D81D;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-44;refseq.start=224656581;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=Intersection GT 1/1
|
|
chr1 224990128 . G T 271.56 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=165;Dels=0.00;HRun=0;HaplotypeScore=8.07;MQ=98.31;MQ0=0;OQ=2507.34;QD=15.20;RankSumP=0.0633404;SB=-1163.60;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1655C>A;refseq.codonCoord=552;refseq.end=224990128;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1995;refseq.name=NM_002221;refseq.name2=ITPKB;refseq.positionType=CDS;refseq.proteinCoordStr=p.P552Q;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-278;refseq.start=224990128;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 224990561 . A C 137.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=155;Dels=0.00;HRun=0;HaplotypeScore=8.63;MQ=98.85;MQ0=0;OQ=2132.20;QD=13.76;RankSumP=0.0927053;SB=-304.83;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1222T>G;refseq.codonCoord=408;refseq.end=224990561;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1562;refseq.name=NM_002221;refseq.name2=ITPKB;refseq.positionType=CDS;refseq.proteinCoordStr=p.S408A;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-711;refseq.start=224990561;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 0/1
|
|
chr1 224991265 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=98.83;MQ0=0;OQ=1094.73;QD=15.64;RankSumP=0.240044;SB=-308.20;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.518G>A;refseq.codonCoord=173;refseq.end=224991265;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=858;refseq.name=NM_002221;refseq.name2=ITPKB;refseq.positionType=CDS;refseq.proteinCoordStr=p.R173H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=723;refseq.start=224991265;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 0/1
|
|
chr1 225136300 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=168;Dels=0.00;HRun=1;HaplotypeScore=7.44;MQ=98.99;MQ0=0;OQ=2004.51;QD=11.93;RankSumP=0.0493831;SB=-994.97;SecondBestBaseQ=27;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.69T>C;refseq.codingCoordStr_2=c.69T>C;refseq.codonCoord_1=23;refseq.codonCoord_2=23;refseq.end_1=225136300;refseq.end_2=225136300;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=496;refseq.mrnaCoord_2=496;refseq.name2_1=PSEN2;refseq.name2_2=PSEN2;refseq.name_1=NM_000447;refseq.name_2=NM_012486;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A23A;refseq.proteinCoordStr_2=p.A23A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=-73;refseq.spliceDist_2=-73;refseq.start_1=225136300;refseq.start_2=225136300;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;set=Intersection GT 1/0
|
|
chr1 225136360 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.20;MQ=98.94;MQ0=0;OQ=999.36;QD=12.19;RankSumP=0.232711;SB=-241.74;SecondBestBaseQ=27;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.129C>T;refseq.codingCoordStr_2=c.129C>T;refseq.codonCoord_1=43;refseq.codonCoord_2=43;refseq.end_1=225136360;refseq.end_2=225136360;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=556;refseq.mrnaCoord_2=556;refseq.name2_1=PSEN2;refseq.name2_2=PSEN2;refseq.name_1=NM_000447;refseq.name_2=NM_012486;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N43N;refseq.proteinCoordStr_2=p.N43N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-13;refseq.spliceDist_2=-13;refseq.start_1=225136360;refseq.start_2=225136360;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 0/1
|
|
chr1 225138148 . C T 249.88 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=7.27;MQ=98.69;MQ0=0;OQ=1597.19;QD=15.81;RankSumP=0.137694;SB=-630.05;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.261C>T;refseq.codingCoordStr_2=c.261C>T;refseq.codonCoord_1=87;refseq.codonCoord_2=87;refseq.end_1=225138148;refseq.end_2=225138148;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=688;refseq.mrnaCoord_2=688;refseq.name2_1=PSEN2;refseq.name2_2=PSEN2;refseq.name_1=NM_000447;refseq.name_2=NM_012486;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.H87H;refseq.proteinCoordStr_2=p.H87H;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceCodon_1=CAC;refseq.referenceCodon_2=CAC;refseq.spliceDist_1=-96;refseq.spliceDist_2=-96;refseq.start_1=225138148;refseq.start_2=225138148;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=His;refseq.variantAA_2=His;refseq.variantCodon_1=CAT;refseq.variantCodon_2=CAT;set=Intersection GT 0/1
|
|
chr1 225215826 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.70;MQ=96.37;MQ0=0;OQ=1033.85;QD=13.97;RankSumP=0.187290;SB=-197.83;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.117G>A;refseq.codonCoord=39;refseq.end=225215826;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=289;refseq.name=NM_020247;refseq.name2=CABC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A39A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-61;refseq.start=225215826;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 225238913 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=328;Dels=0.00;HRun=2;HaplotypeScore=15.67;MQ=98.95;MQ0=0;OQ=6328.14;QD=19.29;RankSumP=0.457567;SB=-2092.38;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1440C>T;refseq.codonCoord=480;refseq.end=225238913;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1612;refseq.name=NM_020247;refseq.name2=CABC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F480F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=42;refseq.start=225238913;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 0/1
|
|
chr1 225240833 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=208;Dels=0.00;HRun=1;HaplotypeScore=10.83;MQ=99.00;MQ0=0;OQ=2919.71;QD=14.04;RankSumP=0.451643;SB=-144.66;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1716T>C;refseq.codonCoord=572;refseq.end=225240833;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1888;refseq.name=NM_020247;refseq.name2=CABC1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S572S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=57;refseq.start=225240833;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/0
|
|
chr1 225248656 . G A 38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=98.39;MQ0=0;OQ=1358.05;QD=38.80;RankSumP=1.00000;SB=-636.37;SecondBestBaseQ=2;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.5096C>T;refseq.codingCoordStr_2=c.4853C>T;refseq.codonCoord_1=1699;refseq.codonCoord_2=1618;refseq.end_1=225248656;refseq.end_2=225248656;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=6039;refseq.mrnaCoord_2=5796;refseq.name2_1=CDC42BPA;refseq.name2_2=CDC42BPA;refseq.name_1=NM_003607;refseq.name_2=NM_014826;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A1699V;refseq.proteinCoordStr_2=p.A1618V;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.spliceDist_1=68;refseq.spliceDist_2=68;refseq.start_1=225248656;refseq.start_2=225248656;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=Intersection GT 1/1
|
|
chr1 225249198 . A G 74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=386;Dels=0.00;HRun=1;HaplotypeScore=8.94;MQ=98.82;MQ0=0;OQ=12329.86;QD=31.94;RankSumP=1.00000;SB=-5800.28;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.4977T>C;refseq.codingCoordStr_2=c.4734T>C;refseq.codonCoord_1=1659;refseq.codonCoord_2=1578;refseq.end_1=225249198;refseq.end_2=225249198;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=5920;refseq.mrnaCoord_2=5677;refseq.name2_1=CDC42BPA;refseq.name2_2=CDC42BPA;refseq.name_1=NM_003607;refseq.name_2=NM_014826;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S1659S;refseq.proteinCoordStr_2=p.S1578S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCT;refseq.referenceCodon_2=TCT;refseq.spliceDist_1=-52;refseq.spliceDist_2=-52;refseq.start_1=225249198;refseq.start_2=225249198;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCC;refseq.variantCodon_2=TCC;set=Intersection GT 1/1
|
|
chr1 225394027 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1263T>G;refseq.codingCoordStr_2=c.1263T>G;refseq.codonCoord_1=421;refseq.codonCoord_2=421;refseq.end_1=225394027;refseq.end_2=225394027;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2206;refseq.mrnaCoord_2=2206;refseq.name2_1=CDC42BPA;refseq.name2_2=CDC42BPA;refseq.name_1=NM_003607;refseq.name_2=NM_014826;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G421G;refseq.proteinCoordStr_2=p.G421G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=40;refseq.spliceDist_2=40;refseq.start_1=225394027;refseq.start_2=225394027;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 0/1
|
|
chr1 225989704 . G A 73.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=26;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=95.33;MQ0=0;OQ=661.97;QD=28.78;RankSumP=1.00000;SB=-348.33;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.32C>T;refseq.codingCoordStr_2=c.32C>T;refseq.codingCoordStr_3=c.-30G>A;refseq.codonCoord_1=11;refseq.codonCoord_2=11;refseq.end_1=225989704;refseq.end_2=225989704;refseq.end_3=225989704;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=false;refseq.mrnaCoord_1=32;refseq.mrnaCoord_2=32;refseq.mrnaCoord_3=385;refseq.name2_1=JMJD4;refseq.name2_2=JMJD4;refseq.name2_3=SNAP47;refseq.name_1=NM_001161465;refseq.name_2=NM_023007;refseq.name_3=NM_053052;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=utr5;refseq.proteinCoordStr_1=p.A11V;refseq.proteinCoordStr_2=p.A11V;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.spliceDist_3=-120;refseq.start_1=225989704;refseq.start_2=225989704;refseq.start_3=225989704;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=Intersection GT 1/1
|
|
chr1 226099820 . A G 110.24 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=119;Dels=0.00;HRun=1;HaplotypeScore=3.74;MQ=98.31;MQ0=0;OQ=1647.54;QD=13.84;RankSumP=0.152635;SB=-417.63;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.610A>G;refseq.codonCoord=204;refseq.end=226099820;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=610;refseq.name=NM_183062;refseq.name2=PRSS38;refseq.positionType=CDS;refseq.proteinCoordStr=p.M204V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=27;refseq.start=226099820;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 0/1
|
|
chr1 226179786 . A G 17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=25;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=189.49;QD=21.05;RankSumP=1.00000;SB=-86.37;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.153T>C;refseq.codonCoord=51;refseq.end=226179786;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=241;refseq.name=NM_003395;refseq.name2=WNT9A;refseq.positionType=CDS;refseq.proteinCoordStr=p.A51A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=58;refseq.start=226179786;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=filterInsoap-gatk GT 1/1
|
|
chr1 226352311 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.520T>G;refseq.codingCoordStr_2=c.520T>G;refseq.codingCoordStr_3=c.520T>G;refseq.codingCoordStr_4=c.520T>G;refseq.codonCoord_1=174;refseq.codonCoord_2=174;refseq.codonCoord_3=174;refseq.codonCoord_4=174;refseq.end_1=226352311;refseq.end_2=226352311;refseq.end_3=226352311;refseq.end_4=226352311;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=748;refseq.mrnaCoord_2=782;refseq.mrnaCoord_3=760;refseq.mrnaCoord_4=663;refseq.name2_1=ARF1;refseq.name2_2=ARF1;refseq.name2_3=ARF1;refseq.name2_4=ARF1;refseq.name_1=NM_001024226;refseq.name_2=NM_001024227;refseq.name_3=NM_001024228;refseq.name_4=NM_001658;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.S174A;refseq.proteinCoordStr_2=p.S174A;refseq.proteinCoordStr_3=p.S174A;refseq.proteinCoordStr_4=p.S174A;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_1=TCC;refseq.referenceCodon_2=TCC;refseq.referenceCodon_3=TCC;refseq.referenceCodon_4=TCC;refseq.spliceDist_1=136;refseq.spliceDist_2=136;refseq.spliceDist_3=136;refseq.spliceDist_4=136;refseq.start_1=226352311;refseq.start_2=226352311;refseq.start_3=226352311;refseq.start_4=226352311;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;refseq.variantCodon_3=GCC;refseq.variantCodon_4=GCC;set=FilteredInAll GT 1/0
|
|
chr1 226362033 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.chr_8=chr1;refseq.codingCoordStr_1=c.187A>C;refseq.codingCoordStr_2=c.187A>C;refseq.codingCoordStr_3=c.187A>C;refseq.codingCoordStr_4=c.187A>C;refseq.codingCoordStr_5=c.295A>C;refseq.codingCoordStr_6=c.187A>C;refseq.codingCoordStr_7=c.187A>C;refseq.codingCoordStr_8=c.187A>C;refseq.codonCoord_1=63;refseq.codonCoord_2=63;refseq.codonCoord_3=63;refseq.codonCoord_4=63;refseq.codonCoord_5=99;refseq.codonCoord_6=63;refseq.codonCoord_7=63;refseq.codonCoord_8=63;refseq.end_1=226362033;refseq.end_2=226362033;refseq.end_3=226362033;refseq.end_4=226362033;refseq.end_5=226362033;refseq.end_6=226362033;refseq.end_7=226362033;refseq.end_8=226362033;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=G;refseq.haplotypeAlternate_8=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.haplotypeReference_5=T;refseq.haplotypeReference_6=T;refseq.haplotypeReference_7=T;refseq.haplotypeReference_8=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=409;refseq.mrnaCoord_2=402;refseq.mrnaCoord_3=405;refseq.mrnaCoord_4=447;refseq.mrnaCoord_5=584;refseq.mrnaCoord_6=476;refseq.mrnaCoord_7=364;refseq.mrnaCoord_8=297;refseq.name2_1=MRPL55;refseq.name2_2=MRPL55;refseq.name2_3=MRPL55;refseq.name2_4=MRPL55;refseq.name2_5=MRPL55;refseq.name2_6=MRPL55;refseq.name2_7=MRPL55;refseq.name2_8=MRPL55;refseq.name_1=NM_181441;refseq.name_2=NM_181454;refseq.name_3=NM_181455;refseq.name_4=NM_181456;refseq.name_5=NM_181462;refseq.name_6=NM_181463;refseq.name_7=NM_181464;refseq.name_8=NM_181465;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.T63P;refseq.proteinCoordStr_2=p.T63P;refseq.proteinCoordStr_3=p.T63P;refseq.proteinCoordStr_4=p.T63P;refseq.proteinCoordStr_5=p.T99P;refseq.proteinCoordStr_6=p.T63P;refseq.proteinCoordStr_7=p.T63P;refseq.proteinCoordStr_8=p.T63P;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceAA_6=Thr;refseq.referenceAA_7=Thr;refseq.referenceAA_8=Thr;refseq.referenceCodon_1=ACC;refseq.referenceCodon_2=ACC;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.referenceCodon_5=ACC;refseq.referenceCodon_6=ACC;refseq.referenceCodon_7=ACC;refseq.referenceCodon_8=ACC;refseq.spliceDist_1=-42;refseq.spliceDist_2=-42;refseq.spliceDist_3=-42;refseq.spliceDist_4=-42;refseq.spliceDist_5=-42;refseq.spliceDist_6=-42;refseq.spliceDist_7=-42;refseq.spliceDist_8=-42;refseq.start_1=226362033;refseq.start_2=226362033;refseq.start_3=226362033;refseq.start_4=226362033;refseq.start_5=226362033;refseq.start_6=226362033;refseq.start_7=226362033;refseq.start_8=226362033;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;refseq.transcriptStrand_5=-;refseq.transcriptStrand_6=-;refseq.transcriptStrand_7=-;refseq.transcriptStrand_8=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Pro;refseq.variantAA_6=Pro;refseq.variantAA_7=Pro;refseq.variantAA_8=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;refseq.variantCodon_5=CCC;refseq.variantCodon_6=CCC;refseq.variantCodon_7=CCC;refseq.variantCodon_8=CCC;set=FilteredInAll GT 1/0
|
|
chr1 226420274 . G C 62.58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=91.33;MQ0=0;OQ=79.51;QD=15.90;RankSumP=0.600000;SB=-6.99;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.134G>C;refseq.codonCoord=45;refseq.end=226420274;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=223;refseq.name=NM_001010867;refseq.name2=C1orf69;refseq.positionType=CDS;refseq.proteinCoordStr=p.G45A;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-208;refseq.start=226420274;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 226429305 . G A 90 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=99.00;MQ0=0;OQ=375.02;QD=20.83;RankSumP=0.233525;SB=-123.61;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.631G>A;refseq.codonCoord=211;refseq.end=226429305;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=720;refseq.name=NM_001010867;refseq.name2=C1orf69;refseq.positionType=CDS;refseq.proteinCoordStr=p.G211S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=-49;refseq.start=226429305;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/0
|
|
chr1 226655421 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.602A>G;refseq.codonCoord=201;refseq.end=226655421;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=857;refseq.name=NM_145214;refseq.name2=TRIM11;refseq.positionType=CDS;refseq.proteinCoordStr=p.E201G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=98;refseq.start=226655421;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 226668119 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=3;RankSumP=0.00000;SecondBestBaseQ=16;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.525+2;refseq.codingCoordStr_2=c.444+2;refseq.codingCoordStr_3=c.525+2;refseq.codingCoordStr_4=c.525+2;refseq.end_1=226668119;refseq.end_2=226668119;refseq.end_3=226668119;refseq.end_4=226668119;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.name2_1=TRIM17;refseq.name2_2=TRIM17;refseq.name2_3=TRIM17;refseq.name2_4=TRIM17;refseq.name_1=NM_001024940;refseq.name_2=NM_001024941;refseq.name_3=NM_001134855;refseq.name_4=NM_016102;refseq.numMatchingRecords=4;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=intron;refseq.positionType_4=intron;refseq.spliceDist_1=2;refseq.spliceDist_2=2;refseq.spliceDist_3=2;refseq.spliceDist_4=2;refseq.spliceInfo_1=splice-donor_2;refseq.spliceInfo_2=splice-donor_2;refseq.spliceInfo_3=splice-donor_2;refseq.spliceInfo_4=splice-donor_2;refseq.start_1=226668119;refseq.start_2=226668119;refseq.start_3=226668119;refseq.start_4=226668119;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=-;set=FilteredInAll GT 0/1
|
|
chr1 226679461 . G T 273.91 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=5.18;MQ=96.96;MQ0=0;OQ=7082.55;QD=34.22;RankSumP=1.00000;SB=-3369.22;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.189C>A;refseq.codonCoord=63;refseq.end=226679461;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=189;refseq.name=NM_003493;refseq.name2=HIST3H3;refseq.positionType=CDS;refseq.proteinCoordStr=p.I63I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=189;refseq.start=226679461;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/1
|
|
chr1 226679560 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=2.61249e-08;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.90A>C;refseq.codonCoord=30;refseq.end=226679560;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=90;refseq.name=NM_003493;refseq.name2=HIST3H3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A30A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=90;refseq.start=226679560;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 226938316 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=156;Dels=0.00;HRun=1;HaplotypeScore=6.56;MQ=98.83;MQ0=0;OQ=2146.81;QD=13.76;RankSumP=0.404884;SB=-822.79;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.204C>T;refseq.codonCoord=68;refseq.end=226938316;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=825;refseq.name=NM_021205;refseq.name2=RHOU;refseq.positionType=CDS;refseq.proteinCoordStr=p.S68S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=-59;refseq.start=226938316;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=Intersection GT 0/1
|
|
chr1 227527647 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=583;Dels=0.00;HRun=0;HaplotypeScore=23.08;MQ=98.67;MQ0=0;OQ=10914.72;QD=18.72;RankSumP=0.267279;SB=-4536.60;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.771G>A;refseq.codonCoord=257;refseq.end=227527647;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=849;refseq.name=NM_145257;refseq.name2=C1orf96;refseq.positionType=CDS;refseq.proteinCoordStr=p.P257P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=135;refseq.start=227527647;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 227529174 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=25;HRun=4;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.570A>G;refseq.codonCoord=190;refseq.end=227529174;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=648;refseq.name=NM_145257;refseq.name2=C1orf96;refseq.positionType=CDS;refseq.proteinCoordStr=p.G190G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-67;refseq.start=227529174;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 227673030 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=1;RankSumP=0.00000;SecondBestBaseQ=12;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1996A>C;refseq.codonCoord=666;refseq.end=227673030;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2088;refseq.name=NM_018230;refseq.name2=NUP133;refseq.positionType=CDS;refseq.proteinCoordStr=p.T666P;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-81;refseq.start=227673030;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 227734027 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=170;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=97.91;MQ0=0;OQ=2848.20;QD=16.75;RankSumP=0.496218;SB=-1250.88;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1414G>C;refseq.codonCoord=472;refseq.end=227734027;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1457;refseq.name=NM_012089;refseq.name2=ABCB10;refseq.positionType=CDS;refseq.proteinCoordStr=p.E472Q;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-22;refseq.start=227734027;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 227797075 . G A 225.93 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=98.76;MQ0=0;OQ=1446.66;QD=16.44;RankSumP=0.00550039;SB=-687.69;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1362C>T;refseq.codonCoord=454;refseq.end=227797075;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1528;refseq.name=NM_014409;refseq.name2=TAF5L;refseq.positionType=CDS;refseq.proteinCoordStr=p.S454S;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=390;refseq.start=227797075;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGT;set=filterInsoap-gatk GT 1/0
|
|
chr1 227804793 . T G 238.97 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=536;Dels=0.00;HRun=0;HaplotypeScore=9.22;MQ=98.47;MQ0=0;OQ=9306.52;QD=17.36;RankSumP=0.00570363;SB=-3530.10;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.744A>C;refseq.codingCoordStr_2=c.744A>C;refseq.codonCoord_1=248;refseq.codonCoord_2=248;refseq.end_1=227804793;refseq.end_2=227804793;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=910;refseq.mrnaCoord_2=910;refseq.name2_1=TAF5L;refseq.name2_2=TAF5L;refseq.name_1=NM_001025247;refseq.name_2=NM_014409;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R248R;refseq.proteinCoordStr_2=p.R248R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.spliceDist_1=497;refseq.spliceDist_2=-229;refseq.start_1=227804793;refseq.start_2=227804793;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGC;refseq.variantCodon_2=CGC;set=filterInsoap-gatk GT 1/0
|
|
chr1 227804859 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=309;Dels=0.00;HRun=0;HaplotypeScore=35.45;MQ=97.72;MQ0=0;OQ=6234.52;QD=20.18;RankSumP=0.122594;SB=-2129.09;SecondBestBaseQ=29;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.678C>T;refseq.codingCoordStr_2=c.678C>T;refseq.codonCoord_1=226;refseq.codonCoord_2=226;refseq.end_1=227804859;refseq.end_2=227804859;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=844;refseq.mrnaCoord_2=844;refseq.name2_1=TAF5L;refseq.name2_2=TAF5L;refseq.name_1=NM_001025247;refseq.name_2=NM_014409;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.P226P;refseq.proteinCoordStr_2=p.P226P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceCodon_1=CCC;refseq.referenceCodon_2=CCC;refseq.spliceDist_1=431;refseq.spliceDist_2=-295;refseq.start_1=227804859;refseq.start_2=227804859;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantCodon_1=CCT;refseq.variantCodon_2=CCT;set=Intersection GT 1/0
|
|
chr1 227839316 . T G 151.71 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=162;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=99.00;MQ0=0;OQ=2757.37;QD=17.02;RankSumP=0.187246;SB=-775.05;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2333T>G;refseq.codonCoord=778;refseq.end=227839316;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2469;refseq.name=NM_014777;refseq.name2=URB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V778G;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-1302;refseq.start=227839316;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/0
|
|
chr1 227853653 . G A 351.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=207;Dels=0.00;HRun=0;HaplotypeScore=6.97;MQ=98.71;MQ0=0;OQ=4235.68;QD=20.46;RankSumP=0.461823;SB=-1631.07;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4198G>A;refseq.codonCoord=1400;refseq.end=227853653;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4334;refseq.name=NM_014777;refseq.name2=URB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1400M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-40;refseq.start=227853653;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/0
|
|
chr1 227856671 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=462;Dels=0.00;HRun=1;HaplotypeScore=7.69;MQ=98.93;MQ0=0;OQ=8933.29;QD=19.34;RankSumP=0.0682883;SB=-3642.60;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4290A>G;refseq.codonCoord=1430;refseq.end=227856671;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=4426;refseq.name=NM_014777;refseq.name2=URB2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1430R;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=53;refseq.start=227856671;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 0/1
|
|
chr1 228438406 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=3;RankSumP=0.00000;SecondBestBaseQ=3;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.398T>G;refseq.codonCoord=133;refseq.end=228438406;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=470;refseq.name=NM_004481;refseq.name2=GALNT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V133G;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=24;refseq.start=228438406;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 228451560 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=4.98;MQ=98.80;MQ0=0;OQ=663.66;QD=9.22;RankSumP=0.383965;SB=-298.15;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.825T>C;refseq.codonCoord=275;refseq.end=228451560;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=897;refseq.name=NM_004481;refseq.name2=GALNT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.D275D;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=8;refseq.spliceInfo=splice-acceptor_8;refseq.start=228451560;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/0
|
|
chr1 228481771 . G A 184.64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=144;Dels=0.00;HRun=0;HaplotypeScore=4.65;MQ=98.99;MQ0=0;OQ=1941.38;QD=13.48;RankSumP=0.0536179;SB=-709.52;SecondBestBaseQ=29;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1660G>A;refseq.codonCoord=554;refseq.end=228481771;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1732;refseq.name=NM_004481;refseq.name2=GALNT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V554M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=100;refseq.start=228481771;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/0
|
|
chr1 228908310 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=4.63;MQ=98.74;MQ0=0;OQ=1371.98;QD=13.72;RankSumP=0.412703;SB=-428.19;SecondBestBaseQ=28;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1116A>G;refseq.codonCoord=372;refseq.end=228908310;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1624;refseq.name=NM_000029;refseq.name2=AGT;refseq.positionType=CDS;refseq.proteinCoordStr=p.L372L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=228908310;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/0
|
|
chr1 228912417 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;DB;DP=165;Dels=0.00;HRun=0;HaplotypeScore=30.06;MQ=98.71;MQ0=0;OQ=1609.44;QD=9.75;RankSumP=0.261996;SB=-0.98;SecondBestBaseQ=25;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.803T>C;refseq.codonCoord=268;refseq.end=228912417;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1311;refseq.name=NM_000029;refseq.name2=AGT;refseq.positionType=CDS;refseq.proteinCoordStr=p.M268T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-54;refseq.start=228912417;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 0/1
|
|
chr1 228965117 . C T 120.68 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=228;Dels=0.00;HRun=0;HaplotypeScore=4.37;MQ=98.92;MQ0=0;OQ=2757.96;QD=12.10;RankSumP=0.179266;SB=-674.56;SecondBestBaseQ=32;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.498C>T;refseq.codingCoordStr_2=c.498C>T;refseq.codonCoord_1=166;refseq.codonCoord_2=166;refseq.end_1=228965117;refseq.end_2=228965117;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=611;refseq.mrnaCoord_2=580;refseq.name2_1=CAPN9;refseq.name2_2=CAPN9;refseq.name_1=NM_006615;refseq.name_2=NM_016452;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N166N;refseq.proteinCoordStr_2=p.N166N;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=-39;refseq.spliceDist_2=-39;refseq.start_1=228965117;refseq.start_2=228965117;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Asn;refseq.variantAA_2=Asn;refseq.variantCodon_1=AAT;refseq.variantCodon_2=AAT;set=Intersection GT 0/1
|
|
chr1 228969973 . T C 148.06 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=239;Dels=0.00;HRun=1;HaplotypeScore=5.27;MQ=98.72;MQ0=0;OQ=3108.32;QD=13.01;RankSumP=0.208284;SB=-1442.48;SecondBestBaseQ=31;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.600T>C;refseq.codingCoordStr_2=c.600T>C;refseq.codonCoord_1=200;refseq.codonCoord_2=200;refseq.end_1=228969973;refseq.end_2=228969973;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=713;refseq.mrnaCoord_2=682;refseq.name2_1=CAPN9;refseq.name2_2=CAPN9;refseq.name_1=NM_006615;refseq.name_2=NM_016452;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T200T;refseq.proteinCoordStr_2=p.T200T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACT;refseq.referenceCodon_2=ACT;refseq.spliceDist_1=64;refseq.spliceDist_2=64;refseq.start_1=228969973;refseq.start_2=228969973;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=Intersection GT 1/0
|
|
chr1 228981422 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1034C>G;refseq.codingCoordStr_2=c.956C>G;refseq.codonCoord_1=345;refseq.codonCoord_2=319;refseq.end_1=228981422;refseq.end_2=228981422;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1147;refseq.mrnaCoord_2=1038;refseq.name2_1=CAPN9;refseq.name2_2=CAPN9;refseq.name_1=NM_006615;refseq.name_2=NM_016452;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A345G;refseq.proteinCoordStr_2=p.A319G;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=-81;refseq.spliceDist_2=-81;refseq.start_1=228981422;refseq.start_2=228981422;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 229109355 . T A 197.06 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=162;Dels=0.00;HRun=1;HaplotypeScore=4.16;MQ=98.74;MQ0=0;OQ=2559.36;QD=15.80;RankSumP=0.438693;SB=-782.23;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2343A>T;refseq.codingCoordStr_2=c.2502A>T;refseq.codonCoord_1=781;refseq.codonCoord_2=834;refseq.end_1=229109355;refseq.end_2=229109355;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2374;refseq.mrnaCoord_2=2533;refseq.name2_1=TTC13;refseq.name2_2=TTC13;refseq.name_1=NM_001122835;refseq.name_2=NM_024525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.V781V;refseq.proteinCoordStr_2=p.V834V;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceCodon_1=GTA;refseq.referenceCodon_2=GTA;refseq.spliceDist_1=34;refseq.spliceDist_2=34;refseq.start_1=229109355;refseq.start_2=229109355;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTT;refseq.variantCodon_2=GTT;set=Intersection GT 1/0
|
|
chr1 229123870 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=98.79;MQ0=0;OQ=739.97;QD=10.57;RankSumP=0.407744;SB=-224.55;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1659T>A;refseq.codingCoordStr_2=c.1818T>A;refseq.codonCoord_1=553;refseq.codonCoord_2=606;refseq.end_1=229123870;refseq.end_2=229123870;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1690;refseq.mrnaCoord_2=1849;refseq.name2_1=TTC13;refseq.name2_2=TTC13;refseq.name_1=NM_001122835;refseq.name_2=NM_024525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G553G;refseq.proteinCoordStr_2=p.G606G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGT;refseq.referenceCodon_2=GGT;refseq.spliceDist_1=4;refseq.spliceDist_2=4;refseq.spliceInfo_1=splice-acceptor_4;refseq.spliceInfo_2=splice-acceptor_4;refseq.start_1=229123870;refseq.start_2=229123870;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGA;refseq.variantCodon_2=GGA;set=Intersection GT 0/1
|
|
chr1 229141813 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=14;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.683A>C;refseq.codingCoordStr_2=c.842A>C;refseq.codonCoord_1=228;refseq.codonCoord_2=281;refseq.end_1=229141813;refseq.end_2=229141813;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=714;refseq.mrnaCoord_2=873;refseq.name2_1=TTC13;refseq.name2_2=TTC13;refseq.name_1=NM_001122835;refseq.name_2=NM_024525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.N228T;refseq.proteinCoordStr_2=p.N281T;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.spliceDist_1=53;refseq.spliceDist_2=53;refseq.start_1=229141813;refseq.start_2=229141813;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACC;refseq.variantCodon_2=ACC;set=FilteredInAll GT 1/0
|
|
chr1 229181088 . C G 14.25 BadSOAPSNP;LowQual AC=2;AF=1.00;AN=2;BestBaseQ=18;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=14.25;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.112G>C;refseq.codingCoordStr_2=c.112G>C;refseq.codonCoord_1=38;refseq.codonCoord_2=38;refseq.end_1=229181088;refseq.end_2=229181088;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=143;refseq.mrnaCoord_2=143;refseq.name2_1=TTC13;refseq.name2_2=TTC13;refseq.name_1=NM_001122835;refseq.name_2=NM_024525;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G38R;refseq.proteinCoordStr_2=p.G38R;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGG;refseq.referenceCodon_2=GGG;refseq.spliceDist_1=143;refseq.spliceDist_2=143;refseq.start_1=229181088;refseq.start_2=229181088;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;set=FilteredInAll GT 1/1
|
|
chr1 229443429 . G C 209.49 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=4.96;MQ=98.82;MQ0=0;OQ=1439.12;QD=14.39;RankSumP=0.343108;SB=-593.91;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.82C>G;refseq.codonCoord=28;refseq.end=229443429;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=119;refseq.name=NM_152379;refseq.name2=C1orf131;refseq.positionType=CDS;refseq.proteinCoordStr=p.L28V;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=-37;refseq.start=229443429;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 0/1
|
|
chr1 229468525 . G A 61.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=430;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=98.84;MQ0=0;OQ=8571.79;QD=19.93;RankSumP=0.00000;SB=-3588.17;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.915G>A;refseq.codonCoord=305;refseq.end=229468525;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1121;refseq.name=NM_014236;refseq.name2=GNPAT;refseq.positionType=CDS;refseq.proteinCoordStr=p.E305E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-10;refseq.spliceInfo=splice-donor_-10;refseq.start=229468525;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=filterInsoap-gatk GT 1/0
|
|
chr1 229479890 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2022A>C;refseq.codonCoord=674;refseq.end=229479890;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=2228;refseq.name=NM_014236;refseq.name2=GNPAT;refseq.positionType=CDS;refseq.proteinCoordStr=p.K674N;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=23;refseq.start=229479890;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 0/1
|
|
chr1 229539291 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=4;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.824A>G;refseq.codonCoord=275;refseq.end=229539291;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=911;refseq.name=NM_175876;refseq.name2=EXOC8;refseq.positionType=CDS;refseq.proteinCoordStr=p.E275G;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=911;refseq.start=229539291;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=FilteredInAll GT 1/0
|
|
chr1 229555147 . C T 138.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=127;Dels=0.00;HRun=1;HaplotypeScore=3.26;MQ=98.56;MQ0=0;OQ=1854.50;QD=14.60;RankSumP=0.416461;SB=-525.56;SecondBestBaseQ=32;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.*1172C>T;refseq.codingCoordStr_2=c.887C>T;refseq.codonCoord_2=296;refseq.end_1=229555147;refseq.end_2=229555147;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2373;refseq.mrnaCoord_2=1335;refseq.name2_1=C1orf124;refseq.name2_2=C1orf124;refseq.name_1=NM_001010984;refseq.name_2=NM_032018;refseq.numMatchingRecords=2;refseq.positionType_1=utr3;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.P296L;refseq.referenceAA_2=Pro;refseq.referenceCodon_2=CCT;refseq.spliceDist_1=-1466;refseq.spliceDist_2=169;refseq.start_1=229555147;refseq.start_2=229555147;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Leu;refseq.variantCodon_2=CTT;set=Intersection GT 0/1
|
|
chr1 229896918 . G A 227.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=99.00;MQ0=0;OQ=1440.95;QD=17.79;RankSumP=0.143677;SB=-402.89;SecondBestBaseQ=31;refseq.changesAA_10=true;refseq.changesAA_11=true;refseq.changesAA_12=true;refseq.changesAA_13=true;refseq.changesAA_14=true;refseq.changesAA_15=true;refseq.changesAA_16=true;refseq.changesAA_17=true;refseq.changesAA_18=true;refseq.changesAA_19=true;refseq.changesAA_20=true;refseq.changesAA_21=true;refseq.changesAA_22=true;refseq.changesAA_23=true;refseq.changesAA_24=true;refseq.changesAA_25=true;refseq.changesAA_26=true;refseq.changesAA_27=true;refseq.changesAA_28=true;refseq.changesAA_29=true;refseq.changesAA_30=true;refseq.changesAA_31=true;refseq.chr_1=chr1;refseq.chr_10=chr1;refseq.chr_11=chr1;refseq.chr_12=chr1;refseq.chr_13=chr1;refseq.chr_14=chr1;refseq.chr_15=chr1;refseq.chr_16=chr1;refseq.chr_17=chr1;refseq.chr_18=chr1;refseq.chr_19=chr1;refseq.chr_2=chr1;refseq.chr_20=chr1;refseq.chr_21=chr1;refseq.chr_22=chr1;refseq.chr_23=chr1;refseq.chr_24=chr1;refseq.chr_25=chr1;refseq.chr_26=chr1;refseq.chr_27=chr1;refseq.chr_28=chr1;refseq.chr_29=chr1;refseq.chr_3=chr1;refseq.chr_30=chr1;refseq.chr_31=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.chr_8=chr1;refseq.chr_9=chr1;refseq.codingCoordStr_10=c.791G>A;refseq.codingCoordStr_11=c.791G>A;refseq.codingCoordStr_12=c.791G>A;refseq.codingCoordStr_13=c.791G>A;refseq.codingCoordStr_14=c.791G>A;refseq.codingCoordStr_15=c.791G>A;refseq.codingCoordStr_16=c.791G>A;refseq.codingCoordStr_17=c.791G>A;refseq.codingCoordStr_18=c.791G>A;refseq.codingCoordStr_19=c.791G>A;refseq.codingCoordStr_20=c.791G>A;refseq.codingCoordStr_21=c.791G>A;refseq.codingCoordStr_22=c.791G>A;refseq.codingCoordStr_23=c.791G>A;refseq.codingCoordStr_24=c.791G>A;refseq.codingCoordStr_25=c.791G>A;refseq.codingCoordStr_26=c.791G>A;refseq.codingCoordStr_27=c.791G>A;refseq.codingCoordStr_28=c.791G>A;refseq.codingCoordStr_29=c.791G>A;refseq.codingCoordStr_30=c.791G>A;refseq.codingCoordStr_31=c.791G>A;refseq.codonCoord_10=264;refseq.codonCoord_11=264;refseq.codonCoord_12=264;refseq.codonCoord_13=264;refseq.codonCoord_14=264;refseq.codonCoord_15=264;refseq.codonCoord_16=264;refseq.codonCoord_17=264;refseq.codonCoord_18=264;refseq.codonCoord_19=264;refseq.codonCoord_20=264;refseq.codonCoord_21=264;refseq.codonCoord_22=264;refseq.codonCoord_23=264;refseq.codonCoord_24=264;refseq.codonCoord_25=264;refseq.codonCoord_26=264;refseq.codonCoord_27=264;refseq.codonCoord_28=264;refseq.codonCoord_29=264;refseq.codonCoord_30=264;refseq.codonCoord_31=264;refseq.end_1=229952284;refseq.end_10=229896918;refseq.end_11=229896918;refseq.end_12=229896918;refseq.end_13=229896918;refseq.end_14=229896918;refseq.end_15=229896918;refseq.end_16=229896918;refseq.end_17=229896918;refseq.end_18=229896918;refseq.end_19=229896918;refseq.end_2=229896918;refseq.end_20=229896918;refseq.end_21=229896918;refseq.end_22=229896918;refseq.end_23=229896918;refseq.end_24=229896918;refseq.end_25=229896918;refseq.end_26=229896918;refseq.end_27=229896918;refseq.end_28=229896918;refseq.end_29=229896918;refseq.end_3=229896918;refseq.end_30=229896918;refseq.end_31=229896918;refseq.end_4=229896918;refseq.end_5=229896918;refseq.end_6=229896918;refseq.end_7=229896918;refseq.end_8=229896918;refseq.end_9=229896918;refseq.frame_10=1;refseq.frame_11=1;refseq.frame_12=1;refseq.frame_13=1;refseq.frame_14=1;refseq.frame_15=1;refseq.frame_16=1;refseq.frame_17=1;refseq.frame_18=1;refseq.frame_19=1;refseq.frame_20=1;refseq.frame_21=1;refseq.frame_22=1;refseq.frame_23=1;refseq.frame_24=1;refseq.frame_25=1;refseq.frame_26=1;refseq.frame_27=1;refseq.frame_28=1;refseq.frame_29=1;refseq.frame_30=1;refseq.frame_31=1;refseq.functionalClass_10=missense;refseq.functionalClass_11=missense;refseq.functionalClass_12=missense;refseq.functionalClass_13=missense;refseq.functionalClass_14=missense;refseq.functionalClass_15=missense;refseq.functionalClass_16=missense;refseq.functionalClass_17=missense;refseq.functionalClass_18=missense;refseq.functionalClass_19=missense;refseq.functionalClass_20=missense;refseq.functionalClass_21=missense;refseq.functionalClass_22=missense;refseq.functionalClass_23=missense;refseq.functionalClass_24=missense;refseq.functionalClass_25=missense;refseq.functionalClass_26=missense;refseq.functionalClass_27=missense;refseq.functionalClass_28=missense;refseq.functionalClass_29=missense;refseq.functionalClass_30=missense;refseq.functionalClass_31=missense;refseq.haplotypeAlternate_10=A;refseq.haplotypeAlternate_11=A;refseq.haplotypeAlternate_12=A;refseq.haplotypeAlternate_13=A;refseq.haplotypeAlternate_14=A;refseq.haplotypeAlternate_15=A;refseq.haplotypeAlternate_16=A;refseq.haplotypeAlternate_17=A;refseq.haplotypeAlternate_18=A;refseq.haplotypeAlternate_19=A;refseq.haplotypeAlternate_2=*;refseq.haplotypeAlternate_20=A;refseq.haplotypeAlternate_21=A;refseq.haplotypeAlternate_22=A;refseq.haplotypeAlternate_23=A;refseq.haplotypeAlternate_24=A;refseq.haplotypeAlternate_25=A;refseq.haplotypeAlternate_26=A;refseq.haplotypeAlternate_27=A;refseq.haplotypeAlternate_28=A;refseq.haplotypeAlternate_29=A;refseq.haplotypeAlternate_3=*;refseq.haplotypeAlternate_30=A;refseq.haplotypeAlternate_31=A;refseq.haplotypeAlternate_4=*;refseq.haplotypeAlternate_5=*;refseq.haplotypeAlternate_6=*;refseq.haplotypeAlternate_7=*;refseq.haplotypeAlternate_8=*;refseq.haplotypeAlternate_9=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_10=G;refseq.haplotypeReference_11=G;refseq.haplotypeReference_12=G;refseq.haplotypeReference_13=G;refseq.haplotypeReference_14=G;refseq.haplotypeReference_15=G;refseq.haplotypeReference_16=G;refseq.haplotypeReference_17=G;refseq.haplotypeReference_18=G;refseq.haplotypeReference_19=G;refseq.haplotypeReference_2=*;refseq.haplotypeReference_20=G;refseq.haplotypeReference_21=G;refseq.haplotypeReference_22=G;refseq.haplotypeReference_23=G;refseq.haplotypeReference_24=G;refseq.haplotypeReference_25=G;refseq.haplotypeReference_26=G;refseq.haplotypeReference_27=G;refseq.haplotypeReference_28=G;refseq.haplotypeReference_29=G;refseq.haplotypeReference_3=*;refseq.haplotypeReference_30=G;refseq.haplotypeReference_31=G;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=*;refseq.haplotypeReference_6=*;refseq.haplotypeReference_7=*;refseq.haplotypeReference_8=*;refseq.haplotypeReference_9=*;refseq.inCodingRegion_1=false;refseq.inCodingRegion_10=true;refseq.inCodingRegion_11=true;refseq.inCodingRegion_12=true;refseq.inCodingRegion_13=true;refseq.inCodingRegion_14=true;refseq.inCodingRegion_15=true;refseq.inCodingRegion_16=true;refseq.inCodingRegion_17=true;refseq.inCodingRegion_18=true;refseq.inCodingRegion_19=true;refseq.inCodingRegion_20=true;refseq.inCodingRegion_21=true;refseq.inCodingRegion_22=true;refseq.inCodingRegion_23=true;refseq.inCodingRegion_24=true;refseq.inCodingRegion_25=true;refseq.inCodingRegion_26=true;refseq.inCodingRegion_27=true;refseq.inCodingRegion_28=true;refseq.inCodingRegion_29=true;refseq.inCodingRegion_30=true;refseq.inCodingRegion_31=true;refseq.mrnaCoord_10=844;refseq.mrnaCoord_11=844;refseq.mrnaCoord_12=844;refseq.mrnaCoord_13=844;refseq.mrnaCoord_14=844;refseq.mrnaCoord_15=844;refseq.mrnaCoord_16=844;refseq.mrnaCoord_17=844;refseq.mrnaCoord_18=844;refseq.mrnaCoord_19=844;refseq.mrnaCoord_2=1512;refseq.mrnaCoord_20=844;refseq.mrnaCoord_21=844;refseq.mrnaCoord_22=844;refseq.mrnaCoord_23=844;refseq.mrnaCoord_24=844;refseq.mrnaCoord_25=844;refseq.mrnaCoord_26=844;refseq.mrnaCoord_27=844;refseq.mrnaCoord_28=844;refseq.mrnaCoord_29=844;refseq.mrnaCoord_3=1640;refseq.mrnaCoord_30=844;refseq.mrnaCoord_31=844;refseq.mrnaCoord_4=1640;refseq.mrnaCoord_5=1512;refseq.mrnaCoord_6=1377;refseq.mrnaCoord_7=1131;refseq.mrnaCoord_8=1747;refseq.mrnaCoord_9=1619;refseq.name2_1=DISC1;refseq.name2_10=DISC1;refseq.name2_11=DISC1;refseq.name2_12=DISC1;refseq.name2_13=DISC1;refseq.name2_14=DISC1;refseq.name2_15=DISC1;refseq.name2_16=DISC1;refseq.name2_17=DISC1;refseq.name2_18=DISC1;refseq.name2_19=DISC1;refseq.name2_2=TSNAX-DISC1;refseq.name2_20=DISC1;refseq.name2_21=DISC1;refseq.name2_22=DISC1;refseq.name2_23=DISC1;refseq.name2_24=DISC1;refseq.name2_25=DISC1;refseq.name2_26=DISC1;refseq.name2_27=DISC1;refseq.name2_28=DISC1;refseq.name2_29=DISC1;refseq.name2_3=TSNAX-DISC1;refseq.name2_30=DISC1;refseq.name2_31=DISC1;refseq.name2_4=TSNAX-DISC1;refseq.name2_5=TSNAX-DISC1;refseq.name2_6=TSNAX-DISC1;refseq.name2_7=TSNAX-DISC1;refseq.name2_8=TSNAX-DISC1;refseq.name2_9=TSNAX-DISC1;refseq.name_1=NM_001164556;refseq.name_10=NM_001012957;refseq.name_11=NM_001012958;refseq.name_12=NM_001012959;refseq.name_13=NM_001164537;refseq.name_14=NM_001164538;refseq.name_15=NM_001164539;refseq.name_16=NM_001164540;refseq.name_17=NM_001164541;refseq.name_18=NM_001164542;refseq.name_19=NM_001164544;refseq.name_2=NR_028393;refseq.name_20=NM_001164545;refseq.name_21=NM_001164546;refseq.name_22=NM_001164547;refseq.name_23=NM_001164548;refseq.name_24=NM_001164549;refseq.name_25=NM_001164550;refseq.name_26=NM_001164551;refseq.name_27=NM_001164552;refseq.name_28=NM_001164553;refseq.name_29=NM_001164554;refseq.name_3=NR_028394;refseq.name_30=NM_001164555;refseq.name_31=NM_018662;refseq.name_4=NR_028395;refseq.name_5=NR_028396;refseq.name_6=NR_028397;refseq.name_7=NR_028398;refseq.name_8=NR_028399;refseq.name_9=NR_028400;refseq.numMatchingRecords=31;refseq.positionType_1=intron;refseq.positionType_10=CDS;refseq.positionType_11=CDS;refseq.positionType_12=CDS;refseq.positionType_13=CDS;refseq.positionType_14=CDS;refseq.positionType_15=CDS;refseq.positionType_16=CDS;refseq.positionType_17=CDS;refseq.positionType_18=CDS;refseq.positionType_19=CDS;refseq.positionType_2=non_coding_exon;refseq.positionType_20=CDS;refseq.positionType_21=CDS;refseq.positionType_22=CDS;refseq.positionType_23=CDS;refseq.positionType_24=CDS;refseq.positionType_25=CDS;refseq.positionType_26=CDS;refseq.positionType_27=CDS;refseq.positionType_28=CDS;refseq.positionType_29=CDS;refseq.positionType_3=non_coding_exon;refseq.positionType_30=CDS;refseq.positionType_31=CDS;refseq.positionType_4=non_coding_exon;refseq.positionType_5=non_coding_exon;refseq.positionType_6=non_coding_exon;refseq.positionType_7=non_coding_exon;refseq.positionType_8=non_coding_exon;refseq.positionType_9=non_coding_exon;refseq.proteinCoordStr_10=p.R264Q;refseq.proteinCoordStr_11=p.R264Q;refseq.proteinCoordStr_12=p.R264Q;refseq.proteinCoordStr_13=p.R264Q;refseq.proteinCoordStr_14=p.R264Q;refseq.proteinCoordStr_15=p.R264Q;refseq.proteinCoordStr_16=p.R264Q;refseq.proteinCoordStr_17=p.R264Q;refseq.proteinCoordStr_18=p.R264Q;refseq.proteinCoordStr_19=p.R264Q;refseq.proteinCoordStr_20=p.R264Q;refseq.proteinCoordStr_21=p.R264Q;refseq.proteinCoordStr_22=p.R264Q;refseq.proteinCoordStr_23=p.R264Q;refseq.proteinCoordStr_24=p.R264Q;refseq.proteinCoordStr_25=p.R264Q;refseq.proteinCoordStr_26=p.R264Q;refseq.proteinCoordStr_27=p.R264Q;refseq.proteinCoordStr_28=p.R264Q;refseq.proteinCoordStr_29=p.R264Q;refseq.proteinCoordStr_30=p.R264Q;refseq.proteinCoordStr_31=p.R264Q;refseq.referenceAA_10=Arg;refseq.referenceAA_11=Arg;refseq.referenceAA_12=Arg;refseq.referenceAA_13=Arg;refseq.referenceAA_14=Arg;refseq.referenceAA_15=Arg;refseq.referenceAA_16=Arg;refseq.referenceAA_17=Arg;refseq.referenceAA_18=Arg;refseq.referenceAA_19=Arg;refseq.referenceAA_20=Arg;refseq.referenceAA_21=Arg;refseq.referenceAA_22=Arg;refseq.referenceAA_23=Arg;refseq.referenceAA_24=Arg;refseq.referenceAA_25=Arg;refseq.referenceAA_26=Arg;refseq.referenceAA_27=Arg;refseq.referenceAA_28=Arg;refseq.referenceAA_29=Arg;refseq.referenceAA_30=Arg;refseq.referenceAA_31=Arg;refseq.referenceCodon_10=CGG;refseq.referenceCodon_11=CGG;refseq.referenceCodon_12=CGG;refseq.referenceCodon_13=CGG;refseq.referenceCodon_14=CGG;refseq.referenceCodon_15=CGG;refseq.referenceCodon_16=CGG;refseq.referenceCodon_17=CGG;refseq.referenceCodon_18=CGG;refseq.referenceCodon_19=CGG;refseq.referenceCodon_20=CGG;refseq.referenceCodon_21=CGG;refseq.referenceCodon_22=CGG;refseq.referenceCodon_23=CGG;refseq.referenceCodon_24=CGG;refseq.referenceCodon_25=CGG;refseq.referenceCodon_26=CGG;refseq.referenceCodon_27=CGG;refseq.referenceCodon_28=CGG;refseq.referenceCodon_29=CGG;refseq.referenceCodon_30=CGG;refseq.referenceCodon_31=CGG;refseq.spliceDist_10=-257;refseq.spliceDist_11=-257;refseq.spliceDist_12=-257;refseq.spliceDist_13=-257;refseq.spliceDist_14=-257;refseq.spliceDist_15=-257;refseq.spliceDist_16=-257;refseq.spliceDist_17=-257;refseq.spliceDist_18=-257;refseq.spliceDist_19=-257;refseq.spliceDist_2=-257;refseq.spliceDist_20=-257;refseq.spliceDist_21=-257;refseq.spliceDist_22=-257;refseq.spliceDist_23=-257;refseq.spliceDist_24=-257;refseq.spliceDist_25=-257;refseq.spliceDist_26=-257;refseq.spliceDist_27=-257;refseq.spliceDist_28=-257;refseq.spliceDist_29=-257;refseq.spliceDist_3=-257;refseq.spliceDist_30=-257;refseq.spliceDist_31=-257;refseq.spliceDist_4=-257;refseq.spliceDist_5=-257;refseq.spliceDist_6=-257;refseq.spliceDist_7=-257;refseq.spliceDist_8=-257;refseq.spliceDist_9=-257;refseq.start_1=229829314;refseq.start_10=229896918;refseq.start_11=229896918;refseq.start_12=229896918;refseq.start_13=229896918;refseq.start_14=229896918;refseq.start_15=229896918;refseq.start_16=229896918;refseq.start_17=229896918;refseq.start_18=229896918;refseq.start_19=229896918;refseq.start_2=229896918;refseq.start_20=229896918;refseq.start_21=229896918;refseq.start_22=229896918;refseq.start_23=229896918;refseq.start_24=229896918;refseq.start_25=229896918;refseq.start_26=229896918;refseq.start_27=229896918;refseq.start_28=229896918;refseq.start_29=229896918;refseq.start_3=229896918;refseq.start_30=229896918;refseq.start_31=229896918;refseq.start_4=229896918;refseq.start_5=229896918;refseq.start_6=229896918;refseq.start_7=229896918;refseq.start_8=229896918;refseq.start_9=229896918;refseq.transcriptStrand_1=+;refseq.transcriptStrand_10=+;refseq.transcriptStrand_11=+;refseq.transcriptStrand_12=+;refseq.transcriptStrand_13=+;refseq.transcriptStrand_14=+;refseq.transcriptStrand_15=+;refseq.transcriptStrand_16=+;refseq.transcriptStrand_17=+;refseq.transcriptStrand_18=+;refseq.transcriptStrand_19=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_20=+;refseq.transcriptStrand_21=+;refseq.transcriptStrand_22=+;refseq.transcriptStrand_23=+;refseq.transcriptStrand_24=+;refseq.transcriptStrand_25=+;refseq.transcriptStrand_26=+;refseq.transcriptStrand_27=+;refseq.transcriptStrand_28=+;refseq.transcriptStrand_29=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_30=+;refseq.transcriptStrand_31=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.transcriptStrand_9=+;refseq.variantAA_10=Gln;refseq.variantAA_11=Gln;refseq.variantAA_12=Gln;refseq.variantAA_13=Gln;refseq.variantAA_14=Gln;refseq.variantAA_15=Gln;refseq.variantAA_16=Gln;refseq.variantAA_17=Gln;refseq.variantAA_18=Gln;refseq.variantAA_19=Gln;refseq.variantAA_20=Gln;refseq.variantAA_21=Gln;refseq.variantAA_22=Gln;refseq.variantAA_23=Gln;refseq.variantAA_24=Gln;refseq.variantAA_25=Gln;refseq.variantAA_26=Gln;refseq.variantAA_27=Gln;refseq.variantAA_28=Gln;refseq.variantAA_29=Gln;refseq.variantAA_30=Gln;refseq.variantAA_31=Gln;refseq.variantCodon_10=CAG;refseq.variantCodon_11=CAG;refseq.variantCodon_12=CAG;refseq.variantCodon_13=CAG;refseq.variantCodon_14=CAG;refseq.variantCodon_15=CAG;refseq.variantCodon_16=CAG;refseq.variantCodon_17=CAG;refseq.variantCodon_18=CAG;refseq.variantCodon_19=CAG;refseq.variantCodon_20=CAG;refseq.variantCodon_21=CAG;refseq.variantCodon_22=CAG;refseq.variantCodon_23=CAG;refseq.variantCodon_24=CAG;refseq.variantCodon_25=CAG;refseq.variantCodon_26=CAG;refseq.variantCodon_27=CAG;refseq.variantCodon_28=CAG;refseq.variantCodon_29=CAG;refseq.variantCodon_30=CAG;refseq.variantCodon_31=CAG;set=Intersection GT 1/0
|
|
chr1 230020724 . C T 121.95 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=269;Dels=0.00;HRun=1;HaplotypeScore=10.81;MQ=98.74;MQ0=0;OQ=5878.92;QD=21.85;RankSumP=0.440930;SB=-2436.24;SecondBestBaseQ=33;refseq.changesAA_10=true;refseq.changesAA_11=true;refseq.changesAA_12=true;refseq.changesAA_13=true;refseq.changesAA_14=true;refseq.changesAA_15=true;refseq.changesAA_16=true;refseq.changesAA_17=true;refseq.changesAA_18=true;refseq.changesAA_19=false;refseq.changesAA_22=true;refseq.chr_1=chr1;refseq.chr_10=chr1;refseq.chr_11=chr1;refseq.chr_12=chr1;refseq.chr_13=chr1;refseq.chr_14=chr1;refseq.chr_15=chr1;refseq.chr_16=chr1;refseq.chr_17=chr1;refseq.chr_18=chr1;refseq.chr_19=chr1;refseq.chr_2=chr1;refseq.chr_20=chr1;refseq.chr_21=chr1;refseq.chr_22=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.chr_6=chr1;refseq.chr_7=chr1;refseq.chr_8=chr1;refseq.chr_9=chr1;refseq.codingCoordStr_10=c.1819C>T;refseq.codingCoordStr_11=c.1819C>T;refseq.codingCoordStr_12=c.1915C>T;refseq.codingCoordStr_13=c.1819C>T;refseq.codingCoordStr_14=c.1819C>T;refseq.codingCoordStr_15=c.1453C>T;refseq.codingCoordStr_16=c.1819C>T;refseq.codingCoordStr_17=c.1819C>T;refseq.codingCoordStr_18=c.1819C>T;refseq.codingCoordStr_19=c.1716C>T;refseq.codingCoordStr_20=c.*5C>T;refseq.codingCoordStr_21=c.*5C>T;refseq.codingCoordStr_22=c.1819C>T;refseq.codonCoord_10=607;refseq.codonCoord_11=607;refseq.codonCoord_12=639;refseq.codonCoord_13=607;refseq.codonCoord_14=607;refseq.codonCoord_15=485;refseq.codonCoord_16=607;refseq.codonCoord_17=607;refseq.codonCoord_18=607;refseq.codonCoord_19=572;refseq.codonCoord_22=607;refseq.end_1=230161186;refseq.end_10=230020724;refseq.end_11=230020724;refseq.end_12=230020724;refseq.end_13=230020724;refseq.end_14=230020724;refseq.end_15=230020724;refseq.end_16=230020724;refseq.end_17=230020724;refseq.end_18=230020724;refseq.end_19=230020724;refseq.end_2=230161186;refseq.end_20=230020724;refseq.end_21=230020724;refseq.end_22=230020724;refseq.end_3=230020724;refseq.end_4=230020724;refseq.end_5=230020724;refseq.end_6=230020724;refseq.end_7=230020724;refseq.end_8=230020724;refseq.end_9=230020724;refseq.frame_10=0;refseq.frame_11=0;refseq.frame_12=0;refseq.frame_13=0;refseq.frame_14=0;refseq.frame_15=0;refseq.frame_16=0;refseq.frame_17=0;refseq.frame_18=0;refseq.frame_19=2;refseq.frame_22=0;refseq.functionalClass_10=missense;refseq.functionalClass_11=missense;refseq.functionalClass_12=missense;refseq.functionalClass_13=missense;refseq.functionalClass_14=missense;refseq.functionalClass_15=missense;refseq.functionalClass_16=missense;refseq.functionalClass_17=missense;refseq.functionalClass_18=missense;refseq.functionalClass_19=silent;refseq.functionalClass_22=missense;refseq.haplotypeAlternate_10=T;refseq.haplotypeAlternate_11=T;refseq.haplotypeAlternate_12=T;refseq.haplotypeAlternate_13=T;refseq.haplotypeAlternate_14=T;refseq.haplotypeAlternate_15=T;refseq.haplotypeAlternate_16=T;refseq.haplotypeAlternate_17=T;refseq.haplotypeAlternate_18=T;refseq.haplotypeAlternate_19=T;refseq.haplotypeAlternate_20=T;refseq.haplotypeAlternate_21=T;refseq.haplotypeAlternate_22=T;refseq.haplotypeAlternate_3=*;refseq.haplotypeAlternate_4=*;refseq.haplotypeAlternate_5=*;refseq.haplotypeAlternate_6=*;refseq.haplotypeAlternate_7=*;refseq.haplotypeAlternate_8=*;refseq.haplotypeAlternate_9=*;refseq.haplotypeReference_1=*;refseq.haplotypeReference_10=C;refseq.haplotypeReference_11=C;refseq.haplotypeReference_12=C;refseq.haplotypeReference_13=C;refseq.haplotypeReference_14=C;refseq.haplotypeReference_15=C;refseq.haplotypeReference_16=C;refseq.haplotypeReference_17=C;refseq.haplotypeReference_18=C;refseq.haplotypeReference_19=C;refseq.haplotypeReference_2=*;refseq.haplotypeReference_20=C;refseq.haplotypeReference_21=C;refseq.haplotypeReference_22=C;refseq.haplotypeReference_3=*;refseq.haplotypeReference_4=*;refseq.haplotypeReference_5=*;refseq.haplotypeReference_6=*;refseq.haplotypeReference_7=*;refseq.haplotypeReference_8=*;refseq.haplotypeReference_9=*;refseq.inCodingRegion_1=false;refseq.inCodingRegion_10=true;refseq.inCodingRegion_11=true;refseq.inCodingRegion_12=true;refseq.inCodingRegion_13=true;refseq.inCodingRegion_14=true;refseq.inCodingRegion_15=true;refseq.inCodingRegion_16=true;refseq.inCodingRegion_17=true;refseq.inCodingRegion_18=true;refseq.inCodingRegion_19=true;refseq.inCodingRegion_2=false;refseq.inCodingRegion_20=false;refseq.inCodingRegion_21=false;refseq.inCodingRegion_22=true;refseq.mrnaCoord_10=1872;refseq.mrnaCoord_11=1872;refseq.mrnaCoord_12=1968;refseq.mrnaCoord_13=1872;refseq.mrnaCoord_14=1872;refseq.mrnaCoord_15=1506;refseq.mrnaCoord_16=1872;refseq.mrnaCoord_17=1872;refseq.mrnaCoord_18=1872;refseq.mrnaCoord_19=1769;refseq.mrnaCoord_20=1714;refseq.mrnaCoord_21=664;refseq.mrnaCoord_22=1872;refseq.mrnaCoord_3=163;refseq.mrnaCoord_4=2485;refseq.mrnaCoord_5=2668;refseq.mrnaCoord_6=2565;refseq.mrnaCoord_7=2540;refseq.mrnaCoord_8=2405;refseq.mrnaCoord_9=2159;refseq.name2_1=DISC1;refseq.name2_10=DISC1;refseq.name2_11=DISC1;refseq.name2_12=DISC1;refseq.name2_13=DISC1;refseq.name2_14=DISC1;refseq.name2_15=DISC1;refseq.name2_16=DISC1;refseq.name2_17=DISC1;refseq.name2_18=DISC1;refseq.name2_19=DISC1;refseq.name2_2=DISC1;refseq.name2_20=DISC1;refseq.name2_21=DISC1;refseq.name2_22=DISC1;refseq.name2_3=DISC2;refseq.name2_4=TSNAX-DISC1;refseq.name2_5=TSNAX-DISC1;refseq.name2_6=TSNAX-DISC1;refseq.name2_7=TSNAX-DISC1;refseq.name2_8=TSNAX-DISC1;refseq.name2_9=TSNAX-DISC1;refseq.name_1=NM_001164546;refseq.name_10=NM_001012957;refseq.name_11=NM_001012959;refseq.name_12=NM_001164537;refseq.name_13=NM_001164538;refseq.name_14=NM_001164539;refseq.name_15=NM_001164540;refseq.name_16=NM_001164541;refseq.name_17=NM_001164542;refseq.name_18=NM_001164544;refseq.name_19=NM_001164545;refseq.name_2=NM_001164547;refseq.name_20=NM_001164548;refseq.name_21=NM_001164556;refseq.name_22=NM_018662;refseq.name_3=NR_002227;refseq.name_4=NR_028393;refseq.name_5=NR_028394;refseq.name_6=NR_028395;refseq.name_7=NR_028396;refseq.name_8=NR_028397;refseq.name_9=NR_028398;refseq.numMatchingRecords=22;refseq.positionType_1=intron;refseq.positionType_10=CDS;refseq.positionType_11=CDS;refseq.positionType_12=CDS;refseq.positionType_13=CDS;refseq.positionType_14=CDS;refseq.positionType_15=CDS;refseq.positionType_16=CDS;refseq.positionType_17=CDS;refseq.positionType_18=CDS;refseq.positionType_19=CDS;refseq.positionType_2=intron;refseq.positionType_20=utr3;refseq.positionType_21=utr3;refseq.positionType_22=CDS;refseq.positionType_3=non_coding_exon;refseq.positionType_4=non_coding_exon;refseq.positionType_5=non_coding_exon;refseq.positionType_6=non_coding_exon;refseq.positionType_7=non_coding_exon;refseq.positionType_8=non_coding_exon;refseq.positionType_9=non_coding_exon;refseq.proteinCoordStr_10=p.L607F;refseq.proteinCoordStr_11=p.L607F;refseq.proteinCoordStr_12=p.L639F;refseq.proteinCoordStr_13=p.L607F;refseq.proteinCoordStr_14=p.L607F;refseq.proteinCoordStr_15=p.L485F;refseq.proteinCoordStr_16=p.L607F;refseq.proteinCoordStr_17=p.L607F;refseq.proteinCoordStr_18=p.L607F;refseq.proteinCoordStr_19=p.T572T;refseq.proteinCoordStr_22=p.L607F;refseq.referenceAA_10=Leu;refseq.referenceAA_11=Leu;refseq.referenceAA_12=Leu;refseq.referenceAA_13=Leu;refseq.referenceAA_14=Leu;refseq.referenceAA_15=Leu;refseq.referenceAA_16=Leu;refseq.referenceAA_17=Leu;refseq.referenceAA_18=Leu;refseq.referenceAA_19=Thr;refseq.referenceAA_22=Leu;refseq.referenceCodon_10=CTC;refseq.referenceCodon_11=CTC;refseq.referenceCodon_12=CTC;refseq.referenceCodon_13=CTC;refseq.referenceCodon_14=CTC;refseq.referenceCodon_15=CTC;refseq.referenceCodon_16=CTC;refseq.referenceCodon_17=CTC;refseq.referenceCodon_18=CTC;refseq.referenceCodon_19=ACC;refseq.referenceCodon_22=CTC;refseq.spliceDist_10=27;refseq.spliceDist_11=27;refseq.spliceDist_12=27;refseq.spliceDist_13=27;refseq.spliceDist_14=27;refseq.spliceDist_15=27;refseq.spliceDist_16=27;refseq.spliceDist_17=27;refseq.spliceDist_18=27;refseq.spliceDist_19=27;refseq.spliceDist_20=27;refseq.spliceDist_21=27;refseq.spliceDist_22=27;refseq.spliceDist_3=163;refseq.spliceDist_4=27;refseq.spliceDist_5=27;refseq.spliceDist_6=27;refseq.spliceDist_7=27;refseq.spliceDist_8=27;refseq.spliceDist_9=27;refseq.start_1=229973450;refseq.start_10=230020724;refseq.start_11=230020724;refseq.start_12=230020724;refseq.start_13=230020724;refseq.start_14=230020724;refseq.start_15=230020724;refseq.start_16=230020724;refseq.start_17=230020724;refseq.start_18=230020724;refseq.start_19=230020724;refseq.start_2=229973450;refseq.start_20=230020724;refseq.start_21=230020724;refseq.start_22=230020724;refseq.start_3=230020724;refseq.start_4=230020724;refseq.start_5=230020724;refseq.start_6=230020724;refseq.start_7=230020724;refseq.start_8=230020724;refseq.start_9=230020724;refseq.transcriptStrand_1=+;refseq.transcriptStrand_10=+;refseq.transcriptStrand_11=+;refseq.transcriptStrand_12=+;refseq.transcriptStrand_13=+;refseq.transcriptStrand_14=+;refseq.transcriptStrand_15=+;refseq.transcriptStrand_16=+;refseq.transcriptStrand_17=+;refseq.transcriptStrand_18=+;refseq.transcriptStrand_19=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_20=+;refseq.transcriptStrand_21=+;refseq.transcriptStrand_22=+;refseq.transcriptStrand_3=-;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.transcriptStrand_9=+;refseq.variantAA_10=Phe;refseq.variantAA_11=Phe;refseq.variantAA_12=Phe;refseq.variantAA_13=Phe;refseq.variantAA_14=Phe;refseq.variantAA_15=Phe;refseq.variantAA_16=Phe;refseq.variantAA_17=Phe;refseq.variantAA_18=Phe;refseq.variantAA_19=Thr;refseq.variantAA_22=Phe;refseq.variantCodon_10=TTC;refseq.variantCodon_11=TTC;refseq.variantCodon_12=TTC;refseq.variantCodon_13=TTC;refseq.variantCodon_14=TTC;refseq.variantCodon_15=TTC;refseq.variantCodon_16=TTC;refseq.variantCodon_17=TTC;refseq.variantCodon_18=TTC;refseq.variantCodon_19=ACT;refseq.variantCodon_22=TTC;set=Intersection GT 0/1
|
|
chr1 230601580 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=159;Dels=0.00;HRun=1;HaplotypeScore=2.11;MQ=98.87;MQ0=0;OQ=1916.67;QD=12.05;RankSumP=0.280862;SB=-772.72;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5085A>G;refseq.codonCoord=1695;refseq.end=230601580;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5243;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1695R;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=63;refseq.start=230601580;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 1/0
|
|
chr1 230628019 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=7.55;MQ=98.64;MQ0=0;OQ=788.63;QD=11.77;RankSumP=0.229234;SB=-188.53;SecondBestBaseQ=27;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4569A>G;refseq.codonCoord=1523;refseq.end=230628019;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4727;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1523P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-62;refseq.start=230628019;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=Intersection GT 1/0
|
|
chr1 230630920 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=322;Dels=0.00;HRun=1;HaplotypeScore=10.57;MQ=98.62;MQ0=0;OQ=6407.04;QD=19.90;RankSumP=0.446958;SB=-2636.63;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4270A>T;refseq.codonCoord=1424;refseq.end=230630920;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4428;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.M1424L;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=14;refseq.start=230630920;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/0
|
|
chr1 230634671 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4201A>G;refseq.codonCoord=1401;refseq.end=230634671;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4359;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1401E;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-56;refseq.start=230634671;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=FilteredInAll GT 1/0
|
|
chr1 230641544 . T C 219.30 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=199;Dels=0.00;HRun=0;HaplotypeScore=8.45;MQ=98.61;MQ0=0;OQ=6793.82;QD=34.14;RankSumP=1.00000;SB=-2836.70;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3964A>G;refseq.codonCoord=1322;refseq.end=230641544;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4122;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1322A;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-68;refseq.start=230641544;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=Intersection GT 1/1
|
|
chr1 230648059 . G A 275.72 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.66;MQ0=0;OQ=1071.67;QD=34.57;RankSumP=1.00000;SB=-555.30;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3192C>T;refseq.codonCoord=1064;refseq.end=230648059;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3350;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1064T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=97;refseq.start=230648059;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 230717373 . A G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=641;Dels=0.00;HRun=1;HaplotypeScore=10.85;MQ=98.80;MQ0=0;OQ=24490.00;QD=38.21;RankSumP=1.00000;SB=-10328.78;SecondBestBaseQ=23;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.336T>C;refseq.codonCoord=112;refseq.end=230717373;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=494;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.S112S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=494;refseq.start=230717373;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 230717490 . C T 98 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=366;Dels=0.00;HRun=2;HaplotypeScore=50.26;MQ=97.11;MQ0=0;OQ=13917.10;QD=38.02;RankSumP=1.00000;SB=-6405.69;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.219G>A;refseq.codonCoord=73;refseq.end=230717490;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=377;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.K73K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=377;refseq.start=230717490;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=soap-filterIngatk GT 1/1
|
|
chr1 230717526 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=5;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.183T>G;refseq.codonCoord=61;refseq.end=230717526;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=341;refseq.name=NM_020808;refseq.name2=SIPA1L2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G61G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=341;refseq.start=230717526;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 231153079 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=27;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=6.24;MQ=98.44;MQ0=0;OQ=1465.04;QD=12.96;RankSumP=0.0261275;SB=-725.64;SecondBestBaseQ=31;refseq.chr=chr1;refseq.codingCoordStr=c.-1T>C;refseq.end=231153079;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.mrnaCoord=87;refseq.name=NM_032324;refseq.name2=C1orf57;refseq.positionType=utr5;refseq.spliceDist=-35;refseq.start=231153079;refseq.transcriptStrand=+;set=Intersection GT 1/0
|
|
chr1 231564649 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=287;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.75;MQ0=0;OQ=5696.94;QD=19.85;RankSumP=0.245745;SB=-2405.28;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1539C>T;refseq.codonCoord=513;refseq.end=231564649;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1800;refseq.name=NM_032435;refseq.name2=KIAA1804;refseq.positionType=CDS;refseq.proteinCoordStr=p.I513I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-14;refseq.start=231564649;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 231581749 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=3;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2374T>C;refseq.codonCoord=792;refseq.end=231581749;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2635;refseq.name=NM_032435;refseq.name2=KIAA1804;refseq.positionType=CDS;refseq.proteinCoordStr=p.S792P;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=-331;refseq.start=231581749;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 232107940 . C T 91 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=98.45;MQ0=0;OQ=269.20;QD=8.41;RankSumP=0.616965;SB=-112.93;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.96C>T;refseq.codonCoord=32;refseq.end=232107940;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=241;refseq.name=NM_173508;refseq.name2=SLC35F3;refseq.positionType=CDS;refseq.proteinCoordStr=p.S32S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=43;refseq.start=232107940;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 0/1
|
|
chr1 232108045 . G C 82 PASS AC=2;AF=1.00;AN=2;BestBaseQ=27;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=98.23;MQ0=0;OQ=2320.44;QD=38.04;RankSumP=1.00000;SB=-1035.17;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.201G>C;refseq.codonCoord=67;refseq.end=232108045;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=346;refseq.name=NM_173508;refseq.name2=SLC35F3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P67P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-83;refseq.start=232108045;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=Intersection GT 1/1
|
|
chr1 232519032 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.890A>C;refseq.codonCoord=297;refseq.end=232519032;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1035;refseq.name=NM_173508;refseq.name2=SLC35F3;refseq.positionType=CDS;refseq.proteinCoordStr=p.H297P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=62;refseq.start=232519032;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 0/1
|
|
chr1 232596175 . C T 235.62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=98.84;MQ0=0;OQ=2586.16;QD=21.20;RankSumP=0.155198;SB=-777.70;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4275G>A;refseq.codonCoord=1425;refseq.end=232596175;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=4275;refseq.name=NM_005646;refseq.name2=TARBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1425A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=32;refseq.start=232596175;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 0/1
|
|
chr1 232596193 . G A 111.40 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=111;Dels=0.00;HRun=1;HaplotypeScore=4.99;MQ=98.66;MQ0=0;OQ=2194.04;QD=19.77;RankSumP=0.304840;SB=-567.73;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4257C>T;refseq.codonCoord=1419;refseq.end=232596193;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4257;refseq.name=NM_005646;refseq.name2=TARBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1419V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=14;refseq.start=232596193;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/0
|
|
chr1 232612868 . C T 153.20 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=148;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=98.78;MQ0=0;OQ=2008.91;QD=13.57;RankSumP=0.346202;SB=-917.76;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3738G>A;refseq.codonCoord=1246;refseq.end=232612868;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3738;refseq.name=NM_005646;refseq.name2=TARBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1246T;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=33;refseq.start=232612868;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACA;set=Intersection GT 0/1
|
|
chr1 232649274 . T C 95 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=573;Dels=0.00;HRun=1;HaplotypeScore=12.83;MQ=98.98;MQ0=0;OQ=23309.75;QD=40.68;RankSumP=1.00000;SB=-10894.11;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2032A>G;refseq.codonCoord=678;refseq.end=232649274;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2032;refseq.name=NM_005646;refseq.name2=TARBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S678G;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=71;refseq.start=232649274;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 1/1
|
|
chr1 232650854 . C T 159.14 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=6.95;MQ=98.07;MQ0=0;OQ=2630.88;QD=38.13;RankSumP=1.00000;SB=-481.34;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1956G>A;refseq.codonCoord=652;refseq.end=232650854;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1956;refseq.name=NM_005646;refseq.name2=TARBP1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q652Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=-6;refseq.spliceInfo=splice-donor_-6;refseq.start=232650854;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/1
|
|
chr1 232810873 . G A 203.69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=105;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=98.97;MQ0=0;OQ=1678.96;QD=15.99;RankSumP=0.198273;SB=-859.32;SecondBestBaseQ=30;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.991C>T;refseq.codingCoordStr_2=c.991C>T;refseq.codonCoord_1=331;refseq.codonCoord_2=331;refseq.end_1=232810873;refseq.end_2=232810873;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1022;refseq.mrnaCoord_2=1022;refseq.name2_1=IRF2BP2;refseq.name2_2=IRF2BP2;refseq.name_1=NM_001077397;refseq.name_2=NM_182972;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L331L;refseq.proteinCoordStr_2=p.L331L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.spliceDist_1=-10;refseq.spliceDist_2=-58;refseq.spliceInfo_1=splice-donor_-10;refseq.start_1=232810873;refseq.start_2=232810873;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantCodon_1=TTG;refseq.variantCodon_2=TTG;set=Intersection GT 1/0
|
|
chr1 232811036 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=21;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=3.97;MQ=98.78;MQ0=0;OQ=251.60;QD=11.44;RankSumP=0.668599;SB=-10.00;SecondBestBaseQ=21;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.828G>T;refseq.codingCoordStr_2=c.828G>T;refseq.codonCoord_1=276;refseq.codonCoord_2=276;refseq.end_1=232811036;refseq.end_2=232811036;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=859;refseq.mrnaCoord_2=859;refseq.name2_1=IRF2BP2;refseq.name2_2=IRF2BP2;refseq.name_1=NM_001077397;refseq.name_2=NM_182972;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A276A;refseq.proteinCoordStr_2=p.A276A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=-173;refseq.spliceDist_2=-221;refseq.start_1=232811036;refseq.start_2=232811036;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCT;refseq.variantCodon_2=GCT;set=Intersection GT 1/0
|
|
chr1 232811103 . G A 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.595238;SecondBestBaseQ=32;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.761C>T;refseq.codingCoordStr_2=c.761C>T;refseq.codonCoord_1=254;refseq.codonCoord_2=254;refseq.end_1=232811103;refseq.end_2=232811103;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=792;refseq.mrnaCoord_2=792;refseq.name2_1=IRF2BP2;refseq.name2_2=IRF2BP2;refseq.name_1=NM_001077397;refseq.name_2=NM_182972;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A254V;refseq.proteinCoordStr_2=p.A254V;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.spliceDist_1=-240;refseq.spliceDist_2=-288;refseq.start_1=232811103;refseq.start_2=232811103;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;set=FilteredInAll GT 1/0
|
|
chr1 233390921 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=173;Dels=0.00;HRun=0;HaplotypeScore=14.77;MQ=98.22;MQ0=0;OQ=2624.80;QD=15.17;RankSumP=0.131588;SB=-913.58;SecondBestBaseQ=28;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_2=c.138A>G;refseq.codingCoordStr_3=c.138A>G;refseq.codonCoord_2=46;refseq.codonCoord_3=46;refseq.end_1=233390921;refseq.end_2=233390921;refseq.end_3=233390921;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=168;refseq.mrnaCoord_2=168;refseq.mrnaCoord_3=168;refseq.name2_1=RBM34;refseq.name2_2=RBM34;refseq.name2_3=RBM34;refseq.name_1=NR_027762;refseq.name_2=NM_001161533;refseq.name_3=NM_015014;refseq.numMatchingRecords=3;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_2=p.E46E;refseq.proteinCoordStr_3=p.E46E;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_2=GAA;refseq.referenceCodon_3=GAA;refseq.spliceDist_1=85;refseq.spliceDist_2=85;refseq.spliceDist_3=85;refseq.start_1=233390921;refseq.start_2=233390921;refseq.start_3=233390921;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_2=Glu;refseq.variantAA_3=Glu;refseq.variantCodon_2=GAG;refseq.variantCodon_3=GAG;set=Intersection GT 1/0
|
|
chr1 233407785 . C T 99 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=18;DP=646;Dels=0.00;HRun=4;HaplotypeScore=75.29;MQ=98.18;MQ0=0;OQ=1089.83;QD=1.69;RankSumP=0.00453582;SB=595.02;SecondBestBaseQ=21;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.3401G>A;refseq.codingCoordStr_2=c.3143G>A;refseq.codonCoord_1=1134;refseq.codonCoord_2=1048;refseq.end_1=233407785;refseq.end_2=233407785;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3899;refseq.mrnaCoord_2=3641;refseq.name2_1=ARID4B;refseq.name2_2=ARID4B;refseq.name_1=NM_016374;refseq.name_2=NM_031371;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.R1134K;refseq.proteinCoordStr_2=p.R1048K;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceCodon_1=AGA;refseq.referenceCodon_2=AGA;refseq.spliceDist_1=-48;refseq.spliceDist_2=-48;refseq.start_1=233407785;refseq.start_2=233407785;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;set=FilteredInAll GT 0/1
|
|
chr1 233449811 . A G 425.18 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=201;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=7814.80;QD=38.88;RankSumP=1.00000;SB=-1774.38;SecondBestBaseQ=34;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1503T>C;refseq.codingCoordStr_2=c.1503T>C;refseq.codonCoord_1=501;refseq.codonCoord_2=501;refseq.end_1=233449811;refseq.end_2=233449811;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2001;refseq.mrnaCoord_2=2001;refseq.name2_1=ARID4B;refseq.name2_2=ARID4B;refseq.name_1=NM_016374;refseq.name_2=NM_031371;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.D501D;refseq.proteinCoordStr_2=p.D501D;refseq.referenceAA_1=Asp;refseq.referenceAA_2=Asp;refseq.referenceCodon_1=GAT;refseq.referenceCodon_2=GAT;refseq.spliceDist_1=-81;refseq.spliceDist_2=-81;refseq.start_1=233449811;refseq.start_2=233449811;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Asp;refseq.variantAA_2=Asp;refseq.variantCodon_1=GAC;refseq.variantCodon_2=GAC;set=Intersection GT 1/1
|
|
chr1 233459169 . T C 188.69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=90;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=3771.29;QD=41.90;RankSumP=1.00000;SB=-1208.45;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.897A>G;refseq.codingCoordStr_2=c.897A>G;refseq.codonCoord_1=299;refseq.codonCoord_2=299;refseq.end_1=233459169;refseq.end_2=233459169;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1395;refseq.mrnaCoord_2=1395;refseq.name2_1=ARID4B;refseq.name2_2=ARID4B;refseq.name_1=NM_016374;refseq.name_2=NM_031371;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.E299E;refseq.proteinCoordStr_2=p.E299E;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceCodon_1=GAA;refseq.referenceCodon_2=GAA;refseq.spliceDist_1=-1;refseq.spliceDist_2=-1;refseq.spliceInfo_1=splice-donor_-1;refseq.spliceInfo_2=splice-donor_-1;refseq.start_1=233459169;refseq.start_2=233459169;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Glu;refseq.variantAA_2=Glu;refseq.variantCodon_1=GAG;refseq.variantCodon_2=GAG;set=Intersection GT 1/1
|
|
chr1 233680263 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1384T>G;refseq.codonCoord=462;refseq.end=233680263;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1613;refseq.name=NM_152490;refseq.name2=B3GALNT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C462G;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=16;refseq.start=233680263;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 233684206 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=1.30520e-08;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1196A>G;refseq.codonCoord=399;refseq.end=233684206;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1425;refseq.name=NM_152490;refseq.name2=B3GALNT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.E399G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=45;refseq.start=233684206;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 233719136 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=708;Dels=0.00;HRun=1;HaplotypeScore=17.75;MQ=98.96;MQ0=0;OQ=13043.35;QD=18.42;RankSumP=0.449970;SB=-4089.02;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.321A>G;refseq.codonCoord=107;refseq.end=233719136;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=550;refseq.name=NM_152490;refseq.name2=B3GALNT2;refseq.positionType=CDS;refseq.proteinCoordStr=p.E107E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-41;refseq.start=233719136;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/0
|
|
chr1 233782146 . A G 257.93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=152;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=98.79;MQ0=0;OQ=5509.55;QD=36.25;RankSumP=1.00000;SB=-2648.41;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.114T>C;refseq.codingCoordStr_2=c.114T>C;refseq.codingCoordStr_3=c.114T>C;refseq.codonCoord_1=38;refseq.codonCoord_2=38;refseq.codonCoord_3=38;refseq.end_1=233782146;refseq.end_2=233782146;refseq.end_3=233782146;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=442;refseq.mrnaCoord_2=568;refseq.mrnaCoord_3=330;refseq.name2_1=GNG4;refseq.name2_2=GNG4;refseq.name2_3=GNG4;refseq.name_1=NM_001098721;refseq.name_2=NM_001098722;refseq.name_3=NM_004485;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.A38A;refseq.proteinCoordStr_2=p.A38A;refseq.proteinCoordStr_3=p.A38A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceCodon_1=GCT;refseq.referenceCodon_2=GCT;refseq.referenceCodon_3=GCT;refseq.spliceDist_1=15;refseq.spliceDist_2=15;refseq.spliceDist_3=15;refseq.start_1=233782146;refseq.start_2=233782146;refseq.start_3=233782146;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.transcriptStrand_3=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantCodon_1=GCC;refseq.variantCodon_2=GCC;refseq.variantCodon_3=GCC;set=Intersection GT 1/1
|
|
chr1 233892908 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.11361A>C;refseq.codonCoord=3787;refseq.end=233892908;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=11536;refseq.name=NM_000081;refseq.name2=LYST;refseq.positionType=CDS;refseq.proteinCoordStr=p.K3787N;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=94;refseq.start=233892908;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 1/0
|
|
chr1 233981276 . A C 0.01 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=166;Dels=0.00;HRun=1;HaplotypeScore=21.63;MQ=97.26;MQ0=0;OQ=118.36;QD=0.71;RankSumP=0.00000;SB=164.56;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.7637T>G;refseq.codonCoord=2546;refseq.end=233981276;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=7812;refseq.name=NM_000081;refseq.name2=LYST;refseq.positionType=CDS;refseq.proteinCoordStr=p.V2546G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=10;refseq.spliceInfo=splice-acceptor_10;refseq.start=233981276;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 234007073 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=256;Dels=0.00;HRun=3;HaplotypeScore=0.32;MQ=98.92;MQ0=0;OQ=5393.14;QD=21.07;RankSumP=0.397974;SB=-1374.27;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5373G>A;refseq.codonCoord=1791;refseq.end=234007073;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=5548;refseq.name=NM_000081;refseq.name2=LYST;refseq.positionType=CDS;refseq.proteinCoordStr=p.K1791K;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-88;refseq.start=234007073;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAA;set=Intersection GT 0/1
|
|
chr1 234011917 . T C 356.56 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=98.83;MQ0=0;OQ=5666.67;QD=20.38;RankSumP=0.464131;SB=-2150.71;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.4956A>G;refseq.codonCoord=1652;refseq.end=234011917;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5131;refseq.name=NM_000081;refseq.name2=LYST;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1652L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=-68;refseq.start=234011917;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/0
|
|
chr1 234021795 . T G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=30;DP=475;Dels=0.00;HRun=2;HaplotypeScore=47.52;MQ=98.51;MQ0=0;OQ=186.01;QD=0.39;RankSumP=0.00000;SB=561.59;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4370A>C;refseq.codonCoord=1457;refseq.end=234021795;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=4545;refseq.name=NM_000081;refseq.name2=LYST;refseq.positionType=CDS;refseq.proteinCoordStr=p.H1457P;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-174;refseq.start=234021795;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 234039058 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=571;Dels=0.00;HRun=0;HaplotypeScore=25.27;MQ=98.86;MQ0=0;OQ=12624.29;QD=22.11;RankSumP=0.0233794;SB=-3781.73;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1683A>G;refseq.codonCoord=561;refseq.end=234039058;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1858;refseq.name=NM_000081;refseq.name2=LYST;refseq.positionType=CDS;refseq.proteinCoordStr=p.L561L;refseq.referenceAA=Leu;refseq.referenceCodon=CTA;refseq.spliceDist=-681;refseq.start=234039058;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/0
|
|
chr1 234039490 . T C 230.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=354;Dels=0.00;HRun=0;HaplotypeScore=8.11;MQ=98.68;MQ0=0;OQ=7449.22;QD=21.04;RankSumP=0.321676;SB=-2977.74;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1251A>G;refseq.codonCoord=417;refseq.end=234039490;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1426;refseq.name=NM_000081;refseq.name2=LYST;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q417Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAA;refseq.spliceDist=968;refseq.start=234039490;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 1/0
|
|
chr1 234207797 . T C 199.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=329;Dels=0.00;HRun=1;HaplotypeScore=2.85;MQ=98.14;MQ0=0;OQ=5457.90;QD=16.59;RankSumP=0.165807;SB=-2052.72;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3737A>G;refseq.codonCoord=1246;refseq.end=234207797;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3839;refseq.name=NM_002508;refseq.name2=NID1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q1246R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=115;refseq.start=234207797;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/0
|
|
chr1 234207843 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3691A>C;refseq.codonCoord=1231;refseq.end=234207843;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=3793;refseq.name=NM_002508;refseq.name2=NID1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T1231P;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=69;refseq.start=234207843;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT 1/0
|
|
chr1 234211574 . A G 203.47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=151;Dels=0.00;HRun=1;HaplotypeScore=2.87;MQ=98.56;MQ0=0;OQ=3065.22;QD=20.30;RankSumP=0.235552;SB=-1088.91;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3187T>C;refseq.codonCoord=1063;refseq.end=234211574;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3289;refseq.name=NM_002508;refseq.name2=NID1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1063L;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-41;refseq.start=234211574;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 0/1
|
|
chr1 234220809 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=287;Dels=0.00;HRun=0;HaplotypeScore=6.26;MQ=98.61;MQ0=0;OQ=4790.58;QD=16.69;RankSumP=0.300317;SB=-1465.34;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2928G>A;refseq.codonCoord=976;refseq.end=234220809;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3030;refseq.name=NM_002508;refseq.name2=NID1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P976P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-1;refseq.spliceInfo=splice-donor_-1;refseq.start=234220809;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 0/1
|
|
chr1 234241962 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=26;DB;DP=212;Dels=0.00;HRun=1;HaplotypeScore=38.35;MQ=97.90;MQ0=0;OQ=2686.34;QD=12.67;RankSumP=0.315768;SB=-168.31;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2409A>G;refseq.codonCoord=803;refseq.end=234241962;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2511;refseq.name=NM_002508;refseq.name2=NID1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V803V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=5;refseq.spliceInfo=splice-acceptor_5;refseq.start=234241962;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 234275396 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=196;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=99.00;MQ0=0;OQ=4026.04;QD=20.54;RankSumP=0.425403;SB=-385.43;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.736G>A;refseq.codonCoord=246;refseq.end=234275396;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=838;refseq.name=NM_002508;refseq.name2=NID1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V246I;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-17;refseq.start=234275396;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 0/1
|
|
chr1 234448448 . G C 218.73 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=5.31;MQ=99.00;MQ0=0;OQ=1778.59;QD=15.07;RankSumP=0.364517;SB=-486.83;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1395C>G;refseq.codonCoord=465;refseq.end=234448448;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1651;refseq.name=NM_019891;refseq.name2=ERO1LB;refseq.positionType=CDS;refseq.proteinCoordStr=p.H465Q;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=52;refseq.start=234448448;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAG;set=Intersection GT 0/1
|
|
chr1 234479853 . T A 127.51 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=194;Dels=0.00;HRun=2;HaplotypeScore=6.01;MQ=98.86;MQ0=0;OQ=3081.91;QD=15.89;RankSumP=0.0463111;SB=-1317.45;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.386A>T;refseq.codonCoord=129;refseq.end=234479853;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=642;refseq.name=NM_019891;refseq.name2=ERO1LB;refseq.positionType=CDS;refseq.proteinCoordStr=p.D129V;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=38;refseq.start=234479853;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/0
|
|
chr1 234624394 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=706;Dels=0.00;HRun=0;HaplotypeScore=14.65;MQ=98.82;MQ0=0;OQ=13691.18;QD=19.39;RankSumP=0.0726915;SB=-5564.04;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.27G>A;refseq.codonCoord=9;refseq.end=234624394;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=92;refseq.name=NM_145861;refseq.name2=EDARADD;refseq.positionType=CDS;refseq.proteinCoordStr=p.M9I;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-35;refseq.start=234624394;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/0
|
|
chr1 234767430 . T A 208.30 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=160;Dels=0.00;HRun=0;HaplotypeScore=9.28;MQ=97.73;MQ0=0;OQ=6230.60;QD=38.94;RankSumP=1.00000;SB=-1334.26;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.56T>A;refseq.codingCoordStr_2=c.56T>A;refseq.codingCoordStr_3=c.56T>A;refseq.codingCoordStr_4=c.56T>A;refseq.codonCoord_1=19;refseq.codonCoord_2=19;refseq.codonCoord_3=19;refseq.codonCoord_4=19;refseq.end_1=234767430;refseq.end_2=234767430;refseq.end_3=234767430;refseq.end_4=234767430;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.frame_4=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=437;refseq.mrnaCoord_2=437;refseq.mrnaCoord_3=444;refseq.mrnaCoord_4=256;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.F19Y;refseq.proteinCoordStr_2=p.F19Y;refseq.proteinCoordStr_3=p.F19Y;refseq.proteinCoordStr_4=p.F19Y;refseq.referenceAA_1=Phe;refseq.referenceAA_2=Phe;refseq.referenceAA_3=Phe;refseq.referenceAA_4=Phe;refseq.referenceCodon_1=TTT;refseq.referenceCodon_2=TTT;refseq.referenceCodon_3=TTT;refseq.referenceCodon_4=TTT;refseq.spliceDist_1=11;refseq.spliceDist_2=11;refseq.spliceDist_3=11;refseq.spliceDist_4=11;refseq.start_1=234767430;refseq.start_2=234767430;refseq.start_3=234767430;refseq.start_4=234767430;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantAA_4=Tyr;refseq.variantCodon_1=TAT;refseq.variantCodon_2=TAT;refseq.variantCodon_3=TAT;refseq.variantCodon_4=TAT;set=Intersection GT 1/1
|
|
chr1 234767446 . T C 103.24 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=169;Dels=0.00;HRun=2;HaplotypeScore=3.10;MQ=97.83;MQ0=0;OQ=6718.33;QD=39.75;RankSumP=1.00000;SB=-1997.91;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.72T>C;refseq.codingCoordStr_2=c.72T>C;refseq.codingCoordStr_3=c.72T>C;refseq.codingCoordStr_4=c.72T>C;refseq.codonCoord_1=24;refseq.codonCoord_2=24;refseq.codonCoord_3=24;refseq.codonCoord_4=24;refseq.end_1=234767446;refseq.end_2=234767446;refseq.end_3=234767446;refseq.end_4=234767446;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=453;refseq.mrnaCoord_2=453;refseq.mrnaCoord_3=460;refseq.mrnaCoord_4=272;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.P24P;refseq.proteinCoordStr_2=p.P24P;refseq.proteinCoordStr_3=p.P24P;refseq.proteinCoordStr_4=p.P24P;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.spliceDist_1=27;refseq.spliceDist_2=27;refseq.spliceDist_3=27;refseq.spliceDist_4=27;refseq.start_1=234767446;refseq.start_2=234767446;refseq.start_3=234767446;refseq.start_4=234767446;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Pro;refseq.variantAA_2=Pro;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantCodon_1=CCC;refseq.variantCodon_2=CCC;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;set=Intersection GT 1/1
|
|
chr1 234767480 . C T 319.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=220;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.33;MQ0=0;OQ=9422.23;QD=42.83;RankSumP=1.00000;SB=-4157.34;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.106C>T;refseq.codingCoordStr_2=c.106C>T;refseq.codingCoordStr_3=c.106C>T;refseq.codingCoordStr_4=c.106C>T;refseq.codonCoord_1=36;refseq.codonCoord_2=36;refseq.codonCoord_3=36;refseq.codonCoord_4=36;refseq.end_1=234767480;refseq.end_2=234767480;refseq.end_3=234767480;refseq.end_4=234767480;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=487;refseq.mrnaCoord_2=487;refseq.mrnaCoord_3=494;refseq.mrnaCoord_4=306;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.R36C;refseq.proteinCoordStr_2=p.R36C;refseq.proteinCoordStr_3=p.R36C;refseq.proteinCoordStr_4=p.R36C;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_1=CGT;refseq.referenceCodon_2=CGT;refseq.referenceCodon_3=CGT;refseq.referenceCodon_4=CGT;refseq.spliceDist_1=-29;refseq.spliceDist_2=-29;refseq.spliceDist_3=-29;refseq.spliceDist_4=-29;refseq.start_1=234767480;refseq.start_2=234767480;refseq.start_3=234767480;refseq.start_4=234767480;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantAA_3=Cys;refseq.variantAA_4=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;refseq.variantCodon_3=TGT;refseq.variantCodon_4=TGT;set=Intersection GT 1/1
|
|
chr1 234768832 . C T 66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=20;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=6.37;MQ=97.31;MQ0=0;OQ=1377.66;QD=23.75;RankSumP=1.00000;SB=-176.29;SecondBestBaseQ=2;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.165C>T;refseq.codingCoordStr_2=c.165C>T;refseq.codingCoordStr_3=c.165C>T;refseq.codingCoordStr_4=c.165C>T;refseq.codonCoord_1=55;refseq.codonCoord_2=55;refseq.codonCoord_3=55;refseq.codonCoord_4=55;refseq.end_1=234768832;refseq.end_2=234768832;refseq.end_3=234768832;refseq.end_4=234768832;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeAlternate_4=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=546;refseq.mrnaCoord_2=546;refseq.mrnaCoord_3=553;refseq.mrnaCoord_4=365;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.S55S;refseq.proteinCoordStr_2=p.S55S;refseq.proteinCoordStr_3=p.S55S;refseq.proteinCoordStr_4=p.S55S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceAA_3=Ser;refseq.referenceAA_4=Ser;refseq.referenceCodon_1=AGC;refseq.referenceCodon_2=AGC;refseq.referenceCodon_3=AGC;refseq.referenceCodon_4=AGC;refseq.spliceDist_1=31;refseq.spliceDist_2=31;refseq.spliceDist_3=31;refseq.spliceDist_4=31;refseq.start_1=234768832;refseq.start_2=234768832;refseq.start_3=234768832;refseq.start_4=234768832;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_1=AGT;refseq.variantCodon_2=AGT;refseq.variantCodon_3=AGT;refseq.variantCodon_4=AGT;set=Intersection GT 1/1
|
|
chr1 234768833 . A G 50 PASS AC=2;AF=1.00;AN=2;BestBaseQ=21;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.05;MQ=97.25;MQ0=0;OQ=1446.35;QD=25.83;RankSumP=1.00000;SB=-114.66;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.166A>G;refseq.codingCoordStr_2=c.166A>G;refseq.codingCoordStr_3=c.166A>G;refseq.codingCoordStr_4=c.166A>G;refseq.codonCoord_1=56;refseq.codonCoord_2=56;refseq.codonCoord_3=56;refseq.codonCoord_4=56;refseq.end_1=234768833;refseq.end_2=234768833;refseq.end_3=234768833;refseq.end_4=234768833;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=547;refseq.mrnaCoord_2=547;refseq.mrnaCoord_3=554;refseq.mrnaCoord_4=366;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.M56V;refseq.proteinCoordStr_2=p.M56V;refseq.proteinCoordStr_3=p.M56V;refseq.proteinCoordStr_4=p.M56V;refseq.referenceAA_1=Met;refseq.referenceAA_2=Met;refseq.referenceAA_3=Met;refseq.referenceAA_4=Met;refseq.referenceCodon_1=ATG;refseq.referenceCodon_2=ATG;refseq.referenceCodon_3=ATG;refseq.referenceCodon_4=ATG;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.spliceDist_3=32;refseq.spliceDist_4=32;refseq.start_1=234768833;refseq.start_2=234768833;refseq.start_3=234768833;refseq.start_4=234768833;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Val;refseq.variantAA_2=Val;refseq.variantAA_3=Val;refseq.variantAA_4=Val;refseq.variantCodon_1=GTG;refseq.variantCodon_2=GTG;refseq.variantCodon_3=GTG;refseq.variantCodon_4=GTG;set=Intersection GT 1/1
|
|
chr1 234768997 . G A 70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=229;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=98.93;MQ0=0;OQ=9771.50;QD=42.67;RankSumP=1.00000;SB=-3976.77;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.330G>A;refseq.codingCoordStr_2=c.330G>A;refseq.codingCoordStr_3=c.330G>A;refseq.codingCoordStr_4=c.330G>A;refseq.codonCoord_1=110;refseq.codonCoord_2=110;refseq.codonCoord_3=110;refseq.codonCoord_4=110;refseq.end_1=234768997;refseq.end_2=234768997;refseq.end_3=234768997;refseq.end_4=234768997;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=711;refseq.mrnaCoord_2=711;refseq.mrnaCoord_3=718;refseq.mrnaCoord_4=530;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.L110L;refseq.proteinCoordStr_2=p.L110L;refseq.proteinCoordStr_3=p.L110L;refseq.proteinCoordStr_4=p.L110L;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceAA_3=Leu;refseq.referenceAA_4=Leu;refseq.referenceCodon_1=CTG;refseq.referenceCodon_2=CTG;refseq.referenceCodon_3=CTG;refseq.referenceCodon_4=CTG;refseq.spliceDist_1=-16;refseq.spliceDist_2=-16;refseq.spliceDist_3=-16;refseq.spliceDist_4=-16;refseq.start_1=234768997;refseq.start_2=234768997;refseq.start_3=234768997;refseq.start_4=234768997;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantCodon_1=CTA;refseq.variantCodon_2=CTA;refseq.variantCodon_3=CTA;refseq.variantCodon_4=CTA;set=Intersection GT 1/1
|
|
chr1 234773485 . G C 71 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=234;Dels=0.00;HRun=1;HaplotypeScore=17.25;MQ=98.61;MQ0=0;OQ=10087.79;QD=43.11;RankSumP=1.00000;SB=-3324.92;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.678G>C;refseq.codingCoordStr_2=c.552G>C;refseq.codingCoordStr_3=c.552G>C;refseq.codingCoordStr_4=c.678G>C;refseq.codonCoord_1=226;refseq.codonCoord_2=184;refseq.codonCoord_3=184;refseq.codonCoord_4=226;refseq.end_1=234773485;refseq.end_2=234773485;refseq.end_3=234773485;refseq.end_4=234773485;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1059;refseq.mrnaCoord_2=933;refseq.mrnaCoord_3=940;refseq.mrnaCoord_4=878;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.R226S;refseq.proteinCoordStr_2=p.R184S;refseq.proteinCoordStr_3=p.R184S;refseq.proteinCoordStr_4=p.R226S;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceCodon_1=AGG;refseq.referenceCodon_2=AGG;refseq.referenceCodon_3=AGG;refseq.referenceCodon_4=AGG;refseq.spliceDist_1=3;refseq.spliceDist_2=3;refseq.spliceDist_3=3;refseq.spliceDist_4=3;refseq.spliceInfo_1=splice-acceptor_3;refseq.spliceInfo_2=splice-acceptor_3;refseq.spliceInfo_3=splice-acceptor_3;refseq.spliceInfo_4=splice-acceptor_3;refseq.start_1=234773485;refseq.start_2=234773485;refseq.start_3=234773485;refseq.start_4=234773485;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantAA_4=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;refseq.variantCodon_3=AGC;refseq.variantCodon_4=AGC;set=Intersection GT 1/1
|
|
chr1 234777946 . T C 301.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=237;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=98.75;MQ0=0;OQ=10031.55;QD=42.33;RankSumP=1.00000;SB=-5002.65;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.codingCoordStr_1=c.942T>C;refseq.codingCoordStr_2=c.816T>C;refseq.codingCoordStr_3=c.816T>C;refseq.codingCoordStr_4=c.942T>C;refseq.codonCoord_1=314;refseq.codonCoord_2=272;refseq.codonCoord_3=272;refseq.codonCoord_4=314;refseq.end_1=234777946;refseq.end_2=234777946;refseq.end_3=234777946;refseq.end_4=234777946;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.haplotypeReference_3=T;refseq.haplotypeReference_4=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.mrnaCoord_1=1323;refseq.mrnaCoord_2=1197;refseq.mrnaCoord_3=1204;refseq.mrnaCoord_4=1142;refseq.name2_1=LGALS8;refseq.name2_2=LGALS8;refseq.name2_3=LGALS8;refseq.name2_4=LGALS8;refseq.name_1=NM_006499;refseq.name_2=NM_201543;refseq.name_3=NM_201544;refseq.name_4=NM_201545;refseq.numMatchingRecords=4;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.proteinCoordStr_1=p.Y314Y;refseq.proteinCoordStr_2=p.Y272Y;refseq.proteinCoordStr_3=p.Y272Y;refseq.proteinCoordStr_4=p.Y314Y;refseq.referenceAA_1=Tyr;refseq.referenceAA_2=Tyr;refseq.referenceAA_3=Tyr;refseq.referenceAA_4=Tyr;refseq.referenceCodon_1=TAT;refseq.referenceCodon_2=TAT;refseq.referenceCodon_3=TAT;refseq.referenceCodon_4=TAT;refseq.spliceDist_1=12;refseq.spliceDist_2=12;refseq.spliceDist_3=12;refseq.spliceDist_4=12;refseq.start_1=234777946;refseq.start_2=234777946;refseq.start_3=234777946;refseq.start_4=234777946;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.variantAA_1=Tyr;refseq.variantAA_2=Tyr;refseq.variantAA_3=Tyr;refseq.variantAA_4=Tyr;refseq.variantCodon_1=TAC;refseq.variantCodon_2=TAC;refseq.variantCodon_3=TAC;refseq.variantCodon_4=TAC;set=Intersection GT 1/1
|
|
chr1 234780915 . T A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=18;RankSumP=2.54536e-08;SecondBestBaseQ=18;refseq.chr=chr1;refseq.codingCoordStr=c.6347-2;refseq.end=234780915;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=false;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=intron;refseq.spliceDist=-2;refseq.spliceInfo=splice-acceptor_-2;refseq.start=234780915;refseq.transcriptStrand=-;set=FilteredInAll GT 1/0
|
|
chr1 234783582 . C T 274.20 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=300;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=98.95;MQ0=0;OQ=12692.72;QD=42.31;RankSumP=1.00000;SB=-6153.70;SecondBestBaseQ=12;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.6159G>A;refseq.codonCoord=2053;refseq.end=234783582;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=6284;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S2053S;refseq.referenceAA=Ser;refseq.referenceCodon=TCG;refseq.spliceDist=-79;refseq.start=234783582;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=Intersection GT 1/1
|
|
chr1 234784549 . T C 230.36 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=354;Dels=0.00;HRun=1;HaplotypeScore=7.26;MQ=98.80;MQ0=0;OQ=14437.64;QD=40.78;RankSumP=1.00000;SB=-5763.94;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6050A>G;refseq.codonCoord=2017;refseq.end=234784549;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6175;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E2017G;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-29;refseq.start=234784549;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 234785243 . T C 268.35 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=99.00;MQ0=0;OQ=2297.49;QD=38.29;RankSumP=1.00000;SB=-696.38;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5899A>G;refseq.codonCoord=1967;refseq.end=234785243;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=6024;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1967D;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-25;refseq.start=234785243;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 234785758 . T C 159.28 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=2881.24;QD=39.47;RankSumP=1.00000;SB=-362.70;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5619A>G;refseq.codonCoord=1873;refseq.end=234785758;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5744;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.E1873E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-31;refseq.start=234785758;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=Intersection GT 1/1
|
|
chr1 234785816 . A G 278.44 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=303;Dels=0.00;HRun=0;HaplotypeScore=9.55;MQ=98.80;MQ0=0;OQ=11246.39;QD=37.12;RankSumP=1.00000;SB=-3649.11;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5561T>C;refseq.codonCoord=1854;refseq.end=234785816;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=5686;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V1854A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=47;refseq.start=234785816;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 234788233 . G A 316.86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=301;Dels=0.00;HRun=1;HaplotypeScore=2.71;MQ=98.96;MQ0=0;OQ=12733.47;QD=42.30;RankSumP=1.00000;SB=-4521.72;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5131C>T;refseq.codonCoord=1711;refseq.end=234788233;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=5256;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L1711L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-74;refseq.start=234788233;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/1
|
|
chr1 234788283 . T C 137.44 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=515;Dels=0.00;HRun=0;HaplotypeScore=3.05;MQ=98.86;MQ0=0;OQ=21461.00;QD=41.67;RankSumP=1.00000;SB=-9423.78;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.5081A>G;refseq.codonCoord=1694;refseq.end=234788283;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5206;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N1694S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-124;refseq.start=234788283;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 234788354 . T C 111.68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=395;Dels=0.00;HRun=0;HaplotypeScore=14.56;MQ=98.79;MQ0=0;OQ=14786.45;QD=37.43;RankSumP=1.00000;SB=-5639.62;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.5010A>G;refseq.codonCoord=1670;refseq.end=234788354;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=5135;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1670A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=99;refseq.start=234788354;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 234804238 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3346G>C;refseq.codonCoord=1116;refseq.end=234804238;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3471;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1116P;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=19;refseq.start=234804238;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=FilteredInAll GT 1/0
|
|
chr1 234811335 . C A 177.83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=96.99;MQ0=0;OQ=716.46;QD=35.82;RankSumP=1.00000;SB=-127.17;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2565G>T;refseq.codonCoord=855;refseq.end=234811335;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2690;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V855V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=3;refseq.spliceInfo=splice-acceptor_3;refseq.start=234811335;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/1
|
|
chr1 234813066 . C T 410.16 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.93;MQ0=0;OQ=3578.18;QD=42.60;RankSumP=1.00000;SB=-1582.99;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2295G>A;refseq.codonCoord=765;refseq.end=234813066;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2420;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V765V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=54;refseq.start=234813066;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/1
|
|
chr1 234815128 . T C 246.17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=388;Dels=0.00;HRun=0;HaplotypeScore=10.33;MQ=98.55;MQ0=0;OQ=16632.86;QD=42.87;RankSumP=1.00000;SB=-5332.44;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2061A>G;refseq.codonCoord=687;refseq.end=234815128;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2186;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L687L;refseq.referenceAA=Leu;refseq.referenceCodon=TTA;refseq.spliceDist=12;refseq.start=234815128;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/1
|
|
chr1 234816272 . T C 209.68 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=402;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.69;MQ0=0;OQ=16658.55;QD=41.44;RankSumP=1.00000;SB=-6459.38;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1819A>G;refseq.codonCoord=607;refseq.end=234816272;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1944;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M607V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=104;refseq.start=234816272;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 234822460 . C T 369.48 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.44;MQ0=0;OQ=2046.27;QD=41.76;RankSumP=1.00000;SB=-776.38;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1290G>A;refseq.codonCoord=430;refseq.end=234822460;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1415;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R430R;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-15;refseq.start=234822460;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/1
|
|
chr1 234825510 . T C 257.31 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=317;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=98.97;MQ0=0;OQ=12115.25;QD=38.22;RankSumP=1.00000;SB=-4880.78;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1043A>G;refseq.codonCoord=348;refseq.end=234825510;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=1168;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H348R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=-48;refseq.start=234825510;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/1
|
|
chr1 234833953 . A G 310.27 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=265;Dels=0.00;HRun=1;HaplotypeScore=6.42;MQ=98.30;MQ0=0;OQ=10232.49;QD=38.61;RankSumP=1.00000;SB=-3665.14;SecondBestBaseQ=2;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.66T>C;refseq.codonCoord=22;refseq.end=234833953;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=191;refseq.name=NM_018072;refseq.name2=HEATR1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S22S;refseq.referenceAA=Ser;refseq.referenceCodon=TCT;refseq.spliceDist=-77;refseq.start=234833953;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 234948926 . T C 301.66 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=219;Dels=0.00;HRun=0;HaplotypeScore=6.02;MQ=98.78;MQ0=0;OQ=8023.69;QD=36.64;RankSumP=1.00000;SB=-3628.08;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.351T>C;refseq.codonCoord=117;refseq.end=234948926;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=555;refseq.name=NM_001103;refseq.name2=ACTN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.I117I;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-11;refseq.start=234948926;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/1
|
|
chr1 234950044 . C T 216.06 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=376;Dels=0.00;HRun=0;HaplotypeScore=11.92;MQ=98.92;MQ0=0;OQ=16080.80;QD=42.77;RankSumP=1.00000;SB=-6003.32;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.378C>T;refseq.codonCoord=126;refseq.end=234950044;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=582;refseq.name=NM_001103;refseq.name2=ACTN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.N126N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=17;refseq.start=234950044;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/1
|
|
chr1 235059154 . A C 19.52 ESPStandard;LowQual AC=1;AF=0.50;AN=2;DP=745;Dels=0.00;HRun=2;HaplotypeScore=47.43;MQ=98.50;MQ0=0;QD=0.03;SB=1232.90;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1038A>C;refseq.codonCoord=346;refseq.end=235059154;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1461;refseq.name=NM_000254;refseq.name2=MTR;refseq.positionType=CDS;refseq.proteinCoordStr=p.P346P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-38;refseq.start=235059154;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:462,283:499:-155.53,-150.30,-1676.88:52.31
|
|
chr1 238322206 . C G 13 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=4;RankSumP=0.251748;SecondBestBaseQ=18;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.174C>G;refseq.codonCoord=58;refseq.end=238322206;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=399;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G58G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=399;refseq.start=238322206;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 238323445 . C A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=96.21;MQ0=0;OQ=647.82;QD=17.05;RankSumP=0.139535;SB=-10.00;SecondBestBaseQ=26;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1413C>A;refseq.codonCoord=471;refseq.end=238323445;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1638;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A471A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-203;refseq.start=238323445;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/0
|
|
chr1 238437252 . C G 162.45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=227;Dels=0.00;HRun=0;HaplotypeScore=20.09;MQ=97.88;MQ0=0;OQ=4307.35;QD=18.98;RankSumP=0.0210361;SB=-1715.96;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2517C>G;refseq.codonCoord=839;refseq.end=238437252;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=2742;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.T839T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=531;refseq.start=238437252;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/0
|
|
chr1 238437729 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=16.98;MQ=24.52;MQ0=33;OQ=455.69;QD=5.30;RankSumP=0.431968;SB=-169.65;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.2994C>T;refseq.codonCoord=998;refseq.end=238437729;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3219;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P998P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-927;refseq.start=238437729;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 238437846 . C T 58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=25;DP=83;Dels=0.00;HRun=0;HaplotypeScore=11.48;MQ=21.01;MQ0=59;OQ=218.38;QD=2.63;RankSumP=0.736305;SB=-110.61;SecondBestBaseQ=20;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3111C>T;refseq.codonCoord=1037;refseq.end=238437846;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=3336;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P1037P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-810;refseq.start=238437846;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 0/1
|
|
chr1 238437951 . G A 10 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=83;Dels=0.00;HRun=0;HaplotypeScore=15.75;MQ=17.23;MQ0=68;OQ=71.77;QD=0.86;RankSumP=0.166667;SB=-6.99;SecondBestBaseQ=15;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.3216G>A;refseq.codonCoord=1072;refseq.end=238437951;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=3441;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.A1072A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=-705;refseq.start=238437951;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=filterInsoap-gatk GT 1/0
|
|
chr1 238438177 . A G 23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=1.27;MQ=32.08;MQ0=28;OQ=84.45;QD=2.56;RankSumP=1.00000;SB=-48.96;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.3442A>G;refseq.codonCoord=1148;refseq.end=238438177;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=3667;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1148G;refseq.referenceAA=Arg;refseq.referenceCodon=AGA;refseq.spliceDist=-479;refseq.start=238438177;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/1
|
|
chr1 238559357 . G A 232.14 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=365;Dels=0.00;HRun=0;HaplotypeScore=17.99;MQ=98.90;MQ0=0;OQ=7510.58;QD=20.58;RankSumP=0.203341;SB=-2891.74;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.4403G>A;refseq.codonCoord=1468;refseq.end=238559357;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=4628;refseq.name=NM_020066;refseq.name2=FMN2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R1468H;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-35;refseq.start=238559357;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/0
|
|
chr1 239778757 . C T 272.84 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=98.45;MQ0=0;OQ=3740.98;QD=40.23;RankSumP=1.00000;SB=-720.71;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.60C>T;refseq.codonCoord=20;refseq.end=239778757;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=125;refseq.name=NM_003679;refseq.name2=KMO;refseq.positionType=CDS;refseq.proteinCoordStr=p.G20G;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=6;refseq.spliceInfo=splice-acceptor_6;refseq.start=239778757;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=Intersection GT 1/1
|
|
chr1 239821971 . C T 343.57 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=523;Dels=0.00;HRun=0;HaplotypeScore=11.94;MQ=98.91;MQ0=0;OQ=10489.07;QD=20.06;RankSumP=0.407361;SB=-2540.63;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1354C>T;refseq.codonCoord=452;refseq.end=239821971;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1419;refseq.name=NM_003679;refseq.name2=KMO;refseq.positionType=CDS;refseq.proteinCoordStr=p.R452C;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=94;refseq.start=239821971;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 0/1
|
|
chr1 240087357 . C A 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=2;RankSumP=0.00000;SecondBestBaseQ=6;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.493C>A;refseq.codingCoordStr_2=c.493C>A;refseq.codingCoordStr_3=c.493C>A;refseq.codonCoord_1=165;refseq.codonCoord_2=165;refseq.codonCoord_3=165;refseq.end_1=240087357;refseq.end_2=240087357;refseq.end_3=240087357;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=807;refseq.mrnaCoord_2=807;refseq.mrnaCoord_3=1075;refseq.name2_1=EXO1;refseq.name2_2=EXO1;refseq.name2_3=EXO1;refseq.name_1=NM_003686;refseq.name_2=NM_006027;refseq.name_3=NM_130398;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.Q165K;refseq.proteinCoordStr_2=p.Q165K;refseq.proteinCoordStr_3=p.Q165K;refseq.referenceAA_1=Gln;refseq.referenceAA_2=Gln;refseq.referenceAA_3=Gln;refseq.referenceCodon_1=CAA;refseq.referenceCodon_2=CAA;refseq.referenceCodon_3=CAA;refseq.spliceDist_1=-51;refseq.spliceDist_2=-51;refseq.spliceDist_3=-51;refseq.start_1=240087357;refseq.start_2=240087357;refseq.start_3=240087357;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Lys;refseq.variantAA_2=Lys;refseq.variantAA_3=Lys;refseq.variantCodon_1=AAA;refseq.variantCodon_2=AAA;refseq.variantCodon_3=AAA;set=FilteredInAll GT 1/0
|
|
chr1 240090521 . A G 297.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=478;Dels=0.00;HRun=0;HaplotypeScore=14.15;MQ=98.87;MQ0=0;OQ=9079.57;QD=18.99;RankSumP=0.166102;SB=-3121.88;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.836A>G;refseq.codingCoordStr_2=c.836A>G;refseq.codingCoordStr_3=c.836A>G;refseq.codonCoord_1=279;refseq.codonCoord_2=279;refseq.codonCoord_3=279;refseq.end_1=240090521;refseq.end_2=240090521;refseq.end_3=240090521;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1150;refseq.mrnaCoord_2=1150;refseq.mrnaCoord_3=1418;refseq.name2_1=EXO1;refseq.name2_2=EXO1;refseq.name2_3=EXO1;refseq.name_1=NM_003686;refseq.name_2=NM_006027;refseq.name_3=NM_130398;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.N279S;refseq.proteinCoordStr_2=p.N279S;refseq.proteinCoordStr_3=p.N279S;refseq.referenceAA_1=Asn;refseq.referenceAA_2=Asn;refseq.referenceAA_3=Asn;refseq.referenceCodon_1=AAC;refseq.referenceCodon_2=AAC;refseq.referenceCodon_3=AAC;refseq.spliceDist_1=80;refseq.spliceDist_2=80;refseq.spliceDist_3=80;refseq.start_1=240090521;refseq.start_2=240090521;refseq.start_3=240090521;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantAA_3=Ser;refseq.variantCodon_1=AGC;refseq.variantCodon_2=AGC;refseq.variantCodon_3=AGC;set=Intersection GT 0/1
|
|
chr1 240096774 . A G 375.70 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=345;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=98.88;MQ0=0;OQ=13160.26;QD=38.15;RankSumP=1.00000;SB=-3843.56;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1061A>G;refseq.codingCoordStr_2=c.1061A>G;refseq.codingCoordStr_3=c.1061A>G;refseq.codonCoord_1=354;refseq.codonCoord_2=354;refseq.codonCoord_3=354;refseq.end_1=240096774;refseq.end_2=240096774;refseq.end_3=240096774;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1375;refseq.mrnaCoord_2=1375;refseq.mrnaCoord_3=1643;refseq.name2_1=EXO1;refseq.name2_2=EXO1;refseq.name2_3=EXO1;refseq.name_1=NM_003686;refseq.name_2=NM_006027;refseq.name_3=NM_130398;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.H354R;refseq.proteinCoordStr_2=p.H354R;refseq.proteinCoordStr_3=p.H354R;refseq.referenceAA_1=His;refseq.referenceAA_2=His;refseq.referenceAA_3=His;refseq.referenceCodon_1=CAT;refseq.referenceCodon_2=CAT;refseq.referenceCodon_3=CAT;refseq.spliceDist_1=20;refseq.spliceDist_2=20;refseq.spliceDist_3=20;refseq.start_1=240096774;refseq.start_2=240096774;refseq.start_3=240096774;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantCodon_1=CGT;refseq.variantCodon_2=CGT;refseq.variantCodon_3=CGT;set=Intersection GT 1/1
|
|
chr1 240102061 . G A 142.70 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=172;Dels=0.00;HRun=2;HaplotypeScore=4.86;MQ=98.78;MQ0=0;OQ=2882.34;QD=16.76;RankSumP=0.380541;SB=-1406.37;SecondBestBaseQ=33;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.1372G>A;refseq.codingCoordStr_2=c.1372G>A;refseq.codingCoordStr_3=c.1372G>A;refseq.codonCoord_1=458;refseq.codonCoord_2=458;refseq.codonCoord_3=458;refseq.end_1=240102061;refseq.end_2=240102061;refseq.end_3=240102061;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=1686;refseq.mrnaCoord_2=1686;refseq.mrnaCoord_3=1954;refseq.name2_1=EXO1;refseq.name2_2=EXO1;refseq.name2_3=EXO1;refseq.name_1=NM_003686;refseq.name_2=NM_006027;refseq.name_3=NM_130398;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.V458M;refseq.proteinCoordStr_2=p.V458M;refseq.proteinCoordStr_3=p.V458M;refseq.referenceAA_1=Val;refseq.referenceAA_2=Val;refseq.referenceAA_3=Val;refseq.referenceCodon_1=GTG;refseq.referenceCodon_2=GTG;refseq.referenceCodon_3=GTG;refseq.spliceDist_1=105;refseq.spliceDist_2=105;refseq.spliceDist_3=105;refseq.start_1=240102061;refseq.start_2=240102061;refseq.start_3=240102061;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Met;refseq.variantAA_2=Met;refseq.variantAA_3=Met;refseq.variantCodon_1=ATG;refseq.variantCodon_2=ATG;refseq.variantCodon_3=ATG;set=Intersection GT 1/0
|
|
chr1 240109168 . A G 82 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=164;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=6939.53;QD=42.31;RankSumP=1.00000;SB=-2291.59;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2009A>G;refseq.codingCoordStr_2=c.2009A>G;refseq.codingCoordStr_3=c.2009A>G;refseq.codonCoord_1=670;refseq.codonCoord_2=670;refseq.codonCoord_3=670;refseq.end_1=240109168;refseq.end_2=240109168;refseq.end_3=240109168;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2323;refseq.mrnaCoord_2=2323;refseq.mrnaCoord_3=2591;refseq.name2_1=EXO1;refseq.name2_2=EXO1;refseq.name2_3=EXO1;refseq.name_1=NM_003686;refseq.name_2=NM_006027;refseq.name_3=NM_130398;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.E670G;refseq.proteinCoordStr_2=p.E670G;refseq.proteinCoordStr_3=p.E670G;refseq.referenceAA_1=Glu;refseq.referenceAA_2=Glu;refseq.referenceAA_3=Glu;refseq.referenceCodon_1=GAG;refseq.referenceCodon_2=GAG;refseq.referenceCodon_3=GAG;refseq.spliceDist_1=-101;refseq.spliceDist_2=-101;refseq.spliceDist_3=-101;refseq.start_1=240109168;refseq.start_2=240109168;refseq.start_3=240109168;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantAA_3=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG;refseq.variantCodon_3=GGG;set=Intersection GT 1/1
|
|
chr1 240111898 . C T 331.29 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=240;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=98.81;MQ0=0;OQ=10394.30;QD=43.31;RankSumP=1.00000;SB=-4200.39;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2167C>T;refseq.codingCoordStr_2=c.2167C>T;refseq.codingCoordStr_3=c.2167C>T;refseq.codonCoord_1=723;refseq.codonCoord_2=723;refseq.codonCoord_3=723;refseq.end_1=240111898;refseq.end_2=240111898;refseq.end_3=240111898;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2481;refseq.mrnaCoord_2=2481;refseq.mrnaCoord_3=2749;refseq.name2_1=EXO1;refseq.name2_2=EXO1;refseq.name2_3=EXO1;refseq.name_1=NM_003686;refseq.name_2=NM_006027;refseq.name_3=NM_130398;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.R723C;refseq.proteinCoordStr_2=p.R723C;refseq.proteinCoordStr_3=p.R723C;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceCodon_1=CGT;refseq.referenceCodon_2=CGT;refseq.referenceCodon_3=CGT;refseq.spliceDist_1=-45;refseq.spliceDist_2=-45;refseq.spliceDist_3=-45;refseq.start_1=240111898;refseq.start_2=240111898;refseq.start_3=240111898;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Cys;refseq.variantAA_2=Cys;refseq.variantAA_3=Cys;refseq.variantCodon_1=TGT;refseq.variantCodon_2=TGT;refseq.variantCodon_3=TGT;set=Intersection GT 1/1
|
|
chr1 240115297 . C T 99.58 PASS AC=1;AF=0.50;AN=2;BestBaseQ=29;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=4.49;MQ=98.48;MQ0=0;OQ=1320.92;QD=14.05;RankSumP=0.263765;SB=-335.82;SecondBestBaseQ=29;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.codingCoordStr_1=c.2270C>T;refseq.codingCoordStr_2=c.2270C>T;refseq.codingCoordStr_3=c.2270C>T;refseq.codonCoord_1=757;refseq.codonCoord_2=757;refseq.codonCoord_3=757;refseq.end_1=240115297;refseq.end_2=240115297;refseq.end_3=240115297;refseq.frame_1=1;refseq.frame_2=1;refseq.frame_3=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=missense;refseq.haplotypeAlternate_1=T;refseq.haplotypeAlternate_2=T;refseq.haplotypeAlternate_3=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.mrnaCoord_1=2584;refseq.mrnaCoord_2=2584;refseq.mrnaCoord_3=2852;refseq.name2_1=EXO1;refseq.name2_2=EXO1;refseq.name2_3=EXO1;refseq.name_1=NM_003686;refseq.name_2=NM_006027;refseq.name_3=NM_130398;refseq.numMatchingRecords=3;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.proteinCoordStr_1=p.P757L;refseq.proteinCoordStr_2=p.P757L;refseq.proteinCoordStr_3=p.P757L;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.spliceDist_1=59;refseq.spliceDist_2=59;refseq.spliceDist_3=59;refseq.start_1=240115297;refseq.start_2=240115297;refseq.start_3=240115297;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.variantAA_1=Leu;refseq.variantAA_2=Leu;refseq.variantAA_3=Leu;refseq.variantCodon_1=CTT;refseq.variantCodon_2=CTT;refseq.variantCodon_3=CTT;set=Intersection GT 0/1
|
|
chr1 240495323 . T C 32 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.376557;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.270A>G;refseq.codonCoord=90;refseq.end=240495323;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=780;refseq.name=NM_152666;refseq.name2=PLD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.E90E;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=51;refseq.start=240495323;refseq.transcriptStrand=-;refseq.variantAA=Glu;refseq.variantCodon=GAG;set=soap GT 1/0
|
|
chr1 240495344 . C T 47 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=1;RankSumP=0.542857;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.249G>A;refseq.codonCoord=83;refseq.end=240495344;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=759;refseq.name=NM_152666;refseq.name2=PLD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q83Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=30;refseq.start=240495344;refseq.transcriptStrand=-;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=soap GT 0/1
|
|
chr1 240518299 . T C 72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.289914;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.207A>G;refseq.codonCoord=69;refseq.end=240518299;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=717;refseq.name=NM_152666;refseq.name2=PLD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.P69P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=-13;refseq.start=240518299;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=soap GT 1/0
|
|
chr1 240578027 . T C 6 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.360715;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.47A>G;refseq.codonCoord=16;refseq.end=240578027;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=557;refseq.name=NM_152666;refseq.name2=PLD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.K16R;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=-4;refseq.spliceInfo=splice-donor_-4;refseq.start=240578027;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=FilteredInAll GT 1/0
|
|
chr1 240578032 . G A 69 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.438455;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.42C>T;refseq.codonCoord=14;refseq.end=240578032;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=552;refseq.name=NM_152666;refseq.name2=PLD5;refseq.positionType=CDS;refseq.proteinCoordStr=p.V14V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-9;refseq.spliceInfo=splice-donor_-9;refseq.start=240578032;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=soap GT 1/0
|
|
chr1 241560511 . C G 0 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=138;Dels=0.00;HRun=2;HaplotypeScore=6.00;MQ=97.55;MQ0=0;OQ=128.22;QD=0.93;RankSumP=0.00000;SB=254.89;SecondBestBaseQ=23;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1115C>G;refseq.codonCoord=372;refseq.end=241560511;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1271;refseq.name=NM_006642;refseq.name2=SDCCAG8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A372G;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=47;refseq.start=241560511;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 241560514 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1118A>G;refseq.codonCoord=373;refseq.end=241560514;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1274;refseq.name=NM_006642;refseq.name2=SDCCAG8;refseq.positionType=CDS;refseq.proteinCoordStr=p.E373G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=50;refseq.start=241560514;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 0/1
|
|
chr1 241560530 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=22;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=16.40;MQ=97.43;MQ0=0;OQ=1885.45;QD=14.18;RankSumP=5.36632e-05;SB=-382.80;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1134A>T;refseq.codonCoord=378;refseq.end=241560530;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1290;refseq.name=NM_006642;refseq.name2=SDCCAG8;refseq.positionType=CDS;refseq.proteinCoordStr=p.E378D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=66;refseq.start=241560530;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAT;set=filterInsoap-gatk GT 0/1
|
|
chr1 241645735 . G A 203.86 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=151;Dels=0.00;HRun=1;HaplotypeScore=3.11;MQ=98.94;MQ0=0;OQ=3057.16;QD=20.25;RankSumP=0.456588;SB=-1073.52;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1725G>A;refseq.codonCoord=575;refseq.end=241645735;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1881;refseq.name=NM_006642;refseq.name2=SDCCAG8;refseq.positionType=CDS;refseq.proteinCoordStr=p.E575E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-20;refseq.start=241645735;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/0
|
|
chr1 242647602 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=30;HRun=2;RankSumP=0.00000;SecondBestBaseQ=13;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1021T>G;refseq.codonCoord=341;refseq.end=242647602;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1315;refseq.name=NM_001126;refseq.name2=ADSS;refseq.positionType=CDS;refseq.proteinCoordStr=p.L341V;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=-50;refseq.start=242647602;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=FilteredInAll GT 0/1
|
|
chr1 242790715 . G A 343.48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=269;Dels=0.00;HRun=0;HaplotypeScore=5.63;MQ=98.70;MQ0=0;OQ=5702.61;QD=21.20;RankSumP=0.349336;SB=-2375.14;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1152G>A;refseq.codingCoordStr_2=c.1152G>A;refseq.codonCoord_1=384;refseq.codonCoord_2=384;refseq.end_1=242790715;refseq.end_2=242790715;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1211;refseq.mrnaCoord_2=1211;refseq.name2_1=C1orf101;refseq.name2_2=C1orf101;refseq.name_1=NM_001130957;refseq.name_2=NM_173807;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S384S;refseq.proteinCoordStr_2=p.S384S;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCG;refseq.referenceCodon_2=TCG;refseq.spliceDist_1=123;refseq.spliceDist_2=123;refseq.start_1=242790715;refseq.start_2=242790715;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCA;refseq.variantCodon_2=TCA;set=Intersection GT 1/0
|
|
chr1 242802481 . A G 288.94 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=228;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=98.83;MQ0=0;OQ=4218.57;QD=18.50;RankSumP=2.48023e-08;SB=-1616.85;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1734A>G;refseq.codingCoordStr_2=c.1734A>G;refseq.codonCoord_1=578;refseq.codonCoord_2=578;refseq.end_1=242802481;refseq.end_2=242802481;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1793;refseq.mrnaCoord_2=1793;refseq.name2_1=C1orf101;refseq.name2_2=C1orf101;refseq.name_1=NM_001130957;refseq.name_2=NM_173807;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.T578T;refseq.proteinCoordStr_2=p.T578T;refseq.referenceAA_1=Thr;refseq.referenceAA_2=Thr;refseq.referenceCodon_1=ACA;refseq.referenceCodon_2=ACA;refseq.spliceDist_1=-217;refseq.spliceDist_2=-217;refseq.start_1=242802481;refseq.start_2=242802481;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantCodon_1=ACG;refseq.variantCodon_2=ACG;set=filterInsoap-gatk GT 0/1
|
|
chr1 242823456 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=1;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.2256C>G;refseq.codingCoordStr_2=c.2256C>G;refseq.codonCoord_1=752;refseq.codonCoord_2=752;refseq.end_1=242823456;refseq.end_2=242823456;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=2315;refseq.mrnaCoord_2=2315;refseq.name2_1=C1orf101;refseq.name2_2=C1orf101;refseq.name_1=NM_001130957;refseq.name_2=NM_173807;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.C752W;refseq.proteinCoordStr_2=p.C752W;refseq.referenceAA_1=Cys;refseq.referenceAA_2=Cys;refseq.referenceCodon_1=TGC;refseq.referenceCodon_2=TGC;refseq.spliceDist_1=33;refseq.spliceDist_2=33;refseq.start_1=242823456;refseq.start_2=242823456;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Trp;refseq.variantAA_2=Trp;refseq.variantCodon_1=TGG;refseq.variantCodon_2=TGG;set=FilteredInAll GT 1/0
|
|
chr1 243071961 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=1.32734e-09;SecondBestBaseQ=10;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.135C>G;refseq.codonCoord_2=45;refseq.end_1=243071961;refseq.end_2=243071961;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=*;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=3647;refseq.mrnaCoord_2=513;refseq.name2_1=NCRNA00201;refseq.name2_2=FAM36A;refseq.name_1=NR_026778;refseq.name_2=NM_198076;refseq.numMatchingRecords=2;refseq.positionType_1=non_coding_exon;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.G45G;refseq.referenceAA_2=Gly;refseq.referenceCodon_2=GGC;refseq.spliceDist_1=-1398;refseq.spliceDist_2=-23;refseq.start_1=243071961;refseq.start_2=243071961;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGG;set=FilteredInAll GT 1/0
|
|
chr1 243089227 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=2;RankSumP=0.00000;SecondBestBaseQ=9;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.1033T>G;refseq.codingCoordStr_2=c.1090T>G;refseq.codonCoord_1=345;refseq.codonCoord_2=364;refseq.end_1=243089227;refseq.end_2=243089227;refseq.frame_1=0;refseq.frame_2=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1251;refseq.mrnaCoord_2=1308;refseq.name2_1=HNRNPU;refseq.name2_2=HNRNPU;refseq.name_1=NM_004501;refseq.name_2=NM_031844;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.S345A;refseq.proteinCoordStr_2=p.S364A;refseq.referenceAA_1=Ser;refseq.referenceAA_2=Ser;refseq.referenceCodon_1=TCA;refseq.referenceCodon_2=TCA;refseq.spliceDist_1=-28;refseq.spliceDist_2=-28;refseq.start_1=243089227;refseq.start_2=243089227;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;set=FilteredInAll GT 0/1
|
|
chr1 244088564 . T C 277.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=490;Dels=0.00;HRun=0;HaplotypeScore=10.26;MQ=98.71;MQ0=0;OQ=9161.37;QD=18.70;RankSumP=0.414218;SB=-3535.87;SecondBestBaseQ=33;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.933A>G;refseq.codingCoordStr_2=c.756A>G;refseq.codonCoord_1=311;refseq.codonCoord_2=252;refseq.end_1=244088564;refseq.end_2=244088564;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=1058;refseq.mrnaCoord_2=886;refseq.name2_1=SMYD3;refseq.name2_2=SMYD3;refseq.name_1=NM_001167740;refseq.name_2=NM_022743;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.A311A;refseq.proteinCoordStr_2=p.A252A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceCodon_1=GCA;refseq.referenceCodon_2=GCA;refseq.spliceDist_1=32;refseq.spliceDist_2=32;refseq.start_1=244088564;refseq.start_2=244088564;refseq.transcriptStrand_1=-;refseq.transcriptStrand_2=-;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantCodon_1=GCG;refseq.variantCodon_2=GCG;set=Intersection GT 1/0
|
|
chr1 244781210 . G A 338.79 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=97.44;MQ0=0;OQ=5113.61;QD=41.57;RankSumP=1.00000;SB=-1567.42;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.723C>T;refseq.codonCoord=241;refseq.end=244781210;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=848;refseq.name=NM_022366;refseq.name2=TFB2M;refseq.positionType=CDS;refseq.proteinCoordStr=p.P241P;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=18;refseq.start=244781210;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCT;set=Intersection GT 1/1
|
|
chr1 244787421 . G A 319.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=155;Dels=0.00;HRun=1;HaplotypeScore=1.48;MQ=97.95;MQ0=0;OQ=6695.83;QD=43.20;RankSumP=1.00000;SB=-3020.50;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.441C>T;refseq.codonCoord=147;refseq.end=244787421;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=566;refseq.name=NM_022366;refseq.name2=TFB2M;refseq.positionType=CDS;refseq.proteinCoordStr=p.I147I;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=39;refseq.start=244787421;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATT;set=Intersection GT 1/1
|
|
chr1 244821747 . T C 359.86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.78;MQ0=0;OQ=3443.82;QD=37.43;RankSumP=1.00000;SB=-694.61;SecondBestBaseQ=0;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_1=c.260T>C;refseq.codingCoordStr_2=c.260T>C;refseq.codonCoord_1=87;refseq.codonCoord_2=87;refseq.end_1=244821747;refseq.end_2=244821747;refseq.frame_1=1;refseq.frame_2=1;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=C;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=T;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=764;refseq.mrnaCoord_2=638;refseq.name2_1=CNST;refseq.name2_2=CNST;refseq.name_1=NM_001139459;refseq.name_2=NM_152609;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.L87S;refseq.proteinCoordStr_2=p.L87S;refseq.referenceAA_1=Leu;refseq.referenceAA_2=Leu;refseq.referenceCodon_1=TTG;refseq.referenceCodon_2=TTG;refseq.spliceDist_1=-120;refseq.spliceDist_2=-120;refseq.start_1=244821747;refseq.start_2=244821747;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Ser;refseq.variantAA_2=Ser;refseq.variantCodon_1=TCG;refseq.variantCodon_2=TCG;set=Intersection GT 1/1
|
|
chr1 245072674 . G C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=699;Dels=0.00;HRun=0;HaplotypeScore=82.23;MQ=97.39;MQ0=2;OQ=15702.53;QD=22.46;RankSumP=0.0414048;SB=-5607.29;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6580C>G;refseq.codonCoord=2194;refseq.end=245072674;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6677;refseq.name=NM_015446;refseq.name2=AHCTF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L2194V;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=28;refseq.start=245072674;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=soap-filterIngatk GT 0/1
|
|
chr1 245079923 . G T 45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.465368;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.6035C>A;refseq.codonCoord=2012;refseq.end=245079923;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=6132;refseq.name=NM_015446;refseq.name2=AHCTF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.P2012H;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=-384;refseq.start=245079923;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=soap GT 0/1
|
|
chr1 245115457 . T C 406.60 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=155;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=90.12;MQ0=9;OQ=6262.04;QD=40.40;RankSumP=1.00000;SB=-2940.85;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.2648A>G;refseq.codonCoord=883;refseq.end=245115457;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=2745;refseq.name=NM_015446;refseq.name2=AHCTF1;refseq.positionType=CDS;refseq.proteinCoordStr=p.N883S;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=-40;refseq.start=245115457;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 245268214 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=855;Dels=0.00;HRun=1;HaplotypeScore=13.49;MQ=98.73;MQ0=0;OQ=16927.42;QD=19.80;RankSumP=0.0511429;SB=-5904.87;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.330A>G;refseq.codonCoord=110;refseq.end=245268214;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=501;refseq.name=NM_033213;refseq.name2=ZNF670;refseq.positionType=CDS;refseq.proteinCoordStr=p.K110K;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=139;refseq.start=245268214;refseq.transcriptStrand=-;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/0
|
|
chr1 245654100 . G A 284.17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=187;Dels=0.00;HRun=0;HaplotypeScore=8.86;MQ=98.70;MQ0=0;OQ=7414.65;QD=39.65;RankSumP=1.00000;SB=-3379.43;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.732G>A;refseq.codingCoordStr_2=c.732G>A;refseq.codingCoordStr_3=c.732G>A;refseq.codingCoordStr_4=c.732G>A;refseq.codingCoordStr_5=c.732G>A;refseq.codonCoord_1=244;refseq.codonCoord_2=244;refseq.codonCoord_3=244;refseq.codonCoord_4=244;refseq.codonCoord_5=244;refseq.end_1=245654100;refseq.end_2=245654100;refseq.end_3=245654100;refseq.end_4=245654100;refseq.end_5=245654100;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=A;refseq.haplotypeAlternate_4=A;refseq.haplotypeAlternate_5=A;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=870;refseq.mrnaCoord_2=1512;refseq.mrnaCoord_3=1478;refseq.mrnaCoord_4=1478;refseq.mrnaCoord_5=1478;refseq.name2_1=NLRP3;refseq.name2_2=NLRP3;refseq.name2_3=NLRP3;refseq.name2_4=NLRP3;refseq.name2_5=NLRP3;refseq.name_1=NM_001079821;refseq.name_2=NM_001127461;refseq.name_3=NM_001127462;refseq.name_4=NM_004895;refseq.name_5=NM_183395;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.A244A;refseq.proteinCoordStr_2=p.A244A;refseq.proteinCoordStr_3=p.A244A;refseq.proteinCoordStr_4=p.A244A;refseq.proteinCoordStr_5=p.A244A;refseq.referenceAA_1=Ala;refseq.referenceAA_2=Ala;refseq.referenceAA_3=Ala;refseq.referenceAA_4=Ala;refseq.referenceAA_5=Ala;refseq.referenceCodon_1=GCG;refseq.referenceCodon_2=GCG;refseq.referenceCodon_3=GCG;refseq.referenceCodon_4=GCG;refseq.referenceCodon_5=GCG;refseq.spliceDist_1=329;refseq.spliceDist_2=329;refseq.spliceDist_3=329;refseq.spliceDist_4=329;refseq.spliceDist_5=329;refseq.start_1=245654100;refseq.start_2=245654100;refseq.start_3=245654100;refseq.start_4=245654100;refseq.start_5=245654100;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_1=Ala;refseq.variantAA_2=Ala;refseq.variantAA_3=Ala;refseq.variantAA_4=Ala;refseq.variantAA_5=Ala;refseq.variantCodon_1=GCA;refseq.variantCodon_2=GCA;refseq.variantCodon_3=GCA;refseq.variantCodon_4=GCA;refseq.variantCodon_5=GCA;set=Intersection GT 1/1
|
|
chr1 245654154 . A G 135.17 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=275;Dels=0.00;HRun=1;HaplotypeScore=11.04;MQ=98.78;MQ0=0;OQ=11033.53;QD=40.12;RankSumP=1.00000;SB=-3767.84;SecondBestBaseQ=0;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_1=c.786A>G;refseq.codingCoordStr_2=c.786A>G;refseq.codingCoordStr_3=c.786A>G;refseq.codingCoordStr_4=c.786A>G;refseq.codingCoordStr_5=c.786A>G;refseq.codonCoord_1=262;refseq.codonCoord_2=262;refseq.codonCoord_3=262;refseq.codonCoord_4=262;refseq.codonCoord_5=262;refseq.end_1=245654154;refseq.end_2=245654154;refseq.end_3=245654154;refseq.end_4=245654154;refseq.end_5=245654154;refseq.frame_1=2;refseq.frame_2=2;refseq.frame_3=2;refseq.frame_4=2;refseq.frame_5=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeAlternate_3=G;refseq.haplotypeAlternate_4=G;refseq.haplotypeAlternate_5=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_1=924;refseq.mrnaCoord_2=1566;refseq.mrnaCoord_3=1532;refseq.mrnaCoord_4=1532;refseq.mrnaCoord_5=1532;refseq.name2_1=NLRP3;refseq.name2_2=NLRP3;refseq.name2_3=NLRP3;refseq.name2_4=NLRP3;refseq.name2_5=NLRP3;refseq.name_1=NM_001079821;refseq.name_2=NM_001127461;refseq.name_3=NM_001127462;refseq.name_4=NM_004895;refseq.name_5=NM_183395;refseq.numMatchingRecords=5;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_1=p.R262R;refseq.proteinCoordStr_2=p.R262R;refseq.proteinCoordStr_3=p.R262R;refseq.proteinCoordStr_4=p.R262R;refseq.proteinCoordStr_5=p.R262R;refseq.referenceAA_1=Arg;refseq.referenceAA_2=Arg;refseq.referenceAA_3=Arg;refseq.referenceAA_4=Arg;refseq.referenceAA_5=Arg;refseq.referenceCodon_1=CGA;refseq.referenceCodon_2=CGA;refseq.referenceCodon_3=CGA;refseq.referenceCodon_4=CGA;refseq.referenceCodon_5=CGA;refseq.spliceDist_1=383;refseq.spliceDist_2=383;refseq.spliceDist_3=383;refseq.spliceDist_4=383;refseq.spliceDist_5=383;refseq.start_1=245654154;refseq.start_2=245654154;refseq.start_3=245654154;refseq.start_4=245654154;refseq.start_5=245654154;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_1=Arg;refseq.variantAA_2=Arg;refseq.variantAA_3=Arg;refseq.variantAA_4=Arg;refseq.variantAA_5=Arg;refseq.variantCodon_1=CGG;refseq.variantCodon_2=CGG;refseq.variantCodon_3=CGG;refseq.variantCodon_4=CGG;refseq.variantCodon_5=CGG;set=Intersection GT 1/1
|
|
chr1 245665953 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.chr_3=chr1;refseq.chr_4=chr1;refseq.chr_5=chr1;refseq.codingCoordStr_3=c.2557A>C;refseq.codingCoordStr_4=c.2386A>C;refseq.codingCoordStr_5=c.2557A>C;refseq.codonCoord_3=853;refseq.codonCoord_4=796;refseq.codonCoord_5=853;refseq.end_1=245673886;refseq.end_2=245673886;refseq.end_3=245665953;refseq.end_4=245665953;refseq.end_5=245665953;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=*;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.mrnaCoord_3=2695;refseq.mrnaCoord_4=3132;refseq.mrnaCoord_5=3303;refseq.name2_1=NLRP3;refseq.name2_2=NLRP3;refseq.name2_3=NLRP3;refseq.name2_4=NLRP3;refseq.name2_5=NLRP3;refseq.name_1=NM_001127461;refseq.name_2=NM_183395;refseq.name_3=NM_001079821;refseq.name_4=NM_001127462;refseq.name_5=NM_004895;refseq.numMatchingRecords=5;refseq.positionType_1=intron;refseq.positionType_2=intron;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.proteinCoordStr_3=p.T853P;refseq.proteinCoordStr_4=p.T796P;refseq.proteinCoordStr_5=p.T853P;refseq.referenceAA_3=Thr;refseq.referenceAA_4=Thr;refseq.referenceAA_5=Thr;refseq.referenceCodon_3=ACC;refseq.referenceCodon_4=ACC;refseq.referenceCodon_5=ACC;refseq.spliceDist_3=59;refseq.spliceDist_4=59;refseq.spliceDist_5=59;refseq.start_1=245664209;refseq.start_2=245664209;refseq.start_3=245665953;refseq.start_4=245665953;refseq.start_5=245665953;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Pro;refseq.variantCodon_3=CCC;refseq.variantCodon_4=CCC;refseq.variantCodon_5=CCC;set=FilteredInAll GT 0/1
|
|
chr1 245681316 . C T 447.09 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=97.74;MQ0=0;OQ=3393.61;QD=40.89;RankSumP=1.00000;SB=-1572.07;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.592G>A;refseq.codonCoord=198;refseq.end=245681316;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=592;refseq.name=NM_001004492;refseq.name2=OR2B11;refseq.positionType=CDS;refseq.proteinCoordStr=p.V198M;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-363;refseq.start=245681316;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/1
|
|
chr1 245681519 . A C 76.38 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=161;Dels=0.00;HRun=0;HaplotypeScore=14.63;MQ=98.11;MQ0=0;OQ=5745.14;QD=35.68;RankSumP=1.00000;SB=-2420.54;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.389T>G;refseq.codonCoord=130;refseq.end=245681519;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=389;refseq.name=NM_001004492;refseq.name2=OR2B11;refseq.positionType=CDS;refseq.proteinCoordStr=p.I130S;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=389;refseq.start=245681519;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 245721121 . G A 265.66 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=226;Dels=0.00;HRun=0;HaplotypeScore=6.73;MQ=98.91;MQ0=0;OQ=4288.66;QD=18.98;RankSumP=0.404747;SB=-1616.33;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.69G>A;refseq.codonCoord=23;refseq.end=245721121;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=129;refseq.name=NM_001004698;refseq.name2=OR2W5;refseq.positionType=CDS;refseq.proteinCoordStr=p.L23L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=129;refseq.start=245721121;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTA;set=Intersection GT 1/0
|
|
chr1 245762050 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=111;Dels=0.00;HRun=2;HaplotypeScore=4.49;MQ=98.58;MQ0=0;OQ=2447.45;QD=22.05;RankSumP=0.218881;SB=-1153.21;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.387G>C;refseq.codonCoord=129;refseq.end=245762050;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=749;refseq.name=NM_198074;refseq.name2=OR2C3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R129S;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=416;refseq.start=245762050;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/0
|
|
chr1 245762235 . G A 285.41 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=304;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=98.98;MQ0=0;OQ=12755.07;QD=41.96;RankSumP=1.00000;SB=-5771.73;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.202C>T;refseq.codonCoord=68;refseq.end=245762235;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=564;refseq.name=NM_198074;refseq.name2=OR2C3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P68S;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=231;refseq.start=245762235;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=Intersection GT 1/1
|
|
chr1 245762379 . T C 370.92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=206;Dels=0.00;HRun=0;HaplotypeScore=4.65;MQ=98.88;MQ0=0;OQ=7690.94;QD=37.33;RankSumP=1.00000;SB=-2389.29;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.58A>G;refseq.codonCoord=20;refseq.end=245762379;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=420;refseq.name=NM_198074;refseq.name2=OR2C3;refseq.positionType=CDS;refseq.proteinCoordStr=p.T20A;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=87;refseq.start=245762379;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 245818354 . C G 121.60 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=388;Dels=0.00;HRun=0;HaplotypeScore=15.11;MQ=98.77;MQ0=0;OQ=9697.52;QD=24.99;RankSumP=0.472247;SB=-3251.41;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.70C>G;refseq.codonCoord=24;refseq.end=245818354;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=70;refseq.name=NM_001001915;refseq.name2=OR2G2;refseq.positionType=CDS;refseq.proteinCoordStr=p.P24A;refseq.referenceAA=Pro;refseq.referenceCodon=CCT;refseq.spliceDist=70;refseq.start=245818354;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/0
|
|
chr1 245818642 . G C 69 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=890;Dels=0.00;HRun=0;HaplotypeScore=19.75;MQ=98.63;MQ0=0;OQ=40450.58;QD=45.45;RankSumP=1.00000;SB=-16763.67;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.358G>C;refseq.codonCoord=120;refseq.end=245818642;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=358;refseq.name=NM_001001915;refseq.name2=OR2G2;refseq.positionType=CDS;refseq.proteinCoordStr=p.V120L;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=358;refseq.start=245818642;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 245818784 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=938;Dels=0.00;HRun=3;HaplotypeScore=18.87;MQ=98.81;MQ0=0;OQ=15888.10;QD=16.94;RankSumP=3.26930e-06;SB=-5981.97;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.500T>C;refseq.codonCoord=167;refseq.end=245818784;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=500;refseq.name=NM_001001915;refseq.name2=OR2G2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L167P;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=-455;refseq.start=245818784;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=filterInsoap-gatk GT 1/0
|
|
chr1 245818990 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=262;Dels=0.00;HRun=2;HaplotypeScore=12.44;MQ=98.81;MQ0=0;OQ=4597.74;QD=17.55;RankSumP=0.176169;SB=-1616.85;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.706A>G;refseq.codonCoord=236;refseq.end=245818990;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=706;refseq.name=NM_001001915;refseq.name2=OR2G2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R236G;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=-249;refseq.start=245818990;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=Intersection GT 0/1
|
|
chr1 245836215 . C T 264.98 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=208;Dels=0.00;HRun=0;HaplotypeScore=7.24;MQ=98.88;MQ0=0;OQ=4138.26;QD=19.90;RankSumP=0.289540;SB=-655.14;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.705C>T;refseq.codonCoord=235;refseq.end=245836215;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=705;refseq.name=NM_001001914;refseq.name2=OR2G3;refseq.positionType=CDS;refseq.proteinCoordStr=p.H235H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-226;refseq.start=245836215;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 0/1
|
|
chr1 245902297 . G A 170.16 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=4.74;MQ=99.00;MQ0=0;OQ=1999.22;QD=16.66;RankSumP=0.255645;SB=-570.74;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.670C>T;refseq.codonCoord=224;refseq.end=245902297;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=670;refseq.name=NM_001005487;refseq.name2=OR13G1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R224C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-255;refseq.start=245902297;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/0
|
|
chr1 245902531 . T A 187.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=222;Dels=0.00;HRun=1;HaplotypeScore=5.09;MQ=98.62;MQ0=0;OQ=4215.99;QD=18.99;RankSumP=0.0634081;SB=-1699.44;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.436A>T;refseq.codonCoord=146;refseq.end=245902531;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=436;refseq.name=NM_001005487;refseq.name2=OR13G1;refseq.positionType=CDS;refseq.proteinCoordStr=p.M146L;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=436;refseq.start=245902531;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 1/0
|
|
chr1 245902573 . T C 336.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=209;Dels=0.00;HRun=0;HaplotypeScore=6.67;MQ=98.68;MQ0=0;OQ=4350.85;QD=20.82;RankSumP=0.0226868;SB=-1498.82;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.394A>G;refseq.codonCoord=132;refseq.end=245902573;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=394;refseq.name=NM_001005487;refseq.name2=OR13G1;refseq.positionType=CDS;refseq.proteinCoordStr=p.I132V;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=394;refseq.start=245902573;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=Intersection GT 1/0
|
|
chr1 245902631 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=168;Dels=0.00;HRun=2;HaplotypeScore=4.14;MQ=98.82;MQ0=0;OQ=3038.88;QD=18.09;RankSumP=0.428697;SB=-1325.04;SecondBestBaseQ=31;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.336C>T;refseq.codonCoord=112;refseq.end=245902631;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=336;refseq.name=NM_001005487;refseq.name2=OR13G1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F112F;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=336;refseq.start=245902631;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTT;set=Intersection GT 1/0
|
|
chr1 245902773 . A C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=29;HRun=1;RankSumP=0.00000;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.194T>G;refseq.codonCoord=65;refseq.end=245902773;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=194;refseq.name=NM_001005487;refseq.name2=OR13G1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V65G;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=194;refseq.start=245902773;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGT;set=FilteredInAll GT 0/1
|
|
chr1 245902830 . T A 231.31 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=226;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=99.00;MQ0=0;OQ=4259.47;QD=18.85;RankSumP=0.334001;SB=-1551.99;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.137A>T;refseq.codonCoord=46;refseq.end=245902830;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=137;refseq.name=NM_001005487;refseq.name2=OR13G1;refseq.positionType=CDS;refseq.proteinCoordStr=p.K46I;refseq.referenceAA=Lys;refseq.referenceCodon=AAA;refseq.spliceDist=137;refseq.start=245902830;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=Intersection GT 1/0
|
|
chr1 245942231 . C G 151.59 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=99.00;MQ0=0;OQ=621.01;QD=14.79;RankSumP=0.166128;SB=-263.36;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.450G>C;refseq.codonCoord=150;refseq.end=245942231;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=450;refseq.name=NM_001005286;refseq.name2=OR6F1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V150V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=450;refseq.start=245942231;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 1/0
|
|
chr1 245987723 . T G 454.96 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=175;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=98.03;MQ0=0;OQ=6624.19;QD=37.85;RankSumP=1.00000;SB=-2354.26;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.609A>C;refseq.codonCoord=203;refseq.end=245987723;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=609;refseq.name=NM_012353;refseq.name2=OR1C1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G203G;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=-337;refseq.start=245987723;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 245987975 . C T 345.57 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=271;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=98.81;MQ0=0;OQ=11096.72;QD=40.95;RankSumP=1.00000;SB=-4033.30;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.357G>A;refseq.codonCoord=119;refseq.end=245987975;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=357;refseq.name=NM_012353;refseq.name2=OR1C1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A119A;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=357;refseq.start=245987975;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=Intersection GT 1/1
|
|
chr1 246044942 . A G 283.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=223;Dels=0.00;HRun=0;HaplotypeScore=6.88;MQ=98.90;MQ0=0;OQ=9190.26;QD=41.21;RankSumP=1.00000;SB=-3245.31;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.713T>C;refseq.codonCoord=238;refseq.end=246044942;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=713;refseq.name=NM_001001966;refseq.name2=OR14A16;refseq.positionType=CDS;refseq.proteinCoordStr=p.I238T;refseq.referenceAA=Ile;refseq.referenceCodon=ATT;refseq.spliceDist=-218;refseq.start=246044942;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 246045619 . A G 343.07 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=145;Dels=0.00;HRun=0;HaplotypeScore=5.14;MQ=99.00;MQ0=0;OQ=2755.62;QD=19.00;RankSumP=0.176564;SB=-1213.21;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.36T>C;refseq.codonCoord=12;refseq.end=246045619;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=36;refseq.name=NM_001001966;refseq.name2=OR14A16;refseq.positionType=CDS;refseq.proteinCoordStr=p.L12L;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=36;refseq.start=246045619;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 0/1
|
|
chr1 246070919 . A G 329.78 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=233;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=99.00;MQ0=0;OQ=4754.96;QD=20.41;RankSumP=0.227084;SB=-1741.22;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.903T>C;refseq.codonCoord=301;refseq.end=246070919;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=903;refseq.name=NM_001001959;refseq.name2=OR11L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V301V;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=-67;refseq.start=246070919;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=Intersection GT 0/1
|
|
chr1 246071237 . G A 166.22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=98.89;MQ0=0;OQ=1253.01;QD=14.24;RankSumP=0.336031;SB=-560.94;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.585C>T;refseq.codonCoord=195;refseq.end=246071237;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=585;refseq.name=NM_001001959;refseq.name2=OR11L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.T195T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=-385;refseq.start=246071237;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/0
|
|
chr1 246071310 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=166;Dels=0.00;HRun=1;HaplotypeScore=12.70;MQ=97.76;MQ0=0;OQ=2687.54;QD=16.19;RankSumP=0.00761408;SB=-791.82;SecondBestBaseQ=27;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.512G>C;refseq.codonCoord=171;refseq.end=246071310;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=512;refseq.name=NM_001001959;refseq.name2=OR11L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.R171P;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-458;refseq.start=246071310;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCC;set=filterInsoap-gatk GT 1/0
|
|
chr1 246071398 . C T 301.41 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=167;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=98.38;MQ0=0;OQ=3100.39;QD=18.57;RankSumP=0.197850;SB=-914.97;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.424G>A;refseq.codonCoord=142;refseq.end=246071398;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=424;refseq.name=NM_001001959;refseq.name2=OR11L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A142T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=424;refseq.start=246071398;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=Intersection GT 0/1
|
|
chr1 246071471 . G C 155.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=30;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=98.13;MQ0=0;OQ=1165.24;QD=22.41;RankSumP=0.643262;SB=-603.75;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.351C>G;refseq.codonCoord=117;refseq.end=246071471;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=351;refseq.name=NM_001001959;refseq.name2=OR11L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.F117L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=351;refseq.start=246071471;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=Intersection GT 0/1
|
|
chr1 246071500 . C T 208.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=97.71;MQ0=0;OQ=1277.12;QD=19.95;RankSumP=0.459641;SB=-379.49;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.322G>A;refseq.codonCoord=108;refseq.end=246071500;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=322;refseq.name=NM_001001959;refseq.name2=OR11L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.G108S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=322;refseq.start=246071500;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 0/1
|
|
chr1 246071507 . T C 133.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=97.89;MQ0=0;OQ=1278.21;QD=17.27;RankSumP=0.496283;SB=-372.40;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.315A>G;refseq.codonCoord=105;refseq.end=246071507;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=315;refseq.name=NM_001001959;refseq.name2=OR11L1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V105V;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=315;refseq.start=246071507;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/0
|
|
chr1 246087179 . G C 200.74 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=150.54;QD=37.63;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.8G>C;refseq.codonCoord=3;refseq.end=246087179;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=56;refseq.name=NM_015431;refseq.name2=TRIM58;refseq.positionType=CDS;refseq.proteinCoordStr=p.W3S;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=56;refseq.start=246087179;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCG;set=filterInsoap-gatk GT 1/1
|
|
chr1 246094842 . G A 76.37 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;OQ=217.14;QD=19.74;RankSumP=0.273810;SB=-93.32;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.729G>A;refseq.codonCoord=243;refseq.end=246094842;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=777;refseq.name=NM_015431;refseq.name2=TRIM58;refseq.positionType=CDS;refseq.proteinCoordStr=p.P243P;refseq.referenceAA=Pro;refseq.referenceCodon=CCG;refseq.spliceDist=-19;refseq.start=246094842;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCA;set=Intersection GT 1/0
|
|
chr1 246105917 . G A 215.02 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=195;Dels=0.00;HRun=0;HaplotypeScore=6.62;MQ=98.77;MQ0=0;OQ=2673.18;QD=13.71;RankSumP=0.0296422;SB=-1216.13;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.964G>A;refseq.codonCoord=322;refseq.end=246105917;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1012;refseq.name=NM_015431;refseq.name2=TRIM58;refseq.positionType=CDS;refseq.proteinCoordStr=p.V322I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=93;refseq.start=246105917;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/0
|
|
chr1 246106074 . C T 350.72 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=394;Dels=0.00;HRun=0;HaplotypeScore=10.58;MQ=98.60;MQ0=0;OQ=7124.67;QD=18.08;RankSumP=0.108986;SB=-2306.83;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.1121C>T;refseq.codonCoord=374;refseq.end=246106074;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=1169;refseq.name=NM_015431;refseq.name2=TRIM58;refseq.positionType=CDS;refseq.proteinCoordStr=p.T374M;refseq.referenceAA=Thr;refseq.referenceCodon=ACG;refseq.spliceDist=250;refseq.start=246106074;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 246106336 . A G 263.88 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=447;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=98.89;MQ0=0;OQ=17578.15;QD=39.32;RankSumP=1.00000;SB=-5623.03;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.1383A>G;refseq.codonCoord=461;refseq.end=246106336;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=1431;refseq.name=NM_015431;refseq.name2=TRIM58;refseq.positionType=CDS;refseq.proteinCoordStr=p.T461T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=512;refseq.start=246106336;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 246126046 . C T 326.29 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=355;Dels=0.00;HRun=0;HaplotypeScore=13.71;MQ=98.49;MQ0=0;OQ=6660.15;QD=18.76;RankSumP=0.272777;SB=-2484.08;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.535C>T;refseq.codonCoord=179;refseq.end=246126046;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=535;refseq.name=NM_001001957;refseq.name2=OR2W3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R179C;refseq.referenceAA=Arg;refseq.referenceCodon=CGT;refseq.spliceDist=-411;refseq.start=246126046;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 0/1
|
|
chr1 246126079 . G A 285.62 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=415;Dels=0.00;HRun=0;HaplotypeScore=16.06;MQ=98.46;MQ0=0;OQ=8154.90;QD=19.65;RankSumP=0.179609;SB=-2376.43;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.568G>A;refseq.codonCoord=190;refseq.end=246126079;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=568;refseq.name=NM_001001957;refseq.name2=OR2W3;refseq.positionType=CDS;refseq.proteinCoordStr=p.V190I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-378;refseq.start=246126079;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=Intersection GT 1/0
|
|
chr1 246126099 . A C 217.73 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=481;Dels=0.00;HRun=0;HaplotypeScore=6.80;MQ=98.39;MQ0=0;OQ=16695.37;QD=34.71;RankSumP=1.00000;SB=-5670.25;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.588A>C;refseq.codonCoord=196;refseq.end=246126099;refseq.frame=2;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=588;refseq.name=NM_001001957;refseq.name2=OR2W3;refseq.positionType=CDS;refseq.proteinCoordStr=p.E196D;refseq.referenceAA=Glu;refseq.referenceCodon=GAA;refseq.spliceDist=-358;refseq.start=246126099;refseq.transcriptStrand=+;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=Intersection GT 1/1
|
|
chr1 246126326 . T A 225.10 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=396;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=98.86;MQ0=0;OQ=15851.16;QD=40.03;RankSumP=1.00000;SB=-5275.92;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.815T>A;refseq.codonCoord=272;refseq.end=246126326;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=815;refseq.name=NM_001001957;refseq.name2=OR2W3;refseq.positionType=CDS;refseq.proteinCoordStr=p.M272K;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-131;refseq.start=246126326;refseq.transcriptStrand=+;refseq.variantAA=Lys;refseq.variantCodon=AAG;set=Intersection GT 1/1
|
|
chr1 246126335 . T C 310.11 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=355;Dels=0.00;HRun=0;HaplotypeScore=4.70;MQ=98.86;MQ0=0;OQ=13209.58;QD=37.21;RankSumP=1.00000;SB=-4381.43;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.824T>C;refseq.codonCoord=275;refseq.end=246126335;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=824;refseq.name=NM_001001957;refseq.name2=OR2W3;refseq.positionType=CDS;refseq.proteinCoordStr=p.M275T;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-122;refseq.start=246126335;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 246151057 . G A 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=558;Dels=0.00;HRun=0;HaplotypeScore=46.62;MQ=47.87;MQ0=398;OQ=6682.33;QD=11.98;RankSumP=1.00000;SB=-419.68;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.115G>A;refseq.codonCoord=39;refseq.end=246151057;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=115;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.G39S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=115;refseq.start=246151057;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=Intersection GT 1/1
|
|
chr1 246151063 . T G 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.416514;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.121T>G;refseq.codonCoord=41;refseq.end=246151063;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=121;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.S41A;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=121;refseq.start=246151063;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCC;set=FilteredInAll GT 1/0
|
|
chr1 246151087 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=670;Dels=0.00;HRun=1;HaplotypeScore=16.10;MQ=32.22;MQ0=457;OQ=4287.25;QD=6.40;RankSumP=0.373918;SB=-1528.93;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.145T>C;refseq.codonCoord=49;refseq.end=246151087;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=145;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.W49R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=145;refseq.start=246151087;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=Intersection GT 1/0
|
|
chr1 246151134 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=980;Dels=0.00;HRun=0;HaplotypeScore=22.12;MQ=28.83;MQ0=316;OQ=464.94;QD=0.47;RankSumP=0.527179;SB=280.20;SecondBestBaseQ=29;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.192T>C;refseq.codonCoord=64;refseq.end=246151134;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=192;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.L64L;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=192;refseq.start=246151134;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/0
|
|
chr1 246151202 . G A 65 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=2;RankSumP=0.625874;SecondBestBaseQ=26;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.260G>A;refseq.codonCoord=87;refseq.end=246151202;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=260;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.S87N;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=260;refseq.start=246151202;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=soap GT 1/0
|
|
chr1 246151219 . G A 10 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=0;RankSumP=0.400000;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.277G>A;refseq.codonCoord=93;refseq.end=246151219;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=277;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A93T;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=277;refseq.start=246151219;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=FilteredInAll GT 1/0
|
|
chr1 246151232 . C T 0.99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=18.81;MQ=27.41;MQ0=99;OQ=366.32;QD=3.05;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.290C>T;refseq.codonCoord=97;refseq.end=246151232;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=290;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A97V;refseq.referenceAA=Ala;refseq.referenceCodon=GCG;refseq.spliceDist=290;refseq.start=246151232;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTG;set=filterInsoap-gatk GT 1/1
|
|
chr1 246151248 rs6692365 C G 176.44 ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=21.98;MQ=25.00;MQ0=94;QD=1.68;SB=-10.00;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.306C>G;refseq.codonCoord=102;refseq.end=246151248;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=306;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.L102L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=306;refseq.start=246151248;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:24,80:6:-22.73,-1.81,-5.19:33.86
|
|
chr1 246151250 . C T 152.45 BadSOAPSNP;ESPStandard;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=22.30;MQ=23.62;MQ0=90;QD=1.52;RankSumP=0.114286;SB=-10.00;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.308C>T;refseq.codonCoord=103;refseq.end=246151250;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=308;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.P103L;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=308;refseq.start=246151250;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=FilteredInAll GT 0/1
|
|
chr1 246151254 . A C 162.17 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=25.93;MQ=21.17;MQ0=95;QD=1.56;RankSumP=0.190476;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.312A>C;refseq.codonCoord=104;refseq.end=246151254;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=312;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.T104T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=312;refseq.start=246151254;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap-filterIngatk GT 0/1
|
|
chr1 246151370 . A C 3 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.428A>C;refseq.codonCoord=143;refseq.end=246151370;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=428;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.N143T;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=428;refseq.start=246151370;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT 1/1
|
|
chr1 246151372 . C A 3 PASS AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=8.99;MQ0=46;OQ=93.31;QD=1.67;RankSumP=1.00000;SB=-71.87;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.430C>A;refseq.codonCoord=144;refseq.end=246151372;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=430;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.L144M;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=430;refseq.start=246151372;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=filterInsoap-gatk GT 1/1
|
|
chr1 246151421 rs61857491 C T 0.05 PASS AC=1;AF=0.50;AN=2;DB;DP=256;Dels=0.00;HRun=1;HaplotypeScore=4.45;MQ=12.76;MQ0=177;OQ=245.84;QD=0.96;SB=56.22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.479C>T;refseq.codonCoord=160;refseq.end=246151421;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=479;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A160V;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-461;refseq.start=246151421;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTT;set=gatk GT:AD:DP:GL:GQ 0/1:137,119:45:-41.42,-13.55,-136.44:99
|
|
chr1 246151448 . C T 25 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=344;Dels=0.00;HRun=0;HaplotypeScore=6.38;MQ=18.31;MQ0=183;OQ=988.68;QD=2.87;RankSumP=0.400000;SB=-194.30;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.506C>T;refseq.codonCoord=169;refseq.end=246151448;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=506;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A169V;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-434;refseq.start=246151448;refseq.transcriptStrand=+;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 0/1
|
|
chr1 246151532 rs34508376 T G 34.15 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=396;Dels=0.00;HRun=1;HaplotypeScore=12.85;MQ=6.23;MQ0=388;QD=0.09;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.590T>G;refseq.codonCoord=197;refseq.end=246151532;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=590;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.M197R;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=-350;refseq.start=246151532;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:310,86:3:-7.60,-0.90,-4.00:30.92
|
|
chr1 246151603 rs4362017 G T 0.03 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=420;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=10.21;MQ0=414;OQ=216.97;QD=0.52;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.661G>T;refseq.codonCoord=221;refseq.end=246151603;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=661;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.A221S;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-279;refseq.start=246151603;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:278,142:6:-25.27,-1.81,-0.00:18.06
|
|
chr1 246151731 . C T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=404;Dels=0.00;HRun=0;HaplotypeScore=36.03;MQ=61.21;MQ0=204;OQ=7253.09;QD=17.95;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.789C>T;refseq.codonCoord=263;refseq.end=246151731;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=789;refseq.name=NM_001005522;refseq.name2=OR2T8;refseq.positionType=CDS;refseq.proteinCoordStr=p.H263H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-151;refseq.start=246151731;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=Intersection GT 1/1
|
|
chr1 246179250 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=724;Dels=0.00;HRun=0;HaplotypeScore=20.36;MQ=28.74;MQ0=218;OQ=17373.42;QD=24.00;RankSumP=1.00000;SB=-6179.98;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.468T>C;refseq.codonCoord_2=156;refseq.end_1=246328565;refseq.end_2=246179250;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=468;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.C156C;refseq.referenceAA_2=Cys;refseq.referenceCodon_2=TGT;refseq.spliceDist_2=468;refseq.start_1=246167320;refseq.start_2=246179250;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Cys;refseq.variantCodon_2=TGC;set=Intersection GT 1/1
|
|
chr1 246179368 . G T 269.75 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=143;Dels=0.00;HRun=0;HaplotypeScore=6.32;MQ=50.67;MQ0=70;OQ=2650.38;QD=18.53;RankSumP=1.00000;SB=-848.89;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.586G>T;refseq.codonCoord_2=196;refseq.end_1=246328565;refseq.end_2=246179368;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=586;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.G196C;refseq.referenceAA_2=Gly;refseq.referenceCodon_2=GGC;refseq.spliceDist_2=-354;refseq.start_1=246167320;refseq.start_2=246179368;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Cys;refseq.variantCodon_2=TGC;set=Intersection GT 1/1
|
|
chr1 246179385 . T C 3682.15 BadSOAPSNP;SnpCluster AC=2;AF=1.00;AN=2;BestBaseQ=18;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=72.45;MQ0=6;QD=37.96;RankSumP=1.00000;SB=-619.46;SecondBestBaseQ=0;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.603T>C;refseq.codonCoord_2=201;refseq.end_1=246328565;refseq.end_2=246179385;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=603;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.S201S;refseq.referenceAA_2=Ser;refseq.referenceCodon_2=AGT;refseq.spliceDist_2=-337;refseq.start_1=246167320;refseq.start_2=246179385;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ser;refseq.variantCodon_2=AGC;set=FilteredInAll GT 1/1
|
|
chr1 246179386 rs4925790 G A 3881.05 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=73.27;MQ0=5;QD=40.01;SB=-572.76;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.604G>A;refseq.codonCoord_2=202;refseq.end_1=246328565;refseq.end_2=246179386;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=604;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A202T;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCC;refseq.spliceDist_2=-336;refseq.start_1=246167320;refseq.start_2=246179386;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Thr;refseq.variantCodon_2=ACC;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:0,97:92:-387.10,-27.71,-0.02:99
|
|
chr1 246179394 rs4925791 C T 6552.09 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=154;Dels=0.00;HRun=3;HaplotypeScore=5.00;MQ=83.79;MQ0=1;QD=42.55;SB=-1975.44;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.612C>T;refseq.codonCoord_2=204;refseq.end_1=246328565;refseq.end_2=246179394;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=612;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.I204I;refseq.referenceAA_2=Ile;refseq.referenceCodon_2=ATC;refseq.spliceDist_2=-328;refseq.start_1=246167320;refseq.start_2=246179394;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ile;refseq.variantCodon_2=ATT;set=FilteredInAll GT:AD:DP:GL:GQ 1/1:0,154:153:-654.21,-46.07,-0.02:99
|
|
chr1 246179432 . A G 282.01 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=414;Dels=0.00;HRun=0;HaplotypeScore=5.31;MQ=87.91;MQ0=0;OQ=17615.50;QD=42.55;RankSumP=1.00000;SB=-6453.90;SecondBestBaseQ=34;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.650A>G;refseq.codonCoord_2=217;refseq.end_1=246328565;refseq.end_2=246179432;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=650;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.Y217C;refseq.referenceAA_2=Tyr;refseq.referenceCodon_2=TAT;refseq.spliceDist_2=-290;refseq.start_1=246167320;refseq.start_2=246179432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Cys;refseq.variantCodon_2=TGT;set=Intersection GT 1/1
|
|
chr1 246179459 . A G 86 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=532;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=85.89;MQ0=2;OQ=20337.11;QD=38.23;RankSumP=1.00000;SB=-9125.33;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.677A>G;refseq.codonCoord_2=226;refseq.end_1=246328565;refseq.end_2=246179459;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=677;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.H226R;refseq.referenceAA_2=His;refseq.referenceCodon_2=CAC;refseq.spliceDist_2=-263;refseq.start_1=246167320;refseq.start_2=246179459;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Arg;refseq.variantCodon_2=CGC;set=Intersection GT 1/1
|
|
chr1 246179649 . T A 93 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=468;Dels=0.00;HRun=1;HaplotypeScore=10.66;MQ=39.28;MQ0=183;OQ=10196.29;QD=21.79;RankSumP=1.00000;SB=-4299.46;SecondBestBaseQ=16;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.867T>A;refseq.codonCoord_2=289;refseq.end_1=246328565;refseq.end_2=246179649;refseq.frame_2=2;refseq.functionalClass_2=nonsense;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=867;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.Y289*;refseq.referenceAA_2=Tyr;refseq.referenceCodon_2=TAT;refseq.spliceDist_2=-73;refseq.start_1=246167320;refseq.start_2=246179649;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Stop;refseq.variantCodon_2=TAA;set=Intersection GT 1/1
|
|
chr1 246179663 . A G 92 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=440;Dels=0.00;HRun=2;HaplotypeScore=6.24;MQ=38.60;MQ0=240;OQ=6905.82;QD=15.70;RankSumP=1.00000;SB=-3190.11;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.881A>G;refseq.codonCoord_2=294;refseq.end_1=246328565;refseq.end_2=246179663;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=881;refseq.name2_1=OR2L13;refseq.name2_2=OR2L8;refseq.name_1=NM_175911;refseq.name_2=NM_001001963;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.K294R;refseq.referenceAA_2=Lys;refseq.referenceCodon_2=AAG;refseq.spliceDist_2=-59;refseq.start_1=246167320;refseq.start_2=246179663;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Arg;refseq.variantCodon_2=AGG;set=Intersection GT 1/1
|
|
chr1 246195368 . A G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=27;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.112A>G;refseq.codonCoord_2=38;refseq.end_1=246328565;refseq.end_2=246195368;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=112;refseq.name2_1=OR2L13;refseq.name2_2=OR2AK2;refseq.name_1=NM_175911;refseq.name_2=NM_001004491;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.I38V;refseq.referenceAA_2=Ile;refseq.referenceCodon_2=ATA;refseq.spliceDist_2=112;refseq.start_1=246167320;refseq.start_2=246195368;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Val;refseq.variantCodon_2=GTA;set=FilteredInAll GT 0/1
|
|
chr1 246195863 . G A 225.90 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=247;Dels=0.00;HRun=0;HaplotypeScore=7.29;MQ=98.72;MQ0=0;OQ=10226.70;QD=41.40;RankSumP=1.00000;SB=-1927.43;SecondBestBaseQ=0;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.607G>A;refseq.codonCoord_2=203;refseq.end_1=246328565;refseq.end_2=246195863;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=A;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=607;refseq.name2_1=OR2L13;refseq.name2_2=OR2AK2;refseq.name_1=NM_175911;refseq.name_2=NM_001004491;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V203M;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTG;refseq.spliceDist_2=-402;refseq.start_1=246167320;refseq.start_2=246195863;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Met;refseq.variantCodon_2=ATG;set=Intersection GT 1/1
|
|
chr1 246268912 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=759;Dels=0.00;HRun=0;HaplotypeScore=15.18;MQ=94.58;MQ0=5;OQ=16054.19;QD=21.15;RankSumP=0.00596652;SB=-5278.71;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.720T>C;refseq.codonCoord_2=240;refseq.end_1=246328565;refseq.end_2=246268912;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=816;refseq.name2_1=OR2L13;refseq.name2_2=OR2L2;refseq.name_1=NM_175911;refseq.name_2=NM_001004686;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.C240C;refseq.referenceAA_2=Cys;refseq.referenceCodon_2=TGT;refseq.spliceDist_2=-319;refseq.start_1=246167320;refseq.start_2=246268912;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Cys;refseq.variantCodon_2=TGC;set=filterInsoap-gatk GT 1/0
|
|
chr1 246291074 . T C 39 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=3.32702e-06;SecondBestBaseQ=27;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.468T>C;refseq.codonCoord_2=156;refseq.end_1=246328565;refseq.end_2=246291074;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=C;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=T;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=468;refseq.name2_1=OR2L13;refseq.name2_2=OR2L3;refseq.name_1=NM_175911;refseq.name_2=NM_001004687;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.C156C;refseq.referenceAA_2=Cys;refseq.referenceCodon_2=TGT;refseq.spliceDist_2=468;refseq.start_1=246167320;refseq.start_2=246291074;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Cys;refseq.variantCodon_2=TGC;set=FilteredInAll GT 1/0
|
|
chr1 246291112 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=642;Dels=0.00;HRun=0;HaplotypeScore=22.26;MQ=36.50;MQ0=135;OQ=944.48;QD=1.47;RankSumP=0.0960248;SB=609.52;SecondBestBaseQ=32;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.506A>G;refseq.codonCoord_2=169;refseq.end_1=246328565;refseq.end_2=246291112;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=506;refseq.name2_1=OR2L13;refseq.name2_2=OR2L3;refseq.name_1=NM_175911;refseq.name_2=NM_001004687;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.Q169R;refseq.referenceAA_2=Gln;refseq.referenceCodon_2=CAA;refseq.spliceDist_2=-434;refseq.start_1=246167320;refseq.start_2=246291112;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Arg;refseq.variantCodon_2=CGA;set=soap-filterIngatk GT 0/1
|
|
chr1 246291192 . G T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1005;Dels=0.00;HRun=0;HaplotypeScore=16.69;MQ=49.00;MQ0=257;OQ=9553.97;QD=9.51;RankSumP=0.406829;SB=-3310.62;SecondBestBaseQ=33;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.586G>T;refseq.codonCoord_2=196;refseq.end_1=246328565;refseq.end_2=246291192;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=586;refseq.name2_1=OR2L13;refseq.name2_2=OR2L3;refseq.name_1=NM_175911;refseq.name_2=NM_001004687;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.G196C;refseq.referenceAA_2=Gly;refseq.referenceCodon_2=GGC;refseq.spliceDist_2=-354;refseq.start_1=246167320;refseq.start_2=246291192;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Cys;refseq.variantCodon_2=TGC;set=soap-filterIngatk GT 0/1
|
|
chr1 246291218 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1018;Dels=0.00;HRun=3;HaplotypeScore=22.14;MQ=50.88;MQ0=196;OQ=10139.09;QD=9.96;RankSumP=0.0736263;SB=-2625.67;SecondBestBaseQ=33;refseq.changesAA_2=false;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.612C>T;refseq.codonCoord_2=204;refseq.end_1=246328565;refseq.end_2=246291218;refseq.frame_2=2;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=612;refseq.name2_1=OR2L13;refseq.name2_2=OR2L3;refseq.name_1=NM_175911;refseq.name_2=NM_001004687;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.I204I;refseq.referenceAA_2=Ile;refseq.referenceCodon_2=ATC;refseq.spliceDist_2=-328;refseq.start_1=246167320;refseq.start_2=246291218;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Ile;refseq.variantCodon_2=ATT;set=soap-filterIngatk GT 0/1
|
|
chr1 246291241 . C G 0.46 PASS AC=1;AF=0.50;AN=2;DP=871;Dels=0.00;HRun=1;HaplotypeScore=12.50;MQ=42.28;MQ0=268;OQ=3109.33;QD=3.57;SB=-895.91;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.635C>G;refseq.codonCoord_2=212;refseq.end_1=246328565;refseq.end_2=246291241;refseq.frame_2=1;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=C;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=635;refseq.name2_1=OR2L13;refseq.name2_2=OR2L3;refseq.name_1=NM_175911;refseq.name_2=NM_001004687;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.A212G;refseq.referenceAA_2=Ala;refseq.referenceCodon_2=GCT;refseq.spliceDist_2=-305;refseq.start_1=246167320;refseq.start_2=246291241;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Gly;refseq.variantCodon_2=GGT;set=gatk GT:AD:DP:GL:GQ 0/1:765,106:582:-489.47,-175.25,-2360.38:99
|
|
chr1 246291369 . G T 64 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=615;Dels=0.00;HRun=4;HaplotypeScore=11.47;MQ=32.12;MQ0=359;OQ=9064.61;QD=14.74;RankSumP=0.277582;SB=-3162.93;SecondBestBaseQ=34;refseq.changesAA_2=true;refseq.chr_1=chr1;refseq.chr_2=chr1;refseq.codingCoordStr_2=c.763G>T;refseq.codonCoord_2=255;refseq.end_1=246328565;refseq.end_2=246291369;refseq.frame_2=0;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_2=T;refseq.haplotypeReference_1=*;refseq.haplotypeReference_2=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=true;refseq.mrnaCoord_2=763;refseq.name2_1=OR2L13;refseq.name2_2=OR2L3;refseq.name_1=NM_175911;refseq.name_2=NM_001004687;refseq.numMatchingRecords=2;refseq.positionType_1=intron;refseq.positionType_2=CDS;refseq.proteinCoordStr_2=p.V255F;refseq.referenceAA_2=Val;refseq.referenceCodon_2=GTC;refseq.spliceDist_2=-177;refseq.start_1=246167320;refseq.start_2=246291369;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_2=Phe;refseq.variantCodon_2=TTC;set=Intersection GT 0/1
|
|
chr1 246330094 . G A 163.54 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=475;Dels=0.00;HRun=0;HaplotypeScore=9.75;MQ=98.62;MQ0=0;OQ=8461.92;QD=17.81;RankSumP=0.495223;SB=-3518.85;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.794G>A;refseq.codonCoord=265;refseq.end=246330094;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=1131;refseq.name=NM_175911;refseq.name2=OR2L13;refseq.positionType=CDS;refseq.proteinCoordStr=p.R265H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-754;refseq.start=246330094;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/0
|
|
chr1 246375360 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.00000;SecondBestBaseQ=7;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.288T>G;refseq.codonCoord=96;refseq.end=246375360;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=288;refseq.name=NM_001004690;refseq.name2=OR2M5;refseq.positionType=CDS;refseq.proteinCoordStr=p.G96G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=288;refseq.start=246375360;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 246375643 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1210;Dels=0.00;HRun=1;HaplotypeScore=39.80;MQ=48.69;MQ0=31;OQ=730.11;QD=0.60;SB=367.01;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.571G>A;refseq.codonCoord=191;refseq.end=246375643;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=571;refseq.name=NM_001004690;refseq.name2=OR2M5;refseq.positionType=CDS;refseq.proteinCoordStr=p.D191N;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-369;refseq.start=246375643;refseq.transcriptStrand=+;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1068,142:1156:-424.35,-348.06,-4423.81:99
|
|
chr1 246410166 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1308;Dels=0.00;HRun=1;HaplotypeScore=43.59;MQ=58.69;MQ0=612;OQ=12035.61;QD=9.20;RankSumP=0.414003;SB=-4204.70;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.256C>T;refseq.codonCoord=86;refseq.end=246410166;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=256;refseq.name=NM_001004688;refseq.name2=OR2M2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L86L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=256;refseq.start=246410166;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=soap-filterIngatk GT 0/1
|
|
chr1 246410198 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=23;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.288T>G;refseq.codonCoord=96;refseq.end=246410198;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=288;refseq.name=NM_001004688;refseq.name2=OR2M2;refseq.positionType=CDS;refseq.proteinCoordStr=p.G96G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=288;refseq.start=246410198;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 246410568 . C G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1387;Dels=0.00;HRun=1;HaplotypeScore=23.90;MQ=36.53;MQ0=273;OQ=8349.73;QD=6.02;RankSumP=0.314673;SB=-2216.09;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.658C>G;refseq.codonCoord=220;refseq.end=246410568;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=658;refseq.name=NM_001004688;refseq.name2=OR2M2;refseq.positionType=CDS;refseq.proteinCoordStr=p.R220G;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=-387;refseq.start=246410568;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGA;set=Intersection GT 1/0
|
|
chr1 246410613 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1140;Dels=0.00;HRun=0;HaplotypeScore=26.06;MQ=42.01;MQ0=223;OQ=2281.56;QD=2.00;RankSumP=0.353567;SB=31.17;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.703T>C;refseq.codonCoord=235;refseq.end=246410613;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=703;refseq.name=NM_001004688;refseq.name2=OR2M2;refseq.positionType=CDS;refseq.proteinCoordStr=p.C235R;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-342;refseq.start=246410613;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGC;set=Intersection GT 1/0
|
|
chr1 246433280 . T G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=22;HRun=2;RankSumP=0.00000;SecondBestBaseQ=8;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.288T>G;refseq.codonCoord=96;refseq.end=246433280;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=288;refseq.name=NM_001004689;refseq.name2=OR2M3;refseq.positionType=CDS;refseq.proteinCoordStr=p.G96G;refseq.referenceAA=Gly;refseq.referenceCodon=GGT;refseq.spliceDist=288;refseq.start=246433280;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|
|
chr1 246433325 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=1070;Dels=0.00;HRun=1;HaplotypeScore=17.43;MQ=90.96;MQ0=0;OQ=22204.94;QD=20.75;RankSumP=0.218356;SB=-8576.80;SecondBestBaseQ=25;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.333G>A;refseq.codonCoord=111;refseq.end=246433325;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=333;refseq.name=NM_001004689;refseq.name2=OR2M3;refseq.positionType=CDS;refseq.proteinCoordStr=p.E111E;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=333;refseq.start=246433325;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=Intersection GT 1/0
|
|
chr1 246433929 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=139;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=84.80;MQ0=0;OQ=2064.58;QD=14.85;RankSumP=0.131504;SB=-222.76;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.937T>A;refseq.codonCoord=313;refseq.end=246433929;refseq.frame=0;refseq.functionalClass=readthrough;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=937;refseq.name=NM_001004689;refseq.name2=OR2M3;refseq.positionType=CDS;refseq.proteinCoordStr=p.*313R;refseq.referenceAA=Stop;refseq.referenceCodon=TGA;refseq.spliceDist=-3;refseq.spliceInfo=splice-donor_-3;refseq.start=246433929;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGA;set=Intersection GT 1/0
|
|
chr1 246469381 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=655;Dels=0.00;HRun=5;HaplotypeScore=7.20;MQ=98.77;MQ0=0;OQ=12499.28;QD=19.08;RankSumP=0.101962;SB=-5077.20;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.528C>T;refseq.codonCoord=176;refseq.end=246469381;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=528;refseq.name=NM_017504;refseq.name2=OR2M4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H176H;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-409;refseq.start=246469381;refseq.transcriptStrand=+;refseq.variantAA=His;refseq.variantCodon=CAT;set=soap-filterIngatk GT 0/1
|
|
chr1 246503079 . C A 21 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=446;Dels=0.00;HRun=0;HaplotypeScore=15.97;MQ=13.41;MQ0=435;QD=0.05;SB=-6.99;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.661G>T;refseq.codonCoord=221;refseq.end=246503079;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=661;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.A221S;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=-303;refseq.start=246503079;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:296,150:11:-8.69,-3.31,-31.46:53.80
|
|
chr1 246503234 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=298;Dels=0.00;HRun=0;HaplotypeScore=21.00;MQ=25.93;MQ0=235;OQ=631.25;QD=2.12;RankSumP=0.377749;SB=-87.09;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.506C>T;refseq.codonCoord=169;refseq.end=246503234;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=506;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.A169V;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=-458;refseq.start=246503234;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTA;set=Intersection GT 1/0
|
|
chr1 246503239 . A G 97 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=306;Dels=0.00;HRun=0;HaplotypeScore=19.13;MQ=26.29;MQ0=222;OQ=1829.85;QD=5.98;RankSumP=1.00000;SB=-156.72;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.501T>C;refseq.codonCoord=167;refseq.end=246503239;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=501;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.C167C;refseq.referenceAA=Cys;refseq.referenceCodon=TGT;refseq.spliceDist=-463;refseq.start=246503239;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=Intersection GT 1/1
|
|
chr1 246503261 rs61857491 A G 0.74 PASS AC=1;AF=0.50;AN=2;DB;DP=475;Dels=0.00;HRun=0;HaplotypeScore=17.40;MQ=34.63;MQ0=207;OQ=1256.25;QD=2.64;SB=-110.91;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.479T>C;refseq.codonCoord=160;refseq.end=246503261;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=479;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.V160A;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=479;refseq.start=246503261;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=gatk GT:AD:DP:GL:GQ 0/1:355,116:189:-185.84,-56.93,-601.72:99
|
|
chr1 246503428 . T G 16927.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1142;Dels=0.00;HRun=1;HaplotypeScore=120.39;MQ=42.39;MQ0=577;QD=14.82;RankSumP=0.191338;SB=-5798.52;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.312A>C;refseq.codonCoord=104;refseq.end=246503428;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=312;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.T104T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=312;refseq.start=246503428;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap-filterIngatk GT 1/0
|
|
chr1 246503430 . T A 48 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.103985;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.310A>T;refseq.codonCoord=104;refseq.end=246503430;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=310;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.T104S;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=310;refseq.start=246503430;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=soap GT 1/0
|
|
chr1 246503432 . G A 10305.80 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1162;Dels=0.00;HRun=0;HaplotypeScore=111.29;MQ=42.40;MQ0=544;QD=8.87;RankSumP=0.708433;SB=-3124.08;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.308C>T;refseq.codonCoord=103;refseq.end=246503432;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=308;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.P103L;refseq.referenceAA=Pro;refseq.referenceCodon=CCC;refseq.spliceDist=308;refseq.start=246503432;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=soap-filterIngatk GT 1/0
|
|
chr1 246503434 . G C 12011.13 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=1196;Dels=0.00;HRun=0;HaplotypeScore=109.16;MQ=42.40;MQ0=540;QD=10.04;RankSumP=0.0720073;SB=-3847.04;SecondBestBaseQ=30;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.306C>G;refseq.codonCoord=102;refseq.end=246503434;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=306;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.L102L;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=306;refseq.start=246503434;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=soap-filterIngatk GT 0/1
|
|
chr1 246503480 . C T 61 PASS AC=1;AF=0.50;AN=2;BestBaseQ=24;HRun=2;RankSumP=0.0923508;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.260G>A;refseq.codonCoord=87;refseq.end=246503480;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=260;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.S87N;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=260;refseq.start=246503480;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=soap GT 0/1
|
|
chr1 246503535 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DP=1149;Dels=0.00;HRun=0;HaplotypeScore=28.82;MQ=25.33;MQ0=425;OQ=774.33;QD=0.67;RankSumP=0.514183;SB=582.38;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.205A>G;refseq.codonCoord=69;refseq.end=246503535;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=205;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.M69V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=205;refseq.start=246503535;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=soap-filterIngatk GT 1/0
|
|
chr1 246503548 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.541512;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.192T>C;refseq.codonCoord=64;refseq.end=246503548;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=192;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.L64L;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=192;refseq.start=246503548;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=soap GT 0/1
|
|
chr1 246503595 . A G 14 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=729;Dels=0.00;HRun=1;HaplotypeScore=25.39;MQ=17.75;MQ0=543;OQ=143.06;QD=0.20;RankSumP=0.175752;SB=143.50;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.145T>C;refseq.codonCoord=49;refseq.end=246503595;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=145;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.W49R;refseq.referenceAA=Trp;refseq.referenceCodon=TGG;refseq.spliceDist=145;refseq.start=246503595;refseq.transcriptStrand=-;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=FilteredInAll GT 0/1
|
|
chr1 246503625 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=577;Dels=0.00;HRun=0;HaplotypeScore=4.88;MQ=13.38;MQ0=531;OQ=153.52;QD=0.27;SB=59.22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.115G>A;refseq.codonCoord=39;refseq.end=246503625;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=115;refseq.name=NM_001004695;refseq.name2=OR2T33;refseq.positionType=CDS;refseq.proteinCoordStr=p.G39S;refseq.referenceAA=Gly;refseq.referenceCodon=GGC;refseq.spliceDist=115;refseq.start=246503625;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=AGC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:449,128:32:-28.27,-9.64,-101.37:99
|
|
chr1 246524602 . C A 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=936;Dels=0.00;HRun=0;HaplotypeScore=22.47;MQ=71.05;MQ0=10;OQ=35219.49;QD=37.63;RankSumP=1.00000;SB=-13437.64;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.902G>T;refseq.codonCoord=301;refseq.end=246524602;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=902;refseq.name=NM_001004692;refseq.name2=OR2T12;refseq.positionType=CDS;refseq.proteinCoordStr=p.R301L;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-62;refseq.start=246524602;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTG;set=Intersection GT 1/1
|
|
chr1 246524984 . G T 2 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.333333;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.520C>A;refseq.codonCoord=174;refseq.end=246524984;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=520;refseq.name=NM_001004692;refseq.name2=OR2T12;refseq.positionType=CDS;refseq.proteinCoordStr=p.H174N;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=-444;refseq.start=246524984;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=FilteredInAll GT 0/1
|
|
chr1 246525194 . T A 32 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=517;Dels=0.00;HRun=0;HaplotypeScore=115.76;MQ=13.22;MQ0=504;OQ=302.90;QD=0.59;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.310A>T;refseq.codonCoord=104;refseq.end=246525194;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=310;refseq.name=NM_001004692;refseq.name2=OR2T12;refseq.positionType=CDS;refseq.proteinCoordStr=p.T104S;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=310;refseq.start=246525194;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCA;set=soap-filterIngatk GT 1/1
|
|
chr1 246525227 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=470;Dels=0.00;HRun=0;HaplotypeScore=24.99;MQ=18.81;MQ0=448;OQ=259.94;QD=0.55;RankSumP=0.151628;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.277G>A;refseq.codonCoord=93;refseq.end=246525227;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=277;refseq.name=NM_001004692;refseq.name2=OR2T12;refseq.positionType=CDS;refseq.proteinCoordStr=p.A93T;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=277;refseq.start=246525227;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=soap-filterIngatk GT 0/1
|
|
chr1 246525299 . T C 106.36 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=228;Dels=0.00;HRun=0;HaplotypeScore=2.59;MQ=56.03;MQ0=138;OQ=3420.86;QD=15.00;RankSumP=1.00000;SB=19.64;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.205A>G;refseq.codonCoord=69;refseq.end=246525299;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=205;refseq.name=NM_001004692;refseq.name2=OR2T12;refseq.positionType=CDS;refseq.proteinCoordStr=p.M69V;refseq.referenceAA=Met;refseq.referenceCodon=ATG;refseq.spliceDist=205;refseq.start=246525299;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 246525312 . A G 161.80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=29;DB;DP=257;Dels=0.00;HRun=0;HaplotypeScore=4.33;MQ=58.18;MQ0=152;OQ=4288.41;QD=16.69;RankSumP=1.00000;SB=-109.04;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.192T>C;refseq.codonCoord=64;refseq.end=246525312;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=192;refseq.name=NM_001004692;refseq.name2=OR2T12;refseq.positionType=CDS;refseq.proteinCoordStr=p.L64L;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=192;refseq.start=246525312;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=Intersection GT 1/1
|
|
chr1 246525340 . C G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=12.95;MQ=71.96;MQ0=74;OQ=7264.37;QD=26.13;RankSumP=1.00000;SB=-1159.53;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.164G>C;refseq.codonCoord=55;refseq.end=246525340;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=164;refseq.name=NM_001004692;refseq.name2=OR2T12;refseq.positionType=CDS;refseq.proteinCoordStr=p.R55T;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=164;refseq.start=246525340;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=Intersection GT 1/1
|
|
chr1 246553923 . C T 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=927;Dels=0.00;HRun=1;HaplotypeScore=20.89;MQ=26.03;MQ0=633;OQ=11160.32;QD=12.04;RankSumP=1.00000;SB=-3841.31;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.571G>A;refseq.codonCoord=191;refseq.end=246553923;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=571;refseq.name=NM_001004691;refseq.name2=OR2M7;refseq.positionType=CDS;refseq.proteinCoordStr=p.D191N;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-369;refseq.start=246553923;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAC;set=Intersection GT 1/1
|
|
chr1 246553961 . C A 87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=864;Dels=0.00;HRun=1;HaplotypeScore=7.45;MQ=22.12;MQ0=657;OQ=7003.04;QD=8.11;RankSumP=1.00000;SB=-3209.60;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.533G>T;refseq.codonCoord=178;refseq.end=246553961;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=533;refseq.name=NM_001004691;refseq.name2=OR2M7;refseq.positionType=CDS;refseq.proteinCoordStr=p.C178F;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-407;refseq.start=246553961;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 1/1
|
|
chr1 246554261 . A G 77 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=1192;Dels=0.00;HRun=0;HaplotypeScore=44.73;MQ=55.71;MQ0=117;OQ=43719.16;QD=36.68;RankSumP=1.00000;SB=-19746.18;SecondBestBaseQ=28;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.233T>C;refseq.codonCoord=78;refseq.end=246554261;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=233;refseq.name=NM_001004691;refseq.name2=OR2M7;refseq.positionType=CDS;refseq.proteinCoordStr=p.V78A;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=233;refseq.start=246554261;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=soap-filterIngatk GT 1/1
|
|
chr1 246554391 . A G 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=960;Dels=0.00;HRun=1;HaplotypeScore=30.40;MQ=80.66;MQ0=32;OQ=37373.93;QD=38.93;RankSumP=1.00000;SB=-18605.44;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.103T>C;refseq.codonCoord=35;refseq.end=246554391;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=103;refseq.name=NM_001004691;refseq.name2=OR2M7;refseq.positionType=CDS;refseq.proteinCoordStr=p.F35L;refseq.referenceAA=Phe;refseq.referenceCodon=TTT;refseq.spliceDist=103;refseq.start=246554391;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTT;set=soap-filterIngatk GT 1/1
|
|
chr1 246578717 . C T 145.04 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=328;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=98.90;MQ0=0;OQ=14193.73;QD=43.27;RankSumP=1.00000;SB=-5257.61;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.18C>T;refseq.codonCoord=6;refseq.end=246578717;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=18;refseq.name=NM_001001918;refseq.name2=OR14C36;refseq.positionType=CDS;refseq.proteinCoordStr=p.T6T;refseq.referenceAA=Thr;refseq.referenceCodon=ACC;refseq.spliceDist=18;refseq.start=246578717;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACT;set=Intersection GT 1/1
|
|
chr1 246579121 . A G 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;DB;DP=391;Dels=0.00;HRun=1;HaplotypeScore=9.55;MQ=98.58;MQ0=0;OQ=6772.60;QD=17.32;RankSumP=0.000617005;SB=-2758.93;SecondBestBaseQ=32;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.422A>G;refseq.codonCoord=141;refseq.end=246579121;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=422;refseq.name=NM_001001918;refseq.name2=OR14C36;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q141R;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=422;refseq.start=246579121;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGG;set=filterInsoap-gatk GT 0/1
|
|
chr1 246579260 . C T 97.34 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=309;Dels=0.00;HRun=1;HaplotypeScore=8.81;MQ=98.83;MQ0=0;OQ=13065.74;QD=42.28;RankSumP=1.00000;SB=-5804.63;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.561C>T;refseq.codonCoord=187;refseq.end=246579260;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=561;refseq.name=NM_001001918;refseq.name2=OR14C36;refseq.positionType=CDS;refseq.proteinCoordStr=p.C187C;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=-379;refseq.start=246579260;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/1
|
|
chr1 246579372 . G A 127.23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=271;Dels=0.00;HRun=0;HaplotypeScore=13.11;MQ=98.41;MQ0=0;OQ=11217.40;QD=41.39;RankSumP=1.00000;SB=-5527.80;SecondBestBaseQ=2;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.673G>A;refseq.codonCoord=225;refseq.end=246579372;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=673;refseq.name=NM_001001918;refseq.name2=OR14C36;refseq.positionType=CDS;refseq.proteinCoordStr=p.G225R;refseq.referenceAA=Gly;refseq.referenceCodon=GGG;refseq.spliceDist=-267;refseq.start=246579372;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 1/1
|
|
chr1 246579390 . G T 227.87 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=277;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=98.64;MQ0=0;OQ=10606.34;QD=38.29;RankSumP=1.00000;SB=-4313.21;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.691G>T;refseq.codonCoord=231;refseq.end=246579390;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=691;refseq.name=NM_001001918;refseq.name2=OR14C36;refseq.positionType=CDS;refseq.proteinCoordStr=p.D231Y;refseq.referenceAA=Asp;refseq.referenceCodon=GAC;refseq.spliceDist=-249;refseq.start=246579390;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/1
|
|
chr1 246591723 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1039;Dels=0.00;HRun=3;HaplotypeScore=30.76;MQ=72.78;MQ0=4;OQ=9699.20;QD=9.34;SB=-2577.81;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.218G>A;refseq.codonCoord=73;refseq.end=246591723;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=218;refseq.name=NM_001004696;refseq.name2=OR2T4;refseq.positionType=CDS;refseq.proteinCoordStr=p.G73E;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=218;refseq.start=246591723;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:810,229:1008:-968.92,-303.51,-3344.05:99
|
|
chr1 246591758 . G A 0.01 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1563;Dels=0.00;HRun=0;HaplotypeScore=44.17;MQ=60.15;MQ0=54;OQ=16759.35;QD=10.72;SB=-4440.98;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.253G>A;refseq.codonCoord=85;refseq.end=246591758;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=253;refseq.name=NM_001004696;refseq.name2=OR2T4;refseq.positionType=CDS;refseq.proteinCoordStr=p.A85T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=253;refseq.start=246591758;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:1131,430:1428:-1674.93,-430.09,-3942.33:99
|
|
chr1 246591761 . C T 45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1615;Dels=0.00;HRun=0;HaplotypeScore=65.13;MQ=59.48;MQ0=71;OQ=17482.34;QD=10.82;RankSumP=0.415078;SB=-4978.79;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.256C>T;refseq.codonCoord=86;refseq.end=246591761;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=256;refseq.name=NM_001004696;refseq.name2=OR2T4;refseq.positionType=CDS;refseq.proteinCoordStr=p.H86Y;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=256;refseq.start=246591761;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=soap-filterIngatk GT 0/1
|
|
chr1 246591908 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=1;RankSumP=0.362915;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.403T>C;refseq.codonCoord=135;refseq.end=246591908;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=403;refseq.name=NM_001004696;refseq.name2=OR2T4;refseq.positionType=CDS;refseq.proteinCoordStr=p.F135L;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=403;refseq.start=246591908;refseq.transcriptStrand=+;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=FilteredInAll GT 1/0
|
|
chr1 246592262 . A C,T 64 PASS AC=1,1;AF=0.50,0.50;AN=2;BestBaseQ=32;RankSumP=0.516422;SecondBestBaseQ=22;set=soap GT 1/2
|
|
chr1 246592263 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;HRun=2;RankSumP=0.165568;SecondBestBaseQ=22;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.758T>C;refseq.codonCoord=253;refseq.end=246592263;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=758;refseq.name=NM_001004696;refseq.name2=OR2T4;refseq.positionType=CDS;refseq.proteinCoordStr=p.I253T;refseq.referenceAA=Ile;refseq.referenceCodon=ATC;refseq.spliceDist=-290;refseq.start=246592263;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap GT 1/0
|
|
chr1 246617599 . T G 83 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=402;Dels=0.00;HRun=1;HaplotypeScore=14.24;MQ=98.64;MQ0=0;OQ=16348.53;QD=40.67;RankSumP=1.00000;SB=-7243.94;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.67T>G;refseq.codonCoord=23;refseq.end=246617599;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=67;refseq.name=NM_001005471;refseq.name2=OR2T6;refseq.positionType=CDS;refseq.proteinCoordStr=p.C23G;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=67;refseq.start=246617599;refseq.transcriptStrand=+;refseq.variantAA=Gly;refseq.variantCodon=GGC;set=Intersection GT 1/1
|
|
chr1 246635992 . A G 250.20 PASS AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=384;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=98.81;MQ0=0;OQ=14436.32;QD=37.59;RankSumP=1.00000;SB=-3958.95;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.74A>G;refseq.codonCoord=25;refseq.end=246635992;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=74;refseq.name=NM_030904;refseq.name2=OR2T1;refseq.positionType=CDS;refseq.proteinCoordStr=p.H25R;refseq.referenceAA=His;refseq.referenceCodon=CAT;refseq.spliceDist=74;refseq.start=246635992;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CGT;set=Intersection GT 1/1
|
|
chr1 246683024 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=1135;Dels=0.00;HRun=1;HaplotypeScore=15.77;MQ=84.21;MQ0=96;OQ=19438.94;QD=17.13;RankSumP=0.316528;SB=-6283.07;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.303G>A;refseq.codonCoord=101;refseq.end=246683024;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=303;refseq.name=NM_001004136;refseq.name2=OR2T2;refseq.positionType=CDS;refseq.proteinCoordStr=p.Q101Q;refseq.referenceAA=Gln;refseq.referenceCodon=CAG;refseq.spliceDist=303;refseq.start=246683024;refseq.transcriptStrand=+;refseq.variantAA=Gln;refseq.variantCodon=CAA;set=Intersection GT 1/0
|
|
chr1 246683031 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1072;Dels=0.00;HRun=1;HaplotypeScore=21.29;MQ=85.83;MQ0=55;OQ=19280.60;QD=17.99;RankSumP=0.432226;SB=-5704.44;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.310C>T;refseq.codonCoord=104;refseq.end=246683031;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=310;refseq.name=NM_001004136;refseq.name2=OR2T2;refseq.positionType=CDS;refseq.proteinCoordStr=p.L104F;refseq.referenceAA=Leu;refseq.referenceCodon=CTC;refseq.spliceDist=310;refseq.start=246683031;refseq.transcriptStrand=+;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=Intersection GT 0/1
|
|
chr1 246703669 . G A 13 BadSOAPSNP;FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=479;Dels=0.00;HRun=0;HaplotypeScore=5.65;MQ=9.08;MQ0=422;OQ=179.29;QD=0.37;RankSumP=0.200000;SB=-10.00;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.395G>A;refseq.codonCoord=132;refseq.end=246703669;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=395;refseq.name=NM_001005495;refseq.name2=OR2T3;refseq.positionType=CDS;refseq.proteinCoordStr=p.C132Y;refseq.referenceAA=Cys;refseq.referenceCodon=TGC;refseq.spliceDist=395;refseq.start=246703669;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=FilteredInAll GT 1/0
|
|
chr1 246703688 . A G 9 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=33;HRun=0;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.414A>G;refseq.codonCoord=138;refseq.end=246703688;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=414;refseq.name=NM_001005495;refseq.name2=OR2T3;refseq.positionType=CDS;refseq.proteinCoordStr=p.P138P;refseq.referenceAA=Pro;refseq.referenceCodon=CCA;refseq.spliceDist=414;refseq.start=246703688;refseq.transcriptStrand=+;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=FilteredInAll GT 1/1
|
|
chr1 246703985 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DP=1680;Dels=0.00;HRun=0;HaplotypeScore=40.36;MQ=25.75;MQ0=246;OQ=10301.50;QD=6.13;RankSumP=0.386967;SB=-1602.23;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.711C>T;refseq.codonCoord=237;refseq.end=246703985;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=711;refseq.name=NM_001005495;refseq.name2=OR2T3;refseq.positionType=CDS;refseq.proteinCoordStr=p.A237A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-247;refseq.start=246703985;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=soap-filterIngatk GT 0/1
|
|
chr1 246704166 . C T 77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=1365;Dels=0.00;HRun=0;HaplotypeScore=27.06;MQ=5.90;MQ0=1273;OQ=365.20;QD=0.27;RankSumP=0.452381;SB=-102.94;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.892C>T;refseq.codonCoord=298;refseq.end=246704166;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=892;refseq.name=NM_001005495;refseq.name2=OR2T3;refseq.positionType=CDS;refseq.proteinCoordStr=p.R298C;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-66;refseq.start=246704166;refseq.transcriptStrand=+;refseq.variantAA=Cys;refseq.variantCodon=TGC;set=soap-filterIngatk GT 0/1
|
|
chr1 246718528 . A T 50 PASS AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.114286;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.16A>T;refseq.codonCoord=6;refseq.end=246718528;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=16;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.R6W;refseq.referenceAA=Arg;refseq.referenceCodon=AGG;refseq.spliceDist=16;refseq.start=246718528;refseq.transcriptStrand=+;refseq.variantAA=Trp;refseq.variantCodon=TGG;set=soap GT 0/1
|
|
chr1 246718550 . A G 77 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=232;Dels=0.00;HRun=1;HaplotypeScore=6.16;MQ=21.50;MQ0=90;OQ=667.83;QD=2.88;RankSumP=0.696970;SB=71.27;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.38A>G;refseq.codonCoord=13;refseq.end=246718550;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=38;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.K13R;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=38;refseq.start=246718550;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=AGG;set=Intersection GT 0/1
|
|
chr1 246718582 . C T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DP=530;Dels=0.00;HRun=0;HaplotypeScore=4.22;MQ=21.39;MQ0=205;OQ=1043.40;QD=1.97;RankSumP=0.410276;SB=-302.37;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.70C>T;refseq.codonCoord=24;refseq.end=246718582;refseq.frame=0;refseq.functionalClass=nonsense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=70;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.R24*;refseq.referenceAA=Arg;refseq.referenceCodon=CGA;refseq.spliceDist=70;refseq.start=246718582;refseq.transcriptStrand=+;refseq.variantAA=Stop;refseq.variantCodon=TGA;set=soap-filterIngatk GT 0/1
|
|
chr1 246718634 . A T 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=812;Dels=0.00;HRun=0;HaplotypeScore=14.01;MQ=14.09;MQ0=633;OQ=877.34;QD=1.08;RankSumP=0.325285;SB=-304.15;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.122A>T;refseq.codonCoord=41;refseq.end=246718634;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=122;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.K41M;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=122;refseq.start=246718634;refseq.transcriptStrand=+;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 246718646 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=860;Dels=0.00;HRun=3;HaplotypeScore=12.91;MQ=9.13;MQ0=795;OQ=404.74;QD=0.47;RankSumP=0.271618;SB=-117.92;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.134G>A;refseq.codonCoord=45;refseq.end=246718646;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=134;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.G45E;refseq.referenceAA=Gly;refseq.referenceCodon=GGA;refseq.spliceDist=134;refseq.start=246718646;refseq.transcriptStrand=+;refseq.variantAA=Glu;refseq.variantCodon=GAA;set=soap-filterIngatk GT 1/0
|
|
chr1 246718681 rs9439352 G A 0.87 PASS AC=2;AF=1.00;AN=2;DB;DP=974;Dels=0.00;HRun=0;HaplotypeScore=12.91;MQ=7.23;MQ0=966;OQ=198.95;QD=0.20;SB=-119.66;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.169G>A;refseq.codonCoord=57;refseq.end=246718681;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=169;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.A57T;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=169;refseq.start=246718681;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=gatk GT:AD:DP:GL:GQ 1/1:915,57:6:-23.47,-1.81,-0.00:18.06
|
|
chr1 246718684 rs9439337 C T 0.59 PASS AC=2;AF=1.00;AN=2;DB;DP=972;Dels=0.00;HRun=0;HaplotypeScore=12.28;MQ=4.69;MQ0=968;OQ=119.33;QD=0.12;SB=-10.00;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.172C>T;refseq.codonCoord=58;refseq.end=246718684;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=172;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.H58Y;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=172;refseq.start=246718684;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=gatk GT:AD:DP:GL:GQ 1/1:922,50:4:-15.47,-1.21,-0.00:12.04
|
|
chr1 246718694 . G C 45 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=994;Dels=0.00;HRun=4;HaplotypeScore=13.32;MQ=4.44;MQ0=992;OQ=69.76;QD=0.07;RankSumP=0.425641;SB=-10.00;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.182G>C;refseq.codonCoord=61;refseq.end=246718694;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=182;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.S61T;refseq.referenceAA=Ser;refseq.referenceCodon=AGC;refseq.spliceDist=182;refseq.start=246718694;refseq.transcriptStrand=+;refseq.variantAA=Thr;refseq.variantCodon=ACC;set=soap-filterIngatk GT 0/1
|
|
chr1 246718798 . G A 10.16 BadSOAPSNP;ESPStandard;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;BestBaseQ=33;DB;DP=773;Dels=0.00;HRun=0;HaplotypeScore=28.33;MQ=3.56;MQ0=772;QD=0.01;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.286G>A;refseq.codonCoord=96;refseq.end=246718798;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=286;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.V96I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=286;refseq.start=246718798;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=FilteredInAll GT 1/1
|
|
chr1 246718973 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=2;RankSumP=0.444444;SecondBestBaseQ=34;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.461T>C;refseq.codonCoord=154;refseq.end=246718973;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=461;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.F154S;refseq.referenceAA=Phe;refseq.referenceCodon=TTC;refseq.spliceDist=461;refseq.start=246718973;refseq.transcriptStrand=+;refseq.variantAA=Ser;refseq.variantCodon=TCC;set=FilteredInAll GT 1/0
|
|
chr1 246719197 . G A 26 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=0;RankSumP=0.700000;SecondBestBaseQ=20;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.685G>A;refseq.codonCoord=229;refseq.end=246719197;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=685;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.V229I;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-264;refseq.start=246719197;refseq.transcriptStrand=+;refseq.variantAA=Ile;refseq.variantCodon=ATC;set=soap GT 1/0
|
|
chr1 246719219 . A C 11.09 BadSOAPSNP;ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;BestBaseQ=34;DB;DP=681;Dels=0.00;HRun=0;HaplotypeScore=17.97;MQ=0.96;MQ0=680;QD=0.02;RankSumP=0.583333;SB=-10.00;SecondBestBaseQ=18;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.707A>C;refseq.codonCoord=236;refseq.end=246719219;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=707;refseq.name=NM_001004697;refseq.name2=OR2T5;refseq.positionType=CDS;refseq.proteinCoordStr=p.E236A;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=-242;refseq.start=246719219;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=FilteredInAll GT 0/1
|
|
chr1 246751876 . T C 99 PASS AC=2;AF=1.00;AN=2;BestBaseQ=28;DB;DP=679;Dels=0.00;HRun=0;HaplotypeScore=20.45;MQ=98.71;MQ0=0;OQ=22613.18;QD=33.30;RankSumP=1.00000;SB=-9230.14;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.306T>C;refseq.codonCoord=102;refseq.end=246751876;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=306;refseq.name=NM_001013355;refseq.name2=OR2G6;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y102Y;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=306;refseq.start=246751876;refseq.transcriptStrand=+;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=Intersection GT 1/1
|
|
chr1 246803882 . C G 17 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=2;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.800G>C;refseq.codonCoord=267;refseq.end=246803882;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=800;refseq.name=NM_001001821;refseq.name2=OR2T34;refseq.positionType=CDS;refseq.proteinCoordStr=p.R267P;refseq.referenceAA=Arg;refseq.referenceCodon=CGG;refseq.spliceDist=-158;refseq.start=246803882;refseq.transcriptStrand=-;refseq.variantAA=Pro;refseq.variantCodon=CCG;set=FilteredInAll GT 1/1
|
|
chr1 246803966 . C T 80 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=110;Dels=0.00;HRun=0;HaplotypeScore=4.95;MQ=17.76;MQ0=101;OQ=129.88;QD=1.18;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.716G>A;refseq.codonCoord=239;refseq.end=246803966;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=716;refseq.name=NM_001001821;refseq.name2=OR2T34;refseq.positionType=CDS;refseq.proteinCoordStr=p.R239H;refseq.referenceAA=Arg;refseq.referenceCodon=CGC;refseq.spliceDist=-242;refseq.start=246803966;refseq.transcriptStrand=-;refseq.variantAA=His;refseq.variantCodon=CAC;set=Intersection GT 1/1
|
|
chr1 246803971 . G A 23 PASS AC=2;AF=1.00;AN=2;BestBaseQ=30;DB;DP=125;Dels=0.00;HRun=0;HaplotypeScore=10.18;MQ=17.23;MQ0=109;OQ=167.75;QD=1.34;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.711C>T;refseq.codonCoord=237;refseq.end=246803971;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=711;refseq.name=NM_001001821;refseq.name2=OR2T34;refseq.positionType=CDS;refseq.proteinCoordStr=p.A237A;refseq.referenceAA=Ala;refseq.referenceCodon=GCC;refseq.spliceDist=-247;refseq.start=246803971;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=Intersection GT 1/1
|
|
chr1 246804218 . A G 17 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.0277778;SecondBestBaseQ=31;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.464T>C;refseq.codonCoord=155;refseq.end=246804218;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=464;refseq.name=NM_001001821;refseq.name2=OR2T34;refseq.positionType=CDS;refseq.proteinCoordStr=p.V155A;refseq.referenceAA=Val;refseq.referenceCodon=GTT;refseq.spliceDist=464;refseq.start=246804218;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCT;set=FilteredInAll GT 0/1
|
|
chr1 246804357 . G A 10.26 BadSOAPSNP;LowQual AC=2;AF=1.00;AN=2;BestBaseQ=34;DB;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=89.00;MQ0=0;QD=10.26;RankSumP=1.00000;SB=-10.00;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.325C>T;refseq.codonCoord=109;refseq.end=246804357;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=325;refseq.name=NM_001001821;refseq.name2=OR2T34;refseq.positionType=CDS;refseq.proteinCoordStr=p.H109Y;refseq.referenceAA=His;refseq.referenceCodon=CAC;refseq.spliceDist=325;refseq.start=246804357;refseq.transcriptStrand=-;refseq.variantAA=Tyr;refseq.variantCodon=TAC;set=FilteredInAll GT 1/1
|
|
chr1 246868535 . C G 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=34;HRun=0;RankSumP=0.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.648G>C;refseq.codonCoord=216;refseq.end=246868535;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=648;refseq.name=NM_001001827;refseq.name2=OR2T35;refseq.positionType=CDS;refseq.proteinCoordStr=p.V216V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-325;refseq.start=246868535;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTC;set=FilteredInAll GT 1/0
|
|
chr1 246868870 . G A 6 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.313C>T;refseq.codonCoord=105;refseq.end=246868870;refseq.frame=0;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=313;refseq.name=NM_001001827;refseq.name2=OR2T35;refseq.positionType=CDS;refseq.proteinCoordStr=p.L105L;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=313;refseq.start=246868870;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=TTG;set=FilteredInAll GT 1/1
|
|
chr1 246868872 . T A 12 BadSOAPSNP;FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;BestBaseQ=34;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=6.48;MQ0=64;OQ=68.29;QD=0.92;RankSumP=1.00000;SB=-3.98;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.311A>T;refseq.codonCoord=104;refseq.end=246868872;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=311;refseq.name=NM_001001827;refseq.name2=OR2T35;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y104F;refseq.referenceAA=Tyr;refseq.referenceCodon=TAC;refseq.spliceDist=311;refseq.start=246868872;refseq.transcriptStrand=-;refseq.variantAA=Phe;refseq.variantCodon=TTC;set=FilteredInAll GT 1/1
|
|
chr1 246869092 . C T 2 BadSOAPSNP AC=2;AF=1.00;AN=2;BestBaseQ=34;HRun=1;RankSumP=1.00000;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.91G>A;refseq.codonCoord=31;refseq.end=246869092;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=91;refseq.name=NM_001001827;refseq.name2=OR2T35;refseq.positionType=CDS;refseq.proteinCoordStr=p.V31I;refseq.referenceAA=Val;refseq.referenceCodon=GTA;refseq.spliceDist=91;refseq.start=246869092;refseq.transcriptStrand=-;refseq.variantAA=Ile;refseq.variantCodon=ATA;set=FilteredInAll GT 1/1
|
|
chr1 246879894 . C A 99 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=32;HRun=1;RankSumP=0.00432116;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.915G>T;refseq.codonCoord=305;refseq.end=246879894;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=915;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.V305V;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=-40;refseq.start=246879894;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTT;set=FilteredInAll GT 1/0
|
|
chr1 246879915 . T C 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;HRun=4;RankSumP=0.309413;SecondBestBaseQ=32;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.894A>G;refseq.codonCoord=298;refseq.end=246879915;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=894;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.T298T;refseq.referenceAA=Thr;refseq.referenceCodon=ACA;refseq.spliceDist=-61;refseq.start=246879915;refseq.transcriptStrand=-;refseq.variantAA=Thr;refseq.variantCodon=ACG;set=soap GT 1/0
|
|
chr1 246879966 . A G 22 PASS AC=1;AF=0.50;AN=2;BestBaseQ=31;HRun=0;RankSumP=0.161548;SecondBestBaseQ=34;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.843T>C;refseq.codonCoord=281;refseq.end=246879966;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=843;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.L281L;refseq.referenceAA=Leu;refseq.referenceCodon=CTT;refseq.spliceDist=-112;refseq.start=246879966;refseq.transcriptStrand=-;refseq.variantAA=Leu;refseq.variantCodon=CTC;set=soap GT 0/1
|
|
chr1 246880170 rs1770073 G C 19.91 PASS AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=31.31;MQ0=3;OQ=57.30;QD=11.46;SB=-54.47;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.639C>G;refseq.codonCoord=213;refseq.end=246880170;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=639;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.V213V;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=-316;refseq.start=246880170;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=gatk GT:AD:DP:GL:GQ 1/1:0,5:2:-9.14,-0.60,-0.00:6.02
|
|
chr1 246880408 rs1782240 A T 21.25 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=315;Dels=0.00;HRun=0;HaplotypeScore=12.07;MQ=26.58;MQ0=139;QD=0.07;SB=233.76;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.401T>A;refseq.codonCoord=134;refseq.end=246880408;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=401;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.V134D;refseq.referenceAA=Val;refseq.referenceCodon=GTC;refseq.spliceDist=401;refseq.start=246880408;refseq.transcriptStrand=-;refseq.variantAA=Asp;refseq.variantCodon=GAC;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:201,110:144:-48.77,-43.36,-507.71:54.06
|
|
chr1 246880450 rs1782241 T C 39.50 ESPStandard;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=407;Dels=0.00;HRun=0;HaplotypeScore=9.42;MQ=19.73;MQ0=196;QD=0.10;SB=227.23;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.359A>G;refseq.codonCoord=120;refseq.end=246880450;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=359;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y120C;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=359;refseq.start=246880450;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=FilteredInAll GT:AD:DP:GL:GQ 0/1:343,63:180:-61.45,-54.21,-695.12:72.34
|
|
chr1 246880524 rs61834487 A T 0.31 PASS AC=1;AF=0.50;AN=2;DB;DP=608;Dels=0.00;HRun=0;HaplotypeScore=13.80;MQ=15.35;MQ0=568;OQ=64.83;QD=0.11;SB=35.14;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.285T>A;refseq.codonCoord=95;refseq.end=246880524;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=T;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=285;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.A95A;refseq.referenceAA=Ala;refseq.referenceCodon=GCT;refseq.spliceDist=285;refseq.start=246880524;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCA;set=gatk GT:AD:DP:GL:GQ 0/1:409,198:29:-18.50,-8.73,-92.78:97.67
|
|
chr1 246880675 . T A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=28;DB;DP=267;Dels=0.00;HRun=0;HaplotypeScore=5.79;MQ=70.23;MQ0=111;OQ=1022.30;QD=3.83;RankSumP=0.0696301;SB=-270.50;SecondBestBaseQ=30;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.134A>T;refseq.codonCoord=45;refseq.end=246880675;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=A;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=134;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.K45M;refseq.referenceAA=Lys;refseq.referenceCodon=AAG;refseq.spliceDist=134;refseq.start=246880675;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 1/0
|
|
chr1 246880703 . A C 278.52 PASS AC=2;AF=1.00;AN=2;BestBaseQ=31;DB;DP=288;Dels=0.00;HRun=0;HaplotypeScore=7.54;MQ=88.10;MQ0=13;OQ=10401.03;QD=36.11;RankSumP=1.00000;SB=-4235.58;SecondBestBaseQ=10;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.106T>G;refseq.codonCoord=36;refseq.end=246880703;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=106;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.L36V;refseq.referenceAA=Leu;refseq.referenceCodon=TTG;refseq.spliceDist=106;refseq.start=246880703;refseq.transcriptStrand=-;refseq.variantAA=Val;refseq.variantCodon=GTG;set=Intersection GT 1/1
|
|
chr1 246880749 . G A 99 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=366;Dels=0.00;HRun=0;HaplotypeScore=5.72;MQ=87.73;MQ0=17;OQ=4527.10;QD=12.37;RankSumP=0.287507;SB=-1599.95;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.60C>T;refseq.codonCoord=20;refseq.end=246880749;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=60;refseq.name=NM_001001824;refseq.name2=OR2T27;refseq.positionType=CDS;refseq.proteinCoordStr=p.N20N;refseq.referenceAA=Asn;refseq.referenceCodon=AAC;refseq.spliceDist=60;refseq.start=246880749;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 1/0
|
|
chr1 246911582 . T C 181.38 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=344;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=98.82;MQ0=0;OQ=7290.48;QD=21.19;RankSumP=0.305755;SB=-3000.82;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.647A>G;refseq.codonCoord=216;refseq.end=246911582;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=647;refseq.name=NM_001004734;refseq.name2=OR14I1;refseq.positionType=CDS;refseq.proteinCoordStr=p.Y216C;refseq.referenceAA=Tyr;refseq.referenceCodon=TAT;refseq.spliceDist=-290;refseq.start=246911582;refseq.transcriptStrand=-;refseq.variantAA=Cys;refseq.variantCodon=TGT;set=Intersection GT 1/0
|
|
chr1 246911720 . C T 225.85 PASS AC=1;AF=0.50;AN=2;BestBaseQ=32;DB;DP=191;Dels=0.00;HRun=1;HaplotypeScore=4.95;MQ=98.66;MQ0=0;OQ=2883.52;QD=15.10;RankSumP=0.353341;SB=-1196.59;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.509G>A;refseq.codonCoord=170;refseq.end=246911720;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=509;refseq.name=NM_001004734;refseq.name2=OR14I1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S170N;refseq.referenceAA=Ser;refseq.referenceCodon=AGT;refseq.spliceDist=-428;refseq.start=246911720;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 246911979 . G T 193.89 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=98.77;MQ0=0;OQ=2456.45;QD=17.55;RankSumP=0.146598;SB=-768.80;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.250C>A;refseq.codonCoord=84;refseq.end=246911979;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=250;refseq.name=NM_001004734;refseq.name2=OR14I1;refseq.positionType=CDS;refseq.proteinCoordStr=p.L84M;refseq.referenceAA=Leu;refseq.referenceCodon=CTG;refseq.spliceDist=250;refseq.start=246911979;refseq.transcriptStrand=-;refseq.variantAA=Met;refseq.variantCodon=ATG;set=Intersection GT 0/1
|
|
chr1 246912034 . G A 155.15 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=254;Dels=0.00;HRun=0;HaplotypeScore=16.33;MQ=98.61;MQ0=0;OQ=4406.02;QD=17.35;RankSumP=0.325650;SB=-1612.33;SecondBestBaseQ=33;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.195C>T;refseq.codonCoord=65;refseq.end=246912034;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=A;refseq.haplotypeReference=G;refseq.inCodingRegion=true;refseq.mrnaCoord=195;refseq.name=NM_001004734;refseq.name2=OR14I1;refseq.positionType=CDS;refseq.proteinCoordStr=p.S65S;refseq.referenceAA=Ser;refseq.referenceCodon=TCC;refseq.spliceDist=195;refseq.start=246912034;refseq.transcriptStrand=-;refseq.variantAA=Ser;refseq.variantCodon=TCT;set=Intersection GT 1/0
|
|
chr1 246912081 . C T 219.82 PASS AC=1;AF=0.50;AN=2;BestBaseQ=33;DB;DP=280;Dels=0.00;HRun=1;HaplotypeScore=2.41;MQ=98.74;MQ0=0;OQ=4502.63;QD=16.08;RankSumP=0.436374;SB=-1648.27;SecondBestBaseQ=33;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.148G>A;refseq.codonCoord=50;refseq.end=246912081;refseq.frame=0;refseq.functionalClass=missense;refseq.haplotypeAlternate=T;refseq.haplotypeReference=C;refseq.inCodingRegion=true;refseq.mrnaCoord=148;refseq.name=NM_001004734;refseq.name2=OR14I1;refseq.positionType=CDS;refseq.proteinCoordStr=p.D50N;refseq.referenceAA=Asp;refseq.referenceCodon=GAT;refseq.spliceDist=148;refseq.start=246912081;refseq.transcriptStrand=-;refseq.variantAA=Asn;refseq.variantCodon=AAT;set=Intersection GT 0/1
|
|
chr1 246912094 . T C 165.16 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=277;Dels=0.00;HRun=1;HaplotypeScore=5.42;MQ=98.87;MQ0=0;OQ=10199.52;QD=36.82;RankSumP=1.00000;SB=-4512.95;SecondBestBaseQ=0;refseq.changesAA=false;refseq.chr=chr1;refseq.codingCoordStr=c.135A>G;refseq.codonCoord=45;refseq.end=246912094;refseq.frame=2;refseq.functionalClass=silent;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=135;refseq.name=NM_001004734;refseq.name2=OR14I1;refseq.positionType=CDS;refseq.proteinCoordStr=p.A45A;refseq.referenceAA=Ala;refseq.referenceCodon=GCA;refseq.spliceDist=135;refseq.start=246912094;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 246912122 . A G 273.56 PASS AC=2;AF=1.00;AN=2;BestBaseQ=32;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=10.35;MQ=98.78;MQ0=0;OQ=10243.67;QD=36.85;RankSumP=1.00000;SB=-4459.43;SecondBestBaseQ=0;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.107T>C;refseq.codonCoord=36;refseq.end=246912122;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=G;refseq.haplotypeReference=A;refseq.inCodingRegion=true;refseq.mrnaCoord=107;refseq.name=NM_001004734;refseq.name2=OR14I1;refseq.positionType=CDS;refseq.proteinCoordStr=p.V36A;refseq.referenceAA=Val;refseq.referenceCodon=GTG;refseq.spliceDist=107;refseq.start=246912122;refseq.transcriptStrand=-;refseq.variantAA=Ala;refseq.variantCodon=GCG;set=Intersection GT 1/1
|
|
chr1 247077705 . T C 0 BadSOAPSNP AC=1;AF=0.50;AN=2;BestBaseQ=26;HRun=2;RankSumP=0.00000;SecondBestBaseQ=11;refseq.changesAA=true;refseq.chr=chr1;refseq.codingCoordStr=c.185A>G;refseq.codonCoord=62;refseq.end=247077705;refseq.frame=1;refseq.functionalClass=missense;refseq.haplotypeAlternate=C;refseq.haplotypeReference=T;refseq.inCodingRegion=true;refseq.mrnaCoord=737;refseq.name=NM_030645;refseq.name2=SH3BP5L;refseq.positionType=CDS;refseq.proteinCoordStr=p.E62G;refseq.referenceAA=Glu;refseq.referenceCodon=GAG;refseq.spliceDist=2;refseq.spliceInfo=splice-acceptor_2;refseq.start=247077705;refseq.transcriptStrand=-;refseq.variantAA=Gly;refseq.variantCodon=GGG;set=FilteredInAll GT 1/0
|