244 lines
51 KiB
Plaintext
244 lines
51 KiB
Plaintext
##fileformat=VCFv4.0
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##FILTER=<ID=ABFilter,Description="AB 0.75 && DP 40">
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##FILTER=<ID=DPFilter,Description="DP 120 || SB -0.10">
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##FILTER=<ID=FDRtranche0.00to0.10,Description="FDR tranche level at qual 0.06">
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##FILTER=<ID=FDRtranche0.10to1.00,Description="FDR tranche level at qual 0.03">
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##FILTER=<ID=FDRtranche1.00to2.00,Description="FDR tranche level at qual 0.02">
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##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual 0.06">
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##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP)) 0.1)">
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##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
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##FILTER=<ID=LowQual,Description="Low quality">
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##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
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##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
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##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">
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##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FilterLiftedVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/tmp/0.069557317373441.sorted.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=FilterLiftedVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
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##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
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##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
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##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
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##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
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##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
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##LiftoverVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/home/radon01/kiran/scr1/projects/DataProcessingPaper/results/newForStacey/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=LiftoverVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub chain=/humgen/gsa-hpprojects/GATK/data/Liftover_Chain_Files/hg18ToHg19.broad.over.chain newSequenceDictionary=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dict"
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##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:10000000-10100000] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.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 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false 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 sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false"
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##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-23/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-24/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-5/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-9/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-6/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-19/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-25/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-4/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-14/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-22/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-2/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-3/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-7/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-16/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-1/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-17/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-8/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-10/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-18/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-20/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-11/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-15/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-21/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-12/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-13/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[chrX] 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,chrX] 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"
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##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/HiSeq.WGS.cleaned.indels.10.mask] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.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"
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##source=SelectVariants
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##source=VariantOptimizer
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
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20 10000117 rs4816203 C T 77.65 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=867.45;QD=13.77;SB=-268.09 GT:AD:DP:GL:GQ 0/1:36,27:63:-109.01,-18.98,-129.63:99
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20 10000211 rs4813908 C T 273.08 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.66;MQ0=0;OQ=913.43;QD=16.61;SB=-383.86 GT:AD:DP:GL:GQ 0/1:28,27:53:-110.59,-15.96,-95.89:99
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20 10000439 rs4816204 T G 489.03 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=2354.98;QD=29.44;SB=-1083.04 GT:AD:DP:GL:GQ 1/1:0,80:77:-239.15,-23.21,-0.06:99
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20 10000598 rs6057087 T A 659.30 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.58;MQ0=0;OQ=1772.11;QD=36.92;SB=-761.69 GT:AD:DP:GL:GQ 1/1:0,48:48:-180.81,-14.46,-0.01:99
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20 10000694 rs6057088 G A 276.41 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=49.18;MQ0=0;OQ=1128.96;QD=14.11;SB=-510.63 GT:AD:DP:GL:GQ 0/1:46,34:80:-140.27,-24.09,-169.48:99
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20 10000758 rs6057089 T A 243.88 PASS AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.23;MQ0=0;OQ=3541.99;QD=38.92;SB=-1671.36 GT:AD:DP:GL:GQ 1/1:0,91:91:-353.20,-27.40,-0.02:99
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20 10001019 rs6077626 T G 401.46 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.70;MQ0=2;OQ=712.45;QD=10.33;SB=-352.52 GT:AD:DP:GL:GQ 0/1:40,29:65:-94.10,-19.57,-146.27:99
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20 10001298 rs1535165 T A 637.39 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.34;MQ0=0;OQ=2708.88;QD=36.61;SB=-1143.40 GT:AD:DP:GL:GQ 1/1:0,73:73:-274.49,-21.99,-0.02:99
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20 10001474 rs1535166 C T 608.02 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.97;MQ0=0;OQ=2678.14;QD=38.26;SB=-1011.68 GT:AD:DP:GL:GQ 1/1:0,70:69:-271.42,-20.79,-0.02:99
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20 10001617 rs2876191 C A 279.42 PASS AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.17;MQ0=0;OQ=1439.09;QD=14.25;SB=-481.71 GT:AD:DP:GL:GQ 0/1:52,49:101:-177.61,-30.42,-186.45:99
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20 10001628 rs1535167 G A 101.37 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.36;MQ0=0;OQ=3780.26;QD=40.22;SB=-1550.04 GT:AD:DP:GL:GQ 1/1:0,93:93:-377.03,-30.13,-2.37:99
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20 10001661 rs1535168 T C 621.16 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.09;MQ0=0;OQ=2787.58;QD=34.41;SB=-1177.74 GT:AD:DP:GL:GQ 1/1:0,81:79:-282.37,-23.79,-0.02:99
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20 10001670 rs1535169 T G 512.38 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.21;MQ0=0;OQ=2852.67;QD=35.22;SB=-1272.32 GT:AD:DP:GL:GQ 1/1:0,81:80:-288.87,-24.09,-0.02:99
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20 10002058 rs4404352 T G 305.05 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.60;MQ0=0;OQ=2628.53;QD=34.14;SB=-934.22 GT:AD:DP:GL:GQ 1/1:1,76:75:-266.46,-22.59,-0.03:99
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20 10002099 rs4555427 C T 2.61 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=5;HaplotypeScore=0.47;MQ=56.02;MQ0=0;OQ=1117.99;QD=17.47;SB=-498.13 GT:AD:DP:GL:GQ 0/1:27,37:61:-133.46,-18.38,-95.58:99
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20 10002138 rs4569544 C G 481.22 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.30;MQ0=0;OQ=2204.77;QD=40.09;SB=-1043.64 GT:AD:DP:GL:GQ 1/1:0,55:51:-224.08,-15.37,-0.01:99
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20 10002142 rs4417777 G C 579.90 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=2117.84;QD=39.22;SB=-975.74 GT:AD:DP:GL:GQ 1/1:0,54:49:-215.38,-14.76,-0.01:99
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20 10002470 rs2327260 C T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=11;HaplotypeScore=1.75;MQ=47.38;MQ0=0;OQ=2328.93;QD=34.25;SB=-1076.99 GT:AD:DP:GL:GQ 1/1:0,68:61:-236.50,-18.38,-0.02:99
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20 10002478 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=7;HaplotypeScore=9.60;MQ=53.59;MQ0=0;OQ=111.85;QD=2.00;SB=59.21 GT:AD:DP:GL:GQ 0/1:47,9:46:-28.33,-13.86,-140.18:99
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20 10002625 rs2144570 G T 624.83 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.02;MQ0=0;OQ=2238.72;QD=36.11;SB=-983.67 GT:AD:DP:GL:GQ 1/1:0,62:61:-227.47,-18.37,-0.01:99
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20 10003021 rs6057090 C T 599.91 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2357.20;QD=38.64;SB=-1005.68 GT:AD:DP:GL:GQ 1/1:0,61:60:-239.32,-18.08,-0.02:99
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20 10003358 rs926982 A C 283.12 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=1239.40;QD=14.58;SB=-411.81 GT:AD:DP:GL:GQ 0/1:43,42:84:-152.52,-25.30,-151.13:99
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20 10003651 rs926984 T C 632.25 PASS AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=3208.86;QD=35.65;SB=-1068.08 GT:AD:DP:GL:GQ 1/1:0,90:89:-324.50,-26.81,-0.03:99
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20 10003692 rs2064653 A G 614.34 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=2247.29;QD=34.05;SB=-940.96 GT:AD:DP:GL:GQ 1/1:0,66:65:-228.34,-19.58,-0.03:99
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20 10003832 rs6057091 G A 453.48 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.79;MQ0=0;OQ=2581.24;QD=40.33;SB=-971.37 GT:AD:DP:GL:GQ 1/1:0,64:64:-261.72,-19.28,-0.01:99
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20 10004094 rs1988590 A C 5.37 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=53.93;MQ0=0;OQ=1571.64;QD=30.82;SB=-600.05 GT:AD:DP:GL:GQ 1/1:0,51:46:-160.77,-13.86,-0.02:99
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20 10004147 rs1988591 A G 22.33 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.77;MQ=56.98;MQ0=0;OQ=1621.26;QD=30.59;SB=-586.00 GT:AD:DP:GL:GQ 1/1:0,53:50:-165.75,-15.08,-0.04:99
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20 10004193 . G T 112 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.87;MQ0=0;OQ=817.22;QD=15.13;SB=-391.14 GT:AD:DP:GL:GQ 0/1:25,29:51:-100.37,-15.36,-82.85:99
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20 10004351 rs6057092 C G 541.07 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2906.33;QD=42.74;SB=-1364.94 GT:AD:DP:GL:GQ 1/1:0,68:67:-294.24,-20.19,-0.02:99
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20 10004389 rs6057093 T G 609.61 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.09;MQ0=0;OQ=2210.27;QD=35.65;SB=-884.11 GT:AD:DP:GL:GQ 1/1:0,62:62:-224.63,-18.68,-0.02:99
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20 10004610 rs2064654 A C 2.26 PASS AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=10.08;MQ=58.45;MQ0=0;OQ=3199.99;QD=35.56;SB=-1545.20 GT:AD:DP:GL:GQ 1/1:1,89:88:-323.60,-26.50,-0.02:99
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20 10004725 rs10485737 A G 457.98 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.27;MQ0=0;OQ=850.43;QD=13.08;SB=-367.17 GT:AD:DP:GL:GQ 0/1:35,30:65:-107.90,-19.58,-141.57:99
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20 10004874 rs725567 A C 315.35 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.30;MQ0=0;OQ=2956.73;QD=35.20;SB=-1190.16 GT:AD:DP:GL:GQ 1/1:0,84:83:-299.28,-25.00,-0.02:99
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20 10004887 rs725566 A G 256.51 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=59.44;MQ0=0;OQ=1129.32;QD=13.61;SB=-455.56 GT:AD:DP:GL:GQ 0/1:44,39:82:-140.92,-24.70,-171.36:99
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20 10005010 rs725565 C T 706.03 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2824.42;QD=39.23;SB=-1089.38 GT:AD:DP:GL:GQ 1/1:0,72:71:-286.04,-21.39,-0.02:99
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|
20 10005427 rs6057094 C T 587.79 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2155.03;QD=39.91;SB=-1081.37 GT:AD:DP:GL:GQ 1/1:0,54:54:-219.10,-16.26,-0.01:99
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20 10005499 rs6077631 A G 634.39 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2607.55;QD=35.72;SB=-1078.12 GT:AD:DP:GL:GQ 1/1:0,73:73:-264.36,-21.99,-0.02:99
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20 10005587 rs6108375 A G 498.17 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1061.48;QD=14.95;SB=-522.04 GT:AD:DP:GL:GQ 0/1:35,36:70:-130.52,-21.08,-138.09:99
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20 10005723 rs6108376 A G 529.34 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2687.35;QD=31.62;SB=-1283.54 GT:AD:DP:GL:GQ 1/1:0,85:83:-272.38,-25.03,-0.06:99
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20 10006291 rs6118856 G A 172.10 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.54;MQ0=0;OQ=908.18;QD=11.08;SB=-459.38 GT:AD:DP:GL:GQ 0/1:53,29:82:-118.80,-24.70,-191.13:99
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20 10006404 rs926985 A C 490.62 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=2586.62;QD=33.59;SB=-921.26 GT:AD:DP:GL:GQ 1/1:0,77:75:-262.28,-22.59,-0.03:99
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20 10006682 rs6057095 T A 131.36 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.43;MQ0=0;OQ=2662.92;QD=36.48;SB=-986.49 GT:AD:DP:GL:GQ 1/1:0,72:71:-269.90,-21.39,-0.02:99
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20 10007150 rs11904989 G C 276.28 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.70;MQ0=0;OQ=742.20;QD=11.78;SB=-296.80 GT:AD:DP:GL:GQ 0/1:38,25:60:-95.59,-18.09,-157.44:99
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20 10007175 rs2207850 C T 90.28 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.69;MQ0=0;OQ=1294.38;QD=21.22;SB=-604.18 GT:AD:DP:GL:GQ 0/1:22,39:58:-150.19,-17.47,-75.88:99
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20 10007352 rs1884399 C T 614.04 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2708.19;QD=39.25;SB=-1162.02 GT:AD:DP:GL:GQ 1/1:0,69:68:-274.43,-20.49,-0.02:99
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20 10007531 rs1884400 A G 493.80 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2611.60;QD=36.78;SB=-843.33 GT:AD:DP:GL:GQ 1/1:0,71:71:-264.76,-21.38,-0.02:99
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20 10007980 rs2876192 A C 668.55 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.73;MQ0=0;OQ=3022.49;QD=34.35;SB=-1434.18 GT:AD:DP:GL:GQ 1/1:0,88:87:-305.86,-26.20,-0.03:99
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20 10008221 rs2876193 T C 510.25 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.18;MQ0=0;OQ=2840.34;QD=36.41;SB=-1397.57 GT:AD:DP:GL:GQ 1/1:0,78:78:-287.64,-23.49,-0.02:99
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20 10008458 rs6087107 T G 157.09 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=52.94;MQ0=0;OQ=2398.43;QD=33.78;SB=-1015.12 GT:AD:DP:GL:GQ 1/1:0,71:68:-243.45,-20.48,-0.02:99
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|
20 10008742 rs12479925 G T 146.75 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=35.86;MQ0=1;OQ=685.54;QD=12.24;SB=-274.47 GT:AD:DP:GL:GQ 0/1:26,30:43:-84.79,-12.96,-61.80:99
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20 10008951 . A C 553.29 Indel AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=16.13;MQ=51.15;MQ0=0;QD=11.77;SB=-184.92 GT:AD:DP:GL:GQ 0/1:23,24:43:-71.58,-12.97,-70.23:99
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20 10009227 rs12481420 A G 523.55 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=1201.44;QD=19.70;SB=-625.90 GT:AD:DP:GL:GQ 0/1:22,39:61:-141.80,-18.37,-90.52:99
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20 10009246 rs4574174 A G 634.47 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.62;MQ0=0;OQ=2711.91;QD=35.68;SB=-1179.49 GT:AD:DP:GL:GQ 1/1:0,76:75:-274.80,-22.59,-0.02:99
|
|
20 10009400 rs6057096 T A 7.09 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2788.17;QD=38.19;SB=-1314.62 GT:AD:DP:GL:GQ 1/1:0,73:73:-282.42,-21.98,-0.01:99
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|
20 10009512 rs6039657 C G 565.55 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.53;MQ0=0;OQ=3160.94;QD=41.59;SB=-1228.86 GT:AD:DP:GL:GQ 1/1:0,76:74:-319.70,-22.30,-0.02:99
|
|
20 10009719 rs6057097 A G 58.27 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.33;MQ0=0;OQ=1551.35;QD=25.02;SB=-585.82 GT:AD:DP:GL:GQ 1/1:0,62:50:-158.78,-15.09,-0.06:99
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|
20 10009795 rs6118861 A G 501.58 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1594.00;QD=35.42;SB=-578.40 GT:AD:DP:GL:GQ 1/1:0,45:45:-163.00,-13.55,-0.01:99
|
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20 10009844 rs6057098 G A 11.23 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.92;MQ=52.80;MQ0=0;OQ=1658.97;QD=30.16;SB=-750.39 GT:AD:DP:GL:GQ 0/1:8,47:51:-184.54,-15.37,-17.54:21.74
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20 10009871 rs6133780 A G 1067.52 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=16.85;MQ=51.54;MQ0=0;QD=18.09;SB=-387.29 GT:AD:DP:GL:GQ 0/1:19,40:49:-124.80,-14.77,-52.03:99
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20 10009875 rs6133781 A G 1106.95 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=19.06;MQ=51.21;MQ0=0;QD=19.42;SB=-410.34 GT:AD:DP:GL:GQ 0/1:16,41:44:-127.23,-13.25,-35.68:99
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20 10009879 . A G 1218.05 SnpCluster AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;HRun=1;HaplotypeScore=20.77;MQ=51.40;MQ0=0;QD=23.88;SB=-543.65 GT:AD:DP:GL:GQ 1/1:5,46:42:-136.91,-12.65,-11.59:10.59
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20 10009883 rs6133782 A G 1399.75 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=11.88;MQ=52.16;MQ0=0;QD=27.45;SB=-484.45 GT:AD:DP:GL:GQ 1/1:2,49:43:-147.73,-12.95,-4.17:87.80
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20 10010393 rs513998 T G 602.85 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=1247.20;QD=16.20;SB=-518.70 GT:AD:DP:GL:GQ 0/1:35,42:76:-150.89,-22.89,-128.62:99
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20 10010766 rs517531 T G 421.91 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2100.93;QD=31.36;SB=-978.12 GT:AD:DP:GL:GQ 1/1:0,66:67:-217.39,-23.46,-3.72:99
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20 10010832 rs582827 T C 733.72 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=2668.46;QD=35.58;SB=-1048.08 GT:AD:DP:GL:GQ 1/1:0,75:75:-270.45,-22.59,-0.02:99
|
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20 10011075 rs6039659 C T 234.23 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=60.00;MQ0=0;OQ=1322.11;QD=15.74;SB=-644.72 GT:AD:DP:GL:GQ 0/1:45,39:82:-160.20,-24.71,-141.60:99
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20 10011309 rs641722 T C 546.02 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=2396.22;QD=30.72;SB=-1026.41 GT:AD:DP:GL:GQ 1/1:0,78:76:-243.28,-22.92,-0.07:99
|
|
20 10011666 rs546821 C T 285.21 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2849.79;QD=40.14;SB=-1187.35 GT:AD:DP:GL:GQ 1/1:0,71:71:-288.58,-21.39,-0.02:99
|
|
20 10011939 rs548863 C T 181.17 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=56.14;MQ0=0;OQ=2488.04;QD=39.49;SB=-885.19 GT:AD:DP:GL:GQ 1/1:0,63:62:-252.40,-18.68,-0.01:99
|
|
20 10012362 rs574425 G T 17.09 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=51.41;MQ0=0;OQ=676.99;QD=28.21;SB=-89.90 GT:AD:DP:GL:GQ 1/1:0,24:20:-71.29,-6.02,-0.01:60.18
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|
20 10012384 rs7270107 T C 128.88 PASS AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=51.62;MQ0=0;OQ=216.13;QD=12.01;SB=-75.35 GT:AD:DP:GL:GQ 0/1:9,9:16:-29.72,-4.82,-34.04:99
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|
20 10012387 rs6057102 T C 18.19 PASS AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=50.47;MQ0=0;OQ=295.02;QD=18.44;SB=-77.36 GT:AD:DP:GL:GQ 1/1:0,16:11:-33.10,-3.32,-0.02:33.06
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20 10012479 rs575394 A G 3.30 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=49.52;MQ0=0;OQ=474.16;QD=23.71;SB=-247.57 GT:AD:DP:GL:GQ 1/1:0,20:16:-51.02,-4.83,-0.02:48.10
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20 10012498 rs657453 C G 2.83 PASS AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=40.06;MQ0=0;OQ=331.25;QD=22.08;SB=-84.82 GT:AD:DP:GL:GQ 1/1:0,15:9:-36.71,-2.71,-0.01:27.09
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20 10012518 rs657490 T C 1.50 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.64;MQ=34.32;MQ0=0;OQ=366.95;QD=22.93;SB=-197.06 GT:AD:DP:GL:GQ 1/1:0,16:12:-40.29,-3.62,-0.01:36.09
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|
20 10012521 rs6141099 C T 33.24 PASS AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=35.97;MQ0=0;OQ=104.02;QD=5.78;SB=-64.27 GT:AD:DP:GL:GQ 0/1:11,7:14:-17.91,-4.23,-28.63:99
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20 10012636 rs57357029 G C 442.35 Indel AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=3;HaplotypeScore=2.47;MQ=46.22;MQ0=1;QD=17.69;SB=-127.71 GT:AD:DP:GL:GQ 0/1:10,15:20:-53.56,-6.04,-26.16:99
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20 10012714 rs577258 G C 4.14 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=54.18;MQ0=0;OQ=1374.69;QD=38.19;SB=-268.50 GT:AD:DP:GL:GQ 1/1:0,36:34:-141.07,-10.25,-0.02:99
|
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20 10012751 rs577383 T C 3.88 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=51.17;MQ0=0;OQ=807.71;QD=26.06;SB=-389.47 GT:AD:DP:GL:GQ 1/1:0,31:26:-84.38,-7.84,-0.03:78.14
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20 10013119 rs670350 C T 14.43 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=53.67;MQ0=0;OQ=1037.37;QD=17.58;SB=-503.12 GT:AD:DP:GL:GQ 0/1:27,32:57:-124.19,-17.17,-93.21:99
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20 10013574 rs6057108 G A 190.67 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.43;MQ0=0;OQ=995.08;QD=15.08;SB=-284.14 GT:AD:DP:GL:GQ 0/1:36,30:66:-122.67,-19.88,-129.26:99
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20 10015679 . C T 4.66 PASS AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=130.84;QD=11.89;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,6:10:-19.38,-3.01,-17.14:99
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20 10015761 rs12106014 T C 188.68 PASS AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=282.39;QD=12.84;SB=-35.94 GT:AD:DP:GL:GQ 0/1:9,13:21:-37.85,-6.33,-34.21:99
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20 10018158 rs512313 G C 152.46 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.79;MQ0=0;OQ=1786.48;QD=20.53;SB=-749.98 GT:AD:DP:GL:GQ 0/1:39,47:85:-207.56,-25.63,-151.93:99
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|
20 10018555 rs570855 G A 501.58 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1507.16;QD=18.61;SB=-748.62 GT:AD:DP:GL:GQ 0/1:36,45:80:-178.09,-24.09,-134.36:99
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20 10019093 rs575534 A G 198.39 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=59.34;MQ0=0;OQ=1097.34;QD=15.68;SB=-511.28 GT:AD:DP:GL:GQ 0/1:34,36:69:-133.80,-20.78,-132.32:99
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20 10020229 rs596203 G A 334.84 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.76;MQ0=0;OQ=1448.48;QD=18.34;SB=-632.66 GT:AD:DP:GL:GQ 0/1:37,42:79:-171.94,-23.81,-120.12:99
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20 10023689 rs4813909 G A 153.20 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.04;MQ0=0;OQ=1887.80;QD=22.74;SB=-948.03 GT:AD:DP:GL:GQ 0/1:30,53:83:-217.06,-25.00,-110.51:99
|
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20 10024107 . C T 114.08 PASS AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.56;MQ0=0;OQ=1618.74;QD=19.04;SB=-735.06 GT:AD:DP:GL:GQ 0/1:38,47:84:-190.47,-25.31,-121.49:99
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20 10024288 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=5;HaplotypeScore=7.93;MQ=51.94;MQ0=0;OQ=68.97;QD=0.97;SB=86.23 GT:AD:DP:GL:GQ 0/1:53,18:57:-27.36,-17.18,-167.04:99
|
|
20 10024294 . C T 19.74 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=5;HaplotypeScore=23.45;MQ=49.01;MQ0=1;QD=0.27;SB=83.26 GT:AD:DP:GL:GQ 0/1:55,18:51:-20.62,-15.37,-156.17:52.53
|
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20 10026357 rs685723 T C 589.98 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1010.93;QD=16.57;SB=-474.08 GT:AD:DP:GL:GQ 0/1:26,35:60:-122.45,-18.07,-104.85:99
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20 10026794 rs687514 C T 152.12 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=60.00;MQ0=0;OQ=1015.27;QD=19.52;SB=-447.00 GT:AD:DP:GL:GQ 0/1:19,32:49:-119.58,-14.77,-61.54:99
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20 10027868 rs514832 A G 410.15 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.47;MQ0=0;OQ=1149.09;QD=13.21;SB=-556.55 GT:AD:DP:GL:GQ 0/1:43,44:87:-144.42,-26.22,-173.75:99
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20 10027872 rs594811 A G 112.59 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.44;MQ0=0;OQ=1351.31;QD=16.28;SB=-565.56 GT:AD:DP:GL:GQ 0/1:39,44:83:-163.41,-25.00,-161.96:99
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20 10030188 rs652633 T A 473.63 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.71;MQ0=0;OQ=1186.53;QD=15.02;SB=-453.42 GT:AD:DP:GL:GQ 0/1:41,38:79:-145.73,-23.79,-157.38:99
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20 10031342 rs668091 G A 109.76 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=60.00;MQ0=0;OQ=1739.31;QD=19.11;SB=-748.28 GT:AD:DP:GL:GQ 0/1:41,50:90:-204.32,-27.11,-145.56:99
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20 10031798 rs669985 G A 353.33 PASS AC=2;AF=1.00;AN=2;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=4247.21;QD=40.84;SB=-1915.55 GT:AD:DP:GL:GQ 1/1:0,104:104:-423.72,-31.33,-0.03:99
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20 10031827 rs558493 C T 27.08 PASS AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.83;MQ0=0;OQ=1957.26;QD=18.12;SB=-1004.58 GT:AD:DP:GL:GQ 0/1:52,56:108:-231.54,-32.53,-189.42:99
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20 10032094 rs681750 G A 562.76 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.21;QD=14.16;SB=-575.44 GT:AD:DP:GL:GQ 0/1:47,36:82:-145.51,-24.71,-151.92:99
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20 10032413 rs683145 T G 535.40 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=698.84;QD=11.09;SB=-317.98 GT:AD:DP:GL:GQ 0/1:33,30:63:-92.15,-18.98,-124.49:99
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20 10032882 rs479039 A T 24.07 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.01;HRun=0;HaplotypeScore=7.14;MQ=58.99;MQ0=0;OQ=1029.41;QD=13.73;SB=-439.55 GT:AD:DP:GL:GQ 0/1:40,34:73:-128.21,-21.99,-155.80:99
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20 10034306 rs604452 T C 170.18 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=59.46;MQ0=0;OQ=667.43;QD=8.67;SB=-359.16 GT:AD:DP:GL:GQ 0/1:47,29:73:-92.02,-22.00,-181.63:99
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20 10037037 rs2327261 C T 271.93 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.97;MQ0=0;OQ=1384.69;QD=17.53;SB=-468.51 GT:AD:DP:GL:GQ 0/1:38,41:74:-164.05,-22.30,-111.89:99
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20 10037709 rs518364 A T 403.99 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.68;MQ0=0;OQ=896.68;QD=12.63;SB=-381.55 GT:AD:DP:GL:GQ 0/1:39,32:70:-114.04,-21.09,-148.36:99
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20 10039371 rs678696 T G 586.43 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1105.57;QD=15.79;SB=-406.66 GT:AD:DP:GL:GQ 0/1:32,38:70:-134.92,-21.08,-120.34:99
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20 10040821 rs6057119 T A 1156.74 Indel AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.03;HRun=6;HaplotypeScore=36.61;MQ=50.69;MQ0=0;QD=15.22;SB=-511.29 GT:AD:DP:GL:GQ 0/1:35,39:75:-140.95,-21.99,-129.69:99
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20 10041304 rs559129 C T 83.54 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.92;MQ=59.66;MQ0=0;OQ=2692.91;QD=39.60;SB=-1319.36 GT:AD:DP:GL:GQ 1/1:0,68:67:-272.89,-20.18,-0.01:99
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20 10042319 rs631317 C T 711.90 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.00;MQ0=0;OQ=2553.65;QD=39.29;SB=-1137.05 GT:AD:DP:GL:GQ 1/1:0,65:64:-258.97,-19.28,-0.02:99
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20 10042761 rs633445 A G 631.29 PASS AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3233.06;QD=35.53;SB=-1142.81 GT:AD:DP:GL:GQ 1/1:0,91:88:-327.18,-26.51,-0.02:99
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20 10042829 rs633841 A G 305.65 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.76;MQ0=0;OQ=2746.23;QD=35.21;SB=-1237.83 GT:AD:DP:GL:GQ 1/1:0,78:77:-278.24,-23.20,-0.03:99
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20 10043002 . A T 147.57 PASS AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1103.68;QD=13.14;SB=-535.28 GT:AD:DP:GL:GQ 0/1:48,36:84:-138.95,-25.30,-175.62:99
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20 10044849 rs663380 A G 242.12 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1840.58;QD=31.20;SB=-654.96 GT:AD:DP:GL:GQ 1/1:0,59:57:-187.68,-17.18,-0.04:99
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20 10045078 rs674630 G T 86.82 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=1.98;MQ=58.99;MQ0=0;OQ=2874.89;QD=36.39;SB=-1368.13 GT:AD:DP:GL:GQ 1/1:0,79:78:-291.09,-23.49,-0.02:99
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20 10045642 rs572752 G C 658.72 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3374.18;QD=42.18;SB=-1455.16 GT:AD:DP:GL:GQ 1/1:0,80:79:-336.42,-23.81,-0.03:99
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20 10046537 rs583827 A G 86.68 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.76;MQ=54.17;MQ0=0;OQ=719.43;QD=12.40;SB=-246.31 GT:AD:DP:GL:GQ 0/1:29,29:55:-91.80,-16.57,-108.67:99
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20 10050828 rs660454 T C 314.94 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.73;MQ0=0;OQ=1072.85;QD=12.62;SB=-513.86 GT:AD:DP:GL:GQ 0/1:48,37:84:-135.87,-25.30,-193.36:99
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20 10051448 rs565455 T C 358.13 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=59.41;MQ0=0;OQ=1005.69;QD=14.16;SB=-400.33 GT:AD:DP:GL:GQ 0/1:36,35:69:-124.64,-20.79,-133.98:99
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20 10052688 . C A 247.91 PASS AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=928.77;QD=12.06;SB=-460.78 GT:AD:DP:GL:GQ 0/1:45,32:77:-119.35,-23.19,-165.26:99
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20 10058022 rs531797 T C 82.90 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=6.22;MQ=58.46;MQ0=0;OQ=872.91;QD=12.47;SB=-339.92 GT:AD:DP:GL:GQ 0/1:38,32:67:-110.76,-20.18,-144.54:99
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20 10067090 rs507568 C A 124.11 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=55.67;MQ0=0;OQ=1789.54;QD=33.76;SB=-802.84 GT:AD:DP:GL:GQ 1/1:0,53:50:-182.55,-15.06,-0.02:99
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20 10067264 rs530271 G A 217.29 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.68;MQ0=0;OQ=2865.42;QD=39.80;SB=-1324.28 GT:AD:DP:GL:GQ 1/1:0,72:72:-290.15,-21.69,-0.02:99
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20 10067722 rs604416 A C 278.06 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1822.34;QD=35.05;SB=-862.09 GT:AD:DP:GL:GQ 1/1:0,52:52:-185.83,-15.66,-0.02:99
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20 10068981 rs490505 G A 49.73 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=1.07;MQ=59.55;MQ0=0;OQ=2469.03;QD=39.82;SB=-1135.04 GT:AD:DP:GL:GQ 1/1:0,62:61:-250.50,-18.37,-0.01:99
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20 10070602 rs6039684 T C 187.72 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.71;MQ0=0;OQ=2364.76;QD=32.84;SB=-1139.10 GT:AD:DP:GL:GQ 1/1:0,72:69:-240.09,-20.79,-0.03:99
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20 10070936 . T A 3050.87 Indel AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=2.65;MQ=58.76;MQ0=0;QD=37.67;SB=-1399.42 GT:AD:DP:GL:GQ 1/1:0,81:80:-308.69,-24.09,-0.02:99
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20 10071135 rs552048 C T 173.64 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=59.09;MQ0=0;OQ=3089.23;QD=40.65;SB=-1301.70 GT:AD:DP:GL:GQ 1/1:0,76:76:-312.53,-22.89,-0.02:99
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20 10071187 rs6032780 G A 696.17 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=3367.02;QD=40.57;SB=-1247.04 GT:AD:DP:GL:GQ 1/1:0,83:82:-335.70,-24.70,-0.02:99
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20 10071890 rs6039685 T C 547.16 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1748.72;QD=30.68;SB=-861.55 GT:AD:DP:GL:GQ 1/1:0,57:56:-178.51,-16.89,-0.05:99
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20 10072505 rs6032786 A G 465.42 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1789.94;QD=28.41;SB=-916.44 GT:AD:DP:GL:GQ 1/1:0,63:57:-182.63,-17.19,-0.05:99
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20 10074187 . A G 68.82 PASS AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=2702.25;QD=35.09;SB=-1331.57 GT:AD:DP:GL:GQ 1/1:0,77:77:-273.84,-23.20,-0.03:99
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20 10074240 rs614270 T C 574.99 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2989.29;QD=34.76;SB=-1439.46 GT:AD:DP:GL:GQ 1/1:0,85:83:-302.53,-25.00,-0.02:99
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20 10074716 rs2327236 G A 207.80 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=2351.97;QD=35.10;SB=-934.35 GT:AD:DP:GL:GQ 1/1:0,67:62:-238.81,-18.69,-0.03:99
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20 10074806 rs2327237 G A 618.46 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2806.22;QD=38.98;SB=-1369.05 GT:AD:DP:GL:GQ 1/1:0,72:71:-284.22,-21.39,-0.02:99
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20 10075043 rs617891 T C 295.12 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2170.63;QD=35.58;SB=-943.96 GT:AD:DP:GL:GQ 1/1:0,61:61:-220.67,-18.37,-0.02:99
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20 10075168 rs6032787 C T 590.04 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=3524.41;QD=40.05;SB=-1505.51 GT:AD:DP:GL:GQ 1/1:0,88:86:-351.44,-25.90,-0.02:99
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20 10076250 rs644043 A G 293.27 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.71;MQ0=0;OQ=915.84;QD=11.59;SB=-456.82 GT:AD:DP:GL:GQ 0/1:41,38:77:-118.08,-23.21,-160.58:99
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20 10076339 rs644160 A G 242.68 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=59.35;MQ0=0;OQ=1102.11;QD=15.52;SB=-557.03 GT:AD:DP:GL:GQ 0/1:33,38:71:-134.88,-21.39,-128.30:99
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20 10076399 rs506458 G A 360.39 PASS AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1756.48;QD=18.69;SB=-796.27 GT:AD:DP:GL:GQ 0/1:44,50:94:-207.24,-28.31,-163.43:99
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20 10077752 . T C 195.33 PASS AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1175.95;QD=14.89;SB=-463.61 GT:AD:DP:GL:GQ 0/1:34,45:79:-144.69,-23.81,-137.94:99
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20 10081750 rs473369 C A 178.19 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1188.67;QD=14.50;SB=-583.96 GT:AD:DP:GL:GQ 0/1:43,39:82:-146.85,-24.69,-154.74:99
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20 10081800 rs474169 C T 600.41 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1088.62;QD=16.25;SB=-544.01 GT:AD:DP:GL:GQ 0/1:34,33:67:-132.33,-20.18,-122.19:99
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20 10082892 rs644145 C T 208.97 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=1601.32;QD=38.13;SB=-762.50 GT:AD:DP:GL:GQ 1/1:0,42:41:-163.73,-12.35,-0.01:99
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20 10085211 rs685573 A T 447.96 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.51;MQ0=0;OQ=1024.78;QD=13.48;SB=-509.23 GT:AD:DP:GL:GQ 0/1:42,34:75:-128.35,-22.59,-157.06:99
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20 10086110 rs592026 G A 451.70 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.14;MQ0=0;OQ=1254.60;QD=15.49;SB=-639.16 GT:AD:DP:GL:GQ 0/1:43,38:81:-153.14,-24.40,-157.02:99
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20 10086283 rs592889 G T 230.49 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=882.77;QD=10.51;SB=-462.82 GT:AD:DP:GL:GQ 0/1:52,32:84:-116.86,-25.30,-180.39:99
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20 10086619 rs513535 T A 1.86 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=5;HaplotypeScore=1.00;MQ=59.68;MQ0=0;OQ=746.98;QD=10.52;SB=-282.61 GT:AD:DP:GL:GQ 0/1:45,26:69:-98.76,-20.78,-164.07:99
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20 10086853 rs127733 G A 343.14 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.75;MQ0=0;OQ=945.98;QD=12.78;SB=-472.45 GT:AD:DP:GL:GQ 0/1:42,32:71:-119.28,-21.40,-133.60:99
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20 10086954 rs595987 G A 578.38 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1076.10;QD=16.06;SB=-401.89 GT:AD:DP:GL:GQ 0/1:33,34:66:-130.79,-19.89,-110.09:99
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20 10087230 rs607331 A G 497.44 PASS AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=1624.42;QD=17.10;SB=-744.63 GT:AD:DP:GL:GQ 0/1:41,54:95:-194.34,-28.62,-167.75:99
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20 10087394 rs608188 T G 410.26 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=1428.70;QD=17.21;SB=-695.70 GT:AD:DP:GL:GQ 0/1:35,48:83:-171.15,-25.00,-131.95:99
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20 10087754 rs544718 T G 209.96 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=60.45;MQ0=0;OQ=1195.66;QD=15.33;SB=-504.83 GT:AD:DP:GL:GQ 0/1:36,42:77:-146.04,-23.19,-131.14:99
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20 10087804 rs609932 C T 337.95 PASS AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=60.49;MQ0=0;OQ=1534.51;QD=15.35;SB=-666.41 GT:AD:DP:GL:GQ 0/1:50,50:93:-184.76,-28.03,-153.45:99
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20 10088063 rs621673 C T 498.25 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.79;MQ0=0;OQ=1322.79;QD=15.20;SB=-531.00 GT:AD:DP:GL:GQ 0/1:46,41:84:-160.88,-25.32,-143.12:99
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20 10088699 rs498420 C T 139.69 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.78;MQ=54.80;MQ0=0;OQ=803.84;QD=12.18;SB=-217.49 GT:AD:DP:GL:GQ 0/1:38,28:61:-102.06,-18.39,-112.29:99
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20 10088730 rs624398 G A 180.64 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=52.02;MQ0=0;OQ=706.21;QD=12.39;SB=-215.65 GT:AD:DP:GL:GQ 0/1:29,26:51:-89.27,-15.37,-99.20:99
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20 10088736 rs624401 A C 166.23 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=51.41;MQ0=0;OQ=755.82;QD=12.81;SB=-289.77 GT:AD:DP:GL:GQ 0/1:29,29:53:-94.83,-15.97,-94.03:99
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20 10088747 rs624419 A G 458.31 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.80;MQ0=0;OQ=732.27;QD=13.31;SB=-319.26 GT:AD:DP:GL:GQ 0/1:25,30:54:-92.79,-16.28,-99.03:99
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20 10088799 rs624824 G A 1.58 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=54.24;MQ0=0;OQ=1015.57;QD=18.46;SB=-384.14 GT:AD:DP:GL:GQ 0/1:24,31:54:-121.12,-16.28,-76.29:99
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20 10088895 rs500269 C T 289 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.39;MQ0=0;OQ=522.39;QD=12.74;SB=-237.72 GT:AD:DP:GL:GQ 0/1:24,17:39:-67.28,-11.76,-70.34:99
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20 10088985 rs2876185 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=28.26;MQ=49.95;MQ0=0;OQ=805.93;QD=10.20;SB=-330.82 GT:AD:DP:GL:GQ 0/1:43,35:73:-105.88,-22.00,-156.93:99
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20 10089441 rs637625 A G 358.05 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=992.46;QD=13.23;SB=-330.00 GT:AD:DP:GL:GQ 0/1:37,38:73:-124.53,-22.00,-148.03:99
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20 10089525 rs526819 C T 411.15 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.84;MQ0=0;OQ=1526.59;QD=17.96;SB=-694.71 GT:AD:DP:GL:GQ 0/1:41,44:82:-180.66,-24.71,-123.55:99
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20 10090764 rs670562 A G 90.49 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=5.75;MQ=59.44;MQ0=0;OQ=705.16;QD=10.52;SB=-326.14 GT:AD:DP:GL:GQ 0/1:37,30:65:-93.39,-19.59,-148.34:99
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20 10090970 rs671426 T C 386.71 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.73;MQ0=0;OQ=1093.51;QD=15.62;SB=-550.11 GT:AD:DP:GL:GQ 0/1:33,37:67:-132.81,-20.18,-125.76:99
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20 10091214 rs563455 C T 321.47 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.75;MQ0=0;OQ=1276.23;QD=17.02;SB=-480.51 GT:AD:DP:GL:GQ 0/1:36,39:73:-152.90,-21.99,-128.97:99
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20 10092415 rs590717 A G 409.50 PASS AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1457.26;QD=14.57;SB=-743.58 GT:AD:DP:GL:GQ 0/1:51,49:100:-179.13,-30.12,-213.26:99
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20 10092927 . G T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=8.09;MQ=59.09;MQ0=0;OQ=102.52;QD=1.35;SB=110.34 GT:AD:DP:GL:GQ 0/1:58,17:57:-30.71,-17.17,-163.94:99
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20 10093923 rs2423481 T A 501.25 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=952.53;QD=14.65;SB=-490.92 GT:AD:DP:GL:GQ 0/1:33,32:64:-117.81,-19.28,-126.25:99
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20 10094251 rs543895 T A 466.65 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.29;QD=18.66;SB=-397.80 GT:AD:DP:GL:GQ 0/1:26,37:59:-138.58,-17.77,-89.00:99
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20 10094582 rs56124148 A G 315.13 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.72;MQ0=0;OQ=736.10;QD=11.15;SB=-314.87 GT:AD:DP:GL:GQ 0/1:38,28:65:-96.47,-19.58,-152.04:99
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20 10094774 rs570383 C T 361.89 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=1017.49;QD=13.75;SB=-374.10 GT:AD:DP:GL:GQ 0/1:39,35:69:-125.82,-20.79,-130.93:99
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20 10095741 rs489548 A G 80.02 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.33;MQ=57.01;MQ0=0;OQ=943.34;QD=13.29;SB=-405.22 GT:AD:DP:GL:GQ 0/1:36,34:68:-118.10,-20.48,-142.28:99
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20 10096293 rs515940 C T 94.01 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.19;MQ0=0;OQ=1320.58;QD=17.61;SB=-665.71 GT:AD:DP:GL:GQ 0/1:37,38:74:-157.63,-22.29,-130.19:99
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20 10096596 rs518701 C T 23.57 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.03;MQ0=0;OQ=1543.46;QD=17.95;SB=-788.95 GT:AD:DP:GL:GQ 0/1:40,46:85:-183.24,-25.61,-136.84:99
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20 10096768 rs520453 A C 398.10 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=1343.01;QD=15.44;SB=-695.73 GT:AD:DP:GL:GQ 0/1:42,45:87:-163.78,-26.20,-154.89:99
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20 10096899 rs652086 G T 1162.66 Indel AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.76;MQ0=0;QD=14.72;SB=-335.13 GT:AD:DP:GL:GQ 0/1:39,40:78:-143.04,-23.49,-142.37:99
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20 10096933 rs652126 G C 307.07 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.78;MQ0=0;OQ=1416.78;QD=16.87;SB=-379.18 GT:AD:DP:GL:GQ 0/1:45,39:83:-169.97,-25.01,-193.85:99
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20 10096958 rs652494 G A 342.18 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.79;MQ0=0;OQ=1501.31;QD=16.68;SB=-462.96 GT:AD:DP:GL:GQ 0/1:45,45:87:-179.62,-26.20,-157.70:99
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20 10097075 rs6077657 T G 299.81 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.69;MQ0=0;OQ=1264.80;QD=13.75;SB=-586.94 GT:AD:DP:GL:GQ 0/1:44,48:90:-156.87,-27.11,-157.64:99
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20 10097437 rs11698147 T C 519.38 Indel AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.01;HRun=1;HaplotypeScore=8.62;MQ=55.90;MQ0=0;QD=7.75;SB=-133.24 GT:AD:DP:GL:GQ 0/1:45,21:62:-73.60,-18.38,-162.59:99
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20 10097465 . C T 31.87 LowQual AC=1;AF=0.50;AN=2;DP=49;Dels=0.02;HRun=3;HaplotypeScore=12.58;MQ=57.18;MQ0=0;QD=0.61;SB=-33.97 GT:AD:DP:GL:GQ 0/1:46,5:49:-20.93,-14.46,-150.67:64.70
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20 10097626 rs665397 C A 205.18 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.09;MQ0=0;OQ=521.22;QD=11.33;SB=-241.94 GT:AD:DP:GL:GQ 0/1:27,19:45:-68.96,-13.55,-93.68:99
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20 10097789 rs550824 T C 40.64 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.80;MQ=57.53;MQ0=1;OQ=609.05;QD=10.15;SB=-279.29 GT:AD:DP:GL:GQ 0/1:35,25:57:-81.36,-17.17,-136.53:99
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20 10097928 rs666732 G A 147.74 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=57.09;MQ0=0;OQ=647.39;QD=16.60;SB=-318.83 GT:AD:DP:GL:GQ 0/1:17,22:38:-79.48,-11.45,-61.53:99
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20 10098110 rs6108402 G C 43.99 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=639.58;QD=17.77;SB=-86.92 GT:AD:DP:GL:GQ 0/1:19,17:35:-77.79,-10.55,-73.75:99
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20 10098135 rs6108403 C A 5.45 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=59.93;MQ0=0;OQ=389.51;QD=10.25;SB=-43.38 GT:AD:DP:GL:GQ 0/1:24,14:38:-53.68,-11.44,-83.52:99
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20 10098237 . A T 39.55 PASS AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.32;MQ0=0;OQ=159.94;QD=12.30;SB=-10.00 GT:AD:DP:GL:GQ 0/1:7,6:13:-23.19,-3.92,-25.88:99
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20 10098265 . T C 37.58 PASS AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.10;MQ0=0;OQ=64.00;QD=12.80;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,3:5:-11.19,-1.51,-7.23:57.28
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20 10098344 . A G 24.50 LowQual AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=6.13;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,2:4:-6.94,-1.20,-8.11:57.33
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20 10098786 . C T 16.33 LowQual AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=54.65;MQ0=0;QD=1.81;SB=-10.00 GT:AD:DP:GL:GQ 0/1:7,2:9:-7.62,-2.71,-21.38:49.06
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20 10098945 rs56176249 T C 5.87 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=51.33;MQ0=0;OQ=363.84;QD=17.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,13:20:-45.69,-6.02,-27.59:99
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20 10098987 . C T 11 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.90;MQ0=0;OQ=342.06;QD=14.87;SB=-3.99 GT:AD:DP:GL:GQ 0/1:10,13:21:-43.82,-6.33,-33.84:99
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20 10099029 rs13044987 T C 3.29 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.87;MQ0=0;OQ=125.69;QD=4.66;SB=2.03 GT:AD:DP:GL:GQ 0/1:18,9:25:-23.39,-7.53,-70.35:99
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20 10099034 rs13043768 C A 139.33 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.19;MQ0=0;OQ=176.63;QD=6.31;SB=-31.94 GT:AD:DP:GL:GQ 0/1:18,10:26:-28.78,-7.84,-59.75:99
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20 10099044 rs13043626 A C 29.61 LowQual AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=51.36;MQ0=0;QD=1.29;SB=-14.48 GT:AD:DP:GL:GQ 0/1:16,7:15:-10.76,-4.52,-43.68:62.44
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20 10099055 rs13045001 T C 65.04 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=48.67;MQ0=0;OQ=222.63;QD=7.95;SB=-64.86 GT:AD:DP:GL:GQ 0/1:16,12:23:-32.47,-6.93,-57.23:99
|
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20 10099079 rs13043786 C T 16.28 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=5.99;MQ=49.66;MQ0=0;OQ=370.70;QD=10.59;SB=-162.25 GT:AD:DP:GL:GQ 0/1:21,14:31:-49.70,-9.35,-56.03:99
|
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20 10099140 rs585009 G T 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=5;HaplotypeScore=2.65;MQ=55.73;MQ0=0;OQ=847.58;QD=14.13;SB=-233.91 GT:AD:DP:GL:GQ 0/1:30,30:58:-105.51,-17.47,-102.15:99
|
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20 10099190 rs508242 G T 210.44 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=57.42;MQ0=0;OQ=860.99;QD=13.25;SB=-270.28 GT:AD:DP:GL:GQ 0/1:33,32:62:-108.05,-18.67,-118.91:99
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20 10099220 rs585404 A G 5.36 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=6.00;MQ=56.96;MQ0=0;OQ=481.07;QD=10.46;SB=-187.61 GT:AD:DP:GL:GQ 0/1:25,21:43:-64.35,-12.96,-100.07:99
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20 10099250 rs585439 G A 100.58 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=56.23;MQ0=0;OQ=672.67;QD=17.70;SB=-330.34 GT:AD:DP:GL:GQ 0/1:17,21:36:-81.41,-10.86,-48.14:99
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20 10099535 rs586791 G A 209.98 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.28;MQ0=0;OQ=1326.40;QD=20.73;SB=-582.88 GT:AD:DP:GL:GQ 0/1:25,38:62:-157.48,-21.55,-76.17:99
|
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20 10099565 rs532882 C T 44.22 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.99;MQ=59.66;MQ0=0;OQ=1282.88;QD=19.15;SB=-617.46 GT:AD:DP:GL:GQ 0/1:30,37:67:-151.75,-20.18,-103.68:99
|
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20 10099755 rs534687 C T 66.98 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=59.00;MQ0=0;OQ=1091.00;QD=16.78;SB=-547.75 GT:AD:DP:GL:GQ 0/1:32,33:64:-131.66,-19.27,-116.96:99
|
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20 10099832 rs534882 A G 477.85 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=927.85;QD=12.89;SB=-445.10 GT:AD:DP:GL:GQ 0/1:39,33:71:-117.45,-21.39,-156.97:99
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