From c2ec2891d1e185b4cc0f30e2dfd18991e2837b69 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 24 Jun 2011 16:56:04 +0000 Subject: [PATCH] Other people besides Mark also wanted VariantContext moved to the GATK, so I listened. I am moving VariantContext and all codecs that rely on it (VCF, SoapSNP, HapMap, and CGvar) to the GATK - including relevant unit tests and data files. Additionally, Matt has modified build.xml to generate the necessary jar files so that people can use our VCF codec with Tribble. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6077 348d0f76-0448-11de-a6fe-93d51630548a --- build.xml | 17 +- .../sting/gatk/GenomeAnalysisEngine.java | 2 +- .../datasources/sample/SampleDataSource.java | 4 +- .../gatk/io/storage/VCFWriterStorage.java | 4 +- .../VCFWriterArgumentTypeDescriptor.java | 2 +- .../sting/gatk/io/stubs/VCFWriterStub.java | 8 +- .../gatk/refdata/RefMetaDataTracker.java | 2 +- .../gatk/refdata/VariantContextAdaptors.java | 16 +- .../features/beagle/BeagleFeature.java | 2 +- .../refdata/utils/helpers/DbSNPHelper.java | 2 +- .../AnalyzeAnnotationsWalker.java | 2 +- .../AnnotationDataManager.java | 4 +- .../gatk/walkers/annotator/AlleleBalance.java | 8 +- .../annotator/AlleleBalanceBySample.java | 7 +- .../walkers/annotator/AnnotationByDepth.java | 2 +- .../gatk/walkers/annotator/BaseCounts.java | 6 +- .../annotator/BaseQualityRankSumTest.java | 6 +- .../walkers/annotator/ChromosomeCounts.java | 10 +- .../walkers/annotator/DepthOfCoverage.java | 8 +- .../annotator/DepthPerAlleleBySample.java | 12 +- .../gatk/walkers/annotator/FisherStrand.java | 8 +- .../gatk/walkers/annotator/GCContent.java | 6 +- .../sting/gatk/walkers/annotator/GLstats.java | 8 +- .../walkers/annotator/HaplotypeScore.java | 10 +- .../gatk/walkers/annotator/HardyWeinberg.java | 8 +- .../walkers/annotator/HomopolymerRun.java | 6 +- .../gatk/walkers/annotator/IndelType.java | 6 +- .../sting/gatk/walkers/annotator/LowMQ.java | 6 +- .../annotator/MappingQualityRankSumTest.java | 6 +- .../walkers/annotator/MappingQualityZero.java | 8 +- .../annotator/MappingQualityZeroBySample.java | 10 +- .../annotator/MappingQualityZeroFraction.java | 7 +- .../gatk/walkers/annotator/NBaseCount.java | 6 +- .../gatk/walkers/annotator/QualByDepth.java | 8 +- .../walkers/annotator/RMSMappingQuality.java | 8 +- .../gatk/walkers/annotator/RankSumTest.java | 6 +- .../ReadDepthAndAllelicFractionBySample.java | 13 +- .../walkers/annotator/ReadPosRankSumTest.java | 6 +- .../gatk/walkers/annotator/SBByDepth.java | 10 +- .../gatk/walkers/annotator/SampleList.java | 10 +- .../walkers/annotator/SpanningDeletions.java | 6 +- .../walkers/annotator/VariantAnnotator.java | 8 +- .../annotator/VariantAnnotatorEngine.java | 6 +- .../genomicannotator/GenomicAnnotation.java | 8 +- .../genomicannotator/GenomicAnnotator.java | 10 +- .../interfaces/GenotypeAnnotation.java | 6 +- .../interfaces/InfoFieldAnnotation.java | 4 +- .../beagle/BeagleOutputToVCFWalker.java | 12 +- .../beagle/ProduceBeagleInputWalker.java | 15 +- .../VariantsToBeagleUnphasedWalker.java | 16 +- .../fasta/FastaAlternateReferenceWalker.java | 2 +- .../gatk/walkers/filters/ClusteredSnps.java | 2 +- .../walkers/filters/FiltrationContext.java | 2 +- .../filters/VariantFiltrationWalker.java | 10 +- .../AlleleFrequencyCalculationModel.java | 6 +- .../BiallelicGenotypeLikelihoods.java | 2 +- .../genotyper/ExactAFCalculationModel.java | 6 +- .../GenotypeLikelihoodsCalculationModel.java | 2 +- .../genotyper/GridSearchAFEstimation.java | 6 +- ...elGenotypeLikelihoodsCalculationModel.java | 4 +- .../MultiallelicGenotypeLikelihoods.java | 2 +- ...NPGenotypeLikelihoodsCalculationModel.java | 4 +- .../walkers/genotyper/UGCalcLikelihoods.java | 4 +- .../walkers/genotyper/UGCallVariants.java | 8 +- .../walkers/genotyper/UnifiedGenotyper.java | 4 +- .../genotyper/UnifiedGenotyperEngine.java | 10 +- .../walkers/genotyper/VariantCallContext.java | 2 +- .../indels/HaplotypeIndelErrorModel.java | 4 +- .../gatk/walkers/indels/IndelRealigner.java | 2 +- .../indels/PairHMMIndelErrorModel.java | 2 +- .../indels/RealignerTargetCreator.java | 2 +- .../indels/SomaticIndelDetectorWalker.java | 11 +- .../gatk/walkers/phasing/AllelePair.java | 4 +- .../walkers/phasing/AnnotateMNPsWalker.java | 12 +- .../gatk/walkers/phasing/MergeMNPsWalker.java | 13 +- ...eSegregatingAlternateAllelesVCFWriter.java | 12 +- ...ergeSegregatingAlternateAllelesWalker.java | 10 +- .../phasing/ReadBackedPhasingWalker.java | 16 +- .../walkers/phasing/RefSeqDataParser.java | 2 +- .../gatk/walkers/phasing/SNPallelePair.java | 4 +- .../sting/gatk/walkers/phasing/WriteVCF.java | 6 +- .../gatk/walkers/qc/ProfileRodSystem.java | 6 +- .../recalibration/CountCovariatesWalker.java | 5 +- .../walkers/sequenom/CreateSequenomMask.java | 2 +- .../walkers/sequenom/PickSequenomProbes.java | 4 +- .../varianteval/VariantEvalWalker.java | 10 +- .../evaluators/CompEvalGenotypes.java | 2 +- .../varianteval/evaluators/CompOverlap.java | 4 +- .../varianteval/evaluators/CountVariants.java | 4 +- .../evaluators/GenotypeConcordance.java | 6 +- .../evaluators/GenotypePhasingEvaluator.java | 4 +- .../evaluators/IndelLengthHistogram.java | 2 +- .../evaluators/IndelMetricsByAC.java | 2 +- .../evaluators/IndelStatistics.java | 4 +- .../MendelianViolationEvaluator.java | 6 +- .../evaluators/PrintMissingComp.java | 2 +- .../evaluators/SamplePreviousGenotypes.java | 2 +- .../evaluators/SimpleMetricsByAC.java | 4 +- .../evaluators/ThetaVariantEvaluator.java | 6 +- .../evaluators/TiTvVariantEvaluator.java | 4 +- .../evaluators/ValidationReport.java | 11 +- .../evaluators/VariantEvaluator.java | 2 +- .../evaluators/VariantQualityScore.java | 6 +- .../stratifications/AlleleCount.java | 4 +- .../stratifications/AlleleFrequency.java | 2 +- .../varianteval/stratifications/CompRod.java | 2 +- .../varianteval/stratifications/Contig.java | 2 +- .../varianteval/stratifications/CpG.java | 2 +- .../stratifications/Degeneracy.java | 2 +- .../varianteval/stratifications/EvalRod.java | 2 +- .../varianteval/stratifications/Filter.java | 2 +- .../stratifications/FunctionalClass.java | 2 +- .../stratifications/JexlExpression.java | 4 +- .../varianteval/stratifications/Novelty.java | 2 +- .../varianteval/stratifications/Sample.java | 2 +- .../stratifications/VariantStratifier.java | 4 +- .../util/NewEvaluationContext.java | 2 +- .../util/SortableJexlVCMatchExp.java | 2 +- .../varianteval/util/VariantEvalUtils.java | 4 +- .../ApplyRecalibration.java | 6 +- .../VQSRCalibrationCurve.java | 2 +- .../VariantDataManager.java | 2 +- .../VariantRecalibrator.java | 4 +- .../walkers/variantutils/CombineVariants.java | 9 +- .../variantutils/FilterLiftedVariants.java | 8 +- .../variantutils/LeftAlignVariants.java | 16 +- .../variantutils/LiftoverVariants.java | 8 +- .../variantutils/RandomlySplitVariants.java | 12 +- .../walkers/variantutils/SelectVariants.java | 17 +- .../variantutils/ValidateVariants.java | 4 +- .../VariantValidationAssessor.java | 11 +- .../walkers/variantutils/VariantsToTable.java | 4 +- .../walkers/variantutils/VariantsToVCF.java | 14 +- .../walkers/AffectedConsistencyWalker.java | 12 +- .../walkers/AlleleBalanceHistogramWalker.java | 2 +- .../walkers/AnnotateTruthROD.java | 14 +- .../AnnotationByAlleleFrequencyWalker.java | 2 +- .../walkers/AssessLikelihoodsAtTruth.java | 6 +- .../walkers/AssessMissingBroadCalls.java | 6 +- .../walkers/AssessSimulatedPerformance.java | 4 +- .../walkers/AssessSnpsNearIndels.java | 12 +- .../walkers/BeagleOutputByDepthWalker.java | 9 +- .../walkers/CNV/CNVstatsWalker.java | 6 +- .../walkers/CalibrateGenotypeLikelihoods.java | 6 +- .../walkers/CreateTiTvTrack.java | 4 +- .../walkers/GenotypeConcordanceTable.java | 4 +- .../walkers/IndelAnnotator.java | 8 +- .../walkers/IndelConsistencyReadCounter.java | 2 +- .../IndelCountCovariatesWalker.java | 4 +- .../walkers/IndelDBRateWalker.java | 14 +- .../oneoffprojects/walkers/MarkIntervals.java | 2 +- .../walkers/MendelianViolationClassifier.java | 18 +- .../walkers/SimulateReadsForVariants.java | 20 +- .../walkers/TestVariantContextWalker.java | 6 +- .../walkers/VCF4WriterTestWalker.java | 6 +- .../walkers/annotator/HammingDistance.java | 8 +- .../annotator/InsertSizeDistribution.java | 6 +- .../ProportionOfNonrefBasesSupportingSNP.java | 6 +- .../walkers/annotator/QualByDepthV2.java | 8 +- .../phasing/CalcFullHaplotypesWalker.java | 8 +- ...ingToTrioPhasingNoRecombinationWalker.java | 16 +- .../CountHetPhasingInIntervalWalker.java | 4 +- .../walkers/phasing/PhaseByTransmission.java | 15 +- .../walkers/phasing/PhasingEval.java | 6 +- .../validation/PickSequenomProbes2.java | 2 +- .../varianteval/PrivatePermutations.java | 4 +- .../vcftools/BootstrapCallsMerger.java | 13 +- .../walkers/vcftools/FixRefBases.java | 13 +- .../gatk/features/maf/MafFeature.java | 8 +- .../walkers/GenotypeAndValidateWalker.java | 14 +- .../gatk/walkers/LocusMismatchWalker.java | 4 +- .../walkers/SnpCallRateByCoverageWalker.java | 4 +- .../gatk/walkers/ValidationGenotyper.java | 2 +- .../gatk/walkers/diagnostics/SNPDensity.java | 2 +- .../phasing/PrintReferenceVariantsWalker.java | 10 +- .../ReadBasedPhasingValidationWalker.java | 6 +- .../ReplicationValidationWalker.java | 6 +- .../validation/DeclareValidityWalker.java | 28 +- .../validation/RodSystemValidationWalker.java | 2 +- .../gatk/walkers/variantutils/CGVarToVCF.java | 8 +- .../sting/playground/tools/SortROD.java | 7 +- .../gatk/ArgumentDefinitionField.java | 2 +- .../queue/extensions/gatk/ArgumentField.java | 2 +- .../sting/utils/IndelUtils.java | 2 +- .../sting/utils/MendelianViolation.java | 4 +- .../sting/utils/SampleUtils.java | 6 +- .../codecs/completegenomics/CGVarCodec.java | 160 + .../utils/codecs/hapmap/HapMapCodec.java | 97 + .../utils/codecs/hapmap/HapMapFeature.java | 194 + .../utils/codecs/soapsnp/SoapSNPCodec.java | 209 + .../utils/codecs/vcf/AbstractVCFCodec.java | 617 + .../codecs/vcf/ManualSortingVCFWriter.java | 52 + .../utils/codecs/vcf/SortingVCFWriter.java | 61 + .../codecs/vcf/SortingVCFWriterBase.java | 168 + .../utils/codecs/vcf/StandardVCFWriter.java | 529 + .../sting/utils/codecs/vcf/VCF3Codec.java | 182 + .../sting/utils/codecs/vcf/VCFCodec.java | 188 + .../codecs/vcf/VCFCompoundHeaderLine.java | 164 + .../sting/utils/codecs/vcf/VCFConstants.java | 109 + .../utils/codecs/vcf/VCFFilterHeaderLine.java | 70 + .../utils/codecs/vcf/VCFFormatHeaderLine.java | 28 + .../sting/utils/codecs/vcf/VCFHeader.java | 191 + .../sting/utils/codecs/vcf/VCFHeaderLine.java | 134 + .../codecs/vcf/VCFHeaderLineTranslator.java | 124 + .../utils/codecs/vcf/VCFHeaderLineType.java | 8 + .../utils/codecs/vcf/VCFHeaderVersion.java | 91 + .../utils/codecs/vcf/VCFInfoHeaderLine.java | 25 + .../utils/codecs/vcf/VCFNamedHeaderLine.java | 30 + .../sting/utils/codecs/vcf/VCFParser.java | 23 + .../utils/{ => codecs}/vcf/VCFUtils.java | 6 +- .../sting/utils/codecs/vcf/VCFWriter.java | 18 + .../sting/utils/exceptions/UserException.java | 4 +- .../sting/utils/genotype/Haplotype.java | 4 +- .../sting/utils/variantcontext/Allele.java | 456 + .../sting/utils/variantcontext/Genotype.java | 279 + .../variantcontext/GenotypeLikelihoods.java | 151 + .../InferredGeneticContext.java | 230 + .../utils/variantcontext/MutableGenotype.java | 80 + .../variantcontext/MutableVariantContext.java | 210 + .../utils/variantcontext/VariantContext.java | 1521 +++ .../variantcontext/VariantContextUtils.java | 7 +- .../variantcontext/VariantJEXLContext.java | 6 +- .../org/broadinstitute/sting/WalkerTest.java | 2 +- .../sample/SampleDataSourceUnitTest.java | 6 +- .../builders/RMDTrackBuilderUnitTest.java | 5 +- .../variantutils/CombineVariantsUnitTest.java | 9 +- .../utils/codecs/hapmap/HapMapUnitTest.java | 162 + .../codecs/vcf/IndexFactoryUnitTest.java | 81 + .../utils/genotype/vcf/VCFHeaderUnitTest.java | 4 +- .../utils/genotype/vcf/VCFWriterUnitTest.java | 8 +- .../utils/variantcontext/AlleleUnitTest.java | 217 + .../GenotypeLikelihoodsUnitTest.java | 78 + .../VariantContextUnitTest.java | 458 + .../VariantJEXLContextUnitTest.java | 4 +- .../sting/queue/util/VCF_BAM_utilities.scala | 4 +- testdata/HiSeq.10000.vcf | 10000 ++++++++++++++++ ...enotypes_chr1_ASW_phase3.3_first500.hapmap | 500 + 237 files changed, 18496 insertions(+), 663 deletions(-) create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java create mode 100644 java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java rename java/src/org/broadinstitute/sting/utils/{ => codecs}/vcf/VCFUtils.java (97%) create mode 100755 java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java create mode 100755 java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java create mode 100755 java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java create mode 100755 java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java create mode 100755 java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java create mode 100755 java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java create mode 100755 java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java create mode 100755 java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java rename java/src/org/broadinstitute/sting/{gatk/contexts => utils}/variantcontext/VariantContextUtils.java (99%) rename java/src/org/broadinstitute/sting/{gatk/contexts => utils}/variantcontext/VariantJEXLContext.java (98%) create mode 100644 java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java create mode 100755 java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java create mode 100755 java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java create mode 100755 java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java create mode 100755 java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java rename java/test/org/broadinstitute/sting/{gatk/contexts => utils}/variantcontext/VariantJEXLContextUnitTest.java (96%) create mode 100644 testdata/HiSeq.10000.vcf create mode 100644 testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap diff --git a/build.xml b/build.xml index 1a9c72bd8..34dcc05fb 100644 --- a/build.xml +++ b/build.xml @@ -403,7 +403,11 @@ - + + + + + @@ -415,6 +419,15 @@ + + + + + + + + + @@ -497,7 +510,7 @@ - + diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index af355ab03..f8527c33b 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -30,7 +30,7 @@ import net.sf.samtools.*; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.ArgumentException; import org.broadinstitute.sting.commandline.ArgumentSource; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.CommandLineUtils; import org.broadinstitute.sting.commandline.ParsingEngine; import org.broadinstitute.sting.commandline.Tags; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java index e85ef80be..0a5981a1b 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java @@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.datasources.sample; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.StingException; diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java index fdac507f7..74176ec35 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java +++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java @@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.io.storage; import org.apache.log4j.Logger; import org.broad.tribble.source.BasicFeatureSource; -import org.broad.tribble.vcf.*; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java index 888f8b36e..7521e754d 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io.stubs; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java index a31a16d50..1a79d2785 100755 --- a/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java +++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java @@ -30,10 +30,10 @@ import java.io.PrintStream; import java.io.OutputStream; import java.util.Collection; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.OutputTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index 239877ccf..43bf6f8e0 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.refdata; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index d2595a39e..7d7a9d32c 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -3,21 +3,19 @@ package org.broadinstitute.sting.gatk.refdata; import org.broad.tribble.Feature; import org.broad.tribble.dbsnp.DbSNPFeature; import org.broad.tribble.gelitext.GeliTextFeature; -import org.broad.tribble.hapmap.HapMapFeature; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.MutableGenotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.MutableGenotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import javax.xml.stream.events.Attribute; import java.util.*; -import java.util.jar.Attributes; /** * A terrible but temporary approach to converting objects to VariantContexts. If you want to add a converter, diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java index dd946287d..c7bf86569 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java @@ -31,7 +31,7 @@ import java.util.ArrayList; import java.util.Map; import net.sf.samtools.util.StringUtil; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Allele; public class BeagleFeature implements Feature { diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java b/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java index d2a5d17ed..75e7c1a32 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata.utils.helpers; import net.sf.samtools.util.SequenceUtil; import org.broad.tribble.annotation.Strand; import org.broad.tribble.dbsnp.DbSNPFeature; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.Utils; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java index 8ffc7d957..54fd0a20c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.analyzeannotations; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java index 726b659e3..2c06b30d6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.analyzeannotations; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index e9f324363..b02dcd8e2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java index b853ed5f3..0be737897 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -1,12 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.vcf.VCFFormatHeaderLine; -import org.broad.tribble.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.gatk.contexts.*; -import org.broad.tribble.util.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; -import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.*; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java index 9b1ee4b4f..51b5381dc 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import java.util.Map; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java index 9d441918f..244627154 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -31,9 +31,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 588a86087..ff916bedd 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 9c5ba40aa..143722d7c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index bc6f71cbf..e56825dbe 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index 2e033a865..754d28dfd 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -1,11 +1,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFCompoundHeaderLine; -import org.broad.tribble.vcf.VCFFormatHeaderLine; -import org.broad.tribble.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 66d927e1c..2115526a6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -32,10 +32,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.vcf.VCFInfoHeaderLine; -import org.broad.tribble.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import cern.jet.math.Arithmetic; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 8dc7b294c..5eaa30bf3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java index 081d43498..3a5db2884 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index cb7bcbeed..bd8c51a41 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -24,11 +24,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java index 05f7fa2e6..ecebfbbd2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java @@ -1,10 +1,10 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broad.tribble.util.popgen.HardyWeinbergCalculation; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 16287491c..099780fa7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java index 2a0ae0290..ee8b01d7d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java index b3e3a742c..33069f1f5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 0f874ed7f..11f86b972 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 665f5c0a4..25a7b286d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java index de64741dd..00cc30309 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java @@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.vcf.VCFConstants; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import java.util.Map; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java index 46beed71d..dc4934ade 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java @@ -1,9 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java index 760f68b9e..ba3e2cc8b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index 2ef9947e2..720984835 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index 4ac4880d3..6e80c7555 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index e5e08472a..1a967293f 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java index 3f0105376..f287549bb 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java @@ -27,19 +27,18 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.vcf.VCFFormatHeaderLine; -import org.broad.tribble.vcf.VCFCompoundHeaderLine; -import org.broad.tribble.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import java.util.Map; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 9d5f2ec1a..2a17cd436 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java index 5e38fd5b2..fc769ac54 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java @@ -1,10 +1,10 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index 3c1c87170..82f16be42 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -25,16 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import java.util.Arrays; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index fb34b56ae..0b6cbcc2e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 0d9ccf738..cd5b6694b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType; @@ -42,7 +42,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 3eb60a54f..54c8be73a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -37,9 +37,9 @@ import java.util.Map; import java.util.Set; import java.util.Map.Entry; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java index caa32fef3..e02c62baf 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java @@ -28,10 +28,10 @@ package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.util.*; import java.util.Map.Entry; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java index f10101328..69a35a584 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java @@ -31,10 +31,10 @@ import java.io.IOException; import java.util.*; import java.util.Map.Entry; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -47,7 +47,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; /** * Annotates variant calls with information from user-specified tabular files. diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java index ee0038ee8..29b256479 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java index c82da908f..5b33395b5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index 3f5dd1396..aa23abc67 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.beagle; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -41,8 +41,8 @@ import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.vcf.VCFUtils; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.*; import java.util.*; import static java.lang.Math.log10; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 98ec7f3d7..93ee0b085 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.beagle; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Input; @@ -36,7 +36,7 @@ import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RMD; @@ -46,13 +46,10 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.io.PrintStream; -import java.text.DecimalFormat; -import java.text.MessageFormat; import java.util.*; /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java index 9a9aff457..18aa3e257 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java @@ -25,17 +25,17 @@ package org.broadinstitute.sting.gatk.walkers.beagle; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; @@ -43,7 +43,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.PrintStream; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 6c8eef9a6..828d39717 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java index a5a74ffa4..b31526987 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java index 4ef007e05..c3849e240 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 61536e758..884d0ac24 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; @@ -39,7 +39,7 @@ import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java index 07e8fc2ce..47be7e6fe 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java @@ -26,11 +26,11 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broad.tribble.util.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import java.io.PrintStream; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java index 2220dd6bc..fbd9c1dbf 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Allele; public class BiallelicGenotypeLikelihoods { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java index 7f4185229..89504b371 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index 5b8a2c761..3902a0b7f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java index ca162c749..c4e315f68 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.collections.Pair; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 1ee658f5c..1f430548b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import net.sf.samtools.SAMRecord; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel; @@ -44,7 +44,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java index a983036f3..2cf149fd0 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.exceptions.StingException; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 9800ea5c7..9f4d4182f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.utils.*; @@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java index 4bfb93e80..cf1c57a05 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.DownsampleType; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java index 4a6ab0eaf..1533e8777 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java @@ -24,14 +24,14 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 0a2b6f503..7a765c602 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.filters.BadMateFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -37,7 +37,7 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; import java.io.PrintStream; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 69c616584..4c9080884 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.GenotypeLikelihoods; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.pileup.*; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import com.google.java.contract.*; import java.io.PrintStream; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java index 8153d9b11..5896e784e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; /** * Created by IntelliJ IDEA. diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java index 5de01392c..7617aa9de 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.walkers.indels; import net.sf.samtools.AlignmentBlock; import net.sf.samtools.SAMRecord; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index c0b170d25..28b88f9f2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -30,7 +30,7 @@ import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.StringUtil; import net.sf.samtools.util.SequenceUtil; import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 56e2ab6b3..89bdd53c8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -29,7 +29,7 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; /*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate; import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index b536a0cb5..048dbd8cb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.filters.BadCigarFilter; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java index 0d9edcde1..c2953d1d7 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java @@ -25,11 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.*; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; @@ -58,6 +57,8 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Hidden; +import net.sf.samtools.*; + import java.io.*; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java index f7e763d8c..869edf784 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java @@ -23,8 +23,8 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java index fac4b5dc1..7989f52db 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java @@ -24,14 +24,14 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature; @@ -43,11 +43,11 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; -import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods; /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java index 5122e10c3..709bc44ce 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java @@ -24,11 +24,10 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -36,11 +35,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; -import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods; /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java index 8acece2ed..abced442e 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java @@ -27,12 +27,12 @@ package org.broadinstitute.sting.gatk.walkers.phasing; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequenceFile; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFWriter; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java index 0c1bc7180..ec6f5c648 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java @@ -24,24 +24,24 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; -import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods; /** * Walks along all variant ROD loci, and merges consecutive sites if some sample has segregating alt alleles in the ROD. diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index 7e2476f8d..e59b29502 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -23,14 +23,14 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -40,15 +40,15 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broad.tribble.vcf.SortingVCFWriter; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import java.io.*; import java.util.*; -import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods; /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java index af3960b1a..55da1c152 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java index 55a877c57..db1f888a1 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java @@ -23,8 +23,8 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java index ddeadee37..f82e48abd 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java @@ -24,9 +24,9 @@ package org.broadinstitute.sting.gatk.walkers.phasing; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; public class WriteVCF { public static void writeVCF(VariantContext vc, VCFWriter writer, Logger logger) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java index 142c383e3..67879a442 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ProfileRodSystem.java @@ -24,10 +24,10 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broad.tribble.util.ParsingUtils; -import org.broad.tribble.vcf.VCFConstants; -import org.broad.tribble.vcf.VCFCodec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broad.tribble.readers.AsciiLineReader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java index 5bf7738ca..ee504b6e7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java @@ -27,9 +27,8 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broad.tribble.bed.BEDCodec; import org.broad.tribble.dbsnp.DbSNPCodec; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCF3Codec; -import org.broad.tribble.vcf.VCFCodec; +import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.commandline.Gather; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java index 19c272bbf..c1c17bda5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.sequenom; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java index 466184da6..f350e7531 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java @@ -28,8 +28,8 @@ package org.broadinstitute.sting.gatk.walkers.sequenom; import net.sf.samtools.util.CloseableIterator; import org.broad.tribble.bed.BEDCodec; import org.broad.tribble.dbsnp.DbSNPCodec; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 2a21bfe41..15d808ebe 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -2,13 +2,13 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; @@ -29,11 +29,9 @@ import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import net.sf.picard.reference.FastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.gatk.walkers.fasta.FastaSequence; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import net.sf.picard.reference.ReferenceSequence; import java.io.FileNotFoundException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java index 00c997a67..787dbe9af 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.GenomeLoc; class NewCompEvalGenotypes { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index 37172617a..76db330ed 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index db4a11960..c4277adc9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java index ad8bfbbe4..4b56cf130 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java index be0b96d3c..3d14dd0e5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 6c8ac3dc6..5daf33a9f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java index c6133acdf..eca6c5193 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java index 410e5da9c..48b06d532 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 6f2f89fcf..85e0b5889 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java index 3085e358c..7d54d0df8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java index c1ba8cccb..5f3e6b0fa 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java index 6be2786d2..deed05508 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index 0d4f4df77..89c67cfe9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index 99b4daec8..8811dc001 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index 8bf317b25..405f35635 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -1,18 +1,15 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; -import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java index 2180bb732..6017ecca3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java index bc8f9a8f8..4af14810b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index 19f207df1..ff59c9e29 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java index 0daad99dc..48b4ffa91 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java index e4d95c514..9942ba8d6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java index 0ce74f518..1a9d31085 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java index 65608f6b7..15b1d41c1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java index 7c41ea58e..65af6090c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java index 6400d612c..7bd15a974 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java index 10e628520..8d8782ab7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index ed9d4d266..fd724d6d1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java index 9fa0eca61..a7ccd3182 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java index ab0fa7f4a..39d2e6b4d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java index 940352246..f909de4f3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java index 96603edaf..218cb23ca 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java index 44248e169..3208c26bb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java index dce08da45..0281653af 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; import org.apache.commons.jexl2.*; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable { /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index 32996a0bc..b8e45e462 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 48deabc14..9877781d1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.NestedHashMap; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.io.FileNotFoundException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java index 4ebe9807b..2914385a4 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantQualityScore; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index 1d6d9a1e4..2fd1326fe 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import cern.jet.random.Normal; import org.apache.log4j.Logger; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 4eb3f7639..e651b62e0 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 4cee70def..597a54dc1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -25,13 +25,12 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import com.sun.tools.internal.xjc.reader.gbind.ElementSets; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Requires; @@ -42,7 +41,7 @@ import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index 298a7e38c..ba6f5e513 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -24,16 +24,16 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFWriter; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.commandline.Output; -import org.broad.tribble.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index bb39e2765..d9dd85f0c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -28,13 +28,13 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.SortingVCFWriter; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -42,7 +42,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 56c5d8db3..7eda54387 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -24,18 +24,18 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.File; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java index 1c9155045..0c41a9728 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -24,11 +24,11 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.StandardVCFWriter; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; @@ -40,7 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 0f1d5221c..963aa0ce5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -24,26 +24,25 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.MendelianViolation; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 19932ca2b..ec7395f85 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.util.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broad.tribble.dbsnp.DbSNPFeature; import org.broad.tribble.TribbleException; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index c3de49a83..482679593 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -25,18 +25,17 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 4aa854946..71dd5df3f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -24,12 +24,12 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 56fb4c75c..7eb49da34 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -28,14 +28,14 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import net.sf.samtools.util.CloseableIterator; import org.broad.tribble.dbsnp.DbSNPCodec; import org.broad.tribble.dbsnp.DbSNPFeature; -import org.broad.tribble.hapmap.HapMapFeature; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.commandline.Argument; @@ -45,7 +45,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java index 044c12cf7..4100b500d 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AffectedConsistencyWalker.java @@ -1,14 +1,14 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; @@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.io.FileNotFoundException; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java index a8c374d63..509d65441 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java index 901a85fd1..3fac966ea 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.java @@ -25,21 +25,21 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.MutableVariantContext; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.MutableVariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.ArrayList; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java index 926842b7f..40bec19f6 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java index 8fa4a3ed1..57d143127 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.GenotypeLikelihoods; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java index 3b134849d..4478bd501 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java index 844a16c3b..47bd82d2f 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSimulatedPerformance.java @@ -24,12 +24,12 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java index f3baf24f7..b7aa1defe 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessSnpsNearIndels.java @@ -25,27 +25,17 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.iterators.DownsampleIterator; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.Reference; -import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.vcf.VCFUtils; import java.io.PrintStream; -import java.io.Writer; -import java.security.PrivilegedActionException; import java.util.*; /** diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java index 5242125db..64e2633da 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java @@ -25,11 +25,10 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; -import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java index 0cdb07e4b..b29917f48 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/CNVstatsWalker.java @@ -24,9 +24,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers.CNV; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java index ff0a9696c..d454dec7e 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CalibrateGenotypeLikelihoods.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers; import net.sf.samtools.SAMReadGroupRecord; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.GenotypeLikelihoods; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java index 60078cbfb..63b17bda3 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java @@ -1,11 +1,11 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.wiggle.WiggleHeader; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java index cfe7fb9a3..d4b73cb59 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/GenotypeConcordanceTable.java @@ -24,8 +24,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java index 13499214e..399a3e6df 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java @@ -1,8 +1,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.FeatureSource; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -12,12 +11,11 @@ import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder; -import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java index fb22c7577..1c7a2d8e4 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.filters.BadMateFilter; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java index a6166be53..a6fcce290 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates; import org.broad.tribble.bed.BEDCodec; import org.broad.tribble.dbsnp.DbSNPCodec; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFCodec; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.commandline.Gather; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java index b90a152dc..189db5206 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java @@ -1,15 +1,15 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.StandardVCFWriter; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; import org.broadinstitute.sting.gatk.walkers.Reference; @@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.PrintStream; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java index 109fa6b40..54bdfdf3f 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java @@ -38,7 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.collections.Pair; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; import java.util.Collection; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java index 4ae95f265..65e09f0db 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java @@ -1,18 +1,18 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.StandardVCFWriter; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; @@ -21,7 +21,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import java.io.PrintStream; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java index bb058a6f1..914a9d745 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimulateReadsForVariants.java @@ -24,37 +24,35 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.vcf.VCFWriter; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils; -import java.io.PrintStream; import java.io.PrintWriter; import java.util.*; import net.sf.samtools.*; + import cern.jet.math.Arithmetic; import cern.jet.random.Poisson; import cern.jet.random.engine.MersenneTwister; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java index 0bd969874..a23b064f1 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java @@ -25,9 +25,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.StandardVCFWriter; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.*; @@ -38,7 +37,6 @@ import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.walkers.Window; import java.util.EnumSet; -import java.io.File; import java.io.PrintStream; /** diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java index 2c476442a..1519aa02e 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers; import org.broad.tribble.readers.AsciiLineReader; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.io.FileInputStream; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java index 95a980a8a..62490b66f 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/HammingDistance.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java index d1618697e..95d4b6bf5 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/InsertSizeDistribution.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java index 51ebfb2db..1af1fa491 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers.annotator; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java index 72079733e..416b7e8c2 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/QualByDepthV2.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers.annotator; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java index 4f8d84965..c0dce0d46 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CalcFullHaplotypesWalker.java @@ -24,9 +24,9 @@ package org.broadinstitute.sting.oneoffprojects.walkers.phasing; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.PrintStream; import java.util.*; -import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods; /** * Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites. diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java index f10062185..a385f870d 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java @@ -24,12 +24,12 @@ package org.broadinstitute.sting.oneoffprojects.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -46,12 +46,12 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.PrintStream; import java.util.*; -import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods; /** * Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites. diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java index 00f34c03e..5c0af0e41 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java @@ -24,8 +24,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.phasing; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java index 27d583b4a..ed5406b8b 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhaseByTransmission.java @@ -1,23 +1,20 @@ package org.broadinstitute.sting.oneoffprojects.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java index 58d007cc2..4a1b51d4c 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/PhasingEval.java @@ -24,8 +24,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.phasing; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -36,7 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.PrintStream; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java index 627b5d59b..045d442a9 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/validation/PickSequenomProbes2.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.oneoffprojects.walkers.validation; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java index 0b0b87981..b6af87637 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/PrivatePermutations.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java index 4d9de6eda..b8937d5dd 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BootstrapCallsMerger.java @@ -1,22 +1,19 @@ package org.broadinstitute.sting.oneoffprojects.walkers.vcftools; import com.google.common.collect.ArrayListMultimap; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import javax.management.NotificationBroadcaster; import java.util.*; /** diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java index f0c4bbf10..933fc629d 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/FixRefBases.java @@ -1,24 +1,23 @@ package org.broadinstitute.sting.oneoffprojects.walkers.vcftools; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.exceptions.*; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java b/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java index e66f1c2b0..49d9713dd 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.playground.gatk.features.maf; import org.broad.tribble.Feature; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; import org.broadinstitute.sting.utils.exceptions.StingException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java index 9e768d166..437fed843 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java @@ -25,16 +25,16 @@ package org.broadinstitute.sting.playground.gatk.walkers; -import org.broad.tribble.util.variantcontext.MutableVariantContext; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.variantcontext.MutableVariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; @@ -44,7 +44,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java index 1a2025d0d..96d3d175a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.playground.gatk.walkers; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java index 12a5f372c..272e9ad26 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java @@ -26,8 +26,8 @@ package org.broadinstitute.sting.playground.gatk.walkers; import net.sf.samtools.SAMRecord; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java index 08a74a431..94df8c69b 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.playground.gatk.walkers; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java index 06632766c..37745c003 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.diagnostics; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java index 725bf140a..eeaa3ff41 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/PrintReferenceVariantsWalker.java @@ -23,10 +23,10 @@ */ package org.broadinstitute.sting.playground.gatk.walkers.phasing; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -34,7 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.phasing.WriteVCF; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java index 698dceee8..b3136b54f 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing; import org.broad.tribble.readers.AsciiLineReader; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java index 489cfca8f..661f746f6 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.replication_validation; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java index 1ebdac489..95266d2e9 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/DeclareValidityWalker.java @@ -24,38 +24,18 @@ package org.broadinstitute.sting.playground.gatk.walkers.validation; -import com.sun.tools.corba.se.idl.constExpr.Not; -import com.sun.tools.internal.xjc.reader.xmlschema.bindinfo.BIConversion; -import org.broad.tribble.Feature; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.io.OutputTracker; -import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.bed.BedParser; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import javax.activation.*; -import java.beans.VetoableChangeSupport; -import java.io.PrintStream; -import java.io.Writer; -import java.security.KeyStore; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java index ce73dfd8c..9e832fde6 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.playground.gatk.walkers.validation; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java index 0263937c8..51951e56c 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantutils/CGVarToVCF.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantutils; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/playground/tools/SortROD.java b/java/src/org/broadinstitute/sting/playground/tools/SortROD.java index 6acb98dab..0a659c010 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/SortROD.java +++ b/java/src/org/broadinstitute/sting/playground/tools/SortROD.java @@ -28,15 +28,14 @@ package org.broadinstitute.sting.playground.tools; import org.apache.log4j.BasicConfigurator; import org.broad.tribble.FeatureCodec; import org.broad.tribble.Feature; -import org.broad.tribble.completegenomics.CGVarCodec; +import org.broadinstitute.sting.utils.codecs.completegenomics.CGVarCodec; import org.broad.tribble.readers.AsciiLineReader; -import org.broad.tribble.soapsnp.SoapSNPCodec; +import org.broadinstitute.sting.utils.codecs.soapsnp.SoapSNPCodec; import org.broad.tribble.gelitext.GeliTextCodec; import org.broad.tribble.dbsnp.DbSNPCodec; import org.broad.tribble.bed.BEDCodec; -import org.broad.tribble.vcf.VCFCodec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.playground.gatk.features.maf.MafCodec; diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java index 0ac08b7f7..fe6758e76 100644 --- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.queue.extensions.gatk; import net.sf.samtools.BAMIndex; import net.sf.samtools.SAMFileWriter; import org.broad.tribble.Tribble; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java index f035892ce..2da427d44 100644 --- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java +++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java @@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter; import org.apache.commons.lang.StringEscapeUtils; import org.apache.commons.lang.StringUtils; import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper; -import org.broad.tribble.vcf.VCFWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter; import java.io.File; import java.io.InputStream; diff --git a/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/java/src/org/broadinstitute/sting/utils/IndelUtils.java index 86363cba0..30e1a3f5b 100755 --- a/java/src/org/broadinstitute/sting/utils/IndelUtils.java +++ b/java/src/org/broadinstitute/sting/utils/IndelUtils.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/java/src/org/broadinstitute/sting/utils/MendelianViolation.java index dab1f51fd..a8089ffe8 100755 --- a/java/src/org/broadinstitute/sting/utils/MendelianViolation.java +++ b/java/src/org/broadinstitute/sting/utils/MendelianViolation.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.sample.Sample; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/java/src/org/broadinstitute/sting/utils/SampleUtils.java index d15eb8e86..c0370064d 100755 --- a/java/src/org/broadinstitute/sting/utils/SampleUtils.java +++ b/java/src/org/broadinstitute/sting/utils/SampleUtils.java @@ -27,12 +27,12 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; -import org.broad.tribble.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import java.io.File; import java.io.FileNotFoundException; diff --git a/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java new file mode 100755 index 000000000..a286ce789 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java @@ -0,0 +1,160 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.completegenomics; + +import org.broad.tribble.Feature; +import org.broad.tribble.FeatureCodec; +import org.broad.tribble.readers.LineReader; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.io.IOException; +import java.util.HashMap; +import java.util.HashSet; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +/** + * a codec for the VAR file types produced by the Complete Genomics Institute + */ +public class CGVarCodec implements FeatureCodec { + + private static final String REF_TYPE = "ref"; + private static final String SNP_TYPE = "snp"; + private static final String DELETION_TYPE = "del"; + private static final String INSERTION_TYPE = "ins"; + private static final String SUBSTITUTION_TYPE = "sub"; + + // the minimum number of features in the CG file line + private static final int minimumFeatureCount = 8; + + /** + * decode the location only + * @param line the input line to decode + * @return a HapMapFeature + */ + public Feature decodeLoc(String line) { + return decode(line); + } + + /** + * decode the CG record + * @param line the input line to decode + * @return a VariantContext + */ + public Feature decode(String line) { + String[] array = line.split("\\s+"); + + // make sure the split was successful - that we got an appropriate number of fields + if ( array.length < minimumFeatureCount ) + return null; + + String type = array[6]; + + long start = Long.valueOf(array[4]); + long end; + Allele ref, alt = null; + + //System.out.println(line); + + if ( type.equals(SNP_TYPE) ) { + ref = Allele.create(array[7], true); + alt = Allele.create(array[8], false); + end = start; + } else if ( type.equals(INSERTION_TYPE) ) { + ref = Allele.create(Allele.NULL_ALLELE_STRING, true); + alt = Allele.create(array[7], false); + end = start; + } else if ( type.equals(DELETION_TYPE) ) { + ref = Allele.create(array[7], true); + alt = Allele.create(Allele.NULL_ALLELE_STRING, false); + end = start + ref.length(); + //} else if ( type.equals(REF_TYPE) ) { + // ref = Allele.create("N", true); // ref bases aren't accurate + // start++; + // end = start; + //} else if ( type.equals(SUBSTITUTION_TYPE) ) { + // ref = Allele.create(array[7], true); + // alt = Allele.create(array[8], false); + // end = start + Math.max(ref.length(), alt.length()); + } else { + return null; // we don't handle other types + } + + HashSet alleles = new HashSet(); + alleles.add(ref); + if ( alt != null ) + alleles.add(alt); + + HashMap attrs = new HashMap(); + String id = array[array.length - 1]; + if ( id.indexOf("dbsnp") != -1 ) { + attrs.put(VariantContext.ID_KEY, parseID(id)); + } + + // create a new feature given the array + return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs); + } + + public Class getFeatureType() { + return VariantContext.class; + } + + // There's no spec and no character to distinguish header lines... + private final static int NUM_HEADER_LINES = 12; + public Object readHeader(LineReader reader) { + return null; + + //String headerLine = null; + //try { + // for (int i = 0; i < NUM_HEADER_LINES; i++) + // headerLine = reader.readLine(); + //} catch (IOException e) { + // throw new IllegalArgumentException("Unable to read a line from the line reader"); + //} + //return headerLine; + } + + private static final Pattern DBSNP_PATTERN = Pattern.compile("^dbsnp\\.\\d+:(.*)"); + private String parseID(String raw) { + StringBuilder sb = null; + + String[] ids = raw.split(";"); + for ( String id : ids ) { + Matcher matcher = DBSNP_PATTERN.matcher(id); + if ( matcher.matches() ) { + String rsID = matcher.group(1); + if ( sb == null ) { + sb = new StringBuilder(rsID); + } else { + sb.append(";"); + sb.append(rsID); + } + } + } + + return sb == null ? null : sb.toString(); + } +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java new file mode 100644 index 000000000..bd95e0f3d --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java @@ -0,0 +1,97 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.hapmap; + +import org.broad.tribble.Feature; +import org.broad.tribble.FeatureCodec; +import org.broad.tribble.annotation.Strand; +import org.broad.tribble.readers.LineReader; + +import java.io.IOException; +import java.util.Arrays; + +/** + * a codec for the file types produced by the HapMap consortium, available on their website: + * http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/ + * + * The format includes eleven standard fields, plus genotypes for each of the samples included + * in the file + * + */ +public class HapMapCodec implements FeatureCodec { + // the minimum number of features in the HapMap file line + private static final int minimumFeatureCount = 11; + + private String headerLine; + /** + * decode the location only + * @param line the input line to decode + * @return a HapMapFeature + */ + public Feature decodeLoc(String line) { + return decode(line); + } + + /** + * decode the hapmap record + * @param line the input line to decode + * @return a HapMapFeature, with the given fields + */ + public Feature decode(String line) { + String[] array = line.split("\\s+"); + + // make sure the split was successful - that we got an appropriate number of fields + if (array.length < minimumFeatureCount) + throw new IllegalArgumentException("Unable to parse line " + line + ", the length of split features is less than the minimum of " + minimumFeatureCount); + + // create a new feature given the array + return new HapMapFeature(array[0], + array[1].split("/"), + array[2], + Long.valueOf(array[3]), + Strand.toStrand(array[4]), + array[5], + array[6], + array[7], + array[8], + array[9], + array[10], + Arrays.copyOfRange(array,11,array.length), + headerLine); + } + + public Class getFeatureType() { + return HapMapFeature.class; + } + + public Object readHeader(LineReader reader) { + try { + headerLine = reader.readLine(); + } catch (IOException e) { + throw new IllegalArgumentException("Unable to read a line from the line reader"); + } + return headerLine; + } +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java new file mode 100755 index 000000000..7a47a4b8d --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java @@ -0,0 +1,194 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.hapmap; + +import org.broad.tribble.Feature; +import org.broad.tribble.annotation.Strand; +import org.broadinstitute.sting.utils.variantcontext.Allele; + +import java.util.HashMap; +import java.util.Map; + +/** + * a feature returned by the HapMap Codec - it represents contig, position, name, + * alleles, other hapmap information, and genotypes for specified samples + */ +public class HapMapFeature implements Feature { + + public static final String INSERTION = "I"; + public static final String DELETION = "D"; + + // the variables we store internally in the class + private final String name; + private final String[] alleles; + private Map actualAlleles = null; + private final String contig ; + private long position; + private final Strand strand; + private final String assembly; + private final String center; + private final String protLSID; + private final String assayLSID; + private final String panelLSID; + private final String qccode; + private final String[] genotypes; + + // we store the header line, if they'd like to get the samples + private final String headerLine; + + /** + * create a HapMap Feature, based on all the records available in the hapmap file + * @param contig the contig name + * @param position the position + * @param strand the strand enum + * @param assembly what assembly this feature is from + * @param center the center that provided this SNP + * @param protLSID ?? + * @param assayLSID ?? + * @param panelLSID ?? + * @param qccode ?? + * @param genotypes a list of strings, representing the genotypes for the list of samples + */ + public HapMapFeature(String name, + String[] alleles, + String contig, + Long position, + Strand strand, + String assembly, + String center, + String protLSID, + String assayLSID, + String panelLSID, + String qccode, + String[] genotypes, + String headerLine) { + this.name = name; + this.alleles = alleles; + this.contig = contig; + this.position = position; + this.strand = strand; + this.assembly = assembly; + this.center = center; + this.protLSID = protLSID ; + this.assayLSID = assayLSID ; + this.panelLSID = panelLSID ; + this.qccode = qccode; + this.genotypes = genotypes; + this.headerLine = headerLine; + } + + /** + * get the contig value + * @return a string representing the contig + */ + public String getChr() { + return contig; + } + + /** + * get the start position, as an integer + * @return an int, representing the start position + */ + public int getStart() { + return (int)position; + } + + /** + * get the end position + * @return get the end position as an int + */ + public int getEnd() { + return (int)position; + } + + /** + * Getter methods + */ + + public Strand getStrand() { + return strand; + } + + public String getAssembly() { + return assembly; + } + + public String getCenter() { + return center; + } + + public String getProtLSID() { + return protLSID; + } + + public String getAssayLSID() { + return assayLSID; + } + + public String getPanelLSID() { + return panelLSID; + } + + public String getQCCode() { + return qccode; + } + + public String getName() { + return name; + } + + public String[] getAlleles() { + return alleles; + } + + public String[] getGenotypes() { + return genotypes; + } + + // This is necessary because HapMap places insertions in the incorrect position + public void updatePosition(long position) { + this.position = position; + } + + public void setActualAlleles(Map alleleMap) { + actualAlleles = new HashMap(alleleMap); + } + + public Map getActualAlleles() { + return actualAlleles; + } + + /** + * get a list of the samples from the header (in order) + * @return a string array of sample names + */ + public String[] getSampleIDs() { + String[] header = headerLine.split("\\s+"); + String[] sample_ids = new String[header.length-11]; + for (int i = 11; i < header.length; i++) + sample_ids[i-11] = header[i]; + return sample_ids; + } +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java new file mode 100755 index 000000000..618d9ce79 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java @@ -0,0 +1,209 @@ +package org.broadinstitute.sting.utils.codecs.soapsnp; + +import org.broad.tribble.Feature; +import org.broad.tribble.FeatureCodec; +import org.broad.tribble.NameAwareCodec; +import org.broad.tribble.TribbleException; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broad.tribble.exception.CodecLineParsingException; +import org.broad.tribble.readers.LineReader; + +import java.util.*; + +/** + * @author depristo + *

+ * a codec for parsing soapsnp files (see http://soap.genomics.org.cn/soapsnp.html#usage2) + *

+ * + * A simple text file format with the following whitespace separated fields: + * +1) Chromosome ID +2) Coordinate on chromosome, start from 1 +3) Reference genotype +4) Consensus genotype +5) Quality score of consensus genotype +6) Best base +7) Average quality score of best base +8) Count of uniquely mapped best base +9) Count of all mapped best base +10) Second best bases +11) Average quality score of second best base +12) Count of uniquely mapped second best base +13) Count of all mapped second best base +14) Sequencing depth of the site +15) Rank sum test p_value +16) Average copy number of nearby region +17) Whether the site is a dbSNP. + */ +public class SoapSNPCodec implements FeatureCodec, NameAwareCodec { + private String[] parts; + + // we store a name to give to each of the variant contexts we emit + private String name = "Unknown"; + + public Feature decodeLoc(String line) { + return decode(line); + } + + /** + * Decode a line as a Feature. + * + * @param line + * + * @return Return the Feature encoded by the line, or null if the line does not represent a feature (e.g. is + * a comment) + */ + public Feature decode(String line) { + try { + // parse into lines + parts = line.trim().split("\\s+"); + + // check that we got the correct number of tokens in the split + if (parts.length != 18) + throw new CodecLineParsingException("Invalid SoapSNP row found -- incorrect element count. Expected 18, got " + parts.length + " line = " + line); + + String contig = parts[0]; + long start = Long.valueOf(parts[1]); + AlleleAndGenotype allelesAndGenotype = parseAlleles(parts[2], parts[3], line); + + double negLog10PError = Integer.valueOf(parts[4]) / 10.0; + + Map attributes = new HashMap(); + attributes.put("BestBaseQ", parts[6]); + attributes.put("SecondBestBaseQ", parts[10]); + attributes.put("RankSumP", parts[15]); + // add info to keys + + //System.out.printf("Alleles = " + allelesAndGenotype.alleles); + //System.out.printf("genotype = " + allelesAndGenotype.genotype); + + VariantContext vc = new VariantContext(name, contig, start, start, allelesAndGenotype.alleles, allelesAndGenotype.genotype, negLog10PError, VariantContext.PASSES_FILTERS, attributes); + + //System.out.printf("line = %s%n", line); + //System.out.printf("vc = %s%n", vc); + + return vc; + } catch (CodecLineParsingException e) { + throw new TribbleException("Unable to parse line " + line,e); + } catch (NumberFormatException e) { + e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. + throw new TribbleException("Unable to parse line " + line,e); + } + } + + private static class AlleleAndGenotype { + Collection alleles; + Collection genotype; + + public AlleleAndGenotype(Collection alleles, Genotype genotype) { + this.alleles = alleles; + this.genotype = new HashSet(); + this.genotype.add(genotype); + } + } + + private AlleleAndGenotype parseAlleles(String ref, String consensusGenotype, String line) { + /* A Adenine + C Cytosine + G Guanine + T (or U) Thymine (or Uracil) + R A or G + Y C or T + S G or C + W A or T + K G or T + M A or C + B C or G or T + D A or G or T + H A or C or T + V A or C or G + N any base + . or - gap + */ + if ( ref.equals(consensusGenotype) ) + throw new TribbleException.InternalCodecException("Ref base and consensus genotype are the same " + ref); + + Allele refAllele = Allele.create(ref, true); + List genotypeAlleles = null; + + char base = consensusGenotype.charAt(0); + + switch ( base ) { + case 'A': case 'C': case 'G': case 'T': + Allele a = Allele.create(consensusGenotype); + genotypeAlleles = Arrays.asList(a, a); + break; + case 'R': case 'Y': case 'S': case 'W': case 'K': case 'M': + genotypeAlleles = determineAlt(refAllele, ref.charAt(0), base); + break; + default: + throw new TribbleException("Unexpected consensus genotype " + consensusGenotype + " at line = " + line); + } + + + Collection alleles = new HashSet(genotypeAlleles); + alleles.add(refAllele); + Genotype genotype = new Genotype("unknown", genotypeAlleles); // todo -- probably should include genotype quality + + return new AlleleAndGenotype( alleles, genotype ); + } + + private static final Map IUPAC_SNPS = new HashMap(); + static { + IUPAC_SNPS.put('R', "AG"); + IUPAC_SNPS.put('Y', "CT"); + IUPAC_SNPS.put('S', "GC"); + IUPAC_SNPS.put('W', "AT"); + IUPAC_SNPS.put('K', "GT"); + IUPAC_SNPS.put('M', "AC"); + } + + private List determineAlt(Allele ref, char refbase, char alt) { + String alts = IUPAC_SNPS.get(alt); + if ( alts == null ) + throw new IllegalStateException("BUG: unexpected consensus genotype " + alt); + + Allele a1 = alts.charAt(0) == refbase ? ref : Allele.create((byte)alts.charAt(0)); + Allele a2 = alts.charAt(1) == refbase ? ref : Allele.create((byte)alts.charAt(1)); + + //if ( a1 != ref && a2 != ref ) + // throw new IllegalStateException("BUG: unexpected consensus genotype " + alt + " does not contain the reference base " + ref); + + return Arrays.asList(a1, a2); + } + + /** + * @return VariantContext + */ + public Class getFeatureType() { + return VariantContext.class; + } + + public Object readHeader(LineReader reader) { + + return null; // we don't have a meaningful header + } + + /** + * get the name of this codec + * @return our set name + */ + public String getName() { + return name; + } + + /** + * set the name of this codec + * @param name new name + */ + public void setName(String name) { + this.name = name; + } + + public static void main(String[] args) { + System.out.printf("Testing " + args[0]); + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java new file mode 100755 index 000000000..cd0f52c68 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -0,0 +1,617 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.apache.log4j.Logger; +import org.broad.tribble.Feature; +import org.broad.tribble.FeatureCodec; +import org.broad.tribble.NameAwareCodec; +import org.broad.tribble.TribbleException; +import org.broad.tribble.readers.LineReader; +import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.*; + + +public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser { + + protected final static Logger log = Logger.getLogger(VCFCodec.class); + protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column + + protected VCFHeaderVersion version; + + // we have to store the list of strings that make up the header until they're needed + protected VCFHeader header = null; + + // a mapping of the allele + protected Map> alleleMap = new HashMap>(3); + + // for ParsingUtils.split + protected String[] GTValueArray = new String[100]; + protected String[] genotypeKeyArray = new String[100]; + protected String[] infoValueArray = new String[1000]; + + // for performance testing purposes + public static boolean validate = true; + + // a key optimization -- we need a per thread string parts array, so we don't allocate a big array over and over + // todo: make this thread safe? + protected String[] parts = null; + protected String[] genotypeParts = null; + + // for performance we cache the hashmap of filter encodings for quick lookup + protected HashMap> filterHash = new HashMap>(); + + // a mapping of the VCF fields to their type, filter fields, and format fields, for quick lookup to validate against + TreeMap infoFields = new TreeMap(); + TreeMap formatFields = new TreeMap(); + Set filterFields = new HashSet(); + + // we store a name to give to each of the variant contexts we emit + protected String name = "Unknown"; + + protected int lineNo = 0; + + protected Map stringCache = new HashMap(); + + + /** + * @param reader the line reader to take header lines from + * @return the number of header lines + */ + public abstract Object readHeader(LineReader reader); + + /** + * create a genotype map + * @param str the string + * @param alleles the list of alleles + * @param chr chrom + * @param pos position + * @return a mapping of sample name to genotype object + */ + public abstract Map createGenotypeMap(String str, List alleles, String chr, int pos); + + + /** + * parse the filter string, first checking to see if we already have parsed it in a previous attempt + * @param filterString the string to parse + * @return a set of the filters applied + */ + protected abstract Set parseFilters(String filterString); + + /** + * create a VCF header + * @param headerStrings a list of strings that represent all the ## entries + * @param line the single # line (column names) + * @return the count of header lines + */ + protected Object createHeader(List headerStrings, String line) { + + headerStrings.add(line); + + Set metaData = new TreeSet(); + Set auxTags = new LinkedHashSet(); + // iterate over all the passed in strings + for ( String str : headerStrings ) { + if ( !str.startsWith(VCFHeader.METADATA_INDICATOR) ) { + String[] strings = str.substring(1).split(VCFConstants.FIELD_SEPARATOR); + int arrayIndex = 0; + for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) { + try { + if (field != VCFHeader.HEADER_FIELDS.valueOf(strings[arrayIndex])) + throw new TribbleException.InvalidHeader("we were expecting column name '" + field + "' but we saw '" + strings[arrayIndex] + "'"); + } catch (IllegalArgumentException e) { + throw new TribbleException.InvalidHeader("unknown column name '" + strings[arrayIndex] + "'; it does not match a legal column header name."); + } + arrayIndex++; + } + if ( arrayIndex < strings.length ) { + if ( !strings[arrayIndex].equals("FORMAT") ) + throw new TribbleException.InvalidHeader("we were expecting column name 'FORMAT' but we saw '" + strings[arrayIndex] + "'"); + arrayIndex++; + } + + while (arrayIndex < strings.length) + auxTags.add(strings[arrayIndex++]); + + } else { + if ( str.startsWith("##INFO=") ) { + VCFInfoHeaderLine info = new VCFInfoHeaderLine(str.substring(7),version); + metaData.add(info); + infoFields.put(info.getName(), info.getType()); + } else if ( str.startsWith("##FILTER=") ) { + VCFFilterHeaderLine filter = new VCFFilterHeaderLine(str.substring(9),version); + metaData.add(filter); + filterFields.add(filter.getName()); + } else if ( str.startsWith("##FORMAT=") ) { + VCFFormatHeaderLine format = new VCFFormatHeaderLine(str.substring(9),version); + metaData.add(format); + formatFields.put(format.getName(), format.getType()); + } else { + int equals = str.indexOf("="); + if ( equals != -1 ) + metaData.add(new VCFHeaderLine(str.substring(2, equals), str.substring(equals+1))); + } + } + } + + header = new VCFHeader(metaData, auxTags); + return header; + } + + /** + * the fast decode function + * @param line the line of text for the record + * @return a feature, (not guaranteed complete) that has the correct start and stop + */ + public Feature decodeLoc(String line) { + return reallyDecode(line); + } + + /** + * decode the line into a feature (VariantContext) + * @param line the line + * @return a VariantContext + */ + public Feature decode(String line) { + return reallyDecode(line); + } + + private Feature reallyDecode(String line) { + try { + // the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line + if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null; + + // our header cannot be null, we need the genotype sample names and counts + if (header == null) throw new IllegalStateException("VCF Header cannot be null when decoding a record"); + + if (parts == null) + parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)]; + + int nParts = ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR, true); + + // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns. Otherwise check that we have nine (normal colummns + genotyping data) + if (( (header == null || (header != null && !header.hasGenotypingData())) && nParts != NUM_STANDARD_FIELDS) || + (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) ) + throw new IllegalArgumentException("There aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) + + " tokens, and saw " + nParts + " )"); + + return parseVCFLine(parts); + } catch (TribbleException e) { + throw new TribbleException.InvalidDecodeLine(e.getMessage(), line); + } + } + + protected void generateException(String message) { + throw new TribbleException.InvalidDecodeLine(message, lineNo); + } + + /** + * parse out the VCF line + * + * @param parts the parts split up + * @return a variant context object + */ + private VariantContext parseVCFLine(String[] parts) { + // increment the line count + lineNo++; + + // parse out the required fields + String contig = getCachedString(parts[0]); + long pos = Long.valueOf(parts[1]); + String id = null; + if ( parts[2].length() == 0 ) + generateException("The VCF specification requires a valid ID field"); + else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) + id = VCFConstants.EMPTY_ID_FIELD; + else + id = new String(parts[2]); + String ref = getCachedString(parts[3].toUpperCase()); + String alts = getCachedString(parts[4].toUpperCase()); + Double qual = parseQual(parts[5]); + String filter = getCachedString(parts[6]); + String info = new String(parts[7]); + + // get our alleles, filters, and setup an attribute map + List alleles = parseAlleles(ref, alts, lineNo); + Set filters = parseFilters(filter); + Map attributes = parseInfo(info, id); + + // find out our current location, and clip the alleles down to their minimum length + long loc = pos; + // ref alleles don't need to be single bases for monomorphic sites + if ( alleles.size() == 1 ) { + loc = pos + alleles.get(0).length() - 1; + } else if ( !isSingleNucleotideEvent(alleles) ) { + ArrayList newAlleles = new ArrayList(); + loc = clipAlleles(pos, ref, alleles, newAlleles); + alleles = newAlleles; + } + + // do we have genotyping data + if (parts.length > NUM_STANDARD_FIELDS) { + attributes.put(VariantContext.UNPARSED_GENOTYPE_MAP_KEY, new String(parts[8])); + attributes.put(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY, this); + } + + VariantContext vc = null; + try { + vc = new VariantContext(name, contig, pos, loc, alleles, qual, filters, attributes); + } catch (Exception e) { + generateException(e.getMessage()); + } + + // did we resort the sample names? If so, we need to load the genotype data + if ( !header.samplesWereAlreadySorted() ) + vc.getGenotypes(); + + // Trim bases of all alleles if necessary + return createVariantContextWithTrimmedAlleles(vc); + } + + /** + * + * @return the type of record + */ + public Class getFeatureType() { + return VariantContext.class; + } + + /** + * get the name of this codec + * @return our set name + */ + public String getName() { + return name; + } + + /** + * set the name of this codec + * @param name new name + */ + public void setName(String name) { + this.name = name; + } + + /** + * Return a cached copy of the supplied string. + * + * @param str string + * @return interned string + */ + protected String getCachedString(String str) { + String internedString = stringCache.get(str); + if ( internedString == null ) { + internedString = new String(str); + stringCache.put(internedString, internedString); + } + return internedString; + } + + /** + * parse out the info fields + * @param infoField the fields + * @param id the indentifier + * @return a mapping of keys to objects + */ + private Map parseInfo(String infoField, String id) { + Map attributes = new HashMap(); + + if ( infoField.length() == 0 ) + generateException("The VCF specification requires a valid info field"); + + if ( !infoField.equals(VCFConstants.EMPTY_INFO_FIELD) ) { + int infoValueSplitSize = ParsingUtils.split(infoField, infoValueArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR); + for (int i = 0; i < infoValueSplitSize; i++) { + String key; + Object value; + + int eqI = infoValueArray[i].indexOf("="); + if ( eqI != -1 ) { + key = infoValueArray[i].substring(0, eqI); + String str = infoValueArray[i].substring(eqI+1, infoValueArray[i].length()); + + // lets see if the string contains a , separator + if ( str.contains(",") ) + value = Arrays.asList(str.split(",")); + else + value = str; + } else { + key = infoValueArray[i]; + value = true; + } + + attributes.put(key, value); + } + } + + attributes.put(VariantContext.ID_KEY, id); + return attributes; + } + + /** + * create a an allele from an index and an array of alleles + * @param index the index + * @param alleles the alleles + * @return an Allele + */ + protected static Allele oneAllele(String index, List alleles) { + if ( index.equals(VCFConstants.EMPTY_ALLELE) ) + return Allele.NO_CALL; + int i = Integer.valueOf(index); + if ( i >= alleles.size() ) + throw new TribbleException.InternalCodecException("The allele with index " + index + " is not defined in the REF/ALT columns in the record"); + return alleles.get(i); + } + + + /** + * parse genotype alleles from the genotype string + * @param GT GT string + * @param alleles list of possible alleles + * @param cache cache of alleles for GT + * @return the allele list for the GT string + */ + protected static List parseGenotypeAlleles(String GT, List alleles, Map> cache) { + // cache results [since they are immutable] and return a single object for each genotype + List GTAlleles = cache.get(GT); + + if ( GTAlleles == null ) { + StringTokenizer st = new StringTokenizer(GT, VCFConstants.PHASING_TOKENS); + GTAlleles = new ArrayList(st.countTokens()); + while ( st.hasMoreTokens() ) { + String genotype = st.nextToken(); + GTAlleles.add(oneAllele(genotype, alleles)); + } + cache.put(GT, GTAlleles); + } + + return GTAlleles; + } + + /** + * parse out the qual value + * @param qualString the quality string + * @return return a double + */ + protected static Double parseQual(String qualString) { + // if we're the VCF 4 missing char, return immediately + if ( qualString.equals(VCFConstants.MISSING_VALUE_v4)) + return VariantContext.NO_NEG_LOG_10PERROR; + + Double val = Double.valueOf(qualString); + + // check to see if they encoded the missing qual score in VCF 3 style, with either the -1 or -1.0. check for val < 0 to save some CPU cycles + if ((val < 0) && (Math.abs(val - VCFConstants.MISSING_QUALITY_v3_DOUBLE) < VCFConstants.VCF_ENCODING_EPSILON)) + return VariantContext.NO_NEG_LOG_10PERROR; + + // scale and return the value + return val / 10.0; + } + + /** + * parse out the alleles + * @param ref the reference base + * @param alts a string of alternates to break into alleles + * @param lineNo the line number for this record + * @return a list of alleles, and a pair of the shortest and longest sequence + */ + protected static List parseAlleles(String ref, String alts, int lineNo) { + List alleles = new ArrayList(2); // we are almost always biallelic + // ref + checkAllele(ref, true, lineNo); + Allele refAllele = Allele.create(ref, true); + alleles.add(refAllele); + + if ( alts.indexOf(",") == -1 ) // only 1 alternatives, don't call string split + parseSingleAltAllele(alleles, alts, lineNo); + else + for ( String alt : alts.split(",") ) + parseSingleAltAllele(alleles, alt, lineNo); + + return alleles; + } + + /** + * check to make sure the allele is an acceptable allele + * @param allele the allele to check + * @param isRef are we the reference allele? + * @param lineNo the line number for this record + */ + private static void checkAllele(String allele, boolean isRef, int lineNo) { + if ( allele == null || allele.length() == 0 ) + generateException("Empty alleles are not permitted in VCF records", lineNo); + + if ( isSymbolicAllele(allele) ) { + if ( isRef ) { + generateException("Symbolic alleles not allowed as reference allele: " + allele, lineNo); + } + } else { + // check for VCF3 insertions or deletions + if ( (allele.charAt(0) == VCFConstants.DELETION_ALLELE_v3) || (allele.charAt(0) == VCFConstants.INSERTION_ALLELE_v3) ) + generateException("Insertions/Deletions are not supported when reading 3.x VCF's. Please" + + " convert your file to VCF4 using VCFTools, available at http://vcftools.sourceforge.net/index.html", lineNo); + + if (!Allele.acceptableAlleleBases(allele)) + generateException("Unparsable vcf record with allele " + allele, lineNo); + + if ( isRef && allele.equals(VCFConstants.EMPTY_ALLELE) ) + generateException("The reference allele cannot be missing", lineNo); + } + } + + /** + * return true if this is a symbolic allele (e.g. ) otherwise false + * @param allele the allele to check + * @return true if the allele is a symbolic allele, otherwise false + */ + private static boolean isSymbolicAllele(String allele) { + return (allele != null && allele.startsWith("<") && allele.endsWith(">") && allele.length() > 2); + } + + /** + * parse a single allele, given the allele list + * @param alleles the alleles available + * @param alt the allele to parse + * @param lineNo the line number for this record + */ + private static void parseSingleAltAllele(List alleles, String alt, int lineNo) { + checkAllele(alt, false, lineNo); + + Allele allele = Allele.create(alt, false); + if ( ! allele.isNoCall() ) + alleles.add(allele); + } + + protected static boolean isSingleNucleotideEvent(List alleles) { + for ( Allele a : alleles ) { + if ( a.length() != 1 ) + return false; + } + return true; + } + + private static void generateException(String message, int lineNo) { + throw new TribbleException.InvalidDecodeLine(message, lineNo); + } + + private static int computeForwardClipping(List unclippedAlleles, String ref) { + boolean clipping = true; + // Note that the computation of forward clipping here is meant only to see whether there is a common + // base to all alleles, and to correctly compute reverse clipping, + // but it is not used for actually changing alleles - this is done in function + // createVariantContextWithTrimmedAlleles() below. + + for (Allele a : unclippedAlleles) { + if (a.isSymbolic()) { + continue; + } + if (a.length() < 1 || (a.getBases()[0] != ref.getBytes()[0])) { + clipping = false; + } + } + return (clipping) ? 1 : 0; + + } + + /** + * clip the alleles, based on the reference + * + * @param position the unadjusted start position (pre-clipping) + * @param ref the reference string + * @param unclippedAlleles the list of unclipped alleles + * @param clippedAlleles output list of clipped alleles + * @return a list of alleles, clipped to the reference + */ + protected static long clipAlleles(long position, String ref, List unclippedAlleles, List clippedAlleles) { + + // Note that the computation of forward clipping here is meant only to see whether there is a common + // base to all alleles, and to correctly compute reverse clipping, + // but it is not used for actually changing alleles - this is done in function + // createVariantContextWithTrimmedAlleles() below. + + int forwardClipping = computeForwardClipping(unclippedAlleles, ref); + + int reverseClipped = 0; + boolean clipping = true; + while (clipping) { + for (Allele a : unclippedAlleles) { + if (a.isSymbolic()) { + continue; + } + if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0) + clipping = false; + else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1]) + clipping = false; + } + if (clipping) reverseClipped++; + } + + for (Allele a : unclippedAlleles) { + if (a.isSymbolic()) { + clippedAlleles.add(a); + } else { + clippedAlleles.add(Allele.create(Arrays.copyOfRange(a.getBases(),0,a.getBases().length-reverseClipped),a.isReference())); + } + } + + // the new reference length + int refLength = ref.length() - reverseClipped; + + return position+Math.max(refLength - 1,0); + } + + public static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) { + // see if we need to trim common reference base from all alleles + boolean trimVC; + + // We need to trim common reference base from all alleles in all genotypes if a ref base is common to all alleles + Allele refAllele = inputVC.getReference(); + if (!inputVC.isVariant()) + trimVC = false; + else if (refAllele.isNull()) + trimVC = false; + else { + trimVC = (computeForwardClipping(new ArrayList(inputVC.getAlternateAlleles()), + inputVC.getReference().getDisplayString()) > 0); + } + + // nothing to do if we don't need to trim bases + if (trimVC) { + List alleles = new ArrayList(); + Map genotypes = new TreeMap(); + + // set the reference base for indels in the attributes + Map attributes = new TreeMap(inputVC.getAttributes()); + attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(inputVC.getReference().getBases()[0])); + + Map originalToTrimmedAlleleMap = new HashMap(); + + for (Allele a : inputVC.getAlleles()) { + if (a.isSymbolic()) { + alleles.add(a); + originalToTrimmedAlleleMap.put(a, a); + } else { + // get bases for current allele and create a new one with trimmed bases + byte[] newBases = Arrays.copyOfRange(a.getBases(), 1, a.length()); + Allele trimmedAllele = Allele.create(newBases, a.isReference()); + alleles.add(trimmedAllele); + originalToTrimmedAlleleMap.put(a, trimmedAllele); + } + } + + // detect case where we're trimming bases but resulting vc doesn't have any null allele. In that case, we keep original representation + // example: mixed records such as {TA*,TGA,TG} + boolean hasNullAlleles = false; + + for (Allele a: originalToTrimmedAlleleMap.values()) { + if (a.isNull()) + hasNullAlleles = true; + if (a.isReference()) + refAllele = a; + } + + if (!hasNullAlleles) + return inputVC; + // now we can recreate new genotypes with trimmed alleles + for ( Map.Entry sample : inputVC.getGenotypes().entrySet() ) { + + List originalAlleles = sample.getValue().getAlleles(); + List trimmedAlleles = new ArrayList(); + for ( Allele a : originalAlleles ) { + if ( a.isCalled() ) + trimmedAlleles.add(originalToTrimmedAlleleMap.get(a)); + else + trimmedAlleles.add(Allele.NO_CALL); + } + genotypes.put(sample.getKey(), Genotype.modifyAlleles(sample.getValue(), trimmedAlleles)); + + } + return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVC.filtersWereApplied() ? inputVC.getFilters() : null, attributes); + + } + + return inputVC; + } +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java new file mode 100755 index 000000000..7dcdab924 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java @@ -0,0 +1,52 @@ +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +/** + * this class writes VCF files, allowing records to be passed in unsorted. + */ +public class ManualSortingVCFWriter extends SortingVCFWriterBase { + + /** + * create a local-sorting VCF writer, given an inner VCF writer to write to + * + * @param innerWriter the VCFWriter to write to + * @param takeOwnershipOfInner Should this Writer close innerWriter when it's done with it + */ + public ManualSortingVCFWriter(VCFWriter innerWriter, boolean takeOwnershipOfInner) { + super(innerWriter, takeOwnershipOfInner); + } + + public ManualSortingVCFWriter(VCFWriter innerWriter) { + super(innerWriter); + } + + // Note that if mostUpstreamWritableLoc = null, then ALL records will be emitted (since not currently waiting for anything) + public void setmostUpstreamWritableLocus(Integer mostUpstreamWritableLoc) { + this.mostUpstreamWritableLoc = mostUpstreamWritableLoc; + emitSafeRecords(); + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java new file mode 100755 index 000000000..7ece5edf8 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java @@ -0,0 +1,61 @@ +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +/** + * this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away) + */ +public class SortingVCFWriter extends SortingVCFWriterBase { + + // the maximum START distance between records that we'll cache + private int maxCachingStartDistance; + + /** + * create a local-sorting VCF writer, given an inner VCF writer to write to + * + * @param innerWriter the VCFWriter to write to + * @param maxCachingStartDistance the maximum start distance between records that we'll cache + * @param takeOwnershipOfInner Should this Writer close innerWriter when it's done with it + */ + public SortingVCFWriter(VCFWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner) { + super(innerWriter, takeOwnershipOfInner); + this.maxCachingStartDistance = maxCachingStartDistance; + } + + public SortingVCFWriter(VCFWriter innerWriter, int maxCachingStartDistance) { + this(innerWriter, maxCachingStartDistance, false); // by default, don't own inner + } + + protected void noteCurrentRecord(VariantContext vc) { + super.noteCurrentRecord(vc); // first, check for errors + + // then, update mostUpstreamWritableLoc: + int mostUpstreamWritableIndex = vc.getStart() - maxCachingStartDistance; + this.mostUpstreamWritableLoc = Math.max(BEFORE_MOST_UPSTREAM_LOC, mostUpstreamWritableIndex); + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java new file mode 100755 index 000000000..311aaecf7 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java @@ -0,0 +1,168 @@ +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.util.Comparator; +import java.util.PriorityQueue; +import java.util.Set; +import java.util.TreeSet; + +/** + * This class writes VCF files, allowing records to be passed in unsorted. + * It also enforces that it is never passed records of the same chromosome with any other chromosome in between them. + */ +public abstract class SortingVCFWriterBase implements VCFWriter { + + // The VCFWriter to which to actually write the sorted VCF records + private VCFWriter innerWriter = null; + + // the current queue of un-emitted records + private PriorityQueue queue = null; + + // The locus until which we are permitted to write out (inclusive) + protected Integer mostUpstreamWritableLoc; + protected static final int BEFORE_MOST_UPSTREAM_LOC = 0; // No real locus index is <= 0 + + // The set of chromosomes already passed over and to which it is forbidden to return + private Set finishedChromosomes = null; + + // Should we call innerWriter.close() in close() + private boolean takeOwnershipOfInner; + + /** + * create a local-sorting VCF writer, given an inner VCF writer to write to + * + * @param innerWriter the VCFWriter to write to + * @param takeOwnershipOfInner Should this Writer close innerWriter when it's done with it + */ + public SortingVCFWriterBase(VCFWriter innerWriter, boolean takeOwnershipOfInner) { + this.innerWriter = innerWriter; + this.queue = new PriorityQueue(50, new VariantContextComparator()); + this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC; + this.finishedChromosomes = new TreeSet(); + this.takeOwnershipOfInner = takeOwnershipOfInner; + } + + public SortingVCFWriterBase(VCFWriter innerWriter) { + this(innerWriter, false); // by default, don't own inner + } + + public void writeHeader(VCFHeader header) { + innerWriter.writeHeader(header); + } + + /** + * attempt to close the VCF file; we need to flush the queue first + */ + public void close() { + stopWaitingToSort(); + + if (takeOwnershipOfInner) + innerWriter.close(); + } + + private void stopWaitingToSort() { + emitRecords(true); + mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC; + } + + protected void emitSafeRecords() { + emitRecords(false); + } + + protected void noteCurrentRecord(VariantContext vc) { + // did the user break the contract by giving a record too late? + if (mostUpstreamWritableLoc != null && vc.getStart() < mostUpstreamWritableLoc) // went too far back, since may have already written anything that is <= mostUpstreamWritableLoc + throw new IllegalArgumentException("Permitted to write any record upstream of position " + mostUpstreamWritableLoc + ", but a record at " + vc.getChr() + ":" + vc.getStart() + " was just added."); + } + + /** + * add a record to the file + * + * @param vc the Variant Context object + * @param refBase the ref base + */ + public void add(VariantContext vc, byte refBase) { + /* Note that the code below does not prevent the successive add()-ing of: (chr1, 10), (chr20, 200), (chr15, 100) + since there is no implicit ordering of chromosomes: + */ + VCFRecord firstRec = queue.peek(); + if (firstRec != null && !vc.getChr().equals(firstRec.vc.getChr())) { // if we hit a new contig, flush the queue + if (finishedChromosomes.contains(vc.getChr())) + throw new IllegalArgumentException("Added a record at " + vc.getChr() + ":" + vc.getStart() + ", but already finished with chromosome" + vc.getChr()); + + finishedChromosomes.add(firstRec.vc.getChr()); + stopWaitingToSort(); + } + + noteCurrentRecord(vc); // possibly overwritten + + queue.add(new VCFRecord(vc, refBase)); + emitSafeRecords(); + } + + private void emitRecords(boolean emitUnsafe) { + while (!queue.isEmpty()) { + VCFRecord firstRec = queue.peek(); + + // No need to wait, waiting for nothing, or before what we're waiting for: + if (emitUnsafe || mostUpstreamWritableLoc == null || firstRec.vc.getStart() <= mostUpstreamWritableLoc) { + queue.poll(); + innerWriter.add(firstRec.vc, firstRec.refBase); + } + else { + break; + } + } + } + + /** + * Gets a string representation of this object. + * @return + */ + @Override + public String toString() { + return getClass().getName(); + } + + private static class VariantContextComparator implements Comparator { + public int compare(VCFRecord r1, VCFRecord r2) { + return r1.vc.getStart() - r2.vc.getStart(); + } + } + + private static class VCFRecord { + public VariantContext vc; + public byte refBase; + + public VCFRecord(VariantContext vc, byte refBase) { + this.vc = vc; + this.refBase = refBase; + } + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java new file mode 100755 index 000000000..31251c089 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java @@ -0,0 +1,529 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broad.tribble.Tribble; +import org.broad.tribble.TribbleException; +import org.broad.tribble.index.DynamicIndexCreator; +import org.broad.tribble.index.Index; +import org.broad.tribble.index.IndexFactory; +import org.broad.tribble.util.LittleEndianOutputStream; +import org.broad.tribble.util.ParsingUtils; +import org.broad.tribble.util.PositionalStream; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; + +import java.io.*; +import java.util.*; +import java.lang.reflect.Array; + +/** + * this class writes VCF files + */ +public class StandardVCFWriter implements VCFWriter { + + // the VCF header we're storing + protected VCFHeader mHeader = null; + + // the print stream we're writing to + protected BufferedWriter mWriter; + protected PositionalStream positionalStream = null; + + // were filters applied? + protected boolean filtersWereAppliedToContext = false; + + // should we write genotypes or just sites? + protected boolean doNotWriteGenotypes = false; + + protected DynamicIndexCreator indexer = null; + protected File indexFile = null; + LittleEndianOutputStream idxStream = null; + File location = null; + + /** + * create a VCF writer, given a file to write to + * + * @param location the file location to write to + */ + public StandardVCFWriter(File location) { + this(location, openOutputStream(location), true, false); + } + + public StandardVCFWriter(File location, boolean enableOnTheFlyIndexing) { + this(location, openOutputStream(location), enableOnTheFlyIndexing, false); + } + + /** + * create a VCF writer, given a stream to write to + * + * @param output the file location to write to + */ + public StandardVCFWriter(OutputStream output) { + this(output, false); + } + + /** + * create a VCF writer, given a stream to write to + * + * @param output the file location to write to + * @param doNotWriteGenotypes do not write genotypes + */ + public StandardVCFWriter(OutputStream output, boolean doNotWriteGenotypes) { + mWriter = new BufferedWriter(new OutputStreamWriter(output)); + this.doNotWriteGenotypes = doNotWriteGenotypes; + } + + public StandardVCFWriter(File location, OutputStream output, boolean enableOnTheFlyIndexing, boolean doNotWriteGenotypes) { + this.location = location; + + if ( enableOnTheFlyIndexing ) { + indexFile = Tribble.indexFile(location); + try { + idxStream = new LittleEndianOutputStream(new FileOutputStream(indexFile)); + //System.out.println("Creating index on the fly for " + location); + indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); + indexer.initialize(location, indexer.defaultBinSize()); + positionalStream = new PositionalStream(output); + output = positionalStream; + } catch ( IOException ex ) { + // No matter what we keep going, since we don't care if we can't create the index file + } + } + + //mWriter = new BufferedWriter(new OutputStreamWriter(new PositionalStream(output))); + mWriter = new BufferedWriter(new OutputStreamWriter(output)); + this.doNotWriteGenotypes = doNotWriteGenotypes; + } + + public void writeHeader(VCFHeader header) { + mHeader = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header; + + try { + // the file format field needs to be written first + mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_0.getFormatString() + "=" + VCFHeaderVersion.VCF4_0.getVersionString() + "\n"); + + for ( VCFHeaderLine line : mHeader.getMetaData() ) { + if ( line.getKey().equals(VCFHeaderVersion.VCF4_0.getFormatString()) || + line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) || + line.getKey().equals(VCFHeaderVersion.VCF3_2.getFormatString()) ) + continue; + + // are the records filtered (so we know what to put in the FILTER column of passing records) ? + if ( line instanceof VCFFilterHeaderLine) + filtersWereAppliedToContext = true; + + mWriter.write(VCFHeader.METADATA_INDICATOR); + mWriter.write(line.toString()); + mWriter.write("\n"); + } + + // write out the column line + mWriter.write(VCFHeader.HEADER_INDICATOR); + for ( VCFHeader.HEADER_FIELDS field : mHeader.getHeaderFields() ) { + mWriter.write(field.toString()); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + } + + if ( mHeader.hasGenotypingData() ) { + mWriter.write("FORMAT"); + for ( String sample : mHeader.getGenotypeSamples() ) { + mWriter.write(VCFConstants.FIELD_SEPARATOR); + mWriter.write(sample); + } + } + + mWriter.write("\n"); + mWriter.flush(); // necessary so that writing to an output stream will work + } + catch (IOException e) { + throw new TribbleException("IOException writing the VCF header to " + locationString(), e); + } + } + + private String locationString() { + return location == null ? mWriter.toString() : location.getAbsolutePath(); + } + + /** + * attempt to close the VCF file + */ + public void close() { + // try to close the vcf stream + try { + mWriter.flush(); + mWriter.close(); + } catch (IOException e) { + throw new TribbleException("Unable to close " + locationString() + " because of " + e.getMessage()); + } + + // try to close the index stream (keep it separate to help debugging efforts) + if ( indexer != null ) { + try { + Index index = indexer.finalizeIndex(positionalStream.getPosition()); + index.write(idxStream); + idxStream.close(); + } catch (IOException e) { + throw new TribbleException("Unable to close index for " + locationString() + " because of " + e.getMessage()); + } + } + } + + protected static OutputStream openOutputStream(File location) { + try { + return new FileOutputStream(location); + } catch (FileNotFoundException e) { + throw new TribbleException("Unable to create VCF file at location: " + location); + } + } + + /** + * add a record to the file + * + * @param vc the Variant Context object + * @param refBase the ref base used for indels + */ + public void add(VariantContext vc, byte refBase) { + add(vc, refBase, false); + } + + /** + * add a record to the file + * + * @param vc the Variant Context object + * @param refBase the ref base used for indels + * @param refBaseShouldBeAppliedToEndOfAlleles *** THIS SHOULD BE FALSE EXCEPT FOR AN INDEL AT THE EXTREME BEGINNING OF A CONTIG (WHERE THERE IS NO PREVIOUS BASE, SO WE USE THE BASE AFTER THE EVENT INSTEAD) + */ + public void add(VariantContext vc, byte refBase, boolean refBaseShouldBeAppliedToEndOfAlleles) { + if ( mHeader == null ) + throw new IllegalStateException("The VCF Header must be written before records can be added: " + locationString()); + + if ( doNotWriteGenotypes ) + vc = VariantContext.modifyGenotypes(vc, null); + + try { + vc = VariantContext.createVariantContextWithPaddedAlleles(vc, refBase, refBaseShouldBeAppliedToEndOfAlleles); + + // if we are doing on the fly indexing, add the record ***before*** we write any bytes + if ( indexer != null ) indexer.addFeature(vc, positionalStream.getPosition()); + + Map alleleMap = new HashMap(vc.getAlleles().size()); + alleleMap.put(Allele.NO_CALL, VCFConstants.EMPTY_ALLELE); // convenience for lookup + + // CHROM + mWriter.write(vc.getChr()); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + // POS + mWriter.write(String.valueOf(vc.getStart())); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + // ID + String ID = vc.hasID() ? vc.getID() : VCFConstants.EMPTY_ID_FIELD; + mWriter.write(ID); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + // REF + alleleMap.put(vc.getReference(), "0"); + String refString = vc.getReference().getDisplayString(); + mWriter.write(refString); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + // ALT + if ( vc.isVariant() ) { + Allele altAllele = vc.getAlternateAllele(0); + alleleMap.put(altAllele, "1"); + String alt = altAllele.getDisplayString(); + mWriter.write(alt); + + for (int i = 1; i < vc.getAlternateAlleles().size(); i++) { + altAllele = vc.getAlternateAllele(i); + alleleMap.put(altAllele, String.valueOf(i+1)); + alt = altAllele.getDisplayString(); + mWriter.write(","); + mWriter.write(alt); + } + } else { + mWriter.write(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD); + } + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + // QUAL + if ( !vc.hasNegLog10PError() ) + mWriter.write(VCFConstants.MISSING_VALUE_v4); + else + mWriter.write(getQualValue(vc.getPhredScaledQual())); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + // FILTER + String filters = vc.isFiltered() ? ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())) : (filtersWereAppliedToContext || vc.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED); + mWriter.write(filters); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + // INFO + Map infoFields = new TreeMap(); + for ( Map.Entry field : vc.getAttributes().entrySet() ) { + String key = field.getKey(); + if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) ) + continue; + + String outputValue = formatVCFField(field.getValue()); + if ( outputValue != null ) + infoFields.put(key, outputValue); + } + writeInfoString(infoFields); + + // FORMAT + if ( vc.hasAttribute(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) ) { + mWriter.write(VCFConstants.FIELD_SEPARATOR); + mWriter.write(vc.getAttributeAsString(VariantContext.UNPARSED_GENOTYPE_MAP_KEY, "")); + } else { + List genotypeAttributeKeys = new ArrayList(); + if ( vc.hasGenotypes() ) { + genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY); + for ( String key : calcVCFGenotypeKeys(vc) ) { + genotypeAttributeKeys.add(key); + } + } else if ( mHeader.hasGenotypingData() ) { + // this needs to be done in case all samples are no-calls + genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY); + } + + if ( genotypeAttributeKeys.size() > 0 ) { + String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys); + mWriter.write(VCFConstants.FIELD_SEPARATOR); + mWriter.write(genotypeFormatString); + + addGenotypeData(vc, alleleMap, genotypeAttributeKeys); + } + } + + mWriter.write("\n"); + mWriter.flush(); // necessary so that writing to an output stream will work + } catch (IOException e) { + throw new RuntimeException("Unable to write the VCF object to " + locationString()); + } + + } + + private String getQualValue(double qual) { + String s = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual); + if ( s.endsWith(VCFConstants.DOUBLE_PRECISION_INT_SUFFIX) ) + s = s.substring(0, s.length() - VCFConstants.DOUBLE_PRECISION_INT_SUFFIX.length()); + return s; + } + + /** + * create the info string; assumes that no values are null + * + * @param infoFields a map of info fields + * @throws IOException for writer + */ + private void writeInfoString(Map infoFields) throws IOException { + if ( infoFields.isEmpty() ) { + mWriter.write(VCFConstants.EMPTY_INFO_FIELD); + return; + } + + boolean isFirst = true; + for ( Map.Entry entry : infoFields.entrySet() ) { + if ( isFirst ) + isFirst = false; + else + mWriter.write(VCFConstants.INFO_FIELD_SEPARATOR); + + String key = entry.getKey(); + mWriter.write(key); + + if ( !entry.getValue().equals("") ) { + int numVals = 1; + VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key); + if ( metaData != null ) + numVals = metaData.getCount(); + + // take care of unbounded encoding + if ( numVals == VCFInfoHeaderLine.UNBOUNDED ) + numVals = 1; + + if ( numVals > 0 ) { + mWriter.write("="); + mWriter.write(entry.getValue()); + } + } + } + } + + /** + * add the genotype data + * + * @param vc the variant context + * @param genotypeFormatKeys Genotype formatting string + * @param alleleMap alleles for this context + * @throws IOException for writer + */ + private void addGenotypeData(VariantContext vc, Map alleleMap, List genotypeFormatKeys) + throws IOException { + + for ( String sample : mHeader.getGenotypeSamples() ) { + mWriter.write(VCFConstants.FIELD_SEPARATOR); + + Genotype g = vc.getGenotype(sample); + if ( g == null ) { + // TODO -- The VariantContext needs to know what the general ploidy is of the samples + // TODO -- We shouldn't be assuming diploid genotypes here! + mWriter.write(VCFConstants.EMPTY_GENOTYPE); + continue; + } + + writeAllele(g.getAllele(0), alleleMap); + for (int i = 1; i < g.getPloidy(); i++) { + mWriter.write(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED); + writeAllele(g.getAllele(i), alleleMap); + } + + List attrs = new ArrayList(genotypeFormatKeys.size()); + for ( String key : genotypeFormatKeys ) { + if ( key.equals(VCFConstants.GENOTYPE_KEY) ) + continue; + + Object val = g.hasAttribute(key) ? g.getAttribute(key) : VCFConstants.MISSING_VALUE_v4; + + // some exceptions + if ( key.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) { + if ( Math.abs(g.getNegLog10PError() - Genotype.NO_NEG_LOG_10PERROR) < 1e-6) + val = VCFConstants.MISSING_VALUE_v4; + else { + val = getQualValue(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL)); + } + } else if ( key.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) { + val = g.isFiltered() ? ParsingUtils.join(";", ParsingUtils.sortList(g.getFilters())) : (g.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED); + } + + VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(key); + if ( metaData != null ) { + int numInFormatField = metaData.getCount(); + if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) { + // If we have a missing field but multiple values are expected, we need to construct a new string with all fields. + // For example, if Number=2, the string has to be ".,." + StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4); + for ( int i = 1; i < numInFormatField; i++ ) { + sb.append(","); + sb.append(VCFConstants.MISSING_VALUE_v4); + } + val = sb.toString(); + } + } + + // assume that if key is absent, then the given string encoding suffices + String outputValue = formatVCFField(val); + if ( outputValue != null ) + attrs.add(outputValue); + } + + // strip off trailing missing values + for (int i = attrs.size()-1; i >= 0; i--) { + if ( isMissingValue(attrs.get(i)) ) + attrs.remove(i); + else + break; + } + + for (String s : attrs ) { + mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR); + mWriter.write(s); + } + } + } + + private boolean isMissingValue(String s) { + // we need to deal with the case that it's a list of missing values + return (countOccurrences(VCFConstants.MISSING_VALUE_v4.charAt(0), s) + countOccurrences(',', s) == s.length()); + } + + private void writeAllele(Allele allele, Map alleleMap) throws IOException { + String encoding = alleleMap.get(allele); + if ( encoding == null ) + throw new TribbleException.InternalCodecException("Allele " + allele + " is not an allele in the variant context"); + mWriter.write(encoding); + } + + private static String formatVCFField(Object val) { + String result; + if ( val == null ) + result = VCFConstants.MISSING_VALUE_v4; + else if ( val instanceof Double ) + result = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, (Double)val); + else if ( val instanceof Boolean ) + result = (Boolean)val ? "" : null; // empty string for true, null for false + else if ( val instanceof List ) { + result = formatVCFField(((List)val).toArray()); + } else if ( val.getClass().isArray() ) { + int length = Array.getLength(val); + if ( length == 0 ) + return formatVCFField(null); + StringBuffer sb = new StringBuffer(formatVCFField(Array.get(val, 0))); + for ( int i = 1; i < length; i++) { + sb.append(","); + sb.append(formatVCFField(Array.get(val, i))); + } + result = sb.toString(); + } else + result = val.toString(); + + return result; + } + + private static List calcVCFGenotypeKeys(VariantContext vc) { + Set keys = new HashSet(); + + boolean sawGoodQual = false; + boolean sawGenotypeFilter = false; + for ( Genotype g : vc.getGenotypes().values() ) { + keys.addAll(g.getAttributes().keySet()); + if ( g.hasNegLog10PError() ) + sawGoodQual = true; + if (g.isFiltered() && g.isCalled()) + sawGenotypeFilter = true; + } + + if ( sawGoodQual ) + keys.add(VCFConstants.GENOTYPE_QUALITY_KEY); + + if (sawGenotypeFilter) + keys.add(VCFConstants.GENOTYPE_FILTER_KEY); + + return ParsingUtils.sortList(new ArrayList(keys)); + } + + + public static int countOccurrences(char c, String s) { + int count = 0; + for (int i = 0; i < s.length(); i++) { + count += s.charAt(i) == c ? 1 : 0; + } + return count; + } + +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java new file mode 100755 index 000000000..f3c99e963 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java @@ -0,0 +1,182 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broad.tribble.TribbleException; +import org.broad.tribble.readers.LineReader; +import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.io.IOException; +import java.util.*; + + +/** + * a feature codec for the VCF 3 specification. Our aim is to read in the records and convert to VariantContext as + * quickly as possible, relying on VariantContext to do the validation of any contradictory (or malformed) record parameters. + */ +public class VCF3Codec extends AbstractVCFCodec { + + /** + * @param reader the line reader to take header lines from + * @return the number of header lines + */ + public Object readHeader(LineReader reader) { + List headerStrings = new ArrayList(); + + String line; + try { + boolean foundHeaderVersion = false; + while ((line = reader.readLine()) != null) { + lineNo++; + if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { + String[] lineFields = line.substring(2).split("="); + if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { + if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) + throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version"); + foundHeaderVersion = true; + version = VCFHeaderVersion.toHeaderVersion(lineFields[1]); + if ( version != VCFHeaderVersion.VCF3_3 && version != VCFHeaderVersion.VCF3_2 ) + throw new TribbleException.InvalidHeader("This codec is strictly for VCFv3 and does not support " + lineFields[1]); + } + headerStrings.add(line); + } + else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) { + if (!foundHeaderVersion) { + throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version"); + } + return createHeader(headerStrings, line); + } + else { + throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file"); + } + + } + } catch (IOException e) { + throw new RuntimeException("IO Exception ", e); + } + throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file"); + } + + + /** + * parse the filter string, first checking to see if we already have parsed it in a previous attempt + * @param filterString the string to parse + * @return a set of the filters applied + */ + protected Set parseFilters(String filterString) { + + // null for unfiltered + if ( filterString.equals(VCFConstants.UNFILTERED) ) + return null; + + // empty set for passes filters + LinkedHashSet fFields = new LinkedHashSet(); + + if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) ) + return fFields; + + if ( filterString.length() == 0 ) + generateException("The VCF specification requires a valid filter status"); + + // do we have the filter string cached? + if ( filterHash.containsKey(filterString) ) + return filterHash.get(filterString); + + // otherwise we have to parse and cache the value + if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 ) + fFields.add(filterString); + else + fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR))); + + filterHash.put(filterString, fFields); + + return fFields; + } + + /** + * create a genotype map + * @param str the string + * @param alleles the list of alleles + * @param chr chrom + * @param pos position + * @return a mapping of sample name to genotype object + */ + public Map createGenotypeMap(String str, List alleles, String chr, int pos) { + if (genotypeParts == null) + genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS]; + + int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR); + + Map genotypes = new LinkedHashMap(nParts); + + // get the format keys + int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR); + + // cycle through the sample names + Iterator sampleNameIterator = header.getGenotypeSamples().iterator(); + + // clear out our allele mapping + alleleMap.clear(); + + // cycle through the genotype strings + for (int genotypeOffset = 1; genotypeOffset < nParts; genotypeOffset++) { + int GTValueSplitSize = ParsingUtils.split(genotypeParts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR); + + double GTQual = VariantContext.NO_NEG_LOG_10PERROR; + Set genotypeFilters = null; + Map gtAttributes = null; + String sampleName = sampleNameIterator.next(); + + // check to see if the value list is longer than the key list, which is a problem + if (nGTKeys < GTValueSplitSize) + generateException("There are too many keys for the sample " + sampleName + ", keys = " + parts[8] + ", values = " + parts[genotypeOffset]); + + int genotypeAlleleLocation = -1; + if (nGTKeys >= 1) { + gtAttributes = new HashMap(nGTKeys - 1); + + for (int i = 0; i < nGTKeys; i++) { + final String gtKey = new String(genotypeKeyArray[i]); + boolean missing = i >= GTValueSplitSize; + + if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) { + if (i != 0) + generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes"); + genotypeAlleleLocation = i; + } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) { + GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]); + } else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) { + genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i])); + } else if ( missing || GTValueArray[i].equals(VCFConstants.MISSING_GENOTYPE_QUALITY_v3) ) { + gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4); + } else { + gtAttributes.put(gtKey, new String(GTValueArray[i])); + } + } + } + + // check to make sure we found a gentoype field + if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field"); + + // todo -- assuming allele list length in the single digits is bad. Fix me. + // Check for > 1 for haploid genotypes + boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|'; + + // add it to the list + try { + genotypes.put(sampleName, new Genotype(sampleName, + parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap), + GTQual, + genotypeFilters, + gtAttributes, + phased)); + } catch (TribbleException e) { + throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos); + } + } + + return genotypes; + } + +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java new file mode 100755 index 000000000..0fb2940bb --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java @@ -0,0 +1,188 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broad.tribble.TribbleException; +import org.broad.tribble.readers.LineReader; +import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +import java.io.IOException; +import java.util.*; + + +/** + * a feature codec for the VCF 4 specification. Our aim is to read in the records and convert to VariantContext as + * quickly as possible, relying on VariantContext to do the validation of any contradictory (or malformed) record parameters. + */ +public class VCFCodec extends AbstractVCFCodec { + + /** + * @param reader the line reader to take header lines from + * @return the number of header lines + */ + public Object readHeader(LineReader reader) { + List headerStrings = new ArrayList(); + + String line; + try { + boolean foundHeaderVersion = false; + while ((line = reader.readLine()) != null) { + lineNo++; + if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { + String[] lineFields = line.substring(2).split("="); + if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { + if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) + throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version"); + foundHeaderVersion = true; + version = VCFHeaderVersion.toHeaderVersion(lineFields[1]); + if ( version == VCFHeaderVersion.VCF3_3 || version == VCFHeaderVersion.VCF3_2 ) + throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4; please use the VCF3 codec for " + lineFields[1]); + if ( version != VCFHeaderVersion.VCF4_0 && version != VCFHeaderVersion.VCF4_1 ) + throw new TribbleException.InvalidHeader("This codec is strictly for VCFv4 and does not support " + lineFields[1]); + } + headerStrings.add(line); + } + else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) { + if (!foundHeaderVersion) { + throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version"); + } + return createHeader(headerStrings, line); + } + else { + throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file"); + } + + } + } catch (IOException e) { + throw new RuntimeException("IO Exception ", e); + } + throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file"); + } + + + /** + * parse the filter string, first checking to see if we already have parsed it in a previous attempt + * + * @param filterString the string to parse + * @return a set of the filters applied or null if filters were not applied to the record (e.g. as per the missing value in a VCF) + */ + protected Set parseFilters(String filterString) { + + // null for unfiltered + if ( filterString.equals(VCFConstants.UNFILTERED) ) + return null; + + // empty set for passes filters + LinkedHashSet fFields = new LinkedHashSet(); + + if ( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) + return fFields; + if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) ) + generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4"); + if ( filterString.length() == 0 ) + generateException("The VCF specification requires a valid filter status"); + + // do we have the filter string cached? + if ( filterHash.containsKey(filterString) ) + return filterHash.get(filterString); + + // otherwise we have to parse and cache the value + if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 ) + fFields.add(filterString); + else + fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR))); + + filterHash.put(filterString, fFields); + + return fFields; + } + + + /** + * create a genotype map + * @param str the string + * @param alleles the list of alleles + * @return a mapping of sample name to genotype object + */ + public Map createGenotypeMap(String str, List alleles, String chr, int pos) { + if (genotypeParts == null) + genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS]; + + int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR); + + Map genotypes = new LinkedHashMap(nParts); + + // get the format keys + int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR); + + // cycle through the sample names + Iterator sampleNameIterator = header.getGenotypeSamples().iterator(); + + // clear out our allele mapping + alleleMap.clear(); + + // cycle through the genotype strings + for (int genotypeOffset = 1; genotypeOffset < nParts; genotypeOffset++) { + int GTValueSplitSize = ParsingUtils.split(genotypeParts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR); + + double GTQual = VariantContext.NO_NEG_LOG_10PERROR; + Set genotypeFilters = null; + Map gtAttributes = null; + String sampleName = sampleNameIterator.next(); + + // check to see if the value list is longer than the key list, which is a problem + if (nGTKeys < GTValueSplitSize) + generateException("There are too many keys for the sample " + sampleName + ", keys = " + parts[8] + ", values = " + parts[genotypeOffset]); + + int genotypeAlleleLocation = -1; + if (nGTKeys >= 1) { + gtAttributes = new HashMap(nGTKeys - 1); + + for (int i = 0; i < nGTKeys; i++) { + final String gtKey = new String(genotypeKeyArray[i]); + boolean missing = i >= GTValueSplitSize; + + // todo -- all of these on the fly parsing of the missing value should be static constants + if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) { + if (i != 0) + generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes"); + genotypeAlleleLocation = i; + } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) { + GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]); + } else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) { + genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i])); + } else if ( missing ) { + gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4); + } else { + gtAttributes.put(gtKey, new String(GTValueArray[i])); + } + } + } + + // check to make sure we found a gentoype field + // TODO -- This is no longer required in v4.1 + if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field"); + + // todo -- assuming allele list length in the single digits is bad. Fix me. + // Check for > 1 for haploid genotypes + boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|'; + + // add it to the list + try { + genotypes.put(sampleName, new Genotype(sampleName, + parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap), + GTQual, + genotypeFilters, + gtAttributes, + phased)); + } catch (TribbleException e) { + throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos); + } + } + + return genotypes; + } + + +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java new file mode 100755 index 000000000..a799161ad --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java @@ -0,0 +1,164 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +import java.util.Arrays; +import java.util.LinkedHashMap; +import java.util.Map; + +/** + * a base class for compound header lines, which include info lines and format lines (so far) + */ +public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine { + public enum SupportedHeaderLineType { + INFO(true), FORMAT(false); + + public final boolean allowFlagValues; + SupportedHeaderLineType(boolean flagValues) { + allowFlagValues = flagValues; + } + } + + // the field types + private String name; + private int count; + private String description; + private VCFHeaderLineType type; + + // access methods + public String getName() { return name; } + public int getCount() { return count; } + public String getDescription() { return description; } + public VCFHeaderLineType getType() { return type; } + + // + public void setNumberToUnbounded() { this.count = UNBOUNDED; } + + // our type of line, i.e. format, info, etc + private final SupportedHeaderLineType lineType; + + // line numerical values are allowed to be unbounded (or unknown), which is + // marked with a dot (.) + public static final int UNBOUNDED = -1; // the value we store internally for unbounded types + + /** + * create a VCF format header line + * + * @param name the name for this header line + * @param count the count for this header line + * @param type the type for this header line + * @param description the description for this header line + */ + protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) { + super(lineType.toString(), ""); + this.name = name; + this.count = count; + this.type = type; + this.description = description; + this.lineType = lineType; + validate(); + } + + /** + * create a VCF format header line + * + * @param line the header line + * @param version the VCF header version + * + */ + protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) { + super(lineType.toString(), ""); + Map mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description")); + name = mapping.get("ID"); + count = (version == VCFHeaderVersion.VCF4_0 || version == VCFHeaderVersion.VCF4_1) ? + mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v4) ? UNBOUNDED : Integer.valueOf(mapping.get("Number")) : + mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v3) ? UNBOUNDED : Integer.valueOf(mapping.get("Number")); + type = VCFHeaderLineType.valueOf(mapping.get("Type")); + if (type == VCFHeaderLineType.Flag && !allowFlagValues()) + throw new IllegalArgumentException("Flag is an unsupported type for this kind of field"); + + description = mapping.get("Description"); + if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided + description = UNBOUND_DESCRIPTION; + + this.lineType = lineType; + + validate(); + } + + private void validate() { + if ( name == null || type == null || description == null || lineType == null ) + throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s type=%s desc=%s lineType=%s", + super.getKey(), name, type, description, lineType )); + } + + /** + * make a string representation of this header line + * @return a string representation + */ + protected String toStringEncoding() { + Map map = new LinkedHashMap(); + map.put("ID", name); + map.put("Number", count == UNBOUNDED ? VCFConstants.UNBOUNDED_ENCODING_v4 : count); + map.put("Type", type); + map.put("Description", description); + return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map); + } + + /** + * returns true if we're equal to another compounder header line + * @param o a compound header line + * @return true if equal + */ + public boolean equals(Object o) { + if ( !(o instanceof VCFCompoundHeaderLine) ) + return false; + VCFCompoundHeaderLine other = (VCFCompoundHeaderLine)o; + return name.equals(other.name) && + count == other.count && + description.equals(other.description) && + type == other.type && + lineType == other.lineType; + } + + public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) { + return count == other.count && + type == other.type && + lineType == other.lineType && + name.equals(other.name); + } + + public boolean sameLineTypeAndName(VCFCompoundHeaderLine other) { + return lineType == other.lineType && + name.equals(other.name); + } + + /** + * do we allow flag (boolean) values? (i.e. booleans where you don't have specify the value, AQ means AQ=true) + * @return true if we do, false otherwise + */ + abstract boolean allowFlagValues(); + +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java new file mode 100755 index 000000000..695c46c27 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java @@ -0,0 +1,109 @@ +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +import java.util.Locale; + +public final class VCFConstants { + public static final Locale VCF_LOCALE = Locale.US; + + // reserved INFO/FORMAT field keys + public static final String ANCESTRAL_ALLELE_KEY = "AA"; + public static final String ALLELE_COUNT_KEY = "AC"; + public static final String ALLELE_FREQUENCY_KEY = "AF"; + public static final String ALLELE_NUMBER_KEY = "AN"; + public static final String RMS_BASE_QUALITY_KEY = "BQ"; + public static final String CIGAR_KEY = "CIGAR"; + public static final String DBSNP_KEY = "DB"; + public static final String DEPTH_KEY = "DP"; + public static final String DOWNSAMPLED_KEY = "DS"; + public static final String EXPECTED_ALLELE_COUNT_KEY = "EC"; + public static final String END_KEY = "END"; + public static final String GENOTYPE_FILTER_KEY = "FT"; + public static final String GENOTYPE_KEY = "GT"; + @Deprecated + public static final String GENOTYPE_LIKELIHOODS_KEY = "GL"; // log10 scaled genotype likelihoods + public static final String GENOTYPE_POSTERIORS_KEY = "GP"; + public static final String GENOTYPE_QUALITY_KEY = "GQ"; + public static final String HAPMAP2_KEY = "H2"; + public static final String HAPMAP3_KEY = "H3"; + public static final String HAPLOTYPE_QUALITY_KEY = "HQ"; + public static final String RMS_MAPPING_QUALITY_KEY = "MQ"; + public static final String MAPPING_QUALITY_ZERO_KEY = "MQ0"; + public static final String SAMPLE_NUMBER_KEY = "NS"; + public static final String PHRED_GENOTYPE_LIKELIHOODS_KEY = "PL"; // phred-scaled genotype likelihoods + public static final String PHASE_QUALITY_KEY = "PQ"; + public static final String PHASE_SET_KEY = "PS"; + public static final String OLD_DEPTH_KEY = "RD"; + public static final String STRAND_BIAS_KEY = "SB"; + public static final String SOMATIC_KEY = "SOMATIC"; + public static final String VALIDATED_KEY = "VALIDATED"; + public static final String THOUSAND_GENOMES_KEY = "1000G"; + + // separators + public static final String FORMAT_FIELD_SEPARATOR = ":"; + public static final String GENOTYPE_FIELD_SEPARATOR = ":"; + public static final char GENOTYPE_FIELD_SEPARATOR_CHAR = ':'; + public static final String FIELD_SEPARATOR = "\t"; + public static final char FIELD_SEPARATOR_CHAR = '\t'; + public static final String FILTER_CODE_SEPARATOR = ";"; + public static final String INFO_FIELD_ARRAY_SEPARATOR = ","; + public static final String ID_FIELD_SEPARATOR = ";"; + public static final String INFO_FIELD_SEPARATOR = ";"; + public static final char INFO_FIELD_SEPARATOR_CHAR = ';'; + public static final String UNPHASED = "/"; + public static final String PHASED = "|"; + public static final String PHASED_SWITCH_PROB_v3 = "\\"; + public static final String PHASING_TOKENS = "/|\\"; + + // old indel alleles + public static final char DELETION_ALLELE_v3 = 'D'; + public static final char INSERTION_ALLELE_v3 = 'I'; + + // missing/default values + public static final String UNFILTERED = "."; + public static final String PASSES_FILTERS_v3 = "0"; + public static final String PASSES_FILTERS_v4 = "PASS"; + public static final String EMPTY_ID_FIELD = "."; + public static final String EMPTY_INFO_FIELD = "."; + public static final String EMPTY_ALTERNATE_ALLELE_FIELD = "."; + public static final String MISSING_VALUE_v4 = "."; + public static final String MISSING_QUALITY_v3 = "-1"; + public static final Double MISSING_QUALITY_v3_DOUBLE = Double.valueOf(MISSING_QUALITY_v3); + + public static final String MISSING_GENOTYPE_QUALITY_v3 = "-1"; + public static final String MISSING_HAPLOTYPE_QUALITY_v3 = "-1"; + public static final String MISSING_DEPTH_v3 = "-1"; + public static final String UNBOUNDED_ENCODING_v4 = "."; + public static final String UNBOUNDED_ENCODING_v3 = "-1"; + public static final String EMPTY_ALLELE = "."; + public static final String EMPTY_GENOTYPE = "./."; + public static final double MAX_GENOTYPE_QUAL = 99.0; + + public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f"; + public static final String DOUBLE_PRECISION_INT_SUFFIX = ".00"; + public static final Double VCF_ENCODING_EPSILON = 0.00005; // when we consider fields equal(), used in the Qual compare +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java new file mode 100755 index 000000000..9176fc16e --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java @@ -0,0 +1,70 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import java.util.Arrays; +import java.util.LinkedHashMap; +import java.util.Map; + + +/** + * @author ebanks + * A class representing a key=value entry for FILTER fields in the VCF header + */ +public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine { + + private String name; + private String description; + + + /** + * create a VCF filter header line + * + * @param name the name for this header line + * @param description the description for this header line + */ + public VCFFilterHeaderLine(String name, String description) { + super("FILTER", ""); + this.name = name; + this.description = description; + + if ( name == null || description == null ) + throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description )); + } + + /** + * create a VCF info header line + * + * @param line the header line + * @param version the vcf header version + */ + protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) { + super("FILTER", ""); + Map mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description")); + name = mapping.get("ID"); + description = mapping.get("Description"); + if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided + description = UNBOUND_DESCRIPTION; + } + + protected String toStringEncoding() { + Map map = new LinkedHashMap(); + map.put("ID", name); + map.put("Description", description); + return "FILTER=" + VCFHeaderLine.toStringEncoding(map); + } + + public boolean equals(Object o) { + if ( !(o instanceof VCFFilterHeaderLine) ) + return false; + VCFFilterHeaderLine other = (VCFFilterHeaderLine)o; + return name.equals(other.name) && + description.equals(other.description); + } + + public String getName() { + return name; + } + + public String getDescription() { + return description; + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java new file mode 100755 index 000000000..352be3e97 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java @@ -0,0 +1,28 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + + +/** + * @author ebanks + *

+ * Class VCFFormatHeaderLine + *

+ * A class representing a key=value entry for genotype FORMAT fields in the VCF header + */ +public class VCFFormatHeaderLine extends VCFCompoundHeaderLine { + + public VCFFormatHeaderLine(String name, int count, VCFHeaderLineType type, String description) { + super(name, count, type, description, SupportedHeaderLineType.FORMAT); + if (type == VCFHeaderLineType.Flag) + throw new IllegalArgumentException("Flag is an unsupported type for format fields"); + } + + protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) { + super(line, version, SupportedHeaderLineType.FORMAT); + } + + // format fields do not allow flag values (that wouldn't make much sense, how would you encode this in the genotype). + @Override + boolean allowFlagValues() { + return false; + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java new file mode 100755 index 000000000..eb01e5dca --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java @@ -0,0 +1,191 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + + +import org.broad.tribble.util.ParsingUtils; + +import java.util.*; + + +/** + * @author aaron + *

+ * Class VCFHeader + *

+ * A class representing the VCF header + */ +public class VCFHeader { + + // the mandatory header fields + public enum HEADER_FIELDS { + CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO + } + + // the associated meta data + private final Set mMetaData; + private final Map mInfoMetaData = new HashMap(); + private final Map mFormatMetaData = new HashMap(); + + // the list of auxillary tags + private final Set mGenotypeSampleNames = new LinkedHashSet(); + + // the character string that indicates meta data + public static final String METADATA_INDICATOR = "##"; + + // the header string indicator + public static final String HEADER_INDICATOR = "#"; + + /** do we have genotying data? */ + private boolean hasGenotypingData = false; + + // were the input samples sorted originally (or are we sorting them)? + private boolean samplesWereAlreadySorted = true; + + + /** + * create a VCF header, given a list of meta data and auxillary tags + * + * @param metaData the meta data associated with this header + */ + public VCFHeader(Set metaData) { + mMetaData = new TreeSet(metaData); + loadVCFVersion(); + loadMetaDataMaps(); + } + + /** + * create a VCF header, given a list of meta data and auxillary tags + * + * @param metaData the meta data associated with this header + * @param genotypeSampleNames the genotype format field, and the sample names + */ + public VCFHeader(Set metaData, Set genotypeSampleNames) { + mMetaData = new TreeSet(); + if ( metaData != null ) + mMetaData.addAll(metaData); + for (String col : genotypeSampleNames) { + if (!col.equals("FORMAT")) + mGenotypeSampleNames.add(col); + } + if (genotypeSampleNames.size() > 0) hasGenotypingData = true; + loadVCFVersion(); + loadMetaDataMaps(); + + samplesWereAlreadySorted = ParsingUtils.isSorted(genotypeSampleNames); + } + + /** + * Adds a header line to the header metadata. + * + * @param headerLine Line to add to the existing metadata component. + */ + public void addMetaDataLine(VCFHeaderLine headerLine) { + mMetaData.add(headerLine); + } + + /** + * check our metadata for a VCF version tag, and throw an exception if the version is out of date + * or the version is not present + */ + public void loadVCFVersion() { + List toRemove = new ArrayList(); + for ( VCFHeaderLine line : mMetaData ) + if ( VCFHeaderVersion.isFormatString(line.getKey())) { + toRemove.add(line); + } + // remove old header lines for now, + mMetaData.removeAll(toRemove); + + } + + /** + * load the format/info meta data maps (these are used for quick lookup by key name) + */ + private void loadMetaDataMaps() { + for ( VCFHeaderLine line : mMetaData ) { + if ( line instanceof VCFInfoHeaderLine ) { + VCFInfoHeaderLine infoLine = (VCFInfoHeaderLine)line; + mInfoMetaData.put(infoLine.getName(), infoLine); + } + else if ( line instanceof VCFFormatHeaderLine ) { + VCFFormatHeaderLine formatLine = (VCFFormatHeaderLine)line; + mFormatMetaData.put(formatLine.getName(), formatLine); + } + } + } + + /** + * get the header fields in order they're presented in the input file (which is now required to be + * the order presented in the spec). + * + * @return a set of the header fields, in order + */ + public Set getHeaderFields() { + Set fields = new LinkedHashSet(); + for (HEADER_FIELDS field : HEADER_FIELDS.values()) + fields.add(field); + return fields; + } + + /** + * get the meta data, associated with this header + * + * @return a set of the meta data + */ + public Set getMetaData() { + Set lines = new LinkedHashSet(); + lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_0.getFormatString(), VCFHeaderVersion.VCF4_0.getVersionString())); + lines.addAll(mMetaData); + return Collections.unmodifiableSet(lines); + } + + /** + * get the genotyping sample names + * + * @return a list of the genotype column names, which may be empty if hasGenotypingData() returns false + */ + public Set getGenotypeSamples() { + return mGenotypeSampleNames; + } + + /** + * do we have genotyping data? + * + * @return true if we have genotyping columns, false otherwise + */ + public boolean hasGenotypingData() { + return hasGenotypingData; + } + + /** + * were the input samples sorted originally? + * + * @return true if the input samples were sorted originally, false otherwise + */ + public boolean samplesWereAlreadySorted() { + return samplesWereAlreadySorted; + } + + /** @return the column count */ + public int getColumnCount() { + return HEADER_FIELDS.values().length + ((hasGenotypingData) ? mGenotypeSampleNames.size() + 1 : 0); + } + + /** + * @param key the header key name + * @return the meta data line, or null if there is none + */ + public VCFInfoHeaderLine getInfoHeaderLine(String key) { + return mInfoMetaData.get(key); + } + + /** + * @param key the header key name + * @return the meta data line, or null if there is none + */ + public VCFFormatHeaderLine getFormatHeaderLine(String key) { + return mFormatMetaData.get(key); + } +} + + + diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java new file mode 100755 index 000000000..162c34d80 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java @@ -0,0 +1,134 @@ +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broad.tribble.TribbleException; + +import java.util.Map; + + +/** + * @author ebanks + *

+ * Class VCFHeaderLine + *

+ * A class representing a key=value entry in the VCF header + */ +public class VCFHeaderLine implements Comparable { + protected static boolean ALLOW_UNBOUND_DESCRIPTIONS = true; + protected static String UNBOUND_DESCRIPTION = "Not provided in original VCF header"; + + private String mKey = null; + private String mValue = null; + + + /** + * create a VCF header line + * + * @param key the key for this header line + * @param value the value for this header line + */ + public VCFHeaderLine(String key, String value) { + if ( key == null ) + throw new IllegalArgumentException("VCFHeaderLine: key cannot be null: key = " + key); + mKey = key; + mValue = value; + } + + /** + * Get the key + * + * @return the key + */ + public String getKey() { + return mKey; + } + + /** + * Get the value + * + * @return the value + */ + public String getValue() { + return mValue; + } + + public String toString() { + return toStringEncoding(); + } + + /** + * Should be overloaded in sub classes to do subclass specific + * + * @return the string encoding + */ + protected String toStringEncoding() { + return mKey + "=" + mValue; + } + + public boolean equals(Object o) { + if ( !(o instanceof VCFHeaderLine) ) + return false; + return mKey.equals(((VCFHeaderLine)o).getKey()) && mValue.equals(((VCFHeaderLine)o).getValue()); + } + + public int compareTo(Object other) { + return toString().compareTo(other.toString()); + } + + /** + * @param line the line + * @return true if the line is a VCF meta data line, or false if it is not + */ + public static boolean isHeaderLine(String line) { + return line != null && line.length() > 0 && VCFHeader.HEADER_INDICATOR.equals(line.substring(0,1)); + } + + /** + * create a string of a mapping pair for the target VCF version + * @param keyValues a mapping of the key->value pairs to output + * @return a string, correctly formatted + */ + public static String toStringEncoding(Map keyValues) { + StringBuilder builder = new StringBuilder(); + builder.append("<"); + boolean start = true; + for (Map.Entry entry : keyValues.entrySet()) { + if (start) start = false; + else builder.append(","); + + if ( entry.getValue() == null ) throw new TribbleException.InternalCodecException("Header problem: unbound value at " + entry + " from " + keyValues); + + builder.append(entry.getKey()); + builder.append("="); + builder.append(entry.getValue().toString().contains(",") || + entry.getValue().toString().contains(" ") || + entry.getKey().equals("Description") ? "\""+ entry.getValue() + "\"" : entry.getValue()); + } + builder.append(">"); + return builder.toString(); + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java new file mode 100755 index 000000000..16f2a3d5a --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java @@ -0,0 +1,124 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import java.util.*; + +/** + * A class for translating between vcf header versions + */ +public class VCFHeaderLineTranslator { + private static Map mapping; + + static { + mapping = new HashMap(); + mapping.put(VCFHeaderVersion.VCF4_0,new VCF4Parser()); + mapping.put(VCFHeaderVersion.VCF4_1,new VCF4Parser()); + mapping.put(VCFHeaderVersion.VCF3_3,new VCF3Parser()); + mapping.put(VCFHeaderVersion.VCF3_2,new VCF3Parser()); + } + + public static Map parseLine(VCFHeaderVersion version, String valueLine, List expectedTagOrder) { + return mapping.get(version).parseLine(valueLine,expectedTagOrder); + } +} + + +interface VCFLineParser { + public Map parseLine(String valueLine, List expectedTagOrder); +} + + +/** + * a class that handles the to and from disk for VCF 4 lines + */ +class VCF4Parser implements VCFLineParser { + Set bracketed = new HashSet(); + + /** + * parse a VCF4 line + * @param valueLine the line + * @return a mapping of the tags parsed out + */ + public Map parseLine(String valueLine, List expectedTagOrder) { + // our return map + Map ret = new LinkedHashMap(); + + // a builder to store up characters as we go + StringBuilder builder = new StringBuilder(); + + // store the key when we're parsing out the values + String key = ""; + + // where are we in the stream of characters? + int index = 0; + + // are we inside a quotation? we don't special case ',' then + boolean inQuote = false; + + // a little switch machine to parse out the tags. Regex ended up being really complicated and ugly [yes, but this machine is getting ugly now... MAD] + for (char c: valueLine.toCharArray()) { + if ( c == '\"' ) { + inQuote = ! inQuote; + } else if ( inQuote ) { + builder.append(c); + } else { + switch (c) { + case ('<') : if (index == 0) break; // if we see a open bracket at the beginning, ignore it + case ('>') : if (index == valueLine.length()-1) ret.put(key,builder.toString().trim()); break; // if we see a close bracket, and we're at the end, add an entry to our list + case ('=') : key = builder.toString().trim(); builder = new StringBuilder(); break; // at an equals, copy the key and reset the builder + case (',') : ret.put(key,builder.toString().trim()); builder = new StringBuilder(); break; // drop the current key value to the return map + default: builder.append(c); // otherwise simply append to the current string + } + } + + index++; + } + + // validate the tags against the expected list + index = 0; + if (ret.size() > expectedTagOrder.size()) throw new IllegalArgumentException("Unexpected tag count " + ret.size() + " in string " + expectedTagOrder.size()); + for (String str : ret.keySet()) { + if (!expectedTagOrder.get(index).equals(str)) throw new IllegalArgumentException("Unexpected tag " + str + " in string " + valueLine); + index++; + } + return ret; + } +} + +class VCF3Parser implements VCFLineParser { + + public Map parseLine(String valueLine, List expectedTagOrder) { + // our return map + Map ret = new LinkedHashMap(); + + // a builder to store up characters as we go + StringBuilder builder = new StringBuilder(); + + // where are we in the stream of characters? + int index = 0; + // where in the expected tag order are we? + int tagIndex = 0; + + // are we inside a quotation? we don't special case ',' then + boolean inQuote = false; + + // a little switch machine to parse out the tags. Regex ended up being really complicated and ugly + for (char c: valueLine.toCharArray()) { + switch (c) { + case ('\"') : inQuote = !inQuote; break; // a quote means we ignore ',' in our strings, keep track of it + case (',') : if (!inQuote) { ret.put(expectedTagOrder.get(tagIndex++),builder.toString()); builder = new StringBuilder(); break; } // drop the current key value to the return map + default: builder.append(c); // otherwise simply append to the current string + } + index++; + } + ret.put(expectedTagOrder.get(tagIndex++),builder.toString()); + + // validate the tags against the expected list + index = 0; + if (tagIndex != expectedTagOrder.size()) throw new IllegalArgumentException("Unexpected tag count " + tagIndex + ", we expected " + expectedTagOrder.size()); + for (String str : ret.keySet()){ + if (!expectedTagOrder.get(index).equals(str)) throw new IllegalArgumentException("Unexpected tag " + str + " in string " + valueLine); + index++; + } + return ret; + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java new file mode 100755 index 000000000..83e272415 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java @@ -0,0 +1,8 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +/** + * the type encodings we use for fields in VCF header lines + */ +public enum VCFHeaderLineType { + Integer, Float, String, Character, Flag; +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java new file mode 100755 index 000000000..c65ce17b9 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java @@ -0,0 +1,91 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broad.tribble.TribbleException; + +/** + * information that identifies each header version + */ +public enum VCFHeaderVersion { + VCF3_2("VCRv3.2","format"), + VCF3_3("VCFv3.3","fileformat"), + VCF4_0("VCFv4.0","fileformat"), + VCF4_1("VCFv4.1","fileformat"); + + private final String versionString; + private final String formatString; + + /** + * create the enum, privately, using: + * @param vString the version string + * @param fString the format string + */ + VCFHeaderVersion(String vString, String fString) { + this.versionString = vString; + this.formatString = fString; + } + + /** + * get the header version + * @param version the version string + * @return a VCFHeaderVersion object + */ + public static VCFHeaderVersion toHeaderVersion(String version) { + version = clean(version); + for (VCFHeaderVersion hv : VCFHeaderVersion.values()) + if (hv.versionString.equals(version)) + return hv; + return null; + } + + /** + * are we a valid version string of some type + * @param version the version string + * @return true if we're valid of some type, false otherwise + */ + public static boolean isVersionString(String version){ + return toHeaderVersion(version) != null; + } + + /** + * are we a valid format string for some type + * @param format the format string + * @return true if we're valid of some type, false otherwise + */ + public static boolean isFormatString(String format){ + format = clean(format); + for (VCFHeaderVersion hv : VCFHeaderVersion.values()) + if (hv.formatString.equals(format)) + return true; + return false; + } + + public static VCFHeaderVersion getHeaderVersion(String versionLine) { + String[] lineFields = versionLine.split("="); + if ( lineFields.length != 2 || !isFormatString(lineFields[0].substring(2)) ) + throw new TribbleException.InvalidHeader(versionLine + " is not a valid VCF version line"); + + if ( !isVersionString(lineFields[1]) ) + throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version"); + + return toHeaderVersion(lineFields[1]); + } + + /** + * Utility function to clean up a VCF header string + * + * @param s string + * @return trimmed version of s + */ + private static String clean(String s) { + return s.trim(); + } + + + public String getVersionString() { + return versionString; + } + + public String getFormatString() { + return formatString; + } +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java new file mode 100755 index 000000000..135a5c1a1 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java @@ -0,0 +1,25 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + + +/** + * @author ebanks + *

+ * Class VCFInfoHeaderLine + *

+ * A class representing a key=value entry for INFO fields in the VCF header + */ +public class VCFInfoHeaderLine extends VCFCompoundHeaderLine { + public VCFInfoHeaderLine(String name, int count, VCFHeaderLineType type, String description) { + super(name, count, type, description, SupportedHeaderLineType.INFO); + } + + protected VCFInfoHeaderLine(String line, VCFHeaderVersion version) { + super(line, version, SupportedHeaderLineType.INFO); + } + + // info fields allow flag values + @Override + boolean allowFlagValues() { + return true; + } +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java new file mode 100755 index 000000000..f78e936b2 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java @@ -0,0 +1,30 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.vcf; + +/** an interface for named header lines **/ +public interface VCFNamedHeaderLine { + String getName(); +} diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java new file mode 100755 index 000000000..dac996494 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java @@ -0,0 +1,23 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import java.util.*; + + +/** + * All VCF codecs need to implement this interface so that we can perform lazy loading. + */ +public interface VCFParser { + + /** + * create a genotype map + * @param str the string + * @param alleles the list of alleles + * @param chr chrom + * @param pos position + * @return a mapping of sample name to genotype object + */ + public Map createGenotypeMap(String str, List alleles, String chr, int pos); + +} diff --git a/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java similarity index 97% rename from java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java rename to java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java index 08de5bf56..e919d5c25 100755 --- a/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java @@ -23,13 +23,11 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.vcf; +package org.broadinstitute.sting.utils.codecs.vcf; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.apache.log4j.Logger; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java new file mode 100755 index 000000000..0d23fe455 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java @@ -0,0 +1,18 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +/** + * this class writes VCF files + */ +public interface VCFWriter { + + public void writeHeader(VCFHeader header); + + /** + * attempt to close the VCF file + */ + public void close(); + + public void add(VariantContext vc, byte refBase); +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 3336eb34f..0be4bec91 100755 --- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -28,8 +28,8 @@ import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.GenomeLoc; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java index e22adc4a6..cb6557408 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java @@ -24,8 +24,8 @@ package org.broadinstitute.sting.utils.genotype; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java new file mode 100755 index 000000000..a9ba46159 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java @@ -0,0 +1,456 @@ +package org.broadinstitute.sting.utils.variantcontext; + +import java.util.Arrays; +import java.util.List; +import java.util.ArrayList; +import java.util.Collection; + +/** + * Immutable representation of an allele + * + * Types of alleles: + * + * Ref: a t C g a // C is the reference base + * + * : a t G g a // C base is a G in some individuals + * + * : a t - g a // C base is deleted w.r.t. the reference + * + * : a t CAg a // A base is inserted w.r.t. the reference sequence + * + * In these cases, where are the alleles? + * + * SNP polymorphism of C/G -> { C , G } -> C is the reference allele + * 1 base deletion of C -> { C , - } -> C is the reference allele + * 1 base insertion of A -> { - ; A } -> Null is the reference allele + * + * Suppose I see a the following in the population: + * + * Ref: a t C g a // C is the reference base + * : a t G g a // C base is a G in some individuals + * : a t - g a // C base is deleted w.r.t. the reference + * + * How do I represent this? There are three segregating alleles: + * + * { C , G , - } + * + * Now suppose I have this more complex example: + * + * Ref: a t C g a // C is the reference base + * : a t - g a + * : a t - - a + * : a t CAg a + * + * There are actually four segregating alleles: + * + * { C g , - g, - -, and CAg } over bases 2-4 + * + * However, the molecular equivalence explicitly listed above is usually discarded, so the actual + * segregating alleles are: + * + * { C g, g, -, C a g } + * + * Critically, it should be possible to apply an allele to a reference sequence to create the + * correct haplotype sequence: + * + * Allele + reference => haplotype + * + * For convenience, we are going to create Alleles where the GenomeLoc of the allele is stored outside of the + * Allele object itself. So there's an idea of an A/C polymorphism independent of it's surrounding context. + * + * Given list of alleles it's possible to determine the "type" of the variation + * + * A / C @ loc => SNP with + * - / A => INDEL + * + * If you know where allele is the reference, you can determine whether the variant is an insertion or deletion. + * + * Alelle also supports is concept of a NO_CALL allele. This Allele represents a haplotype that couldn't be + * determined. This is usually represented by a '.' allele. + * + * Note that Alleles store all bases as bytes, in **UPPER CASE**. So 'atc' == 'ATC' from the perspective of an + * Allele. + + * @author ebanks, depristo + */ +public class Allele implements Comparable { + private static final byte[] EMPTY_ALLELE_BASES = new byte[0]; + + private boolean isRef = false; + private boolean isNull = false; + private boolean isNoCall = false; + private boolean isSymbolic = false; + + private byte[] bases = null; + + public final static String NULL_ALLELE_STRING = "-"; + public final static String NO_CALL_STRING = "."; + /** A generic static NO_CALL allele for use */ + + // no public way to create an allele + private Allele(byte[] bases, boolean isRef) { + // standardize our representation of null allele and bases + if ( wouldBeNullAllele(bases) ) { + bases = EMPTY_ALLELE_BASES; + isNull = true; + } else if ( wouldBeNoCallAllele(bases) ) { + bases = EMPTY_ALLELE_BASES; + isNoCall = true; + if ( isRef ) throw new IllegalArgumentException("Cannot tag a NoCall allele as the reference allele"); + } else if ( wouldBeSymbolicAllele(bases) ) { + isSymbolic = true; + if ( isRef ) throw new IllegalArgumentException("Cannot tag a symbolic allele as the reference allele"); + } +// else +// bases = new String(bases).toUpperCase().getBytes(); // todo -- slow performance + + this.isRef = isRef; + this.bases = bases; + + if ( ! acceptableAlleleBases(bases) ) + throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases)); + } + + private Allele(String bases, boolean isRef) { + this(bases.getBytes(), isRef); + } + + + private final static Allele REF_A = new Allele("A", true); + private final static Allele ALT_A = new Allele("A", false); + private final static Allele REF_C = new Allele("C", true); + private final static Allele ALT_C = new Allele("C", false); + private final static Allele REF_G = new Allele("G", true); + private final static Allele ALT_G = new Allele("G", false); + private final static Allele REF_T = new Allele("T", true); + private final static Allele ALT_T = new Allele("T", false); + private final static Allele REF_N = new Allele("N", true); + private final static Allele ALT_N = new Allele("N", false); + private final static Allele REF_NULL = new Allele(NULL_ALLELE_STRING, true); + private final static Allele ALT_NULL = new Allele(NULL_ALLELE_STRING, false); + public final static Allele NO_CALL = new Allele(NO_CALL_STRING, false); + + // --------------------------------------------------------------------------------------------------------- + // + // creation routines + // + // --------------------------------------------------------------------------------------------------------- + + /** + * Create a new Allele that includes bases and if tagged as the reference allele if isRef == true. If bases + * == '-', a Null allele is created. If bases == '.', a no call Allele is created. + * + * @param bases the DNA sequence of this variation, '-', of '.' + * @param isRef should we make this a reference allele? + * @throws IllegalArgumentException if bases contains illegal characters or is otherwise malformated + */ + public static Allele create(byte[] bases, boolean isRef) { + if ( bases == null ) + throw new IllegalArgumentException("create: the Allele base string cannot be null; use new Allele() or new Allele(\"\") to create a Null allele"); + + if ( bases.length == 1 ) { + // optimization to return a static constant Allele for each single base object + switch (bases[0]) { + case '.': + if ( isRef ) throw new IllegalArgumentException("Cannot tag a NoCall allele as the reference allele"); + return NO_CALL; + case '-': return isRef ? REF_NULL : ALT_NULL; + case 'A': case 'a' : return isRef ? REF_A : ALT_A; + case 'C': case 'c' : return isRef ? REF_C : ALT_C; + case 'G': case 'g' : return isRef ? REF_G : ALT_G; + case 'T': case 't' : return isRef ? REF_T : ALT_T; + case 'N': case 'n' : return isRef ? REF_N : ALT_N; + default: throw new IllegalArgumentException("Illegal base: " + (char)bases[0]); + } + } else { + return new Allele(bases, isRef); + } + } + + public static Allele create(byte base, boolean isRef) { +// public Allele(byte base, boolean isRef) { + return create( new byte[]{ base }, isRef); + } + + public static Allele create(byte base) { + return create( base, false ); + } + + public static Allele extend(Allele left, byte[] right) { + if (left.isSymbolic()) + throw new IllegalArgumentException("Cannot extend a symbolic allele"); + byte[] bases = null; + if ( left.length() == 0 ) + bases = right; + else { + bases = new byte[left.length() + right.length]; + System.arraycopy(left.getBases(), 0, bases, 0, left.length()); + System.arraycopy(right, 0, bases, left.length(), right.length); + } + + return create(bases, left.isReference()); + } + + /** + * @param bases bases representing an allele + * @return true if the bases represent the null allele + */ + public static boolean wouldBeNullAllele(byte[] bases) { + return (bases.length == 1 && bases[0] == '-') || bases.length == 0; + } + + /** + * @param bases bases representing an allele + * @return true if the bases represent the NO_CALL allele + */ + public static boolean wouldBeNoCallAllele(byte[] bases) { + return bases.length == 1 && bases[0] == '.'; + } + + /** + * @param bases bases representing an allele + * @return true if the bases represent a symbolic allele + */ + public static boolean wouldBeSymbolicAllele(byte[] bases) { + return bases.length > 2 && bases[0] == '<' && bases[bases.length-1] == '>'; + } + + /** + * @param bases bases representing an allele + * @return true if the bases represent the well formatted allele + */ + public static boolean acceptableAlleleBases(String bases) { + return acceptableAlleleBases(bases.getBytes()); + } + + /** + * @param bases bases representing an allele + * @return true if the bases represent the well formatted allele + */ + public static boolean acceptableAlleleBases(byte[] bases) { + if ( wouldBeNullAllele(bases) || wouldBeNoCallAllele(bases) || wouldBeSymbolicAllele(bases) ) + return true; + + for ( int i = 0; i < bases.length; i++ ) { + switch (bases[i]) { + case 'A': case 'C': case 'G': case 'T': case 'N' : case 'a': case 'c': case 'g': case 't': case 'n' : + break; + default: + return false; + } + } + + return true; + } + + /** + * @see Allele(byte[], boolean) + * + * @param bases bases representing an allele + * @param isRef is this the reference allele? + */ + public static Allele create(String bases, boolean isRef) { + //public Allele(String bases, boolean isRef) { + return create(bases.getBytes(), isRef); + } + + + /** + * Creates a non-Ref allele. @see Allele(byte[], boolean) for full information + * + * @param bases bases representing an allele + */ + public static Allele create(String bases) { + return create(bases, false); + } + + /** + * Creates a non-Ref allele. @see Allele(byte[], boolean) for full information + * + * @param bases bases representing an allele + */ + public static Allele create(byte[] bases) { + return create(bases, false); + //this(bases, false); + } + + // --------------------------------------------------------------------------------------------------------- + // + // accessor routines + // + // --------------------------------------------------------------------------------------------------------- + + //Returns true if this is the null allele + public boolean isNull() { return isNull; } + // Returns true if this is not the null allele + public boolean isNonNull() { return ! isNull(); } + + // Returns true if this is the NO_CALL allele + public boolean isNoCall() { return isNoCall; } + // Returns true if this is not the NO_CALL allele + public boolean isCalled() { return ! isNoCall(); } + + // Returns true if this Allele is the reference allele + public boolean isReference() { return isRef; } + // Returns true if this Allele is not the reference allele + public boolean isNonReference() { return ! isReference(); } + + // Returns true if this Allele is symbolic (i.e. no well-defined base sequence) + public boolean isSymbolic() { return isSymbolic; } + + // Returns a nice string representation of this object + public String toString() { + return (isNull() ? NULL_ALLELE_STRING : ( isNoCall() ? NO_CALL_STRING : getDisplayString() )) + (isReference() ? "*" : ""); + } + + /** + * Return the DNA bases segregating in this allele. Note this isn't reference polarized, + * so the Null allele is represented by a vector of length 0 + * + * @return the segregating bases + */ + public byte[] getBases() { return isSymbolic ? EMPTY_ALLELE_BASES : bases; } + + /** + * Return the DNA bases segregating in this allele in String format. + * This is useful, because toString() adds a '*' to reference alleles and getBases() returns garbage when you call toString() on it. + * + * @return the segregating bases + */ + public String getBaseString() { return new String(getBases()); } + + /** + * Return the printed representation of this allele. + * Same as getBaseString(), except for symbolic alleles. + * For symbolic alleles, the base string is empty while the display string contains . + * + * @return the allele string representation + */ + public String getDisplayString() { return new String(bases); } + + /** + * @param other the other allele + * + * @return true if these alleles are equal + */ + public boolean equals(Object other) { + return ( ! (other instanceof Allele) ? false : equals((Allele)other, false) ); + } + + /** + * @return hash code + */ + public int hashCode() { + int hash = 1; + for (int i = 0; i < bases.length; i++) + hash += (i+1) * bases[i]; + return hash; + } + + /** + * Returns true if this and other are equal. If ignoreRefState is true, then doesn't require both alleles has the + * same ref tag + * + * @param other allele to compare to + * @param ignoreRefState if true, ignore ref state in comparison + * @return true if this and other are equal + */ + public boolean equals(Allele other, boolean ignoreRefState) { + return this == other || (isRef == other.isRef || ignoreRefState) && isNull == other.isNull && isNoCall == other.isNoCall && (bases == other.bases || Arrays.equals(bases, other.bases)); + } + + /** + * @param test bases to test against + * + * @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles + */ + public boolean basesMatch(byte[] test) { return !isSymbolic && (bases == test || Arrays.equals(bases, test)); } + + /** + * @param test bases to test against + * + * @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles + */ + public boolean basesMatch(String test) { return basesMatch(test.toUpperCase().getBytes()); } + + /** + * @param test allele to test against + * + * @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles + */ + public boolean basesMatch(Allele test) { return basesMatch(test.getBases()); } + + /** + * @return the length of this allele. Null and NO_CALL alleles have 0 length. + */ + public int length() { + return isSymbolic ? 0 : bases.length; + } + + // --------------------------------------------------------------------------------------------------------- + // + // useful static functions + // + // --------------------------------------------------------------------------------------------------------- + + public static Allele getMatchingAllele(Collection allAlleles, String alleleBases) { + return getMatchingAllele(allAlleles, alleleBases.getBytes()); + } + + public static Allele getMatchingAllele(Collection allAlleles, byte[] alleleBases) { + for ( Allele a : allAlleles ) { + if ( a.basesMatch(alleleBases) ) { + return a; + } + } + + if ( wouldBeNoCallAllele(alleleBases) ) + return NO_CALL; + else + return null; // couldn't find anything + } + + public static List resolveAlleles(List possibleAlleles, List alleleStrings) { + List myAlleles = new ArrayList(alleleStrings.size()); + + for ( String alleleString : alleleStrings ) { + Allele allele = getMatchingAllele(possibleAlleles, alleleString); + + if ( allele == null ) { + if ( Allele.wouldBeNoCallAllele(alleleString.getBytes()) ) { + allele = create(alleleString); + } else { + throw new IllegalArgumentException("Allele " + alleleString + " not present in the list of alleles " + possibleAlleles); + } + } + + myAlleles.add(allele); + } + + return myAlleles; + } + + public int compareTo(Allele other) { + if ( isReference() && other.isNonReference() ) + return -1; + else if ( isNonReference() && other.isReference() ) + return 1; + else + return getBaseString().compareTo(other.getBaseString()); // todo -- potential performance issue + } + + public static boolean oneIsPrefixOfOther(Allele a1, Allele a2) { + if ( a1.isNull() || a2.isNull() ) + return true; + + if ( a2.length() >= a1.length() ) + return firstIsPrefixOfSecond(a1, a2); + else + return firstIsPrefixOfSecond(a2, a1); + } + + private static boolean firstIsPrefixOfSecond(Allele a1, Allele a2) { + String a1String = a1.getBaseString(); + return a2.getBaseString().substring(0, a1String.length()).equals(a1String); + } +} diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java new file mode 100755 index 000000000..3a87f1196 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java @@ -0,0 +1,279 @@ +package org.broadinstitute.sting.utils.variantcontext; + + +import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; + +import java.util.*; + +/** + * This class encompasses all the basic information about a genotype. It is immutable. + * + * @author Mark DePristo + */ +public class Genotype { + + public final static String PHASED_ALLELE_SEPARATOR = "|"; + public final static String UNPHASED_ALLELE_SEPARATOR = "/"; + + protected InferredGeneticContext commonInfo; + public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; + protected List alleles = null; // new ArrayList(); + + protected boolean isPhased = false; + private boolean filtersWereAppliedToContext; + + public Genotype(String sampleName, List alleles, double negLog10PError, Set filters, Map attributes, boolean isPhased) { + this.alleles = Collections.unmodifiableList(alleles); + commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes); + filtersWereAppliedToContext = filters != null; + this.isPhased = isPhased; + validate(); + } + + public Genotype(String sampleName, List alleles, double negLog10PError) { + this(sampleName, alleles, negLog10PError, null, null, false); + } + + public Genotype(String sampleName, List alleles) { + this(sampleName, alleles, NO_NEG_LOG_10PERROR, null, null, false); + } + + + // --------------------------------------------------------------------------------------------------------- + // + // Partial-cloning routines (because Genotype is immutable). + // + // --------------------------------------------------------------------------------------------------------- + + public static Genotype modifyName(Genotype g, String name) { + return new Genotype(name, g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.isPhased()); + } + + public static Genotype modifyAttributes(Genotype g, Map attributes) { + return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attributes, g.isPhased()); + } + + public static Genotype modifyAlleles(Genotype g, List alleles) { + return new Genotype(g.getSampleName(), alleles, g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.isPhased()); + } + + /** + * @return the alleles for this genotype + */ + public List getAlleles() { + return alleles; + } + + public List getAlleles(Allele allele) { + List al = new ArrayList(); + for ( Allele a : alleles ) + if ( a.equals(allele) ) + al.add(a); + + return Collections.unmodifiableList(al); + } + + public Allele getAllele(int i) { + return alleles.get(i); + } + + public boolean isPhased() { return isPhased; } + + /** + * @return the ploidy of this genotype + */ + public int getPloidy() { return alleles.size(); } + + public enum Type { + NO_CALL, + HOM_REF, + HET, + HOM_VAR + } + + public Type getType() { + Allele firstAllele = alleles.get(0); + + if ( firstAllele.isNoCall() ) { + return Type.NO_CALL; + } + + for (Allele a : alleles) { + if ( ! firstAllele.equals(a) ) + return Type.HET; + } + return firstAllele.isReference() ? Type.HOM_REF : Type.HOM_VAR; + } + + /** + * @return true if all observed alleles are the same (regardless of whether they are ref or alt) + */ + public boolean isHom() { return isHomRef() || isHomVar(); } + public boolean isHomRef() { return getType() == Type.HOM_REF; } + public boolean isHomVar() { return getType() == Type.HOM_VAR; } + + /** + * @return true if we're het (observed alleles differ) + */ + public boolean isHet() { return getType() == Type.HET; } + + /** + * @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF) + */ + public boolean isNoCall() { return getType() == Type.NO_CALL; } + public boolean isCalled() { return getType() != Type.NO_CALL; } + + // + // Useful methods for getting genotype likelihoods for a genotype object, if present + // + public boolean hasLikelihoods() { + return (hasAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) && !getAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)) || + (hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)); + } + + public GenotypeLikelihoods getLikelihoods() { + GenotypeLikelihoods x = getLikelihoods(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, true); + if ( x != null ) + return x; + else { + x = getLikelihoods(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, false); + if ( x != null ) return x; + else + throw new IllegalStateException("BUG: genotype likelihood field in " + this.getSampleName() + " sample are not either a string or a genotype likelihood class!"); + } + } + + private GenotypeLikelihoods getLikelihoods(String key, boolean asPL) { + Object x = getAttribute(key); + if ( x instanceof String ) { + if ( asPL ) + return GenotypeLikelihoods.fromPLField((String)x); + else + return GenotypeLikelihoods.fromGLField((String)x); + } + else if ( x instanceof GenotypeLikelihoods ) return (GenotypeLikelihoods)x; + else return null; + } + + public void validate() { + if ( alleles == null ) throw new IllegalArgumentException("BUG: alleles cannot be null in setAlleles"); + if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0 in setAlleles"); + + int nNoCalls = 0; + for ( Allele allele : alleles ) { + if ( allele == null ) + throw new IllegalArgumentException("BUG: allele cannot be null in Genotype"); + nNoCalls += allele.isNoCall() ? 1 : 0; + } + if ( nNoCalls > 0 && nNoCalls != alleles.size() ) + throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this); + } + + public String getGenotypeString() { + return getGenotypeString(true); + } + + public String getGenotypeString(boolean ignoreRefState) { + // Notes: + // 1. Make sure to use the appropriate separator depending on whether the genotype is phased + // 2. If ignoreRefState is true, then we want just the bases of the Alleles (ignoring the '*' indicating a ref Allele) + // 3. So that everything is deterministic with regards to integration tests, we sort Alleles (when the genotype isn't phased, of course) + return ParsingUtils.join(isPhased() ? PHASED_ALLELE_SEPARATOR : UNPHASED_ALLELE_SEPARATOR, + ignoreRefState ? getAlleleStrings() : (isPhased() ? getAlleles() : ParsingUtils.sortList(getAlleles()))); + } + + private List getAlleleStrings() { + List al = new ArrayList(); + for ( Allele a : alleles ) + al.add(a.getBaseString()); + + return al; + } + + public String toString() { + int Q = (int)Math.round(getPhredScaledQual()); + return String.format("[%s %s Q%s %s]", getSampleName(), getGenotypeString(false), + Q == -10 ? "." : String.format("%2d",Q), sortedString(getAttributes())); + } + + public String toBriefString() { + return String.format("%s:Q%.2f", getGenotypeString(false), getPhredScaledQual()); + } + + public boolean sameGenotype(Genotype other) { + return sameGenotype(other, true); + } + + public boolean sameGenotype(Genotype other, boolean ignorePhase) { + if (getPloidy() != other.getPloidy()) + return false; // gotta have the same number of allele to be equal + + // By default, compare the elements in the lists of alleles, element-by-element + Collection thisAlleles = this.getAlleles(); + Collection otherAlleles = other.getAlleles(); + + if (ignorePhase) { // do not care about order, only identity of Alleles + thisAlleles = new TreeSet(thisAlleles); //implemented Allele.compareTo() + otherAlleles = new TreeSet(otherAlleles); + } + + return thisAlleles.equals(otherAlleles); + } + + /** + * a utility method for generating sorted strings from a map key set. + * @param c the map + * @param the key type + * @param the value type + * @return a sting, enclosed in {}, with comma seperated key value pairs in order of the keys + */ + public static , V> String sortedString(Map c) { + List t = new ArrayList(c.keySet()); + Collections.sort(t); + + List pairs = new ArrayList(); + for (T k : t) { + pairs.add(k + "=" + c.get(k)); + } + + return "{" + ParsingUtils.join(", ", pairs.toArray(new String[pairs.size()])) + "}"; + } + + + // --------------------------------------------------------------------------------------------------------- + // + // get routines to access context info fields + // + // --------------------------------------------------------------------------------------------------------- + public String getSampleName() { return commonInfo.getName(); } + public Set getFilters() { return commonInfo.getFilters(); } + public boolean isFiltered() { return commonInfo.isFiltered(); } + public boolean isNotFiltered() { return commonInfo.isNotFiltered(); } + public boolean filtersWereApplied() { return filtersWereAppliedToContext; } + public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); } + public double getNegLog10PError() { return commonInfo.getNegLog10PError(); } + public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); } + + public Map getAttributes() { return commonInfo.getAttributes(); } + public boolean hasAttribute(String key) { return commonInfo.hasAttribute(key); } + public Object getAttribute(String key) { return commonInfo.getAttribute(key); } + + public Object getAttribute(String key, Object defaultValue) { + return commonInfo.getAttribute(key, defaultValue); + } + + public String getAttributeAsString(String key) { return commonInfo.getAttributeAsString(key); } + public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); } + public int getAttributeAsInt(String key) { return commonInfo.getAttributeAsInt(key); } + public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); } + public double getAttributeAsDouble(String key) { return commonInfo.getAttributeAsDouble(key); } + public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); } + public boolean getAttributeAsBoolean(String key) { return commonInfo.getAttributeAsBoolean(key); } + public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); } + + public Integer getAttributeAsIntegerNoException(String key) { return commonInfo.getAttributeAsIntegerNoException(key); } + public Double getAttributeAsDoubleNoException(String key) { return commonInfo.getAttributeAsDoubleNoException(key); } + public String getAttributeAsStringNoException(String key) { return commonInfo.getAttributeAsStringNoException(key); } + public Boolean getAttributeAsBooleanNoException(String key) { return commonInfo.getAttributeAsBooleanNoException(key); } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java new file mode 100755 index 000000000..3feaf5e1c --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java @@ -0,0 +1,151 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.variantcontext; + +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broad.tribble.TribbleException; + +public class GenotypeLikelihoods { + public static final boolean CAP_PLS = false; + public static final int PL_CAP = 255; + + // + // There are two objects here because we are lazy in creating both representations + // for this object: a vector of log10 Probs and the PL phred-scaled string. Supports + // having one set during initializating, and dynamic creation of the other, if needed + // + private double[] log10Likelihoods = null; + private String likelihoodsAsString_PLs = null; + + public final static GenotypeLikelihoods fromPLField(String PLs) { + return new GenotypeLikelihoods(PLs); + } + + public final static GenotypeLikelihoods fromGLField(String GLs) { + return new GenotypeLikelihoods(parseDeprecatedGLString(GLs)); + } + + public final static GenotypeLikelihoods fromLog10Likelihoods(double[] log10Likelihoods) { + return new GenotypeLikelihoods(log10Likelihoods); + } + + // + // You must use the factory methods now + // + protected GenotypeLikelihoods(String asString) { + likelihoodsAsString_PLs = asString; + } + + protected GenotypeLikelihoods(double[] asVector) { + log10Likelihoods = asVector; + } + + /** + * Returns the genotypes likelihoods in negative log10 vector format. pr{AA} = x, this + * vector returns math.log10(x) for each of the genotypes. Can return null if the + * genotype likelihoods are "missing". + * + * @return + */ + public double[] getAsVector() { + // assumes one of the likelihoods vector or the string isn't null + if ( log10Likelihoods == null ) { + // make sure we create the GL string if it doesn't already exist + log10Likelihoods = parsePLsIntoLikelihoods(likelihoodsAsString_PLs); + } + + return log10Likelihoods; + } + + public String toString() { + return getAsString(); + } + + public String getAsString() { + if ( likelihoodsAsString_PLs == null ) { + // todo -- should we accept null log10Likelihoods and set PLs as MISSING? + if ( log10Likelihoods == null ) + throw new TribbleException("BUG: Attempted to get likelihoods as strings and neither the vector nor the string is set!"); + likelihoodsAsString_PLs = convertLikelihoodsToPLString(log10Likelihoods); + } + + return likelihoodsAsString_PLs; + } + + private final static double[] parsePLsIntoLikelihoods(String likelihoodsAsString_PLs) { + if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) { + String[] strings = likelihoodsAsString_PLs.split(","); + double[] likelihoodsAsVector = new double[strings.length]; + for ( int i = 0; i < strings.length; i++ ) { + likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0; + } + return likelihoodsAsVector; + } else + return null; + } + + /** + * Back-compatibility function to read old style GL formatted genotype likelihoods in VCF format + * @param GLString + * @return + */ + private final static double[] parseDeprecatedGLString(String GLString) { + if ( !GLString.equals(VCFConstants.MISSING_VALUE_v4) ) { + String[] strings = GLString.split(","); + double[] likelihoodsAsVector = new double[strings.length]; + for ( int i = 0; i < strings.length; i++ ) { + likelihoodsAsVector[i] = Double.parseDouble(strings[i]); + } + return likelihoodsAsVector; + } + + return null; + } + + private final static String convertLikelihoodsToPLString(double[] GLs) { + if ( GLs == null ) + return VCFConstants.MISSING_VALUE_v4; + + StringBuilder s = new StringBuilder(); + + double adjust = Double.NEGATIVE_INFINITY; + for ( double l : GLs ) adjust = Math.max(adjust, l); + + boolean first = true; + for ( double l : GLs ) { + if ( ! first ) + s.append(","); + else + first = false; + + long PL = Math.round(-10 * (l - adjust)); + if ( CAP_PLS ) + PL = Math.min(PL, PL_CAP); + s.append(Long.toString(PL)); + } + + return s.toString(); + } +} diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java new file mode 100755 index 000000000..3d162adb0 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java @@ -0,0 +1,230 @@ +package org.broadinstitute.sting.utils.variantcontext; + + +import java.util.*; + + +/** + * Common utility routines for VariantContext and Genotype + * + * @author depristo + */ +public final class InferredGeneticContext { + public static final double NO_NEG_LOG_10PERROR = -1.0; + + private static Set NO_FILTERS = Collections.unmodifiableSet(new HashSet()); + private static Map NO_ATTRIBUTES = Collections.unmodifiableMap(new HashMap()); + + private double negLog10PError = NO_NEG_LOG_10PERROR; + private String name = null; + private Set filters = NO_FILTERS; + private Map attributes = NO_ATTRIBUTES; + +// public InferredGeneticContext(String name) { +// this.name = name; +// } +// +// public InferredGeneticContext(String name, double negLog10PError) { +// this(name); +// setNegLog10PError(negLog10PError); +// } + + public InferredGeneticContext(String name, double negLog10PError, Set filters, Map attributes) { + this.name = name; + setNegLog10PError(negLog10PError); + if ( filters != null ) + setFilters(filters); + if ( attributes != null ) + setAttributes(attributes); + } + + /** + * @return the name + */ + public String getName() { + return name; + } + + /** + * Sets the name + * + * @param name the name associated with this information + */ + public void setName(String name) { + if ( name == null ) throw new IllegalArgumentException("Name cannot be null " + this); + this.name = name; + } + + + // --------------------------------------------------------------------------------------------------------- + // + // Filter + // + // --------------------------------------------------------------------------------------------------------- + + public Set getFilters() { + return Collections.unmodifiableSet(filters); + } + + public boolean isFiltered() { + return filters.size() > 0; + } + + public boolean isNotFiltered() { + return ! isFiltered(); + } + + public void addFilter(String filter) { + if ( filters == NO_FILTERS ) // immutable -> mutable + filters = new HashSet(filters); + + if ( filter == null ) throw new IllegalArgumentException("BUG: Attempting to add null filter " + this); + if ( getFilters().contains(filter) ) throw new IllegalArgumentException("BUG: Attempting to add duplicate filter " + filter + " at " + this); + filters.add(filter); + } + + public void addFilters(Collection filters) { + if ( filters == null ) throw new IllegalArgumentException("BUG: Attempting to add null filters at" + this); + for ( String f : filters ) + addFilter(f); + } + + public void clearFilters() { + filters = new HashSet(); + } + + public void setFilters(Collection filters) { + clearFilters(); + addFilters(filters); + } + + // --------------------------------------------------------------------------------------------------------- + // + // Working with log error rates + // + // --------------------------------------------------------------------------------------------------------- + + public boolean hasNegLog10PError() { + return getNegLog10PError() != NO_NEG_LOG_10PERROR; + } + + /** + * @return the -1 * log10-based error estimate + */ + public double getNegLog10PError() { return negLog10PError; } + public double getPhredScaledQual() { return getNegLog10PError() * 10; } + + public void setNegLog10PError(double negLog10PError) { + if ( negLog10PError < 0 && negLog10PError != NO_NEG_LOG_10PERROR ) throw new IllegalArgumentException("BUG: negLog10PError cannot be < than 0 : " + negLog10PError); + if ( Double.isInfinite(negLog10PError) ) throw new IllegalArgumentException("BUG: negLog10PError should not be Infinity"); + if ( Double.isNaN(negLog10PError) ) throw new IllegalArgumentException("BUG: negLog10PError should not be NaN"); + + this.negLog10PError = negLog10PError; + } + + // --------------------------------------------------------------------------------------------------------- + // + // Working with attributes + // + // --------------------------------------------------------------------------------------------------------- + public void clearAttributes() { + attributes = new HashMap(); + } + + /** + * @return the attribute map + */ + public Map getAttributes() { + return Collections.unmodifiableMap(attributes); + } + + // todo -- define common attributes as enum + + public void setAttributes(Map map) { + clearAttributes(); + putAttributes(map); + } + + public void putAttribute(String key, Object value) { + putAttribute(key, value, false); + } + + public void putAttribute(String key, Object value, boolean allowOverwrites) { + if ( ! allowOverwrites && hasAttribute(key) ) + throw new IllegalStateException("Attempting to overwrite key->value binding: key = " + key + " this = " + this); + + if ( attributes == NO_ATTRIBUTES ) // immutable -> mutable + attributes = new HashMap(); + + attributes.put(key, value); + } + + public void removeAttribute(String key) { + if ( attributes == NO_ATTRIBUTES ) // immutable -> mutable + attributes = new HashMap(); + attributes.remove(key); + } + + public void putAttributes(Map map) { + if ( map != null ) { + // for efficiency, we can skip the validation if the map is empty + if ( attributes.size() == 0 ) { + if ( attributes == NO_ATTRIBUTES ) // immutable -> mutable + attributes = new HashMap(); + attributes.putAll(map); + } else { + for ( Map.Entry elt : map.entrySet() ) { + putAttribute(elt.getKey(), elt.getValue(), false); + } + } + } + } + + public boolean hasAttribute(String key) { + return attributes.containsKey(key); + } + + public int getNumAttributes() { + return attributes.size(); + } + + /** + * @param key the attribute key + * + * @return the attribute value for the given key (or null if not set) + */ + public Object getAttribute(String key) { + return attributes.get(key); + } + + public Object getAttribute(String key, Object defaultValue) { + if ( hasAttribute(key) ) + return attributes.get(key); + else + return defaultValue; + } + +// public AttributedObject getAttributes(Collection keys) { +// AttributedObject selected = new AttributedObject(); +// +// for ( Object key : keys ) +// selected.putAttribute(key, this.getAttribute(key)); +// +// return selected; +// } + + public String getAttributeAsString(String key) { return (String.valueOf(getAttribute(key))); } // **NOTE**: will turn a null Object into the String "null" + public int getAttributeAsInt(String key) { Object x = getAttribute(key); return x instanceof Integer ? (Integer)x : Integer.valueOf((String)x); } + public double getAttributeAsDouble(String key) { Object x = getAttribute(key); return x instanceof Double ? (Double)x : Double.valueOf((String)x); } + public boolean getAttributeAsBoolean(String key) { Object x = getAttribute(key); return x instanceof Boolean ? (Boolean)x : Boolean.valueOf((String)x); } + + public String getAttributeAsString(String key, String defaultValue) { return (String)getAttribute(key, defaultValue); } + public int getAttributeAsInt(String key, int defaultValue) { return (Integer)getAttribute(key, defaultValue); } + public double getAttributeAsDouble(String key, double defaultValue) { return (Double)getAttribute(key, defaultValue); } + public boolean getAttributeAsBoolean(String key, boolean defaultValue){ return (Boolean)getAttribute(key, defaultValue); } + + public Integer getAttributeAsIntegerNoException(String key) { try {return getAttributeAsInt(key);} catch (Exception e) {return null;} } + public Double getAttributeAsDoubleNoException(String key) { try {return getAttributeAsDouble(key);} catch (Exception e) {return null;} } + public String getAttributeAsStringNoException(String key) { if (getAttribute(key) == null) return null; return getAttributeAsString(key); } + public Boolean getAttributeAsBooleanNoException(String key) { try {return getAttributeAsBoolean(key);} catch (Exception e) {return null;} } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java new file mode 100755 index 000000000..0cd684cb6 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java @@ -0,0 +1,80 @@ +package org.broadinstitute.sting.utils.variantcontext; + +import java.util.*; + +/** + * This class emcompasses all the basic information about a genotype. It is immutable. + * + * @author Mark DePristo + */ +public class MutableGenotype extends Genotype { + public MutableGenotype(Genotype parent) { + super(parent.getSampleName(), parent.getAlleles(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes(), parent.isPhased()); + } + + public MutableGenotype(String sampleName, Genotype parent) { + super(sampleName, parent.getAlleles(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes(), parent.isPhased()); + } + + + public MutableGenotype(String sampleName, List alleles, double negLog10PError, Set filters, Map attributes, boolean genotypesArePhased) { + super(sampleName, alleles, negLog10PError, filters, attributes, genotypesArePhased); + } + + public MutableGenotype(String sampleName, List alleles, double negLog10PError) { + super(sampleName, alleles, negLog10PError); + } + + public MutableGenotype(String sampleName, List alleles) { + super(sampleName, alleles); + } + + public Genotype unmodifiableGenotype() { + return new Genotype(getSampleName(), getAlleles(), getNegLog10PError(), getFilters(), getAttributes(), isPhased()); + } + + + /** + * + * @param alleles list of alleles + */ + public void setAlleles(List alleles) { + this.alleles = new ArrayList(alleles); + + // todo -- add validation checking here + + if ( alleles == null ) throw new IllegalArgumentException("BUG: alleles cannot be null in setAlleles"); + if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0 in setAlleles"); + + int nNoCalls = 0; + for ( Allele allele : alleles ) { nNoCalls += allele.isNoCall() ? 1 : 0; } + if ( nNoCalls > 0 && nNoCalls != alleles.size() ) + throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this); + + for ( Allele allele : alleles ) + if ( allele == null ) throw new IllegalArgumentException("BUG: Cannot add a null allele to a genotype"); + } + + public void setPhase(boolean isPhased) { + super.isPhased = isPhased; + } + + // --------------------------------------------------------------------------------------------------------- + // + // InferredGeneticContext mutation operators + // + // --------------------------------------------------------------------------------------------------------- + public void setName(String name) { commonInfo.setName(name); } + public void addFilter(String filter) { commonInfo.addFilter(filter); } + public void addFilters(Collection filters) { commonInfo.addFilters(filters); } + public void clearFilters() { commonInfo.clearFilters(); } + public void setFilters(Collection filters) { commonInfo.setFilters(filters); } + public void setAttributes(Map map) { commonInfo.setAttributes(map); } + public void clearAttributes() { commonInfo.clearAttributes(); } + public void putAttribute(String key, Object value) { commonInfo.putAttribute(key, value); } + public void removeAttribute(String key) { commonInfo.removeAttribute(key); } + public void putAttributes(Map map) { commonInfo.putAttributes(map); } + public void setNegLog10PError(double negLog10PError) { commonInfo.setNegLog10PError(negLog10PError); } + public void putAttribute(String key, Object value, boolean allowOverwrites) { commonInfo.putAttribute(key, value, allowOverwrites); } + +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java new file mode 100755 index 000000000..4efba8825 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java @@ -0,0 +1,210 @@ +package org.broadinstitute.sting.utils.variantcontext; + + +import java.util.*; + +/** + * Mutable version of VariantContext + * + * @author depristo + */ +public class MutableVariantContext extends VariantContext { + // --------------------------------------------------------------------------------------------------------- + // + // constructors + // + // --------------------------------------------------------------------------------------------------------- + + public MutableVariantContext(String source, String contig, long start, long stop, Collection alleles, Collection genotypes, double negLog10PError, Set filters, Map attributes) { + super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes); + } + + public MutableVariantContext(String source, String contig, long start, long stop, Collection alleles, Map genotypes, double negLog10PError, Set filters, Map attributes) { + super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes); + } + + public MutableVariantContext(String source, String contig, long start, long stop, Collection alleles) { + this(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); + } + + public MutableVariantContext(String source, String contig, long start, long stop, Collection alleles, Collection genotypes) { + this(source, contig, start, stop, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); + } + + public MutableVariantContext(VariantContext parent) { + this(parent.getSource(), parent.contig, parent.start, parent.stop, parent.getAlleles(), parent.getGenotypes(), parent.getNegLog10PError(), parent.getFilters(), parent.getAttributes()); + } + + /** + * Sets the alleles segregating in this context to the collect of alleles. Each of which must be unique according + * to equals() in Allele. Validate() should be called when you are done modifying the context. + * + * @param alleles + */ + public void setAlleles(Collection alleles) { + this.alleles.clear(); + for ( Allele a : alleles ) + addAllele(a); + } + + /** + * Adds allele to the segregating allele list in this context to the collection of alleles. The new + * allele must be be unique according to equals() in Allele. + * Validate() should be called when you are done modifying the context. + * + * @param allele + */ + public void addAllele(Allele allele) { + final boolean allowDuplicates = false; // used to be a parameter + + type = null; + + for ( Allele a : alleles ) { + if ( a.basesMatch(allele) && ! allowDuplicates ) + throw new IllegalArgumentException("Duplicate allele added to VariantContext" + this); + } + + // we are a novel allele + alleles.add(allele); + } + + public void clearGenotypes() { + genotypes = new TreeMap(); + } + + /** + * Adds this single genotype to the context, not allowing duplicate genotypes to be added + * @param genotype + */ + public void addGenotypes(Genotype genotype) { + putGenotype(genotype.getSampleName(), genotype, false); + } + + /** + * Adds these genotypes to the context, not allowing duplicate genotypes to be added + * @param genotypes + */ + public void addGenotypes(Collection genotypes) { + for ( Genotype g : genotypes ) { + addGenotype(g); + } + } + + /** + * Adds these genotype to the context, not allowing duplicate genotypes to be added. + * @param genotypes + */ + public void addGenotypes(Map genotypes) { + + for ( Map.Entry elt : genotypes.entrySet() ) { + addGenotype(elt.getValue()); + } + } + + /** + * Adds these genotypes to the context. + * + * @param genotypes + */ + public void putGenotypes(Map genotypes) { + for ( Map.Entry g : genotypes.entrySet() ) + putGenotype(g.getKey(), g.getValue()); + } + + /** + * Adds these genotypes to the context. + * + * @param genotypes + */ + public void putGenotypes(Collection genotypes) { + for ( Genotype g : genotypes ) + putGenotype(g); + } + + /** + * Adds this genotype to the context, throwing an error if it's already bound. + * + * @param genotype + */ + public void addGenotype(Genotype genotype) { + addGenotype(genotype.getSampleName(), genotype); + } + + /** + * Adds this genotype to the context, throwing an error if it's already bound. + * + * @param genotype + */ + public void addGenotype(String sampleName, Genotype genotype) { + putGenotype(sampleName, genotype, false); + } + + /** + * Adds this genotype to the context. + * + * @param genotype + */ + public void putGenotype(Genotype genotype) { + putGenotype(genotype.getSampleName(), genotype); + } + + /** + * Adds this genotype to the context. + * + * @param genotype + */ + public void putGenotype(String sampleName, Genotype genotype) { + putGenotype(sampleName, genotype, true); + } + + private void putGenotype(String sampleName, Genotype genotype, boolean allowOverwrites) { + if ( hasGenotype(sampleName) && ! allowOverwrites ) + throw new IllegalStateException("Attempting to overwrite sample->genotype binding: " + sampleName + " this=" + this); + + if ( ! sampleName.equals(genotype.getSampleName()) ) + throw new IllegalStateException("Sample name doesn't equal genotype.getSample(): " + sampleName + " genotype=" + genotype); + + this.genotypes.put(sampleName, genotype); + } + + /** + * Removes the binding from sampleName to genotype. If this doesn't exist, throws an IllegalArgumentException + * @param sampleName + */ + public void removeGenotype(String sampleName) { + if ( ! this.genotypes.containsKey(sampleName) ) + throw new IllegalArgumentException("Sample name isn't contained in genotypes " + sampleName + " genotypes =" + genotypes); + + this.genotypes.remove(sampleName); + } + + /** + * Removes genotype from the context. If this doesn't exist, throws an IllegalArgumentException + * @param genotype + */ + public void removeGenotype(Genotype genotype) { + removeGenotype(genotype.getSampleName()); + } + + // todo -- add replace genotype routine + + // --------------------------------------------------------------------------------------------------------- + // + // InferredGeneticContext mutation operators + // + // --------------------------------------------------------------------------------------------------------- + + public void setSource(String source) { commonInfo.setName(source); } + public void addFilter(String filter) { commonInfo.addFilter(filter); } + public void addFilters(Collection filters) { commonInfo.addFilters(filters); } + public void clearFilters() { commonInfo.clearFilters(); } + public void setFilters(Collection filters) { commonInfo.setFilters(filters); } + public void setAttributes(Map map) { commonInfo.setAttributes(map); } + public void clearAttributes() { commonInfo.clearAttributes(); } + public void putAttribute(String key, Object value) { commonInfo.putAttribute(key, value); } + public void removeAttribute(String key) { commonInfo.removeAttribute(key); } + public void putAttributes(Map map) { commonInfo.putAttributes(map); } + public void setNegLog10PError(double negLog10PError) { commonInfo.setNegLog10PError(negLog10PError); } + public void putAttribute(String key, Object value, boolean allowOverwrites) { commonInfo.putAttribute(key, value, allowOverwrites); } + public void setID(String id) { putAttribute(ID_KEY, id, true); } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java new file mode 100755 index 000000000..87466e21b --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -0,0 +1,1521 @@ +package org.broadinstitute.sting.utils.variantcontext; + +import org.broad.tribble.Feature; +import org.broad.tribble.TribbleException; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFParser; + +import java.util.*; + +/** + * Class VariantContext + * + * == High-level overview == + * + * The VariantContext object is a single general class system for representing genetic variation data composed of: + * + * * Allele: representing single genetic haplotypes (A, T, ATC, -) + * * Genotype: an assignment of alleles for each chromosome of a single named sample at a particular locus + * * VariantContext: an abstract class holding all segregating alleles at a locus as well as genotypes + * for multiple individuals containing alleles at that locus + * + * The class system works by defining segregating alleles, creating a variant context representing the segregating + * information at a locus, and potentially creating and associating genotypes with individuals in the context. + * + * All of the classes are highly validating -- call validate() if you modify them -- so you can rely on the + * self-consistency of the data once you have a VariantContext in hand. The system has a rich set of assessor + * and manipulator routines, as well as more complex static support routines in VariantContextUtils. + * + * The VariantContext (and Genotype) objects are attributed (supporting addition of arbitrary key/value pairs) and + * filtered (can represent a variation that is viewed as suspect). + * + * VariantContexts are dynamically typed, so whether a VariantContext is a SNP, Indel, or NoVariant depends + * on the properties of the alleles in the context. See the detailed documentation on the Type parameter below. + * + * It's also easy to create subcontexts based on selected genotypes. + * + * == Working with Variant Contexts == + * By default, VariantContexts are immutable. In order to access (in the rare circumstances where you need them) + * setter routines, you need to create MutableVariantContexts and MutableGenotypes. + * + * === Some example data === + * + * Allele A, Aref, T, Tref; + * Allele del, delRef, ATC, ATCref; + * + * A [ref] / T at 10 + * GenomeLoc snpLoc = GenomeLocParser.createGenomeLoc("chr1", 10, 10); + * + * - / ATC [ref] from 20-23 + * GenomeLoc delLoc = GenomeLocParser.createGenomeLoc("chr1", 20, 22); + * + * // - [ref] / ATC immediately after 20 + * GenomeLoc insLoc = GenomeLocParser.createGenomeLoc("chr1", 20, 20); + * + * === Alleles === + * + * See the documentation in the Allele class itself + * + * What are they? + * + * Alleles can be either reference or non-reference + * + * Example alleles used here: + * + * del = new Allele("-"); + * A = new Allele("A"); + * Aref = new Allele("A", true); + * T = new Allele("T"); + * ATC = new Allele("ATC"); + * + * === Creating variant contexts === + * + * ==== By hand ==== + * + * Here's an example of a A/T polymorphism with the A being reference: + * + * 
+ * VariantContext vc = new VariantContext(name, snpLoc, Arrays.asList(Aref, T));
+ *
+ * + * If you want to create a non-variant site, just put in a single reference allele + * + * 
+ * VariantContext vc = new VariantContext(name, snpLoc, Arrays.asList(Aref));
+ *
+ * + * A deletion is just as easy: + * + * 
+ * VariantContext vc = new VariantContext(name, delLoc, Arrays.asList(ATCref, del));
+ *
+ * + * The only 2 things that distinguishes between a insertion and deletion are the reference allele + * and the location of the variation. An insertion has a Null reference allele and at least + * one non-reference Non-Null allele. Additionally, the location of the insertion is immediately after + * a 1-bp GenomeLoc (at say 20). + * + * 
+ * VariantContext vc = new VariantContext("name", insLoc, Arrays.asList(delRef, ATC));
+ *
+ * + * ==== Converting rods and other data structures to VCs ==== + * + * You can convert many common types into VariantContexts using the general function: + * + * 
+ * VariantContextAdaptors.convertToVariantContext(name, myObject)
+ *
+ * + * dbSNP and VCFs, for example, can be passed in as myObject and a VariantContext corresponding to that + * object will be returned. A null return type indicates that the type isn't yet supported. This is the best + * and easiest way to create contexts using RODs. + * + * + * === Working with genotypes === + * + * 
+ * List alleles = Arrays.asList(Aref, T);
+ * Genotype g1 = new Genotype(Arrays.asList(Aref, Aref), "g1", 10);
+ * Genotype g2 = new Genotype(Arrays.asList(Aref, T), "g2", 10);
+ * Genotype g3 = new Genotype(Arrays.asList(T, T), "g3", 10);
+ * VariantContext vc = new VariantContext(snpLoc, alleles, Arrays.asList(g1, g2, g3));
+ *
+ * + * At this point we have 3 genotypes in our context, g1-g3. + * + * You can assess a good deal of information about the genotypes through the VariantContext: + * + * 
+ * vc.hasGenotypes()
+ * vc.isMonomorphic()
+ * vc.isPolymorphic()
+ * vc.getSampleNames().size()
+ *
+ * vc.getGenotypes()
+ * vc.getGenotypes().get("g1")
+ * vc.hasGenotype("g1")
+ *
+ * vc.getChromosomeCount()
+ * vc.getChromosomeCount(Aref)
+ * vc.getChromosomeCount(T)
+ *
+ * + * === NO_CALL alleles === + * + * The system allows one to create Genotypes carrying special NO_CALL alleles that aren't present in the + * set of context alleles and that represent undetermined alleles in a genotype: + * + * Genotype g4 = new Genotype(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), "NO_DATA_FOR_SAMPLE", 10); + * + * + * === subcontexts === + * It's also very easy get subcontext based only the data in a subset of the genotypes: + * + * 
+ * VariantContext vc12 = vc.subContextFromGenotypes(Arrays.asList(g1,g2));
+ * VariantContext vc1 = vc.subContextFromGenotypes(Arrays.asList(g1));
+ *
+ * + * @author depristo + */ +public class VariantContext implements Feature { // to enable tribble intergration + protected InferredGeneticContext commonInfo = null; + public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; + public final static String REFERENCE_BASE_FOR_INDEL_KEY = "_REFERENCE_BASE_FOR_INDEL_"; + public final static String UNPARSED_GENOTYPE_MAP_KEY = "_UNPARSED_GENOTYPE_MAP_"; + public final static String UNPARSED_GENOTYPE_PARSER_KEY = "_UNPARSED_GENOTYPE_PARSER_"; + public final static String ID_KEY = "ID"; + + public final static Set PASSES_FILTERS = Collections.unmodifiableSet(new LinkedHashSet()); + + /** The location of this VariantContext */ + protected String contig; + protected long start; + protected long stop; + + /** The type (cached for performance reasons) of this context */ + protected Type type = null; + + /** A set of the alleles segregating in this context */ + protected LinkedHashSet alleles = null; + + /** A mapping from sampleName -> genotype objects for all genotypes associated with this context */ + protected Map genotypes = null; + + /** Counts for each of the possible Genotype types in this context */ + protected int[] genotypeCounts = null; + + public final static Map NO_GENOTYPES = Collections.unmodifiableMap(new HashMap()); + + // a fast cached access point to the ref / alt alleles for biallelic case + private Allele REF = null; + + // set to the alt allele when biallelic, otherwise == null + private Allele ALT = null; + + // were filters applied? + private boolean filtersWereAppliedToContext; + + // --------------------------------------------------------------------------------------------------------- + // + // constructors + // + // --------------------------------------------------------------------------------------------------------- + + + /** + * the complete constructor. Makes a complete VariantContext from its arguments + * + * @param source source + * @param contig the contig + * @param start the start base (one based) + * @param stop the stop reference base (one based) + * @param alleles alleles + * @param genotypes genotypes map + * @param negLog10PError qual + * @param filters filters: use null for unfiltered and empty set for passes filters + * @param attributes attributes + */ + public VariantContext(String source, String contig, long start, long stop, Collection alleles, Map genotypes, double negLog10PError, Set filters, Map attributes) { + this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, false); + } + + /** + * Makes a VariantContext from its arguments without parsing the genotypes. + * Note that this constructor assumes that if there is genotype data, then it's been put into + * the attributes with the UNPARSED_GENOTYPE_MAP_KEY and that the codec has been added with the + * UNPARSED_GENOTYPE_PARSER_KEY. It doesn't validate that this is the case because it's possible + * that there is no genotype data. + * + * @param source source + * @param contig the contig + * @param start the start base (one based) + * @param stop the stop reference base (one based) + * @param alleles alleles + * @param negLog10PError qual + * @param filters filters: use null for unfiltered and empty set for passes filters + * @param attributes attributes + */ + public VariantContext(String source, String contig, long start, long stop, Collection alleles, double negLog10PError, Set filters, Map attributes) { + this(source, contig, start, stop, alleles, NO_GENOTYPES, negLog10PError, filters, attributes, true); + } + + /** + * Create a new VariantContext + * + * @param source source + * @param contig the contig + * @param start the start base (one based) + * @param stop the stop reference base (one based) + * @param alleles alleles + * @param genotypes genotypes set + * @param negLog10PError qual + * @param filters filters: use null for unfiltered and empty set for passes filters + * @param attributes attributes + */ + public VariantContext(String source, String contig, long start, long stop, Collection alleles, Collection genotypes, double negLog10PError, Set filters, Map attributes) { + this(source, contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap(), genotypes) : null, negLog10PError, filters, attributes, false); + } + + /** + * Create a new variant context without genotypes and no Perror, no filters, and no attributes + * + * @param source source + * @param contig the contig + * @param start the start base (one based) + * @param stop the stop reference base (one based) + * @param alleles alleles + */ + public VariantContext(String source, String contig, long start, long stop, Collection alleles) { + this(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, false); + } + + /** + * Create a new variant context without genotypes and no Perror, no filters, and no attributes + * + * @param source source + * @param contig the contig + * @param start the start base (one based) + * @param stop the stop reference base (one based) + * @param alleles alleles + * @param genotypes genotypes + */ + public VariantContext(String source, String contig, long start, long stop, Collection alleles, Collection genotypes) { + this(source, contig, start, stop, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); + } + + /** + * Copy constructor + * + * @param other the VariantContext to copy + */ + public VariantContext(VariantContext other) { + this(other.getSource(), other.getChr(), other.getStart(), other.getEnd() , other.getAlleles(), other.getGenotypes(), other.getNegLog10PError(), other.filtersWereApplied() ? other.getFilters() : null, other.getAttributes(), false); + } + + /** + * the actual constructor. Private access only + * + * @param source source + * @param contig the contig + * @param start the start base (one based) + * @param stop the stop reference base (one based) + * @param alleles alleles + * @param genotypes genotypes map + * @param negLog10PError qual + * @param filters filters: use null for unfiltered and empty set for passes filters + * @param attributes attributes + */ + private VariantContext(String source, String contig, long start, long stop, Collection alleles, Map genotypes, double negLog10PError, Set filters, Map attributes, boolean genotypesAreUnparsed) { + if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); } + this.contig = contig; + this.start = start; + this.stop = stop; + + if ( !genotypesAreUnparsed && attributes != null ) { + if ( attributes.containsKey(UNPARSED_GENOTYPE_MAP_KEY) ) + attributes.remove(UNPARSED_GENOTYPE_MAP_KEY); + if ( attributes.containsKey(UNPARSED_GENOTYPE_PARSER_KEY) ) + attributes.remove(UNPARSED_GENOTYPE_PARSER_KEY); + } + + this.commonInfo = new InferredGeneticContext(source, negLog10PError, filters, attributes); + filtersWereAppliedToContext = filters != null; + + if ( alleles == null ) { throw new IllegalArgumentException("Alleles cannot be null"); } + + // we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles + this.alleles = alleleCollectionToSet(new LinkedHashSet(), alleles); + + + if ( genotypes == null ) { genotypes = NO_GENOTYPES; } + this.genotypes = Collections.unmodifiableMap(genotypes); + + // cache the REF and ALT alleles + int nAlleles = alleles.size(); + for ( Allele a : alleles ) { + if ( a.isReference() ) { + REF = a; + } else if ( nAlleles == 2 ) { // only cache ALT when biallelic + ALT = a; + } + } + + validate(); + } + + // --------------------------------------------------------------------------------------------------------- + // + // Partial-cloning routines (because Variant Context is immutable). + // Note that we don't call vc.getGenotypes() because that triggers the lazy loading. + // Also note that we need to create a new attributes map because it's unmodifiable and the constructor may try to modify it. + // + // --------------------------------------------------------------------------------------------------------- + + public static VariantContext modifyGenotypes(VariantContext vc, Map genotypes) { + return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap(vc.getAttributes()), false); + } + + public static VariantContext modifyLocation(VariantContext vc, String chr, int start, int end) { + return new VariantContext(vc.getSource(), chr, start, end, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap(vc.getAttributes()), true); + } + + public static VariantContext modifyFilters(VariantContext vc, Set filters) { + return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd() , vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), filters, new HashMap(vc.getAttributes()), true); + } + + public static VariantContext modifyAttributes(VariantContext vc, Map attributes) { + return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, true); + } + + public static VariantContext modifyPErrorFiltersAndAttributes(VariantContext vc, double negLog10PError, Set filters, Map attributes) { + return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, negLog10PError, filters, attributes, true); + } + + // --------------------------------------------------------------------------------------------------------- + // + // Selectors + // + // --------------------------------------------------------------------------------------------------------- + + /** + * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotype + * genotype and alleles in genotype. This is the right way to test if a single genotype is actually + * variant or not. + * + * @param genotype genotype + * @return vc subcontext + */ + public VariantContext subContextFromGenotypes(Genotype genotype) { + return subContextFromGenotypes(Arrays.asList(genotype)); + } + + + /** + * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotypes + * genotypes and alleles in these genotypes. This is the right way to test if a single genotype is actually + * variant or not. + * + * @param genotypes genotypes + * @return vc subcontext + */ + public VariantContext subContextFromGenotypes(Collection genotypes) { + return subContextFromGenotypes(genotypes, allelesOfGenotypes(genotypes)) ; + } + + /** + * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotypes + * genotypes. Also, the resulting variant context will contain the alleles provided, not only those found in genotypes + * + * @param genotypes genotypes + * @param alleles the set of allele segregating alleles at this site. Must include those in genotypes, but may be more + * @return vc subcontext + */ + public VariantContext subContextFromGenotypes(Collection genotypes, Set alleles) { + return new VariantContext(getSource(), contig, start, stop, alleles, genotypes, getNegLog10PError(), getFilters(), getAttributes()); + } + + + /** + * helper routine for subcontext + * @param genotypes genotypes + * @return allele set + */ + private Set allelesOfGenotypes(Collection genotypes) { + Set alleles = new HashSet(); + + boolean addedref = false; + for ( Genotype g : genotypes ) { + for ( Allele a : g.getAlleles() ) { + addedref = addedref || a.isReference(); + if ( a.isCalled() ) + alleles.add(a); + } + } + if ( ! addedref ) alleles.add(getReference()); + + return alleles; + } + + // --------------------------------------------------------------------------------------------------------- + // + // type operations + // + // --------------------------------------------------------------------------------------------------------- + + /** + * see: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch5&rendertype=table&id=ch5.ch5_t3 + * + * Format: + * dbSNP variation class + * Rules for assigning allele classes + * Sample allele definition + * + * Single Nucleotide Polymorphisms (SNPs)a + * Strictly defined as single base substitutions involving A, T, C, or G. + * A/T + * + * Deletion/Insertion Polymorphisms (DIPs) + * Designated using the full sequence of the insertion as one allele, and either a fully + * defined string for the variant allele or a '-' character to specify the deleted allele. + * This class will be assigned to a variation if the variation alleles are of different lengths or + * if one of the alleles is deleted ('-'). + * T/-/CCTA/G + * + * No-variation + * Reports may be submitted for segments of sequence that are assayed and determined to be invariant + * in the sample. + * (NoVariation) + * + * Mixed + * Mix of other classes + * + * Also supports NO_VARIATION type, used to indicate that the site isn't polymorphic in the population + * + * + * Not currently supported: + * + * Heterozygous sequencea + * The term heterozygous is used to specify a region detected by certain methods that do not + * resolve the polymorphism into a specific sequence motif. In these cases, a unique flanking + * sequence must be provided to define a sequence context for the variation. + * (heterozygous) + * + * Microsatellite or short tandem repeat (STR) + * Alleles are designated by providing the repeat motif and the copy number for each allele. + * Expansion of the allele repeat motif designated in dbSNP into full-length sequence will + * be only an approximation of the true genomic sequence because many microsatellite markers are + * not fully sequenced and are resolved as size variants only. + * (CAC)8/9/10/11 + * + * Named variant + * Applies to insertion/deletion polymorphisms of longer sequence features, such as retroposon + * dimorphism for Alu or line elements. These variations frequently include a deletion '-' indicator + * for the absent allele. + * (alu) / - + * + * Multi-Nucleotide Polymorphism (MNP) + * Assigned to variations that are multi-base variations of a single, common length + * GGA/AGT + */ + public enum Type { + NO_VARIATION, + SNP, + MNP, // a multi-nucleotide polymorphism + INDEL, + SYMBOLIC, + MIXED, + } + + /** + * Determines (if necessary) and returns the type of this variation by examining the alleles it contains. + * + * @return the type of this VariantContext + **/ + public Type getType() { + if ( type == null ) + determineType(); + + return type; + } + + /** + * convenience method for SNPs + * + * @return true if this is a SNP, false otherwise + */ + public boolean isSNP() { return getType() == Type.SNP; } + + + /** + * convenience method for variants + * + * @return true if this is a variant allele, false if it's reference + */ + public boolean isVariant() { return getType() != Type.NO_VARIATION; } + + /** + * convenience method for point events + * + * @return true if this is a SNP or ref site, false if it's an indel or mixed event + */ + public boolean isPointEvent() { return isSNP() || !isVariant(); } + + /** + * convenience method for indels + * + * @return true if this is an indel, false otherwise + */ + public boolean isIndel() { return getType() == Type.INDEL; } + + /** + * @return true if the alleles indicate a simple insertion (i.e., the reference allele is Null) + */ + public boolean isInsertion() { + // can't just call !isDeletion() because of complex indels + return getType() == Type.INDEL && getReference().isNull(); + } + + /** + * @return true if the alleles indicate a simple deletion (i.e., a single alt allele that is Null) + */ + public boolean isDeletion() { + // can't just call !isInsertion() because of complex indels + return getType() == Type.INDEL && getAlternateAllele(0).isNull(); + } + + public boolean isSymbolic() { + return getType() == Type.SYMBOLIC; + } + + /** + * convenience method for indels + * + * @return true if this is an mixed variation, false otherwise + */ + public boolean isMixed() { return getType() == Type.MIXED; } + + + // --------------------------------------------------------------------------------------------------------- + // + // Generic accessors + // + // --------------------------------------------------------------------------------------------------------- + + public boolean hasID() { + return commonInfo.hasAttribute(ID_KEY); + } + + public String getID() { + return (String)commonInfo.getAttribute(ID_KEY); + } + + // --------------------------------------------------------------------------------------------------------- + // + // get routines to access context info fields + // + // --------------------------------------------------------------------------------------------------------- + public String getSource() { return commonInfo.getName(); } + public Set getFilters() { return commonInfo.getFilters(); } + public boolean isFiltered() { return commonInfo.isFiltered(); } + public boolean isNotFiltered() { return commonInfo.isNotFiltered(); } + public boolean filtersWereApplied() { return filtersWereAppliedToContext; } + public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); } + public double getNegLog10PError() { return commonInfo.getNegLog10PError(); } + public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); } + + public Map getAttributes() { return commonInfo.getAttributes(); } + public boolean hasAttribute(String key) { return commonInfo.hasAttribute(key); } + public Object getAttribute(String key) { return commonInfo.getAttribute(key); } + + public Object getAttribute(String key, Object defaultValue) { + return commonInfo.getAttribute(key, defaultValue); + } + + public String getAttributeAsString(String key) { return commonInfo.getAttributeAsString(key); } + public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); } + public int getAttributeAsInt(String key) { return commonInfo.getAttributeAsInt(key); } + public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); } + public double getAttributeAsDouble(String key) { return commonInfo.getAttributeAsDouble(key); } + public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); } + public boolean getAttributeAsBoolean(String key) { return commonInfo.getAttributeAsBoolean(key); } + public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); } + + public Integer getAttributeAsIntegerNoException(String key) { return commonInfo.getAttributeAsIntegerNoException(key); } + public Double getAttributeAsDoubleNoException(String key) { return commonInfo.getAttributeAsDoubleNoException(key); } + public String getAttributeAsStringNoException(String key) { return commonInfo.getAttributeAsStringNoException(key); } + public Boolean getAttributeAsBooleanNoException(String key) { return commonInfo.getAttributeAsBooleanNoException(key); } + + + // --------------------------------------------------------------------------------------------------------- + // + // Working with alleles + // + // --------------------------------------------------------------------------------------------------------- + + /** + * @return the reference allele for this context + */ + public Allele getReference() { + Allele ref = REF; + if ( ref == null ) + throw new IllegalStateException("BUG: no reference allele found at " + this); + return ref; + } + + /** Private helper routine that grabs the reference allele but doesn't throw an error if there's no such allele */ + +// private Allele getReferenceWithoutError() { +// for ( Allele allele : getAlleles() ) { +// if ( allele.isReference() ) { +// return allele; +// } +// } +// +// return null; +// } + + /** + * @return true if the context is strictly bi-allelic + */ + public boolean isBiallelic() { + return getNAlleles() == 2; + } + + /** + * @return The number of segregating alleles in this context + */ + public int getNAlleles() { + return alleles.size(); + } + + /** + * @return The allele sharing the same bases as this String. A convenience method; better to use byte[] + */ + public Allele getAllele(String allele) { + return getAllele(allele.getBytes()); + } + + /** + * @return The allele sharing the same bases as this byte[], or null if no such allele is present. + */ + public Allele getAllele(byte[] allele) { + return Allele.getMatchingAllele(getAlleles(), allele); + } + + /** + * @return True if this context contains Allele allele, or false otherwise + */ + public boolean hasAllele(Allele allele) { + return hasAllele(allele, false); + } + + public boolean hasAllele(Allele allele, boolean ignoreRefState) { + if ( allele == REF || allele == ALT ) // optimization for cached cases + return true; + + for ( Allele a : getAlleles() ) { + if ( a.equals(allele, ignoreRefState) ) + return true; + } + + return false; + } + + + /** + * Gets the alleles. This method should return all of the alleles present at the location, + * including the reference allele. There are no constraints imposed on the ordering of alleles + * in the set. If the reference is not an allele in this context it will not be included. + * + * @return the set of alleles + */ + public Set getAlleles() { return alleles; } + + /** + * Gets the alternate alleles. This method should return all the alleles present at the location, + * NOT including the reference allele. There are no constraints imposed on the ordering of alleles + * in the set. + * + * @return the set of alternate alleles + */ + public Set getAlternateAlleles() { + LinkedHashSet altAlleles = new LinkedHashSet(); + for ( Allele allele : alleles ) { + if ( allele.isNonReference() ) + altAlleles.add(allele); + } + + return Collections.unmodifiableSet(altAlleles); + } + + /** + * Gets the sizes of the alternate alleles if they are insertion/deletion events, and returns a list of their sizes + * + * @return a list of indel lengths ( null if not of type indel or mixed ) + */ + public List getIndelLengths() { + if ( getType() != Type.INDEL && getType() != Type.MIXED ) { + return null; + } + + List lengths = new ArrayList(); + for ( Allele a : getAlternateAlleles() ) { + lengths.add(a.length() - getReference().length()); + } + + return lengths; + } + + /** + * @param i -- the ith allele (from 0 to n - 2 for a context with n alleles including a reference allele) + * @return the ith non-reference allele in this context + * @throws IllegalArgumentException if i is invalid + */ + public Allele getAlternateAllele(int i) { + int n = 0; + + for ( Allele allele : alleles ) { + if ( allele.isNonReference() && n++ == i ) + return allele; + } + + throw new IllegalArgumentException("Requested " + i + " alternative allele but there are only " + n + " alternative alleles " + this); + } + + // --------------------------------------------------------------------------------------------------------- + // + // Working with genotypes + // + // --------------------------------------------------------------------------------------------------------- + + private void loadGenotypes() { + if ( !hasAttribute(UNPARSED_GENOTYPE_MAP_KEY) ) + return; + + Object parserObj = getAttribute(UNPARSED_GENOTYPE_PARSER_KEY); + if ( parserObj == null || !(parserObj instanceof VCFParser) ) + throw new IllegalStateException("There is no VCF parser stored to unparse the genotype data"); + VCFParser parser = (VCFParser)parserObj; + + Object mapObj = getAttribute(UNPARSED_GENOTYPE_MAP_KEY); + if ( mapObj == null ) + throw new IllegalStateException("There is no mapping string stored to unparse the genotype data"); + + genotypes = parser.createGenotypeMap(mapObj.toString(), new ArrayList(alleles), getChr(), getStart()); + + commonInfo.removeAttribute(UNPARSED_GENOTYPE_MAP_KEY); + commonInfo.removeAttribute(UNPARSED_GENOTYPE_PARSER_KEY); + + validateGenotypes(); + } + + /** + * @return the number of samples in the context + */ + public int getNSamples() { + loadGenotypes(); + return genotypes.size(); + } + + /** + * @return true if the context has associated genotypes + */ + public boolean hasGenotypes() { + loadGenotypes(); + return genotypes.size() > 0; + } + + public boolean hasGenotypes(Collection sampleNames) { + loadGenotypes(); + for ( String name : sampleNames ) { + if ( ! genotypes.containsKey(name) ) + return false; + } + return true; + } + + /** + * @return set of all Genotypes associated with this context + */ + public Map getGenotypes() { + loadGenotypes(); + return genotypes; + } + + public List getGenotypesSortedByName() { + loadGenotypes(); + Collection types = new TreeMap(genotypes).values(); + return new ArrayList(types); + } + + /** + * Returns a map from sampleName -> Genotype for the genotype associated with sampleName. Returns a map + * for consistency with the multi-get function. + * + * @param sampleName + * @return + * @throws IllegalArgumentException if sampleName isn't bound to a genotype + */ + public Map getGenotypes(String sampleName) { + return getGenotypes(Arrays.asList(sampleName)); + } + + /** + * Returns a map from sampleName -> Genotype for each sampleName in sampleNames. Returns a map + * for consistency with the multi-get function. + * + * @param sampleNames a unique list of sample names + * @return + * @throws IllegalArgumentException if sampleName isn't bound to a genotype + */ + public Map getGenotypes(Collection sampleNames) { + HashMap map = new HashMap(); + + for ( String name : sampleNames ) { + if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames); + map.put(name, getGenotype(name)); + } + + return map; + } + + /** + * @return the set of all sample names in this context + */ + public Set getSampleNames() { + return getGenotypes().keySet(); + } + + /** + * @param sample the sample name + * + * @return the Genotype associated with the given sample in this context or null if the sample is not in this context + */ + public Genotype getGenotype(String sample) { + return getGenotypes().get(sample); + } + + public boolean hasGenotype(String sample) { + return getGenotypes().containsKey(sample); + } + + public Genotype getGenotype(int ith) { + return getGenotypesSortedByName().get(ith); + } + + + /** + * Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS + * + * @return chromosome count + */ + public int getChromosomeCount() { + int n = 0; + + for ( Genotype g : getGenotypes().values() ) { + n += g.isNoCall() ? 0 : g.getPloidy(); + } + + return n; + } + + /** + * Returns the number of chromosomes carrying allele A in the genotypes + * + * @param a allele + * @return chromosome count + */ + public int getChromosomeCount(Allele a) { + int n = 0; + + for ( Genotype g : getGenotypes().values() ) { + n += g.getAlleles(a).size(); + } + + return n; + } + + /** + * Genotype-specific functions -- are the genotypes monomorphic w.r.t. to the alleles segregating at this + * site? That is, is the number of alternate alleles among all fo the genotype == 0? + * + * @return true if it's monomorphic + */ + public boolean isMonomorphic() { + return ! isVariant() || getChromosomeCount(getReference()) == getChromosomeCount(); + } + + /** + * Genotype-specific functions -- are the genotypes polymorphic w.r.t. to the alleles segregating at this + * site? That is, is the number of alternate alleles among all fo the genotype > 0? + * + * @return true if it's polymorphic + */ + public boolean isPolymorphic() { + return ! isMonomorphic(); + } + + private void calculateGenotypeCounts() { + if ( genotypeCounts == null ) { + genotypeCounts = new int[Genotype.Type.values().length]; + + for ( Genotype g : getGenotypes().values() ) { + if ( g.isNoCall() ) + genotypeCounts[Genotype.Type.NO_CALL.ordinal()]++; + else if ( g.isHomRef() ) + genotypeCounts[Genotype.Type.HOM_REF.ordinal()]++; + else if ( g.isHet() ) + genotypeCounts[Genotype.Type.HET.ordinal()]++; + else if ( g.isHomVar() ) + genotypeCounts[Genotype.Type.HOM_VAR.ordinal()]++; + else + throw new IllegalStateException("Genotype of unknown type: " + g); + } + } + } + + /** + * Genotype-specific functions -- how many no-calls are there in the genotypes? + * + * @return number of no calls + */ + public int getNoCallCount() { + calculateGenotypeCounts(); + return genotypeCounts[Genotype.Type.NO_CALL.ordinal()]; + } + + /** + * Genotype-specific functions -- how many hom ref calls are there in the genotypes? + * + * @return number of hom ref calls + */ + public int getHomRefCount() { + calculateGenotypeCounts(); + return genotypeCounts[Genotype.Type.HOM_REF.ordinal()]; + } + + /** + * Genotype-specific functions -- how many het calls are there in the genotypes? + * + * @return number of het calls + */ + public int getHetCount() { + calculateGenotypeCounts(); + return genotypeCounts[Genotype.Type.HET.ordinal()]; + } + + /** + * Genotype-specific functions -- how many hom var calls are there in the genotypes? + * + * @return number of hom var calls + */ + public int getHomVarCount() { + return genotypeCounts[Genotype.Type.HOM_VAR.ordinal()]; + } + + // --------------------------------------------------------------------------------------------------------- + // + // validation: extra-strict validation routines for paranoid users + // + // --------------------------------------------------------------------------------------------------------- + + /** + * Run all extra-strict validation tests on a Variant Context object + * + * @param reference the true reference allele + * @param rsIDs the true dbSNP IDs + */ + public void extraStrictValidation(Allele reference, Set rsIDs) { + // validate the reference + validateReferenceBases(reference); + + // validate the RS IDs + validateRSIDs(rsIDs); + + // validate the altenate alleles + validateAlternateAlleles(); + + // validate the AN and AC fields + validateChromosomeCounts(); + + // TODO: implement me + //checkReferenceTrack(); + } + + public void validateReferenceBases(Allele reference) { + // don't validate if we're an insertion + if ( !reference.isNull() && !reference.basesMatch(getReference()) ) { + throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString())); + } + } + + public void validateRSIDs(Set rsIDs) { + if ( rsIDs != null && hasAttribute(VariantContext.ID_KEY) ) { + for ( String id : getID().split(VCFConstants.ID_FIELD_SEPARATOR) ) { + if ( id.startsWith("rs") && !rsIDs.contains(id) ) + throw new TribbleException.InternalCodecException(String.format("the rsID %s for the record at position %s:%d is not in dbSNP", id, getChr(), getStart())); + } + } + } + + public void validateAlternateAlleles() { + if ( !hasGenotypes() ) + return; + + Set reportedAlleles = getAlleles(); + Set observedAlleles = new HashSet(); + observedAlleles.add(getReference()); + for ( Genotype g : getGenotypes().values() ) { + if ( g.isCalled() ) + observedAlleles.addAll(g.getAlleles()); + } + + if ( reportedAlleles.size() != observedAlleles.size() ) + throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-sample genotypes", getChr(), getStart())); + + int originalSize = reportedAlleles.size(); + // take the intersection and see if things change + observedAlleles.retainAll(reportedAlleles); + if ( observedAlleles.size() != originalSize ) + throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-sample genotypes", getChr(), getStart())); + } + + public void validateChromosomeCounts() { + Map observedAttrs = calculateChromosomeCounts(); + + // AN + if ( hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) { + int reportedAN = Integer.valueOf(getAttribute(VCFConstants.ALLELE_NUMBER_KEY).toString()); + int observedAN = (Integer)observedAttrs.get(VCFConstants.ALLELE_NUMBER_KEY); + if ( reportedAN != observedAN ) + throw new TribbleException.InternalCodecException(String.format("the Allele Number (AN) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedAN, observedAN)); + } + + // AC + if ( hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { + List observedACs = (List)observedAttrs.get(VCFConstants.ALLELE_COUNT_KEY); + if ( getAttribute(VCFConstants.ALLELE_COUNT_KEY) instanceof List ) { + Collections.sort(observedACs); + List reportedACs = (List)getAttribute(VCFConstants.ALLELE_COUNT_KEY); + Collections.sort(reportedACs); + if ( observedACs.size() != reportedACs.size() ) + throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag doesn't have the correct number of values for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedACs.size(), observedACs.size())); + for (int i = 0; i < observedACs.size(); i++) { + if ( Integer.valueOf(reportedACs.get(i).toString()) != observedACs.get(i) ) + throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedACs.get(i), observedACs.get(i))); + } + } else { + if ( observedACs.size() != 1 ) + throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag doesn't have enough values for the record at position %s:%d", getChr(), getStart())); + int reportedAC = Integer.valueOf(getAttribute(VCFConstants.ALLELE_COUNT_KEY).toString()); + if ( reportedAC != observedACs.get(0) ) + throw new TribbleException.InternalCodecException(String.format("the Allele Count (AC) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedAC, observedACs.get(0))); + } + } + } + + private Map calculateChromosomeCounts() { + Map attributes = new HashMap(); + + attributes.put(VCFConstants.ALLELE_NUMBER_KEY, getChromosomeCount()); + ArrayList alleleFreqs = new ArrayList(); + ArrayList alleleCounts = new ArrayList(); + + // if there are alternate alleles, record the relevant tags + if ( getAlternateAlleles().size() > 0 ) { + for ( Allele allele : getAlternateAlleles() ) { + alleleCounts.add(getChromosomeCount(allele)); + alleleFreqs.add((double)getChromosomeCount(allele) / (double)getChromosomeCount()); + } + } + // otherwise, set them to 0 + else { + alleleCounts.add(0); + alleleFreqs.add(0.0); + } + + attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts); + attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs); + return attributes; + } + + // --------------------------------------------------------------------------------------------------------- + // + // validation: the normal validation routines are called automatically upon creation of the VC + // + // --------------------------------------------------------------------------------------------------------- + + /** + * To be called by any modifying routines + */ + private boolean validate() { + return validate(true); + } + + private boolean validate(boolean throwException) { + try { + validateAlleles(); + validateGenotypes(); + } catch ( IllegalArgumentException e ) { + if ( throwException ) + throw e; + else + return false; + } + + return true; + } + + private void validateAlleles() { + // check alleles + boolean alreadySeenRef = false, alreadySeenNull = false; + for ( Allele allele : alleles ) { + // make sure there's only one reference allele + if ( allele.isReference() ) { + if ( alreadySeenRef ) throw new IllegalArgumentException("BUG: Received two reference tagged alleles in VariantContext " + alleles + " this=" + this); + alreadySeenRef = true; + } + + if ( allele.isNoCall() ) { + throw new IllegalArgumentException("BUG: Cannot add a no call allele to a variant context " + alleles + " this=" + this); + } + + // make sure there's only one null allele + if ( allele.isNull() ) { + if ( alreadySeenNull ) throw new IllegalArgumentException("BUG: Received two null alleles in VariantContext " + alleles + " this=" + this); + alreadySeenNull = true; + } + } + + // make sure there's one reference allele + if ( ! alreadySeenRef ) + throw new IllegalArgumentException("No reference allele found in VariantContext"); + +// if ( getType() == Type.INDEL ) { +// if ( getReference().length() != (getLocation().size()-1) ) { + long length = (stop - start) + 1; + if ( (getReference().isNull() && length != 1 ) || + (getReference().isNonNull() && (length - getReference().length() > 1))) { + throw new IllegalStateException("BUG: GenomeLoc " + contig + ":" + start + "-" + stop + " has a size == " + length + " but the variation reference allele has length " + getReference().length() + " this = " + this); + } + } + + private void validateGenotypes() { + if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null"); + + for ( Map.Entry elt : this.genotypes.entrySet() ) { + String name = elt.getKey(); + Genotype g = elt.getValue(); + + if ( ! name.equals(g.getSampleName()) ) throw new IllegalStateException("Bound sample name " + name + " does not equal the name of the genotype " + g.getSampleName()); + + for ( Allele gAllele : g.getAlleles() ) { + if ( ! hasAllele(gAllele) && gAllele.isCalled() ) + throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles); + } + } + } + + // --------------------------------------------------------------------------------------------------------- + // + // utility routines + // + // --------------------------------------------------------------------------------------------------------- + + // the indel base that gets stripped off for indels + public boolean hasReferenceBaseForIndel() { + return hasAttribute(REFERENCE_BASE_FOR_INDEL_KEY); + } + + // the indel base that gets stripped off for indels + public byte getReferenceBaseForIndel() { + return hasReferenceBaseForIndel() ? (Byte)getAttribute(REFERENCE_BASE_FOR_INDEL_KEY) : (byte)'N'; + } + + private void determineType() { + if ( type == null ) { + switch ( getNAlleles() ) { + case 0: + throw new IllegalStateException("Unexpected error: requested type of VariantContext with no alleles!" + this); + case 1: + // note that this doesn't require a reference allele. You can be monomorphic independent of having a + // reference allele + type = Type.NO_VARIATION; + break; + default: + determinePolymorphicType(); + } + } + } + + private void determinePolymorphicType() { + type = null; + + // do a pairwise comparison of all alleles against the reference allele + for ( Allele allele : alleles ) { + if ( allele == REF ) + continue; + + // find the type of this allele relative to the reference + Type biallelicType = typeOfBiallelicVariant(REF, allele); + + // for the first alternate allele, set the type to be that one + if ( type == null ) { + type = biallelicType; + } + // if the type of this allele is different from that of a previous one, assign it the MIXED type and quit + else if ( biallelicType != type ) { + type = Type.MIXED; + return; + } + } + } + + private static Type typeOfBiallelicVariant(Allele ref, Allele allele) { + if ( ref.isSymbolic() ) + throw new IllegalStateException("Unexpected error: encountered a record with a symbolic reference allele"); + + if ( allele.isSymbolic() ) + return Type.SYMBOLIC; + + if ( ref.length() == allele.length() ) { + if ( allele.length() == 1 ) + return Type.SNP; + else + return Type.MNP; + } + + // Important note: previously we were checking that one allele is the prefix of the other. However, that's not an + // appropriate check as can be seen from the following example: + // REF = CTTA and ALT = C,CT,CA + // This should be assigned the INDEL type but was being marked as a MIXED type because of the prefix check. + // In truth, it should be absolutely impossible to return a MIXED type from this method because it simply + // performs a pairwise comparison of a single alternate allele against the reference allele (whereas the MIXED type + // is reserved for cases of multiple alternate alleles of different types). Therefore, if we've reached this point + // in the code (so we're not a SNP, MNP, or symbolic allele), we absolutely must be an INDEL. + return Type.INDEL; + + // old incorrect logic: + // if (oneIsPrefixOfOther(ref, allele)) + // return Type.INDEL; + // else + // return Type.MIXED; + } + + public String toString() { + return String.format("[VC %s @ %s of type=%s alleles=%s attr=%s GT=%s", + getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), this.getType(), + ParsingUtils.sortList(this.getAlleles()), ParsingUtils.sortedString(this.getAttributes()), this.getGenotypesSortedByName()); + } + + // protected basic manipulation routines + private static LinkedHashSet alleleCollectionToSet(LinkedHashSet dest, Collection alleles) { + for ( Allele a : alleles ) { + for ( Allele b : dest ) { + if ( a.equals(b, true) ) + throw new IllegalArgumentException("Duplicate allele added to VariantContext: " + a); + } + + dest.add(a); + } + + return dest; + } + + public static Map genotypeCollectionToMap(Map dest, Collection genotypes) { + for ( Genotype g : genotypes ) { + if ( dest.containsKey(g.getSampleName() ) ) + throw new IllegalArgumentException("Duplicate genotype added to VariantContext: " + g); + dest.put(g.getSampleName(), g); + } + + return dest; + } + + // --------------------------------------------------------------------------------------------------------- + // + // tribble integration routines -- not for public consumption + // + // --------------------------------------------------------------------------------------------------------- + public String getChr() { + return contig; + } + + public int getStart() { + return (int)start; + } + + public int getEnd() { + return (int)stop; + } + + public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase, boolean refBaseShouldBeAppliedToEndOfAlleles) { + Allele refAllele = inputVC.getReference(); + + // see if we need to pad common reference base from all alleles + boolean padVC; + + // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext. + // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention). + long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1; + if (refAllele.length() == locLength) + padVC = false; + else if (refAllele.length() == locLength-1) + padVC = true; + else throw new IllegalArgumentException("Badly formed variant context at location " + String.valueOf(inputVC.getStart()) + + " in contig " + inputVC.getChr() + ". Reference length must be at most one base shorter than location size"); + + + // nothing to do if we don't need to pad bases + if (padVC) { + Byte refByte; + + Map attributes = inputVC.getAttributes(); + + // upper-case for consistency; note that we can safely make these casts because the input is constrained to be a byte + inputRefBase = (byte)Character.toUpperCase((char)inputRefBase); + if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY)) + refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY); + else if (inputRefBase == 'A' || inputRefBase == 'T' || inputRefBase == 'C' || inputRefBase == 'G' || inputRefBase == 'N') + refByte = inputRefBase; + else + throw new IllegalArgumentException("Error when trying to pad Variant Context at location " + String.valueOf(inputVC.getStart()) + + " in contig " + inputVC.getChr() + + ". Either input reference base ("+(char)inputRefBase+ + ", ascii code="+inputRefBase+") must be a regular base, or input VC must contain reference base key"); + + List alleles = new ArrayList(); + Map genotypes = new TreeMap(); + + Map inputGenotypes = inputVC.getGenotypes(); + + for (Allele a : inputVC.getAlleles()) { + // get bases for current allele and create a new one with trimmed bases + if (a.isSymbolic()) { + alleles.add(a); + } else { + String newBases; + if ( refBaseShouldBeAppliedToEndOfAlleles ) + newBases = a.getBaseString() + new String(new byte[]{refByte}); + else + newBases = new String(new byte[]{refByte}) + a.getBaseString(); + alleles.add(Allele.create(newBases,a.isReference())); + } + } + + // now we can recreate new genotypes with trimmed alleles + for (String sample : inputVC.getSampleNames()) { + Genotype g = inputGenotypes.get(sample); + + List inAlleles = g.getAlleles(); + List newGenotypeAlleles = new ArrayList(); + for (Allele a : inAlleles) { + if (a.isCalled()) { + if (a.isSymbolic()) { + newGenotypeAlleles.add(a); + } else { + String newBases; + if ( refBaseShouldBeAppliedToEndOfAlleles ) + newBases = a.getBaseString() + new String(new byte[]{refByte}); + else + newBases = new String(new byte[]{refByte}) + a.getBaseString(); + newGenotypeAlleles.add(Allele.create(newBases,a.isReference())); + } + } + else { + // add no-call allele + newGenotypeAlleles.add(Allele.NO_CALL); + } + } + genotypes.put(sample, new Genotype(sample, newGenotypeAlleles, g.getNegLog10PError(), + g.getFilters(),g.getAttributes(),g.isPhased())); + + } + + // Do not change the filter state if filters were not applied to this context + Set inputVCFilters = inputVC.filtersWereAppliedToContext ? inputVC.getFilters() : null; + return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), + inputVCFilters, attributes); + + + + } + else + return inputVC; + + } + + public ArrayList getTwoAllelesWithHighestAlleleCounts() { + // first idea: get two alleles with highest AC + int maxAC1 = 0, maxAC2=0,maxAC1ind =0, maxAC2ind = 0; + int i=0; + int[] alleleCounts = new int[this.getAlleles().size()]; + ArrayList alleleArray = new ArrayList(); + for (Allele a:this.getAlleles()) { + int ac = this.getChromosomeCount(a); + if (ac >=maxAC1) { + maxAC1 = ac; + maxAC1ind = i; + } + alleleArray.add(a); + alleleCounts[i++] = ac; + } + // now get second best allele + for (i=0; i < alleleCounts.length; i++) { + if (i == maxAC1ind) + continue; + if (alleleCounts[i] >= maxAC2) { + maxAC2 = alleleCounts[i]; + maxAC2ind = i; + } + } + + Allele alleleA, alleleB; + if (alleleArray.get(maxAC1ind).isReference()) { + alleleA = alleleArray.get(maxAC1ind); + alleleB = alleleArray.get(maxAC2ind); + } + else if (alleleArray.get(maxAC2ind).isReference()) { + alleleA = alleleArray.get(maxAC2ind); + alleleB = alleleArray.get(maxAC1ind); + } else { + alleleA = alleleArray.get(maxAC1ind); + alleleB = alleleArray.get(maxAC2ind); + } + ArrayList a = new ArrayList(); + a.add(alleleA); + a.add(alleleB); + return a; + } + public Allele getAltAlleleWithHighestAlleleCount() { + // first idea: get two alleles with highest AC + Allele best = null; + int maxAC1 = 0; + for (Allele a:this.getAlternateAlleles()) { + int ac = this.getChromosomeCount(a); + if (ac >=maxAC1) { + maxAC1 = ac; + best = a; + } + + } + return best; + } + + public int[] getGLIndecesOfAllele(Allele inputAllele) { + int[] idxVector = new int[3]; + int numAlleles = this.getAlleles().size(); + + int idxDiag = numAlleles; + int incr = numAlleles - 1; + int k=1; + for (Allele a: getAlternateAlleles()) { + // multi-allelic approximation, part 1: Ideally + // for each alt allele compute marginal (suboptimal) posteriors - + // compute indices for AA,AB,BB for current allele - genotype likelihoods are a linear vector that can be thought of + // as a row-wise upper triangular matrix of likelihoods. + // So, for example, with 2 alt alleles, likelihoods have AA,AB,AC,BB,BC,CC. + // 3 alt alleles: AA,AB,AC,AD BB BC BD CC CD DD + + int idxAA = 0; + int idxAB = k++; + // yy is always element on the diagonal. + // 2 alleles: BBelement 2 + // 3 alleles: BB element 3. CC element 5 + // 4 alleles: + int idxBB = idxDiag; + + if (a.equals(inputAllele)) { + idxVector[0] = idxAA; + idxVector[1] = idxAB; + idxVector[2] = idxBB; + break; + } + idxDiag += incr--; + } + return idxVector; + } +} diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java similarity index 99% rename from java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java rename to java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index c848a300b..5d58954aa 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -21,7 +21,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.contexts.variantcontext; +package org.broadinstitute.sting.utils.variantcontext; import java.io.Serializable; import java.util.*; @@ -31,11 +31,10 @@ import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.samtools.util.StringUtil; import org.apache.commons.jexl2.*; import org.broad.tribble.util.popgen.HardyWeinbergCalculation; -import org.broad.tribble.util.variantcontext.*; -import org.broad.tribble.vcf.AbstractVCFCodec; +import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec; import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; import org.broadinstitute.sting.utils.*; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java rename to java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java index e29054893..c5a3b6f2a 100644 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java +++ b/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java @@ -21,14 +21,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.contexts.variantcontext; +package org.broadinstitute.sting.utils.variantcontext; import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.MapContext; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.utils.Utils; -import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.*; diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java index 822034720..dacaf2738 100755 --- a/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/java/test/org/broadinstitute/sting/WalkerTest.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting; import org.apache.commons.lang.StringUtils; import org.broad.tribble.Tribble; import org.broad.tribble.index.IndexFactory; -import org.broad.tribble.vcf.VCFCodec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java index 8e04fd24e..59405c065 100644 --- a/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSourceUnitTest.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.gatk.datasources.sample; import net.sf.samtools.SAMFileHeader; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.StingException; diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java index 218948c52..e475e732d 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java @@ -28,9 +28,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.Tribble; import org.broad.tribble.index.Index; -import org.broad.tribble.vcf.VCF3Codec; -import org.broad.tribble.vcf.VCFCodec; -import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; +import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java index 2eef77400..a64d0b5ab 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java @@ -1,18 +1,17 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broad.tribble.readers.AsciiLineReader; -import org.broad.tribble.vcf.VCFCodec; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.testng.Assert; import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderUnitTest; -import org.broadinstitute.sting.utils.vcf.VCFUtils; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.testng.annotations.Test; import java.io.StringBufferInputStream; import java.util.ArrayList; -import java.util.List; import java.util.Set; /** diff --git a/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java b/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java new file mode 100644 index 000000000..2e618d5eb --- /dev/null +++ b/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java @@ -0,0 +1,162 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.codecs.hapmap; + +import org.broad.tribble.annotation.Strand; +import org.broad.tribble.readers.AsciiLineReader; +import org.testng.Assert; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.IOException; + +/** + * Unit tests for the HapMap codec + */ +public class HapMapUnitTest { + // our sample hapmap file + private final static File hapMapFile = new File("testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap"); + private final static String knownLine = "rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_r" + + "s2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TC TT CT CC CC CC CC CC CC CC CC CC"; + /** + * test reading the header off of the file. We take in the file, read off the first line, + * close the reader, and then ask the HapMap decoder for the header with a new reader. These should + * be equal (i.e. they return the same object). + */ + @Test + public void testReadHeader() { + HapMapCodec codec = new HapMapCodec(); + AsciiLineReader reader = getReader(); + try { + String header = reader.readLine(); + reader.close(); + Assert.assertTrue(header.equals((String)codec.readHeader(getReader()))); + } catch (IOException e) { + Assert.fail("Unable to read from file " + hapMapFile); + } + reader.close(); + } + + @Test + public void testKnownRecordConversion() { + HapMapCodec codec = new HapMapCodec(); + HapMapFeature feature = (HapMapFeature)codec.decode(knownLine); + + + // check that the alleles are right + Assert.assertEquals(feature.getAlleles().length,2); + Assert.assertTrue("C".equals(feature.getAlleles()[0])); + Assert.assertTrue("T".equals(feature.getAlleles()[1])); + + // check the name + Assert.assertTrue("rs2185539".equals(feature.getName())); + + // check the position + Assert.assertEquals(feature.getStart(),556738); + Assert.assertEquals(feature.getEnd(),556738); + + // check the contig + Assert.assertTrue("chr1".equals(feature.getChr())); + + // check the assembly, center, protLSID, assayLSID, panelLSID, and qccode + Assert.assertTrue("ncbi_b36".equals(feature.getAssembly())); + Assert.assertTrue("bbs".equals(feature.getCenter())); + Assert.assertTrue("urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1".equals(feature.getProtLSID())); + Assert.assertTrue("urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2185539:1".equals(feature.getAssayLSID())); + Assert.assertTrue("urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4".equals(feature.getPanelLSID())); + Assert.assertTrue("QC+".equals(feature.getQCCode())); + + // check the strand + Assert.assertEquals(feature.getStrand(),Strand.POSITIVE); + + // check the genotypes + int x = 0; + for (; x < feature.getGenotypes().length; x++) { + switch (x) { + case 1: Assert.assertTrue("TC".equals(feature.getGenotypes()[x])); break; + case 2: Assert.assertTrue("TT".equals(feature.getGenotypes()[x])); break; + case 3: Assert.assertTrue("CT".equals(feature.getGenotypes()[x])); break; + default: Assert.assertTrue("CC".equals(feature.getGenotypes()[x])); break; + } + } + // assert that we found the correct number of records + Assert.assertEquals(x,13); + } + + @Test + public void testReadCorrectNumberOfRecords() { + // setup the record for reading our 500 line file (499 records, 1 header line) + HapMapCodec codec = new HapMapCodec(); + AsciiLineReader reader = getReader(); + + String line = null; + int count = 0; + try { + codec.readHeader(reader); + line = reader.readLine(); + while (line != null) { + HapMapFeature feature = (HapMapFeature) codec.decode(line); + line = reader.readLine(); + ++count; + } + } catch (IOException e) { + Assert.fail("IOException " + e.getMessage()); + } + reader.close(); + Assert.assertEquals(count,499); + } + + @Test + public void testGetSampleNames() { + // setup the record for reading our 500 line file (499 records, 1 header line) + HapMapCodec codec = new HapMapCodec(); + AsciiLineReader reader = getReader(); + + String line = null; + try { + codec.readHeader(reader); + line = reader.readLine(); + HapMapFeature feature = (HapMapFeature) codec.decode(line); + Assert.assertEquals(feature.getSampleIDs().length,87); + + } catch (IOException e) { + Assert.fail("IOException " + e.getMessage()); + } + reader.close(); + } + + + public AsciiLineReader getReader() { + try { + return new AsciiLineReader(new FileInputStream(hapMapFile)); + } catch (FileNotFoundException e) { + Assert.fail("Unable to open hapmap file : " + hapMapFile); + } + return null; // for intellij, it doesn't know that assert.fail is fatal + } + +} diff --git a/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java new file mode 100755 index 000000000..3929ff388 --- /dev/null +++ b/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java @@ -0,0 +1,81 @@ +package org.broadinstitute.sting.utils.codecs.vcf; + +import org.broad.tribble.Tribble; +import org.broad.tribble.index.*; +import org.broad.tribble.iterators.CloseableTribbleIterator; +import org.broad.tribble.source.BasicFeatureSource; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.testng.Assert; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.IOException; +import java.util.*; + +/** + * tests out the various functions in the index factory class + */ +public class IndexFactoryUnitTest { + + File inputFile = new File("testdata/HiSeq.10000.vcf"); + File outputFile = new File("testdata/onTheFlyOutputTest.vcf"); + File outputFileIndex = Tribble.indexFile(outputFile); + + /** + * test out scoring the indexes + */ + @Test + public void testScoreIndexes() { + /*// make a list of indexes to score + Map creators = new HashMap(); + // add a linear index with the default bin size + LinearIndexCreator linearNormal = new LinearIndexCreator(); + linearNormal.initialize(inputFile, linearNormal.defaultBinSize()); + creators.add(LInearIndexlinearNormal); + + // create a tree index with a small index size + IntervalIndexCreator treeSmallBin = new IntervalIndexCreator(); + treeSmallBin.initialize(inputFile, Math.max(200,treeSmallBin.defaultBinSize()/10)); + creators.add(treeSmallBin); + + List indexes = new ArrayList(); + for (IndexCreator creator : creators) + indexes.add(creator.finalizeIndex(0)); + + ArrayList scores = IndexFactory.scoreIndexes(0.5,indexes,100, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); + System.err.println("scores are : "); + for (Double score : scores) { + System.err.println(score); +*/ + } + + // + // test out scoring the indexes + // + @Test + public void testOnTheFlyIndexing1() throws IOException { + Index indexFromInputFile = IndexFactory.createIndex(inputFile, new VCFCodec()); + if ( outputFileIndex.exists() ) { + System.err.println("Deleting " + outputFileIndex); + outputFileIndex.delete(); + } + + for ( int maxRecords : Arrays.asList(0, 1, 10, 100, 1000, -1)) { + BasicFeatureSource source = new BasicFeatureSource(inputFile.getAbsolutePath(), indexFromInputFile, new VCFCodec()); + + int counter = 0; + VCFWriter writer = new StandardVCFWriter(outputFile); + writer.writeHeader((VCFHeader)source.getHeader()); + CloseableTribbleIterator it = source.iterator(); + while (it.hasNext() && (counter++ < maxRecords || maxRecords == -1) ) { + VariantContext vc = it.next(); + writer.add(vc, vc.getReferenceBaseForIndel()); + } + writer.close(); + + // test that the input index is the same as the one created from the identical input file + // test that the dynamic index is the same as the output index, which is equal to the input index + Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(outputFile, outputFileIndex, new VCFCodec())); + } + } +} diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java index 88c1b8294..c4ca6a551 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils.genotype.vcf; import org.broad.tribble.readers.AsciiLineReader; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; @@ -11,8 +11,6 @@ import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.io.StringBufferInputStream; -import java.util.ArrayList; -import java.util.List; /** * Created by IntelliJ IDEA. diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java index 3552af037..34a2e616a 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java @@ -2,10 +2,10 @@ package org.broadinstitute.sting.utils.genotype.vcf; import org.broad.tribble.Tribble; import org.broad.tribble.readers.AsciiLineReader; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.Genotype; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; diff --git a/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java new file mode 100755 index 000000000..ed9805d19 --- /dev/null +++ b/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java @@ -0,0 +1,217 @@ +/* + * Copyright (c) 2010 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +// our package +package org.broadinstitute.sting.utils.variantcontext; + + +// the imports for unit testing. + +import org.testng.Assert; +import org.testng.annotations.BeforeSuite; +import org.testng.annotations.BeforeTest; +import org.testng.annotations.Test; + +// public Allele(byte[] bases, boolean isRef) { +// public Allele(boolean isRef) { +// public Allele(String bases, boolean isRef) { +// public boolean isNullAllele() { return length() == 0; } +// public boolean isNonNullAllele() { return ! isNullAllele(); } +// public boolean isReference() { return isRef; } +// public boolean isNonReference() { return ! isReference(); } +// public byte[] getBases() { return bases; } +// public boolean equals(Allele other) { +// public int length() { + +/** + * Basic unit test for RecalData + */ +public class AlleleUnitTest { + Allele ARef, del, delRef, A, T, ATIns, ATCIns, NoCall; + + @BeforeSuite + public void before() { + del = Allele.create("-"); + delRef = Allele.create("-", true); + + A = Allele.create("A"); + ARef = Allele.create("A", true); + T = Allele.create("T"); + + ATIns = Allele.create("AT"); + ATCIns = Allele.create("ATC"); + + NoCall = Allele.create("."); + } + + @Test + public void testCreatingSNPAlleles() { + Assert.assertTrue(A.isNonReference()); + Assert.assertFalse(A.isReference()); + Assert.assertTrue(A.basesMatch("A")); + Assert.assertEquals(A.length(), 1); + Assert.assertTrue(A.isNonNull()); + Assert.assertFalse(A.isNull()); + + Assert.assertTrue(ARef.isReference()); + Assert.assertFalse(ARef.isNonReference()); + Assert.assertTrue(ARef.basesMatch("A")); + Assert.assertFalse(ARef.basesMatch("T")); + + Assert.assertTrue(T.isNonReference()); + Assert.assertFalse(T.isReference()); + Assert.assertTrue(T.basesMatch("T")); + Assert.assertFalse(T.basesMatch("A")); + } + + @Test + public void testCreatingNoCallAlleles() { + Assert.assertTrue(NoCall.isNonReference()); + Assert.assertFalse(NoCall.isReference()); + Assert.assertFalse(NoCall.basesMatch(".")); + Assert.assertEquals(NoCall.length(), 0); + Assert.assertTrue(NoCall.isNonNull()); + Assert.assertFalse(NoCall.isNull()); + } + + + @Test + public void testCreatingIndelAlleles() { + Assert.assertEquals(ATIns.length(), 2); + Assert.assertEquals(ATCIns.length(), 3); + Assert.assertEquals(ATIns.getBases(), "AT".getBytes()); + Assert.assertEquals(ATCIns.getBases(), "ATC".getBytes()); + + Assert.assertTrue(del.isNonReference()); + Assert.assertFalse(delRef.isNonReference()); + Assert.assertFalse(del.isReference()); + Assert.assertTrue(delRef.isReference()); + Assert.assertFalse(del.basesMatch("-")); + Assert.assertTrue(del.basesMatch("")); + Assert.assertEquals(del.length(), 0); + Assert.assertFalse(del.isNonNull()); + Assert.assertTrue(del.isNull()); + } + + + @Test + public void testConstructors1() { + Allele a1 = Allele.create("A"); + Allele a2 = Allele.create("A".getBytes()); + Allele a3 = Allele.create("A"); + Allele a4 = Allele.create("A", true); + + Assert.assertTrue(a1.equals(a2)); + Assert.assertTrue(a1.equals(a3)); + Assert.assertFalse(a1.equals(a4)); + } + + @Test + public void testDelConstructors() { + Allele a1 = Allele.create("-"); + Allele a2 = Allele.create("-".getBytes()); + Allele a3 = Allele.create(""); + Allele a4 = Allele.create("", true); + + Assert.assertTrue(a1.equals(a2)); + Assert.assertTrue(a1.equals(a3)); + Assert.assertFalse(a1.equals(a4)); + } + + @Test + public void testInsConstructors() { + Allele a1 = Allele.create("AC"); + Allele a2 = Allele.create("AC".getBytes()); + Allele a3 = Allele.create("AC"); + Allele a4 = Allele.create("AC", true); + + Assert.assertTrue(a1.equals(a2)); + Assert.assertTrue(a1.equals(a3)); + Assert.assertFalse(a1.equals(a4)); + } + + @Test + public void testEquals() { + Assert.assertTrue(ARef.basesMatch(A)); + Assert.assertFalse(ARef.equals(A)); + Assert.assertFalse(ARef.equals(del)); + Assert.assertFalse(ARef.equals(ATIns)); + Assert.assertFalse(ARef.equals(ATCIns)); + + Assert.assertTrue(T.basesMatch(T)); + Assert.assertFalse(T.basesMatch(A)); + Assert.assertFalse(T.equals(A)); + + Assert.assertTrue(del.basesMatch(del)); + Assert.assertTrue(del.basesMatch(delRef)); + Assert.assertTrue(del.equals(del)); + Assert.assertFalse(del.equals(delRef)); + + Assert.assertTrue(ATIns.equals(ATIns)); + Assert.assertFalse(ATIns.equals(ATCIns)); + Assert.assertTrue(ATIns.basesMatch("AT")); + Assert.assertFalse(ATIns.basesMatch("A")); + Assert.assertFalse(ATIns.basesMatch("ATC")); + + Assert.assertTrue(ATIns.basesMatch("AT")); + Assert.assertFalse(ATIns.basesMatch("ATC")); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs1() { + byte[] foo = null; + Allele.create(foo); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs2() { + Allele.create("x"); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs3() { + Allele.create("--"); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs4() { + Allele.create("-A"); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs5() { + Allele.create("A A"); + } + + @Test + public void testExtend() { + Assert.assertEquals("AT", Allele.extend(Allele.create("A"), "T".getBytes()).toString()); + Assert.assertEquals("ATA", Allele.extend(Allele.create("A"), "TA".getBytes()).toString()); + Assert.assertEquals("A", Allele.extend(Allele.create("-"), "A".getBytes()).toString()); + Assert.assertEquals("A", Allele.extend(Allele.NO_CALL, "A".getBytes()).toString()); + Assert.assertEquals("ATCGA", Allele.extend(Allele.create("AT"), "CGA".getBytes()).toString()); + Assert.assertEquals("ATCGA", Allele.extend(Allele.create("ATC"), "GA".getBytes()).toString()); + } +} \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java new file mode 100755 index 000000000..9243588ab --- /dev/null +++ b/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java @@ -0,0 +1,78 @@ +/* + * Copyright (c) 2010, The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +// our package +package org.broadinstitute.sting.utils.variantcontext; + + +// the imports for unit testing. + + +import org.testng.Assert; +import org.testng.annotations.Test; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; + + +/** + * Basic unit test for Genotype likelihoods objects + */ +public class GenotypeLikelihoodsUnitTest { + double [] v = new double[]{-10.5, -1.25, -5.11}; + final static String vGLString = "-10.50,-1.25,-5.11"; + final static String vPLString = "93,0,39"; + + @Test + public void testFromVector2() { + GenotypeLikelihoods gl = new GenotypeLikelihoods(v); + assertDoubleArraysAreEqual(gl.getAsVector(), v); + Assert.assertEquals(gl.getAsString(), vPLString); + } + + @Test + public void testFromString1() { + GenotypeLikelihoods gl = new GenotypeLikelihoods(vPLString); + assertDoubleArraysAreEqual(gl.getAsVector(), new double[]{-9.3, 0, -3.9}); + Assert.assertEquals(gl.getAsString(), vPLString); + } + + @Test + public void testFromString2() { + GenotypeLikelihoods gl = GenotypeLikelihoods.fromGLField(vGLString); + assertDoubleArraysAreEqual(gl.getAsVector(), v); + Assert.assertEquals(gl.getAsString(), vPLString); + } + + @Test (expectedExceptions = NumberFormatException.class) + public void testErrorBadFormat() { + GenotypeLikelihoods gl = new GenotypeLikelihoods("adf,b,c"); + gl.getAsVector(); + } + + private void assertDoubleArraysAreEqual(double[] v1, double[] v2) { + Assert.assertEquals(v1.length, v2.length); + for ( int i = 0; i < v1.length; i++ ) { + Assert.assertEquals(v1[i], v2[i], 1e-6); + } + } +} \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java new file mode 100755 index 000000000..e82817714 --- /dev/null +++ b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java @@ -0,0 +1,458 @@ +// our package +package org.broadinstitute.sting.utils.variantcontext; + + +// the imports for unit testing. + + +import org.testng.Assert; +import org.testng.annotations.BeforeSuite; +import org.testng.annotations.BeforeTest; +import org.testng.annotations.Test; + +import java.util.Arrays; +import java.util.List; + + +/** + * Basic unit test for RecalData + */ +public class VariantContextUnitTest { + Allele A, Aref, T, Tref; + Allele del, delRef, ATC, ATCref; + + // A [ref] / T at 10 + String snpLoc = "chr1"; + int snpLocStart = 10; + int snpLocStop = 10; + + // - / ATC [ref] from 20-23 + String delLoc = "chr1"; + int delLocStart = 20; + int delLocStop = 23; + + // - [ref] / ATC from 20-20 + String insLoc = "chr1"; + int insLocStart = 20; + int insLocStop = 20; + + // - / A / T / ATC [ref] from 20-23 + String mixedLoc = "chr1"; + int mixedLocStart = 20; + int mixedLocStop = 23; + + @BeforeSuite + public void before() { + del = Allele.create("-"); + delRef = Allele.create("-", true); + + A = Allele.create("A"); + Aref = Allele.create("A", true); + T = Allele.create("T"); + Tref = Allele.create("T", true); + + ATC = Allele.create("ATC"); + ATCref = Allele.create("ATC", true); + } + + @Test + public void testDetermineTypes() { + Allele ACref = Allele.create("AC", true); + Allele AC = Allele.create("AC"); + Allele AT = Allele.create("AT"); + Allele C = Allele.create("C"); + Allele CAT = Allele.create("CAT"); + Allele TAref = Allele.create("TA", true); + Allele TA = Allele.create("TA"); + Allele TC = Allele.create("TC"); + Allele symbolic = Allele.create(""); + + // test REF + List alleles = Arrays.asList(Tref); + VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.NO_VARIATION); + + // test SNPs + alleles = Arrays.asList(Tref, A); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.SNP); + + alleles = Arrays.asList(Tref, A, C); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.SNP); + + // test MNPs + alleles = Arrays.asList(ACref, TA); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.MNP); + + alleles = Arrays.asList(ATCref, CAT, Allele.create("GGG")); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.MNP); + + // test INDELs + alleles = Arrays.asList(Aref, ATC); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); + + alleles = Arrays.asList(ATCref, A); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); + + alleles = Arrays.asList(Tref, TA, TC); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); + + alleles = Arrays.asList(ATCref, A, AC); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); + + alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC")); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); + + // test MIXED + alleles = Arrays.asList(TAref, T, TC); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); + + alleles = Arrays.asList(TAref, T, AC); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); + + alleles = Arrays.asList(ACref, ATC, AT); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); + + alleles = Arrays.asList(Aref, T, symbolic); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); + + // test SYMBOLIC + alleles = Arrays.asList(Tref, symbolic); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC); + } + + @Test + public void testCreatingSNPVariantContext() { + + List alleles = Arrays.asList(Aref, T); + VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + + Assert.assertEquals(vc.getChr(), snpLoc); + Assert.assertEquals(vc.getStart(), snpLocStart); + Assert.assertEquals(vc.getEnd(), snpLocStop); + Assert.assertEquals(vc.getType(), VariantContext.Type.SNP); + Assert.assertTrue(vc.isSNP()); + Assert.assertFalse(vc.isIndel()); + Assert.assertFalse(vc.isInsertion()); + Assert.assertFalse(vc.isDeletion()); + Assert.assertFalse(vc.isMixed()); + Assert.assertTrue(vc.isBiallelic()); + Assert.assertEquals(vc.getNAlleles(), 2); + + Assert.assertEquals(vc.getReference(), Aref); + Assert.assertEquals(vc.getAlleles().size(), 2); + Assert.assertEquals(vc.getAlternateAlleles().size(), 1); + Assert.assertEquals(vc.getAlternateAllele(0), T); + + Assert.assertFalse(vc.hasGenotypes()); + + Assert.assertEquals(vc.getSampleNames().size(), 0); + } + + @Test + public void testCreatingRefVariantContext() { + List alleles = Arrays.asList(Aref); + VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); + + Assert.assertEquals(vc.getChr(), snpLoc); + Assert.assertEquals(vc.getStart(), snpLocStart); + Assert.assertEquals(vc.getEnd(), snpLocStop); + Assert.assertEquals(VariantContext.Type.NO_VARIATION, vc.getType()); + Assert.assertFalse(vc.isSNP()); + Assert.assertFalse(vc.isIndel()); + Assert.assertFalse(vc.isInsertion()); + Assert.assertFalse(vc.isDeletion()); + Assert.assertFalse(vc.isMixed()); + Assert.assertFalse(vc.isBiallelic()); + Assert.assertEquals(vc.getNAlleles(), 1); + + Assert.assertEquals(vc.getReference(), Aref); + Assert.assertEquals(vc.getAlleles().size(), 1); + Assert.assertEquals(vc.getAlternateAlleles().size(), 0); + //Assert.assertEquals(vc.getAlternateAllele(0), T); + + Assert.assertFalse(vc.hasGenotypes()); + Assert.assertEquals(vc.getSampleNames().size(), 0); + } + + @Test + public void testCreatingDeletionVariantContext() { + List alleles = Arrays.asList(ATCref, del); + VariantContext vc = new VariantContext("test", delLoc, delLocStart, delLocStop, alleles); + + Assert.assertEquals(vc.getChr(), delLoc); + Assert.assertEquals(vc.getStart(), delLocStart); + Assert.assertEquals(vc.getEnd(), delLocStop); + Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); + Assert.assertFalse(vc.isSNP()); + Assert.assertTrue(vc.isIndel()); + Assert.assertFalse(vc.isInsertion()); + Assert.assertTrue(vc.isDeletion()); + Assert.assertFalse(vc.isMixed()); + Assert.assertTrue(vc.isBiallelic()); + Assert.assertEquals(vc.getNAlleles(), 2); + + Assert.assertEquals(vc.getReference(), ATCref); + Assert.assertEquals(vc.getAlleles().size(), 2); + Assert.assertEquals(vc.getAlternateAlleles().size(), 1); + Assert.assertEquals(vc.getAlternateAllele(0), del); + + Assert.assertFalse(vc.hasGenotypes()); + + Assert.assertEquals(vc.getSampleNames().size(), 0); + } + + @Test + public void testCreatingInsertionVariantContext() { + List alleles = Arrays.asList(delRef, ATC); + VariantContext vc = new VariantContext("test", insLoc, insLocStart, insLocStop, alleles); + + Assert.assertEquals(vc.getChr(), insLoc); + Assert.assertEquals(vc.getStart(), insLocStart); + Assert.assertEquals(vc.getEnd(), insLocStop); + Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); + Assert.assertFalse(vc.isSNP()); + Assert.assertTrue(vc.isIndel()); + Assert.assertTrue(vc.isInsertion()); + Assert.assertFalse(vc.isDeletion()); + Assert.assertFalse(vc.isMixed()); + Assert.assertTrue(vc.isBiallelic()); + Assert.assertEquals(vc.getNAlleles(), 2); + + Assert.assertEquals(vc.getReference(), delRef); + Assert.assertEquals(vc.getAlleles().size(), 2); + Assert.assertEquals(vc.getAlternateAlleles().size(), 1); + Assert.assertEquals(vc.getAlternateAllele(0), ATC); + Assert.assertFalse(vc.hasGenotypes()); + + Assert.assertEquals(vc.getSampleNames().size(), 0); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs1() { + new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref)); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs2() { + new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del)); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgs3() { + new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(del)); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgsDuplicateAlleles1() { + new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, T, T)); + } + + @Test (expectedExceptions = IllegalArgumentException.class) + public void testBadConstructorArgsDuplicateAlleles2() { + new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, A)); + } + + @Test (expectedExceptions = IllegalStateException.class) + public void testBadLoc1() { + List alleles = Arrays.asList(Aref, T, del); + new VariantContext("test", delLoc, delLocStart, delLocStop, alleles); + } + + @Test + public void testAccessingSimpleSNPGenotypes() { + List alleles = Arrays.asList(Aref, T); + + Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10); + Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10); + Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10); + + VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3)); + + Assert.assertTrue(vc.hasGenotypes()); + Assert.assertFalse(vc.isMonomorphic()); + Assert.assertTrue(vc.isPolymorphic()); + Assert.assertEquals(vc.getSampleNames().size(), 3); + + Assert.assertEquals(vc.getGenotypes().size(), 3); + Assert.assertEquals(vc.getGenotypes().get("AA"), g1); + Assert.assertEquals(vc.getGenotype("AA"), g1); + Assert.assertEquals(vc.getGenotypes().get("AT"), g2); + Assert.assertEquals(vc.getGenotype("AT"), g2); + Assert.assertEquals(vc.getGenotypes().get("TT"), g3); + Assert.assertEquals(vc.getGenotype("TT"), g3); + + Assert.assertTrue(vc.hasGenotype("AA")); + Assert.assertTrue(vc.hasGenotype("AT")); + Assert.assertTrue(vc.hasGenotype("TT")); + Assert.assertFalse(vc.hasGenotype("foo")); + Assert.assertFalse(vc.hasGenotype("TTT")); + Assert.assertFalse(vc.hasGenotype("at")); + Assert.assertFalse(vc.hasGenotype("tt")); + + Assert.assertEquals(vc.getChromosomeCount(), 6); + Assert.assertEquals(vc.getChromosomeCount(Aref), 3); + Assert.assertEquals(vc.getChromosomeCount(T), 3); + } + + @Test + public void testAccessingCompleteGenotypes() { + List alleles = Arrays.asList(Aref, T, del); + + Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10); + Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10); + Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10); + Genotype g4 = new Genotype("Td", Arrays.asList(T, del), 10); + Genotype g5 = new Genotype("dd", Arrays.asList(del, del), 10); + Genotype g6 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10); + + VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3, g4, g5, g6)); + + Assert.assertTrue(vc.hasGenotypes()); + Assert.assertFalse(vc.isMonomorphic()); + Assert.assertTrue(vc.isPolymorphic()); + Assert.assertEquals(vc.getGenotypes().size(), 6); + + Assert.assertEquals(3, vc.getGenotypes(Arrays.asList("AA", "Td", "dd")).size()); + + Assert.assertEquals(10, vc.getChromosomeCount()); + Assert.assertEquals(3, vc.getChromosomeCount(Aref)); + Assert.assertEquals(4, vc.getChromosomeCount(T)); + Assert.assertEquals(3, vc.getChromosomeCount(del)); + Assert.assertEquals(2, vc.getChromosomeCount(Allele.NO_CALL)); + } + + @Test + public void testAccessingRefGenotypes() { + List alleles1 = Arrays.asList(Aref, T); + List alleles2 = Arrays.asList(Aref); + List alleles3 = Arrays.asList(Aref, T, del); + for ( List alleles : Arrays.asList(alleles1, alleles2, alleles3)) { + Genotype g1 = new Genotype("AA1", Arrays.asList(Aref, Aref), 10); + Genotype g2 = new Genotype("AA2", Arrays.asList(Aref, Aref), 10); + Genotype g3 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10); + VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3)); + + Assert.assertTrue(vc.hasGenotypes()); + Assert.assertTrue(vc.isMonomorphic()); + Assert.assertFalse(vc.isPolymorphic()); + Assert.assertEquals(vc.getGenotypes().size(), 3); + + Assert.assertEquals(4, vc.getChromosomeCount()); + Assert.assertEquals(4, vc.getChromosomeCount(Aref)); + Assert.assertEquals(0, vc.getChromosomeCount(T)); + Assert.assertEquals(2, vc.getChromosomeCount(Allele.NO_CALL)); + } + } + + @Test + public void testFilters() { + List alleles = Arrays.asList(Aref, T, del); + Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10); + Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10); + MutableVariantContext vc = new MutableVariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2)); + + Assert.assertTrue(vc.isNotFiltered()); + Assert.assertFalse(vc.isFiltered()); + Assert.assertEquals(0, vc.getFilters().size()); + + vc.addFilter("BAD_SNP_BAD!"); + + Assert.assertFalse(vc.isNotFiltered()); + Assert.assertTrue(vc.isFiltered()); + Assert.assertEquals(1, vc.getFilters().size()); + + vc.addFilters(Arrays.asList("REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE")); + + Assert.assertFalse(vc.isNotFiltered()); + Assert.assertTrue(vc.isFiltered()); + Assert.assertEquals(3, vc.getFilters().size()); + + vc.clearFilters(); + + Assert.assertTrue(vc.isNotFiltered()); + Assert.assertFalse(vc.isFiltered()); + Assert.assertEquals(0, vc.getFilters().size()); + } + + @Test + public void testVCromGenotypes() { + List alleles = Arrays.asList(Aref, T, del); + Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10); + Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10); + Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10); + Genotype g4 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10); + Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10); + VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5)); + + VariantContext vc12 = vc.subContextFromGenotypes(Arrays.asList(g1,g2)); + VariantContext vc1 = vc.subContextFromGenotypes(Arrays.asList(g1)); + VariantContext vc23 = vc.subContextFromGenotypes(Arrays.asList(g2, g3)); + VariantContext vc4 = vc.subContextFromGenotypes(Arrays.asList(g4)); + VariantContext vc14 = vc.subContextFromGenotypes(Arrays.asList(g1, g4)); + VariantContext vc5 = vc.subContextFromGenotypes(Arrays.asList(g5)); + + Assert.assertTrue(vc12.isPolymorphic()); + Assert.assertTrue(vc23.isPolymorphic()); + Assert.assertTrue(vc1.isMonomorphic()); + Assert.assertTrue(vc4.isMonomorphic()); + Assert.assertTrue(vc14.isMonomorphic()); + Assert.assertTrue(vc5.isPolymorphic()); + + Assert.assertTrue(vc12.isSNP()); + Assert.assertTrue(vc12.isVariant()); + Assert.assertTrue(vc12.isBiallelic()); + + Assert.assertFalse(vc1.isSNP()); + Assert.assertFalse(vc1.isVariant()); + Assert.assertFalse(vc1.isBiallelic()); + + Assert.assertTrue(vc23.isSNP()); + Assert.assertTrue(vc23.isVariant()); + Assert.assertTrue(vc23.isBiallelic()); + + Assert.assertFalse(vc4.isSNP()); + Assert.assertFalse(vc4.isVariant()); + Assert.assertFalse(vc4.isBiallelic()); + + Assert.assertFalse(vc14.isSNP()); + Assert.assertFalse(vc14.isVariant()); + Assert.assertFalse(vc14.isBiallelic()); + + Assert.assertTrue(vc5.isIndel()); + Assert.assertTrue(vc5.isDeletion()); + Assert.assertTrue(vc5.isVariant()); + Assert.assertTrue(vc5.isBiallelic()); + + Assert.assertEquals(3, vc12.getChromosomeCount(Aref)); + Assert.assertEquals(1, vc23.getChromosomeCount(Aref)); + Assert.assertEquals(2, vc1.getChromosomeCount(Aref)); + Assert.assertEquals(0, vc4.getChromosomeCount(Aref)); + Assert.assertEquals(2, vc14.getChromosomeCount(Aref)); + Assert.assertEquals(0, vc5.getChromosomeCount(Aref)); + } + + + @Test + public void testManipulatingAlleles() { + // todo -- add tests that call add/set/remove + } + + @Test + public void testManipulatingGenotypes() { + // todo -- add tests that call add/set/remove + } +} diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java similarity index 96% rename from java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java rename to java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java index 4de413334..b5f6b1b1a 100644 --- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java @@ -21,11 +21,9 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.contexts.variantcontext; +package org.broadinstitute.sting.utils.variantcontext; import net.sf.samtools.SAMFileHeader; -import org.broad.tribble.util.variantcontext.Allele; -import org.broad.tribble.util.variantcontext.VariantContext; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala index 91b7bd874..f2592e05c 100644 --- a/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala +++ b/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala @@ -5,7 +5,7 @@ import org.apache.commons.io.FilenameUtils import scala.io.Source._ import net.sf.samtools.SAMFileReader import org.broad.tribble.source.BasicFeatureSource -import org.broad.tribble.vcf.{VCFHeader, VCFCodec} +import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec} import scala.collection.JavaConversions._ object VCF_BAM_utilities { @@ -56,4 +56,4 @@ object VCF_BAM_utilities { val l: List[File] = Nil return l ++ findBAMsForSamplesHelper(samples) } -} \ No newline at end of file +} diff --git a/testdata/HiSeq.10000.vcf b/testdata/HiSeq.10000.vcf new file mode 100644 index 000000000..ac0107746 --- /dev/null +++ b/testdata/HiSeq.10000.vcf @@ -0,0 +1,10000 @@ +##fileformat=VCFv4.0 +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= 0.06"> +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##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" +##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" +##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.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.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=[QUAL < 50.0, MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1), AB > 0.75 && DP > 40, DP > 120 || SB > -0.10] filterName=[LowQual, HARD_TO_VALIDATE, ABFilter, DPFilter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=10 maskName=Mask NO_HEADER=false" +##source=VariantOptimizer +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +chr1 109 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1019;Dels=0.00;HRun=0;HaplotypeScore=686.65;MQ=19.20;MQ0=288;OQ=2175.54;QD=2.13;SB=-1042.18 GT:AD:DP:GL:GQ 0/1:610,327:308:-316.30,-95.47,-803.03:99 +chr1 147 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=348;Dels=0.01;HRun=2;HaplotypeScore=268.66;MQ=20.23;MQ0=105;OQ=196.24;QD=0.56;SB=-76.48 GT:AD:DP:GL:GQ 0/1:294,49:118:-57.87,-34.96,-338.46:99 +chr1 177 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=432;Dels=0.02;HRun=2;HaplotypeScore=404.17;MQ=17.76;MQ0=153;OQ=697.20;QD=1.61;SB=-140.54 GT:AD:DP:GL:GQ 0/1:283,140:122:-108.58,-35.57,-292.84:99 +chr1 180 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=630;Dels=0.01;HRun=2;HaplotypeScore=495.41;MQ=14.22;MQ0=327;OQ=885.33;QD=1.41;SB=-412.44 GT:AD:DP:GL:GQ 0/1:466,154:104:-122.27,-30.46,-246.17:99 +chr1 234 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=336;Dels=0.00;HRun=1;HaplotypeScore=423.95;MQ=19.45;MQ0=111;OQ=596.60;QD=1.78;SB=-230.12 GT:AD:DP:GL:GQ 0/1:267,67:106:-94.87,-31.93,-297.68:99 +chr1 235 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=326;Dels=0.00;HRun=2;HaplotypeScore=391.04;MQ=19.68;MQ0=106;OQ=580.03;QD=1.78;SB=-219.50 GT:AD:DP:GL:GQ 0/1:274,47:105:-99.60,-38.31,-293.27:99 +chr1 250 . A C 22.88 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=182;Dels=0.01;HRun=3;HaplotypeScore=244.83;MQ=21.91;MQ0=52;QD=0.13;SB=-23.67 GT:AD:DP:GL:GQ 0/1:148,33:70:-26.66,-21.09,-215.78:55.69 +chr1 291 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=284.50;MQ=20.72;MQ0=39;OQ=529.94;QD=3.93;SB=-160.31 GT:AD:DP:GL:GQ 0/1:87,43:32:-69.55,-13.28,-54.44:99 +chr1 297 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=214.52;MQ=20.93;MQ0=36;OQ=101.21;QD=0.82;SB=-38.97 GT:AD:DP:GL:GQ 0/1:98,15:30:-33.20,-19.79,-87.91:99 +chr1 309 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=153.70;MQ=21.12;MQ0=35;OQ=53.98;QD=0.46;SB=-50.01 GT:AD:DP:GL:GQ 0/1:103,9:32:-18.33,-9.64,-96.32:86.82 +chr1 321 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=612.30;MQ=19.11;MQ0=29;OQ=136.39;QD=0.67;SB=-61.25 GT:AD:DP:GL:GQ 0/1:171,23:33:-33.14,-16.22,-92.98:99 +chr1 327 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=3;HaplotypeScore=227.75;MQ=19.74;MQ0=24;OQ=143.34;QD=0.69;SB=-63.56 GT:AD:DP:GL:GQ 0/1:183,21:38:-34.61,-16.99,-113.13:99 +chr1 352 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=325;Dels=0.00;HRun=1;HaplotypeScore=437.89;MQ=18.90;MQ0=142;OQ=774.23;QD=2.38;SB=-355.54 GT:AD:DP:GL:GQ 0/1:238,84:81:-104.82,-24.11,-183.81:99 +chr1 354 . C A 24.89 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=486;Dels=0.01;HRun=1;HaplotypeScore=281.11;MQ=16.12;MQ0=261;QD=0.05;SB=17.54 GT:AD:DP:GL:GQ 0/1:459,24:90:-32.28,-26.51,-269.47:57.71 +chr1 469 . C A 22.04 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=82.51;MQ=26.50;MQ0=12;QD=0.39;SB=-7.00 GT:AD:DP:GL:GQ 0/1:34,21:20:-11.52,-6.03,-45.07:54.85 +chr1 664 . C G 30.66 PASS AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=50.85;QD=25.42;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-8.49,-0.60,-0.00:6.02 +chr1 666 . C G 10.99 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=10.99;SB=-10.00 GT:AD:DP:GL:GQ 0/1:0,1:1:-4.35,-0.30,-0.00:1.76 +chr1 2646 rs62635284 G A 0.15 PASS AC=2;AF=1.00;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=9.27;MQ=6.23;MQ0=107;OQ=89.13;QD=0.70;SB=-10.00 GT:AD:DP:GL:GQ 1/1:53,75:3:-12.40,-0.90,-0.00:9.03 +chr1 2979 rs62635286 T G 83.67 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=11.99;MQ0=41;OQ=300.29;QD=4.77;SB=-10.00 GT:AD:DP:GL:GQ 1/1:31,32:9:-33.61,-2.71,-0.00:27.09 +chr1 2981 rs62028691 A G 14.69 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=11.89;MQ0=42;OQ=285.31;QD=4.46;SB=-10.00 GT:AD:DP:GL:GQ 1/1:31,33:9:-32.12,-2.71,-0.00:27.08 +chr1 3759 . C A 0.19 PASS AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=9.71;MQ0=116;OQ=458.45;QD=3.14;SB=-211.61 GT:AD:DP:GL:GQ 0/1:106,40:25:-56.66,-7.53,-33.77:99 +chr1 4536 rs11582131 G C 0.18 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=9.63;MQ=12.37;MQ0=52;OQ=335.66;QD=4.48;SB=8.06 GT:AD:DP:GL:GQ 0/1:42,33:16:-41.67,-4.82,-26.29:99 +chr1 4540 . G A 47.71 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=2;HaplotypeScore=11.12;MQ=11.52;MQ0=49;QD=0.67;SB=8.05 GT:AD:DP:GL:GQ 0/1:66,5:13:-11.97,-3.92,-35.35:80.54 +chr1 4562 rs11490464 C G 0.14 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=2.62;MQ=11.28;MQ0=37;OQ=136.40;QD=2.44;SB=-10.00 GT:AD:DP:GL:GQ 0/1:26,30:9:-19.64,-2.72,-14.87:99 +chr1 4770 rs6682375 A G 0.32 PASS AC=2;AF=1.00;AN=2;DB;DP=121;Dels=0.00;HRun=1;HaplotypeScore=1.93;MQ=26.23;MQ0=31;OQ=2992.25;QD=24.73;SB=-1410.84 GT:AD:DP:GL:GQ 1/1:9,111:84:-306.27,-28.58,-3.46:99 +chr1 4793 rs6682385 A G 0.15 PASS AC=2;AF=1.00;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=8.98;MQ=29.61;MQ0=5;OQ=3517.41;QD=29.56;SB=-1722.01 GT:AD:DP:GL:GQ 1/1:4,115:109:-350.74,-32.88,-0.10:99 +chr1 5074 rs11586607 T G 0.01 FDRtranche2.00to10.00 AC=2;AF=1.00;AN=2;DB;DP=126;Dels=0.00;HRun=1;HaplotypeScore=24.34;MQ=21.42;MQ0=68;OQ=1230.02;QD=9.76;SB=-234.94 GT:AD:DP:GL:GQ 1/1:29,97:39:-130.41,-11.75,-3.82:79.31 +chr1 5137 rs62636497 A T 140.49 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=21.69;MQ0=25;OQ=1453.92;QD=17.73;SB=-222.33 GT:AD:DP:GL:GQ 1/1:0,74:39:-148.99,-11.75,-0.01:99 +chr1 5966 . T G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=129;Dels=0.18;HRun=5;HaplotypeScore=140.84;MQ=21.40;MQ0=8;OQ=1764.68;QD=13.68;SB=-234.42 GT:AD:DP:GL:GQ 1/1:0,106:53:-180.07,-15.66,-0.02:99 +chr1 6092 . C A 11.16 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=9.08;MQ=27.90;MQ0=10;QD=0.08;SB=14.05 GT:AD:DP:GL:GQ 0/1:125,11:94:-32.68,-28.32,-307.61:43.65 +chr1 6120 rs11489794 G C 0.46 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=27.31;MQ0=11;OQ=181.15;QD=2.01;SB=8.06 GT:AD:DP:GL:GQ 0/1:73,17:66:-41.29,-19.89,-251.91:99 +chr1 6151 rs62028673 C G 0.34 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=22.13;MQ0=10;OQ=58.79;QD=1.73;SB=-6.99 GT:AD:DP:GL:GQ 0/1:24,10:14:-13.38,-4.22,-45.26:91.62 +chr1 6241 rs17041382 T C 5.47 PASS AC=1;AF=0.50;AN=2;DB;DP=138;Dels=0.00;HRun=0;HaplotypeScore=4.98;MQ=14.62;MQ0=74;OQ=755.36;QD=5.47;SB=-258.37 GT:AD:DP:GL:GQ 0/1:39,99:33:-88.77,-9.95,-20.05:99 +chr1 6358 rs3210724 G C 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=174;Dels=0.00;HRun=0;HaplotypeScore=19.20;MQ=25.41;MQ0=15;OQ=678.86;QD=3.90;SB=-150.77 GT:AD:DP:GL:GQ 0/1:131,42:113:-105.24,-34.07,-360.44:99 +chr1 6360 rs7359297 A G 49.26 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=2;HaplotypeScore=19.20;MQ=25.54;MQ0=15;QD=0.29;SB=20.10 GT:AD:DP:GL:GQ 0/1:155,16:111:-41.64,-33.43,-398.12:82.10 +chr1 6397 rs15642 C T 157.37 PASS AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=21.39;MQ0=24;OQ=850.53;QD=7.88;SB=-122.64 GT:AD:DP:GL:GQ 0/1:45,63:33:-98.28,-9.94,-33.57:99 +chr1 7270 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=0;HaplotypeScore=18.12;MQ=8.37;MQ0=128;OQ=66.01;QD=0.43;SB=-47.55 GT:AD:DP:GL:GQ 0/1:137,16:8:-12.30,-2.42,-14.38:98.84 +chr1 7558 rs7357853 G A 28.66 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=11.88;MQ0=88;QD=0.23;SB=-10.00 GT:AD:DP:GL:GQ 0/1:113,10:21:-12.48,-6.33,-62.63:61.49 +chr1 7609 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=4.53;MQ=19.87;MQ0=60;OQ=69.47;QD=0.58;SB=-10.00 GT:AD:DP:GL:GQ 0/1:98,22:48:-24.69,-14.46,-166.38:99 +chr1 7766 . C T 24.46 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=9.88;MQ=9.94;MQ0=60;QD=0.35;SB=-10.00 GT:AD:DP:GL:GQ 0/1:66,3:7:-7.84,-2.11,-15.08:57.28 +chr1 9089 rs28609851 T A 1.71 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=14.01;MQ0=34;OQ=172.68;QD=2.93;SB=-37.66 GT:AD:DP:GL:GQ 0/1:50,9:19:-26.28,-5.72,-45.27:99 +chr1 9185 rs2974813 C T 45.14 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=3.92;MQ0=67;QD=0.65;SB=-47.56 GT:AD:DP:GL:GQ 1/1:67,2:2:-7.92,-0.60,-0.00:6.02 +chr1 9721 rs12354145 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=2;HaplotypeScore=26.09;MQ=12.03;MQ0=77;OQ=197.90;QD=1.55;SB=-10.00 GT:AD:DP:GL:GQ 0/1:97,31:18:-28.50,-5.42,-36.05:99 +chr1 9805 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=10.83;MQ0=134;OQ=142.73;QD=0.73;SB=-10.00 GT:AD:DP:GL:GQ 0/1:171,24:24:-24.81,-7.25,-68.77:99 +chr1 9993 rs7354882 G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=155;Dels=0.00;HRun=0;HaplotypeScore=22.48;MQ=21.20;MQ0=19;OQ=727.76;QD=4.70;SB=-285.16 GT:AD:DP:GL:GQ 0/1:126,29:124:-113.46,-37.39,-308.40:99 +chr1 10108 rs6682921 G A 129.70 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=249;Dels=0.00;HRun=1;HaplotypeScore=98.13;MQ=8.71;MQ0=185;QD=0.52;SB=-64.03 GT:AD:DP:GL:GQ 0/1:175,74:25:-23.78,-7.53,-70.54:99 +chr1 10113 rs11490226 T C 60.45 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=252;Dels=0.00;HRun=0;HaplotypeScore=99.00;MQ=8.29;MQ0=191;QD=0.24;SB=-6.56 GT:AD:DP:GL:GQ 0/1:200,52:22:-15.96,-6.63,-68.61:93.28 +chr1 10117 . G A 27.78 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=251;Dels=0.00;HRun=0;HaplotypeScore=92.18;MQ=8.29;MQ0=191;QD=0.11;SB=-12.58 GT:AD:DP:GL:GQ 0/1:210,41:21:-12.39,-6.33,-58.67:60.61 +chr1 10375 rs6683179 G T 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=229;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=7.78;MQ0=173;OQ=50.55;QD=0.22;SB=-10.00 GT:AD:DP:GL:GQ 0/1:152,76:16:-13.16,-4.82,-44.89:83.39 +chr1 10410 rs11489908 A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=236;Dels=0.00;HRun=2;HaplotypeScore=3.67;MQ=7.06;MQ0=196;OQ=84.39;QD=0.36;SB=-10.00 GT:AD:DP:GL:GQ 0/1:188,48:18:-17.15,-5.42,-52.83:99 +chr1 16862 rs376349 A G 0.50 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=2.47;MQ=20.73;MQ0=3;OQ=399.27;QD=24.95;SB=-188.41 GT:AD:DP:GL:GQ 1/1:2,14:12:-43.52,-3.61,-0.00:36.11 +chr1 18110 rs4413987 G A 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=114;Dels=0.00;HRun=0;HaplotypeScore=6.99;MQ=6.98;MQ0=101;OQ=80.12;QD=0.70;SB=-10.00 GT:AD:DP:GL:GQ 0/1:95,19:5:-12.80,-1.51,-7.39:58.87 +chr1 18357 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=8.76;MQ=5.01;MQ0=96;OQ=60.18;QD=0.60;SB=-6.99 GT:AD:DP:GL:GQ 0/1:80,21:4:-10.51,-1.20,-3.97:27.63 +chr1 18421 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=23.14;MQ=14.44;MQ0=48;OQ=339.38;QD=4.35;SB=-90.89 GT:AD:DP:GL:GQ 0/1:55,23:25:-44.76,-7.53,-46.87:99 +chr1 18426 rs4099234 A G 0.05 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=22.14;MQ=14.77;MQ0=46;OQ=857.23;QD=11.13;SB=-429.56 GT:AD:DP:GL:GQ 1/1:24,53:25:-89.32,-7.53,-0.01:75.22 +chr1 18451 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=15;HaplotypeScore=19.76;MQ=19.64;MQ0=16;OQ=152.23;QD=2.67;SB=-85.40 GT:AD:DP:GL:GQ 0/1:45,12:33:-28.45,-9.95,-82.12:99 +chr1 18454 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=47.13;MQ=19.20;MQ0=19;OQ=58.45;QD=0.99;SB=-20.71 GT:AD:DP:GL:GQ 0/1:53,6:35:-19.67,-10.55,-115.15:91.28 +chr1 18526 rs2418705 T A 37.69 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=4.16;MQ0=59;QD=0.62;SB=-10.00 GT:AD:DP:GL:GQ 1/1:52,9:2:-7.18,-0.60,-0.00:6.02 +chr1 18698 rs3871714 A G 0.86 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=9.06;MQ0=38;OQ=98.37;QD=2.19;SB=-10.00 GT:AD:DP:GL:GQ 1/1:27,18:4:-13.37,-1.21,-0.00:12.03 +chr1 18726 rs16924801 C A 45.81 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=3.57;MQ=10.40;MQ0=25;QD=1.27;SB=-10.00 GT:AD:DP:GL:GQ 1/1:31,5:2:-7.99,-0.60,-0.00:6.02 +chr1 20391 rs4248192 C T 0.40 PASS AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=17.17;MQ0=74;OQ=114.21;QD=1.08;SB=-10.00 GT:AD:DP:GL:GQ 0/1:95,11:32:-24.34,-9.64,-88.28:99 +chr1 20411 rs62028215 T G 8.08 PASS AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=3.84;MQ=18.51;MQ0=71;OQ=573.84;QD=5.26;SB=-10.00 GT:AD:DP:GL:GQ 0/1:56,53:38:-72.12,-11.45,-46.57:99 +chr1 20723 rs28673882 G C 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=9.28;MQ=29.99;MQ0=37;OQ=163.32;QD=1.45;SB=40.84 GT:AD:DP:GL:GQ 0/1:100,13:69:-40.42,-20.80,-251.48:99 +chr1 20786 rs806731 G T 139.58 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=34.31;MQ0=5;OQ=1407.60;QD=31.99;SB=-624.57 GT:AD:DP:GL:GQ 1/1:0,44:38:-144.35,-11.44,-0.01:99 +chr1 21158 rs806729 A C 233.61 PASS AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.41;MQ0=5;OQ=71.14;QD=7.90;SB=-10.00 GT:AD:DP:GL:GQ 1/1:6,3:3:-10.60,-0.90,-0.00:9.03 +chr1 30569 rs62101646 G A 24.23 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=13.59;MQ0=55;QD=0.37;SB=-0.99 GT:AD:DP:GL:GQ 0/1:53,12:8:-8.12,-2.41,-18.79:57.05 +chr1 30757 rs56954914 G A 38.24 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=7.79;MQ0=81;QD=0.44;SB=-10.00 GT:AD:DP:GL:GQ 0/1:56,30:4:-8.31,-1.20,-6.94:57.33 +chr1 30916 . C T 44.25 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=6.25;MQ0=41;QD=1.03;SB=-10.00 GT:AD:DP:GL:GQ 1/1:40,3:2:-7.83,-0.60,-0.00:6.02 +chr1 41536 rs2531251 T C 28.51 LowQual AC=1;AF=0.50;AN=2;DB;DP=6;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=19.20;MQ0=3;QD=4.75;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,2:3:-7.04,-0.90,-3.46:25.52 +chr1 41761 . C A 0.43 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=27.62;MQ0=8;OQ=172.06;QD=5.55;SB=14.07 GT:AD:DP:GL:GQ 0/1:17,14:19:-26.21,-5.72,-39.58:99 +chr1 41791 . G A 3.24 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.83;MQ=30.13;MQ0=12;OQ=368.88;QD=8.20;SB=14.07 GT:AD:DP:GL:GQ 0/1:28,17:31:-49.51,-9.34,-69.71:99 +chr1 42101 rs2691277 T G 379.72 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.14;MQ0=8;OQ=1117.45;QD=27.25;SB=-498.06 GT:AD:DP:GL:GQ 1/1:0,41:32:-115.34,-9.64,-0.01:96.29 +chr1 44243 rs2691279 T C 13.38 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=44.42;MQ0=2;QD=0.32;SB=29.13 GT:AD:DP:GL:GQ 0/1:35,7:40:-16.65,-12.05,-143.10:46.01 +chr1 44449 . T C 10.02 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=30.96;MQ0=0;QD=0.25;SB=38.15 GT:AD:DP:GL:GQ 0/1:31,9:34:-14.48,-10.24,-121.45:42.40 +chr1 44539 rs2462492 C T 2.85 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=48.14;MQ0=0;OQ=219.90;QD=4.40;SB=-111.03 GT:AD:DP:GL:GQ 0/1:40,10:50:-40.33,-15.06,-146.68:99 +chr1 44571 . G C 349.91 SnpCluster AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=22.88;MQ=46.02;MQ0=0;QD=5.74;SB=-120.67 GT:AD:DP:GL:GQ 0/1:43,18:49:-53.04,-14.77,-155.67:99 +chr1 44573 . A T 77.97 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=5;HaplotypeScore=28.86;MQ=46.27;MQ0=0;QD=1.22;SB=18.79 GT:AD:DP:GL:GQ 0/1:55,9:53:-27.05,-15.97,-167.03:99 +chr1 44575 . T C 100.77 SnpCluster AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=36.58;MQ=45.60;MQ0=1;QD=1.53;SB=-17.16 GT:AD:DP:GL:GQ 0/1:57,9:54:-29.63,-16.27,-179.47:99 +chr1 44579 . C T 185.88 SnpCluster AC=1;AF=0.50;AN=2;DP=83;Dels=0.04;HRun=5;HaplotypeScore=85.91;MQ=43.82;MQ0=2;QD=2.24;SB=-100.05 GT:AD:DP:GL:GQ 0/1:66,14:58:-39.34,-17.47,-169.22:99 +chr1 44707 . G A 14.95 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=25.67;MQ0=14;OQ=285.82;QD=6.35;SB=-102.92 GT:AD:DP:GL:GQ 0/1:29,16:26:-39.70,-7.83,-56.06:99 +chr1 44948 . T A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=3.69;MQ=36.35;MQ0=4;OQ=152.52;QD=2.99;SB=0.17 GT:AD:DP:GL:GQ 0/1:39,12:36:-29.38,-10.84,-106.91:99 +chr1 45027 rs3091274 C A 22.40 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=21.32;MQ0=9;OQ=324.14;QD=13.51;SB=-88.90 GT:AD:DP:GL:GQ 1/1:0,24:10:-36.00,-3.01,-0.00:30.09 +chr1 45162 rs10399749 C T 268.24 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=27.59;MQ0=3;OQ=1749.04;QD=37.21;SB=-889.19 GT:AD:DP:GL:GQ 1/1:1,46:44:-178.50,-13.25,-0.01:99 +chr1 45189 rs3107975 T C 528.74 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.64;MQ0=0;OQ=1690.04;QD=36.74;SB=-682.96 GT:AD:DP:GL:GQ 1/1:0,46:46:-172.60,-13.85,-0.01:99 +chr1 45408 rs28396308 C T 25.10 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=23.65;MQ0=4;OQ=659.03;QD=19.97;SB=-174.67 GT:AD:DP:GL:GQ 1/1:0,33:17:-69.49,-5.12,-0.00:51.17 +chr1 46501 rs2691308 C T 1.65 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=36.83;MQ0=2;OQ=218.70;QD=3.22;SB=47.17 GT:AD:DP:GL:GQ 0/1:55,13:65:-44.73,-19.58,-190.42:99 +chr1 46662 rs2691309 T C 45.27 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=41.65;MQ0=3;QD=1.29;SB=26.11 GT:AD:DP:GL:GQ 0/1:27,8:32:-17.45,-9.64,-107.04:78.10 +chr1 46896 rs2691311 T C 94.73 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=47.00;MQ0=0;OQ=492.79;QD=6.48;SB=-211.35 GT:AD:DP:GL:GQ 0/1:55,21:75:-75.15,-22.59,-219.09:99 +chr1 46927 rs2548884 G A 0.20 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=44.33;MQ0=0;OQ=115.48;QD=1.89;SB=-71.32 GT:AD:DP:GL:GQ 0/1:53,8:60:-32.90,-18.07,-195.48:99 +chr1 47021 rs6658003 G C 0.57 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=8.74;MQ0=44;OQ=79.96;QD=1.45;SB=-46.90 GT:AD:DP:GL:GQ 0/1:36,19:6:-13.09,-1.81,-12.99:99 +chr1 47109 rs2691313 C G 35.94 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=36.99;MQ0=0;OQ=346.71;QD=6.80;SB=47.18 GT:AD:DP:GL:GQ 0/1:38,13:51:-53.32,-15.37,-164.95:99 +chr1 47155 . C T 135.45 PASS AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=34.92;MQ0=10;OQ=1281.86;QD=17.56;SB=-510.08 GT:AD:DP:GL:GQ 0/1:34,39:60:-149.57,-18.10,-69.03:99 +chr1 47239 rs2854673 C T 32.39 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=43.73;MQ0=3;OQ=244.39;QD=4.61;SB=47.16 GT:AD:DP:GL:GQ 0/1:39,14:49:-42.48,-14.76,-140.73:99 +chr1 47719 . T A 0.78 PASS AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=2;HaplotypeScore=3.14;MQ=19.08;MQ0=29;OQ=670.79;QD=8.49;SB=-194.63 GT:AD:DP:GL:GQ 0/1:47,32:46:-84.22,-13.86,-89.29:99 +chr1 48074 rs2691335 A G 2.10 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.51;MQ0=2;OQ=156.22;QD=22.32;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:5:-19.18,-1.51,-0.00:15.05 +chr1 48634 . T C 2.39 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.66;MQ=33.49;MQ0=8;OQ=733.26;QD=12.22;SB=-133.25 GT:AD:DP:GL:GQ 0/1:32,28:50:-91.67,-15.06,-103.96:99 +chr1 50195 rs62637816 T C 137.58 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=17.45;MQ0=31;OQ=544.88;QD=7.46;SB=-273.42 GT:AD:DP:GL:GQ 0/1:46,26:42:-70.43,-12.65,-88.66:99 +chr1 50884 rs3844232 G A 43.24 PASS AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.69;MQ0=8;OQ=74.12;QD=4.12;SB=-10.00 GT:AD:DP:GL:GQ 0/1:11,7:6:-12.50,-1.81,-9.19:73.80 +chr1 51151 . T A 30.50 LowQual AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.43;MQ0=2;QD=5.08;SB=-37.96 GT:AD:DP:GL:GQ 0/1:4,2:4:-7.54,-1.20,-7.68:63.33 +chr1 51152 . A G 76.91 PASS AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.59;MQ0=2;OQ=62.44;QD=8.92;SB=-39.93 GT:AD:DP:GL:GQ 0/1:4,3:5:-11.03,-1.51,-8.33:68.29 +chr1 51305 rs2531261 A G 318.95 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.94;MQ0=3;OQ=1035.37;QD=25.88;SB=-471.86 GT:AD:DP:GL:GQ 1/1:0,40:29:-107.13,-8.73,-0.01:87.27 +chr1 51850 . A G 82.68 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=39.81;MQ0=7;OQ=720.99;QD=12.22;SB=-171.50 GT:AD:DP:GL:GQ 0/1:32,27:50:-90.45,-15.06,-94.52:99 +chr1 51852 . G C 25.49 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=40.15;MQ0=6;OQ=1021.36;QD=17.61;SB=-245.09 GT:AD:DP:GL:GQ 0/1:31,27:50:-120.48,-15.06,-101.09:99 +chr1 52066 rs28402963 T C 139.56 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=39.80;MQ0=3;OQ=684.28;QD=9.50;SB=-320.22 GT:AD:DP:GL:GQ 0/1:42,30:68:-92.19,-20.48,-169.52:99 +chr1 52134 rs28599927 A G 180.85 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=31.13;MQ0=5;OQ=314.17;QD=8.73;SB=-124.71 GT:AD:DP:GL:GQ 0/1:23,13:30:-43.74,-9.04,-73.62:99 +chr1 52441 rs2531315 G A 15.83 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.89;MQ0=7;OQ=286.62;QD=17.91;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,16:8:-32.24,-2.41,-0.00:24.08 +chr1 52640 rs3844233 A T 1.57 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=20.92;MQ0=32;OQ=114.33;QD=2.04;SB=-23.31 GT:AD:DP:GL:GQ 0/1:45,11:17:-19.84,-5.12,-46.79:99 +chr1 53560 . T C 39.15 PASS AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=25.49;MQ0=11;OQ=919.76;QD=11.22;SB=-454.58 GT:AD:DP:GL:GQ 0/1:47,35:69:-116.05,-20.79,-145.77:99 +chr1 54476 rs1627939 T A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=2;HaplotypeScore=1.16;MQ=27.48;MQ0=38;OQ=233.94;QD=2.36;SB=-139.05 GT:AD:DP:GL:GQ 0/1:84,15:50:-41.74,-15.06,-148.46:99 +chr1 54790 rs996010 G T 31.78 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=23.12;MQ0=20;QD=0.47;SB=29.08 GT:AD:DP:GL:GQ 0/1:55,13:40:-18.51,-12.05,-121.17:64.61 +chr1 54839 rs2854687 C T 10.60 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=27.08;MQ0=0;OQ=1633.87;QD=34.04;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,48:40:-166.98,-12.05,-0.01:99 +chr1 55660 . T C 47.12 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=8.71;MQ0=70;QD=0.52;SB=-10.00 GT:AD:DP:GL:GQ 0/1:73,17:9:-10.71,-2.71,-24.43:79.96 +chr1 55735 . T G 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=7.24;MQ0=61;OQ=58.14;QD=0.81;SB=-10.00 GT:AD:DP:GL:GQ 0/1:55,17:5:-10.60,-1.51,-6.69:51.83 +chr1 56025 rs62639105 A T 0.18 PASS AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=3;HaplotypeScore=1.00;MQ=23.00;MQ0=0;OQ=377.29;QD=31.44;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,11:12:-44.38,-3.61,-3.44:2.23 +chr1 60591 . C T 1.69 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=14.15;MQ0=46;OQ=324.67;QD=4.39;SB=-159.64 GT:AD:DP:GL:GQ 0/1:50,24:28:-44.18,-8.43,-61.59:99 +chr1 60624 . T C 29.51 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=5.38;MQ0=69;QD=0.40;SB=-6.99 GT:AD:DP:GL:GQ 0/1:53,20:3:-7.14,-0.90,-3.77:28.64 +chr1 63704 rs3020697 C T 122.92 PASS AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.04;MQ=34.36;MQ0=1;OQ=168.10;QD=12.93;SB=-51.56 GT:AD:DP:GL:GQ 1/1:0,13:6:-20.39,-1.81,-0.01:18.05 +chr1 64418 . A G 43.84 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;HRun=1;HaplotypeScore=8.82;MQ=6.47;MQ0=82;QD=0.45;SB=-10.00 GT:AD:DP:GL:GQ 1/1:82,16:2:-7.79,-0.60,-0.00:6.02 +chr1 64433 . T A 31.10 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=7.92;MQ0=71;QD=0.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:82,12:3:-7.30,-0.90,-3.84:29.36 +chr1 64544 rs13328683 G T 4.16 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.57;MQ=18.78;MQ0=9;OQ=435.52;QD=13.61;SB=-10.00 GT:AD:DP:GL:GQ 1/1:10,22:12:-47.14,-3.61,-0.00:36.12 +chr1 67325 rs2462497 G A 48.02 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.51;MQ0=2;QD=12.01;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,4:2:-8.21,-0.60,-0.00:6.02 +chr1 72009 . A G 32.65 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=5.60;MQ=18.28;MQ0=7;QD=1.72;SB=-38.67 GT:AD:DP:GL:GQ 0/1:14,5:11:-9.86,-3.31,-31.53:65.48 +chr1 72112 rs1851945 A G 1.46 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=25.77;MQ0=4;OQ=504.38;QD=26.55;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,15:15:-54.03,-4.52,-0.00:45.14 +chr1 72166 rs2907073 T C 81.98 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.95;MQ0=1;OQ=468.64;QD=33.47;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,14:13:-50.45,-3.91,-0.00:39.13 +chr1 72179 rs2260604 A C 22.50 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.51;MQ0=4;OQ=244.12;QD=17.44;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,10:10:-28.01,-3.01,-0.01:30.03 +chr1 72195 . T C 61.39 PASS AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.33;MQ0=10;OQ=206.79;QD=10.34;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,7:10:-26.97,-3.01,-11.90:88.90 +chr1 73690 . A G 59.97 Indel AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=8.93;MQ=23.64;MQ0=3;QD=4.28;SB=-6.99 GT:AD:DP:GL:GQ 0/1:7,7:8:-11.69,-2.41,-21.22:92.80 +chr1 73692 . G A 71.09 Indel AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=3;HaplotypeScore=9.93;MQ=23.64;MQ0=3;QD=5.08;SB=-6.99 GT:AD:DP:GL:GQ 0/1:7,7:8:-12.80,-2.41,-18.45:99 +chr1 73996 . A T 22.55 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=27.59;MQ0=22;OQ=466.23;QD=7.40;SB=-57.87 GT:AD:DP:GL:GQ 0/1:36,27:38:-61.35,-11.44,-82.94:99 +chr1 74170 rs4118012 C A 85.72 PASS AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=197.97;QD=32.99;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,6:6:-23.37,-1.81,-0.00:18.06 +chr1 74355 rs3871778 C G 11.43 PASS AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.46;MQ0=2;OQ=92.52;QD=18.50;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:3:-12.74,-0.90,-0.00:9.03 +chr1 74885 . G A 80.42 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=18.46;MQ0=14;OQ=538.01;QD=13.12;SB=-187.68 GT:AD:DP:GL:GQ 0/1:20,21:26:-64.92,-7.83,-36.63:99 +chr1 80719 . G A 41.54 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=8.20;MQ0=31;QD=1.19;SB=-10.00 GT:AD:DP:GL:GQ 0/1:32,2:3:-8.34,-0.91,-2.50:15.90 +chr1 81004 rs4245761 G T 39.81 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=13.75;MQ0=7;QD=3.32;SB=-10.00 GT:AD:DP:GL:GQ 1/1:7,5:2:-7.39,-0.60,-0.00:6.02 +chr1 81077 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=13;HaplotypeScore=2.26;MQ=18.21;MQ0=7;OQ=85.86;QD=5.05;SB=-62.92 GT:AD:DP:GL:GQ 0/1:11,6:5:-13.38,-1.51,-3.74:22.35 +chr1 81199 rs4245763 A T 30.68 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=13.70;MQ0=7;QD=3.07;SB=-10.00 GT:AD:DP:GL:GQ 1/1:6,4:2:-6.48,-0.60,-0.00:6.01 +chr1 81378 . A C 3.99 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=33.30;MQ0=0;OQ=188.72;QD=4.72;SB=-114.61 GT:AD:DP:GL:GQ 0/1:31,9:34:-32.39,-10.24,-89.64:99 +chr1 81399 rs6702460 G T 307.92 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=32.81;MQ0=0;OQ=1379.58;QD=33.65;SB=-370.87 GT:AD:DP:GL:GQ 1/1:0,41:37:-141.55,-11.14,-0.01:99 +chr1 81444 rs1524604 G A 325.75 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.68;MQ0=1;OQ=1101.93;QD=36.73;SB=-340.44 GT:AD:DP:GL:GQ 1/1:0,30:28:-113.78,-8.43,-0.01:84.28 +chr1 81611 rs4256762 C T 100.30 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=17.29;MQ0=34;OQ=684.35;QD=12.01;SB=-10.00 GT:AD:DP:GL:GQ 1/1:14,43:19:-75.91,-5.72,-3.90:18.23 +chr1 82517 . T C 0.75 PASS AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=13.00;MQ0=6;OQ=70.17;QD=3.19;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,22:3:-10.51,-0.90,-0.00:9.03 +chr1 86134 . C G 0.28 PASS AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=17.64;MQ0=31;OQ=214.58;QD=2.38;SB=-33.05 GT:AD:DP:GL:GQ 0/1:81,9:51:-40.11,-15.36,-187.83:99 +chr1 88546 . G A 0.08 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.25;MQ0=8;OQ=736.28;QD=19.90;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,24:26:-84.74,-7.83,-23.08:99 +chr1 88616 rs4504463 T C 1.95 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.27;MQ0=29;OQ=80.37;QD=1.55;SB=-10.00 GT:AD:DP:GL:GQ 0/1:43,9:21:-17.65,-6.33,-64.09:99 +chr1 88704 . G A 26.43 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=13.14;MQ0=25;QD=0.76;SB=-10.00 GT:AD:DP:GL:GQ 0/1:33,2:8:-8.34,-2.41,-22.88:59.26 +chr1 88715 . A G 0.29 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=13.96;MQ0=21;OQ=53.96;QD=1.74;SB=-10.00 GT:AD:DP:GL:GQ 0/1:28,3:8:-11.09,-2.41,-20.54:86.80 +chr1 88808 . C T 3.03 PASS AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.56;MQ0=9;OQ=459.05;QD=18.36;SB=-49.56 GT:AD:DP:GL:GQ 1/1:1,24:12:-49.49,-3.61,-0.00:36.12 +chr1 88856 rs1851939 G A 178.37 HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=30.10;MQ0=10;QD=3.64;SB=-37.62 GT:AD:DP:GL:GQ 0/1:36,12:37:-32.26,-11.14,-102.50:99 +chr1 88918 . C A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=6.89;MQ=32.20;MQ0=8;OQ=309.74;QD=3.64;SB=-68.70 GT:AD:DP:GL:GQ 0/1:64,21:74:-56.55,-22.29,-199.33:99 +chr1 88963 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=30.09;MQ=26.41;MQ0=31;OQ=291.13;QD=2.62;SB=-116.74 GT:AD:DP:GL:GQ 0/1:88,23:71:-53.80,-21.40,-203.68:99 +chr1 88966 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=24.42;MQ=26.07;MQ0=32;OQ=253.10;QD=2.32;SB=-149.24 GT:AD:DP:GL:GQ 0/1:88,21:67:-48.78,-20.19,-197.64:99 +chr1 89000 . A G 0.14 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=15.31;MQ0=39;OQ=157.34;QD=2.76;SB=-51.84 GT:AD:DP:GL:GQ 0/1:48,9:10:-22.04,-3.02,-12.09:90.71 +chr1 89029 . C T 23.46 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.84;MQ=12.16;MQ0=50;QD=0.36;SB=5.02 GT:AD:DP:GL:GQ 0/1:50,16:9:-8.34,-2.71,-21.03:56.28 +chr1 89043 . T C 25.04 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=9.57;MQ0=58;QD=0.36;SB=-0.97 GT:AD:DP:GL:GQ 0/1:54,16:6:-7.59,-1.81,-16.33:57.86 +chr1 89188 . C T 0.06 PASS AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=2.43;MQ=17.90;MQ0=10;OQ=61.10;QD=3.39;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,3:7:-11.50,-2.11,-14.49:93.93 +chr1 89528 . C T 1.15 PASS AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.04;MQ0=0;OQ=168.19;QD=24.03;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,6:5:-20.38,-1.51,-0.00:15.05 +chr1 90974 rs62639107 G T 14.16 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=10.20;MQ0=34;QD=0.33;SB=-0.97 GT:AD:DP:GL:GQ 0/1:33,10:6:-6.49,-1.81,-14.67:46.83 +chr1 91131 . G A 0.50 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=10.39;MQ0=55;OQ=206.73;QD=2.79;SB=-10.00 GT:AD:DP:GL:GQ 0/1:41,33:9:-26.67,-2.71,-7.60:48.84 +chr1 91212 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=134;Dels=0.01;HRun=13;HaplotypeScore=35.68;MQ=19.40;MQ0=63;OQ=147.19;QD=1.10;SB=-6.99 GT:AD:DP:GL:GQ 0/1:107,25:41:-30.37,-12.37,-109.55:99 +chr1 91252 . A C 43.23 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=1;HaplotypeScore=36.75;MQ=16.93;MQ0=85;QD=0.29;SB=-10.00 GT:AD:DP:GL:GQ 0/1:138,10:43:-20.56,-12.95,-127.64:76.06 +chr1 91549 . A G 49.47 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=209;Dels=0.00;HRun=0;HaplotypeScore=15.98;MQ=27.81;MQ0=39;QD=0.24;SB=65.80 GT:AD:DP:GL:GQ 0/1:179,30:144:-51.61,-43.38,-519.29:82.31 +chr1 91758 . G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=22.49;MQ0=25;OQ=143.40;QD=2.17;SB=15.64 GT:AD:DP:GL:GQ 0/1:56,10:34:-27.86,-10.24,-97.22:99 +chr1 91835 . T C 60.94 PASS AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.01;MQ0=36;OQ=785.45;QD=10.47;SB=-10.00 GT:AD:DP:GL:GQ 0/1:43,32:33:-91.79,-9.96,-12.24:22.78 +chr1 91851 rs4109800 G C 35.73 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.96;MQ0=33;OQ=1198.57;QD=15.98;SB=-10.00 GT:AD:DP:GL:GQ 0/1:41,34:33:-133.08,-9.94,-16.89:69.53 +chr1 91938 . G A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=2.53;MQ=14.92;MQ0=47;OQ=298.50;QD=3.21;SB=-10.00 GT:AD:DP:GL:GQ 0/1:77,15:21:-39.46,-6.32,-39.15:99 +chr1 92459 rs3912701 G A 1.57 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=1.98;MQ=17.65;MQ0=34;OQ=809.52;QD=14.99;SB=-10.00 GT:AD:DP:GL:GQ 1/1:30,24:20:-84.54,-6.02,-0.00:60.20 +chr1 92527 rs4618909 A G 1.05 PASS AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=1;HaplotypeScore=7.26;MQ=22.11;MQ0=40;OQ=1083.35;QD=10.62;SB=-10.00 GT:AD:DP:GL:GQ 0/1:55,47:51:-126.98,-15.36,-75.91:99 +chr1 92632 rs3872168 C A 251.56 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.40;MQ0=16;OQ=274.62;QD=10.98;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,25:9:-31.05,-2.71,-0.00:27.07 +chr1 92814 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=1;HaplotypeScore=9.83;MQ=30.05;MQ0=21;OQ=659.75;QD=3.88;SB=-292.33 GT:AD:DP:GL:GQ 0/1:135,35:144:-112.64,-43.38,-415.54:99 +chr1 93070 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=1;HaplotypeScore=8.90;MQ=17.00;MQ0=65;OQ=190.64;QD=1.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:83,17:34:-32.59,-10.25,-92.04:99 +chr1 93104 rs62642109 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=24.91;MQ=20.20;MQ0=60;OQ=819.40;QD=6.83;SB=-0.98 GT:AD:DP:GL:GQ 0/1:72,48:57:-102.42,-17.19,-99.00:99 +chr1 93113 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=17.60;MQ=21.02;MQ0=51;OQ=474.12;QD=4.23;SB=5.03 GT:AD:DP:GL:GQ 0/1:79,33:56:-67.57,-16.87,-129.01:99 +chr1 93181 . T C 7.86 PASS AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=15.97;MQ0=67;OQ=759.85;QD=7.17;SB=20.10 GT:AD:DP:GL:GQ 0/1:53,53:35:-89.81,-10.54,-44.53:99 +chr1 93248 rs62639110 G A 30.22 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=8.07;MQ0=76;QD=0.36;SB=-10.00 GT:AD:DP:GL:GQ 0/1:62,22:6:-8.11,-1.81,-14.17:63.05 +chr1 93307 . G A 47.02 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=5.80;MQ0=48;QD=0.94;SB=-10.00 GT:AD:DP:GL:GQ 1/1:44,6:2:-8.11,-0.60,-0.00:6.02 +chr1 93757 . T C 30.28 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=10.09;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,2:2:-6.44,-0.60,-0.00:6.01 +chr1 93896 rs4287120 T C 0.17 PASS AC=2;AF=1.00;AN=2;DB;DP=174;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=4.84;MQ0=151;OQ=128.63;QD=0.74;SB=-81.37 GT:AD:DP:GL:GQ 1/1:41,133:5:-16.43,-1.51,-0.00:15.04 +chr1 93971 rs4492556 A G 12.01 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=2.58;MQ=7.18;MQ0=71;QD=0.15;SB=-31.93 GT:AD:DP:GL:GQ 0/1:47,34:7:-6.57,-2.11,-19.60:44.57 +chr1 94001 . G T 0.94 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=16.11;MQ0=45;OQ=194.11;QD=3.35;SB=-41.38 GT:AD:DP:GL:GQ 0/1:51,7:13:-26.61,-3.91,-21.51:99 +chr1 94049 rs4288537 T C 0.39 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=10.96;MQ=20.93;MQ0=24;OQ=438.79;QD=10.45;SB=-71.88 GT:AD:DP:GL:GQ 0/1:18,24:17:-52.28,-5.12,-8.24:31.18 +chr1 94088 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.06;MQ=13.40;MQ0=57;OQ=79.42;QD=1.15;SB=-38.36 GT:AD:DP:GL:GQ 0/1:64,5:10:-14.24,-3.02,-19.96:99 +chr1 94312 . C A 18.04 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=10.70;MQ0=65;QD=0.24;SB=-10.00 GT:AD:DP:GL:GQ 0/1:72,2:9:-7.79,-2.71,-24.60:50.81 +chr1 98160 rs4109806 A C 199.96 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.46;MQ0=21;OQ=505.68;QD=12.97;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,39:15:-54.16,-4.52,-0.00:45.14 +chr1 98173 . T C 2.30 PASS AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=16.05;MQ0=20;OQ=109.74;QD=3.05;SB=-45.95 GT:AD:DP:GL:GQ 0/1:14,22:12:-17.87,-3.61,-27.89:99 +chr1 98191 rs4109805 A G 15.99 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=16.84;MQ0=14;QD=0.50;SB=5.05 GT:AD:DP:GL:GQ 0/1:28,4:15:-9.39,-4.52,-49.05:48.72 +chr1 98276 rs4457511 T G 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=9.15;MQ=5.64;MQ0=97;OQ=125.84;QD=1.20;SB=-67.98 GT:AD:DP:GL:GQ 0/1:81,24:6:-17.67,-1.81,-3.90:20.89 +chr1 99188 . T C 0.10 PASS AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=8.00;MQ0=82;OQ=57.15;QD=0.64;SB=-10.00 GT:AD:DP:GL:GQ 0/1:85,4:6:-10.81,-1.81,-11.97:89.99 +chr1 99237 . G A 48.25 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=4.41;MQ0=117;QD=0.40;SB=-10.00 GT:AD:DP:GL:GQ 1/1:114,6:2:-8.23,-0.60,-0.00:6.02 +chr1 99503 rs4126043 T A 232.13 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.79;MQ0=3;OQ=79.29;QD=11.33;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:3:-11.42,-0.90,-0.00:9.03 +chr1 110568 rs4117992 T C 36.28 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=12.09;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:2:-7.04,-0.60,-0.00:6.02 +chr1 110846 . C T 29.97 PASS AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=21.24;MQ0=9;OQ=175.53;QD=12.54;SB=-93.11 GT:AD:DP:GL:GQ 1/1:6,8:5:-21.11,-1.51,-0.00:15.05 +chr1 110872 rs1851943 C T 61.13 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.59;MQ0=3;OQ=127.11;QD=18.16;SB=-91.11 GT:AD:DP:GL:GQ 1/1:0,7:4:-16.25,-1.20,-0.00:12.04 +chr1 117436 . G A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=9.09;MQ0=104;OQ=195.33;QD=1.58;SB=-97.57 GT:AD:DP:GL:GQ 0/1:100,24:19:-28.54,-5.73,-40.13:99 +chr1 119192 . C G 13.29 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=6.87;MQ0=19;QD=0.58;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,8:1:-4.59,-0.30,-0.00:1.76 +chr1 125911 rs11531330 C T 87.12 PASS AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=18.40;MQ0=3;OQ=89.79;QD=11.22;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,3:3:-12.47,-0.90,-0.00:9.03 +chr1 217782 . A T 46.88 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.40;MQ0=4;QD=5.86;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:2:-8.10,-0.60,-0.00:6.02 +chr1 219536 rs6678242 A C 214.27 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.88;MQ0=9;OQ=112.38;QD=6.61;SB=-45.01 GT:AD:DP:GL:GQ 1/1:0,17:4:-14.77,-1.20,-0.00:12.04 +chr1 219731 . C T 12.21 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.96;MQ0=44;QD=0.17;SB=38.14 GT:AD:DP:GL:GQ 0/1:62,9:27:-12.61,-8.14,-82.06:44.77 +chr1 219921 rs12239119 T G 63.08 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.26;MQ0=4;OQ=606.74;QD=25.28;SB=-312.56 GT:AD:DP:GL:GQ 1/1:0,24:18:-64.26,-5.42,-0.01:54.16 +chr1 221068 rs10047119 T A 39.88 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=254;Dels=0.00;HRun=1;HaplotypeScore=6.12;MQ=8.79;MQ0=135;QD=0.16;SB=-10.00 GT:AD:DP:GL:GQ 1/1:167,87:2:-7.40,-0.60,-0.00:6.02 +chr1 221077 rs10047174 C A 38.69 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=271;Dels=0.00;HRun=0;HaplotypeScore=6.64;MQ=8.55;MQ0=150;QD=0.14;SB=-10.00 GT:AD:DP:GL:GQ 1/1:181,90:2:-7.28,-0.60,-0.00:6.02 +chr1 221092 rs10047175 C A 39.69 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=283;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=7.57;MQ0=174;QD=0.14;SB=-10.00 GT:AD:DP:GL:GQ 1/1:201,82:2:-7.38,-0.60,-0.00:6.02 +chr1 221109 rs10047121 T C 34.28 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=275;Dels=0.00;HRun=0;HaplotypeScore=3.23;MQ=7.06;MQ0=184;QD=0.12;SB=-10.00 GT:AD:DP:GL:GQ 1/1:197,78:2:-6.84,-0.60,-0.00:6.02 +chr1 221318 . T A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=241;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=19.94;MQ0=85;OQ=462.52;QD=1.92;SB=39.55 GT:AD:DP:GL:GQ 0/1:212,29:108:-82.07,-32.53,-323.83:99 +chr1 221343 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=261;Dels=0.00;HRun=0;HaplotypeScore=2.12;MQ=22.79;MQ0=47;OQ=408.64;QD=1.57;SB=-215.29 GT:AD:DP:GL:GQ 0/1:222,38:157:-91.46,-47.31,-595.18:99 +chr1 221367 rs10047230 G A 0.14 PASS AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=11.19;MQ=25.20;MQ0=11;OQ=1571.46;QD=5.65;SB=-527.77 GT:AD:DP:GL:GQ 0/1:197,80:212:-224.34,-63.91,-509.11:99 +chr1 221389 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=260;Dels=0.00;HRun=1;HaplotypeScore=1.74;MQ=24.37;MQ0=22;OQ=840.34;QD=3.23;SB=-412.02 GT:AD:DP:GL:GQ 0/1:209,50:201:-147.86,-60.54,-597.88:99 +chr1 221420 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=1;HaplotypeScore=4.60;MQ=20.04;MQ0=77;OQ=83.18;QD=0.40;SB=26.98 GT:AD:DP:GL:GQ 0/1:192,14:117:-46.84,-35.24,-385.27:99 +chr1 222364 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=186;Dels=0.03;HRun=0;HaplotypeScore=32.96;MQ=22.76;MQ0=12;OQ=2072.95;QD=11.14;SB=59.21 GT:AD:DP:GL:GQ 0/1:70,111:137:-251.84,-41.26,-268.25:99 +chr1 222793 . C G 25.72 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=260;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=16.62;MQ0=87;QD=0.10;SB=81.54 GT:AD:DP:GL:GQ 0/1:230,30:110:-38.99,-33.14,-447.79:58.55 +chr1 223336 . C G 28.20 PASS AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=35.25;MQ0=2;OQ=1925.92;QD=21.40;SB=-854.31 GT:AD:DP:GL:GQ 0/1:39,51:87:-222.09,-26.21,-160.96:99 +chr1 224095 rs8179512 G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=229;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=15.51;MQ0=125;OQ=91.58;QD=0.40;SB=-45.96 GT:AD:DP:GL:GQ 0/1:203,26:89:-39.28,-26.84,-255.40:99 +chr1 224171 rs7195389 A G 40.71 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=269;Dels=0.00;HRun=0;HaplotypeScore=47.18;MQ=22.11;MQ0=18;QD=0.15;SB=122.50 GT:AD:DP:GL:GQ 0/1:232,36:234:-77.87,-70.51,-842.48:73.55 +chr1 224176 rs56055731 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=276;Dels=0.00;HRun=1;HaplotypeScore=39.67;MQ=21.41;MQ0=32;OQ=545.76;QD=1.98;SB=-248.71 GT:AD:DP:GL:GQ 0/1:242,34:226:-125.93,-68.07,-709.89:99 +chr1 224241 rs62053733 A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.00;HRun=0;HaplotypeScore=20.29;MQ=17.49;MQ0=74;OQ=1752.30;QD=8.11;SB=-714.08 GT:AD:DP:GL:GQ 0/1:103,113:104:-209.87,-31.36,-152.51:99 +chr1 224344 rs8179403 T A 166.23 PASS AC=1;AF=0.50;AN=2;DB;DP=163;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=23.92;MQ0=45;OQ=2824.26;QD=17.33;SB=-725.16 GT:AD:DP:GL:GQ 0/1:38,125:108:-318.26,-32.55,-66.31:99 +chr1 224419 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=1;HaplotypeScore=18.87;MQ=14.35;MQ0=100;OQ=127.03;QD=0.68;SB=8.05 GT:AD:DP:GL:GQ 0/1:161,26:49:-30.75,-14.76,-153.48:99 +chr1 224472 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=261;Dels=0.00;HRun=1;HaplotypeScore=6.53;MQ=15.44;MQ0=125;OQ=992.61;QD=3.80;SB=-39.67 GT:AD:DP:GL:GQ 0/1:177,84:84:-127.86,-25.32,-192.69:99 +chr1 224623 rs7548182 A T 1.19 PASS AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=3;HaplotypeScore=1.37;MQ=26.54;MQ0=23;OQ=863.08;QD=8.07;SB=50.19 GT:AD:DP:GL:GQ 0/1:39,68:64:-108.87,-19.28,-138.61:99 +chr1 225707 rs6603780 C G 0.19 PASS AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=6.28;MQ=15.73;MQ0=150;OQ=1742.87;QD=6.27;SB=-566.38 GT:AD:DP:GL:GQ 0/1:147,131:57:-194.74,-17.17,-58.86:99 +chr1 225839 rs6422503 C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=215;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=34.58;MQ0=26;OQ=4599.62;QD=21.39;SB=-1688.57 GT:AD:DP:GL:GQ 0/1:70,145:162:-458.96,-48.79,-124.49:99 +chr1 226216 . T C 24.03 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=3.20;MQ=9.23;MQ0=93;QD=0.13;SB=-10.00 GT:AD:DP:GL:GQ 0/1:162,19:7:-7.79,-2.11,-21.54:56.85 +chr1 227048 . C A 43.64 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=9.30;MQ0=121;QD=0.28;SB=-44.79 GT:AD:DP:GL:GQ 0/1:134,21:22:-14.27,-6.63,-62.25:76.48 +chr1 227333 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=5.51;MQ=14.65;MQ0=59;OQ=58.63;QD=0.42;SB=-10.00 GT:AD:DP:GL:GQ 0/1:125,16:25:-16.68,-7.54,-70.62:91.47 +chr1 227353 . C A 20.49 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=1;HaplotypeScore=4.94;MQ=14.92;MQ0=62;QD=0.15;SB=-10.00 GT:AD:DP:GL:GQ 0/1:122,18:29:-14.07,-8.74,-90.83:53.29 +chr1 227461 rs28618397 A G 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=144;Dels=0.00;HRun=0;HaplotypeScore=6.94;MQ=8.17;MQ0=115;OQ=63.90;QD=0.44;SB=-10.00 GT:AD:DP:GL:GQ 0/1:131,13:8:-12.09,-2.41,-14.97:96.73 +chr1 227626 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=4.92;MQ=20.49;MQ0=18;OQ=315.55;QD=1.73;SB=-168.42 GT:AD:DP:GL:GQ 0/1:163,19:138:-76.40,-41.57,-437.40:99 +chr1 227735 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=14.30;MQ=17.08;MQ0=35;OQ=66.90;QD=0.75;SB=20.77 GT:AD:DP:GL:GQ 0/1:78,11:41:-22.33,-12.35,-159.24:99 +chr1 230298 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=1;HaplotypeScore=4.58;MQ=24.72;MQ0=17;OQ=319.24;QD=2.47;SB=-97.27 GT:AD:DP:GL:GQ 0/1:109,19:104:-66.59,-31.38,-356.71:99 +chr1 230890 . G A 0.28 PASS AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=4.05;MQ=28.42;MQ0=10;OQ=452.11;QD=3.77;SB=-186.08 GT:AD:DP:GL:GQ 0/1:99,21:95:-77.11,-28.62,-272.62:99 +chr1 231027 rs1917217 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=16;HaplotypeScore=20.40;MQ=32.62;MQ0=10;OQ=363.52;QD=5.05;SB=32.11 GT:AD:DP:GL:GQ 0/1:47,24:50:-54.70,-15.07,-118.26:99 +chr1 231044 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=16;HaplotypeScore=28.71;MQ=27.06;MQ0=9;OQ=128.09;QD=1.69;SB=39.29 GT:AD:DP:GL:GQ 0/1:63,12:57:-36.63,-20.54,-166.03:99 +chr1 231045 . A T 16.10 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=26.04;MQ=26.31;MQ0=9;QD=0.22;SB=44.16 GT:AD:DP:GL:GQ 0/1:63,8:54:-21.15,-16.27,-182.36:48.82 +chr1 231183 . A G 0.09 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=8.45;MQ=28.02;MQ0=10;OQ=325.16;QD=6.25;SB=-110.63 GT:AD:DP:GL:GQ 0/1:19,32:27:-43.95,-8.15,-48.50:99 +chr1 231232 rs11490246 C T 142.56 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=27.55;MQ0=9;OQ=1010.69;QD=16.84;SB=-258.84 GT:AD:DP:GL:GQ 1/1:0,59:26:-104.66,-7.83,-0.01:78.25 +chr1 234887 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=0;HaplotypeScore=14.30;MQ=23.11;MQ0=12;OQ=591.52;QD=2.82;SB=-248.32 GT:AD:DP:GL:GQ 0/1:173,36:184:-117.86,-55.42,-542.00:99 +chr1 235002 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=3;HaplotypeScore=1.45;MQ=7.75;MQ0=92;OQ=65.10;QD=0.63;SB=-6.99 GT:AD:DP:GL:GQ 0/1:88,15:7:-11.90,-2.11,-15.26:97.93 +chr1 235268 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=1;HaplotypeScore=31.21;MQ=26.04;MQ0=17;OQ=96.26;QD=2.53;SB=-57.31 GT:AD:DP:GL:GQ 0/1:24,12:15:-17.43,-4.52,-39.23:99 +chr1 235318 . C G 0.88 PASS AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=31.66;MQ0=1;OQ=172.25;QD=9.57;SB=-27.84 GT:AD:DP:GL:GQ 0/1:12,6:17:-25.63,-5.12,-44.90:99 +chr1 237291 rs62639107 G T 22.08 PASS AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=12.32;MQ0=83;OQ=830.85;QD=6.59;SB=-342.75 GT:AD:DP:GL:GQ 0/1:51,75:34:-96.61,-10.24,-28.48:99 +chr1 237573 . T C 21.25 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=174;Dels=0.00;HRun=0;HaplotypeScore=8.41;MQ=14.44;MQ0=98;QD=0.12;SB=17.09 GT:AD:DP:GL:GQ 0/1:155,19:37:-16.55,-11.15,-125.38:54.05 +chr1 238151 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=9.86;MQ0=83;OQ=59.88;QD=0.63;SB=-10.00 GT:AD:DP:GL:GQ 0/1:91,4:10:-12.29,-3.01,-24.61:92.72 +chr1 238167 rs4109800 G C 1.40 PASS AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=9.69;MQ0=81;OQ=122.76;QD=1.31;SB=-10.00 GT:AD:DP:GL:GQ 0/1:83,11:9:-18.27,-2.71,-21.24:99 +chr1 238254 . G A 14.34 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=10.94;MQ0=73;QD=0.13;SB=-10.00 GT:AD:DP:GL:GQ 0/1:101,9:10:-7.71,-3.01,-28.55:47.01 +chr1 242992 rs4109808 G C 0.33 PASS AC=1;AF=0.50;AN=2;DB;DP=205;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=17.96;MQ0=77;OQ=316.33;QD=1.54;SB=11.07 GT:AD:DP:GL:GQ 0/1:143,62:81:-59.32,-24.40,-284.11:99 +chr1 244543 rs62639119 A G 39.09 PASS AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=13.13;MQ0=71;OQ=645.60;QD=5.98;SB=-100.72 GT:AD:DP:GL:GQ 0/1:56,52:34:-78.09,-10.25,-42.39:99 +chr1 244959 rs4096710 C T 45.82 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=3.93;MQ=13.07;MQ0=59;QD=0.54;SB=-26.62 GT:AD:DP:GL:GQ 0/1:74,11:15:-12.39,-4.52,-39.32:78.66 +chr1 245030 rs4247528 T G 34.76 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=14.80;MQ0=42;QD=0.49;SB=8.04 GT:AD:DP:GL:GQ 0/1:62,9:14:-10.98,-4.22,-38.66:67.59 +chr1 245496 . A G 44.84 LowQual AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.49;MQ0=2;QD=7.47;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:2:-7.89,-0.60,-0.00:6.02 +chr1 314685 . A T 13.26 PASS AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.75;MQ=14.76;MQ0=13;OQ=314.43;QD=11.65;SB=-42.39 GT:AD:DP:GL:GQ 1/1:12,15:9:-35.03,-2.71,-0.00:27.09 +chr1 314938 . G C 1.97 PASS AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=12.45;MQ0=16;OQ=80.86;QD=3.23;SB=-10.00 GT:AD:DP:GL:GQ 1/1:16,9:3:-11.58,-0.91,-0.00:9.03 +chr1 314990 . T C 42.83 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=12.15;MQ0=12;QD=2.14;SB=-10.00 GT:AD:DP:GL:GQ 1/1:10,10:2:-7.69,-0.60,-0.00:6.02 +chr1 354114 rs3905534 G T 4.20 PASS AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=1.96;MQ=17.14;MQ0=8;OQ=149.39;QD=8.30;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,8:10:-21.23,-3.01,-14.53:99 +chr1 374336 rs4959767 C G 48.85 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=9.01;MQ=5.04;MQ0=75;QD=0.57;SB=-10.00 GT:AD:DP:GL:GQ 1/1:78,7:2:-8.29,-0.60,-0.00:6.02 +chr1 374388 rs4120938 C T 0.16 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=7.85;MQ=3.88;MQ0=74;OQ=50.25;QD=0.61;SB=-10.00 GT:AD:DP:GL:GQ 1/1:76,7:2:-8.43,-0.60,-0.00:6.02 +chr1 374916 . A C 6.13 PASS AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.92;MQ0=3;OQ=209.71;QD=17.48;SB=-40.56 GT:AD:DP:GL:GQ 1/1:2,10:8:-24.56,-2.41,-0.01:24.03 +chr1 391491 . T G 33.28 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=1;HaplotypeScore=4.00;MQ=5.85;MQ0=67;QD=0.45;SB=-10.00 GT:AD:DP:GL:GQ 0/1:70,4:3:-7.51,-0.90,-3.44:25.36 +chr1 394166 . C T 0.46 PASS AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=7.89;MQ0=95;OQ=178.49;QD=1.75;SB=-10.00 GT:AD:DP:GL:GQ 0/1:96,6:7:-23.23,-2.11,-3.57:14.61 +chr1 394272 . T G 16.31 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=17.93;MQ0=35;OQ=484.03;QD=7.81;SB=-10.00 GT:AD:DP:GL:GQ 0/1:39,23:22:-58.31,-6.63,-19.38:99 +chr1 394291 rs12121306 C T 153.03 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=16.59;MQ0=30;OQ=364.11;QD=7.75;SB=-10.00 GT:AD:DP:GL:GQ 0/1:31,16:14:-43.91,-4.22,-11.01:67.92 +chr1 394310 . C T 0.18 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=12.47;MQ0=36;OQ=147.86;QD=3.21;SB=-10.00 GT:AD:DP:GL:GQ 0/1:41,5:8:-20.48,-2.41,-10.61:81.97 +chr1 394537 . G A 2.58 PASS AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=6.78;MQ=23.70;MQ0=52;OQ=1238.38;QD=11.79;SB=-421.21 GT:AD:DP:GL:GQ 0/1:65,40:50:-142.19,-15.07,-44.99:99 +chr1 394765 . A G 0.18 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=7.43;MQ0=57;OQ=65.19;QD=1.07;SB=-10.00 GT:AD:DP:GL:GQ 0/1:58,3:4:-11.01,-1.20,-3.46:22.51 +chr1 394834 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.99;MQ=12.79;MQ0=47;OQ=202.79;QD=3.56;SB=-10.00 GT:AD:DP:GL:GQ 0/1:49,8:10:-26.57,-3.01,-12.50:94.91 +chr1 394837 . A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=7.99;MQ=12.80;MQ0=51;OQ=216.52;QD=3.49;SB=-10.00 GT:AD:DP:GL:GQ 0/1:48,14:11:-28.25,-3.31,-11.97:86.56 +chr1 404035 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=20.45;MQ=17.63;MQ0=51;OQ=155.60;QD=2.22;SB=-84.79 GT:AD:DP:GL:GQ 0/1:62,8:17:-23.97,-5.12,-38.73:99 +chr1 511466 rs3902909 G A 114.88 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.37;MQ0=1;OQ=299.83;QD=6.00;SB=-10.00 GT:AD:DP:GL:GQ 0/1:35,15:40:-45.34,-12.07,-85.80:99 +chr1 513688 rs61767343 C T 0.33 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=21.22;MQ0=15;OQ=264.79;QD=2.88;SB=32.01 GT:AD:DP:GL:GQ 0/1:78,14:66:-49.68,-19.91,-161.21:99 +chr1 522943 . G A 31.72 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=14;HaplotypeScore=31.16;MQ=21.11;MQ0=30;QD=0.33;SB=74.23 GT:AD:DP:GL:GQ 0/1:84,11:55:-23.03,-16.58,-166.54:64.56 +chr1 523155 . C T 20.46 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=7.86;MQ=11.23;MQ0=37;QD=0.34;SB=-10.00 GT:AD:DP:GL:GQ 0/1:56,5:10:-8.34,-3.02,-25.17:53.26 +chr1 523163 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=7.11;MQ=11.49;MQ0=30;OQ=99.30;QD=1.99;SB=-10.00 GT:AD:DP:GL:GQ 0/1:37,13:9:-15.92,-2.71,-17.34:99 +chr1 523812 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=9.50;MQ=11.52;MQ0=31;OQ=145.45;QD=2.05;SB=-10.00 GT:AD:DP:GL:GQ 0/1:61,10:10:-20.85,-3.02,-13.58:99 +chr1 523821 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=9.21;MQ=15.64;MQ0=25;OQ=121.38;QD=1.84;SB=-10.00 GT:AD:DP:GL:GQ 0/1:57,9:12:-19.04,-3.62,-21.78:99 +chr1 523868 . G A 13.34 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.79;MQ0=4;OQ=177.69;QD=5.08;SB=-10.00 GT:AD:DP:GL:GQ 0/1:21,14:15:-25.58,-4.53,-24.67:99 +chr1 524029 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=26.24;MQ0=29;OQ=72.18;QD=0.99;SB=-17.85 GT:AD:DP:GL:GQ 0/1:58,15:34:-20.75,-10.24,-100.17:99 +chr1 524055 rs6680723 C T 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=2;HaplotypeScore=11.94;MQ=30.97;MQ0=23;OQ=525.09;QD=5.30;SB=-269.67 GT:AD:DP:GL:GQ 0/1:68,31:65:-75.37,-19.58,-166.45:99 +chr1 524061 rs6680725 C T 44.53 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=14.45;MQ=31.89;MQ0=22;QD=0.42;SB=98.20 GT:AD:DP:GL:GQ 0/1:92,13:70:-28.85,-21.11,-204.21:77.37 +chr1 524105 rs2792879 C T 49.58 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=35.66;MQ0=5;QD=0.40;SB=82.58 GT:AD:DP:GL:GQ 0/1:106,18:95:-36.89,-28.65,-274.71:82.42 +chr1 524187 . G T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=13.69;MQ=38.72;MQ0=2;OQ=392.49;QD=8.18;SB=-133.62 GT:AD:DP:GL:GQ 0/1:25,22:25:-49.77,-7.23,-31.06:99 +chr1 524410 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=27.66;MQ=40.25;MQ0=9;OQ=582.52;QD=5.34;SB=-205.05 GT:AD:DP:GL:GQ 0/1:82,27:83:-86.53,-25.00,-225.34:99 +chr1 524592 rs61767348 C T 0.12 PASS AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=35.17;MQ0=0;OQ=230.33;QD=1.84;SB=-71.36 GT:AD:DP:GL:GQ 0/1:109,16:125:-63.96,-37.65,-391.79:99 +chr1 524704 . C G 0.30 PASS AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=15.62;MQ0=42;OQ=247.71;QD=3.26;SB=-10.00 GT:AD:DP:GL:GQ 0/1:63,13:16:-32.88,-4.82,-37.64:99 +chr1 525671 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=0;HaplotypeScore=16.72;MQ=18.80;MQ0=44;OQ=189.70;QD=1.52;SB=-93.64 GT:AD:DP:GL:GQ 0/1:113,12:40:-34.30,-12.05,-118.97:99 +chr1 525779 . A G 0.63 PASS AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=22.14;MQ0=11;OQ=348.30;QD=4.15;SB=-47.83 GT:AD:DP:GL:GQ 0/1:66,18:49:-52.88,-14.76,-137.92:99 +chr1 525958 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=25.63;MQ=21.45;MQ0=28;OQ=60.59;QD=0.61;SB=-44.97 GT:AD:DP:GL:GQ 0/1:86,13:50:-24.43,-15.08,-139.15:93.42 +chr1 526007 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=23.90;MQ=27.74;MQ0=20;OQ=72.77;QD=0.52;SB=-61.14 GT:AD:DP:GL:GQ 0/1:119,22:81:-34.97,-24.41,-279.63:99 +chr1 526679 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=6.10;MQ=15.23;MQ0=50;OQ=159.06;QD=1.64;SB=-10.00 GT:AD:DP:GL:GQ 0/1:72,25:19:-24.93,-5.74,-37.85:99 +chr1 526910 . C T 33.12 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=15.09;MQ=12.21;MQ0=78;QD=0.31;SB=8.05 GT:AD:DP:GL:GQ 0/1:95,11:28:-15.03,-8.43,-86.21:65.95 +chr1 527066 rs1109924 C T 18.08 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.21;MQ=24.80;MQ0=20;QD=0.22;SB=56.20 GT:AD:DP:GL:GQ 0/1:74,8:55:-21.66,-16.57,-168.07:50.84 +chr1 527350 rs1105044 C T 0.77 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=5.45;MQ=30.46;MQ0=9;OQ=109.38;QD=3.91;SB=5.03 GT:AD:DP:GL:GQ 0/1:19,9:14:-18.45,-4.22,-27.73:99 +chr1 527399 . C G 0.15 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.45;MQ=22.48;MQ0=26;OQ=195.21;QD=3.42;SB=2.03 GT:AD:DP:GL:GQ 0/1:49,8:23:-29.74,-6.93,-66.80:99 +chr1 527400 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=5.09;MQ=22.50;MQ0=26;OQ=149.94;QD=2.50;SB=3.82 GT:AD:DP:GL:GQ 0/1:51,8:23:-28.15,-9.87,-58.83:99 +chr1 527445 . C G 0.06 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=15.27;MQ0=33;OQ=120.74;QD=2.05;SB=-43.89 GT:AD:DP:GL:GQ 0/1:47,12:21:-21.68,-6.33,-71.74:99 +chr1 530476 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=20.30;MQ0=34;OQ=101.99;QD=0.68;SB=16.46 GT:AD:DP:GL:GQ 0/1:135,15:110:-46.63,-33.14,-338.24:99 +chr1 534258 rs61769278 G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=9.91;MQ0=64;OQ=75.11;QD=0.62;SB=-10.00 GT:AD:DP:GL:GQ 0/1:81,40:6:-12.60,-1.81,-10.89:90.82 +chr1 534650 rs61769279 G C 10.23 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=22.82;MQ0=11;OQ=171.47;QD=4.76;SB=-10.00 GT:AD:DP:GL:GQ 0/1:26,10:21:-26.76,-6.33,-62.71:99 +chr1 536560 rs12025928 A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=3;HaplotypeScore=20.90;MQ=24.04;MQ0=6;OQ=206.19;QD=3.49;SB=8.06 GT:AD:DP:GL:GQ 0/1:26,33:37:-35.06,-11.16,-99.03:99 +chr1 536665 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=53.76;MQ=25.56;MQ0=32;OQ=200.39;QD=1.71;SB=-106.47 GT:AD:DP:GL:GQ 0/1:92,25:66:-43.22,-19.90,-241.56:99 +chr1 536668 rs61769283 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=116;Dels=0.00;HRun=0;HaplotypeScore=52.49;MQ=25.44;MQ0=31;OQ=176.14;QD=1.52;SB=-101.57 GT:AD:DP:GL:GQ 0/1:89,25:62:-39.59,-18.70,-187.95:99 +chr1 536745 rs9438485 T C 0.12 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=10.16;MQ=22.38;MQ0=21;OQ=208.92;QD=2.37;SB=-117.20 GT:AD:DP:GL:GQ 0/1:59,28:39:-35.93,-11.75,-108.78:99 +chr1 536815 rs9438487 T C 0.71 PASS AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=5.65;MQ=26.07;MQ0=22;OQ=487.78;QD=3.81;SB=-195.14 GT:AD:DP:GL:GQ 0/1:76,52:82:-76.77,-24.71,-234.35:99 +chr1 536828 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=25.55;MQ0=22;OQ=75.76;QD=0.57;SB=28.89 GT:AD:DP:GL:GQ 0/1:122,12:82:-35.59,-24.73,-235.80:99 +chr1 537100 . G A 12.85 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=13.16;MQ0=46;QD=0.12;SB=-7.00 GT:AD:DP:GL:GQ 0/1:81,22:25:-12.08,-7.53,-73.93:45.46 +chr1 537113 . C T 31 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=12.14;MQ0=51;QD=0.29;SB=-6.99 GT:AD:DP:GL:GQ 0/1:84,22:18:-11.81,-5.42,-56.12:63.83 +chr1 537596 . G A 46.75 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=0;HaplotypeScore=23.62;MQ=12.88;MQ0=95;QD=0.28;SB=83.26 GT:AD:DP:GL:GQ 0/1:155,15:50:-23.03,-15.07,-148.87:79.59 +chr1 537643 rs9438495 T C 0.24 PASS AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=12.92;MQ0=56;OQ=64.59;QD=0.65;SB=29.12 GT:AD:DP:GL:GQ 0/1:83,15:29:-18.49,-8.74,-88.70:97.43 +chr1 540378 . T C 1.66 PASS AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=10.44;MQ0=61;OQ=250.82;QD=2.82;SB=-10.00 GT:AD:DP:GL:GQ 0/1:69,20:17:-33.49,-5.12,-26.69:99 +chr1 543605 . G A 0.71 PASS AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=19.26;MQ0=44;OQ=534.14;QD=4.38;SB=-165.55 GT:AD:DP:GL:GQ 0/1:95,27:72:-78.41,-21.71,-168.45:99 +chr1 544671 rs4120954 G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=1;HaplotypeScore=17.61;MQ=20.21;MQ0=40;OQ=184.77;QD=1.55;SB=-112.49 GT:AD:DP:GL:GQ 0/1:103,16:61:-40.15,-18.39,-172.29:99 +chr1 549231 . A G 0.07 PASS AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=20.37;MQ0=37;OQ=179.14;QD=2.21;SB=30.55 GT:AD:DP:GL:GQ 0/1:67,14:40:-33.25,-12.05,-121.81:99 +chr1 549235 . C G 0.42 PASS AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=21.34;MQ0=35;OQ=329.96;QD=4.12;SB=-9.65 GT:AD:DP:GL:GQ 0/1:65,15:43:-49.24,-12.96,-142.49:99 +chr1 549756 . G A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=4.27;MQ=22.29;MQ0=22;OQ=255.07;QD=4.40;SB=-111.11 GT:AD:DP:GL:GQ 0/1:45,13:33:-38.73,-9.94,-83.62:99 +chr1 551019 . T G 0.10 PASS AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=26.98;MQ0=20;OQ=197.80;QD=2.50;SB=4.26 GT:AD:DP:GL:GQ 0/1:67,12:53:-39.03,-15.96,-159.29:99 +chr1 551526 rs3908981 C A 0.27 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=9.51;MQ0=72;OQ=83.63;QD=0.93;SB=-10.00 GT:AD:DP:GL:GQ 0/1:72,18:8:-14.06,-2.41,-15.23:99 +chr1 552065 . T G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=19.90;MQ0=42;OQ=77.24;QD=1.04;SB=-15.93 GT:AD:DP:GL:GQ 0/1:68,6:22:-17.64,-6.63,-61.21:99 +chr1 553226 . C T 0.19 PASS AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=3;HaplotypeScore=1.62;MQ=24.97;MQ0=44;OQ=605.74;QD=6.51;SB=-203.18 GT:AD:DP:GL:GQ 0/1:67,26:42:-76.51,-12.65,-84.24:99 +chr1 553488 . T C 0.79 PASS AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=309.81;QD=34.42;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:9:-34.57,-2.71,-0.00:27.09 +chr1 555282 rs55668158 C G 1.90 PASS AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=7.94;MQ=40.12;MQ0=17;OQ=1152.38;QD=10.38;SB=-595.15 GT:AD:DP:GL:GQ 0/1:77,33:92:-146.24,-27.72,-249.40:99 +chr1 555454 rs7416152 C T 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.00;HRun=0;HaplotypeScore=6.80;MQ=46.34;MQ0=10;OQ=133.21;QD=0.99;SB=31.52 GT:AD:DP:GL:GQ 0/1:100,33:107:-48.84,-32.23,-339.95:99 +chr1 555839 rs9283151 C T 3.01 PASS AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=45.60;MQ0=9;OQ=549.78;QD=4.07;SB=-291.62 GT:AD:DP:GL:GQ 0/1:100,35:123:-95.32,-37.06,-353.94:99 +chr1 555911 rs6421780 G A 0.18 PASS AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=39.59;MQ0=14;OQ=584.19;QD=4.56;SB=-299.10 GT:AD:DP:GL:GQ 0/1:90,32:104:-93.03,-31.32,-293.74:99 +chr1 557751 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=2961;Dels=0.00;HRun=2;HaplotypeScore=55.38;MQ=12.90;MQ0=2051;OQ=15633.32;QD=5.28;SB=59.42 GT:AD:DP:GL:GQ 0/1:109,2851:490:-1562.33,-147.66,-305.00:99 +chr1 558077 . C T 9.05 PASS AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=45.73;MQ0=8;OQ=1080.95;QD=8.72;SB=-436.58 GT:AD:DP:GL:GQ 0/1:87,37:109:-144.24,-32.87,-230.68:99 +chr1 559290 rs55665739 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=606;Dels=0.00;HRun=3;HaplotypeScore=17.31;MQ=15.96;MQ0=469;OQ=1033.33;QD=1.71;SB=-487.92 GT:AD:DP:GL:GQ 0/1:561,45:103:-137.67,-31.06,-222.34:99 +chr1 559575 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=286;Dels=0.00;HRun=0;HaplotypeScore=67.59;MQ=29.40;MQ0=143;OQ=1081.89;QD=3.78;SB=-504.88 GT:AD:DP:GL:GQ 0/1:248,38:131:-150.96,-39.49,-301.87:99 +chr1 560501 rs3912527 T C 0.59 PASS AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=42.53;MQ0=1;OQ=256.32;QD=2.44;SB=101.36 GT:AD:DP:GL:GQ 0/1:81,24:98:-58.45,-29.53,-320.39:99 +chr1 561486 rs4951848 T G 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=3;HaplotypeScore=1.10;MQ=14.41;MQ0=91;OQ=408.98;QD=3.27;SB=-10.00 GT:AD:DP:GL:GQ 0/1:75,49:28:-52.62,-8.43,-47.04:99 +chr1 561492 rs4951847 T C 0.48 PASS AC=1;AF=0.50;AN=2;DB;DP=117;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=12.50;MQ0=93;OQ=266.80;QD=2.28;SB=-10.00 GT:AD:DP:GL:GQ 0/1:73,44:19:-35.69,-5.72,-37.10:99 +chr1 561756 rs4092521 C A 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=234;Dels=0.00;HRun=0;HaplotypeScore=3.92;MQ=28.08;MQ0=93;OQ=133.54;QD=0.57;SB=-15.37 GT:AD:DP:GL:GQ 0/1:211,23:136:-57.61,-40.97,-421.13:99 +chr1 574427 rs4317776 G T 26.75 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=197;Dels=0.00;HRun=9;HaplotypeScore=3.53;MQ=6.95;MQ0=179;QD=0.14;SB=-30.89 GT:AD:DP:GL:GQ 0/1:180,17:17:-11.08,-5.12,-48.02:59.57 +chr1 575363 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=0;HaplotypeScore=13.77;MQ=11.89;MQ0=66;OQ=93.79;QD=0.87;SB=-10.00 GT:AD:DP:GL:GQ 0/1:97,11:18:-18.09,-5.43,-51.57:99 +chr1 575571 . A G 44.95 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=12.50;MQ0=35;QD=0.49;SB=-7.00 GT:AD:DP:GL:GQ 0/1:88,3:9:-10.49,-2.71,-23.69:77.78 +chr1 575656 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=0;HaplotypeScore=17.86;MQ=21.34;MQ0=33;OQ=102.29;QD=0.86;SB=-15.11 GT:AD:DP:GL:GQ 0/1:101,18:60:-31.59,-18.08,-183.63:99 +chr1 577203 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=2;HaplotypeScore=18.06;MQ=18.60;MQ0=50;OQ=68.56;QD=0.90;SB=-15.46 GT:AD:DP:GL:GQ 0/1:71,5:16:-14.96,-4.82,-42.28:99 +chr1 578945 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=108;Dels=0.01;HRun=3;HaplotypeScore=26.60;MQ=35.12;MQ0=11;OQ=422.46;QD=3.91;SB=-212.09 GT:AD:DP:GL:GQ 0/1:86,21:88:-72.04,-26.51,-252.61:99 +chr1 581862 rs428603 C T 12.84 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=117;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=16.17;MQ0=62;QD=0.11;SB=5.04 GT:AD:DP:GL:GQ 0/1:112,5:25:-12.07,-7.53,-76.64:45.44 +chr1 582131 rs2808300 G T 0.12 PASS AC=1;AF=0.50;AN=2;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=20.19;MQ0=60;OQ=103.03;QD=0.77;SB=74.25 GT:AD:DP:GL:GQ 0/1:113,20:71:-34.97,-21.38,-223.52:99 +chr1 590341 . G A 2.32 PASS AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=31.66;MQ0=1;OQ=697.92;QD=5.91;SB=-148.83 GT:AD:DP:GL:GQ 0/1:88,30:101:-103.52,-30.45,-248.69:99 +chr1 591004 . C T 96.57 PASS AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=34.15;MQ0=0;OQ=697.04;QD=7.58;SB=-276.23 GT:AD:DP:GL:GQ 0/1:66,26:89:-99.83,-26.84,-204.19:99 +chr1 591498 rs2531322 C A 0.53 PASS AC=1;AF=0.50;AN=2;DB;DP=129;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=32.80;MQ0=0;OQ=356.51;QD=2.76;SB=131.06 GT:AD:DP:GL:GQ 0/1:108,21:125:-76.61,-37.67,-331.80:99 +chr1 592316 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=5.89;MQ=8.09;MQ0=42;OQ=58.17;QD=0.88;SB=-10.00 GT:AD:DP:GL:GQ 0/1:52,12:5:-10.61,-1.51,-6.31:48.04 +chr1 592508 rs2686868 C T 15.96 PASS AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=1;HaplotypeScore=3.16;MQ=34.52;MQ0=0;OQ=1500.76;QD=12.61;SB=-645.23 GT:AD:DP:GL:GQ 0/1:71,48:113:-187.40,-34.04,-240.50:99 +chr1 616184 rs2808330 A G 13.87 PASS AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.61;MQ0=5;OQ=348.18;QD=3.38;SB=86.31 GT:AD:DP:GL:GQ 0/1:75,28:95:-66.73,-28.63,-299.16:99 +chr1 625884 rs3857304 G A 2.14 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=6.38;MQ0=48;OQ=115.97;QD=2.23;SB=-51.67 GT:AD:DP:GL:GQ 1/1:47,5:4:-15.13,-1.21,-0.00:12.03 +chr1 625907 rs4030160 G A 213.52 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=11.50;MQ0=27;OQ=320.38;QD=8.90;SB=-93.34 GT:AD:DP:GL:GQ 1/1:25,11:9:-35.62,-2.71,-0.00:27.09 +chr1 625979 rs3871845 G C 249.04 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=11.96;MQ0=27;OQ=358.10;QD=9.68;SB=-129.40 GT:AD:DP:GL:GQ 1/1:26,11:9:-39.40,-2.71,-0.00:27.09 +chr1 626181 rs3873089 G A 177.45 PASS AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.43;MQ0=3;OQ=376.84;QD=28.99;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,13:10:-41.27,-3.01,-0.00:30.10 +chr1 638976 . C T 0.12 PASS AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=4.06;MQ=23.85;MQ0=8;OQ=648.49;QD=24.02;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,27:17:-68.44,-5.12,-0.00:51.17 +chr1 640686 . A G 25.04 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=6.84;MQ0=102;QD=0.23;SB=-10.00 GT:AD:DP:GL:GQ 0/1:98,10:6:-7.60,-1.81,-15.47:57.87 +chr1 641012 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=157;Dels=0.00;HRun=1;HaplotypeScore=5.72;MQ=12.45;MQ0=138;OQ=282.66;QD=1.80;SB=-113.62 GT:AD:DP:GL:GQ 0/1:142,15:18:-36.97,-5.42,-32.71:99 +chr1 647651 . G C 91.46 PASS AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=15.14;MQ0=31;OQ=441.56;QD=9.39;SB=-238.61 GT:AD:DP:GL:GQ 1/1:28,19:11:-47.74,-3.31,-0.00:33.11 +chr1 652720 rs62639125 G A 47.02 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=8.82;MQ0=19;QD=1.42;SB=-10.00 GT:AD:DP:GL:GQ 1/1:13,20:2:-8.11,-0.60,-0.00:6.02 +chr1 652960 rs61769340 G C 105.13 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=20.58;MQ0=11;OQ=1522.59;QD=27.68;SB=-684.47 GT:AD:DP:GL:GQ 1/1:10,45:39:-155.88,-11.77,-0.03:99 +chr1 656406 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=11.93;MQ0=83;OQ=127.34;QD=1.14;SB=-0.98 GT:AD:DP:GL:GQ 0/1:95,17:17:-21.14,-5.12,-45.67:99 +chr1 662072 . G A 11.72 PASS AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=27.50;MQ0=7;OQ=1481.48;QD=11.06;SB=-511.41 GT:AD:DP:GL:GQ 0/1:80,54:118:-187.00,-35.57,-233.79:99 +chr1 662535 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=1;HaplotypeScore=4.63;MQ=12.94;MQ0=86;OQ=221.86;QD=1.71;SB=-10.00 GT:AD:DP:GL:GQ 0/1:117,13:31:-34.81,-9.34,-77.61:99 +chr1 664297 . A T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=1;HaplotypeScore=8.91;MQ=25.89;MQ0=44;OQ=139.99;QD=0.72;SB=29.32 GT:AD:DP:GL:GQ 0/1:135,59:118:-52.83,-35.54,-396.03:99 +chr1 664319 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=1;HaplotypeScore=4.98;MQ=25.84;MQ0=39;OQ=562.89;QD=2.86;SB=-70.36 GT:AD:DP:GL:GQ 0/1:152,44:131:-101.81,-42.24,-385.33:99 +chr1 665009 . G A 0.15 PASS AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=7.66;MQ=13.29;MQ0=30;OQ=394.21;QD=6.36;SB=-10.00 GT:AD:DP:GL:GQ 1/1:20,42:11:-43.01,-3.32,-0.01:33.10 +chr1 665981 . C T 314.88 PASS AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.49;MQ0=9;OQ=1228.86;QD=15.36;SB=-521.03 GT:AD:DP:GL:GQ 0/1:42,38:68:-146.65,-20.48,-114.04:99 +chr1 678857 . T C 37.39 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=9.96;MQ0=52;QD=0.58;SB=-41.94 GT:AD:DP:GL:GQ 0/1:58,5:10:-10.04,-3.02,-24.70:70.23 +chr1 681407 . T A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;HRun=13;HaplotypeScore=8.39;MQ=28.14;MQ0=23;OQ=991.49;QD=17.71;SB=-487.41 GT:AD:DP:GL:GQ 1/1:17,39:33:-109.19,-9.95,-6.46:34.91 +chr1 681927 . C G 40.97 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=4.89;MQ=4.61;MQ0=72;QD=0.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:72,2:3:-8.29,-0.90,-4.05:31.44 +chr1 684740 rs1829739 A C 31.20 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=3;HaplotypeScore=24.15;MQ=12.41;MQ0=41;QD=0.60;SB=-34.97 GT:AD:DP:GL:GQ 0/1:47,5:9:-9.12,-2.71,-21.21:64.03 +chr1 684742 . C A 14.57 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=37.61;MQ=12.41;MQ0=41;QD=0.28;SB=-31.35 GT:AD:DP:GL:GQ 0/1:46,6:9:-7.44,-2.71,-24.53:47.25 +chr1 684781 . C T 48.14 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.66;MQ=4.69;MQ0=46;QD=1.00;SB=-49.56 GT:AD:DP:GL:GQ 1/1:40,8:2:-8.22,-0.60,-0.00:6.02 +chr1 684978 . A T 38.37 PASS AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.29;MQ0=2;OQ=86.08;QD=14.35;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,6:3:-12.10,-0.90,-0.00:9.03 +chr1 690691 rs6685320 T A 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=41.41;MQ0=1;OQ=71.22;QD=0.76;SB=149.48 GT:AD:DP:GL:GQ 0/1:83,11:90:-37.51,-27.11,-298.94:99 +chr1 692785 . C T 0.89 PASS AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.63;MQ0=14;OQ=282.72;QD=2.30;SB=-80.41 GT:AD:DP:GL:GQ 0/1:107,16:98:-61.07,-29.52,-300.46:99 +chr1 692834 . C T 2.02 PASS AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=26.70;MQ0=10;OQ=722.71;QD=6.12;SB=-381.76 GT:AD:DP:GL:GQ 0/1:89,29:108:-108.08,-32.53,-294.03:99 +chr1 692878 rs12124557 G C 71.38 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.28;MQ0=34;OQ=350.61;QD=4.61;SB=-168.38 GT:AD:DP:GL:GQ 0/1:61,15:41:-50.70,-12.35,-126.27:99 +chr1 694230 rs9727436 T C 8.89 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=32.48;MQ0=2;OQ=333.56;QD=17.56;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,18:12:-36.95,-3.62,-0.01:36.08 +chr1 695745 . G A 102.02 PASS AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=41.82;MQ0=0;OQ=1169.68;QD=16.02;SB=-501.47 GT:AD:DP:GL:GQ 0/1:36,37:71:-141.66,-21.41,-112.07:99 +chr1 696231 rs12029736 A G 92.82 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=39.21;MQ0=1;OQ=1205.31;QD=20.78;SB=-587.73 GT:AD:DP:GL:GQ 0/1:5,53:49:-138.60,-14.79,-16.39:15.94 +chr1 696641 . G A 0.05 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=11.92;MQ=21.76;MQ0=28;OQ=1527.01;QD=18.18;SB=-47.56 GT:AD:DP:GL:GQ 1/1:26,58:39:-156.30,-11.75,-0.02:99 +chr1 704290 rs12028261 G A 67.98 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.14;MQ=38.97;MQ0=0;OQ=1407.21;QD=35.18;SB=-656.37 GT:AD:DP:GL:GQ 1/1:0,40:36:-144.32,-10.85,-0.01:99 +chr1 705211 rs3131984 T G 181.58 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=48.59;MQ0=0;OQ=1797.71;QD=32.69;SB=-808.10 GT:AD:DP:GL:GQ 1/1:0,55:52:-183.37,-15.66,-0.02:99 +chr1 705859 rs4614203 A T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=9;HaplotypeScore=9.09;MQ=20.66;MQ0=19;OQ=690.18;QD=13.80;SB=-46.39 GT:AD:DP:GL:GQ 1/1:1,48:20:-72.61,-6.03,-0.01:60.18 +chr1 708249 rs10900602 A G 1.62 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.93;MQ=25.93;MQ0=21;OQ=1118.18;QD=17.47;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,63:38:-115.46,-11.48,-0.05:99 +chr1 708418 rs10751453 T C 415.24 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.69;MQ0=5;OQ=1667.51;QD=27.79;SB=-566.12 GT:AD:DP:GL:GQ 1/1:4,56:54:-174.43,-16.28,-4.09:99 +chr1 710103 rs3121393 T C 439.85 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.62;MQ0=19;OQ=1791.16;QD=20.59;SB=-717.22 GT:AD:DP:GL:GQ 1/1:0,87:51:-182.72,-15.36,-0.02:99 +chr1 710660 rs3115846 G A 23.98 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=32.94;MQ0=7;OQ=1843.21;QD=32.91;SB=-738.02 GT:AD:DP:GL:GQ 1/1:0,56:47:-187.92,-14.16,-0.01:99 +chr1 713754 rs2977670 G C 680.35 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.16;MQ0=0;OQ=1954.35;QD=36.87;SB=-819.16 GT:AD:DP:GL:GQ 1/1:0,53:49:-199.05,-14.78,-0.03:99 +chr1 714052 . G A 38.81 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=1;HaplotypeScore=27.06;MQ=47.82;MQ0=13;QD=0.40;SB=-19.66 GT:AD:DP:GL:GQ 0/1:88,9:69:-27.95,-20.79,-220.66:71.64 +chr1 714724 rs12123401 G A 77.21 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=38.16;MQ=32.18;MQ0=19;QD=1.19;SB=53.18 GT:AD:DP:GL:GQ 0/1:50,14:32:-20.64,-9.64,-97.41:99 +chr1 714732 rs12735556 C A 597.50 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=35.96;MQ=32.37;MQ0=15;QD=9.34;SB=-186.20 GT:AD:DP:GL:GQ 0/1:31,30:31:-72.37,-9.34,-42.36:99 +chr1 714734 rs12735557 C G 606.51 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=32.96;MQ=32.01;MQ0=15;QD=9.48;SB=-232.37 GT:AD:DP:GL:GQ 0/1:31,33:32:-73.58,-9.64,-63.94:99 +chr1 714811 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=1;HaplotypeScore=105.18;MQ=32.80;MQ0=13;OQ=394.82;QD=4.11;SB=-25.79 GT:AD:DP:GL:GQ 0/1:48,48:42:-55.42,-12.65,-93.88:99 +chr1 714830 . G A 44.58 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=2;HaplotypeScore=123.02;MQ=32.55;MQ0=17;QD=0.46;SB=2.03 GT:AD:DP:GL:GQ 0/1:60,27:26:-15.57,-7.83,-82.81:77.42 +chr1 714865 . G A 118.87 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=2;HaplotypeScore=72.07;MQ=36.16;MQ0=17;QD=1.19;SB=45.52 GT:AD:DP:GL:GQ 0/1:83,11:39:-26.94,-11.77,-99.77:99 +chr1 714869 . G A 210.22 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=70.54;MQ=36.82;MQ0=18;QD=2.08;SB=89.30 GT:AD:DP:GL:GQ 0/1:78,22:52:-39.97,-15.66,-154.79:99 +chr1 714870 . G C 132.10 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=64.77;MQ=36.96;MQ0=18;QD=1.33;SB=86.32 GT:AD:DP:GL:GQ 0/1:81,18:51:-31.86,-15.37,-195.72:99 +chr1 714885 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=11.63;MQ=42.34;MQ0=19;OQ=59.67;QD=0.80;SB=57.28 GT:AD:DP:GL:GQ 0/1:59,16:42:-21.91,-12.66,-130.29:92.50 +chr1 714965 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.06;HRun=0;HaplotypeScore=109.90;MQ=37.50;MQ0=15;OQ=104.38;QD=1.12;SB=93.07 GT:AD:DP:GL:GQ 0/1:76,7:50:-34.61,-20.89,-189.48:99 +chr1 714987 . A T 75.82 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=80;Dels=0.03;HRun=1;HaplotypeScore=85.54;MQ=37.34;MQ0=12;QD=0.95;SB=77.28 GT:AD:DP:GL:GQ 0/1:70,6:44:-26.77,-15.90,-141.85:99 +chr1 714990 . A G 169.75 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=75;Dels=0.04;HRun=1;HaplotypeScore=76.84;MQ=38.08;MQ0=11;QD=2.26;SB=1.07 GT:AD:DP:GL:GQ 0/1:50,19:44:-36.22,-15.96,-136.58:99 +chr1 714991 . A G 49.83 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=75;Dels=0.01;HRun=0;HaplotypeScore=63.75;MQ=38.08;MQ0=11;QD=0.66;SB=86.30 GT:AD:DP:GL:GQ 0/1:68,6:44:-21.52,-13.26,-154.68:82.67 +chr1 714995 . C A 39.02 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=2;HaplotypeScore=68.11;MQ=38.07;MQ0=12;QD=0.54;SB=48.86 GT:AD:DP:GL:GQ 0/1:52,10:39:-31.66,-24.48,-125.33:71.86 +chr1 715012 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=28.31;MQ=43.81;MQ0=11;OQ=81.07;QD=1.33;SB=77.26 GT:AD:DP:GL:GQ 0/1:50,6:42:-27.43,-16.04,-129.03:99 +chr1 715014 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=28.31;MQ=44.76;MQ0=10;OQ=135.00;QD=2.29;SB=80.30 GT:AD:DP:GL:GQ 0/1:48,10:43:-29.74,-12.96,-149.46:99 +chr1 715704 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=1;HaplotypeScore=25.25;MQ=54.80;MQ0=2;OQ=145.06;QD=1.23;SB=-43.38 GT:AD:DP:GL:GQ 0/1:97,21:107:-50.01,-32.22,-342.89:99 +chr1 716048 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=178;Dels=0.00;HRun=1;HaplotypeScore=18.47;MQ=39.54;MQ0=8;OQ=52.50;QD=0.29;SB=34.27 GT:AD:DP:GL:GQ 0/1:78,99:81:-32.94,-24.40,-274.16:85.34 +chr1 716061 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=21.67;MQ=39.51;MQ0=6;OQ=115.15;QD=0.62;SB=43.85 GT:AD:DP:GL:GQ 0/1:135,49:85:-40.41,-25.61,-331.38:99 +chr1 716222 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=2;HaplotypeScore=139.36;MQ=31.95;MQ0=27;OQ=92.92;QD=0.79;SB=-50.76 GT:AD:DP:GL:GQ 0/1:103,13:47:-26.73,-14.16,-149.22:99 +chr1 716344 rs3131980 T G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=39.71;MQ=55.45;MQ0=6;OQ=2415.81;QD=31.79;SB=-1086.51 GT:AD:DP:GL:GQ 1/1:2,74:68:-245.18,-20.48,-0.02:99 +chr1 716802 rs4520358 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=160;Dels=0.00;HRun=0;HaplotypeScore=127.95;MQ=28.01;MQ0=48;OQ=1542.52;QD=9.64;SB=-717.92 GT:AD:DP:GL:GQ 0/1:109,49:76:-180.46,-22.93,-134.20:99 +chr1 716807 rs3131979 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.00;HRun=1;HaplotypeScore=146.45;MQ=27.53;MQ0=52;OQ=2520.74;QD=14.92;SB=-1257.54 GT:AD:DP:GL:GQ 0/1:69,89:79:-286.20,-30.85,-56.55:99 +chr1 717392 . A G 3.52 PASS AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.37;MQ=24.74;MQ0=13;OQ=554.36;QD=8.66;SB=-175.95 GT:AD:DP:GL:GQ 0/1:36,28:38:-70.17,-11.45,-77.18:99 +chr1 717776 . A G 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=36.84;MQ0=8;OQ=198.21;QD=1.82;SB=-48.31 GT:AD:DP:GL:GQ 0/1:82,26:93:-51.12,-28.02,-315.62:99 +chr1 717825 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=45.12;MQ0=3;OQ=93.24;QD=0.90;SB=-41.95 GT:AD:DP:GL:GQ 0/1:87,17:97:-41.83,-29.22,-341.26:99 +chr1 718022 rs3131978 C T 227.01 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=24.78;MQ0=12;OQ=2206.38;QD=27.93;SB=-528.20 GT:AD:DP:GL:GQ 1/1:0,79:55:-224.24,-16.57,-0.01:99 +chr1 718105 rs3131977 C G 701.77 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.42;MQ0=9;OQ=2564.24;QD=33.30;SB=-886.52 GT:AD:DP:GL:GQ 1/1:0,77:61:-260.03,-18.38,-0.02:99 +chr1 718468 rs2977661 C A 0.97 PASS AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=44.88;MQ0=1;OQ=306.65;QD=3.13;SB=125.41 GT:AD:DP:GL:GQ 0/1:81,17:92:-61.67,-27.72,-254.10:99 +chr1 719542 rs4951859 C G 20.03 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=0.73;MQ=51.87;MQ0=0;OQ=2314.11;QD=40.60;SB=-1158.05 GT:AD:DP:GL:GQ 1/1:0,57:55:-235.02,-16.58,-0.02:99 +chr1 722635 . G A 178.90 PASS AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.65;MQ0=17;OQ=703.25;QD=9.38;SB=-329.31 GT:AD:DP:GL:GQ 0/1:40,35:48:-88.07,-14.46,-95.92:99 +chr1 723861 rs3094321 C T 2.53 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=4.03;MQ=14.10;MQ0=13;OQ=171.30;QD=5.53;SB=-52.67 GT:AD:DP:GL:GQ 1/1:0,31:5:-20.69,-1.51,-0.00:15.05 +chr1 723905 rs3115866 G A 435.39 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.45;MQ0=11;OQ=1488.74;QD=31.02;SB=-417.55 GT:AD:DP:GL:GQ 1/1:0,48:37:-152.47,-11.14,-0.01:99 +chr1 724152 rs2427932 G A 28.59 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=40.65;MQ0=10;OQ=544.36;QD=7.78;SB=29.11 GT:AD:DP:GL:GQ 0/1:46,24:57:-74.91,-17.19,-123.40:99 +chr1 724325 rs12564807 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.02;HRun=14;HaplotypeScore=12.95;MQ=25.23;MQ0=25;OQ=486.84;QD=10.36;SB=-195.27 GT:AD:DP:GL:GQ 0/1:7,39:20:-57.99,-6.03,-17.33:99 +chr1 724354 rs7518433 T C 213.81 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=16.24;MQ0=8;OQ=108.50;QD=7.23;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:4:-14.38,-1.21,-0.00:12.04 +chr1 724429 . G A 5.67 PASS AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=39.71;MQ0=12;OQ=1919.08;QD=16.26;SB=-856.39 GT:AD:DP:GL:GQ 0/1:56,62:102:-225.91,-30.72,-172.49:99 +chr1 724483 rs2427930 A G 156.88 PASS AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=45.92;MQ0=8;OQ=1015.40;QD=8.46;SB=-368.74 GT:AD:DP:GL:GQ 0/1:73,47:110:-137.96,-33.13,-289.42:99 +chr1 724814 rs61770166 A G 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.01;HRun=0;HaplotypeScore=8.00;MQ=38.81;MQ0=11;OQ=57.16;QD=0.57;SB=101.37 GT:AD:DP:GL:GQ 0/1:74,25:85:-34.30,-25.30,-302.54:90 +chr1 725289 rs10900603 G A 319.30 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.84;MQ0=12;OQ=1308.47;QD=22.56;SB=-614.32 GT:AD:DP:GL:GQ 1/1:0,58:33:-134.44,-9.94,-0.01:99 +chr1 727603 rs3893479 G A 3.33 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=20.83;MQ0=35;OQ=241.46;QD=3.71;SB=-122.11 GT:AD:DP:GL:GQ 0/1:49,15:27:-35.56,-8.14,-65.14:99 +chr1 729005 rs2340527 T A 17.56 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=11;HaplotypeScore=0.00;MQ=42.93;MQ0=12;QD=0.18;SB=2.25 GT:AD:DP:GL:GQ 0/1:70,25:68:-25.52,-20.49,-222.57:50.31 +chr1 729073 rs2427917 A G 0.66 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=3;HaplotypeScore=1.32;MQ=36.83;MQ0=11;OQ=1725.34;QD=25.00;SB=-386.59 GT:AD:DP:GL:GQ 1/1:8,61:54:-180.20,-16.27,-4.08:99 +chr1 729289 rs3131973 A G 242.97 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.01;MQ0=22;OQ=768.10;QD=13.48;SB=-48.96 GT:AD:DP:GL:GQ 1/1:0,57:23:-80.40,-6.93,-0.01:69.20 +chr1 729391 rs3094317 G A 25.41 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=29.31;MQ0=14;OQ=1050.45;QD=23.87;SB=-501.02 GT:AD:DP:GL:GQ 1/1:0,44:27:-108.64,-8.13,-0.01:81.26 +chr1 731442 rs3115865 T C 10.98 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=14.78;MQ0=18;OQ=257.65;QD=3.79;SB=-147.73 GT:AD:DP:GL:GQ 1/1:0,68:9:-29.35,-2.71,-0.01:27.07 +chr1 732688 . A G 132.94 PASS AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=40.79;MQ0=0;OQ=1231.30;QD=15.02;SB=-638.22 GT:AD:DP:GL:GQ 0/1:40,42:81:-150.81,-24.40,-157.55:99 +chr1 732884 rs2488925 T C 45.12 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=12.78;MQ0=54;QD=0.47;SB=-0.97 GT:AD:DP:GL:GQ 0/1:72,25:9:-10.51,-2.71,-24.07:77.96 +chr1 732935 rs2488505 C A 405.73 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=25.42;MQ0=21;OQ=984.68;QD=12.62;SB=-456.35 GT:AD:DP:GL:GQ 1/1:10,68:28:-102.06,-8.43,-0.01:84.26 +chr1 734986 rs61823337 A C 21.52 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=22.23;MQ0=45;QD=0.18;SB=23.10 GT:AD:DP:GL:GQ 0/1:104,17:71:-26.81,-21.38,-234.10:54.33 +chr1 735210 rs2488501 T C 0.42 PASS AC=1;AF=0.50;AN=2;DB;DP=117;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=29.20;MQ0=16;OQ=204.37;QD=1.75;SB=-126.97 GT:AD:DP:GL:GQ 0/1:101,16:100:-53.85,-30.13,-340.21:99 +chr1 736231 rs3925106 C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=38.77;MQ0=4;OQ=87.62;QD=1.33;SB=28.85 GT:AD:DP:GL:GQ 0/1:58,8:62:-30.72,-18.67,-192.09:99 +chr1 736257 rs28622890 G A 34.58 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=41.58;MQ0=5;QD=0.43;SB=53.57 GT:AD:DP:GL:GQ 0/1:73,8:73:-28.75,-22.01,-217.76:67.42 +chr1 737271 rs2427896 G A 1.34 PASS AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.89;MQ0=27;OQ=95.91;QD=0.96;SB=26.10 GT:AD:DP:GL:GQ 0/1:78,22:62:-31.55,-18.68,-198.47:99 +chr1 737583 rs2488922 A G 0.48 PASS AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=42.10;MQ0=2;OQ=266.56;QD=2.17;SB=-121.05 GT:AD:DP:GL:GQ 0/1:92,31:105:-61.60,-31.66,-333.56:99 +chr1 738741 rs2519043 G T 42.42 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=26.82;MQ0=11;OQ=2109.65;QD=29.30;SB=-875.26 GT:AD:DP:GL:GQ 1/1:7,65:57:-214.56,-17.17,-0.01:99 +chr1 739128 rs2519041 G A 43.02 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=8.37;MQ0=49;QD=0.61;SB=-10.00 GT:AD:DP:GL:GQ 1/1:19,51:2:-7.71,-0.60,-0.00:6.02 +chr1 739546 rs12184332 C T 184.94 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=12.22;MQ0=29;OQ=412.05;QD=9.81;SB=-172.22 GT:AD:DP:GL:GQ 1/1:0,15:11:-44.79,-3.31,-0.00:33.11 +chr1 739719 rs12409679 C T 476.33 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.16;MQ0=31;OQ=1249.90;QD=19.53;SB=-559.74 GT:AD:DP:GL:GQ 1/1:9,55:32:-128.58,-9.64,-0.01:96.31 +chr1 739852 rs12409693 C T 32.23 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=4;HaplotypeScore=0.83;MQ=11.24;MQ0=16;QD=1.29;SB=-3.98 GT:AD:DP:GL:GQ 0/1:9,16:4:-7.71,-1.20,-7.59:63.88 +chr1 739860 rs12410209 A G 6.46 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=11.03;MQ0=14;OQ=69.01;QD=3.14;SB=-6.99 GT:AD:DP:GL:GQ 0/1:7,15:4:-11.39,-1.20,-4.06:28.52 +chr1 742429 rs3094315 G A 709.48 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.17;MQ0=0;OQ=3081.43;QD=40.02;SB=-1319.35 GT:AD:DP:GL:GQ 1/1:0,77:77:-311.75,-23.19,-0.02:99 +chr1 742584 rs3131972 A G 25.55 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=43.52;MQ0=0;OQ=2970.98;QD=35.37;SB=-1399.49 GT:AD:DP:GL:GQ 1/1:0,84:83:-300.71,-25.00,-0.02:99 +chr1 742757 rs3131971 T C 41.65 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.21;MQ=23.17;MQ0=17;OQ=516.07;QD=12.59;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,37:19:-55.23,-5.74,-0.04:57.08 +chr1 743132 rs3115861 C G 14.67 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=27.06;MQ0=17;OQ=1234.23;QD=26.26;SB=-15.29 GT:AD:DP:GL:GQ 1/1:0,46:29:-129.86,-11.46,-2.85:86.17 +chr1 743268 rs3115860 C A 75.43 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.75;MQ0=7;OQ=486.16;QD=22.10;SB=-153.55 GT:AD:DP:GL:GQ 1/1:0,22:14:-52.20,-4.22,-0.00:42.13 +chr1 743288 rs3131970 T C 362.63 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.31;MQ0=12;OQ=231.44;QD=11.57;SB=-100.85 GT:AD:DP:GL:GQ 1/1:0,20:8:-26.73,-2.41,-0.01:24.06 +chr1 743337 rs2073814 C G 1.55 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=4;HaplotypeScore=1.47;MQ=27.30;MQ0=10;OQ=1125.84;QD=30.43;SB=-429.30 GT:AD:DP:GL:GQ 1/1:1,36:27:-116.18,-8.13,-0.01:81.27 +chr1 743712 rs56101360 G T 37.36 PASS AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=10.96;MQ0=18;OQ=73.40;QD=3.50;SB=-44.39 GT:AD:DP:GL:GQ 1/1:0,21:3:-10.83,-0.90,-0.00:9.03 +chr1 744045 rs3131969 A G 233.56 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.14;MQ0=6;OQ=1104.31;QD=23.50;SB=-502.19 GT:AD:DP:GL:GQ 1/1:0,47:36:-114.05,-10.86,-0.03:99 +chr1 744055 rs3131968 A G 489.63 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.65;MQ0=5;OQ=1245.81;QD=27.08;SB=-566.90 GT:AD:DP:GL:GQ 1/1:0,46:40:-128.20,-12.07,-0.04:99 +chr1 744197 rs3131967 T C 119.26 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=53.80;MQ0=2;OQ=2119.16;QD=28.26;SB=-841.48 GT:AD:DP:GL:GQ 1/1:1,74:67:-215.56,-20.21,-0.06:99 +chr1 744366 rs3115859 G A 143.80 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.48;MQ0=0;OQ=2152.98;QD=37.77;SB=-958.79 GT:AD:DP:GL:GQ 1/1:0,55:55:-218.90,-16.57,-0.02:99 +chr1 744827 rs3131966 C T 120.29 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=47.82;MQ0=1;OQ=2882.74;QD=38.96;SB=-1406.06 GT:AD:DP:GL:GQ 1/1:1,73:72:-291.88,-21.69,-0.02:99 +chr1 745638 rs3131965 A G 37.34 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=59.56;MQ0=0;OQ=1308.09;QD=25.16;SB=-645.91 GT:AD:DP:GL:GQ 1/1:2,50:45:-138.61,-13.58,-4.21:93.63 +chr1 745750 rs3131964 C G 3.97 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=53.42;MQ0=0;OQ=1959.71;QD=42.60;SB=-541.05 GT:AD:DP:GL:GQ 1/1:0,46:45:-199.57,-13.56,-0.01:99 +chr1 745753 rs3115858 A T 53.72 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=52.51;MQ0=0;OQ=1749.78;QD=37.23;SB=-548.77 GT:AD:DP:GL:GQ 1/1:0,47:47:-178.57,-14.15,-0.01:99 +chr1 745791 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=2;HaplotypeScore=18.24;MQ=43.86;MQ0=9;OQ=50.05;QD=0.65;SB=68.26 GT:AD:DP:GL:GQ 0/1:71,6:65:-27.87,-19.59,-256.05:82.88 +chr1 745803 rs3115857 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=56.59;MQ=40.14;MQ0=10;OQ=1678.77;QD=22.69;SB=-752.72 GT:AD:DP:GL:GQ 0/1:24,50:53:-187.11,-15.98,-16.89:9.18 +chr1 745905 . G C 40.04 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=109.46;MQ=39.52;MQ0=1;QD=0.47;SB=41.16 GT:AD:DP:GL:GQ 0/1:44,42:46:-21.15,-13.87,-174.52:72.88 +chr1 745926 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=71.25;MQ=39.59;MQ0=1;OQ=190.93;QD=2.22;SB=53.16 GT:AD:DP:GL:GQ 0/1:47,39:55:-38.95,-16.57,-157.39:99 +chr1 745944 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=34.08;MQ=37.55;MQ0=2;OQ=183.15;QD=2.23;SB=41.15 GT:AD:DP:GL:GQ 0/1:68,13:63:-40.58,-18.98,-189.40:99 +chr1 745947 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=35.45;MQ=37.64;MQ0=2;OQ=144.60;QD=1.76;SB=41.13 GT:AD:DP:GL:GQ 0/1:61,21:63:-36.72,-18.98,-195.32:99 +chr1 745969 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=26.39;MQ=43.31;MQ0=1;OQ=191.12;QD=2.62;SB=65.24 GT:AD:DP:GL:GQ 0/1:56,17:62:-41.07,-18.68,-205.74:99 +chr1 745970 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=53.14;MQ=43.05;MQ0=1;OQ=181.87;QD=2.46;SB=65.22 GT:AD:DP:GL:GQ 0/1:57,13:62:-40.15,-18.68,-186.08:99 +chr1 746120 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=2;HaplotypeScore=45.83;MQ=41.92;MQ0=5;OQ=178.43;QD=2.66;SB=1.10 GT:AD:DP:GL:GQ 0/1:36,31:38:-32.58,-11.45,-99.35:99 +chr1 746127 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=64.18;MQ=39.79;MQ0=5;OQ=90.17;QD=1.29;SB=23.10 GT:AD:DP:GL:GQ 0/1:61,9:40:-24.35,-12.05,-113.93:99 +chr1 746131 rs12567639 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=86.22;MQ=40.15;MQ0=5;OQ=1193.97;QD=14.74;SB=-198.46 GT:AD:DP:GL:GQ 0/1:23,47:41:-137.40,-14.72,-24.14:94.15 +chr1 746140 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=67.36;MQ=39.96;MQ0=6;OQ=451.51;QD=4.47;SB=-226.37 GT:AD:DP:GL:GQ 0/1:64,37:56:-65.31,-16.87,-128.04:99 +chr1 746183 rs61768169 G A 45.64 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=15.14;MQ=43.93;MQ0=4;QD=0.48;SB=0.06 GT:AD:DP:GL:GQ 0/1:84,10:80:-31.96,-24.11,-251.75:78.48 +chr1 746197 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=9.62;MQ=45.83;MQ0=2;OQ=266.46;QD=3.10;SB=-143.52 GT:AD:DP:GL:GQ 0/1:62,24:69:-50.72,-20.79,-191.84:99 +chr1 746210 . C G 29.36 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=1;HaplotypeScore=12.28;MQ=48.57;MQ0=1;QD=0.39;SB=83.30 GT:AD:DP:GL:GQ 0/1:61,15:60:-24.30,-18.08,-232.38:62.19 +chr1 746211 . A C 19.28 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=12.28;MQ=48.88;MQ0=1;QD=0.26;SB=56.68 GT:AD:DP:GL:GQ 0/1:55,20:60:-23.28,-18.07,-191.05:52.07 +chr1 746241 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=1;HaplotypeScore=37.04;MQ=43.41;MQ0=2;OQ=460.88;QD=4.90;SB=-102.94 GT:AD:DP:GL:GQ 0/1:66,28:77:-72.58,-23.21,-260.56:99 +chr1 746243 rs3131963 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=38.28;MQ=42.00;MQ0=2;OQ=2225.83;QD=20.61;SB=-986.67 GT:AD:DP:GL:GQ 0/1:37,71:77:-249.07,-23.20,-37.48:99 +chr1 746259 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=53.13;MQ=42.82;MQ0=2;OQ=115.63;QD=1.04;SB=-45.40 GT:AD:DP:GL:GQ 0/1:89,21:81:-39.28,-24.43,-223.64:99 +chr1 746271 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=0;HaplotypeScore=62.70;MQ=43.89;MQ0=1;OQ=73.67;QD=0.68;SB=-12.36 GT:AD:DP:GL:GQ 0/1:82,19:79:-37.12,-26.47,-271.48:99 +chr1 746467 rs3131962 A G 256.08 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.92;MQ0=2;OQ=1247.82;QD=23.54;SB=-557.88 GT:AD:DP:GL:GQ 1/1:1,52:40:-128.40,-12.06,-0.04:99 +chr1 747503 rs3115853 G A 25.12 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=3.30;MQ=58.23;MQ0=2;OQ=3098.30;QD=37.78;SB=-1549.56 GT:AD:DP:GL:GQ 1/1:0,81:79:-317.18,-27.31,-3.76:99 +chr1 747597 rs4951929 C T 626.13 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=2652.10;QD=38.44;SB=-1324.28 GT:AD:DP:GL:GQ 1/1:0,69:67:-268.81,-20.18,-0.02:99 +chr1 747799 rs4951862 C A 77.67 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=57.90;MQ0=0;OQ=1743.44;QD=32.90;SB=-442.30 GT:AD:DP:GL:GQ 1/1:0,53:51:-177.95,-15.36,-0.02:99 +chr1 748007 rs3131956 A G 613.10 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=1973.59;QD=34.03;SB=-931.61 GT:AD:DP:GL:GQ 1/1:0,58:58:-200.97,-17.48,-0.03:99 +chr1 748187 rs3131955 T C 137.90 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=57.23;MQ0=0;OQ=1684.65;QD=30.08;SB=-868.87 GT:AD:DP:GL:GQ 1/1:0,56:51:-172.08,-15.37,-0.03:99 +chr1 748489 rs3131954 C T 606.26 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.38;MQ0=0;OQ=1957.02;QD=37.63;SB=-957.97 GT:AD:DP:GL:GQ 1/1:0,52:51:-199.31,-15.37,-0.02:99 +chr1 749563 rs3115852 T C 295.01 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.43;MQ0=19;OQ=1638.73;QD=24.46;SB=-694.62 GT:AD:DP:GL:GQ 1/1:0,67:46:-167.47,-13.85,-0.01:99 +chr1 749700 rs3115851 T A 246.72 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=37.92;MQ0=12;OQ=2113.34;QD=28.18;SB=-566.84 GT:AD:DP:GL:GQ 1/1:0,75:55:-214.93,-16.56,-0.01:99 +chr1 750775 rs1048488 C T 147.65 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=55.79;MQ0=0;OQ=2544.23;QD=37.42;SB=-1282.72 GT:AD:DP:GL:GQ 1/1:0,68:64:-258.02,-19.28,-0.02:99 +chr1 751010 rs3115850 T C 532.65 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.77;MQ0=0;OQ=2501.23;QD=35.73;SB=-1116.81 GT:AD:DP:GL:GQ 1/1:0,70:69:-253.73,-20.78,-0.02:99 +chr1 751595 rs2286139 C T 599.50 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=41.46;MQ0=7;OQ=1283.06;QD=32.08;SB=-543.21 GT:AD:DP:GL:GQ 1/1:0,40:32:-131.90,-9.64,-0.01:96.32 +chr1 751615 rs1057213 C T 31.34 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=31.78;MQ0=12;OQ=906.27;QD=25.17;SB=-453.10 GT:AD:DP:GL:GQ 1/1:0,36:23:-94.22,-6.93,-0.00:69.23 +chr1 751674 rs1057212 G A 293.40 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=15.73;MQ0=12;OQ=176.65;QD=10.39;SB=-51.56 GT:AD:DP:GL:GQ 1/1:0,17:5:-21.22,-1.51,-0.00:15.05 +chr1 752136 rs3115849 G A 60.54 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.04;MQ0=8;OQ=733.35;QD=26.19;SB=-160.21 GT:AD:DP:GL:GQ 1/1:0,28:19:-76.93,-5.73,-0.01:57.18 +chr1 752452 rs3115848 G C 110.74 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=44.19;MQ0=1;OQ=1521.80;QD=34.59;SB=-621.54 GT:AD:DP:GL:GQ 1/1:1,43:40:-155.80,-12.08,-0.04:99 +chr1 752455 rs3131950 C G 3.82 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=4.46;MQ=42.62;MQ0=2;OQ=1386.15;QD=32.24;SB=-555.07 GT:AD:DP:GL:GQ 1/1:1,42:36:-142.24,-10.87,-0.04:99 +chr1 752464 rs3131949 T C 84.88 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=40.87;MQ0=2;OQ=1077.25;QD=28.35;SB=-454.51 GT:AD:DP:GL:GQ 1/1:1,37:32:-111.32,-9.64,-0.01:96.27 +chr1 752495 rs3131948 T A 77.80 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=37.91;MQ0=2;OQ=926.17;QD=28.94;SB=-390.81 GT:AD:DP:GL:GQ 1/1:1,31:26:-96.21,-7.83,-0.01:78.23 +chr1 753257 rs3115847 G A 0.46 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=27.21;MQ0=9;OQ=840.10;QD=24.71;SB=-20.92 GT:AD:DP:GL:GQ 1/1:5,28:22:-89.90,-8.89,-2.30:65.88 +chr1 755968 rs2519015 T A 366.75 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.21;MQ0=48;OQ=1019.18;QD=12.90;SB=-121.94 GT:AD:DP:GL:GQ 1/1:23,56:29:-105.51,-8.74,-0.01:87.26 +chr1 757643 rs2905042 G A 71.81 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=34.85;MQ0=1;OQ=1607.55;QD=32.81;SB=-663.38 GT:AD:DP:GL:GQ 1/1:0,49:41:-164.35,-12.35,-0.01:99 +chr1 758116 rs2977608 A C 58.89 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=47.69;MQ0=11;OQ=2396.98;QD=30.34;SB=-914.67 GT:AD:DP:GL:GQ 1/1:4,75:68:-243.30,-20.48,-0.02:99 +chr1 759692 rs2977607 C A 65.29 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=47.39;MQ0=6;OQ=1539.69;QD=31.42;SB=-733.73 GT:AD:DP:GL:GQ 1/1:0,49:42:-157.56,-12.65,-0.01:99 +chr1 759938 rs2977606 C T 514.72 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.63;MQ0=7;OQ=1693.07;QD=33.20;SB=-574.34 GT:AD:DP:GL:GQ 1/1:0,51:44:-172.91,-13.26,-0.01:99 +chr1 760431 rs3131943 A G 213.11 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=31.32;MQ0=2;OQ=527.61;QD=27.77;SB=-87.92 GT:AD:DP:GL:GQ 1/1:0,19:16:-56.35,-4.82,-0.00:48.14 +chr1 760781 rs3095826 T G 40.05 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=15.14;MQ0=8;QD=3.64;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,11:2:-7.41,-0.60,-0.00:6.02 +chr1 761273 rs2519006 C T 29.93 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.96;MQ=27.71;MQ0=20;OQ=1719.34;QD=22.33;SB=-558.69 GT:AD:DP:GL:GQ 1/1:18,59:45:-179.00,-13.55,-3.48:99 +chr1 761686 rs2977605 T C 284.90 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.99;MQ0=4;OQ=744.87;QD=26.60;SB=-283.54 GT:AD:DP:GL:GQ 1/1:0,28:24:-78.09,-7.24,-0.02:72.16 +chr1 762618 rs2905039 A C 494.84 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.90;MQ0=0;OQ=1864.52;QD=29.13;SB=-798.77 GT:AD:DP:GL:GQ 1/1:0,64:60:-190.09,-18.09,-0.06:99 +chr1 764599 rs28830877 A C 154.63 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=49.78;MQ0=3;OQ=2217.13;QD=30.37;SB=-1008.12 GT:AD:DP:GL:GQ 1/1:0,73:64:-225.32,-19.28,-0.02:99 +chr1 764648 rs28873693 G A 193.89 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=40.27;MQ0=2;OQ=1900.97;QD=32.22;SB=-951.98 GT:AD:DP:GL:GQ 1/1:0,59:49:-193.70,-14.76,-0.02:99 +chr1 764732 rs55994826 G A 15.73 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=36.88;MQ0=1;QD=0.58;SB=17.08 GT:AD:DP:GL:GQ 0/1:24,3:23:-11.77,-6.93,-72.32:48.45 +chr1 764737 rs28810152 A C 715.74 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=38.33;MQ0=0;QD=28.63;SB=-297.55 GT:AD:DP:GL:GQ 1/1:0,25:22:-75.17,-6.63,-0.01:66.18 +chr1 764742 . A T 46.72 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=39.13;MQ0=0;QD=2.03;SB=-38.86 GT:AD:DP:GL:GQ 0/1:19,4:18:-13.38,-5.42,-51.11:79.56 +chr1 764746 . G A 393.33 SnpCluster AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=40.70;MQ0=1;QD=17.88;SB=-221.92 GT:AD:DP:GL:GQ 0/1:8,14:19:-48.34,-5.72,-22.76:99 +chr1 764763 rs28797844 C G 118.37 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=44.74;MQ0=1;OQ=234.91;QD=8.39;SB=-89.25 GT:AD:DP:GL:GQ 0/1:20,8:26:-34.62,-7.84,-73.94:99 +chr1 764786 rs28769076 G C 293.91 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=38.71;MQ0=4;OQ=1154.38;QD=32.98;SB=-346.74 GT:AD:DP:GL:GQ 1/1:0,35:27:-119.03,-8.14,-0.01:81.27 +chr1 765119 . T G 7.65 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=15.72;MQ0=15;OQ=87.25;QD=4.15;SB=-66.98 GT:AD:DP:GL:GQ 0/1:15,6:6:-13.82,-1.81,-7.64:58.28 +chr1 765289 rs2905037 G A 284.46 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=48.40;MQ0=0;OQ=3000.65;QD=37.51;SB=-1455.38 GT:AD:DP:GL:GQ 1/1:0,80:75:-303.67,-22.59,-0.02:99 +chr1 765522 rs2905035 A G 84.99 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=40.77;MQ0=3;OQ=2096.78;QD=30.39;SB=-645.26 GT:AD:DP:GL:GQ 1/1:0,68:58:-213.28,-17.47,-0.02:99 +chr1 766409 rs12124819 A G 273.30 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=3.66;MQ=51.01;MQ0=0;OQ=1354.31;QD=15.75;SB=-621.86 GT:AD:DP:GL:GQ 0/1:41,45:85:-164.32,-25.60,-163.76:99 +chr1 766985 rs2980319 A T 684.18 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.93;MQ0=0;OQ=2347.43;QD=37.26;SB=-849.94 GT:AD:DP:GL:GQ 1/1:0,63:62:-238.35,-18.68,-0.02:99 +chr1 768432 rs2977615 A G 315.81 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.80;MQ0=5;OQ=1414.86;QD=25.27;SB=-618.23 GT:AD:DP:GL:GQ 1/1:0,56:46:-145.13,-13.88,-0.05:99 +chr1 769890 rs2977613 G T 314.36 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=53.23;MQ0=0;OQ=2549.06;QD=34.45;SB=-1034.15 GT:AD:DP:GL:GQ 1/1:0,74:70:-258.51,-21.09,-0.02:99 +chr1 770648 rs2977612 T A 316.89 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.02;MQ0=0;OQ=2471.78;QD=34.81;SB=-1070.63 GT:AD:DP:GL:GQ 1/1:1,70:68:-253.32,-20.49,-2.56:99 +chr1 773167 rs2980295 T C 625.67 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.46;MQ0=0;OQ=2479.28;QD=34.43;SB=-1064.87 GT:AD:DP:GL:GQ 1/1:0,72:71:-251.54,-21.39,-0.02:99 +chr1 774913 rs2905062 G A 647.91 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.25;MQ0=0;OQ=2057.09;QD=38.09;SB=-793.69 GT:AD:DP:GL:GQ 1/1:0,54:52:-209.31,-15.66,-0.01:99 +chr1 775852 rs2980300 T C 398.92 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.91;MQ0=0;OQ=1925.83;QD=36.34;SB=-289.45 GT:AD:DP:GL:GQ 1/1:0,53:52:-196.18,-15.66,-0.01:99 +chr1 776110 rs59319764 G A 135.46 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.95;MQ0=5;OQ=708.27;QD=21.46;SB=-330.44 GT:AD:DP:GL:GQ 1/1:5,28:18:-74.41,-5.42,-0.00:54.18 +chr1 776673 rs2905061 G A 271.44 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.77;MQ0=2;OQ=243.21;QD=12.80;SB=-51.67 GT:AD:DP:GL:GQ 1/1:0,19:7:-27.90,-2.11,-0.00:21.07 +chr1 776882 rs2905060 C T 28.05 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.47;MQ0=13;OQ=680.11;QD=21.25;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,32:18:-71.60,-5.42,-0.01:54.17 +chr1 776908 . C G 26.94 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=23.04;MQ0=7;QD=1.35;SB=-10.00 GT:AD:DP:GL:GQ 0/1:11,8:6:-7.79,-1.82,-13.09:59.77 +chr1 776998 rs28753393 A G 1.62 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=22.78;MQ0=8;OQ=492.59;QD=20.52;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,24:14:-52.85,-4.22,-0.00:42.13 +chr1 777048 rs2905058 G A 64.34 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=17.04;MQ0=12;OQ=310.80;QD=12.43;SB=-128.67 GT:AD:DP:GL:GQ 1/1:0,25:9:-34.67,-2.71,-0.01:27.08 +chr1 777068 rs2905057 G A 256.67 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=15.61;MQ0=17;OQ=265.15;QD=9.14;SB=-131.67 GT:AD:DP:GL:GQ 1/1:0,29:8:-30.10,-2.41,-0.01:24.07 +chr1 777125 rs2905056 C G 369.51 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=42.20;MQ0=14;OQ=1716.63;QD=32.39;SB=-514.60 GT:AD:DP:GL:GQ 1/1:0,53:39:-175.26,-11.75,-0.01:99 +chr1 777262 rs2905055 G T 436.57 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=43.93;MQ0=5;OQ=1457.00;QD=33.11;SB=-678.96 GT:AD:DP:GL:GQ 1/1:0,44:39:-149.29,-11.74,-0.01:99 +chr1 777290 . C T 29.42 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=32.80;MQ0=5;OQ=855.45;QD=17.11;SB=-308.80 GT:AD:DP:GL:GQ 0/1:21,29:44:-102.09,-13.26,-62.10:99 +chr1 777548 rs2905054 G T 500.83 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.40;MQ0=0;OQ=2267.93;QD=36.00;SB=-851.89 GT:AD:DP:GL:GQ 1/1:0,63:62:-230.39,-18.67,-0.01:99 +chr1 777707 rs2905053 C T 334.21 PASS AC=2;AF=1.00;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=44.44;MQ0=2;OQ=3957.07;QD=39.57;SB=-1940.72 GT:AD:DP:GL:GQ 1/1:0,100:95:-394.71,-28.61,-0.02:99 +chr1 778576 rs2980306 T C 128.68 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=33.51;MQ0=34;OQ=1562.02;QD=19.05;SB=-268.41 GT:AD:DP:GL:GQ 1/1:13,69:45:-159.81,-13.56,-0.02:99 +chr1 778703 rs10157303 T C 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=3;HaplotypeScore=7.41;MQ=38.85;MQ0=14;OQ=444.81;QD=5.30;SB=-42.81 GT:AD:DP:GL:GQ 0/1:40,44:57:-64.95,-17.19,-138.39:99 +chr1 778707 rs10159337 C G 0.38 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=6.67;MQ=39.47;MQ0=14;OQ=423.04;QD=5.29;SB=32.36 GT:AD:DP:GL:GQ 0/1:47,33:53:-61.57,-15.98,-162.13:99 +chr1 778752 rs10159341 C T 0.26 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=43.79;MQ0=4;OQ=82.84;QD=1.45;SB=53.17 GT:AD:DP:GL:GQ 0/1:50,7:44:-24.83,-13.27,-122.87:99 +chr1 778808 . G C 4.86 PASS AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=23.40;MQ0=13;OQ=99.43;QD=5.52;SB=-51.47 GT:AD:DP:GL:GQ 1/1:11,7:3:-13.43,-0.90,-0.00:9.03 +chr1 778958 . C G 0.12 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=6.83;MQ=13.77;MQ0=12;OQ=373.21;QD=7.46;SB=-3.98 GT:AD:DP:GL:GQ 0/1:40,10:17:-45.73,-5.12,-29.92:99 +chr1 778962 rs10158938 G A 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=6.77;MQ=13.74;MQ0=12;OQ=114.14;QD=2.24;SB=-77.09 GT:AD:DP:GL:GQ 0/1:17,34:17:-19.83,-5.13,-36.56:99 +chr1 779001 . C G 62.18 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=43.25;MQ=17.50;MQ0=24;QD=0.60;SB=-3.98 GT:AD:DP:GL:GQ 0/1:92,11:44:-22.76,-13.26,-160.88:95.02 +chr1 779004 . G C 379.18 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=41.31;MQ=17.52;MQ0=26;QD=3.61;SB=-3.98 GT:AD:DP:GL:GQ 0/1:83,21:42:-55.98,-14.78,-128.84:99 +chr1 779007 . G C 125.98 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=41.47;MQ=17.84;MQ0=24;QD=1.21;SB=-3.98 GT:AD:DP:GL:GQ 0/1:82,22:45:-29.45,-13.56,-167.32:99 +chr1 779046 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=13.36;MQ=16.85;MQ0=30;OQ=85.18;QD=0.76;SB=-0.98 GT:AD:DP:GL:GQ 0/1:103,9:39:-23.55,-11.75,-110.84:99 +chr1 779119 rs3131939 T C 14.51 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=38.97;MQ0=6;OQ=1691.71;QD=26.03;SB=-847.52 GT:AD:DP:GL:GQ 1/1:0,65:53:-172.80,-15.99,-0.05:99 +chr1 782126 rs1044922 A G 199.05 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=35.10;MQ0=8;OQ=1304.52;QD=20.38;SB=-463.86 GT:AD:DP:GL:GQ 1/1:3,61:42:-134.08,-12.67,-0.04:99 +chr1 782343 rs2905036 C T 605.33 PASS AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.88;MQ0=2;OQ=3789.97;QD=39.07;SB=-1780.39 GT:AD:DP:GL:GQ 1/1:0,97:94:-378.00,-28.32,-0.03:99 +chr1 783071 rs2905029 C G 4.69 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=24.02;MQ0=7;OQ=636.50;QD=15.91;SB=29.13 GT:AD:DP:GL:GQ 0/1:20,20:32:-76.58,-9.64,-67.00:99 +chr1 783292 rs2519067 T C 14.72 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=32.87;MQ0=7;OQ=1046.72;QD=28.29;SB=-162.84 GT:AD:DP:GL:GQ 1/1:5,32:30:-108.26,-9.03,-0.01:90.27 +chr1 785455 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=20;HaplotypeScore=3.33;MQ=47.34;MQ0=4;OQ=246.17;QD=4.48;SB=-56.75 GT:AD:DP:GL:GQ 0/1:43,12:47:-42.06,-14.16,-132.17:99 +chr1 786397 . T C 0.59 PASS AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=41.18;MQ0=9;OQ=325.37;QD=4.52;SB=-24.72 GT:AD:DP:GL:GQ 0/1:50,22:59:-53.59,-17.77,-179.67:99 +chr1 786590 rs2909612 G T 160.63 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=27.34;MQ0=10;OQ=1960.56;QD=30.63;SB=-1001.80 GT:AD:DP:GL:GQ 1/1:0,64:54:-199.65,-16.26,-0.01:99 +chr1 786630 rs12076540 G A 0.40 PASS AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=7.41;MQ=41.01;MQ0=13;OQ=2659.94;QD=26.60;SB=-1327.51 GT:AD:DP:GL:GQ 0/1:23,77:83:-294.28,-25.01,-36.59:99 +chr1 786634 rs2909613 T C 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=7.24;MQ=42.00;MQ0=12;OQ=84.11;QD=0.83;SB=12.37 GT:AD:DP:GL:GQ 0/1:80,21:85:-37.30,-25.61,-300.66:99 +chr1 786902 . A G 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=48.19;MQ0=15;OQ=198.92;QD=1.55;SB=-72.06 GT:AD:DP:GL:GQ 0/1:96,32:111:-56.61,-33.43,-385.87:99 +chr1 787026 . G A 14.82 LowQual AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=46.76;MQ0=8;QD=0.17;SB=-27.80 GT:AD:DP:GL:GQ 0/1:74,15:80:-28.85,-24.10,-261.80:47.51 +chr1 787041 . A T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=44.71;MQ0=13;OQ=84.25;QD=0.90;SB=-23.86 GT:AD:DP:GL:GQ 0/1:71,22:80:-37.92,-26.21,-271.06:99 +chr1 787889 rs4951864 C T 266.17 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=45.78;MQ0=1;OQ=2714.18;QD=38.77;SB=-989.31 GT:AD:DP:GL:GQ 1/1:1,69:67:-275.02,-20.18,-0.01:99 +chr1 789326 rs4245756 T C 211.89 PASS AC=2;AF=1.00;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=58.75;MQ0=0;OQ=3107.92;QD=34.53;SB=-1502.55 GT:AD:DP:GL:GQ 1/1:0,90:89:-314.41,-26.81,-0.04:99 +chr1 789870 rs6681049 T C 615.97 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=47.06;MQ0=1;OQ=2660.56;QD=34.55;SB=-1115.14 GT:AD:DP:GL:GQ 1/1:0,77:73:-269.66,-21.99,-0.02:99 +chr1 790246 rs4951931 C T 190.77 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=47.97;MQ0=4;OQ=2808.35;QD=36.95;SB=-1258.17 GT:AD:DP:GL:GQ 1/1:1,75:70:-284.44,-21.09,-0.02:99 +chr1 791806 rs7516866 C T 78.65 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=49.91;MQ0=4;OQ=2127.43;QD=34.88;SB=-1017.37 GT:AD:DP:GL:GQ 1/1:0,61:56:-216.36,-16.88,-0.03:99 +chr1 791858 rs7553084 G A 0.25 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=36.92;MQ0=13;OQ=63.33;QD=1.47;SB=-33.64 GT:AD:DP:GL:GQ 0/1:29,14:21:-15.95,-6.33,-55.40:96.17 +chr1 791869 rs9700144 T C 36.55 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=30.98;MQ0=16;OQ=499.95;QD=11.90;SB=-156.35 GT:AD:DP:GL:GQ 0/1:18,24:19:-59.00,-5.72,-11.19:54.70 +chr1 791956 rs7553197 G A 67.79 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=36.93;MQ0=8;OQ=1294.09;QD=27.53;SB=-402.66 GT:AD:DP:GL:GQ 1/1:3,44:34:-133.00,-10.24,-0.01:99 +chr1 792054 . G A 0.09 PASS AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=30.80;MQ0=19;OQ=223.16;QD=2.37;SB=-57.50 GT:AD:DP:GL:GQ 0/1:66,28:40:-37.67,-12.07,-95.70:99 +chr1 792085 rs61768213 G A 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=11.76;MQ=27.41;MQ0=19;OQ=204.34;QD=1.93;SB=-8.44 GT:AD:DP:GL:GQ 0/1:88,18:55:-40.31,-16.60,-140.17:99 +chr1 792094 rs59334306 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=46.76;MQ=26.45;MQ0=20;OQ=280.32;QD=2.64;SB=-7.86 GT:AD:DP:GL:GQ 0/1:75,30:53:-47.28,-15.96,-151.37:99 +chr1 792103 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=25.85;MQ=29.18;MQ0=20;OQ=339.53;QD=3.09;SB=-172.66 GT:AD:DP:GL:GQ 0/1:84,26:61:-55.65,-18.41,-142.90:99 +chr1 792163 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=94;Dels=0.02;HRun=3;HaplotypeScore=9.77;MQ=36.34;MQ0=8;OQ=472.25;QD=5.02;SB=-153.68 GT:AD:DP:GL:GQ 0/1:49,43:64:-69.50,-18.99,-156.72:99 +chr1 792183 . G A 7.22 PASS AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=42.20;MQ0=9;OQ=1359.41;QD=15.27;SB=-245.27 GT:AD:DP:GL:GQ 0/1:36,53:59:-157.01,-17.79,-57.64:99 +chr1 792201 . G A 0.06 PASS AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=43.46;MQ0=8;OQ=234.21;QD=2.47;SB=6.27 GT:AD:DP:GL:GQ 0/1:68,27:69:-47.53,-20.82,-170.85:99 +chr1 792244 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=3.46;MQ=47.18;MQ0=4;OQ=75.38;QD=1.05;SB=92.33 GT:AD:DP:GL:GQ 0/1:49,23:53:-26.79,-15.97,-181.50:99 +chr1 793978 rs9725068 G A 105.15 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.47;MQ0=13;OQ=1474.93;QD=26.34;SB=-321.42 GT:AD:DP:GL:GQ 1/1:0,56:37:-151.09,-11.15,-0.01:99 +chr1 794403 rs11240778 T C 115.53 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.32;MQ0=0;OQ=2475.68;QD=30.95;SB=-1150.98 GT:AD:DP:GL:GQ 1/1:0,80:77:-251.22,-23.23,-0.07:99 +chr1 797375 rs10751454 A G 614.93 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.93;MQ0=1;OQ=2184.15;QD=34.67;SB=-971.41 GT:AD:DP:GL:GQ 1/1:0,63:61:-222.02,-18.37,-0.02:99 +chr1 797624 rs4951932 C A 532.14 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.69;MQ0=0;OQ=2699.27;QD=36.48;SB=-1270.15 GT:AD:DP:GL:GQ 1/1:0,74:72:-273.52,-21.68,-0.01:99 +chr1 798086 rs4951933 G C 74.24 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=48.23;MQ0=3;OQ=1918.57;QD=25.24;SB=-881.14 GT:AD:DP:GL:GQ 1/1:5,71:54:-198.81,-16.33,-3.37:99 +chr1 798494 rs11240779 G A 160.91 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=54.32;MQ0=0;OQ=2346.63;QD=37.85;SB=-859.15 GT:AD:DP:GL:GQ 1/1:0,62:60:-238.27,-18.08,-0.02:99 +chr1 798785 rs6594027 G A 211.91 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.48;MQ=43.75;MQ0=6;OQ=1743.42;QD=29.06;SB=-625.73 GT:AD:DP:GL:GQ 1/1:3,57:47:-180.84,-14.16,-2.92:99 +chr1 798791 rs11240780 C T 1.58 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.98;MQ=44.87;MQ0=5;OQ=1874.68;QD=30.73;SB=-625.19 GT:AD:DP:GL:GQ 1/1:3,58:49:-194.73,-14.76,-3.68:99 +chr1 801153 rs6683530 G C 58.35 Indel AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=7.29;SB=-48.46 GT:AD:DP:GL:GQ 0/1:3,5:6:-10.93,-1.81,-12.15:91.19 +chr1 801443 . G C 0.04 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=38.48;MQ0=1;OQ=52.85;QD=17.62;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:2:-8.69,-0.60,-0.00:6.02 +chr1 801493 . G A 49.74 LowQual AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=43.23;MQ0=0;QD=5.53;SB=-18.25 GT:AD:DP:GL:GQ 0/1:2,4:4:-12.63,-4.37,-6.30:19.25 +chr1 801563 . C G 14.05 LowQual AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=3.71;MQ=42.60;MQ0=0;QD=1.40;SB=-3.98 GT:AD:DP:GL:GQ 0/1:8,2:7:-6.79,-2.12,-21.33:46.71 +chr1 801598 . T C 10.44 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=49.26;MQ0=0;OQ=130.47;QD=6.21;SB=-25.63 GT:AD:DP:GL:GQ 0/1:13,8:15:-20.85,-4.52,-36.05:99 +chr1 801628 . C T 6.09 PASS AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=52.56;MQ0=0;OQ=245.60;QD=14.45;SB=-39.65 GT:AD:DP:GL:GQ 0/1:7,10:12:-31.46,-3.62,-11.96:83.42 +chr1 802130 rs7541694 A G 69.50 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.34;MQ=55.65;MQ0=0;OQ=1955.23;QD=29.18;SB=-933.35 GT:AD:DP:GL:GQ 1/1:0,67:63:-199.17,-19.00,-0.06:99 +chr1 802147 rs7545373 C G 33.64 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=3.57;MQ=55.54;MQ0=0;OQ=2348.31;QD=37.27;SB=-1198.48 GT:AD:DP:GL:GQ 1/1:2,61:60:-246.74,-18.09,-8.33:97.66 +chr1 802165 . G A 18.16 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.79;MQ=55.42;MQ0=0;QD=0.31;SB=71.21 GT:AD:DP:GL:GQ 0/1:51,8:51:-20.46,-15.37,-155.58:50.93 +chr1 802175 . C T 26.53 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=55.08;MQ0=0;QD=0.48;SB=56.20 GT:AD:DP:GL:GQ 0/1:46,8:48:-20.39,-14.46,-154.35:59.35 +chr1 802189 . G A 11.38 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=55.49;MQ0=0;QD=0.20;SB=56.19 GT:AD:DP:GL:GQ 0/1:49,8:51:-19.75,-15.37,-163.52:43.89 +chr1 802470 . T C 21.38 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=54.38;MQ0=1;QD=0.34;SB=62.23 GT:AD:DP:GL:GQ 0/1:57,6:59:-23.19,-17.77,-210.98:54.19 +chr1 802488 . G T 29.03 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=53.89;MQ0=1;QD=0.53;SB=65.21 GT:AD:DP:GL:GQ 0/1:49,6:52:-21.85,-15.66,-163.62:61.86 +chr1 802614 rs4246500 T C 405.83 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1600.84;QD=34.80;SB=-568.88 GT:AD:DP:GL:GQ 1/1:0,46:45:-163.68,-13.56,-0.02:99 +chr1 803503 rs16973606 A G 11.51 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.56;MQ=28.75;MQ0=1;OQ=1669.54;QD=28.30;SB=-566.93 GT:AD:DP:GL:GQ 1/1:0,58:52:-170.59,-15.68,-0.05:99 +chr1 803610 rs4970388 G A 620.03 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.63;MQ0=0;OQ=2297.43;QD=38.94;SB=-1171.71 GT:AD:DP:GL:GQ 1/1:0,59:58:-233.34,-17.47,-0.02:99 +chr1 803950 . C A 24.11 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=7.91;MQ=35.01;MQ0=10;QD=0.32;SB=59.14 GT:AD:DP:GL:GQ 0/1:54,21:50:-20.76,-15.06,-152.32:56.93 +chr1 803957 rs61768235 A G 0.17 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=7.75;MQ=34.03;MQ0=10;OQ=322.16;QD=4.30;SB=35.12 GT:AD:DP:GL:GQ 0/1:42,30:47:-49.67,-14.18,-120.05:99 +chr1 803968 . C T 1.63 PASS AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=30.80;MQ0=12;OQ=418.55;QD=4.81;SB=59.13 GT:AD:DP:GL:GQ 0/1:53,34:61:-63.53,-18.39,-146.32:99 +chr1 804010 rs4268301 G C 0.65 PASS AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=6.53;MQ=32.14;MQ0=12;OQ=1062.36;QD=10.84;SB=53.20 GT:AD:DP:GL:GQ 0/1:43,55:71:-130.91,-21.39,-167.36:99 +chr1 804023 . C G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=2;HaplotypeScore=7.44;MQ=36.24;MQ0=5;OQ=967.44;QD=10.63;SB=62.24 GT:AD:DP:GL:GQ 0/1:48,43:70:-121.12,-21.09,-190.26:99 +chr1 804036 . A T 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=7.15;MQ=36.45;MQ0=7;OQ=717.66;QD=8.34;SB=65.21 GT:AD:DP:GL:GQ 0/1:47,38:68:-95.53,-20.48,-155.46:99 +chr1 804078 rs4468103 A G 426.89 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=12.81;MQ=43.94;MQ0=3;QD=5.62;SB=77.26 GT:AD:DP:GL:GQ 0/1:53,23:63:-64.96,-18.98,-178.46:99 +chr1 804080 rs34234497 C A 381.14 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=12.71;MQ=43.70;MQ0=3;QD=4.95;SB=89.27 GT:AD:DP:GL:GQ 0/1:53,24:67:-61.57,-20.18,-178.60:99 +chr1 804083 . C A 27.31 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=12.71;MQ=43.58;MQ0=4;QD=0.34;SB=86.24 GT:AD:DP:GL:GQ 0/1:70,11:67:-26.19,-20.18,-214.42:60.14 +chr1 804127 rs4571914 C T 3.06 PASS AC=2;AF=1.00;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=47.10;MQ0=4;OQ=2988.66;QD=31.13;SB=-1433.34 GT:AD:DP:GL:GQ 1/1:3,93:75:-302.47,-22.59,-0.02:99 +chr1 804160 . T A 1.44 PASS AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=46.18;MQ0=5;OQ=470.49;QD=4.06;SB=48.91 GT:AD:DP:GL:GQ 0/1:72,44:82:-75.03,-24.70,-237.11:99 +chr1 804163 . T A 0.61 PASS AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=45.72;MQ0=5;OQ=536.43;QD=4.62;SB=45.90 GT:AD:DP:GL:GQ 0/1:71,45:81:-81.32,-24.40,-231.88:99 +chr1 804176 . C T 0.11 PASS AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=42.84;MQ0=5;OQ=284.28;QD=2.41;SB=31.59 GT:AD:DP:GL:GQ 0/1:90,28:84:-57.01,-25.30,-251.94:99 +chr1 804255 rs61768236 C T 415.82 PASS AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.82;MQ0=7;OQ=1235.94;QD=11.44;SB=-464.41 GT:AD:DP:GL:GQ 0/1:49,59:70:-147.96,-21.08,-123.48:99 +chr1 804268 rs61768237 T C 267.05 PASS AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.38;MQ0=8;OQ=1449.21;QD=11.32;SB=-624.62 GT:AD:DP:GL:GQ 0/1:53,75:88:-174.71,-26.51,-156.34:99 +chr1 804322 . T C 170.65 PASS AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.67;MQ0=9;OQ=1734.45;QD=11.19;SB=-540.49 GT:AD:DP:GL:GQ 0/1:72,83:118:-212.27,-35.54,-249.66:99 +chr1 804353 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=4;HaplotypeScore=24.21;MQ=44.77;MQ0=2;OQ=299.39;QD=2.32;SB=-27.46 GT:AD:DP:GL:GQ 0/1:106,23:112:-66.96,-33.74,-330.98:99 +chr1 804358 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=1;HaplotypeScore=23.14;MQ=46.13;MQ0=0;OQ=958.19;QD=8.33;SB=-257.80 GT:AD:DP:GL:GQ 0/1:68,47:100:-129.23,-30.12,-232.16:99 +chr1 804472 . A T 0.19 PASS AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=48.14;MQ0=4;OQ=798.74;QD=6.89;SB=107.38 GT:AD:DP:GL:GQ 0/1:75,41:98:-112.67,-29.52,-266.53:99 +chr1 804474 . A C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=2;HaplotypeScore=5.00;MQ=47.90;MQ0=4;OQ=704.41;QD=6.18;SB=101.34 GT:AD:DP:GL:GQ 0/1:73,41:96:-102.63,-28.91,-247.09:99 +chr1 804544 . A T 0.11 PASS AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=3.62;MQ=40.45;MQ0=6;OQ=406.04;QD=3.15;SB=95.34 GT:AD:DP:GL:GQ 0/1:99,30:89:-70.69,-26.81,-271.16:99 +chr1 804557 . A C 0.23 PASS AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=3.14;MQ=40.10;MQ0=5;OQ=416.51;QD=3.82;SB=86.28 GT:AD:DP:GL:GQ 0/1:65,43:73:-66.93,-21.99,-180.79:99 +chr1 804573 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=8.85;MQ=43.02;MQ0=4;OQ=579.16;QD=6.16;SB=83.29 GT:AD:DP:GL:GQ 0/1:56,38:69:-81.99,-20.79,-176.35:99 +chr1 804594 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=7.80;MQ=47.78;MQ0=4;OQ=294.82;QD=3.04;SB=104.36 GT:AD:DP:GL:GQ 0/1:66,31:74:-55.06,-22.29,-235.53:99 +chr1 804605 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=13.95;MQ=49.87;MQ0=3;OQ=284.24;QD=2.81;SB=113.40 GT:AD:DP:GL:GQ 0/1:73,28:82:-56.44,-24.73,-279.54:99 +chr1 804976 . T C 11.87 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=17.62;MQ=47.74;MQ0=10;QD=0.07;SB=128.44 GT:AD:DP:GL:GQ 0/1:107,52:112:-38.18,-33.74,-401.64:44.42 +chr1 805001 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=241;Dels=0.00;HRun=1;HaplotypeScore=76.93;MQ=42.40;MQ0=12;OQ=1246.68;QD=5.17;SB=146.50 GT:AD:DP:GL:GQ 0/1:129,112:153:-174.09,-46.14,-468.17:99 +chr1 805002 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=75.93;MQ=42.40;MQ0=13;OQ=1673.16;QD=6.89;SB=-6.76 GT:AD:DP:GL:GQ 0/1:105,138:154:-217.01,-46.41,-335.99:99 +chr1 805021 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=298;Dels=0.00;HRun=1;HaplotypeScore=153.68;MQ=38.48;MQ0=13;OQ=1337.90;QD=4.49;SB=-19.37 GT:AD:DP:GL:GQ 0/1:146,152:156:-184.06,-46.99,-421.14:99 +chr1 805031 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=318;Dels=0.00;HRun=0;HaplotypeScore=207.07;MQ=37.99;MQ0=12;OQ=1684.06;QD=5.30;SB=131.37 GT:AD:DP:GL:GQ 0/1:175,143:165:-221.39,-49.70,-405.98:99 +chr1 805042 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=340;Dels=0.00;HRun=0;HaplotypeScore=155.12;MQ=37.32;MQ0=17;OQ=677.06;QD=1.99;SB=140.48 GT:AD:DP:GL:GQ 0/1:285,55:199:-130.92,-59.93,-605.02:99 +chr1 805044 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=339;Dels=0.00;HRun=1;HaplotypeScore=156.13;MQ=36.94;MQ0=19;OQ=889.27;QD=2.62;SB=-0.09 GT:AD:DP:GL:GQ 0/1:243,95:179:-146.12,-53.91,-499.80:99 +chr1 805060 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=354;Dels=0.00;HRun=0;HaplotypeScore=82.46;MQ=36.20;MQ0=28;OQ=262.53;QD=0.74;SB=131.47 GT:AD:DP:GL:GQ 0/1:269,85:206:-91.58,-62.05,-725.20:99 +chr1 805070 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=335;Dels=0.00;HRun=0;HaplotypeScore=72.27;MQ=36.04;MQ0=29;OQ=243.31;QD=0.73;SB=122.43 GT:AD:DP:GL:GQ 0/1:284,51:196:-86.65,-59.04,-686.22:99 +chr1 805096 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=276;Dels=0.00;HRun=1;HaplotypeScore=49.35;MQ=36.73;MQ0=27;OQ=2126.16;QD=7.70;SB=101.36 GT:AD:DP:GL:GQ 0/1:81,194:152:-261.68,-45.78,-320.28:99 +chr1 805097 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=277;Dels=0.00;HRun=0;HaplotypeScore=50.14;MQ=36.84;MQ0=27;OQ=2166.21;QD=7.82;SB=104.34 GT:AD:DP:GL:GQ 0/1:80,196:153:-269.55,-49.64,-287.57:99 +chr1 805200 . G T 14.62 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=163;Dels=0.00;HRun=0;HaplotypeScore=25.70;MQ=44.88;MQ0=22;QD=0.09;SB=134.45 GT:AD:DP:GL:GQ 0/1:137,26:122:-41.47,-36.74,-399.49:47.31 +chr1 805236 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=3;HaplotypeScore=58.62;MQ=48.88;MQ0=19;OQ=385.49;QD=2.77;SB=18.48 GT:AD:DP:GL:GQ 0/1:87,52:105:-73.46,-31.63,-322.22:99 +chr1 805261 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=234;Dels=0.00;HRun=0;HaplotypeScore=375.75;MQ=40.95;MQ0=20;OQ=701.87;QD=3.00;SB=-184.24 GT:AD:DP:GL:GQ 0/1:132,101:136:-114.44,-40.97,-420.32:99 +chr1 805262 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=0;HaplotypeScore=355.61;MQ=40.41;MQ0=21;OQ=112.78;QD=0.47;SB=-10.32 GT:AD:DP:GL:GQ 0/1:195,42:136:-62.96,-48.40,-549.49:99 +chr1 805283 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=350;Dels=0.00;HRun=0;HaplotypeScore=86.54;MQ=35.73;MQ0=32;OQ=70.17;QD=0.20;SB=7.66 GT:AD:DP:GL:GQ 0/1:314,35:208:-72.95,-62.65,-681.33:99 +chr1 805284 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=355;Dels=0.00;HRun=0;HaplotypeScore=88.37;MQ=35.41;MQ0=32;OQ=4656.41;QD=13.12;SB=-1324.68 GT:AD:DP:GL:GQ 0/1:83,272:209:-464.64,-62.96,-333.94:99 +chr1 805326 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=520;Dels=0.00;HRun=0;HaplotypeScore=98.56;MQ=31.27;MQ0=33;OQ=692.81;QD=1.33;SB=-240.64 GT:AD:DP:GL:GQ 0/1:439,81:305:-164.43,-91.87,-1058.15:99 +chr1 805332 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=545;Dels=0.00;HRun=2;HaplotypeScore=105.70;MQ=31.02;MQ0=35;OQ=141.69;QD=0.26;SB=-23.90 GT:AD:DP:GL:GQ 0/1:483,62:326:-115.64,-98.18,-1059.59:99 +chr1 805355 . A G 982.52 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=566;Dels=0.00;HRun=0;HaplotypeScore=511.67;MQ=31.08;MQ0=42;QD=1.74;SB=-163.90 GT:AD:DP:GL:GQ 0/1:444,82:337:-230.52,-128.98,-1164.43:99 +chr1 805360 . A G 1795.44 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=565;Dels=0.00;HRun=0;HaplotypeScore=478.07;MQ=31.09;MQ0=46;QD=3.18;SB=-791.73 GT:AD:DP:GL:GQ 0/1:432,132:335:-287.21,-104.38,-1038.16:99 +chr1 805365 . T C 1655.74 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=542;Dels=0.00;HRun=0;HaplotypeScore=449.89;MQ=31.32;MQ0=44;QD=3.05;SB=-765.34 GT:AD:DP:GL:GQ 0/1:385,157:321:-265.54,-96.68,-1024.45:99 +chr1 805383 rs61768238 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=498;Dels=0.00;HRun=3;HaplotypeScore=98.26;MQ=31.16;MQ0=41;OQ=7913.78;QD=15.89;SB=-2299.71 GT:AD:DP:GL:GQ 0/1:75,423:268:-790.38,-80.71,-278.68:99 +chr1 805386 rs61768239 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=483;Dels=0.00;HRun=1;HaplotypeScore=91.10;MQ=31.39;MQ0=41;OQ=3141.51;QD=6.50;SB=-667.16 GT:AD:DP:GL:GQ 0/1:227,256:265:-397.24,-79.81,-626.74:99 +chr1 805419 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=411;Dels=0.00;HRun=1;HaplotypeScore=30.13;MQ=32.93;MQ0=34;OQ=719.57;QD=1.75;SB=-330.57 GT:AD:DP:GL:GQ 0/1:225,186:205:-136.99,-61.75,-686.74:99 +chr1 805436 rs61768240 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=352;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=34.71;MQ0=24;OQ=2408.76;QD=6.84;SB=-1167.64 GT:AD:DP:GL:GQ 0/1:93,259:163:-293.26,-49.10,-323.35:99 +chr1 805464 . T C 90.93 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=2;HaplotypeScore=145.78;MQ=37.92;MQ0=13;QD=0.36;SB=50.70 GT:AD:DP:GL:GQ 0/1:218,34:131:-51.84,-39.46,-473.80:99 +chr1 805469 . G A 411.01 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=0;HaplotypeScore=129.65;MQ=39.23;MQ0=10;QD=1.77;SB=-144.72 GT:AD:DP:GL:GQ 0/1:163,68:125:-82.03,-37.65,-380.30:99 +chr1 805474 . C T 980.44 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=4;HaplotypeScore=70.79;MQ=41.63;MQ0=7;QD=4.83;SB=-326.68 GT:AD:DP:GL:GQ 0/1:87,114:116:-136.29,-34.97,-264.49:99 +chr1 805480 . G T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=1;HaplotypeScore=5.97;MQ=42.07;MQ0=5;OQ=803.65;QD=4.10;SB=-259.91 GT:AD:DP:GL:GQ 0/1:87,109:116:-118.58,-34.93,-301.30:99 +chr1 805558 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=0;HaplotypeScore=21.59;MQ=45.69;MQ0=3;OQ=812.25;QD=4.51;SB=-279.67 GT:AD:DP:GL:GQ 0/1:110,69:130:-123.67,-39.16,-392.54:99 +chr1 805591 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=34.23;MQ=41.40;MQ0=5;OQ=1850.17;QD=8.49;SB=-635.41 GT:AD:DP:GL:GQ 0/1:84,134:148:-232.88,-44.58,-338.13:99 +chr1 805603 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=0;HaplotypeScore=49.54;MQ=40.33;MQ0=6;OQ=1757.35;QD=7.35;SB=-559.93 GT:AD:DP:GL:GQ 0/1:109,130:154:-225.41,-46.39,-351.31:99 +chr1 805620 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=274;Dels=0.00;HRun=0;HaplotypeScore=50.16;MQ=37.51;MQ0=8;OQ=230.26;QD=0.84;SB=134.91 GT:AD:DP:GL:GQ 0/1:246,28:171:-77.81,-51.50,-552.70:99 +chr1 805666 . G A 1332.87 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=339;Dels=0.00;HRun=0;HaplotypeScore=203.60;MQ=35.75;MQ0=0;QD=3.93;SB=119.41 GT:AD:DP:GL:GQ 0/1:281,58:223:-203.73,-67.16,-610.84:99 +chr1 805667 . T G 1225.05 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=341;Dels=0.00;HRun=2;HaplotypeScore=286.55;MQ=35.76;MQ0=2;QD=3.59;SB=122.41 GT:AD:DP:GL:GQ 0/1:261,66:222:-230.10,-104.31,-623.63:99 +chr1 805699 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=311;Dels=0.00;HRun=0;HaplotypeScore=73.71;MQ=35.76;MQ0=12;OQ=1765.48;QD=5.68;SB=-47.39 GT:AD:DP:GL:GQ 0/1:139,171:182:-234.66,-54.83,-454.10:99 +chr1 805716 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=281;Dels=0.00;HRun=1;HaplotypeScore=131.75;MQ=37.99;MQ0=12;OQ=2170.35;QD=7.72;SB=-121.23 GT:AD:DP:GL:GQ 0/1:87,193:163:-269.41,-49.09,-357.63:99 +chr1 805720 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=145.61;MQ=38.29;MQ0=13;OQ=527.98;QD=1.87;SB=137.43 GT:AD:DP:GL:GQ 0/1:237,44:165:-105.78,-49.70,-509.42:99 +chr1 805742 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=47.83;MQ=40.90;MQ0=15;OQ=1225.89;QD=5.11;SB=-296.81 GT:AD:DP:GL:GQ 0/1:97,143:138:-167.44,-41.57,-348.72:99 +chr1 805786 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=3.15;MQ=44.26;MQ0=7;OQ=155.59;QD=0.86;SB=-81.22 GT:AD:DP:GL:GQ 0/1:95,86:108:-51.37,-32.53,-383.93:99 +chr1 805792 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=9.50;MQ=44.61;MQ0=6;OQ=192.56;QD=1.10;SB=-88.24 GT:AD:DP:GL:GQ 0/1:93,82:108:-55.07,-32.53,-377.29:99 +chr1 805825 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=46.58;MQ0=3;OQ=327.36;QD=1.98;SB=-101.34 GT:AD:DP:GL:GQ 0/1:95,70:115:-70.67,-34.65,-378.60:99 +chr1 805831 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=0;HaplotypeScore=10.96;MQ=47.14;MQ0=3;OQ=324.94;QD=2.11;SB=-17.64 GT:AD:DP:GL:GQ 0/1:97,57:110:-68.91,-33.13,-331.34:99 +chr1 805897 . G T 104.51 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=35.45;MQ=51.05;MQ0=2;QD=0.74;SB=119.34 GT:AD:DP:GL:GQ 0/1:121,19:121:-50.18,-36.44,-386.79:99 +chr1 805898 . C A 129.42 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=35.61;MQ=51.05;MQ0=2;QD=0.91;SB=116.38 GT:AD:DP:GL:GQ 0/1:123,19:121:-52.67,-36.45,-375.35:99 +chr1 805905 . T G 13.51 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=25.14;MQ=52.44;MQ0=2;QD=0.10;SB=92.42 GT:AD:DP:GL:GQ 0/1:98,32:107:-36.84,-32.23,-356.89:46.15 +chr1 806044 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=16.71;MQ=40.59;MQ0=35;OQ=921.37;QD=5.06;SB=-438.60 GT:AD:DP:GL:GQ 0/1:71,111:106:-127.34,-31.92,-261.51:99 +chr1 806066 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=250;Dels=0.00;HRun=1;HaplotypeScore=9.43;MQ=37.37;MQ0=38;OQ=287.57;QD=1.15;SB=103.29 GT:AD:DP:GL:GQ 0/1:214,36:146:-76.01,-43.97,-467.77:99 +chr1 806081 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=255;Dels=0.00;HRun=0;HaplotypeScore=39.62;MQ=37.88;MQ0=27;OQ=908.24;QD=3.56;SB=97.71 GT:AD:DP:GL:GQ 0/1:178,77:158:-141.71,-47.60,-556.49:99 +chr1 806157 . T C 806.81 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=0;HaplotypeScore=71.06;MQ=40.64;MQ0=4;QD=3.75;SB=110.40 GT:AD:DP:GL:GQ 0/1:92,123:126:-121.92,-37.95,-368.73:99 +chr1 806159 . A C 141.17 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=219;Dels=0.00;HRun=0;HaplotypeScore=72.96;MQ=40.68;MQ0=4;QD=0.64;SB=110.38 GT:AD:DP:GL:GQ 0/1:166,49:128:-59.78,-42.38,-415.09:99 +chr1 806180 . A G 18.74 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=200;Dels=0.00;HRun=0;HaplotypeScore=59.33;MQ=41.65;MQ0=4;QD=0.09;SB=116.41 GT:AD:DP:GL:GQ 0/1:140,60:110:-38.29,-33.13,-408.92:51.52 +chr1 806197 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=1;HaplotypeScore=58.42;MQ=43.62;MQ0=5;OQ=190.94;QD=0.95;SB=134.47 GT:AD:DP:GL:GQ 0/1:110,91:116:-57.32,-34.94,-409.71:99 +chr1 806222 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=4;HaplotypeScore=6.94;MQ=47.96;MQ0=4;OQ=291.81;QD=1.80;SB=146.43 GT:AD:DP:GL:GQ 0/1:98,64:114:-66.80,-34.33,-354.69:99 +chr1 806232 . T A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=1;HaplotypeScore=11.98;MQ=49.02;MQ0=3;OQ=233.87;QD=1.55;SB=140.48 GT:AD:DP:GL:GQ 0/1:96,55:110:-59.80,-33.13,-362.79:99 +chr1 806258 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=0;HaplotypeScore=10.30;MQ=50.03;MQ0=8;OQ=407.17;QD=2.51;SB=100.40 GT:AD:DP:GL:GQ 0/1:106,56:126:-81.95,-37.95,-384.61:99 +chr1 806268 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=1;HaplotypeScore=25.82;MQ=48.78;MQ0=9;OQ=670.14;QD=4.09;SB=84.39 GT:AD:DP:GL:GQ 0/1:109,55:126:-108.24,-37.95,-362.57:99 +chr1 806273 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=0;HaplotypeScore=24.82;MQ=48.14;MQ0=9;OQ=549.55;QD=3.23;SB=88.59 GT:AD:DP:GL:GQ 0/1:119,51:130:-97.39,-39.15,-372.33:99 +chr1 806316 . T G 0.95 PASS AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=0;HaplotypeScore=6.00;MQ=41.01;MQ0=11;OQ=1685.25;QD=7.49;SB=-248.74 GT:AD:DP:GL:GQ 0/1:86,139:148:-216.38,-44.57,-322.16:99 +chr1 806332 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=267;Dels=0.00;HRun=0;HaplotypeScore=118.47;MQ=40.66;MQ0=10;OQ=669.93;QD=2.51;SB=-242.01 GT:AD:DP:GL:GQ 0/1:204,61:176:-123.31,-53.03,-632.31:99 +chr1 806338 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=0;HaplotypeScore=122.42;MQ=40.64;MQ0=8;OQ=2439.01;QD=9.17;SB=-856.79 GT:AD:DP:GL:GQ 0/1:98,144:180:-333.38,-86.20,-389.89:99 +chr1 806349 . G A 3132.30 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=280;Dels=0.07;HRun=0;HaplotypeScore=186.48;MQ=39.25;MQ0=4;QD=11.19;SB=-1153.15 GT:AD:DP:GL:GQ 0/1:91,170:182:-371.34,-54.83,-329.61:99 +chr1 806378 rs61768241 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=371;Dels=0.00;HRun=0;HaplotypeScore=37.20;MQ=35.74;MQ0=10;OQ=1136.07;QD=3.06;SB=-392.71 GT:AD:DP:GL:GQ 0/1:284,87:244:-190.38,-73.49,-742.15:99 +chr1 806405 . A T 171.83 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=402;Dels=0.02;HRun=5;HaplotypeScore=383.28;MQ=34.90;MQ0=14;QD=0.43;SB=-100.81 GT:AD:DP:GL:GQ 0/1:350,43:240:-91.25,-70.78,-803.92:99 +chr1 806411 . A T 5745.19 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=405;Dels=0.00;HRun=5;HaplotypeScore=552.66;MQ=35.31;MQ0=14;QD=14.19;SB=-2306.85 GT:AD:DP:GL:GQ 0/1:102,301:243:-573.52,-72.58,-344.41:99 +chr1 806412 . A T 2395.75 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=407;Dels=0.00;HRun=0;HaplotypeScore=506.57;MQ=35.27;MQ0=14;QD=5.89;SB=-1049.34 GT:AD:DP:GL:GQ 0/1:219,186:244:-315.74,-72.89,-600.57:99 +chr1 806419 . G T 930.64 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=433;Dels=0.00;HRun=4;HaplotypeScore=220.68;MQ=34.42;MQ0=17;QD=2.15;SB=-419.01 GT:AD:DP:GL:GQ 0/1:342,91:258:-174.05,-77.70,-758.54:99 +chr1 806424 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=450;Dels=0.00;HRun=4;HaplotypeScore=249.41;MQ=33.94;MQ0=20;OQ=971.28;QD=2.16;SB=-437.51 GT:AD:DP:GL:GQ 0/1:358,92:263:-179.62,-79.21,-806.78:99 +chr1 806430 rs61768242 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=441;Dels=0.01;HRun=1;HaplotypeScore=160.65;MQ=34.18;MQ0=22;OQ=1511.20;QD=3.43;SB=-624.36 GT:AD:DP:GL:GQ 0/1:304,134:257:-231.81,-77.41,-730.64:99 +chr1 806460 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=368;Dels=0.01;HRun=0;HaplotypeScore=18.13;MQ=35.78;MQ0=21;OQ=826.67;QD=2.25;SB=-89.07 GT:AD:DP:GL:GQ 0/1:306,59:217:-150.70,-64.75,-660.76:99 +chr1 806471 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=38.11;MQ0=12;OQ=2295.87;QD=7.92;SB=-836.85 GT:AD:DP:GL:GQ 0/1:88,202:166:-282.86,-49.99,-314.28:99 +chr1 806472 . T G 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=38.55;MQ0=12;OQ=2108.07;QD=7.42;SB=-683.52 GT:AD:DP:GL:GQ 0/1:91,193:165:-263.78,-49.69,-338.75:99 +chr1 806498 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=2;HaplotypeScore=28.30;MQ=42.69;MQ0=9;OQ=436.81;QD=2.11;SB=-20.91 GT:AD:DP:GL:GQ 0/1:161,46:144:-90.38,-43.41,-400.65:99 +chr1 806543 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=1;HaplotypeScore=100.50;MQ=43.92;MQ0=14;OQ=975.93;QD=5.00;SB=-107.11 GT:AD:DP:GL:GQ 0/1:89,101:124:-149.49,-48.61,-281.82:99 +chr1 806545 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=211;Dels=0.00;HRun=0;HaplotypeScore=104.33;MQ=43.14;MQ0=16;OQ=1451.12;QD=6.88;SB=-262.10 GT:AD:DP:GL:GQ 0/1:103,108:137:-189.66,-41.27,-324.56:99 +chr1 806559 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=338;Dels=0.00;HRun=5;HaplotypeScore=96.33;MQ=38.72;MQ0=24;OQ=1155.72;QD=3.42;SB=-374.82 GT:AD:DP:GL:GQ 0/1:243,83:209:-199.57,-80.72,-560.52:99 +chr1 806579 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=382;Dels=0.00;HRun=0;HaplotypeScore=77.21;MQ=36.57;MQ0=25;OQ=319.95;QD=0.84;SB=31.35 GT:AD:DP:GL:GQ 0/1:306,63:241:-152.76,-117.48,-790.42:99 +chr1 806588 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=408;Dels=0.00;HRun=0;HaplotypeScore=158.67;MQ=35.58;MQ0=25;OQ=4390.20;QD=10.76;SB=-833.37 GT:AD:DP:GL:GQ 0/1:156,252:245:-438.02,-73.80,-510.93:99 +chr1 806591 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=423;Dels=0.00;HRun=0;HaplotypeScore=153.73;MQ=35.14;MQ0=25;OQ=116.80;QD=0.28;SB=22.12 GT:AD:DP:GL:GQ 0/1:359,64:250:-90.26,-75.29,-922.92:99 +chr1 806599 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=465;Dels=0.00;HRun=3;HaplotypeScore=92.78;MQ=34.88;MQ0=25;OQ=533.96;QD=1.15;SB=-62.62 GT:AD:DP:GL:GQ 0/1:398,67:259:-134.68,-78.00,-790.36:99 +chr1 806614 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=552;Dels=0.00;HRun=4;HaplotypeScore=128.97;MQ=33.43;MQ0=27;OQ=171.34;QD=0.31;SB=81.53 GT:AD:DP:GL:GQ 0/1:512,39:328:-122.57,-102.16,-1083.77:99 +chr1 806616 . A C 48.77 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=560;Dels=0.00;HRun=0;HaplotypeScore=145.79;MQ=33.35;MQ0=27;QD=0.09;SB=125.19 GT:AD:DP:GL:GQ 0/1:521,38:333:-108.15,-99.99,-1104.08:81.61 +chr1 806647 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=500;Dels=0.00;HRun=1;HaplotypeScore=106.37;MQ=33.16;MQ0=15;OQ=6479.54;QD=12.96;SB=-2653.75 GT:AD:DP:GL:GQ 0/1:87,413:252:-646.95,-75.89,-317.53:99 +chr1 806652 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=463;Dels=0.00;HRun=0;HaplotypeScore=119.18;MQ=33.47;MQ0=16;OQ=6167.91;QD=13.32;SB=-2596.35 GT:AD:DP:GL:GQ 0/1:76,386:224:-615.79,-67.46,-279.43:99 +chr1 806659 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=412;Dels=0.00;HRun=0;HaplotypeScore=138.09;MQ=33.68;MQ0=14;OQ=4821.66;QD=11.70;SB=-2064.94 GT:AD:DP:GL:GQ 0/1:127,285:208:-481.17,-62.64,-276.81:99 +chr1 806663 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=403;Dels=0.00;HRun=1;HaplotypeScore=116.74;MQ=34.29;MQ0=14;OQ=4902.23;QD=12.16;SB=-2019.44 GT:AD:DP:GL:GQ 0/1:76,327:212:-489.22,-63.85,-279.67:99 +chr1 806698 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=346;Dels=0.00;HRun=0;HaplotypeScore=104.08;MQ=36.06;MQ0=23;OQ=205.16;QD=0.59;SB=41.51 GT:AD:DP:GL:GQ 0/1:305,41:216:-88.85,-65.05,-740.73:99 +chr1 806719 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=0;HaplotypeScore=400.08;MQ=40.22;MQ0=20;OQ=582.43;QD=2.75;SB=89.75 GT:AD:DP:GL:GQ 0/1:145,66:134:-101.59,-40.07,-419.05:99 +chr1 806735 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=24.14;MQ=41.77;MQ0=24;OQ=129.16;QD=0.59;SB=143.49 GT:AD:DP:GL:GQ 0/1:169,49:138:-57.78,-41.58,-482.40:99 +chr1 806755 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=0;HaplotypeScore=72.66;MQ=42.05;MQ0=23;OQ=1702.34;QD=7.99;SB=-97.29 GT:AD:DP:GL:GQ 0/1:86,127:148:-218.09,-44.57,-348.93:99 +chr1 806758 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=0;HaplotypeScore=66.82;MQ=42.51;MQ0=24;OQ=101.05;QD=0.48;SB=140.48 GT:AD:DP:GL:GQ 0/1:180,31:147:-57.67,-44.28,-533.12:99 +chr1 806774 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=33.98;MQ=43.76;MQ0=28;OQ=1370.17;QD=7.29;SB=4.43 GT:AD:DP:GL:GQ 0/1:94,94:136:-181.26,-40.96,-326.53:99 +chr1 806807 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=247;Dels=0.00;HRun=1;HaplotypeScore=84.17;MQ=41.43;MQ0=32;OQ=1901.04;QD=7.70;SB=-364.66 GT:AD:DP:GL:GQ 0/1:93,133:161:-255.61,-62.23,-399.73:99 +chr1 806819 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=264;Dels=0.00;HRun=1;HaplotypeScore=51.78;MQ=39.46;MQ0=35;OQ=117.55;QD=0.45;SB=-52.87 GT:AD:DP:GL:GQ 0/1:235,29:167:-65.33,-50.29,-569.53:99 +chr1 806835 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=24.93;MQ=38.15;MQ0=32;OQ=3184.79;QD=11.46;SB=-1086.54 GT:AD:DP:GL:GQ 0/1:75,203:179:-375.67,-53.91,-276.38:99 +chr1 806857 . A G 426.69 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=388;Dels=0.00;HRun=0;HaplotypeScore=416.26;MQ=36.42;MQ0=33;QD=1.10;SB=-205.00 GT:AD:DP:GL:GQ 0/1:336,52:260:-124.27,-78.32,-915.07:99 +chr1 806858 . A C 2180.12 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=390;Dels=0.00;HRun=1;HaplotypeScore=419.10;MQ=36.36;MQ0=33;QD=5.59;SB=-410.18 GT:AD:DP:GL:GQ 0/1:135,134:259:-523.35,-302.06,-691.29:99 +chr1 806860 . T C 364.40 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=414;Dels=0.02;HRun=1;HaplotypeScore=391.10;MQ=36.35;MQ0=33;QD=0.88;SB=-200.49 GT:AD:DP:GL:GQ 0/1:360,44:277:-126.33,-86.61,-1004.70:99 +chr1 806864 . G A 1874.70 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=430;Dels=0.00;HRun=0;HaplotypeScore=443.75;MQ=36.02;MQ0=32;QD=4.36;SB=-378.35 GT:AD:DP:GL:GQ 0/1:340,90:284:-276.29,-85.54,-766.79:99 +chr1 806872 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=439;Dels=0.00;HRun=3;HaplotypeScore=61.91;MQ=35.95;MQ0=27;OQ=241.94;QD=0.55;SB=-56.85 GT:AD:DP:GL:GQ 0/1:394,45:294:-116.03,-88.55,-994.05:99 +chr1 806914 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=433;Dels=0.00;HRun=1;HaplotypeScore=82.84;MQ=36.13;MQ0=15;OQ=91.45;QD=0.21;SB=145.33 GT:AD:DP:GL:GQ 0/1:380,53:292:-100.38,-87.95,-1073.99:99 +chr1 806929 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=394;Dels=0.00;HRun=1;HaplotypeScore=53.78;MQ=36.16;MQ0=12;OQ=628.62;QD=1.60;SB=165.96 GT:AD:DP:GL:GQ 0/1:300,94:257:-143.55,-77.40,-778.57:99 +chr1 806933 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=384;Dels=0.00;HRun=1;HaplotypeScore=52.56;MQ=36.30;MQ0=13;OQ=624.21;QD=1.63;SB=148.11 GT:AD:DP:GL:GQ 0/1:298,86:253:-141.91,-76.20,-801.85:99 +chr1 807097 rs4970387 A T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=141;Dels=0.00;HRun=4;HaplotypeScore=35.71;MQ=49.47;MQ0=9;OQ=3569.50;QD=25.32;SB=-1647.14 GT:AD:DP:GL:GQ 1/1:0,141:95:-355.95,-28.62,-0.03:99 +chr1 807120 . C T 28.74 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=5;HaplotypeScore=8.47;MQ=47.00;MQ0=10;QD=0.19;SB=107.30 GT:AD:DP:GL:GQ 0/1:82,66:90:-33.27,-27.11,-295.41:61.57 +chr1 807127 . C G 240.31 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=32.57;MQ=46.64;MQ0=10;QD=1.61;SB=107.38 GT:AD:DP:GL:GQ 0/1:80,69:92:-55.04,-27.72,-340.23:99 +chr1 807132 . T C 652.10 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=1;HaplotypeScore=41.20;MQ=46.24;MQ0=10;QD=4.29;SB=107.38 GT:AD:DP:GL:GQ 0/1:77,75:102:-99.22,-30.73,-310.86:99 +chr1 807136 . C A 59.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=2;HaplotypeScore=75.46;MQ=45.64;MQ0=10;QD=0.36;SB=6.21 GT:AD:DP:GL:GQ 0/1:135,27:108:-41.72,-32.53,-330.47:91.87 +chr1 807137 . T G 132.15 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=74.46;MQ=45.79;MQ0=10;QD=0.83;SB=113.39 GT:AD:DP:GL:GQ 0/1:140,19:114:-50.84,-34.34,-356.98:99 +chr1 807144 . G C 321.19 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=33.44;MQ=44.89;MQ0=10;QD=1.96;SB=17.66 GT:AD:DP:GL:GQ 0/1:131,27:122:-82.39,-46.99,-445.41:99 +chr1 807168 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=236.47;MQ=42.45;MQ0=9;OQ=1209.57;QD=6.91;SB=-394.74 GT:AD:DP:GL:GQ 0/1:124,51:131:-163.71,-39.47,-414.74:99 +chr1 807169 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=262.45;MQ=42.56;MQ0=9;OQ=108.48;QD=0.61;SB=74.80 GT:AD:DP:GL:GQ 0/1:162,17:135:-54.79,-40.66,-456.43:99 +chr1 807188 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=186;Dels=0.01;HRun=8;HaplotypeScore=227.66;MQ=43.88;MQ0=1;OQ=1264.52;QD=6.80;SB=-460.79 GT:AD:DP:GL:GQ 0/1:118,67:149:-174.32,-44.58,-377.47:99 +chr1 807190 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=246.34;MQ=43.75;MQ0=1;OQ=529.31;QD=2.86;SB=137.46 GT:AD:DP:GL:GQ 0/1:148,37:145:-99.89,-43.67,-443.33:99 +chr1 807204 . A C 36.37 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=12.98;MQ=42.45;MQ0=6;QD=0.19;SB=109.90 GT:AD:DP:GL:GQ 0/1:167,21:153:-53.00,-46.08,-519.54:69.21 +chr1 807245 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=1;HaplotypeScore=17.90;MQ=38.97;MQ0=18;OQ=1145.58;QD=6.94;SB=-550.34 GT:AD:DP:GL:GQ 0/1:87,78:121:-154.28,-36.44,-312.35:99 +chr1 807259 . G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=39.36;MQ0=20;OQ=646.71;QD=4.25;SB=-192.93 GT:AD:DP:GL:GQ 0/1:96,56:108:-100.48,-32.53,-300.21:99 +chr1 807350 rs4082611 G A 0.14 PASS AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=9.97;MQ=44.42;MQ0=8;OQ=866.67;QD=5.70;SB=98.31 GT:AD:DP:GL:GQ 0/1:80,69:106:-125.51,-35.56,-282.07:99 +chr1 807353 . C A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=8.92;MQ=43.77;MQ0=8;OQ=867.33;QD=5.45;SB=95.29 GT:AD:DP:GL:GQ 0/1:76,83:108:-122.54,-32.52,-265.26:99 +chr1 807384 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=0;HaplotypeScore=61.52;MQ=40.31;MQ0=13;OQ=503.09;QD=2.47;SB=116.39 GT:AD:DP:GL:GQ 0/1:145,57:132:-93.37,-39.78,-338.75:99 +chr1 807385 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=1;HaplotypeScore=61.52;MQ=40.32;MQ0=13;OQ=1779.01;QD=8.76;SB=73.73 GT:AD:DP:GL:GQ 0/1:76,126:131:-220.64,-39.46,-278.09:99 +chr1 807400 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=1;HaplotypeScore=26.31;MQ=38.88;MQ0=12;OQ=2472.80;QD=10.18;SB=76.74 GT:AD:DP:GL:GQ 0/1:81,162:155:-297.25,-46.69,-297.33:99 +chr1 807412 rs4082610 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=262;Dels=0.00;HRun=4;HaplotypeScore=30.19;MQ=38.31;MQ0=9;OQ=2516.42;QD=9.60;SB=119.38 GT:AD:DP:GL:GQ 0/1:109,153:168:-305.53,-50.60,-311.50:99 +chr1 807432 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=262;Dels=0.00;HRun=0;HaplotypeScore=25.55;MQ=38.32;MQ0=6;OQ=4433.84;QD=16.92;SB=-160.81 GT:AD:DP:GL:GQ 0/1:80,182:176:-442.38,-53.03,-343.20:99 +chr1 807469 . C T 416.75 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=0;HaplotypeScore=92.28;MQ=41.14;MQ0=1;QD=1.98;SB=-49.34 GT:AD:DP:GL:GQ 0/1:84,126:97:-74.18,-29.22,-280.73:99 +chr1 807471 . A C 318.15 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=2;HaplotypeScore=90.45;MQ=41.29;MQ0=1;QD=1.49;SB=-31.35 GT:AD:DP:GL:GQ 0/1:85,128:99:-64.91,-29.81,-297.50:99 +chr1 807475 . C T 356.15 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=0;HaplotypeScore=174.77;MQ=40.93;MQ0=2;QD=1.67;SB=-36.29 GT:AD:DP:GL:GQ 0/1:85,128:101:-69.35,-30.45,-273.00:99 +chr1 807484 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=1;HaplotypeScore=266.19;MQ=40.31;MQ0=2;OQ=100.09;QD=0.47;SB=95.09 GT:AD:DP:GL:GQ 0/1:168,47:127:-51.55,-38.26,-450.15:99 +chr1 807508 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=1;HaplotypeScore=7.00;MQ=41.28;MQ0=4;OQ=211.72;QD=1.14;SB=90.69 GT:AD:DP:GL:GQ 0/1:142,43:119:-60.30,-35.84,-379.49:99 +chr1 807527 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=161;Dels=0.00;HRun=2;HaplotypeScore=9.95;MQ=41.68;MQ0=7;OQ=177.85;QD=1.10;SB=146.44 GT:AD:DP:GL:GQ 0/1:119,42:108:-53.60,-32.53,-346.10:99 +chr1 807556 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=1;HaplotypeScore=66.91;MQ=41.77;MQ0=6;OQ=532.40;QD=3.89;SB=-236.01 GT:AD:DP:GL:GQ 0/1:68,69:85:-82.13,-25.60,-230.23:99 +chr1 807561 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=0;HaplotypeScore=70.93;MQ=41.65;MQ0=7;OQ=124.65;QD=0.89;SB=101.32 GT:AD:DP:GL:GQ 0/1:96,44:87:-41.95,-26.20,-282.69:99 +chr1 807571 rs34106744 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=3;HaplotypeScore=33.63;MQ=41.31;MQ0=9;OQ=377.46;QD=2.80;SB=-157.65 GT:AD:DP:GL:GQ 0/1:62,73:80:-65.12,-24.09,-230.06:99 +chr1 807588 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=29.86;MQ=39.35;MQ0=12;OQ=1527.96;QD=9.32;SB=-255.65 GT:AD:DP:GL:GQ 0/1:60,104:105:-187.72,-31.65,-191.88:99 +chr1 807611 . G C 0.98 PASS AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=7.78;MQ=38.64;MQ0=13;OQ=1984.90;QD=11.81;SB=-213.08 GT:AD:DP:GL:GQ 0/1:60,108:111:-235.21,-33.44,-245.33:99 +chr1 807628 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=0;HaplotypeScore=15.09;MQ=38.17;MQ0=13;OQ=1889.96;QD=9.74;SB=-59.93 GT:AD:DP:GL:GQ 0/1:68,126:123:-229.33,-37.05,-239.27:99 +chr1 807662 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=324;Dels=0.00;HRun=0;HaplotypeScore=5.25;MQ=35.02;MQ0=24;OQ=5029.36;QD=15.52;SB=-1355.57 GT:AD:DP:GL:GQ 0/1:79,245:206:-501.94,-62.04,-299.38:99 +chr1 807698 rs61768243 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=413;Dels=0.00;HRun=1;HaplotypeScore=119.83;MQ=33.65;MQ0=41;OQ=7356.92;QD=17.81;SB=-2911.42 GT:AD:DP:GL:GQ 0/1:85,328:252:-734.69,-75.92,-368.28:99 +chr1 807726 rs61768244 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=451;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=33.55;MQ0=36;OQ=2315.76;QD=5.13;SB=-928.19 GT:AD:DP:GL:GQ 0/1:303,148:263:-314.08,-79.22,-727.35:99 +chr1 807759 rs4034377 A C 755.20 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=336;Dels=0.00;HRun=0;HaplotypeScore=236.06;MQ=33.74;MQ0=39;QD=2.25;SB=-109.97 GT:AD:DP:GL:GQ 0/1:260,76:175:-131.50,-52.70,-521.92:99 +chr1 807761 . A G 2451.79 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=328;Dels=0.00;HRun=0;HaplotypeScore=310.08;MQ=33.84;MQ0=39;QD=7.47;SB=-739.45 GT:AD:DP:GL:GQ 0/1:164,163:171:-299.96,-51.50,-359.62:99 +chr1 807766 rs3969819 A C 564.07 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=320;Dels=0.00;HRun=0;HaplotypeScore=284.38;MQ=33.76;MQ0=45;QD=1.76;SB=-303.05 GT:AD:DP:GL:GQ 0/1:266,53:164:-109.08,-49.39,-509.36:99 +chr1 807787 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=301;Dels=0.00;HRun=1;HaplotypeScore=10.94;MQ=35.09;MQ0=34;OQ=678.04;QD=2.25;SB=50.87 GT:AD:DP:GL:GQ 0/1:179,122:124:-108.43,-37.34,-358.12:99 +chr1 807799 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=330;Dels=0.00;HRun=1;HaplotypeScore=46.01;MQ=35.31;MQ0=34;OQ=1300.39;QD=3.94;SB=-358.87 GT:AD:DP:GL:GQ 0/1:191,139:161:-181.81,-48.48,-410.83:99 +chr1 807817 rs4034379 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=305;Dels=0.00;HRun=0;HaplotypeScore=40.59;MQ=36.43;MQ0=47;OQ=1097.69;QD=3.60;SB=-508.19 GT:AD:DP:GL:GQ 0/1:205,100:154:-159.44,-46.39,-521.49:99 +chr1 807831 rs4034380 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=324;Dels=0.00;HRun=0;HaplotypeScore=53.25;MQ=36.07;MQ0=54;OQ=860.18;QD=2.65;SB=-52.35 GT:AD:DP:GL:GQ 0/1:235,89:165:-139.00,-49.70,-477.57:99 +chr1 807843 rs61768247 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=340;Dels=0.00;HRun=3;HaplotypeScore=25.24;MQ=35.61;MQ0=59;OQ=2917.98;QD=8.58;SB=-1176.92 GT:AD:DP:GL:GQ 0/1:93,247:179:-348.99,-53.91,-340.62:99 +chr1 807878 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=340;Dels=0.00;HRun=3;HaplotypeScore=1.68;MQ=33.99;MQ0=59;OQ=2636.13;QD=7.75;SB=-1148.59 GT:AD:DP:GL:GQ 0/1:141,199:182:-321.71,-54.82,-379.20:99 +chr1 807900 rs61768248 A G 107.46 PASS AC=1;AF=0.50;AN=2;DB;DP=254;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=36.51;MQ0=52;OQ=2423.92;QD=9.54;SB=-510.71 GT:AD:DP:GL:GQ 0/1:72,182:155:-292.36,-46.69,-288.83:99 +chr1 807921 rs4034381 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=238;Dels=0.00;HRun=0;HaplotypeScore=52.91;MQ=37.12;MQ0=38;OQ=730.38;QD=3.07;SB=87.15 GT:AD:DP:GL:GQ 0/1:169,69:152:-122.12,-45.80,-464.61:99 +chr1 807923 rs2311679 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=238;Dels=0.00;HRun=1;HaplotypeScore=53.91;MQ=36.90;MQ0=37;OQ=150.90;QD=0.63;SB=114.49 GT:AD:DP:GL:GQ 0/1:205,33:149:-63.25,-44.87,-483.89:99 +chr1 807940 rs61768249 C T 132.32 PASS AC=1;AF=0.50;AN=2;DB;DP=201;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=39.52;MQ0=18;OQ=2365.28;QD=11.77;SB=-227.57 GT:AD:DP:GL:GQ 0/1:70,131:135:-280.47,-40.66,-242.20:99 +chr1 807969 . G T 0.34 PASS AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=3.99;MQ=40.13;MQ0=16;OQ=852.49;QD=4.24;SB=25.59 GT:AD:DP:GL:GQ 0/1:139,62:138:-130.10,-41.57,-369.51:99 +chr1 807986 . G A 410.65 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=0;HaplotypeScore=37.75;MQ=40.61;MQ0=11;QD=2.15;SB=32.93 GT:AD:DP:GL:GQ 0/1:73,117:91:-71.78,-27.44,-235.41:99 +chr1 807989 . A G 41.79 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=1;HaplotypeScore=63.74;MQ=41.32;MQ0=11;QD=0.24;SB=71.44 GT:AD:DP:GL:GQ 0/1:71,104:80:-31.56,-24.09,-295.20:74.62 +chr1 807990 . G T 63.48 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=1;HaplotypeScore=63.74;MQ=41.32;MQ0=11;QD=0.36;SB=71.41 GT:AD:DP:GL:GQ 0/1:71,104:79:-33.42,-23.79,-250.10:96.32 +chr1 808001 rs2311681 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.00;HRun=1;HaplotypeScore=145.95;MQ=39.96;MQ0=12;OQ=189.55;QD=1.02;SB=-28.87 GT:AD:DP:GL:GQ 0/1:68,100:81:-53.53,-31.29,-271.83:99 +chr1 808002 . C T 30.08 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=1;HaplotypeScore=147.95;MQ=39.81;MQ0=12;QD=0.16;SB=5.97 GT:AD:DP:GL:GQ 0/1:124,64:83:-31.29,-25.00,-266.30:62.91 +chr1 808027 rs3969820 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=178;Dels=0.00;HRun=0;HaplotypeScore=57.38;MQ=38.17;MQ0=19;OQ=723.18;QD=4.06;SB=-165.45 GT:AD:DP:GL:GQ 0/1:134,44:108:-108.14,-32.53,-287.08:99 +chr1 808030 . A G 1086.71 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=0;HaplotypeScore=42.92;MQ=38.47;MQ0=18;QD=6.51;SB=-568.31 GT:AD:DP:GL:GQ 0/1:57,109:99:-141.80,-29.84,-220.97:99 +chr1 808043 . A G 970.86 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=1;HaplotypeScore=39.52;MQ=39.24;MQ0=20;QD=6.11;SB=-490.82 GT:AD:DP:GL:GQ 0/1:58,101:92:-128.08,-27.71,-229.15:99 +chr1 808058 rs4068670 A G 19.55 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=148;Dels=0.00;HRun=0;HaplotypeScore=41.67;MQ=39.19;MQ0=26;QD=0.13;SB=-33.62 GT:AD:DP:GL:GQ 0/1:54,74:61:-37.68,-32.44,-211.21:52.34 +chr1 808064 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=1;HaplotypeScore=40.55;MQ=38.61;MQ0=24;OQ=246.33;QD=1.85;SB=-81.77 GT:AD:DP:GL:GQ 0/1:48,85:54:-44.19,-16.27,-162.59:99 +chr1 808071 . C T 20.12 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=40.24;MQ=40.16;MQ0=22;QD=0.15;SB=14.54 GT:AD:DP:GL:GQ 0/1:54,82:58:-22.76,-17.47,-182.75:52.91 +chr1 808112 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=227;Dels=0.00;HRun=2;HaplotypeScore=125.36;MQ=37.91;MQ0=32;OQ=1776.62;QD=7.83;SB=-160.46 GT:AD:DP:GL:GQ 0/1:73,153:125:-218.60,-37.66,-274.51:99 +chr1 808131 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=257;Dels=0.00;HRun=1;HaplotypeScore=46.49;MQ=37.72;MQ0=22;OQ=2127.72;QD=8.28;SB=-282.13 GT:AD:DP:GL:GQ 0/1:106,150:146:-260.04,-43.99,-307.83:99 +chr1 808143 rs2871830 A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=266;Dels=0.00;HRun=0;HaplotypeScore=22.61;MQ=37.96;MQ0=21;OQ=255.61;QD=0.96;SB=23.44 GT:AD:DP:GL:GQ 0/1:214,51:151:-74.35,-45.50,-504.23:99 +chr1 808170 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=251;Dels=0.00;HRun=1;HaplotypeScore=39.92;MQ=39.75;MQ0=13;OQ=386.02;QD=1.54;SB=116.39 GT:AD:DP:GL:GQ 0/1:201,50:155:-88.58,-46.69,-468.07:99 +chr1 808187 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=220;Dels=0.00;HRun=7;HaplotypeScore=162.06;MQ=41.27;MQ0=11;OQ=363.00;QD=1.65;SB=17.72 GT:AD:DP:GL:GQ 0/1:176,44:136:-80.56,-40.98,-399.39:99 +chr1 808189 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=0;HaplotypeScore=288.29;MQ=41.39;MQ0=11;OQ=708.25;QD=3.28;SB=-149.01 GT:AD:DP:GL:GQ 0/1:142,53:138:-146.61,-72.50,-410.59:99 +chr1 808297 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=0;HaplotypeScore=21.45;MQ=38.78;MQ0=17;OQ=1228.84;QD=6.27;SB=-563.99 GT:AD:DP:GL:GQ 0/1:75,120:104:-157.52,-31.35,-213.62:99 +chr1 808336 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=1;HaplotypeScore=34.12;MQ=34.50;MQ0=28;OQ=414.84;QD=1.47;SB=-185.55 GT:AD:DP:GL:GQ 0/1:228,54:155:-91.47,-46.70,-585.75:99 +chr1 808347 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=78.29;MQ=34.29;MQ0=30;OQ=600.10;QD=2.16;SB=-67.28 GT:AD:DP:GL:GQ 0/1:221,39:151:-138.41,-75.12,-545.71:99 +chr1 808349 rs61768250 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=274;Dels=0.00;HRun=0;HaplotypeScore=172.09;MQ=34.47;MQ0=30;OQ=2858.46;QD=10.43;SB=-822.44 GT:AD:DP:GL:GQ 0/1:82,190:149:-334.02,-44.89,-232.77:99 +chr1 808359 . C T 950.38 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=269;Dels=0.00;HRun=0;HaplotypeScore=192.43;MQ=34.52;MQ0=31;QD=3.53;SB=-243.11 GT:AD:DP:GL:GQ 0/1:178,83:148:-142.90,-44.58,-399.15:99 +chr1 808362 . G A 76.04 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=113.80;MQ=34.64;MQ0=30;QD=0.28;SB=96.15 GT:AD:DP:GL:GQ 0/1:234,29:151:-56.37,-45.49,-495.71:99 +chr1 808363 . C A 14.91 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=113.80;MQ=34.60;MQ0=34;QD=0.05;SB=125.29 GT:AD:DP:GL:GQ 0/1:250,29:157:-52.05,-47.29,-518.11:47.61 +chr1 808367 . G A 731.54 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=120.25;MQ=34.34;MQ0=33;QD=2.52;SB=-82.29 GT:AD:DP:GL:GQ 0/1:229,61:165:-126.14,-49.70,-491.32:99 +chr1 808394 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=235;Dels=0.00;HRun=0;HaplotypeScore=10.16;MQ=37.74;MQ0=26;OQ=126.55;QD=0.54;SB=56.98 GT:AD:DP:GL:GQ 0/1:188,47:147:-60.25,-44.31,-434.17:99 +chr1 808413 . T G 317.98 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=2;HaplotypeScore=72.86;MQ=40.13;MQ0=20;QD=1.94;SB=-24.43 GT:AD:DP:GL:GQ 0/1:121,43:105:-66.71,-31.62,-317.98:99 +chr1 808417 . G A 68.93 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=67.03;MQ=42.13;MQ0=16;QD=0.46;SB=83.26 GT:AD:DP:GL:GQ 0/1:135,13:103:-41.21,-31.03,-340.99:99 +chr1 808421 . G A 1042.35 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=46.56;MQ=44.72;MQ0=15;QD=7.72;SB=-112.51 GT:AD:DP:GL:GQ 0/1:67,68:99:-137.34,-29.83,-234.94:99 +chr1 808447 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=2;HaplotypeScore=11.26;MQ=49.75;MQ0=9;OQ=392.50;QD=3.54;SB=-21.38 GT:AD:DP:GL:GQ 0/1:71,40:86:-68.46,-25.93,-223.10:99 +chr1 808451 . A T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=1;HaplotypeScore=9.78;MQ=50.21;MQ0=9;OQ=368.72;QD=3.29;SB=-63.61 GT:AD:DP:GL:GQ 0/1:73,39:88:-66.66,-26.51,-263.45:99 +chr1 808566 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=42.07;MQ=40.72;MQ0=9;OQ=262.25;QD=1.45;SB=83.19 GT:AD:DP:GL:GQ 0/1:73,108:86:-55.43,-25.93,-233.09:99 +chr1 808594 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=0;HaplotypeScore=18.85;MQ=37.64;MQ0=16;OQ=690.50;QD=2.77;SB=110.37 GT:AD:DP:GL:GQ 0/1:80,169:110:-105.47,-33.14,-280.23:99 +chr1 808641 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=283;Dels=0.00;HRun=1;HaplotypeScore=21.83;MQ=33.64;MQ0=19;OQ=2063.93;QD=7.29;SB=28.04 GT:AD:DP:GL:GQ 0/1:72,211:133:-249.73,-40.06,-265.59:99 +chr1 808664 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=245;Dels=0.00;HRun=1;HaplotypeScore=236.43;MQ=34.77;MQ0=16;OQ=159.51;QD=0.65;SB=12.22 GT:AD:DP:GL:GQ 0/1:197,22:147:-105.83,-86.60,-492.17:99 +chr1 808677 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=233;Dels=0.00;HRun=0;HaplotypeScore=83.64;MQ=35.28;MQ0=11;OQ=206.00;QD=0.88;SB=113.55 GT:AD:DP:GL:GQ 0/1:190,43:144:-67.26,-43.38,-499.53:99 +chr1 808728 . C A 203.60 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=1;HaplotypeScore=31.96;MQ=45.04;MQ0=12;QD=1.82;SB=15.39 GT:AD:DP:GL:GQ 0/1:87,25:80:-47.74,-24.10,-238.32:99 +chr1 808731 . C T 444.24 SnpCluster AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=24.97;MQ=46.65;MQ0=11;QD=4.04;SB=-165.40 GT:AD:DP:GL:GQ 0/1:69,41:86:-73.64,-25.93,-224.50:99 +chr1 808732 . G A 408.16 SnpCluster AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=24.97;MQ=46.65;MQ0=11;QD=3.71;SB=-130.98 GT:AD:DP:GL:GQ 0/1:69,41:85:-69.72,-25.62,-220.30:99 +chr1 808802 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=47.94;MQ=46.85;MQ0=10;OQ=50.85;QD=0.45;SB=55.37 GT:AD:DP:GL:GQ 0/1:67,39:74:-30.66,-22.29,-262.89:83.69 +chr1 808813 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=9.12;MQ=42.90;MQ0=8;OQ=68.22;QD=0.48;SB=65.92 GT:AD:DP:GL:GQ 0/1:121,22:85:-35.73,-25.62,-328.85:99 +chr1 808837 . A G 640.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=0;HaplotypeScore=190.29;MQ=37.94;MQ0=4;QD=3.42;SB=66.67 GT:AD:DP:GL:GQ 0/1:64,123:88:-93.80,-26.51,-252.52:99 +chr1 808839 . G A 725.93 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=188;Dels=0.01;HRun=3;HaplotypeScore=118.63;MQ=37.90;MQ0=4;QD=3.86;SB=63.76 GT:AD:DP:GL:GQ 0/1:65,112:89:-102.68,-26.81,-229.73:99 +chr1 808842 . A G 234.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=1;HaplotypeScore=215.12;MQ=37.45;MQ0=5;QD=1.20;SB=62.67 GT:AD:DP:GL:GQ 0/1:152,43:87:-52.93,-26.20,-300.50:99 +chr1 808844 . C A 211.39 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=1;HaplotypeScore=139.43;MQ=37.30;MQ0=5;QD=1.09;SB=62.33 GT:AD:DP:GL:GQ 0/1:151,43:87:-50.63,-26.20,-257.94:99 +chr1 808878 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=228;Dels=0.00;HRun=0;HaplotypeScore=11.87;MQ=35.54;MQ0=6;OQ=484.59;QD=2.13;SB=67.42 GT:AD:DP:GL:GQ 0/1:69,159:88:-78.25,-26.50,-268.80:99 +chr1 808900 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=211;Dels=0.00;HRun=0;HaplotypeScore=53.01;MQ=34.26;MQ0=7;OQ=319.52;QD=1.51;SB=101.36 GT:AD:DP:GL:GQ 0/1:68,143:78:-58.73,-23.49,-234.89:99 +chr1 808952 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=30.36;MQ0=16;OQ=684.75;QD=4.08;SB=-303.13 GT:AD:DP:GL:GQ 0/1:69,99:91:-99.17,-27.41,-260.34:99 +chr1 808969 rs57185426 C T 0.56 PASS AC=1;AF=0.50;AN=2;DB;DP=167;Dels=0.00;HRun=0;HaplotypeScore=6.98;MQ=27.19;MQ0=22;OQ=1308.35;QD=7.83;SB=-543.36 GT:AD:DP:GL:GQ 0/1:64,103:97:-163.35,-29.23,-183.79:99 +chr1 809028 rs61768251 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=24.74;MQ=37.22;MQ0=19;OQ=1197.89;QD=7.88;SB=-487.91 GT:AD:DP:GL:GQ 0/1:69,83:107:-155.31,-32.23,-252.53:99 +chr1 809058 . T C 0.11 PASS AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=4.46;MQ=47.89;MQ0=8;OQ=300.60;QD=2.95;SB=-111.38 GT:AD:DP:GL:GQ 0/1:71,31:84:-58.65,-25.31,-262.00:99 +chr1 809087 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=12.78;MQ=44.45;MQ0=38;OQ=174.63;QD=1.20;SB=29.35 GT:AD:DP:GL:GQ 0/1:79,66:90:-47.85,-27.11,-283.45:99 +chr1 809147 . A G 708.22 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=385;Dels=0.00;HRun=0;HaplotypeScore=142.43;MQ=32.08;MQ0=67;QD=1.84;SB=-338.08 GT:AD:DP:GL:GQ 0/1:273,112:167:-124.42,-50.31,-531.00:99 +chr1 809152 . A G 2828.87 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=380;Dels=0.00;HRun=0;HaplotypeScore=142.28;MQ=32.36;MQ0=64;QD=7.44;SB=-821.16 GT:AD:DP:GL:GQ 0/1:76,304:165:-335.87,-49.70,-295.78:99 +chr1 809155 . G A 906.28 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=379;Dels=0.00;HRun=1;HaplotypeScore=107.83;MQ=32.25;MQ0=64;QD=2.39;SB=-437.76 GT:AD:DP:GL:GQ 0/1:271,108:165:-143.61,-49.69,-484.11:99 +chr1 809196 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=2;HaplotypeScore=63.80;MQ=34.67;MQ0=22;OQ=1194.90;QD=4.80;SB=-269.68 GT:AD:DP:GL:GQ 0/1:67,182:101:-153.20,-30.42,-236.52:99 +chr1 809260 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=41.08;MQ0=8;OQ=376.66;QD=3.30;SB=116.36 GT:AD:DP:GL:GQ 0/1:80,34:93:-68.96,-28.01,-266.36:99 +chr1 809273 . T C 463.34 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=8.66;MQ=40.73;MQ0=7;QD=3.83;SB=119.42 GT:AD:DP:GL:GQ 0/1:85,36:100:-79.74,-30.12,-319.61:99 +chr1 809278 . T A 448.40 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=0;HaplotypeScore=9.66;MQ=40.70;MQ0=10;QD=3.59;SB=128.40 GT:AD:DP:GL:GQ 0/1:95,30:101:-78.54,-30.42,-301.76:99 +chr1 809279 . C A 472.08 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=9.66;MQ=40.57;MQ0=10;QD=3.72;SB=128.43 GT:AD:DP:GL:GQ 0/1:97,30:103:-81.51,-31.02,-300.46:99 +chr1 809374 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=40.85;MQ=49.25;MQ0=14;OQ=274.74;QD=2.18;SB=128.46 GT:AD:DP:GL:GQ 0/1:85,41:95:-59.38,-28.62,-356.10:99 +chr1 809396 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=153;Dels=0.03;HRun=0;HaplotypeScore=81.33;MQ=46.63;MQ0=11;OQ=370.18;QD=2.42;SB=128.42 GT:AD:DP:GL:GQ 0/1:90,59:107:-71.93,-31.63,-311.43:99 +chr1 809418 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=0;HaplotypeScore=18.59;MQ=42.45;MQ0=17;OQ=1574.87;QD=7.57;SB=-383.90 GT:AD:DP:GL:GQ 0/1:84,123:141:-203.25,-42.48,-331.17:99 +chr1 809463 . T C 270.15 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=113.69;MQ=41.23;MQ0=17;QD=1.24;SB=22.33 GT:AD:DP:GL:GQ 0/1:180,37:141:-72.78,-42.48,-486.18:99 +chr1 809466 . G A 91.66 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=2;HaplotypeScore=122.84;MQ=41.24;MQ0=16;QD=0.43;SB=110.32 GT:AD:DP:GL:GQ 0/1:181,32:144:-55.83,-43.38,-458.71:99 +chr1 809470 . T C 630.75 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=2;HaplotypeScore=238.78;MQ=41.40;MQ0=14;QD=3.03;SB=-114.41 GT:AD:DP:GL:GQ 0/1:153,55:135:-107.03,-40.67,-427.65:99 +chr1 809480 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=103.82;MQ=41.73;MQ0=11;OQ=1974.03;QD=10.79;SB=-338.07 GT:AD:DP:GL:GQ 0/1:66,116:122:-237.45,-36.76,-206.62:99 +chr1 809721 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=3;HaplotypeScore=9.02;MQ=53.95;MQ0=4;OQ=80.85;QD=0.86;SB=59.35 GT:AD:DP:GL:GQ 0/1:75,18:84:-36.67,-25.30,-283.82:99 +chr1 809780 rs6605057 A G 0.76 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=11.81;MQ=56.13;MQ0=2;OQ=3054.85;QD=32.85;SB=-1362.55 GT:AD:DP:GL:GQ 1/1:0,93:85:-309.09,-25.60,-0.02:99 +chr1 809879 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=0;HaplotypeScore=59.97;MQ=40.35;MQ0=14;OQ=622.51;QD=3.19;SB=42.71 GT:AD:DP:GL:GQ 0/1:76,119:98:-95.05,-29.52,-272.29:99 +chr1 809895 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=1;HaplotypeScore=66.59;MQ=38.60;MQ0=19;OQ=465.46;QD=2.28;SB=92.30 GT:AD:DP:GL:GQ 0/1:110,94:92:-77.54,-27.71,-254.54:99 +chr1 809906 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=107.86;MQ=38.19;MQ0=19;OQ=204.28;QD=1.02;SB=98.35 GT:AD:DP:GL:GQ 0/1:163,38:93:-51.72,-28.01,-294.59:99 +chr1 810152 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=23.45;MQ=46.60;MQ0=18;OQ=256.17;QD=1.80;SB=89.22 GT:AD:DP:GL:GQ 0/1:80,62:93:-56.93,-28.03,-260.32:99 +chr1 810179 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=166;Dels=0.00;HRun=0;HaplotypeScore=40.97;MQ=43.29;MQ0=18;OQ=423.48;QD=2.55;SB=-10.82 GT:AD:DP:GL:GQ 0/1:90,76:99:-75.44,-29.81,-289.52:99 +chr1 810200 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=157;Dels=0.00;HRun=0;HaplotypeScore=91.89;MQ=44.44;MQ0=8;OQ=93.53;QD=0.60;SB=79.37 GT:AD:DP:GL:GQ 0/1:113,44:97:-41.85,-29.21,-309.84:99 +chr1 810211 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=3;HaplotypeScore=28.81;MQ=44.83;MQ0=8;OQ=438.48;QD=2.67;SB=-23.86 GT:AD:DP:GL:GQ 0/1:92,72:104:-78.46,-31.33,-303.09:99 +chr1 810249 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=0;HaplotypeScore=54.95;MQ=45.56;MQ0=5;OQ=532.92;QD=3.29;SB=-263.19 GT:AD:DP:GL:GQ 0/1:92,70:108:-89.11,-32.53,-336.39:99 +chr1 810266 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=0;HaplotypeScore=6.95;MQ=49.31;MQ0=7;OQ=320.58;QD=2.31;SB=3.34 GT:AD:DP:GL:GQ 0/1:87,51:105:-66.97,-31.63,-352.01:99 +chr1 810282 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=2;HaplotypeScore=2.11;MQ=50.38;MQ0=7;OQ=214.82;QD=1.51;SB=75.99 GT:AD:DP:GL:GQ 0/1:98,44:111:-58.20,-33.43,-338.53:99 +chr1 810326 . T C 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.92;MQ0=10;OQ=89.69;QD=0.81;SB=59.40 GT:AD:DP:GL:GQ 0/1:87,24:95:-40.87,-28.62,-338.92:99 +chr1 810564 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=14.88;MQ=44.23;MQ0=6;OQ=498.14;QD=2.90;SB=-150.99 GT:AD:DP:GL:GQ 0/1:102,70:118:-88.65,-35.55,-364.99:99 +chr1 810629 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=38.71;MQ=50.61;MQ0=2;OQ=253.97;QD=2.29;SB=-143.03 GT:AD:DP:GL:GQ 0/1:83,27:94:-56.99,-28.31,-290.69:99 +chr1 810683 . T C 21.46 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=45.49;MQ0=13;QD=0.17;SB=104.38 GT:AD:DP:GL:GQ 0/1:80,50:88:-31.93,-26.50,-325.33:54.27 +chr1 810696 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=0;HaplotypeScore=34.97;MQ=44.00;MQ0=14;OQ=294.30;QD=1.91;SB=110.32 GT:AD:DP:GL:GQ 0/1:85,69:98:-62.23,-29.52,-298.08:99 +chr1 810711 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=44.23;MQ=40.46;MQ0=17;OQ=839.07;QD=4.51;SB=107.39 GT:AD:DP:GL:GQ 0/1:81,105:106:-119.13,-31.94,-347.53:99 +chr1 810733 . C A 43.01 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=1;HaplotypeScore=56.61;MQ=40.22;MQ0=16;QD=0.19;SB=125.38 GT:AD:DP:GL:GQ 0/1:192,33:131:-47.04,-39.45,-426.81:75.84 +chr1 810794 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=3;HaplotypeScore=52.64;MQ=44.21;MQ0=2;OQ=1066.68;QD=5.73;SB=31.06 GT:AD:DP:GL:GQ 0/1:92,94:128:-148.50,-38.55,-332.75:99 +chr1 810798 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=60.51;MQ=44.84;MQ0=1;OQ=1224.15;QD=6.69;SB=34.50 GT:AD:DP:GL:GQ 0/1:93,90:127:-163.96,-38.27,-393.95:99 +chr1 810830 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=3;HaplotypeScore=77.56;MQ=44.23;MQ0=2;OQ=74.26;QD=0.42;SB=98.47 GT:AD:DP:GL:GQ 0/1:145,25:125:-59.06,-48.35,-399.04:99 +chr1 810842 . C G 7.71 PASS AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=44.02;MQ0=3;OQ=1687.26;QD=9.37;SB=-373.48 GT:AD:DP:GL:GQ 0/1:84,96:131:-211.48,-39.47,-372.20:99 +chr1 810901 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=76.75;MQ=45.85;MQ0=4;OQ=1193.00;QD=8.40;SB=-508.15 GT:AD:DP:GL:GQ 0/1:72,70:110:-155.72,-33.14,-263.20:99 +chr1 810906 . T C 38.41 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=84.75;MQ=46.22;MQ0=3;QD=0.29;SB=-42.29 GT:AD:DP:GL:GQ 0/1:104,29:99:-36.95,-29.82,-359.79:71.24 +chr1 810914 rs2871831 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=29.97;MQ=47.06;MQ0=6;OQ=781.68;QD=6.20;SB=-314.19 GT:AD:DP:GL:GQ 0/1:70,55:96:-110.36,-28.91,-259.38:99 +chr1 810923 . A T 0.10 PASS AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=1;HaplotypeScore=7.81;MQ=46.94;MQ0=8;OQ=838.41;QD=6.60;SB=-348.34 GT:AD:DP:GL:GQ 0/1:70,57:101:-117.55,-30.42,-266.19:99 +chr1 810974 rs61768253 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.00;HRun=0;HaplotypeScore=90.96;MQ=39.12;MQ0=31;OQ=376.97;QD=2.37;SB=-131.06 GT:AD:DP:GL:GQ 0/1:90,68:97:-70.20,-29.22,-313.33:99 +chr1 810984 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=2;HaplotypeScore=97.32;MQ=34.90;MQ0=35;OQ=108.00;QD=0.52;SB=94.23 GT:AD:DP:GL:GQ 0/1:166,41:109:-46.91,-32.83,-360.50:99 +chr1 810998 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=0;HaplotypeScore=73.35;MQ=33.36;MQ0=43;OQ=73.40;QD=0.31;SB=-50.06 GT:AD:DP:GL:GQ 0/1:185,54:123:-47.67,-37.04,-404.38:99 +chr1 811006 rs61768254 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=248;Dels=0.00;HRun=1;HaplotypeScore=66.91;MQ=33.49;MQ0=48;OQ=832.91;QD=3.36;SB=-277.39 GT:AD:DP:GL:GQ 0/1:106,142:128:-125.13,-38.56,-331.35:99 +chr1 811069 rs35186927 T A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=481;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=31.63;MQ0=35;OQ=1139.00;QD=2.37;SB=-237.78 GT:AD:DP:GL:GQ 0/1:346,135:257:-194.59,-77.40,-784.30:99 +chr1 811112 rs2311684 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=350;Dels=0.00;HRun=0;HaplotypeScore=77.41;MQ=35.82;MQ0=8;OQ=2362.85;QD=6.75;SB=-654.92 GT:AD:DP:GL:GQ 0/1:216,134:219:-305.59,-66.02,-466.00:99 +chr1 811131 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=248;Dels=0.00;HRun=0;HaplotypeScore=87.33;MQ=41.16;MQ0=2;OQ=4074.75;QD=16.43;SB=-1430.41 GT:AD:DP:GL:GQ 0/1:100,147:200:-406.47,-62.90,-355.42:99 +chr1 811184 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=2;HaplotypeScore=27.77;MQ=43.71;MQ0=0;OQ=460.52;QD=3.74;SB=149.45 GT:AD:DP:GL:GQ 0/1:91,32:108:-81.87,-32.53,-317.70:99 +chr1 811205 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=2;HaplotypeScore=18.01;MQ=44.82;MQ0=0;OQ=329.41;QD=2.86;SB=146.50 GT:AD:DP:GL:GQ 0/1:87,28:104:-67.56,-31.33,-345.48:99 +chr1 811285 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=37.25;MQ=40.88;MQ0=3;OQ=828.79;QD=5.53;SB=-15.76 GT:AD:DP:GL:GQ 0/1:66,84:93:-114.20,-28.04,-207.99:99 +chr1 811292 . G C 33.11 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=58.15;MQ=39.23;MQ0=3;QD=0.21;SB=95.35 GT:AD:DP:GL:GQ 0/1:79,14:72:-31.92,-25.33,-286.41:65.95 +chr1 811309 . A C 218.07 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=0;HaplotypeScore=95.42;MQ=36.77;MQ0=3;QD=1.21;SB=75.78 GT:AD:DP:GL:GQ 0/1:95,84:77:-48.28,-23.19,-225.41:99 +chr1 811313 . C A 77.35 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=190;Dels=0.00;HRun=1;HaplotypeScore=126.41;MQ=36.87;MQ0=1;QD=0.41;SB=64.94 GT:AD:DP:GL:GQ 0/1:128,61:85:-36.63,-25.61,-260.99:99 +chr1 811315 . G A 900.17 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=189;Dels=0.00;HRun=1;HaplotypeScore=96.44;MQ=36.96;MQ0=1;QD=4.76;SB=64.69 GT:AD:DP:GL:GQ 0/1:57,131:88:-122.19,-28.89,-207.10:99 +chr1 811336 . T C 533.21 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=37.36;MQ0=1;QD=2.63;SB=59.62 GT:AD:DP:GL:GQ 0/1:62,140:81:-81.01,-24.41,-227.12:99 +chr1 811339 . T C 458.52 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=200;Dels=0.00;HRun=1;HaplotypeScore=44.80;MQ=38.07;MQ0=1;QD=2.29;SB=92.33 GT:AD:DP:GL:GQ 0/1:65,135:85:-74.74,-25.60,-261.77:99 +chr1 811347 . T G 278.98 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=226;Dels=0.00;HRun=3;HaplotypeScore=134.53;MQ=37.01;MQ0=0;QD=1.23;SB=83.27 GT:AD:DP:GL:GQ 0/1:65,161:80:-55.28,-24.10,-233.47:99 +chr1 811354 . C T 677.91 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=233;Dels=0.00;HRun=0;HaplotypeScore=163.01;MQ=36.31;MQ0=0;QD=2.91;SB=83.23 GT:AD:DP:GL:GQ 0/1:63,170:82:-95.80,-24.72,-187.92:99 +chr1 811362 . C T 454.65 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=226.76;MQ=36.80;MQ0=0;QD=1.97;SB=83.14 GT:AD:DP:GL:GQ 0/1:64,167:80:-72.88,-24.13,-190.51:99 +chr1 811364 . T C 196.31 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=1;HaplotypeScore=66.22;MQ=36.51;MQ0=0;QD=0.85;SB=79.92 GT:AD:DP:GL:GQ 0/1:84,145:75:-47.99,-25.07,-244.42:99 +chr1 811375 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=93.49;MQ=37.41;MQ0=0;OQ=1696.08;QD=7.34;SB=71.11 GT:AD:DP:GL:GQ 0/1:93,137:119:-208.77,-35.88,-209.62:99 +chr1 811378 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=1;HaplotypeScore=193.97;MQ=37.86;MQ0=0;OQ=1149.75;QD=4.81;SB=77.23 GT:AD:DP:GL:GQ 0/1:188,51:123:-155.31,-37.05,-314.47:99 +chr1 811386 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=227;Dels=0.00;HRun=2;HaplotypeScore=163.58;MQ=38.25;MQ0=0;OQ=516.99;QD=2.28;SB=29.28 GT:AD:DP:GL:GQ 0/1:149,78:121:-91.43,-36.45,-384.88:99 +chr1 811400 . C T 562.85 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=209;Dels=0.00;HRun=0;HaplotypeScore=151.19;MQ=39.64;MQ0=0;QD=2.69;SB=23.60 GT:AD:DP:GL:GQ 0/1:96,113:102:-90.30,-30.73,-291.44:99 +chr1 811402 . C T 93.97 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=1;HaplotypeScore=101.45;MQ=39.46;MQ0=1;QD=0.46;SB=62.16 GT:AD:DP:GL:GQ 0/1:188,18:99:-42.50,-29.82,-326.30:99 +chr1 811408 . G T 250.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=192;Dels=0.00;HRun=0;HaplotypeScore=79.23;MQ=40.75;MQ0=2;QD=1.30;SB=59.20 GT:AD:DP:GL:GQ 0/1:111,80:98:-57.85,-29.52,-298.59:99 +chr1 811413 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=67.52;MQ=40.58;MQ0=2;OQ=77.44;QD=0.41;SB=62.19 GT:AD:DP:GL:GQ 0/1:97,91:86:-36.94,-25.92,-277.54:99 +chr1 811430 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=4;HaplotypeScore=58.87;MQ=40.65;MQ0=2;OQ=63.77;QD=0.39;SB=65.24 GT:AD:DP:GL:GQ 0/1:88,76:92:-37.38,-27.72,-324.79:96.61 +chr1 811435 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=19.26;MQ=40.95;MQ0=1;OQ=266.78;QD=1.72;SB=71.27 GT:AD:DP:GL:GQ 0/1:84,71:100:-60.08,-30.12,-340.43:99 +chr1 811443 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=2;HaplotypeScore=30.32;MQ=41.18;MQ0=1;OQ=189.19;QD=1.39;SB=77.28 GT:AD:DP:GL:GQ 0/1:79,56:91:-52.39,-30.19,-304.45:99 +chr1 811635 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=82.21;MQ=40.79;MQ0=16;OQ=141.45;QD=0.98;SB=-89.35 GT:AD:DP:GL:GQ 0/1:111,34:74:-39.73,-22.30,-281.80:99 +chr1 811650 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=95.82;MQ=42.47;MQ0=12;OQ=224.58;QD=1.65;SB=-61.36 GT:AD:DP:GL:GQ 0/1:66,70:76:-48.64,-22.89,-228.84:99 +chr1 811656 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=71.17;MQ=43.15;MQ0=11;OQ=112.09;QD=0.87;SB=-75.98 GT:AD:DP:GL:GQ 0/1:102,27:76:-37.39,-22.90,-238.94:99 +chr1 811750 rs6677354 A G 0.61 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=4.05;MQ=50.03;MQ0=0;OQ=1811.37;QD=31.78;SB=-810.16 GT:AD:DP:GL:GQ 1/1:0,56:52:-184.74,-15.66,-0.02:99 +chr1 811789 rs35660652 C G 23.26 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=4.89;MQ=49.27;MQ0=1;OQ=933.21;QD=16.97;SB=-483.19 GT:AD:DP:GL:GQ 0/1:25,30:48:-111.08,-14.47,-94.44:99 +chr1 811811 rs6671445 T C 60.28 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=51.17;MQ0=1;OQ=1096.50;QD=26.11;SB=-519.10 GT:AD:DP:GL:GQ 1/1:0,42:35:-113.27,-10.56,-0.03:99 +chr1 811899 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=32.15;MQ=43.49;MQ0=20;OQ=124.06;QD=1.01;SB=92.32 GT:AD:DP:GL:GQ 0/1:62,60:72:-37.38,-21.69,-248.07:99 +chr1 812359 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=23.61;MQ=48.84;MQ0=1;OQ=66.32;QD=0.77;SB=71.21 GT:AD:DP:GL:GQ 0/1:52,34:57:-27.09,-17.17,-171.46:99 +chr1 812367 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=15.11;MQ=47.39;MQ0=1;OQ=182.54;QD=1.77;SB=-16.56 GT:AD:DP:GL:GQ 0/1:55,46:66:-41.42,-19.89,-213.25:99 +chr1 812395 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=147;Dels=0.00;HRun=0;HaplotypeScore=16.89;MQ=44.59;MQ0=4;OQ=290.02;QD=1.97;SB=-35.46 GT:AD:DP:GL:GQ 0/1:75,71:87:-58.50,-26.21,-278.39:99 +chr1 812396 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=12.57;MQ=44.24;MQ0=4;OQ=510.01;QD=3.40;SB=-121.97 GT:AD:DP:GL:GQ 0/1:77,73:89:-81.09,-26.81,-250.00:99 +chr1 812452 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=237;Dels=0.00;HRun=1;HaplotypeScore=44.19;MQ=38.30;MQ0=6;OQ=174.18;QD=0.73;SB=140.46 GT:AD:DP:GL:GQ 0/1:178,59:128:-59.25,-38.55,-429.97:99 +chr1 812470 . G A 3027.24 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=2;HaplotypeScore=95.67;MQ=37.00;MQ0=5;QD=11.38;SB=-136.01 GT:AD:DP:GL:GQ 0/1:72,177:161:-375.45,-69.45,-279.59:99 +chr1 812474 . A G 225.39 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=98.08;MQ=36.45;MQ0=4;QD=0.80;SB=107.36 GT:AD:DP:GL:GQ 0/1:225,57:173:-77.95,-52.13,-605.26:99 +chr1 812476 . G A 4194.86 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=1;HaplotypeScore=148.97;MQ=36.56;MQ0=4;QD=14.98;SB=-125.96 GT:AD:DP:GL:GQ 0/1:71,208:172:-418.49,-51.81,-254.37:99 +chr1 812496 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=383;Dels=0.00;HRun=3;HaplotypeScore=110.05;MQ=34.24;MQ0=3;OQ=4072.28;QD=10.63;SB=-60.38 GT:AD:DP:GL:GQ 0/1:191,192:229:-406.23,-68.97,-420.64:99 +chr1 812509 . A G 1306.01 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=390;Dels=0.00;HRun=0;HaplotypeScore=338.39;MQ=34.90;MQ0=4;QD=3.35;SB=113.39 GT:AD:DP:GL:GQ 0/1:88,302:134:-174.25,-40.36,-354.14:99 +chr1 812511 . C T 253.04 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=392;Dels=0.00;HRun=1;HaplotypeScore=342.27;MQ=34.93;MQ0=3;QD=0.65;SB=107.37 GT:AD:DP:GL:GQ 0/1:210,181:105:-60.21,-31.62,-326.58:99 +chr1 812536 . C T 6216.93 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=431;Dels=0.00;HRun=0;HaplotypeScore=21.13;MQ=33.82;MQ0=5;QD=14.42;SB=89.30 GT:AD:DP:GL:GQ 0/1:86,345:239:-620.69,-71.99,-300.06:99 +chr1 812546 . A T 6301.61 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=411;Dels=0.00;HRun=5;HaplotypeScore=527.01;MQ=34.23;MQ0=5;QD=15.33;SB=95.32 GT:AD:DP:GL:GQ 0/1:107,219:261:-629.16,-251.98,-546.86:99 +chr1 812557 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=384;Dels=0.00;HRun=0;HaplotypeScore=98.60;MQ=34.24;MQ0=5;OQ=4742.49;QD=12.35;SB=92.31 GT:AD:DP:GL:GQ 0/1:201,182:235:-473.25,-70.78,-414.34:99 +chr1 812581 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=273;Dels=0.00;HRun=0;HaplotypeScore=142.64;MQ=35.76;MQ0=4;OQ=1205.24;QD=4.41;SB=74.26 GT:AD:DP:GL:GQ 0/1:167,71:149:-175.85,-52.04,-375.17:99 +chr1 812582 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=267;Dels=0.00;HRun=0;HaplotypeScore=141.33;MQ=35.99;MQ0=4;OQ=1716.18;QD=6.43;SB=71.26 GT:AD:DP:GL:GQ 0/1:103,164:146:-218.89,-43.99,-346.52:99 +chr1 812608 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=1;HaplotypeScore=67.91;MQ=41.17;MQ0=4;OQ=693.18;QD=4.20;SB=50.19 GT:AD:DP:GL:GQ 0/1:102,63:97:-101.82,-29.21,-294.33:99 +chr1 812623 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=28.33;MQ=46.60;MQ0=1;OQ=165.38;QD=1.61;SB=41.15 GT:AD:DP:GL:GQ 0/1:59,44:68:-40.30,-20.48,-216.18:99 +chr1 812625 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=1;HaplotypeScore=28.33;MQ=46.70;MQ0=1;OQ=134.52;QD=1.27;SB=44.17 GT:AD:DP:GL:GQ 0/1:60,46:69:-37.52,-20.78,-218.11:99 +chr1 812637 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=0;HaplotypeScore=37.48;MQ=47.73;MQ0=2;OQ=214.50;QD=1.87;SB=-61.85 GT:AD:DP:GL:GQ 0/1:67,48:77:-47.94,-23.20,-220.91:99 +chr1 812655 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=33.89;MQ=47.71;MQ0=3;OQ=405.95;QD=3.35;SB=-136.06 GT:AD:DP:GL:GQ 0/1:68,53:87:-70.08,-26.20,-247.74:99 +chr1 812661 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=2;HaplotypeScore=21.84;MQ=47.58;MQ0=5;OQ=365.64;QD=2.95;SB=-168.82 GT:AD:DP:GL:GQ 0/1:87,37:88:-66.35,-26.51,-263.64:99 +chr1 812666 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=21.15;MQ=47.18;MQ0=5;OQ=451.13;QD=3.67;SB=-190.13 GT:AD:DP:GL:GQ 0/1:65,57:86:-74.30,-25.91,-260.71:99 +chr1 812725 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=2;HaplotypeScore=17.99;MQ=47.07;MQ0=7;OQ=51.25;QD=0.37;SB=36.23 GT:AD:DP:GL:GQ 0/1:99,33:95:-37.06,-28.65,-279.36:84.09 +chr1 812740 . T A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=2;HaplotypeScore=10.99;MQ=47.57;MQ0=4;OQ=391.52;QD=3.08;SB=-178.55 GT:AD:DP:GL:GQ 0/1:69,58:85:-68.04,-25.60,-259.04:99 +chr1 812742 . A T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=11.99;MQ=46.41;MQ0=4;OQ=355.87;QD=2.58;SB=-160.38 GT:AD:DP:GL:GQ 0/1:72,66:89:-65.67,-26.80,-277.85:99 +chr1 812772 . C A 4524.81 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=340;Dels=0.00;HRun=1;HaplotypeScore=205.36;MQ=35.68;MQ0=5;QD=13.31;SB=-1151.01 GT:AD:DP:GL:GQ 0/1:83,257:202:-451.48,-60.83,-296.00:99 +chr1 812774 . G A 5465.17 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=359;Dels=0.00;HRun=1;HaplotypeScore=230.04;MQ=35.29;MQ0=5;QD=15.22;SB=-1392.69 GT:AD:DP:GL:GQ 0/1:83,276:217:-545.52,-65.36,-295.35:99 +chr1 812778 . A C 2967.60 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=395;Dels=0.00;HRun=0;HaplotypeScore=217.58;MQ=34.63;MQ0=8;QD=7.51;SB=-725.51 GT:AD:DP:GL:GQ 0/1:219,176:242:-372.92,-72.88,-512.65:99 +chr1 812823 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=734;Dels=0.00;HRun=0;HaplotypeScore=134.36;MQ=30.02;MQ0=41;OQ=617.75;QD=0.84;SB=-157.33 GT:AD:DP:GL:GQ 0/1:653,81:442:-198.19,-133.13,-1425.62:99 +chr1 812838 rs657923 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=716;Dels=0.00;HRun=1;HaplotypeScore=212.74;MQ=29.97;MQ0=41;OQ=1388.92;QD=1.94;SB=-7.94 GT:AD:DP:GL:GQ 0/1:599,117:439:-274.39,-132.21,-1407.52:99 +chr1 812875 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=465;Dels=0.00;HRun=0;HaplotypeScore=110.91;MQ=32.05;MQ0=37;OQ=83.36;QD=0.18;SB=55.37 GT:AD:DP:GL:GQ 0/1:398,67:296:-100.77,-89.15,-980.63:99 +chr1 812885 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=346;Dels=0.00;HRun=1;HaplotypeScore=111.42;MQ=33.27;MQ0=30;OQ=5208.47;QD=15.05;SB=-2233.36 GT:AD:DP:GL:GQ 0/1:69,277:208:-519.85,-62.65,-238.95:99 +chr1 812886 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=335;Dels=0.00;HRun=1;HaplotypeScore=55.46;MQ=33.49;MQ0=30;OQ=451.06;QD=1.35;SB=-154.07 GT:AD:DP:GL:GQ 0/1:302,33:200:-108.62,-60.23,-633.51:99 +chr1 812900 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=14.94;MQ=39.79;MQ0=13;OQ=813.81;QD=4.45;SB=92.87 GT:AD:DP:GL:GQ 0/1:73,110:100:-114.78,-30.12,-260.13:99 +chr1 812923 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=27.88;MQ=50.22;MQ0=2;OQ=306.33;QD=2.95;SB=-30.81 GT:AD:DP:GL:GQ 0/1:70,34:81:-58.31,-24.40,-238.03:99 +chr1 812935 . G A 2.07 PASS AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=2.66;MQ=47.53;MQ0=2;OQ=744.11;QD=5.55;SB=-223.02 GT:AD:DP:GL:GQ 0/1:69,65:96:-106.61,-28.92,-247.13:99 +chr1 812951 . G T 11.25 PASS AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=43.90;MQ0=5;OQ=1351.36;QD=8.72;SB=-400.31 GT:AD:DP:GL:GQ 0/1:63,92:108:-170.95,-32.53,-225.30:99 +chr1 812975 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=0;HaplotypeScore=28.65;MQ=40.87;MQ0=15;OQ=1862.55;QD=9.36;SB=-484.23 GT:AD:DP:GL:GQ 0/1:66,132:123:-230.20,-40.66,-212.95:99 +chr1 812981 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=1;HaplotypeScore=40.75;MQ=39.82;MQ0=15;OQ=1797.82;QD=8.86;SB=-460.63 GT:AD:DP:GL:GQ 0/1:63,140:120:-219.20,-36.14,-217.08:99 +chr1 812999 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=293;Dels=0.00;HRun=3;HaplotypeScore=112.34;MQ=35.70;MQ0=17;OQ=746.50;QD=2.55;SB=103.46 GT:AD:DP:GL:GQ 0/1:201,92:175:-130.64,-52.71,-522.15:99 +chr1 813018 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=409;Dels=0.00;HRun=4;HaplotypeScore=24.00;MQ=34.51;MQ0=18;OQ=2503.76;QD=6.12;SB=-85.25 GT:AD:DP:GL:GQ 0/1:266,142:285:-339.49,-85.83,-765.92:99 +chr1 813030 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=463;Dels=0.00;HRun=0;HaplotypeScore=48.87;MQ=34.17;MQ0=19;OQ=2316.95;QD=5.00;SB=-56.40 GT:AD:DP:GL:GQ 0/1:312,151:338:-336.77,-101.79,-911.65:99 +chr1 813038 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=491;Dels=0.00;HRun=0;HaplotypeScore=299.82;MQ=33.86;MQ0=19;OQ=574.58;QD=1.17;SB=49.00 GT:AD:DP:GL:GQ 0/1:442,49:363:-170.06,-109.32,-1157.10:99 +chr1 813041 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=493;Dels=0.00;HRun=0;HaplotypeScore=391.76;MQ=34.08;MQ0=19;OQ=10262.92;QD=20.82;SB=-1216.69 GT:AD:DP:GL:GQ 0/1:84,408:369:-1025.29,-114.38,-315.19:99 +chr1 813055 . T G 5105.47 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=534;Dels=0.00;HRun=1;HaplotypeScore=573.54;MQ=33.39;MQ0=15;QD=9.56;SB=-804.21 GT:AD:DP:GL:GQ 0/1:355,179:410:-509.55,-123.48,-999.47:99 +chr1 813070 . G T 1334.14 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=573;Dels=0.00;HRun=1;HaplotypeScore=588.05;MQ=33.10;MQ0=9;QD=2.33;SB=-193.13 GT:AD:DP:GL:GQ 0/1:472,101:440:-269.21,-132.51,-1306.87:99 +chr1 813073 . C G 2805.72 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=592;Dels=0.00;HRun=1;HaplotypeScore=532.94;MQ=33.08;MQ0=8;QD=4.74;SB=-566.71 GT:AD:DP:GL:GQ 0/1:469,123:455:-420.94,-137.09,-1553.33:99 +chr1 813077 . G A 139.61 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=606;Dels=0.00;HRun=1;HaplotypeScore=787.16;MQ=33.34;MQ0=7;QD=0.23;SB=20.29 GT:AD:DP:GL:GQ 0/1:564,42:462:-156.39,-139.14,-1597.16:99 +chr1 813078 . C G 7856.82 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=607;Dels=0.00;HRun=1;HaplotypeScore=894.22;MQ=33.34;MQ0=7;QD=12.94;SB=-567.18 GT:AD:DP:GL:GQ 0/1:367,165:476:-784.68,-363.52,-1514.16:99 +chr1 813086 . C G 6412.49 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=625;Dels=0.00;HRun=0;HaplotypeScore=667.82;MQ=33.46;MQ0=7;QD=10.26;SB=-767.41 GT:AD:DP:GL:GQ 0/1:438,186:509:-640.25,-153.35,-1590.01:99 +chr1 813088 . G A 7116.40 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=627;Dels=0.00;HRun=1;HaplotypeScore=625.87;MQ=33.36;MQ0=7;QD=11.35;SB=-863.76 GT:AD:DP:GL:GQ 0/1:405,186:507:-710.64,-256.24,-1344.66:99 +chr1 813094 . C T 2968.23 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=620;Dels=0.00;HRun=0;HaplotypeScore=211.21;MQ=33.22;MQ0=9;QD=4.79;SB=-1023.50 GT:AD:DP:GL:GQ 0/1:481,139:495:-449.19,-149.09,-1385.37:99 +chr1 813107 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=546;Dels=0.00;HRun=0;HaplotypeScore=55.14;MQ=33.11;MQ0=20;OQ=871.93;QD=1.60;SB=-175.62 GT:AD:DP:GL:GQ 0/1:477,69:368:-201.32,-110.84,-1286.63:99 +chr1 813112 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=540;Dels=0.00;HRun=1;HaplotypeScore=215.40;MQ=33.46;MQ0=24;OQ=633.86;QD=1.17;SB=-102.54 GT:AD:DP:GL:GQ 0/1:489,51:349:-171.78,-105.11,-1109.57:99 +chr1 813120 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=452;Dels=0.00;HRun=0;HaplotypeScore=223.96;MQ=34.07;MQ0=26;OQ=8026.64;QD=17.76;SB=-2723.00 GT:AD:DP:GL:GQ 0/1:104,348:294:-801.66,-88.56,-349.63:99 +chr1 813123 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=449;Dels=0.00;HRun=0;HaplotypeScore=337.04;MQ=33.84;MQ0=28;OQ=7271.87;QD=16.20;SB=-2574.23 GT:AD:DP:GL:GQ 0/1:72,377:266:-726.19,-80.11,-257.87:99 +chr1 813133 . G C 2818.75 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=399;Dels=0.00;HRun=0;HaplotypeScore=373.63;MQ=34.21;MQ0=30;QD=7.06;SB=-1307.24 GT:AD:DP:GL:GQ 0/1:279,119:209:-348.13,-62.97,-562.66:99 +chr1 813135 . A G 6195.50 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=391;Dels=0.00;HRun=0;HaplotypeScore=305.70;MQ=34.41;MQ0=29;QD=15.85;SB=-2650.19 GT:AD:DP:GL:GQ 0/1:69,321:237:-618.55,-71.38,-275.07:99 +chr1 813142 . T C 345.82 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=364;Dels=0.00;HRun=1;HaplotypeScore=286.54;MQ=33.82;MQ0=33;QD=0.95;SB=-108.69 GT:AD:DP:GL:GQ 0/1:317,47:188:-94.49,-56.62,-663.95:99 +chr1 813148 . C A 1435.04 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=349;Dels=0.00;HRun=2;HaplotypeScore=161.77;MQ=34.46;MQ0=34;QD=4.11;SB=-365.32 GT:AD:DP:GL:GQ 0/1:282,67:257:-224.19,-77.40,-705.20:99 +chr1 813156 . T A 297.72 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=0;HaplotypeScore=111.01;MQ=35.71;MQ0=35;QD=0.97;SB=9.92 GT:AD:DP:GL:GQ 0/1:276,32:221:-99.61,-66.55,-759.37:99 +chr1 813157 . G C 549.74 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=111.01;MQ=35.86;MQ0=35;QD=1.79;SB=-210.25 GT:AD:DP:GL:GQ 0/1:247,59:221:-124.85,-66.59,-828.88:99 +chr1 813168 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=254;Dels=0.00;HRun=2;HaplotypeScore=4.86;MQ=37.54;MQ0=37;OQ=984.94;QD=3.88;SB=44.86 GT:AD:DP:GL:GQ 0/1:209,45:173:-153.88,-52.11,-496.83:99 +chr1 813186 . G C 76.25 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=160;Dels=0.00;HRun=0;HaplotypeScore=72.20;MQ=40.71;MQ0=36;QD=0.48;SB=71.95 GT:AD:DP:GL:GQ 0/1:148,12:83:-35.91,-25.01,-332.34:99 +chr1 813187 . A G 513.33 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=147;Dels=0.00;HRun=1;HaplotypeScore=71.20;MQ=41.66;MQ0=35;QD=3.49;SB=-73.38 GT:AD:DP:GL:GQ 0/1:75,50:94:-82.93,-28.31,-287.29:99 +chr1 813188 . C A 79.88 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=1;HaplotypeScore=71.20;MQ=41.50;MQ0=35;QD=0.55;SB=44.61 GT:AD:DP:GL:GQ 0/1:120,26:78:-34.77,-23.49,-243.41:99 +chr1 813189 . C A 521.18 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=67.21;MQ=41.65;MQ0=35;QD=3.62;SB=-1.36 GT:AD:DP:GL:GQ 0/1:108,26:91:-101.37,-45.97,-249.59:99 +chr1 813208 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=2;HaplotypeScore=18.83;MQ=43.26;MQ0=23;OQ=418.24;QD=3.37;SB=-54.23 GT:AD:DP:GL:GQ 0/1:61,63:76:-68.00,-22.89,-206.10:99 +chr1 813240 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=2;HaplotypeScore=43.28;MQ=41.04;MQ0=25;OQ=943.89;QD=6.13;SB=-68.91 GT:AD:DP:GL:GQ 0/1:64,90:92:-125.38,-27.71,-227.61:99 +chr1 813250 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=195;Dels=0.00;HRun=0;HaplotypeScore=62.53;MQ=37.95;MQ0=22;OQ=226.25;QD=1.16;SB=14.99 GT:AD:DP:GL:GQ 0/1:153,42:96:-54.82,-28.92,-298.56:99 +chr1 813271 . T C 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=0;HaplotypeScore=8.46;MQ=34.98;MQ0=19;OQ=1147.61;QD=4.61;SB=-134.40 GT:AD:DP:GL:GQ 0/1:63,186:103:-149.07,-31.02,-256.47:99 +chr1 813292 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=382;Dels=0.00;HRun=2;HaplotypeScore=102.43;MQ=30.92;MQ0=23;OQ=1986.60;QD=5.20;SB=-566.46 GT:AD:DP:GL:GQ 0/1:105,277:133:-242.00,-40.06,-276.00:99 +chr1 813307 . A G 32.13 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=535;Dels=0.00;HRun=0;HaplotypeScore=181.84;MQ=30.25;MQ0=27;QD=0.06;SB=46.55 GT:AD:DP:GL:GQ 0/1:504,31:255:-83.31,-76.81,-935.22:64.97 +chr1 813316 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=619;Dels=0.00;HRun=2;HaplotypeScore=75.11;MQ=29.97;MQ0=27;OQ=3157.81;QD=5.10;SB=-1462.71 GT:AD:DP:GL:GQ 0/1:382,237:331:-418.76,-99.69,-846.79:99 +chr1 813335 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=826;Dels=0.00;HRun=1;HaplotypeScore=136.91;MQ=30.11;MQ0=21;OQ=7119.57;QD=8.62;SB=-2280.77 GT:AD:DP:GL:GQ 0/1:537,288:549:-710.96,-165.36,-1364.58:99 +chr1 813362 . A G 16357.98 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=920;Dels=0.00;HRun=1;HaplotypeScore=446.32;MQ=30.10;MQ0=24;QD=17.78;SB=-5014.09 GT:AD:DP:GL:GQ 0/1:273,494:683:-1634.80,-554.43,-1400.88:99 +chr1 813367 . T C 20902.62 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=914;Dels=0.00;HRun=0;HaplotypeScore=426.41;MQ=30.28;MQ0=24;QD=22.87;SB=-7448.46 GT:AD:DP:GL:GQ 0/1:141,716:687:-2089.26,-358.04,-691.48:99 +chr1 813368 rs13302980 T C 206.93 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=916;Dels=0.00;HRun=0;HaplotypeScore=426.41;MQ=30.25;MQ0=24;QD=0.23;SB=-118.41 GT:AD:DP:GL:GQ 0/1:843,73:685:-230.32,-206.34,-2521.41:99 +chr1 813385 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=888;Dels=0.00;HRun=0;HaplotypeScore=40.71;MQ=30.82;MQ0=25;OQ=1088.75;QD=1.23;SB=-408.14 GT:AD:DP:GL:GQ 0/1:783,105:699:-322.70,-210.54,-2232.26:99 +chr1 813404 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=750;Dels=0.00;HRun=2;HaplotypeScore=134.73;MQ=32.26;MQ0=17;OQ=670.55;QD=0.89;SB=-191.51 GT:AD:DP:GL:GQ 0/1:685,65:613:-254.96,-184.62,-2037.75:99 +chr1 813405 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=741;Dels=0.00;HRun=2;HaplotypeScore=133.74;MQ=32.36;MQ0=17;OQ=1633.92;QD=2.21;SB=-672.01 GT:AD:DP:GL:GQ 0/1:597,144:607:-349.50,-182.82,-2122.95:99 +chr1 813418 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=590;Dels=0.00;HRun=0;HaplotypeScore=47.11;MQ=33.33;MQ0=15;OQ=65.79;QD=0.11;SB=206.84 GT:AD:DP:GL:GQ 0/1:544,46:476:-153.22,-143.35,-1574.37:98.63 +chr1 813443 . T G 3848.11 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=0;HaplotypeScore=38.86;MQ=37.99;MQ0=5;QD=13.99;SB=-1241.58 GT:AD:DP:GL:GQ 0/1:79,195:186:-383.81,-56.02,-279.85:99 +chr1 813451 . C T 1033.45 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=197;Dels=0.01;HRun=0;HaplotypeScore=22.13;MQ=41.75;MQ0=4;QD=5.25;SB=-217.95 GT:AD:DP:GL:GQ 0/1:81,115:114:-140.97,-34.34,-279.86:99 +chr1 813452 . A G 765.89 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=186;Dels=0.01;HRun=0;HaplotypeScore=26.12;MQ=42.21;MQ0=4;QD=4.12;SB=-130.38 GT:AD:DP:GL:GQ 0/1:79,106:109:-112.71,-32.84,-316.56:99 +chr1 813514 rs61768255 T A 0.19 PASS AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=40.18;MQ0=52;OQ=194.92;QD=1.28;SB=-18.62 GT:AD:DP:GL:GQ 0/1:64,87:75:-45.36,-22.59,-238.39:99 +chr1 813576 . G T 36.42 DPFilter;Indel;LowQual AC=1;AF=0.50;AN=2;DP=256;Dels=0.00;HRun=0;HaplotypeScore=114.90;MQ=32.12;MQ0=13;QD=0.14;SB=80.27 GT:AD:DP:GL:GQ 0/1:231,25:108:-39.45,-32.53,-355.25:69.25 +chr1 813577 . C T 12.25 DPFilter;Indel;LowQual AC=1;AF=0.50;AN=2;DP=253;Dels=0.00;HRun=0;HaplotypeScore=118.76;MQ=32.29;MQ0=11;QD=0.05;SB=83.28 GT:AD:DP:GL:GQ 0/1:222,24:110:-47.87,-43.39,-370.50:44.82 +chr1 813595 . G A 14.36 DPFilter;Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=304;Dels=0.02;HRun=3;HaplotypeScore=679.47;MQ=32.56;MQ0=1;QD=0.05;SB=59.22 GT:AD:DP:GL:GQ 0/1:279,19:122:-44.63,-39.92,-398.76:47.04 +chr1 813600 . G A 274.89 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=326;Dels=0.00;HRun=2;HaplotypeScore=874.07;MQ=32.03;MQ0=1;QD=0.84;SB=65.24 GT:AD:DP:GL:GQ 0/1:247,78:142:-73.54,-42.77,-440.28:99 +chr1 813603 . G A 897.36 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=326;Dels=0.00;HRun=2;HaplotypeScore=1015.89;MQ=31.94;MQ0=0;QD=2.75;SB=17.55 GT:AD:DP:GL:GQ 0/1:201,125:138:-134.59,-41.57,-374.40:99 +chr1 813618 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=385;Dels=0.01;HRun=2;HaplotypeScore=1064.00;MQ=30.68;MQ0=0;OQ=4144.71;QD=10.77;SB=-60.77 GT:AD:DP:GL:GQ 0/1:139,193:174:-413.47,-52.40,-263.62:99 +chr1 813640 . G A 6008.25 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=492;Dels=0.03;HRun=2;HaplotypeScore=778.76;MQ=30.34;MQ0=0;QD=12.21;SB=-280.67 GT:AD:DP:GL:GQ 0/1:225,249:279:-599.83,-82.23,-444.10:99 +chr1 813644 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=499;Dels=0.00;HRun=2;HaplotypeScore=589.76;MQ=30.13;MQ0=0;OQ=1319.59;QD=2.64;SB=-65.34 GT:AD:DP:GL:GQ 0/1:370,128:286:-221.39,-86.15,-815.48:99 +chr1 813653 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=493;Dels=0.00;HRun=1;HaplotypeScore=439.06;MQ=30.75;MQ0=0;OQ=617.48;QD=1.25;SB=-157.65 GT:AD:DP:GL:GQ 0/1:455,38:256:-142.14,-77.10,-775.99:99 +chr1 813667 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=450;Dels=0.03;HRun=0;HaplotypeScore=1087.09;MQ=31.84;MQ0=0;OQ=612.31;QD=1.36;SB=24.15 GT:AD:DP:GL:GQ 0/1:310,99:290:-203.97,-139.46,-953.68:99 +chr1 813680 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=385;Dels=0.03;HRun=2;HaplotypeScore=1191.21;MQ=32.81;MQ0=0;OQ=1213.04;QD=3.15;SB=-10.63 GT:AD:DP:GL:GQ 0/1:276,97:229:-193.56,-68.97,-645.40:99 +chr1 813720 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=252;Dels=0.06;HRun=1;HaplotypeScore=327.60;MQ=37.03;MQ0=0;OQ=194.28;QD=0.77;SB=110.38 GT:AD:DP:GL:GQ 0/1:205,33:146:-66.38,-43.67,-457.57:99 +chr1 813729 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=0;HaplotypeScore=373.81;MQ=39.70;MQ0=0;OQ=281.23;QD=1.50;SB=15.00 GT:AD:DP:GL:GQ 0/1:127,60:111:-64.84,-33.43,-345.95:99 +chr1 813820 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=81;Dels=0.05;HRun=2;HaplotypeScore=42.41;MQ=49.74;MQ0=3;OQ=162.06;QD=2.00;SB=-100.42 GT:AD:DP:GL:GQ 0/1:56,21:59:-37.26,-17.77,-183.03:99 +chr1 813869 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=73.61;MQ=47.62;MQ0=2;OQ=155.20;QD=1.94;SB=41.14 GT:AD:DP:GL:GQ 0/1:71,9:54:-35.07,-16.26,-160.29:99 +chr1 813877 . G A 25.05 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=66.85;MQ=49.86;MQ0=1;QD=0.34;SB=32.11 GT:AD:DP:GL:GQ 0/1:64,9:51:-21.15,-15.36,-169.54:57.88 +chr1 813907 . G A 23.05 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=73;Dels=0.04;HRun=1;HaplotypeScore=56.30;MQ=49.27;MQ0=1;QD=0.32;SB=38.13 GT:AD:DP:GL:GQ 0/1:63,7:54:-21.25,-15.66,-171.08:55.87 +chr1 813910 . G A 12.29 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=61.37;MQ=49.27;MQ0=1;QD=0.17;SB=35.12 GT:AD:DP:GL:GQ 0/1:63,10:55:-21.06,-16.57,-179.39:44.87 +chr1 813923 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=75;Dels=0.03;HRun=2;HaplotypeScore=23.38;MQ=50.12;MQ0=1;OQ=138.74;QD=1.85;SB=-24.20 GT:AD:DP:GL:GQ 0/1:50,23:55:-33.43,-16.28,-173.24:99 +chr1 813957 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=2;HaplotypeScore=18.68;MQ=43.32;MQ0=1;OQ=871.71;QD=6.86;SB=-275.74 GT:AD:DP:GL:GQ 0/1:65,62:85:-116.06,-25.61,-200.91:99 +chr1 813978 . A C 0.71 PASS AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=39.28;MQ0=4;OQ=705.69;QD=4.77;SB=-252.74 GT:AD:DP:GL:GQ 0/1:54,94:80:-97.95,-24.09,-193.62:99 +chr1 814078 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=6.42;MQ=36.79;MQ0=24;OQ=486.46;QD=2.55;SB=-267.20 GT:AD:DP:GL:GQ 0/1:63,128:82:-76.63,-24.70,-247.64:99 +chr1 814121 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=39.43;MQ=40.45;MQ0=17;OQ=289.94;QD=1.73;SB=-38.08 GT:AD:DP:GL:GQ 0/1:70,98:82:-56.99,-24.71,-295.92:99 +chr1 814147 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=0;HaplotypeScore=14.17;MQ=45.92;MQ0=13;OQ=964.78;QD=6.39;SB=-366.58 GT:AD:DP:GL:GQ 0/1:82,69:112:-133.50,-33.74,-285.66:99 +chr1 814171 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=1;HaplotypeScore=20.78;MQ=44.66;MQ0=14;OQ=904.13;QD=5.38;SB=-364.51 GT:AD:DP:GL:GQ 0/1:83,85:118:-129.23,-35.54,-305.53:99 +chr1 814202 . C A 1692.96 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=197;Dels=0.09;HRun=0;HaplotypeScore=162.31;MQ=41.97;MQ0=8;QD=8.59;SB=-578.48 GT:AD:DP:GL:GQ 0/1:79,100:139:-213.84,-41.26,-286.69:99 +chr1 814220 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=0;HaplotypeScore=50.82;MQ=39.65;MQ0=8;OQ=329.14;QD=1.52;SB=-86.50 GT:AD:DP:GL:GQ 0/1:161,56:136:-77.16,-40.96,-423.94:99 +chr1 814233 . G A 2067.86 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=0;HaplotypeScore=147.47;MQ=38.66;MQ0=13;QD=9.23;SB=-544.97 GT:AD:DP:GL:GQ 0/1:105,119:132:-249.86,-39.79,-228.63:99 +chr1 814239 . A G 1315.30 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=220;Dels=0.00;HRun=1;HaplotypeScore=123.50;MQ=38.45;MQ0=13;QD=5.98;SB=-142.40 GT:AD:DP:GL:GQ 0/1:70,150:114:-169.16,-34.34,-278.17:99 +chr1 814242 . A G 554.64 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=125.56;MQ=38.13;MQ0=16;QD=2.40;SB=-155.01 GT:AD:DP:GL:GQ 0/1:172,59:130:-97.91,-39.16,-422.03:99 +chr1 814256 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=245;Dels=0.00;HRun=0;HaplotypeScore=21.41;MQ=37.07;MQ0=15;OQ=2324.45;QD=9.49;SB=-360.77 GT:AD:DP:GL:GQ 0/1:68,177:144:-279.11,-43.38,-270.96:99 +chr1 814273 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=59.92;MQ=36.71;MQ0=15;OQ=51.68;QD=0.19;SB=122.32 GT:AD:DP:GL:GQ 0/1:221,49:163:-60.05,-51.60,-506.38:84.51 +chr1 814274 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=269;Dels=0.00;HRun=0;HaplotypeScore=59.77;MQ=36.62;MQ0=15;OQ=1850.48;QD=6.88;SB=-407.81 GT:AD:DP:GL:GQ 0/1:149,120:153:-234.45,-46.12,-315.76:99 +chr1 814294 . A G 2410.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=2;HaplotypeScore=103.79;MQ=37.05;MQ0=15;QD=9.06;SB=-443.47 GT:AD:DP:GL:GQ 0/1:75,191:153:-290.38,-46.10,-295.34:99 +chr1 814296 . G A 1211.04 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=274;Dels=0.00;HRun=0;HaplotypeScore=219.20;MQ=36.82;MQ0=15;QD=4.42;SB=-351.23 GT:AD:DP:GL:GQ 0/1:200,74:158:-171.99,-47.60,-420.58:99 +chr1 814301 . A G 978.34 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=274;Dels=0.00;HRun=0;HaplotypeScore=220.77;MQ=36.41;MQ0=15;QD=3.57;SB=-180.08 GT:AD:DP:GL:GQ 0/1:73,201:110:-134.26,-33.14,-291.65:99 +chr1 814305 . T C 45.78 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=232.83;MQ=35.76;MQ0=15;QD=0.16;SB=-43.14 GT:AD:DP:GL:GQ 0/1:206,71:102:-38.59,-30.73,-365.14:78.61 +chr1 814318 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=0;HaplotypeScore=167.17;MQ=36.26;MQ0=13;OQ=2113.99;QD=7.60;SB=-387.55 GT:AD:DP:GL:GQ 0/1:72,191:148:-269.75,-55.07,-295.63:99 +chr1 814320 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=0;HaplotypeScore=167.17;MQ=36.49;MQ0=13;OQ=746.17;QD=2.66;SB=-108.14 GT:AD:DP:GL:GQ 0/1:218,62:140:-120.08,-42.18,-412.31:99 +chr1 814333 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=285;Dels=0.00;HRun=0;HaplotypeScore=281.15;MQ=35.53;MQ0=9;OQ=1990.33;QD=6.98;SB=-447.96 GT:AD:DP:GL:GQ 0/1:95,190:142:-245.09,-42.77,-288.22:99 +chr1 814346 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=251;Dels=0.00;HRun=0;HaplotypeScore=225.23;MQ=36.32;MQ0=4;OQ=1683.84;QD=6.71;SB=-421.88 GT:AD:DP:GL:GQ 0/1:107,144:128:-210.24,-38.57,-269.23:99 +chr1 814360 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=2;HaplotypeScore=149.83;MQ=38.08;MQ0=4;OQ=172.19;QD=0.77;SB=51.61 GT:AD:DP:GL:GQ 0/1:195,28:117:-55.74,-35.24,-362.13:99 +chr1 814384 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=1;HaplotypeScore=42.51;MQ=45.49;MQ0=3;OQ=551.67;QD=3.70;SB=-145.33 GT:AD:DP:GL:GQ 0/1:76,73:99:-88.27,-29.82,-286.26:99 +chr1 814428 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=10.58;MQ=49.14;MQ0=17;OQ=342.52;QD=2.63;SB=-111.49 GT:AD:DP:GL:GQ 0/1:82,48:99:-67.35,-29.82,-298.71:99 +chr1 814439 . C T 20.82 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=47.72;MQ0=20;QD=0.14;SB=152.46 GT:AD:DP:GL:GQ 0/1:137,12:115:-40.00,-34.64,-383.60:53.62 +chr1 814456 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=1;HaplotypeScore=15.28;MQ=46.84;MQ0=26;OQ=753.94;QD=4.65;SB=-138.63 GT:AD:DP:GL:GQ 0/1:92,70:122:-115.43,-36.75,-321.50:99 +chr1 814470 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=189;Dels=0.00;HRun=1;HaplotypeScore=31.58;MQ=44.82;MQ0=39;OQ=884.58;QD=4.68;SB=-229.69 GT:AD:DP:GL:GQ 0/1:97,92:121:-128.25,-36.50,-368.74:99 +chr1 814488 . C A 76.03 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=247;Dels=0.00;HRun=0;HaplotypeScore=105.09;MQ=41.14;MQ0=41;QD=0.31;SB=176.55 GT:AD:DP:GL:GQ 0/1:229,16:148:-55.47,-44.58,-476.50:99 +chr1 814489 . C G 69.13 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=248;Dels=0.00;HRun=0;HaplotypeScore=89.81;MQ=41.12;MQ0=41;QD=0.28;SB=176.62 GT:AD:DP:GL:GQ 0/1:231,17:149:-55.10,-44.90,-596.57:99 +chr1 814495 . T C 1858.16 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=258;Dels=0.00;HRun=0;HaplotypeScore=56.93;MQ=40.44;MQ0=47;QD=7.20;SB=-760.45 GT:AD:DP:GL:GQ 0/1:92,166:157:-236.40,-47.30,-370.00:99 +chr1 814529 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=433;Dels=0.00;HRun=0;HaplotypeScore=120.51;MQ=38.11;MQ0=39;OQ=500.57;QD=1.16;SB=-243.42 GT:AD:DP:GL:GQ 0/1:383,50:261:-131.95,-78.61,-806.43:99 +chr1 814534 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=446;Dels=0.00;HRun=0;HaplotypeScore=107.63;MQ=38.32;MQ0=36;OQ=359.59;QD=0.81;SB=-173.49 GT:AD:DP:GL:GQ 0/1:401,44:272:-121.18,-81.93,-841.90:99 +chr1 814540 . A G 36.54 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=477;Dels=0.00;HRun=1;HaplotypeScore=62.33;MQ=38.25;MQ0=37;QD=0.08;SB=123.17 GT:AD:DP:GL:GQ 0/1:445,32:265:-86.76,-79.83,-986.21:69.37 +chr1 814554 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=529;Dels=0.00;HRun=0;HaplotypeScore=89.36;MQ=37.97;MQ0=32;OQ=9731.93;QD=18.40;SB=-1976.66 GT:AD:DP:GL:GQ 0/1:80,449:318:-972.19,-95.79,-281.92:99 +chr1 814557 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=552;Dels=0.00;HRun=0;HaplotypeScore=97.56;MQ=38.01;MQ0=31;OQ=8661.84;QD=15.69;SB=-1680.73 GT:AD:DP:GL:GQ 0/1:195,357:340:-865.18,-102.42,-472.42:99 +chr1 814572 rs564838 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=625;Dels=0.00;HRun=1;HaplotypeScore=63.63;MQ=38.08;MQ0=27;OQ=2371.32;QD=3.79;SB=-326.77 GT:AD:DP:GL:GQ 0/1:480,145:413:-364.80,-124.39,-1136.05:99 +chr1 814627 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=504;Dels=0.00;HRun=1;HaplotypeScore=183.33;MQ=39.27;MQ0=14;OQ=10984.00;QD=21.79;SB=-1265.89 GT:AD:DP:GL:GQ 0/1:67,203:343:-1097.40,-537.50,-676.52:99 +chr1 814675 . G A 2732.90 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=265;Dels=0.00;HRun=1;HaplotypeScore=261.45;MQ=41.69;MQ0=11;QD=10.31;SB=-108.93 GT:AD:DP:GL:GQ 0/1:161,102:166:-330.09,-53.51,-314.61:99 +chr1 814679 . A G 2402.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=237;Dels=0.00;HRun=1;HaplotypeScore=135.51;MQ=41.79;MQ0=13;QD=10.14;SB=-20.34 GT:AD:DP:GL:GQ 0/1:70,167:146:-287.52,-43.99,-273.83:99 +chr1 814680 . C T 2092.18 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=238;Dels=0.00;HRun=0;HaplotypeScore=134.51;MQ=41.43;MQ0=17;QD=8.79;SB=-7.62 GT:AD:DP:GL:GQ 0/1:151,86:144:-255.88,-43.38,-283.23:99 +chr1 814701 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=219;Dels=0.00;HRun=0;HaplotypeScore=51.82;MQ=41.75;MQ0=19;OQ=1622.55;QD=7.41;SB=-75.48 GT:AD:DP:GL:GQ 0/1:87,132:141:-208.02,-42.48,-267.24:99 +chr1 814708 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=0;HaplotypeScore=76.68;MQ=40.68;MQ0=25;OQ=2028.26;QD=9.14;SB=-58.81 GT:AD:DP:GL:GQ 0/1:84,138:144:-249.49,-43.38,-267.28:99 +chr1 814713 rs563211 T C 1374.69 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=232;Dels=0.00;HRun=0;HaplotypeScore=105.58;MQ=40.40;MQ0=29;QD=5.93;SB=29.72 GT:AD:DP:GL:GQ 0/1:146,86:143:-183.83,-43.08,-359.04:99 +chr1 814720 . T C 689.97 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=108.11;MQ=39.59;MQ0=32;QD=2.84;SB=46.65 GT:AD:DP:GL:GQ 0/1:85,157:115:-106.92,-34.64,-346.63:99 +chr1 814722 . C G 183.01 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=254;Dels=0.00;HRun=0;HaplotypeScore=126.09;MQ=39.61;MQ0=33;QD=0.72;SB=68.61 GT:AD:DP:GL:GQ 0/1:217,37:122:-58.35,-36.76,-472.38:99 +chr1 814737 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=30.86;MQ=38.18;MQ0=38;OQ=2218.82;QD=7.42;SB=-36.77 GT:AD:DP:GL:GQ 0/1:186,113:186:-281.20,-56.03,-416.78:99 +chr1 814767 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=365;Dels=0.00;HRun=2;HaplotypeScore=49.56;MQ=35.63;MQ0=43;OQ=5264.89;QD=14.42;SB=-427.42 GT:AD:DP:GL:GQ 0/1:96,269:216:-525.49,-65.13,-366.09:99 +chr1 814784 . A G 211.71 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=402;Dels=0.00;HRun=0;HaplotypeScore=324.91;MQ=34.66;MQ0=41;QD=0.53;SB=-28.05 GT:AD:DP:GL:GQ 0/1:357,45:243:-97.65,-73.19,-885.32:99 +chr1 814787 . A G 1988.10 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=404;Dels=0.00;HRun=0;HaplotypeScore=288.76;MQ=34.45;MQ0=41;QD=4.92;SB=-448.31 GT:AD:DP:GL:GQ 0/1:239,165:199:-262.08,-59.99,-467.56:99 +chr1 814790 . G A 2076.12 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=406;Dels=0.00;HRun=0;HaplotypeScore=289.81;MQ=34.38;MQ0=42;QD=5.11;SB=-426.20 GT:AD:DP:GL:GQ 0/1:294,112:245:-284.69,-73.80,-651.34:99 +chr1 814794 . G C 5521.90 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=400;Dels=0.00;HRun=0;HaplotypeScore=359.70;MQ=34.34;MQ0=40;QD=13.80;SB=-919.83 GT:AD:DP:GL:GQ 0/1:77,252:207:-551.19,-211.22,-478.27:99 +chr1 814804 . C T 88.70 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=434;Dels=0.00;HRun=1;HaplotypeScore=347.22;MQ=35.87;MQ0=35;QD=0.20;SB=-33.30 GT:AD:DP:GL:GQ 0/1:387,47:188:-68.79,-56.64,-599.68:99 +chr1 814807 . A C 912.16 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=446;Dels=0.00;HRun=1;HaplotypeScore=302.12;MQ=36.31;MQ0=35;QD=2.05;SB=-348.23 GT:AD:DP:GL:GQ 0/1:319,127:242:-167.40,-72.90,-690.79:99 +chr1 814811 . C T 8629.57 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=472;Dels=0.00;HRun=2;HaplotypeScore=321.44;MQ=36.81;MQ0=35;QD=18.28;SB=-2662.56 GT:AD:DP:GL:GQ 0/1:133,339:310:-861.96,-93.38,-350.61:99 +chr1 814815 . G A 1219.97 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=497;Dels=0.00;HRun=1;HaplotypeScore=253.88;MQ=37.19;MQ0=33;QD=2.45;SB=-308.28 GT:AD:DP:GL:GQ 0/1:414,82:332:-225.30,-100.02,-991.58:99 +chr1 814833 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=552;Dels=0.00;HRun=0;HaplotypeScore=30.66;MQ=38.93;MQ0=25;OQ=13138.69;QD=23.80;SB=-5564.86 GT:AD:DP:GL:GQ 0/1:68,484:387:-1312.87,-116.58,-241.99:99 +chr1 814846 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=600;Dels=0.00;HRun=1;HaplotypeScore=69.54;MQ=39.19;MQ0=23;OQ=3136.64;QD=5.23;SB=-1237.78 GT:AD:DP:GL:GQ 0/1:435,165:409:-440.13,-123.18,-1039.78:99 +chr1 814879 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=693;Dels=0.00;HRun=0;HaplotypeScore=388.69;MQ=39.91;MQ0=7;OQ=8125.01;QD=11.72;SB=-2578.04 GT:AD:DP:GL:GQ 0/1:409,284:467:-811.50,-140.66,-960.39:99 +chr1 814880 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=692;Dels=0.00;HRun=2;HaplotypeScore=381.90;MQ=39.95;MQ0=7;OQ=2413.57;QD=3.49;SB=-960.49 GT:AD:DP:GL:GQ 0/1:533,158:465:-387.57,-142.93,-1289.43:99 +chr1 814900 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=699;Dels=0.00;HRun=0;HaplotypeScore=119.56;MQ=39.22;MQ0=14;OQ=14541.95;QD=20.80;SB=-4000.09 GT:AD:DP:GL:GQ 0/1:90,605:445:-1453.20,-134.09,-272.14:99 +chr1 814929 . C T 1261.33 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=562;Dels=0.00;HRun=0;HaplotypeScore=644.78;MQ=37.11;MQ0=29;QD=2.24;SB=-29.99 GT:AD:DP:GL:GQ 0/1:384,176:313:-223.70,-94.28,-953.66:99 +chr1 814931 . T C 7350.11 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=554;Dels=0.00;HRun=4;HaplotypeScore=616.85;MQ=36.93;MQ0=28;QD=13.27;SB=-1896.86 GT:AD:DP:GL:GQ 0/1:148,405:309:-734.01,-93.08,-440.40:99 +chr1 814932 rs4475692 G A 10783.24 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=554;Dels=0.00;HRun=0;HaplotypeScore=621.95;MQ=36.79;MQ0=29;QD=19.46;SB=-2129.22 GT:AD:DP:GL:GQ 0/1:174,298:306:-1077.32,-380.57,-459.91:99 +chr1 814939 . G A 1306.21 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=568;Dels=0.00;HRun=1;HaplotypeScore=479.84;MQ=36.20;MQ0=35;QD=2.30;SB=-170.45 GT:AD:DP:GL:GQ 0/1:402,165:327:-232.39,-98.48,-986.51:99 +chr1 814952 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=543;Dels=0.00;HRun=0;HaplotypeScore=51.53;MQ=35.74;MQ0=35;OQ=140.17;QD=0.26;SB=144.16 GT:AD:DP:GL:GQ 0/1:482,61:349:-122.41,-105.11,-1207.38:99 +chr1 814967 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=541;Dels=0.00;HRun=0;HaplotypeScore=312.71;MQ=35.10;MQ0=40;OQ=7468.20;QD=13.80;SB=-2338.34 GT:AD:DP:GL:GQ 0/1:256,284:360:-745.82,-108.45,-622.35:99 +chr1 814975 . C T 35.90 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=483;Dels=0.00;HRun=0;HaplotypeScore=80.80;MQ=34.88;MQ0=44;QD=0.07;SB=387.40 GT:AD:DP:GL:GQ 0/1:418,42:326:-167.53,-160.66,-1098.08:68.73 +chr1 815007 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=591;Dels=0.00;HRun=1;HaplotypeScore=71.67;MQ=32.27;MQ0=41;OQ=5134.52;QD=8.69;SB=-1587.17 GT:AD:DP:GL:GQ 0/1:388,203:408:-512.45,-122.89,-966.60:99 +chr1 815060 rs7417801 G A 11239.90 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=650;Dels=0.00;HRun=0;HaplotypeScore=316.82;MQ=33.42;MQ0=19;QD=17.29;SB=-4737.34 GT:AD:DP:GL:GQ 0/1:178,470:421:-1122.99,-126.87,-458.77:99 +chr1 815061 . C T 1691.04 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=650;Dels=0.00;HRun=1;HaplotypeScore=315.98;MQ=33.65;MQ0=19;QD=2.60;SB=-738.44 GT:AD:DP:GL:GQ 0/1:537,113:421:-299.19,-126.80,-1266.58:99 +chr1 815070 rs61768257 T C 12258.60 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=631;Dels=0.00;HRun=0;HaplotypeScore=343.15;MQ=33.97;MQ0=16;QD=19.43;SB=-5504.71 GT:AD:DP:GL:GQ 0/1:80,551:412:-1224.86,-124.09,-309.22:99 +chr1 815113 rs61768258 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=470;Dels=0.00;HRun=0;HaplotypeScore=109.35;MQ=33.63;MQ0=24;OQ=6584.76;QD=14.01;SB=-2185.39 GT:AD:DP:GL:GQ 0/1:114,356:254:-657.48,-76.51,-273.29:99 +chr1 815129 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=382;Dels=0.00;HRun=3;HaplotypeScore=48.33;MQ=33.58;MQ0=23;OQ=4485.00;QD=11.74;SB=-986.12 GT:AD:DP:GL:GQ 0/1:120,260:190:-447.50,-57.26,-260.95:99 +chr1 815155 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=321;Dels=0.00;HRun=2;HaplotypeScore=58.38;MQ=34.02;MQ0=21;OQ=1737.47;QD=5.41;SB=15.00 GT:AD:DP:GL:GQ 0/1:189,132:155:-223.72,-46.69,-361.30:99 +chr1 815170 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=270;Dels=0.00;HRun=0;HaplotypeScore=137.94;MQ=34.80;MQ0=19;OQ=2424.70;QD=8.98;SB=14.59 GT:AD:DP:GL:GQ 0/1:64,205:125:-283.44,-37.69,-171.56:99 +chr1 815209 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=4;HaplotypeScore=80.30;MQ=38.66;MQ0=0;OQ=2224.65;QD=10.44;SB=11.50 GT:AD:DP:GL:GQ 0/1:67,146:136:-266.72,-40.97,-258.01:99 +chr1 815222 . C G 180.27 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=2;HaplotypeScore=142.18;MQ=38.40;MQ0=0;QD=0.81;SB=9.29 GT:AD:DP:GL:GQ 0/1:186,36:136:-62.35,-41.04,-500.13:99 +chr1 815223 . G T 2117.77 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=1;HaplotypeScore=129.82;MQ=38.70;MQ0=0;QD=9.80;SB=21.09 GT:AD:DP:GL:GQ 0/1:67,149:140:-257.24,-42.18,-220.42:99 +chr1 815225 . C A 1105.29 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=2;HaplotypeScore=129.82;MQ=38.83;MQ0=0;QD=5.09;SB=62.22 GT:AD:DP:GL:GQ 0/1:119,82:139:-174.62,-60.81,-341.62:99 +chr1 815273 rs13303179 G A 2565.92 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=228;Dels=0.03;HRun=0;HaplotypeScore=354.84;MQ=39.22;MQ0=2;QD=11.25;SB=-1159.78 GT:AD:DP:GL:GQ 0/1:137,80:90:-286.39,-26.51,-60.11:99 +chr1 815278 . G T 761.09 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=623.87;MQ=38.93;MQ0=0;QD=3.17;SB=80.36 GT:AD:DP:GL:GQ 0/1:181,48:118:-132.78,-53.39,-296.79:99 +chr1 815284 . A T 612.72 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=234;Dels=0.01;HRun=0;HaplotypeScore=131.40;MQ=39.54;MQ0=0;QD=2.62;SB=-4.85 GT:AD:DP:GL:GQ 0/1:70,108:89:-96.12,-31.56,-237.53:99 +chr1 815299 . C T 462.61 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=1;HaplotypeScore=228.02;MQ=37.95;MQ0=1;QD=1.71;SB=107.29 GT:AD:DP:GL:GQ 0/1:137,134:104:-80.88,-31.33,-296.80:99 +chr1 815300 . A G 825.50 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=268;Dels=0.00;HRun=0;HaplotypeScore=227.74;MQ=37.73;MQ0=1;QD=3.08;SB=104.37 GT:AD:DP:GL:GQ 0/1:110,156:125:-123.50,-37.66,-346.20:99 +chr1 815308 . A G 1233.06 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=264;Dels=0.00;HRun=0;HaplotypeScore=419.76;MQ=37.40;MQ0=1;QD=4.67;SB=68.40 GT:AD:DP:GL:GQ 0/1:127,137:154:-172.99,-46.40,-402.39:99 +chr1 815312 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=276;Dels=0.00;HRun=0;HaplotypeScore=183.65;MQ=36.17;MQ0=1;OQ=3931.91;QD=14.25;SB=-32.81 GT:AD:DP:GL:GQ 0/1:62,214:156:-392.19,-47.02,-185.37:99 +chr1 815328 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=297;Dels=0.00;HRun=0;HaplotypeScore=61.42;MQ=35.05;MQ0=1;OQ=1563.62;QD=5.26;SB=37.57 GT:AD:DP:GL:GQ 0/1:210,87:190:-216.89,-57.25,-456.11:99 +chr1 815333 . A G 262.79 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=239.02;MQ=35.16;MQ0=1;QD=0.88;SB=12.36 GT:AD:DP:GL:GQ 0/1:257,42:214:-94.06,-64.49,-716.97:99 +chr1 815339 . G A 1298.73 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=1;HaplotypeScore=174.26;MQ=34.74;MQ0=1;QD=4.57;SB=28.57 GT:AD:DP:GL:GQ 0/1:213,70:192:-191.01,-57.85,-488.27:99 +chr1 815340 . C A 157.45 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=166.11;MQ=34.52;MQ0=1;QD=0.56;SB=56.17 GT:AD:DP:GL:GQ 0/1:238,39:195:-77.77,-58.74,-595.87:99 +chr1 815347 . C T 431.68 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=149.67;MQ=34.21;MQ0=1;QD=1.59;SB=13.61 GT:AD:DP:GL:GQ 0/1:219,52:183:-101.60,-55.14,-567.56:99 +chr1 815356 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=134.05;MQ=33.48;MQ0=1;OQ=648.64;QD=2.30;SB=53.15 GT:AD:DP:GL:GQ 0/1:240,42:173:-120.28,-52.13,-519.88:99 +chr1 815363 . G A 778.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=288;Dels=0.00;HRun=0;HaplotypeScore=145.91;MQ=33.47;MQ0=1;QD=2.70;SB=9.52 GT:AD:DP:GL:GQ 0/1:221,66:188:-137.76,-56.63,-540.20:99 +chr1 815371 . T A 4591.13 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=0;HaplotypeScore=258.43;MQ=32.98;MQ0=1;QD=16.70;SB=38.12 GT:AD:DP:GL:GQ 0/1:49,226:171:-458.11,-51.51,-170.42:99 +chr1 815373 . A T 533.41 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=286;Dels=0.00;HRun=2;HaplotypeScore=261.79;MQ=33.03;MQ0=1;QD=1.87;SB=35.14 GT:AD:DP:GL:GQ 0/1:246,39:154:-103.02,-46.39,-455.31:99 +chr1 815376 . C A 1170.34 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=282;Dels=0.00;HRun=0;HaplotypeScore=127.10;MQ=33.82;MQ0=1;QD=4.15;SB=38.15 GT:AD:DP:GL:GQ 0/1:188,94:146:-164.30,-43.98,-347.79:99 +chr1 815381 . G A 252.28 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=149.34;MQ=33.65;MQ0=1;QD=0.84;SB=44.17 GT:AD:DP:GL:GQ 0/1:261,37:167:-78.82,-50.30,-512.70:99 +chr1 815393 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=2;HaplotypeScore=32.62;MQ=34.43;MQ0=1;OQ=361.63;QD=1.32;SB=59.23 GT:AD:DP:GL:GQ 0/1:214,61:130:-78.62,-39.18,-425.44:99 +chr1 815401 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=262;Dels=0.00;HRun=0;HaplotypeScore=139.53;MQ=35.48;MQ0=0;OQ=534.52;QD=2.04;SB=65.23 GT:AD:DP:GL:GQ 0/1:204,58:105:-88.37,-31.63,-309.51:99 +chr1 815405 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=256;Dels=0.00;HRun=0;HaplotypeScore=139.38;MQ=35.34;MQ0=0;OQ=1047.66;QD=4.09;SB=65.23 GT:AD:DP:GL:GQ 0/1:61,195:95:-136.67,-28.62,-215.61:99 +chr1 815412 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=227;Dels=0.00;HRun=1;HaplotypeScore=225.15;MQ=36.20;MQ0=0;OQ=276.35;QD=1.22;SB=65.25 GT:AD:DP:GL:GQ 0/1:61,166:74:-53.21,-22.29,-232.02:99 +chr1 815417 rs4970337 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=202;Dels=0.00;HRun=1;HaplotypeScore=585.49;MQ=36.06;MQ0=0;OQ=1433.41;QD=7.10;SB=-630.86 GT:AD:DP:GL:GQ 1/1:20,53:52:-158.74,-15.68,-11.81:38.71 +chr1 815425 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=183;Dels=0.00;HRun=0;HaplotypeScore=313.15;MQ=35.48;MQ0=0;OQ=58.46;QD=0.32;SB=65.13 GT:AD:DP:GL:GQ 0/1:47,51:54:-25.40,-16.27,-162.78:91.30 +chr1 815458 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=13.84;MQ=40.96;MQ0=1;OQ=53.27;QD=0.51;SB=62.22 GT:AD:DP:GL:GQ 0/1:68,36:55:-25.19,-16.58,-184.48:86.11 +chr1 815470 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=23.44;MQ=43.10;MQ0=1;OQ=126.81;QD=1.44;SB=62.23 GT:AD:DP:GL:GQ 0/1:44,44:50:-31.03,-15.06,-165.46:99 +chr1 815557 . T C 22.78 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=22.31;MQ=51.18;MQ0=1;QD=0.27;SB=2.47 GT:AD:DP:GL:GQ 0/1:71,13:68:-26.06,-20.50,-237.08:55.60 +chr1 815639 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=2;HaplotypeScore=38.60;MQ=52.07;MQ0=2;OQ=197.56;QD=2.27;SB=80.29 GT:AD:DP:GL:GQ 0/1:75,12:73:-45.07,-22.03,-247.37:99 +chr1 815714 rs4549984 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=282;Dels=0.00;HRun=0;HaplotypeScore=45.55;MQ=35.23;MQ0=6;OQ=3065.05;QD=10.87;SB=-490.50 GT:AD:DP:GL:GQ 0/1:131,151:198:-369.43,-59.64,-380.00:99 +chr1 815740 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=388;Dels=0.00;HRun=1;HaplotypeScore=91.19;MQ=33.31;MQ0=8;OQ=203.81;QD=0.53;SB=46.30 GT:AD:DP:GL:GQ 0/1:351,35:273:-111.13,-87.46,-857.56:99 +chr1 815759 . A T 981.66 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=425;Dels=0.00;HRun=0;HaplotypeScore=319.89;MQ=33.30;MQ0=16;QD=2.31;SB=-282.31 GT:AD:DP:GL:GQ 0/1:309,70:292:-258.47,-157.02,-944.68:99 +chr1 815760 . C A 1978.15 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=424;Dels=0.00;HRun=3;HaplotypeScore=319.89;MQ=33.21;MQ0=16;QD=4.67;SB=-361.60 GT:AD:DP:GL:GQ 0/1:311,113:290:-288.45,-87.35,-755.50:99 +chr1 815761 . C A 1757.71 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=422;Dels=0.00;HRun=1;HaplotypeScore=319.47;MQ=33.03;MQ0=16;QD=4.17;SB=-393.48 GT:AD:DP:GL:GQ 0/1:295,112:286:-275.36,-96.30,-763.46:99 +chr1 815762 . A G 1602.96 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=423;Dels=0.00;HRun=0;HaplotypeScore=319.57;MQ=33.04;MQ0=16;QD=3.79;SB=-325.52 GT:AD:DP:GL:GQ 0/1:273,113:288:-310.25,-146.67,-857.16:99 +chr1 815765 . G A 2936.95 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=427;Dels=0.00;HRun=3;HaplotypeScore=320.41;MQ=33.17;MQ0=17;QD=6.88;SB=-566.97 GT:AD:DP:GL:GQ 0/1:277,150:291:-384.73,-87.75,-614.82:99 +chr1 815777 . C T 24.19 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=434;Dels=0.00;HRun=0;HaplotypeScore=73.54;MQ=32.97;MQ0=17;QD=0.06;SB=99.73 GT:AD:DP:GL:GQ 0/1:393,41:292:-93.65,-87.95,-958.63:57.01 +chr1 815780 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=432;Dels=0.00;HRun=1;HaplotypeScore=75.21;MQ=32.79;MQ0=17;OQ=115.11;QD=0.27;SB=79.01 GT:AD:DP:GL:GQ 0/1:399,33:289:-101.84,-87.05,-1076.94:99 +chr1 815810 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=3;HaplotypeScore=40.23;MQ=35.68;MQ0=17;OQ=207.08;QD=0.78;SB=-57.21 GT:AD:DP:GL:GQ 0/1:229,35:180:-78.22,-54.22,-636.76:99 +chr1 815845 . C G 0.13 PASS AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=5.72;MQ=49.45;MQ0=9;OQ=487.79;QD=4.69;SB=-262.79 GT:AD:DP:GL:GQ 0/1:68,36:85:-77.68,-25.61,-285.79:99 +chr1 815857 . T A 21.33 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=5.01;MQ=54.04;MQ0=5;QD=0.23;SB=16.48 GT:AD:DP:GL:GQ 0/1:77,14:82:-30.11,-24.70,-281.02:54.14 +chr1 815931 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=2;HaplotypeScore=25.80;MQ=41.76;MQ0=34;OQ=413.34;QD=2.70;SB=-90.95 GT:AD:DP:GL:GQ 0/1:89,64:100:-74.74,-30.13,-291.31:99 +chr1 815936 . T G 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=41.51;MQ0=35;OQ=307.08;QD=1.93;SB=-87.61 GT:AD:DP:GL:GQ 0/1:91,68:101:-64.41,-30.42,-308.26:99 +chr1 815949 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=1;HaplotypeScore=25.06;MQ=39.71;MQ0=34;OQ=456.33;QD=2.82;SB=-102.31 GT:AD:DP:GL:GQ 0/1:134,28:100:-79.04,-30.12,-319.08:99 +chr1 815979 . A G 1177.05 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=1;HaplotypeScore=140.50;MQ=42.13;MQ0=3;QD=7.18;SB=-203.16 GT:AD:DP:GL:GQ 0/1:88,76:129:-159.86,-38.87,-326.00:99 +chr1 815980 . T C 32.10 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=144.97;MQ=42.03;MQ0=3;QD=0.19;SB=-40.00 GT:AD:DP:GL:GQ 0/1:145,23:122:-43.25,-36.76,-439.68:64.94 +chr1 815986 . A G 296.02 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=2;HaplotypeScore=92.41;MQ=40.86;MQ0=3;QD=1.64;SB=-47.33 GT:AD:DP:GL:GQ 0/1:153,28:121:-69.34,-36.45,-404.50:99 +chr1 816000 . G A 125.95 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=173;Dels=0.00;HRun=1;HaplotypeScore=82.29;MQ=39.25;MQ0=3;QD=0.73;SB=53.66 GT:AD:DP:GL:GQ 0/1:159,14:109:-48.71,-32.83,-348.18:99 +chr1 816001 . G A 216.96 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=171;Dels=0.00;HRun=0;HaplotypeScore=91.06;MQ=39.38;MQ0=3;QD=1.27;SB=50.65 GT:AD:DP:GL:GQ 0/1:127,38:117:-81.21,-56.23,-367.68:99 +chr1 816004 . G A 219.09 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=92.89;MQ=39.19;MQ0=0;QD=1.27;SB=56.64 GT:AD:DP:GL:GQ 0/1:125,47:119:-61.04,-35.85,-362.44:99 +chr1 816007 . G A 88.79 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=173;Dels=0.02;HRun=1;HaplotypeScore=88.30;MQ=38.80;MQ0=0;QD=0.51;SB=95.33 GT:AD:DP:GL:GQ 0/1:131,39:117:-47.40,-35.24,-375.36:99 +chr1 816018 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=1;HaplotypeScore=112.53;MQ=36.89;MQ0=0;OQ=274.62;QD=1.40;SB=-52.14 GT:AD:DP:GL:GQ 0/1:173,23:109:-63.59,-32.85,-401.41:99 +chr1 816026 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=509.63;MQ=37.96;MQ0=0;OQ=1247.86;QD=6.86;SB=56.18 GT:AD:DP:GL:GQ 0/1:108,73:128:-166.63,-38.56,-316.49:99 +chr1 816043 . A G 1178.79 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=281;Dels=0.00;HRun=0;HaplotypeScore=614.45;MQ=34.94;MQ0=1;QD=4.19;SB=56.21 GT:AD:DP:GL:GQ 0/1:198,83:191:-178.71,-57.55,-539.60:99 +chr1 816057 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=287;Dels=0.00;HRun=0;HaplotypeScore=198.13;MQ=34.34;MQ0=4;OQ=1603.81;QD=5.59;SB=62.23 GT:AD:DP:GL:GQ 0/1:144,109:196:-293.22,-129.56,-512.85:99 +chr1 816072 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=0;HaplotypeScore=33.06;MQ=33.48;MQ0=15;OQ=115.32;QD=0.37;SB=71.18 GT:AD:DP:GL:GQ 0/1:282,15:160:-71.44,-56.63,-531.53:99 +chr1 816077 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=299;Dels=0.00;HRun=0;HaplotypeScore=55.33;MQ=33.49;MQ0=15;OQ=4794.59;QD=16.04;SB=68.22 GT:AD:DP:GL:GQ 0/1:81,218:173:-478.46,-52.11,-201.39:99 +chr1 816088 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=278;Dels=0.00;HRun=1;HaplotypeScore=51.57;MQ=34.30;MQ0=16;OQ=4463.53;QD=16.06;SB=62.23 GT:AD:DP:GL:GQ 0/1:58,220:169:-445.35,-50.90,-214.04:99 +chr1 816103 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=237;Dels=0.00;HRun=0;HaplotypeScore=38.99;MQ=36.26;MQ0=16;OQ=1889.47;QD=7.97;SB=68.20 GT:AD:DP:GL:GQ 0/1:61,152:117:-237.42,-45.19,-199.18:99 +chr1 816115 . C T 1441.66 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=202;Dels=0.00;HRun=0;HaplotypeScore=145.73;MQ=37.27;MQ0=15;QD=7.14;SB=68.18 GT:AD:DP:GL:GQ 0/1:132,70:112:-181.22,-33.77,-214.53:99 +chr1 816118 . A T 125.43 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=0;HaplotypeScore=164.12;MQ=38.34;MQ0=15;QD=0.66;SB=77.28 GT:AD:DP:GL:GQ 0/1:145,37:109:-58.41,-42.58,-369.08:99 +chr1 816122 . G C 132.11 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=159.96;MQ=38.91;MQ0=15;QD=0.73;SB=80.30 GT:AD:DP:GL:GQ 0/1:155,27:96:-45.43,-28.94,-364.83:99 +chr1 816123 . A G 766.79 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=157.96;MQ=38.91;MQ0=14;QD=4.28;SB=80.30 GT:AD:DP:GL:GQ 0/1:86,89:106:-121.93,-41.97,-306.67:99 +chr1 816140 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=2;HaplotypeScore=35.96;MQ=45.77;MQ0=9;OQ=496.37;QD=3.82;SB=92.32 GT:AD:DP:GL:GQ 0/1:81,49:95:-81.53,-28.61,-273.48:99 +chr1 817130 rs2879698 C T 1.75 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=7.86;MQ=52.69;MQ0=4;OQ=2390.21;QD=32.30;SB=-1172.34 GT:AD:DP:GL:GQ 1/1:5,69:61:-242.62,-18.38,-0.02:99 +chr1 817140 rs4246498 T C 134.82 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=52.12;MQ0=4;OQ=2043.04;QD=29.61;SB=-1026.82 GT:AD:DP:GL:GQ 1/1:0,69:59:-207.91,-17.78,-0.03:99 +chr1 817186 rs4970386 C T 31.13 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.56;MQ=51.33;MQ0=3;OQ=2194.13;QD=35.39;SB=-970.28 GT:AD:DP:GL:GQ 1/1:3,59:55:-223.01,-16.57,-0.01:99 +chr1 819196 rs9778019 G A 567.53 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.32;MQ0=0;OQ=1941.14;QD=39.62;SB=-968.30 GT:AD:DP:GL:GQ 1/1:0,49:49:-197.71,-14.76,-0.01:99 +chr1 819500 rs4437820 C T 68.03 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=47.44;MQ0=2;OQ=2599.35;QD=37.13;SB=-1006.03 GT:AD:DP:GL:GQ 1/1:0,70:64:-263.53,-19.28,-0.01:99 +chr1 819787 . G A 25.28 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=51.75;MQ0=1;QD=0.29;SB=104.31 GT:AD:DP:GL:GQ 0/1:80,8:75:-28.42,-22.61,-220.79:58.10 +chr1 820044 rs28444699 A G 2.65 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=5.59;MQ=55.18;MQ0=2;OQ=1994.05;QD=28.49;SB=-1022.00 GT:AD:DP:GL:GQ 1/1:9,61:60:-210.82,-18.07,-7.83:99 +chr1 820670 rs6422669 G C 266.94 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=1;OQ=1743.26;QD=40.54;SB=-467.22 GT:AD:DP:GL:GQ 1/1:1,42:42:-177.93,-12.66,-0.02:99 +chr1 821139 rs4024798 C T 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=239;Dels=0.00;HRun=1;HaplotypeScore=9.98;MQ=39.26;MQ0=24;OQ=434.25;QD=1.82;SB=23.91 GT:AD:DP:GL:GQ 0/1:189,50:167:-97.03,-50.32,-487.12:99 +chr1 821171 rs477080 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=308;Dels=0.00;HRun=0;HaplotypeScore=33.10;MQ=34.56;MQ0=43;OQ=282.37;QD=0.92;SB=137.47 GT:AD:DP:GL:GQ 0/1:233,75:190:-88.75,-57.23,-688.44:99 +chr1 821352 rs4970385 C T 0.69 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=12.93;MQ=49.51;MQ0=5;OQ=2978.23;QD=32.02;SB=-1308.26 GT:AD:DP:GL:GQ 1/1:14,79:78:-308.32,-23.50,-6.91:99 +chr1 821772 rs9697642 C T 1.09 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=6.48;MQ=53.07;MQ0=1;OQ=2639.96;QD=38.26;SB=-935.74 GT:AD:DP:GL:GQ 1/1:1,68:65:-267.59,-19.58,-0.01:99 +chr1 821923 rs9697378 G A 628.11 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.85;MQ0=2;OQ=2615.06;QD=34.87;SB=-1164.40 GT:AD:DP:GL:GQ 1/1:9,66:67:-268.90,-20.18,-3.81:99 +chr1 821929 rs9697380 G C 204.81 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=46.00;MQ0=2;OQ=2952.34;QD=37.85;SB=-1375.91 GT:AD:DP:GL:GQ 1/1:9,69:70:-303.53,-21.09,-4.71:99 +chr1 821975 rs9697725 T C 60.31 PASS AC=2;AF=1.00;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=42.31;MQ0=7;OQ=2446.13;QD=25.75;SB=-880.44 GT:AD:DP:GL:GQ 1/1:20,75:74:-256.35,-22.29,-8.15:99 +chr1 822041 rs13302934 A G 54.22 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=37.41;MQ0=11;OQ=2291.03;QD=26.64;SB=-1047.92 GT:AD:DP:GL:GQ 1/1:17,69:67:-236.77,-20.18,-4.08:99 +chr1 822181 rs4500250 C A 165.39 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.49;MQ0=0;OQ=2287.58;QD=33.15;SB=-1055.56 GT:AD:DP:GL:GQ 1/1:2,67:63:-232.36,-18.97,-0.02:99 +chr1 822261 rs4553118 T C 105.61 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=53.16;MQ0=0;OQ=2074.16;QD=32.41;SB=-1031.91 GT:AD:DP:GL:GQ 1/1:0,64:58:-211.02,-17.47,-0.02:99 +chr1 827077 . G C 11.08 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1103.43;QD=20.06;SB=-557.74 GT:AD:DP:GL:GQ 0/1:23,32:50:-128.70,-15.07,-86.51:99 +chr1 832688 rs7519340 A G 206.11 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.92;MQ0=0;OQ=2256.38;QD=34.19;SB=-897.99 GT:AD:DP:GL:GQ 1/1:0,66:64:-229.25,-19.28,-0.02:99 +chr1 833268 rs11516185 A G 180.02 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=58.03;MQ0=0;OQ=720.81;QD=12.65;SB=-270.98 GT:AD:DP:GL:GQ 0/1:24,33:50:-90.45,-15.09,-82.68:99 +chr1 834163 rs61769713 C G 7.44 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=34.66;MQ0=0;OQ=386.18;QD=32.18;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,12:11:-42.22,-3.32,-0.01:33.11 +chr1 834187 rs61769714 G A 6.81 PASS AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=34.17;MQ0=0;OQ=258.44;QD=25.84;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:8:-29.44,-2.42,-0.01:24.06 +chr1 834206 rs61769715 A G 21 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=32.88;MQ0=0;OQ=98.47;QD=14.07;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:4:-13.38,-1.21,-0.00:12.03 +chr1 834961 . T G 0.56 PASS AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=16.23;MQ0=3;OQ=70.14;QD=6.38;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,10:3:-10.50,-0.90,-0.00:9.03 +chr1 835146 rs7366404 G T 7.38 PASS AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=37.00;MQ0=0;OQ=260.28;QD=32.54;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:8:-29.61,-2.41,-0.00:24.08 +chr1 836201 rs4970334 A G 56.75 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=57.95;MQ0=0;OQ=1280.53;QD=26.68;SB=-522.83 GT:AD:DP:GL:GQ 1/1:0,47:43:-131.69,-12.98,-0.05:99 +chr1 836352 rs4970333 T C 54.39 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=58.58;MQ0=0;OQ=1607.31;QD=32.80;SB=-789.15 GT:AD:DP:GL:GQ 1/1:0,49:46:-164.33,-13.86,-0.02:99 +chr1 837113 rs7416129 G A 502.58 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=3431.98;QD=39.91;SB=-1125.99 GT:AD:DP:GL:GQ 1/1:0,85:84:-342.20,-25.31,-0.02:99 +chr1 839861 rs13303222 A G 170.66 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.09;MQ0=0;OQ=2748.15;QD=33.51;SB=-1203.79 GT:AD:DP:GL:GQ 1/1:0,81:78:-278.43,-23.50,-0.03:99 +chr1 840081 rs6664536 T A 113.50 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=58.64;MQ0=0;OQ=1837.58;QD=35.34;SB=-814.88 GT:AD:DP:GL:GQ 1/1:0,52:50:-187.36,-15.06,-0.02:99 +chr1 840234 rs6679046 G T 614.25 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.48;MQ0=0;OQ=2550.23;QD=33.56;SB=-1032.51 GT:AD:DP:GL:GQ 1/1:0,76:73:-258.64,-22.00,-0.04:99 +chr1 840643 rs6657440 C T 589.62 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2334.22;QD=36.47;SB=-836.99 GT:AD:DP:GL:GQ 1/1:0,64:61:-237.03,-18.38,-0.02:99 +chr1 841253 . G T 87.70 PASS AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=59.70;MQ0=0;OQ=1174.44;QD=15.25;SB=-547.82 GT:AD:DP:GL:GQ 0/1:37,40:75:-143.32,-22.59,-125.03:99 +chr1 841362 rs4970465 A G 15.40 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=2.07;MQ=60.00;MQ0=0;OQ=1972.18;QD=30.34;SB=-856.55 GT:AD:DP:GL:GQ 1/1:0,65:61:-200.85,-18.39,-0.05:99 +chr1 841500 . G C 11.73 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=3;HaplotypeScore=11.47;MQ=56.60;MQ0=0;QD=0.26;SB=59.23 GT:AD:DP:GL:GQ 0/1:36,10:33:-14.38,-9.96,-126.72:44.27 +chr1 841620 rs62677860 A G 51.10 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=1201.63;QD=27.31;SB=-317.48 GT:AD:DP:GL:GQ 1/1:0,43:38:-123.78,-11.46,-0.03:99 +chr1 841900 rs4970463 G A 437.16 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=1176.31;QD=36.76;SB=-508.18 GT:AD:DP:GL:GQ 1/1:0,32:31:-121.23,-9.34,-0.01:93.29 +chr1 841926 rs28436996 G A 99.38 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=58.05;MQ0=0;OQ=1247.42;QD=34.65;SB=-580.28 GT:AD:DP:GL:GQ 1/1:0,35:33:-128.34,-9.94,-0.01:99 +chr1 841996 rs7518702 C T 517.92 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1573.23;QD=37.46;SB=-692.34 GT:AD:DP:GL:GQ 1/1:0,41:40:-160.92,-12.05,-0.01:99 +chr1 842738 rs13303369 C T 76.16 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.63;MQ=58.47;MQ0=0;OQ=2145.17;QD=36.99;SB=-908.72 GT:AD:DP:GL:GQ 1/1:0,58:57:-218.13,-17.18,-0.03:99 +chr1 842827 rs4970461 T G 8.55 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.36;MQ=59.03;MQ0=0;OQ=1414.13;QD=29.46;SB=-684.25 GT:AD:DP:GL:GQ 1/1:0,48:47:-145.05,-14.17,-0.05:99 +chr1 843817 rs1806509 C A 190.21 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.61;MQ0=0;OQ=1993.99;QD=33.80;SB=-878.64 GT:AD:DP:GL:GQ 1/1:0,59:57:-203.01,-17.17,-0.02:99 +chr1 844640 rs13303019 A G 51.99 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.20;MQ0=0;OQ=644.86;QD=22.24;SB=-345.42 GT:AD:DP:GL:GQ 1/1:0,29:23:-68.11,-6.95,-0.04:69.10 +chr1 844841 rs13303057 A C 5.18 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=58.36;MQ0=0;OQ=1059.33;QD=26.48;SB=-412.87 GT:AD:DP:GL:GQ 1/1:0,40:35:-109.55,-10.55,-0.04:99 +chr1 844938 rs6673914 C G 24.53 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.27;MQ0=0;OQ=1048.92;QD=37.46;SB=-371.18 GT:AD:DP:GL:GQ 1/1:0,28:26:-108.49,-7.84,-0.02:78.26 +chr1 847591 rs6689107 T G 181.31 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.19;MQ0=0;OQ=1848.72;QD=32.43;SB=-803.49 GT:AD:DP:GL:GQ 1/1:0,57:54:-188.48,-16.27,-0.02:99 +chr1 848664 rs7418179 A G 160.64 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=1692.05;QD=34.53;SB=-783.00 GT:AD:DP:GL:GQ 1/1:0,49:48:-172.81,-14.46,-0.02:99 +chr1 850279 rs61464428 G A 12.90 PASS AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.66;MQ0=0;OQ=337.99;QD=33.80;SB=-134.01 GT:AD:DP:GL:GQ 1/1:0,10:10:-37.39,-3.02,-0.01:30.09 +chr1 850324 rs57465118 G A 8.27 PASS AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=54.65;MQ0=0;OQ=218.19;QD=24.24;SB=-48.67 GT:AD:DP:GL:GQ 1/1:0,9:7:-25.40,-2.11,-0.00:21.06 +chr1 850384 rs57924093 C A 117.02 PASS AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.88;MQ0=0;OQ=151.15;QD=25.19;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:5:-18.67,-1.51,-0.00:15.05 +chr1 850551 rs60837925 G A 175.87 PASS AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=188.60;QD=31.43;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,6:6:-22.43,-1.81,-0.00:18.06 +chr1 850660 . G T 32.80 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=65.19;MQ0=0;QD=16.40;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-6.69,-0.60,-0.00:6.02 +chr1 850717 rs57816555 T C 168.04 PASS AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.96;MQ0=0;OQ=139.82;QD=27.96;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:5:-17.54,-1.51,-0.00:15.04 +chr1 850871 rs28521172 G C 136.83 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=409.27;QD=34.11;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,12:11:-44.52,-3.32,-0.00:33.11 +chr1 851493 rs2879816 G A 181.32 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=58.51;MQ0=0;OQ=1761.97;QD=35.24;SB=-837.99 GT:AD:DP:GL:GQ 1/1:0,50:46:-179.80,-13.86,-0.02:99 +chr1 851671 rs13302982 A G 540.86 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.19;MQ0=0;OQ=1746.20;QD=30.64;SB=-800.68 GT:AD:DP:GL:GQ 1/1:0,57:56:-178.25,-16.89,-0.05:99 +chr1 851956 rs13303291 T C 0.63 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=5;HaplotypeScore=0.79;MQ=59.54;MQ0=0;OQ=1647.69;QD=32.95;SB=-763.57 GT:AD:DP:GL:GQ 1/1:0,50:48:-168.38,-14.46,-0.02:99 +chr1 851987 rs13303101 A G 75.91 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=58.42;MQ0=0;OQ=1718.71;QD=29.13;SB=-814.55 GT:AD:DP:GL:GQ 1/1:0,59:55:-175.51,-16.59,-0.06:99 +chr1 852246 rs6680268 C T 87.18 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.89;MQ0=0;OQ=1535.86;QD=36.57;SB=-649.38 GT:AD:DP:GL:GQ 1/1:0,42:40:-157.19,-12.05,-0.02:99 +chr1 852252 rs6693546 A G 8.74 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=57.97;MQ0=0;OQ=1460.23;QD=31.74;SB=-743.12 GT:AD:DP:GL:GQ 1/1:0,45:42:-149.63,-12.66,-0.02:99 +chr1 852729 rs3892970 C T 119.55 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1397.63;QD=34.09;SB=-551.29 GT:AD:DP:GL:GQ 1/1:0,41:38:-143.37,-11.46,-0.02:99 +chr1 852987 rs4040604 G T 33.76 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=59.28;MQ0=0;OQ=1900.46;QD=32.77;SB=-758.90 GT:AD:DP:GL:GQ 1/1:0,58:55:-193.66,-16.57,-0.02:99 +chr1 853374 rs28626846 T C 176.60 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=56.72;MQ0=0;OQ=383.16;QD=9.12;SB=-198.44 GT:AD:DP:GL:GQ 0/1:24,18:39:-53.37,-11.77,-80.00:99 +chr1 853419 rs7410998 G A 181.10 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=49.05;MQ0=1;OQ=787.22;QD=31.49;SB=-167.67 GT:AD:DP:GL:GQ 1/1:1,24:21:-82.31,-6.33,-0.01:63.20 +chr1 853425 rs7417972 A C 3.94 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=51.24;MQ0=1;OQ=853.26;QD=25.86;SB=-413.26 GT:AD:DP:GL:GQ 1/1:1,32:29:-88.94,-8.74,-0.03:87.12 +chr1 853552 rs7417994 A G 58.67 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=47.89;MQ0=0;OQ=1045.12;QD=27.50;SB=-347.41 GT:AD:DP:GL:GQ 1/1:0,38:34:-108.13,-10.26,-0.03:99 +chr1 854589 rs2340590 T A 319.49 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.35;MQ0=0;OQ=1082.41;QD=34.92;SB=-267.73 GT:AD:DP:GL:GQ 1/1:0,31:30:-111.84,-9.04,-0.02:90.27 +chr1 854618 rs2340589 A G 2.04 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1104.04;QD=28.31;SB=-284.44 GT:AD:DP:GL:GQ 1/1:0,39:37:-114.04,-11.17,-0.05:99 +chr1 854620 rs2340588 G A 306.13 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1407.34;QD=36.09;SB=-288.88 GT:AD:DP:GL:GQ 1/1:0,39:36:-144.33,-10.85,-0.01:99 +chr1 854801 . G A 27.13 PASS AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.52;MQ0=0;OQ=1814.99;QD=37.81;SB=-848.99 GT:AD:DP:GL:GQ 1/1:0,48:46:-185.10,-13.86,-0.01:99 +chr1 856182 rs9988021 G A 414.08 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=1807.60;QD=37.66;SB=-511.65 GT:AD:DP:GL:GQ 1/1:0,48:47:-184.36,-14.16,-0.02:99 +chr1 856756 rs2880024 T C 439.96 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.61;MQ0=0;OQ=1661.89;QD=33.92;SB=-660.32 GT:AD:DP:GL:GQ 1/1:0,49:47:-169.79,-14.16,-0.01:99 +chr1 856783 rs2341361 A G 391.16 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=1555.14;QD=34.56;SB=-535.20 GT:AD:DP:GL:GQ 1/1:0,45:44:-159.12,-13.26,-0.02:99 +chr1 857447 rs2341360 A T 453.14 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1951.43;QD=37.53;SB=-755.79 GT:AD:DP:GL:GQ 1/1:0,51:51:-198.74,-15.36,-0.01:99 +chr1 858192 rs2341359 A C 117.47 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=55.20;MQ0=0;OQ=1194.83;QD=30.64;SB=-603.64 GT:AD:DP:GL:GQ 1/1:0,39:36:-123.08,-10.85,-0.02:99 +chr1 858267 rs13302914 C T 413.34 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.75;MQ0=0;OQ=1181.60;QD=33.76;SB=-589.79 GT:AD:DP:GL:GQ 1/1:0,35:32:-121.76,-9.65,-0.02:96.30 +chr1 858654 rs13303003 C T 431.96 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=892.14;QD=35.69;SB=-459.35 GT:AD:DP:GL:GQ 1/1:1,24:23:-92.80,-6.93,-0.01:69.23 +chr1 858754 rs13303066 A G 117.57 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.96;MQ0=0;OQ=1127.68;QD=32.22;SB=-537.22 GT:AD:DP:GL:GQ 1/1:0,35:32:-116.36,-9.64,-0.01:96.29 +chr1 858844 rs13303037 C T 239.71 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.36;MQ0=0;OQ=920.18;QD=35.39;SB=-178.71 GT:AD:DP:GL:GQ 1/1:0,26:25:-95.62,-7.54,-0.02:75.23 +chr1 859186 rs13303207 T C 5.25 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=1.75;MQ=49.46;MQ0=0;OQ=860.62;QD=31.87;SB=-321.13 GT:AD:DP:GL:GQ 1/1:0,27:25:-89.66,-7.53,-0.01:75.22 +chr1 859220 . G T 15.33 LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=44.47;MQ0=0;QD=0.73;SB=-4.00 GT:AD:DP:GL:GQ 0/1:18,3:16:-9.63,-4.82,-45.13:48.04 +chr1 859232 rs13303328 G T 26.22 PASS AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=42.12;MQ0=0;OQ=238.10;QD=15.87;SB=-41.94 GT:AD:DP:GL:GQ 0/1:4,11:12:-30.71,-3.62,-8.58:49.58 +chr1 859236 rs13303330 G C 2.57 PASS AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=42.12;MQ0=0;OQ=289.97;QD=19.33;SB=-45.46 GT:AD:DP:GL:GQ 0/1:4,11:11:-35.60,-3.32,-10.54:72.26 +chr1 859264 rs13303353 G C 17.54 PASS AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=37.87;MQ0=1;OQ=164.66;QD=13.72;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,7:8:-22.16,-2.41,-12.54:99 +chr1 859992 . G C 97.38 PASS AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.96;MQ0=0;OQ=93.52;QD=10.39;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:3:-12.84,-0.90,-0.00:9.03 +chr1 860032 . G T 37.54 PASS AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.43;MQ0=0;OQ=70.96;QD=5.46;SB=-10.00 GT:AD:DP:GL:GQ 1/1:8,5:3:-10.58,-0.90,-0.00:9.03 +chr1 860180 rs28451560 G A 12.62 PASS AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.95;MQ0=0;OQ=73.11;QD=18.28;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,3:3:-10.80,-0.90,-0.00:9.03 +chr1 860766 rs13303094 T C 16.65 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.17;MQ0=0;OQ=826.94;QD=29.53;SB=-125.69 GT:AD:DP:GL:GQ 1/1:0,28:25:-86.29,-7.54,-0.02:75.20 +chr1 861197 rs4072383 G T 400.06 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.63;MQ0=0;OQ=731.30;QD=30.47;SB=-355.85 GT:AD:DP:GL:GQ 1/1:0,24:22:-76.73,-6.63,-0.01:66.18 +chr1 861546 rs4504834 G A 1.38 PASS AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.70;MQ0=0;OQ=257.15;QD=25.71;SB=-133.67 GT:AD:DP:GL:GQ 1/1:0,10:8:-29.30,-2.41,-0.01:24.07 +chr1 863421 rs1110052 G T 380.03 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1308.42;QD=32.71;SB=-530.08 GT:AD:DP:GL:GQ 1/1:0,40:39:-134.45,-11.76,-0.03:99 +chr1 865499 . C T 29.46 LowQual AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;QD=4.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,2:5:-7.74,-1.51,-8.99:62.30 +chr1 865506 rs7411115 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=5;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=112.00;QD=22.40;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,4:5:-15.99,-1.51,-3.39:18.84 +chr1 866063 . G C 0.28 PASS AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.80;MQ=60.00;MQ0=0;OQ=689.42;QD=21.54;SB=-257.43 GT:AD:DP:GL:GQ 0/1:12,20:31:-81.58,-9.35,-46.59:99 +chr1 866362 rs4372192 A G 0.01 FDRtranche2.00to10.00 AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=6;HaplotypeScore=0.89;MQ=56.86;MQ0=0;OQ=933.15;QD=29.16;SB=-432.49 GT:AD:DP:GL:GQ 1/1:0,31:29:-96.92,-8.74,-0.02:87.21 +chr1 867578 rs6605066 C G 7.06 PASS AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=93.52;QD=31.17;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:3:-12.84,-0.90,-0.00:9.03 +chr1 867694 rs6672356 T C 3.72 PASS AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=52.96;QD=17.65;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:3:-8.79,-0.91,-0.01:9.01 +chr1 868792 . G C 15.78 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=42;Dels=0.02;HRun=2;HaplotypeScore=22.45;MQ=51.57;MQ0=2;QD=0.38;SB=59.22 GT:AD:DP:GL:GQ 0/1:36,4:34:-14.81,-9.96,-119.24:48.50 +chr1 869539 rs6605067 G A 19.27 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=0.58;MQ=56.16;MQ0=0;OQ=2221.47;QD=39.67;SB=-1054.70 GT:AD:DP:GL:GQ 1/1:0,56:55:-225.74,-16.57,-0.01:99 +chr1 869550 rs2839 T C 133.50 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=56.64;MQ0=0;OQ=2001.68;QD=34.51;SB=-1024.77 GT:AD:DP:GL:GQ 1/1:0,58:57:-203.78,-17.17,-0.02:99 +chr1 870101 rs3748592 A G 495.56 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.39;MQ0=0;OQ=1890.23;QD=34.37;SB=-862.36 GT:AD:DP:GL:GQ 1/1:0,55:54:-192.63,-16.27,-0.02:99 +chr1 871490 rs2272757 G A 6.94 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.19;MQ=57.04;MQ0=0;OQ=1394.54;QD=37.69;SB=-510.64 GT:AD:DP:GL:GQ 1/1:0,37:36:-143.05,-10.85,-0.01:99 +chr1 872666 rs2340582 A G 42.12 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.34;MQ=59.14;MQ0=0;OQ=1872.55;QD=34.68;SB=-917.03 GT:AD:DP:GL:GQ 1/1:0,54:54:-190.86,-16.27,-0.02:99 +chr1 873488 rs4970378 A G 248.98 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=1449.35;QD=35.35;SB=-732.23 GT:AD:DP:GL:GQ 1/1:0,41:41:-148.53,-12.35,-0.01:99 +chr1 873762 . T G 3.38 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=3.82;MQ=57.58;MQ0=0;OQ=623.05;QD=12.98;SB=-319.82 GT:AD:DP:GL:GQ 0/1:24,24:47:-79.75,-14.16,-84.17:99 +chr1 873892 . A C 58.62 SnpCluster AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=53.03;MQ0=0;QD=2.09;SB=-41.91 GT:AD:DP:GL:GQ 0/1:23,5:28:-17.58,-8.43,-82.84:91.46 +chr1 873894 . C T 82.90 SnpCluster AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.03;MQ0=0;QD=2.96;SB=-56.23 GT:AD:DP:GL:GQ 0/1:23,5:28:-20.01,-8.43,-84.10:99 +chr1 873895 . C T 48.24 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.20;MQ0=0;QD=1.56;SB=-25.58 GT:AD:DP:GL:GQ 0/1:26,5:28:-16.54,-8.43,-88.26:81.07 +chr1 873901 . T G 115.57 SnpCluster AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.52;MQ0=0;QD=3.50;SB=-81.81 GT:AD:DP:GL:GQ 0/1:26,7:33:-24.78,-9.94,-99.02:99 +chr1 873954 rs7522415 C G 8.33 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.52;MQ=43.40;MQ0=0;OQ=1100.42;QD=22.93;SB=-415.98 GT:AD:DP:GL:GQ 0/1:16,32:45:-126.89,-13.56,-66.90:99 +chr1 873964 rs4970455 A C 1.05 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=3;HaplotypeScore=2.44;MQ=43.46;MQ0=0;OQ=358.55;QD=6.77;SB=-63.88 GT:AD:DP:GL:GQ 0/1:38,15:50:-54.21,-15.07,-122.51:99 +chr1 874630 . G A 13.69 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=47.61;MQ0=0;OQ=1000.31;QD=21.75;SB=-485.51 GT:AD:DP:GL:GQ 0/1:17,29:46:-117.17,-13.86,-57.54:99 +chr1 874678 rs4246503 A G 158.46 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=55.11;MQ0=0;OQ=1771.59;QD=30.03;SB=-814.69 GT:AD:DP:GL:GQ 1/1:0,59:55:-180.79,-16.58,-0.04:99 +chr1 875539 rs4970377 C A 535.35 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.40;MQ0=0;OQ=2636.42;QD=36.12;SB=-1177.36 GT:AD:DP:GL:GQ 1/1:1,72:71:-267.24,-21.38,-0.02:99 +chr1 875552 rs4970452 G A 0.79 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=56.01;MQ0=0;OQ=2730.82;QD=37.93;SB=-1364.34 GT:AD:DP:GL:GQ 1/1:1,71:70:-276.69,-21.09,-0.03:99 +chr1 875562 rs4970376 A G 1.74 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=9.96;MQ=55.41;MQ0=0;OQ=2063.84;QD=30.35;SB=-1045.24 GT:AD:DP:GL:GQ 1/1:1,67:64:-210.02,-19.30,-0.05:99 +chr1 875869 rs4970375 T C 458.99 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.16;MQ0=0;OQ=1904.11;QD=35.26;SB=-492.54 GT:AD:DP:GL:GQ 1/1:0,54:53:-194.01,-15.96,-0.01:99 +chr1 876651 rs10465242 G A 37.22 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=58.78;MQ0=0;OQ=1853.33;QD=37.07;SB=-743.49 GT:AD:DP:GL:GQ 1/1:0,50:47:-188.93,-14.16,-0.01:99 +chr1 876680 rs10465241 C T 139.09 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1420.84;QD=37.39;SB=-598.99 GT:AD:DP:GL:GQ 1/1:0,38:38:-145.68,-11.45,-0.02:99 +chr1 877423 rs3748595 A C 60.20 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.73;MQ0=0;OQ=1913.10;QD=31.88;SB=-946.06 GT:AD:DP:GL:GQ 1/1:0,60:56:-194.92,-16.87,-0.02:99 +chr1 877664 rs3828047 A G 27.25 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.38;MQ0=0;OQ=1254.26;QD=33.90;SB=-513.49 GT:AD:DP:GL:GQ 1/1:0,37:36:-129.02,-10.84,-0.01:99 +chr1 878502 rs3748596 T C 69.46 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=55.26;MQ0=0;OQ=1390.46;QD=33.11;SB=-577.30 GT:AD:DP:GL:GQ 1/1:0,42:41:-142.65,-12.35,-0.02:99 +chr1 878522 rs3748597 T C 420.43 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.43;MQ0=0;OQ=1101.61;QD=31.47;SB=-433.56 GT:AD:DP:GL:GQ 1/1:0,35:33:-113.76,-9.94,-0.02:99 +chr1 879021 rs56262069 G C 15.32 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1649.51;QD=39.27;SB=-490.55 GT:AD:DP:GL:GQ 1/1:0,42:39:-168.56,-11.76,-0.02:99 +chr1 879022 rs13302945 A C 102.46 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1299.59;QD=30.94;SB=-461.34 GT:AD:DP:GL:GQ 1/1:0,42:39:-133.56,-11.75,-0.02:99 +chr1 879501 rs13303206 G C 38.13 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.78;MQ0=0;OQ=1536.75;QD=40.44;SB=-636.90 GT:AD:DP:GL:GQ 1/1:0,38:37:-157.27,-11.15,-0.01:99 +chr1 879576 rs13303051 C A 192.55 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.48;MQ=59.05;MQ0=0;OQ=1663.22;QD=33.94;SB=-850.81 GT:AD:DP:GL:GQ 1/1:1,48:46:-169.92,-13.85,-0.01:99 +chr1 880884 rs13302957 G A 138.98 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=59.32;MQ0=0;OQ=2228.59;QD=40.52;SB=-1097.37 GT:AD:DP:GL:GQ 1/1:0,55:55:-226.45,-16.57,-0.01:99 +chr1 880922 rs13303065 C T 237.80 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2022.89;QD=39.66;SB=-914.68 GT:AD:DP:GL:GQ 1/1:0,51:51:-205.89,-15.36,-0.01:99 +chr1 881808 rs13303106 A G 3.31 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.33;MQ=59.21;MQ0=0;OQ=1343.98;QD=25.36;SB=-644.88 GT:AD:DP:GL:GQ 1/1:0,53:43:-138.03,-12.97,-0.04:99 +chr1 882608 rs13303227 G A 569.43 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=2091.00;QD=38.72;SB=-899.68 GT:AD:DP:GL:GQ 1/1:0,54:53:-212.70,-15.97,-0.01:99 +chr1 883143 rs4970371 G A 143.48 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=57.73;MQ0=0;OQ=2249.45;QD=37.49;SB=-940.26 GT:AD:DP:GL:GQ 1/1:0,60:57:-228.55,-17.17,-0.02:99 +chr1 883494 rs6605069 A G 58.53 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=58.62;MQ0=0;OQ=2094.43;QD=32.73;SB=-870.68 GT:AD:DP:GL:GQ 1/1:0,64:60:-213.05,-18.07,-0.02:99 +chr1 883582 rs4970445 G A 189.37 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.14;MQ0=0;OQ=1807.99;QD=33.48;SB=-798.52 GT:AD:DP:GL:GQ 1/1:1,53:49:-184.42,-14.78,-0.04:99 +chr1 884436 rs13303010 G A 1.14 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=58.63;MQ0=0;OQ=585.11;QD=34.42;SB=-52.67 GT:AD:DP:GL:GQ 1/1:0,17:16:-62.10,-4.82,-0.01:48.15 +chr1 885569 rs13303327 G A 161.74 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=61.07;MQ0=0;OQ=743.89;QD=37.19;SB=-245.00 GT:AD:DP:GL:GQ 1/1:0,20:20:-77.98,-6.03,-0.01:60.19 +chr1 887188 rs4970441 G C 2.34 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=753.54;QD=39.66;SB=-289.25 GT:AD:DP:GL:GQ 1/1:0,19:18:-78.95,-5.42,-0.01:54.18 +chr1 887427 rs13303229 T C 257.67 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1210.82;QD=33.63;SB=-286.61 GT:AD:DP:GL:GQ 1/1:0,36:36:-124.69,-10.85,-0.02:99 +chr1 888186 rs6605071 T C 17.61 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=3.35;MQ=58.67;MQ0=0;OQ=1185.73;QD=33.88;SB=-618.22 GT:AD:DP:GL:GQ 1/1:0,35:34:-122.17,-10.24,-0.01:99 +chr1 889791 rs6677386 G C 245.35 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=39.71;MQ0=0;QD=16.36;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:8:-28.14,-2.43,-0.02:24.07 +chr1 889800 . G T 344.36 SnpCluster AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.12;MQ0=0;QD=28.70;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,12:11:-38.03,-3.31,-0.01:33.08 +chr1 889801 . G C 465.29 SnpCluster AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=39.12;MQ0=0;QD=38.77;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,12:11:-50.12,-3.31,-0.00:33.11 +chr1 889805 . G A 501.88 SnpCluster AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.71;MQ0=0;QD=33.46;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:14:-53.78,-4.22,-0.01:42.13 +chr1 889852 rs6669071 A C 11.50 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=44.10;MQ0=0;OQ=318.72;QD=26.56;SB=-44.57 GT:AD:DP:GL:GQ 1/1:0,12:11:-35.46,-3.31,-0.01:33.07 +chr1 889864 rs28754834 G A 283.84 Indel AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=44.79;MQ0=0;QD=31.54;SB=-93.34 GT:AD:DP:GL:GQ 1/1:0,9:8:-31.97,-2.41,-0.00:24.08 +chr1 889872 rs6704181 C G 264.94 Indel AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=42.50;MQ0=0;QD=33.12;SB=-56.93 GT:AD:DP:GL:GQ 1/1:0,8:7:-30.07,-2.11,-0.00:21.07 +chr1 890148 rs4970435 C T 1.99 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=54.37;MQ0=0;OQ=1059.65;QD=35.32;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,29:28:-109.56,-8.43,-0.01:84.27 +chr1 890149 rs4970434 A G 1.27 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=54.37;MQ0=0;OQ=1048.98;QD=34.97;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,30:29:-108.49,-8.74,-0.01:87.27 +chr1 890161 . C G 0.39 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.89;MQ=54.80;MQ0=0;OQ=464.33;QD=12.55;SB=-10.00 GT:AD:DP:GL:GQ 0/1:16,21:31:-59.09,-9.37,-60.44:99 +chr1 890593 rs3935066 G A 1827.67 Indel AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=54.80;MQ0=0;QD=38.08;SB=-380.50 GT:AD:DP:GL:GQ 1/1:0,48:46:-186.37,-13.86,-0.02:99 +chr1 890835 rs9697711 T G 5.70 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.09;MQ=57.77;MQ0=0;OQ=1087.73;QD=27.19;SB=-563.56 GT:AD:DP:GL:GQ 1/1:0,40:34:-112.38,-10.25,-0.03:99 +chr1 890886 rs13303351 T C 4.74 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=56.17;MQ0=0;OQ=1868.96;QD=27.89;SB=-762.95 GT:AD:DP:GL:GQ 1/1:0,67:61:-190.56,-18.41,-0.08:99 +chr1 891422 rs13303160 G A 335.14 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1009.81;QD=38.84;SB=-456.35 GT:AD:DP:GL:GQ 1/1:0,26:26:-104.57,-7.83,-0.01:78.26 +chr1 891470 rs13302996 C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1288.09;QD=33.03;SB=-383.20 GT:AD:DP:GL:GQ 1/1:0,39:34:-132.43,-10.27,-0.04:99 +chr1 891515 rs2879814 A G 4.78 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.80;MQ=59.05;MQ0=0;OQ=1360.05;QD=30.91;SB=-420.15 GT:AD:DP:GL:GQ 1/1:0,44:40:-139.61,-12.06,-0.03:99 +chr1 892627 rs28416780 C G 985.40 Indel AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.73;MQ=60.94;MQ0=0;QD=29.86;SB=-516.60 GT:AD:DP:GL:GQ 1/1:0,33:26:-102.16,-7.86,-0.03:78.25 +chr1 892860 rs7524174 G A 607.69 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2039.21;QD=35.78;SB=-884.69 GT:AD:DP:GL:GQ 1/1:0,57:52:-207.52,-15.67,-0.02:99 +chr1 893108 rs28690976 A G 19.77 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.31;MQ=59.50;MQ0=0;OQ=1221.87;QD=33.02;SB=-508.55 GT:AD:DP:GL:GQ 1/1:0,37:34:-125.78,-10.24,-0.01:99 +chr1 893184 rs6669800 G A 536.30 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1821.94;QD=35.04;SB=-645.66 GT:AD:DP:GL:GQ 1/1:0,52:47:-185.80,-14.16,-0.02:99 +chr1 895023 rs7555426 C T 0.47 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.03;HRun=0;HaplotypeScore=12.36;MQ=55.36;MQ0=0;OQ=2346.52;QD=37.25;SB=-860.64 GT:AD:DP:GL:GQ 1/1:0,60:62:-238.26,-18.08,-0.02:99 +chr1 895028 rs7522959 A G 167.42 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=55.43;MQ0=0;OQ=2120.68;QD=33.14;SB=-824.97 GT:AD:DP:GL:GQ 1/1:0,63:62:-215.68,-18.68,-0.03:99 +chr1 899282 rs28548431 C T 198.63 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.43;MQ0=0;OQ=508.80;QD=15.42;SB=-237.75 GT:AD:DP:GL:GQ 0/1:15,18:31:-63.51,-9.35,-46.57:99 +chr1 899418 rs2340594 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=1231.29;QD=30.03;SB=-602.23 GT:AD:DP:GL:GQ 1/1:0,41:40:-126.75,-12.06,-0.03:99 +chr1 899631 rs2340593 A G 106.26 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1110.83;QD=35.83;SB=-387.48 GT:AD:DP:GL:GQ 1/1:0,31:31:-114.68,-9.34,-0.01:93.28 +chr1 900257 rs28477686 C T 200.51 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=716.99;QD=16.30;SB=-337.87 GT:AD:DP:GL:GQ 0/1:20,24:40:-87.03,-12.05,-62.41:99 +chr1 900301 rs6685581 A G 61.67 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=58.90;MQ0=0;OQ=1025.59;QD=26.99;SB=-469.48 GT:AD:DP:GL:GQ 1/1:0,38:34:-106.18,-10.26,-0.04:99 +chr1 900766 rs4970429 T C 21.40 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=1255.50;QD=27.90;SB=-520.11 GT:AD:DP:GL:GQ 1/1:0,45:41:-129.18,-12.37,-0.04:99 +chr1 901458 rs7417106 A G 62.69 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=56.69;MQ0=0;OQ=1131.68;QD=22.63;SB=-392.29 GT:AD:DP:GL:GQ 1/1:0,48:37:-116.79,-11.16,-0.04:99 +chr1 901912 rs9803103 T C 68.99 PASS AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.16;MQ0=0;OQ=72.78;QD=4.85;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,5:15:-15.08,-4.52,-39.48:99 +chr1 901966 rs9803017 G A 5.21 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=48.89;MQ0=0;OQ=164.19;QD=23.46;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,5:5:-19.98,-1.51,-0.00:15.05 +chr1 903262 . C T 47.02 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=23.51;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-8.11,-0.60,-0.00:6.02 +chr1 903752 rs2340596 G A 213.15 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=58.63;MQ0=0;OQ=437.08;QD=12.86;SB=-239.73 GT:AD:DP:GL:GQ 0/1:19,15:34:-57.25,-10.26,-59.16:99 +chr1 904055 rs2340595 G C 462.22 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1540.41;QD=36.68;SB=-743.79 GT:AD:DP:GL:GQ 1/1:0,42:38:-157.65,-11.46,-0.02:99 +chr1 904196 rs13302979 C G 14.38 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=60.00;MQ0=0;OQ=238.96;QD=11.95;SB=-110.33 GT:AD:DP:GL:GQ 0/1:12,8:19:-32.91,-5.73,-43.20:99 +chr1 904715 rs13303368 G C 150.50 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=58.83;MQ0=0;OQ=429.52;QD=11.93;SB=-165.16 GT:AD:DP:GL:GQ 0/1:21,15:34:-56.48,-10.25,-87.94:99 +chr1 904739 rs13302983 T C 1.98 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=3.25;MQ=59.49;MQ0=0;OQ=1146.65;QD=25.48;SB=-382.24 GT:AD:DP:GL:GQ 1/1:0,45:37:-118.29,-11.16,-0.04:99 +chr1 904803 rs13303033 T C 97.04 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=3.63;MQ=59.44;MQ0=0;OQ=505.70;QD=12.33;SB=-138.55 GT:AD:DP:GL:GQ 0/1:20,21:40:-65.92,-12.07,-67.38:99 +chr1 905090 rs13303355 A G 1.94 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=8.34;MQ=56.14;MQ0=0;OQ=1675.03;QD=29.39;SB=-822.95 GT:AD:DP:GL:GQ 1/1:1,56:50:-171.12,-15.07,-0.03:99 +chr1 906412 rs6660139 A G 108.89 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=506.06;QD=14.88;SB=-146.57 GT:AD:DP:GL:GQ 0/1:14,20:33:-63.84,-9.95,-51.10:99 +chr1 906453 rs28566954 G A 282.05 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.36;MQ0=0;OQ=491.61;QD=13.66;SB=-253.24 GT:AD:DP:GL:GQ 0/1:20,16:35:-62.99,-10.55,-63.70:99 +chr1 906697 rs6694632 G A 262.48 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.25;MQ0=0;OQ=424.41;QD=13.69;SB=-233.73 GT:AD:DP:GL:GQ 0/1:16,15:29:-54.46,-8.74,-53.31:99 +chr1 906923 rs6605058 C G 4.01 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.45;MQ0=0;OQ=1718.51;QD=40.92;SB=-739.75 GT:AD:DP:GL:GQ 1/1:0,42:41:-175.45,-12.36,-0.02:99 +chr1 907503 rs41285816 G A 149.42 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.47;MQ0=0;OQ=650.11;QD=15.12;SB=-327.85 GT:AD:DP:GL:GQ 0/1:21,22:41:-80.65,-12.35,-76.53:99 +chr1 908101 rs28552711 C G 269.46 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.03;MQ0=0;OQ=561.89;QD=11.71;SB=-234.09 GT:AD:DP:GL:GQ 0/1:27,21:45:-73.04,-13.57,-111.91:99 +chr1 908247 rs13303118 G T 75.04 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.58;MQ0=0;OQ=378.28;QD=8.60;SB=-112.78 GT:AD:DP:GL:GQ 0/1:27,17:40:-53.17,-12.06,-75.89:99 +chr1 908436 rs2341354 A G 288.04 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.09;MQ0=0;OQ=687.85;QD=13.49;SB=-217.36 GT:AD:DP:GL:GQ 0/1:22,29:47:-86.23,-14.17,-83.30:99 +chr1 908990 rs28469033 T C 203.63 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=58.06;MQ0=0;OQ=712.75;QD=12.29;SB=-242.27 GT:AD:DP:GL:GQ 0/1:29,28:55:-91.13,-16.57,-114.97:99 +chr1 909282 rs6605059 T C 230.41 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=181.71;QD=7.57;SB=-100.01 GT:AD:DP:GL:GQ 0/1:13,11:22:-28.09,-6.63,-51.27:99 +chr1 909352 rs61606412 C T 41.71 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=53.76;MQ0=0;OQ=576.99;QD=16.03;SB=-77.09 GT:AD:DP:GL:GQ 0/1:16,19:32:-70.62,-9.64,-54.85:99 +chr1 909718 . G A 32.42 PASS AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.35;MQ0=0;OQ=82.61;QD=6.35;SB=-28.51 GT:AD:DP:GL:GQ 0/1:9,4:13:-15.46,-3.92,-29.36:99 +chr1 909851 . C T 379.69 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=14.99;MQ=38.66;MQ0=0;QD=8.44;SB=-209.86 GT:AD:DP:GL:GQ 0/1:32,13:38:-52.70,-11.44,-90.66:99 +chr1 909854 . C A 33.53 Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=23.31;MQ=39.61;MQ0=0;QD=0.73;SB=-35.83 GT:AD:DP:GL:GQ 0/1:41,3:18:-18.90,-12.26,-52.66:66.37 +chr1 909858 . T A 34.25 Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=85.24;MQ=39.71;MQ0=0;QD=0.69;SB=-24.32 GT:AD:DP:GL:GQ 0/1:46,4:25:-14.24,-7.53,-79.28:67.09 +chr1 909861 rs2341357 A C 442.96 Indel;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=92.23;MQ=37.93;MQ0=0;QD=9.23;SB=-187.18 GT:AD:DP:GL:GQ 0/1:13,31:32:-70.70,-23.12,-57.83:99 +chr1 909862 . T C 28.94 Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=90.34;MQ=37.54;MQ0=1;QD=0.59;SB=-27.89 GT:AD:DP:GL:GQ 0/1:45,4:23:-13.11,-6.93,-76.03:61.77 +chr1 909865 rs55746336 A C 368.04 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=65.88;MQ=38.28;MQ0=1;QD=7.51;SB=-150.94 GT:AD:DP:GL:GQ 0/1:20,29:28:-48.52,-8.43,-49.13:99 +chr1 910511 rs6677020 T C 126.81 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=58.99;MQ0=0;OQ=1842.74;QD=30.71;SB=-555.07 GT:AD:DP:GL:GQ 1/1:0,60:57:-187.90,-17.18,-0.04:99 +chr1 910596 rs6677131 T C 281.37 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=1029.24;QD=25.10;SB=-459.07 GT:AD:DP:GL:GQ 1/1:0,41:35:-106.55,-10.56,-0.04:99 +chr1 911433 rs6662128 T C 65.09 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=42.74;MQ0=0;OQ=1332.64;QD=27.76;SB=-494.18 GT:AD:DP:GL:GQ 1/1:0,48:43:-136.89,-12.97,-0.04:99 +chr1 911523 rs6703008 C T 253.53 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.87;MQ0=0;OQ=592.10;QD=14.44;SB=-247.55 GT:AD:DP:GL:GQ 0/1:21,20:40:-74.55,-12.06,-68.34:99 +chr1 911579 rs13303278 C A 321.21 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=57.82;MQ0=0;OQ=846.22;QD=16.27;SB=-412.14 GT:AD:DP:GL:GQ 0/1:22,30:49:-102.67,-14.76,-65.25:99 +chr1 911872 rs6693747 G A 247.15 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=57.81;MQ0=0;OQ=692.72;QD=11.94;SB=-247.55 GT:AD:DP:GL:GQ 0/1:34,24:51:-87.93,-15.37,-94.90:99 +chr1 912939 rs6605060 A G 422.47 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1569.95;QD=29.62;SB=-431.82 GT:AD:DP:GL:GQ 1/1:0,53:52:-160.64,-15.69,-0.06:99 +chr1 913322 rs9442609 A G 120.23 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=58.95;MQ0=0;OQ=1780.01;QD=28.25;SB=-752.61 GT:AD:DP:GL:GQ 1/1:0,63:58:-181.64,-17.49,-0.06:99 +chr1 913612 rs9442610 T C 76.57 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.45;MQ0=1;OQ=2496.82;QD=28.70;SB=-1150.17 GT:AD:DP:GL:GQ 1/1:1,86:79:-253.33,-23.82,-0.07:99 +chr1 913974 rs28447224 T A 288.86 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.45;MQ0=0;OQ=731.87;QD=12.20;SB=-322.51 GT:AD:DP:GL:GQ 0/1:33,27:58:-93.94,-17.47,-123.87:99 +chr1 914034 . A T 3.99 PASS AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.53;MQ0=0;OQ=328.12;QD=3.57;SB=-36.46 GT:AD:DP:GL:GQ 0/1:74,18:90:-63.21,-27.12,-275.61:99 +chr1 914043 . A T 0.15 PASS AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=53.25;MQ0=0;OQ=310.60;QD=3.20;SB=-88.90 GT:AD:DP:GL:GQ 0/1:71,26:82:-59.05,-24.71,-248.58:99 +chr1 914057 rs36034299 T A 46.78 PASS AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=52.48;MQ0=0;OQ=1254.45;QD=10.20;SB=-515.06 GT:AD:DP:GL:GQ 0/1:78,44:120:-164.87,-36.14,-292.57:99 +chr1 914062 rs34208189 G T 4.13 PASS AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=1;HaplotypeScore=4.71;MQ=52.50;MQ0=0;OQ=1304.79;QD=10.87;SB=-551.46 GT:AD:DP:GL:GQ 0/1:72,47:118:-172.13,-38.37,-252.01:99 +chr1 914098 rs28489602 G A 178.03 PASS AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=53.92;MQ0=0;OQ=1142.45;QD=9.29;SB=-414.29 GT:AD:DP:GL:GQ 0/1:80,43:115:-152.18,-34.65,-273.57:99 +chr1 914111 . T G 3.17 PASS AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=54.02;MQ0=0;OQ=717.31;QD=5.56;SB=-222.67 GT:AD:DP:GL:GQ 0/1:95,34:128:-113.56,-38.55,-355.41:99 +chr1 914118 rs59424352 T G 15.06 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=131;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=54.89;MQ0=0;QD=0.11;SB=-22.32 GT:AD:DP:GL:GQ 0/1:103,28:116:-39.71,-34.94,-387.42:47.76 +chr1 914126 rs28607403 A T 0.47 PASS AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=56.46;MQ0=0;OQ=177.88;QD=1.41;SB=-25.34 GT:AD:DP:GL:GQ 0/1:106,20:118:-56.62,-35.55,-387.33:99 +chr1 914231 rs35562283 C T 2.83 PASS AC=2;AF=1.00;AN=2;DB;DP=100;Dels=0.00;HRun=2;HaplotypeScore=2.10;MQ=59.39;MQ0=0;OQ=4072.19;QD=40.72;SB=-2034.20 GT:AD:DP:GL:GQ 1/1:0,100:100:-406.22,-30.12,-0.03:99 +chr1 914391 rs34712273 C A 51.10 PASS AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=5.23;MQ=56.94;MQ0=0;OQ=1123.83;QD=11.59;SB=-531.23 GT:AD:DP:GL:GQ 0/1:55,42:95:-144.28,-28.62,-196.31:99 +chr1 914466 rs28422907 T C 454.63 PASS AC=2;AF=1.00;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=3679.99;QD=36.08;SB=-1782.71 GT:AD:DP:GL:GQ 1/1:0,102:101:-367.00,-30.42,-0.03:99 +chr1 914492 rs28622096 A G 82.91 PASS AC=2;AF=1.00;AN=2;DB;DP=92;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=2947.74;QD=32.04;SB=-1451.63 GT:AD:DP:GL:GQ 1/1:0,92:91:-298.43,-27.44,-0.07:99 +chr1 914761 rs6665000 C A 607.33 PASS AC=2;AF=1.00;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3789.11;QD=37.15;SB=-1446.45 GT:AD:DP:GL:GQ 1/1:0,101:101:-377.91,-33.59,-3.42:99 +chr1 915547 rs6605061 T C 196.60 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=57.81;MQ0=0;OQ=1982.79;QD=33.05;SB=-855.97 GT:AD:DP:GL:GQ 1/1:0,60:57:-201.89,-17.17,-0.03:99 +chr1 916214 rs6671243 C T 469.30 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2468.85;QD=39.82;SB=-737.98 GT:AD:DP:GL:GQ 1/1:0,62:61:-250.48,-18.37,-0.01:99 +chr1 916294 rs4970403 A T 304.51 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.55;MQ=59.43;MQ0=0;OQ=2680.54;QD=36.72;SB=-1154.05 GT:AD:DP:GL:GQ 1/1:1,72:71:-271.66,-21.39,-0.02:99 +chr1 916484 rs4970351 A C 485.68 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1740.98;QD=35.53;SB=-550.05 GT:AD:DP:GL:GQ 1/1:0,49:49:-177.70,-14.76,-0.01:99 +chr1 917172 rs2341362 T C 555.17 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1855.09;QD=30.92;SB=-890.64 GT:AD:DP:GL:GQ 1/1:0,60:59:-189.15,-17.80,-0.06:99 +chr1 917604 rs6665587 G A 343.04 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=746.63;QD=16.23;SB=-250.74 GT:AD:DP:GL:GQ 0/1:23,23:45:-91.50,-13.55,-86.19:99 +chr1 918279 . G A 19.72 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=64.12;MQ0=0;OQ=347.49;QD=8.91;SB=-127.57 GT:AD:DP:GL:GQ 0/1:25,14:32:-47.68,-9.65,-62.78:99 +chr1 918383 rs35002855 A G 36.80 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.30;MQ0=0;OQ=923.20;QD=27.98;SB=-310.47 GT:AD:DP:GL:GQ 1/1:0,33:30:-95.93,-9.05,-0.03:90.20 +chr1 918441 rs28394749 G A 367.26 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=1345.86;QD=38.45;SB=-480.97 GT:AD:DP:GL:GQ 1/1:0,35:35:-138.18,-10.55,-0.01:99 +chr1 918699 rs9777703 C T 463.81 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.88;MQ0=0;OQ=1525.43;QD=38.14;SB=-621.02 GT:AD:DP:GL:GQ 1/1:0,40:39:-156.14,-11.75,-0.01:99 +chr1 919053 rs9777939 A G 223.28 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1351.32;QD=33.78;SB=-678.95 GT:AD:DP:GL:GQ 1/1:0,40:38:-138.73,-11.45,-0.01:99 +chr1 919179 rs9777893 C T 85.58 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=55.86;MQ0=0;OQ=1631.07;QD=35.46;SB=-540.88 GT:AD:DP:GL:GQ 1/1:0,46:44:-166.72,-13.27,-0.03:99 +chr1 919184 rs13302916 A C 0.11 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=5;HaplotypeScore=2.13;MQ=54.60;MQ0=0;OQ=1536.74;QD=31.36;SB=-480.03 GT:AD:DP:GL:GQ 1/1:0,49:45:-157.28,-13.56,-0.02:99 +chr1 919190 rs13302924 A G 46.51 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=54.92;MQ0=0;OQ=1263.79;QD=24.30;SB=-518.21 GT:AD:DP:GL:GQ 1/1:0,52:42:-130.02,-12.68,-0.06:99 +chr1 919921 . C A 110.32 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=58.99;MQ0=0;OQ=1041.89;QD=15.10;SB=-490.89 GT:AD:DP:GL:GQ 0/1:34,35:65:-127.06,-19.58,-99.23:99 +chr1 920192 rs3128108 C T 194.44 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.69;MQ0=0;OQ=711.37;QD=14.23;SB=-187.15 GT:AD:DP:GL:GQ 0/1:24,26:47:-88.59,-14.17,-77.59:99 +chr1 920240 rs3128109 C T 215.53 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.70;MQ0=0;OQ=1131.05;QD=17.95;SB=-367.88 GT:AD:DP:GL:GQ 0/1:29,34:63:-135.38,-18.99,-92.17:99 +chr1 920396 rs3128110 C G 210.15 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=58.26;MQ0=0;OQ=1157.59;QD=14.84;SB=-599.54 GT:AD:DP:GL:GQ 0/1:41,37:77:-142.27,-23.22,-177.91:99 +chr1 920430 rs3121574 A G 364.31 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.06;MQ0=0;OQ=652.89;QD=9.60;SB=-349.53 GT:AD:DP:GL:GQ 0/1:41,27:65:-88.16,-19.59,-156.95:99 +chr1 920614 rs3128111 C G 139.72 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=58.99;MQ0=0;OQ=1461.73;QD=21.18;SB=-736.36 GT:AD:DP:GL:GQ 0/1:28,41:68:-169.95,-20.49,-124.60:99 +chr1 920786 rs2710882 A G 12.29 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.97;MQ=49.62;MQ0=0;OQ=1291.93;QD=28.71;SB=-670.84 GT:AD:DP:GL:GQ 1/1:0,45:41:-132.82,-12.37,-0.04:99 +chr1 920877 rs2710881 A G 324.40 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=0;OQ=966.43;QD=26.85;SB=-364.34 GT:AD:DP:GL:GQ 1/1:0,36:31:-100.25,-9.35,-0.03:93.22 +chr1 921029 rs2710880 A G 58.88 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.24;MQ=56.56;MQ0=0;OQ=562.50;QD=14.06;SB=-270.38 GT:AD:DP:GL:GQ 0/1:15,25:36:-70.39,-10.85,-55.63:99 +chr1 921225 rs2799060 G A 150.73 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.04;MQ=54.08;MQ0=0;OQ=614.91;QD=17.08;SB=-332.87 GT:AD:DP:GL:GQ 0/1:15,21:29:-73.51,-8.74,-35.50:99 +chr1 921371 rs2799061 T A 126.55 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=52.82;MQ0=0;OQ=1479.30;QD=33.62;SB=-589.54 GT:AD:DP:GL:GQ 1/1:0,44:41:-151.53,-12.35,-0.02:99 +chr1 921411 rs2799062 G T 122.68 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=53.36;MQ0=0;OQ=738.91;QD=16.06;SB=-235.96 GT:AD:DP:GL:GQ 0/1:19,27:43:-90.13,-12.95,-62.40:99 +chr1 921593 rs2005437 A G 3.88 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=3.71;MQ=50.61;MQ0=0;OQ=1146.23;QD=32.75;SB=-497.46 GT:AD:DP:GL:GQ 1/1:0,35:33:-118.22,-9.94,-0.01:99 +chr1 921666 rs1891908 C T 2.08 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.85;MQ=32.06;MQ0=2;OQ=160.89;QD=4.35;SB=-6.43 GT:AD:DP:GL:GQ 0/1:19,17:19:-25.09,-5.72,-45.39:99 +chr1 921743 rs2710878 G A 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=13.34;MQ=30.42;MQ0=11;OQ=92.22;QD=1.77;SB=38.12 GT:AD:DP:GL:GQ 0/1:43,9:31:-21.85,-9.35,-87.56:99 +chr1 921798 rs59581901 T C 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=13.36;MQ=44.02;MQ0=2;OQ=265.71;QD=4.66;SB=-27.22 GT:AD:DP:GL:GQ 0/1:37,20:42:-42.52,-12.66,-114.67:99 +chr1 921802 rs13303155 G A 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=12.88;MQ=43.29;MQ0=2;OQ=165.28;QD=2.85;SB=-96.56 GT:AD:DP:GL:GQ 0/1:44,13:47:-33.98,-14.17,-116.58:99 +chr1 921917 rs13302969 G T 74.55 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.19;MQ=21.41;MQ0=5;OQ=283.37;QD=8.86;SB=-65.73 GT:AD:DP:GL:GQ 0/1:6,26:13:-35.54,-3.92,-11.08:71.59 +chr1 921950 rs4350142 T G 3.51 PASS AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=16.76;MQ0=5;OQ=77.67;QD=4.32;SB=-39.55 GT:AD:DP:GL:GQ 0/1:13,5:9:-13.76,-2.71,-16.22:99 +chr1 922320 rs1891910 G A 55.08 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=54.96;MQ0=0;OQ=908.58;QD=18.93;SB=-365.40 GT:AD:DP:GL:GQ 0/1:20,28:47:-108.30,-14.16,-73.49:99 +chr1 922481 rs3128112 C G 140.23 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.00;MQ0=0;OQ=2826.91;QD=42.19;SB=-1373.36 GT:AD:DP:GL:GQ 1/1:0,67:66:-286.30,-19.89,-0.02:99 +chr1 923653 rs9442392 G A 34.86 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.66;MQ0=0;OQ=346.01;QD=17.30;SB=-99.62 GT:AD:DP:GL:GQ 0/1:8,12:18:-43.31,-5.43,-22.69:99 +chr1 923962 rs2710867 G C 179.76 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.52;MQ0=0;OQ=491.87;QD=30.74;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,16:14:-52.79,-4.24,-0.02:42.13 +chr1 923969 rs2799063 A G 177.71 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.52;MQ0=0;OQ=467.35;QD=31.16;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:15:-50.33,-4.52,-0.01:45.12 +chr1 923984 rs2488989 G A 4.47 PASS AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=52.45;MQ0=0;OQ=54.72;QD=4.21;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,4:12:-12.37,-3.61,-31.32:87.56 +chr1 924007 rs9697551 C G 2.08 PASS AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=52.65;MQ0=0;OQ=378.82;QD=37.88;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,10:10:-41.47,-3.01,-0.00:30.10 +chr1 925085 rs2298214 C A 41.67 PASS AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=126.82;QD=15.85;SB=-10.00 GT:AD:DP:GL:GQ 0/1:3,5:8:-18.37,-2.41,-10.50:80.94 +chr1 925696 rs3128115 C G 0.04 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=341.24;QD=28.44;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,12:10:-37.72,-3.03,-0.02:30.09 +chr1 925974 rs1936360 C T 39.87 PASS AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=58.35;MQ0=0;OQ=214.61;QD=12.62;SB=-42.53 GT:AD:DP:GL:GQ 0/1:9,8:14:-28.97,-4.22,-22.12:99 +chr1 926057 rs3121570 A G 2.88 PASS AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=311.77;QD=28.34;SB=-100.02 GT:AD:DP:GL:GQ 1/1:0,11:11:-34.77,-3.32,-0.01:33.06 +chr1 926073 rs3121569 C A 189.59 PASS AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=295.10;QD=26.83;SB=-77.88 GT:AD:DP:GL:GQ 1/1:0,11:10:-33.10,-3.01,-0.01:30.07 +chr1 927551 rs2489000 T C 23.57 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.20;MQ0=0;OQ=869.96;QD=30.00;SB=-383.48 GT:AD:DP:GL:GQ 1/1:0,29:26:-90.60,-7.84,-0.01:78.21 +chr1 927679 . G T 11.95 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=20;HaplotypeScore=4.44;MQ=51.49;MQ0=1;QD=0.30;SB=29.12 GT:AD:DP:GL:GQ 0/1:35,5:33:-14.39,-9.94,-101.16:44.50 +chr1 927979 rs2710869 T G 68.27 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=52.06;MQ0=0;OQ=1400.53;QD=31.83;SB=-711.32 GT:AD:DP:GL:GQ 1/1:0,44:41:-143.66,-12.35,-0.02:99 +chr1 927988 rs2710868 G A 255.30 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.36;MQ0=0;OQ=410.87;QD=10.02;SB=-73.54 GT:AD:DP:GL:GQ 0/1:27,14:38:-55.83,-11.46,-75.32:99 +chr1 928076 rs2799058 A G 513.54 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.12;MQ0=1;OQ=1982.35;QD=34.78;SB=-956.40 GT:AD:DP:GL:GQ 1/1:0,57:56:-201.84,-16.87,-0.02:99 +chr1 929868 rs2799056 A G 83.40 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=60.00;MQ0=0;OQ=292.67;QD=13.30;SB=-94.98 GT:AD:DP:GL:GQ 0/1:10,12:19:-38.28,-5.73,-31.90:99 +chr1 929959 rs4503294 C T 66.68 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=59.48;MQ0=0;OQ=871.55;QD=19.81;SB=-434.84 GT:AD:DP:GL:GQ 0/1:17,27:40:-102.50,-12.06,-44.62:99 +chr1 931147 rs3128116 C T 186.46 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=58.74;MQ0=0;OQ=584.87;QD=15.81;SB=-318.85 GT:AD:DP:GL:GQ 0/1:17,20:34:-72.02,-10.25,-50.30:99 +chr1 931197 rs57683598 G A 242.64 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.63;MQ0=0;OQ=443.86;QD=13.05;SB=-202.91 GT:AD:DP:GL:GQ 0/1:19,15:33:-57.62,-9.95,-57.41:99 +chr1 931402 rs9778087 C T 103.12 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.28;MQ=58.18;MQ0=0;OQ=521.73;QD=14.49;SB=-147.61 GT:AD:DP:GL:GQ 0/1:17,19:30:-64.50,-9.04,-41.68:99 +chr1 933113 rs3121568 C T 81.24 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=27.66;MQ0=1;OQ=764.02;QD=34.73;SB=-301.68 GT:AD:DP:GL:GQ 1/1:1,21:20:-79.99,-6.02,-0.00:60.20 +chr1 933331 rs3121567 T C 90.20 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=52.92;MQ0=0;OQ=1930.66;QD=28.39;SB=-605.93 GT:AD:DP:GL:GQ 1/1:0,67:59:-196.69,-17.79,-0.04:99 +chr1 933550 rs2465140 G C 10.53 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=52.98;MQ0=0;OQ=1826.77;QD=24.04;SB=-482.83 GT:AD:DP:GL:GQ 0/1:29,47:76:-208.87,-22.91,-115.72:99 +chr1 933770 rs2488992 C G 622.99 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2496.05;QD=39.00;SB=-1249.63 GT:AD:DP:GL:GQ 1/1:1,63:62:-253.23,-18.70,-0.04:99 +chr1 933831 rs13303313 C T 77.45 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=54.98;MQ0=1;OQ=1022.40;QD=21.30;SB=-421.46 GT:AD:DP:GL:GQ 0/1:17,31:46:-119.39,-13.87,-49.73:99 +chr1 934427 rs3128117 T C 70.90 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.79;MQ=59.48;MQ0=0;OQ=1012.81;QD=12.50;SB=-424.88 GT:AD:DP:GL:GQ 0/1:46,35:81:-128.96,-24.40,-186.84:99 +chr1 934959 rs3135457 C T 611.86 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.45;MQ0=0;OQ=2185.20;QD=35.82;SB=-904.70 GT:AD:DP:GL:GQ 1/1:0,61:55:-222.12,-16.57,-0.02:99 +chr1 934974 rs13303172 C T 140.68 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=58.59;MQ0=0;OQ=2216.02;QD=34.63;SB=-887.19 GT:AD:DP:GL:GQ 1/1:0,63:58:-225.21,-17.48,-0.03:99 +chr1 935337 rs3121566 C T 64.84 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=57.82;MQ0=0;OQ=2650.36;QD=37.33;SB=-1265.29 GT:AD:DP:GL:GQ 1/1:0,71:68:-268.65,-20.49,-0.03:99 +chr1 935475 rs3121565 C T 3.95 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=5.58;MQ=54.82;MQ0=0;OQ=1712.26;QD=33.57;SB=-826.14 GT:AD:DP:GL:GQ 1/1:0,51:46:-174.83,-13.86,-0.02:99 +chr1 935997 rs2341364 T G 377.30 Indel AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=10.97;MQ=57.32;MQ0=2;QD=7.12;SB=-202.78 GT:AD:DP:GL:GQ 0/1:37,16:48:-55.47,-14.46,-118.77:99 +chr1 935998 rs9723307 T G 915.61 Indel AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=11.45;MQ=57.32;MQ0=2;QD=17.28;SB=-353.60 GT:AD:DP:GL:GQ 0/1:21,32:48:-109.30,-14.46,-57.43:99 +chr1 936897 rs2465126 G A 228.15 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.52;MQ0=0;OQ=1823.18;QD=37.98;SB=-798.06 GT:AD:DP:GL:GQ 1/1:0,48:47:-185.92,-14.16,-0.02:99 +chr1 937401 rs2465125 C T 186.23 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.20;MQ0=0;OQ=2163.80;QD=37.31;SB=-987.00 GT:AD:DP:GL:GQ 1/1:0,58:56:-219.99,-16.88,-0.02:99 +chr1 938555 rs2341365 G A 140.11 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.55;MQ0=0;OQ=1650.26;QD=34.38;SB=-693.43 GT:AD:DP:GL:GQ 1/1:0,47:44:-168.63,-13.26,-0.02:99 +chr1 938733 rs4615788 C G 63.76 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=59.05;MQ0=0;OQ=1777.68;QD=37.82;SB=-661.48 GT:AD:DP:GL:GQ 1/1:0,47:45:-181.39,-13.58,-0.03:99 +chr1 938784 rs15842 T C 63.77 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=51.15;MQ0=0;OQ=1180.61;QD=25.67;SB=-593.57 GT:AD:DP:GL:GQ 1/1:0,46:38:-121.68,-11.46,-0.04:99 +chr1 939098 rs2465124 G A 101.68 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.32;MQ0=0;OQ=1385.28;QD=35.52;SB=-635.85 GT:AD:DP:GL:GQ 1/1:0,39:36:-142.13,-10.85,-0.02:99 +chr1 939471 rs1921 G A 210.99 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=59.46;MQ0=0;OQ=818.95;QD=19.05;SB=-428.80 GT:AD:DP:GL:GQ 0/1:17,25:41:-97.53,-12.36,-57.36:99 +chr1 939517 rs8997 A G 93.12 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.52;MQ=58.71;MQ0=0;OQ=1127.57;QD=31.32;SB=-511.18 GT:AD:DP:GL:GQ 1/1:0,36:33:-116.36,-9.94,-0.02:99 +chr1 939788 rs2799070 C T 122.12 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=60.00;MQ0=0;OQ=1513.64;QD=36.92;SB=-701.35 GT:AD:DP:GL:GQ 1/1:0,40:39:-154.96,-11.75,-0.01:99 +chr1 940106 rs1891906 A C 58.36 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.38;MQ0=0;OQ=496.04;QD=13.41;SB=-49.04 GT:AD:DP:GL:GQ 0/1:19,18:37:-64.03,-11.14,-68.15:99 +chr1 940540 rs9331223 T C 228.94 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=58.40;MQ0=0;OQ=564.77;QD=13.45;SB=-287.31 GT:AD:DP:GL:GQ 0/1:17,25:39:-71.52,-11.76,-66.74:99 +chr1 940579 rs2799069 A T 132.14 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=57.66;MQ0=0;OQ=1217.27;QD=32.90;SB=-595.76 GT:AD:DP:GL:GQ 1/1:0,37:34:-125.32,-10.24,-0.01:99 +chr1 941146 rs9442363 C T 200.29 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=29.19;MQ0=1;OQ=502.68;QD=12.89;SB=-262.28 GT:AD:DP:GL:GQ 0/1:16,22:28:-61.99,-8.44,-37.57:99 +chr1 941158 rs9442388 C T 75.76 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.38;MQ=27.92;MQ0=1;OQ=496.98;QD=10.80;SB=-155.64 GT:AD:DP:GL:GQ 0/1:24,22:37:-64.14,-11.16,-65.52:99 +chr1 941185 rs9697362 C T 0.27 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=4;HaplotypeScore=0.96;MQ=26.62;MQ0=0;OQ=1253.78;QD=25.59;SB=-636.34 GT:AD:DP:GL:GQ 1/1:0,49:34:-128.98,-10.25,-0.02:99 +chr1 941193 rs9697717 G A 313.44 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.36;MQ0=0;OQ=1030.78;QD=25.77;SB=-468.62 GT:AD:DP:GL:GQ 1/1:0,40:27:-106.67,-8.14,-0.01:81.26 +chr1 941427 rs2465141 A G 200.39 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.01;MQ=50.56;MQ0=1;OQ=585.65;QD=10.65;SB=-303.21 GT:AD:DP:GL:GQ 0/1:29,26:48:-76.32,-14.47,-98.65:99 +chr1 941491 . A T 28.08 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=45.78;MQ0=3;QD=0.52;SB=41.14 GT:AD:DP:GL:GQ 0/1:46,8:45:-19.65,-13.56,-148.74:60.91 +chr1 941866 rs3128118 G A 182.23 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.48;MQ=58.42;MQ0=1;OQ=769.91;QD=13.27;SB=-278.19 GT:AD:DP:GL:GQ 0/1:30,27:54:-96.56,-16.28,-93.17:99 +chr1 942291 rs9442611 G A 158.27 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=58.27;MQ0=0;OQ=928.32;QD=19.34;SB=-479.01 GT:AD:DP:GL:GQ 0/1:19,29:48:-110.59,-14.48,-59.61:99 +chr1 943087 rs4970390 C T 107.20 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=50.43;MQ0=1;OQ=376.23;QD=6.60;SB=-175.84 GT:AD:DP:GL:GQ 0/1:38,19:49:-55.68,-14.78,-111.95:99 +chr1 943217 rs61766298 G A 33.08 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=54.66;MQ0=1;OQ=355.20;QD=4.80;SB=-58.95 GT:AD:DP:GL:GQ 0/1:57,16:65:-58.41,-19.60,-158.72:99 +chr1 943541 rs2952918 T C 3.09 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=5.78;MQ=53.39;MQ0=0;OQ=348.13;QD=8.70;SB=-186.61 GT:AD:DP:GL:GQ 0/1:24,16:38:-49.55,-11.46,-86.70:99 +chr1 943815 rs9442612 G A 205.15 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=57.73;MQ0=0;OQ=533.79;QD=13.02;SB=-257.75 GT:AD:DP:GL:GQ 0/1:22,19:39:-68.42,-11.76,-70.56:99 +chr1 944640 rs61766299 C A 104.63 PASS AC=1;AF=0.50;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=57.66;MQ0=0;OQ=76.34;QD=7.63;SB=-34.38 GT:AD:DP:GL:GQ 0/1:6,4:9:-13.63,-2.71,-15.11:99 +chr1 946715 rs9777931 C T 99.84 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=313.20;QD=12.05;SB=-129.12 GT:AD:DP:GL:GQ 0/1:14,11:22:-41.23,-6.63,-41.31:99 +chr1 949018 rs3845291 G A 42.15 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=1.63;MQ=59.54;MQ0=0;OQ=843.29;QD=16.87;SB=-349.52 GT:AD:DP:GL:GQ 0/1:23,27:47:-101.78,-14.17,-66.18:99 +chr1 949032 rs3845292 G C 180 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.52;MQ0=0;OQ=777.11;QD=16.19;SB=-360.45 GT:AD:DP:GL:GQ 0/1:22,26:45:-94.57,-13.58,-90.66:99 +chr1 949094 rs4039721 G A 273.59 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.09;MQ0=0;OQ=688.73;QD=16.80;SB=-366.42 GT:AD:DP:GL:GQ 0/1:19,22:36:-83.01,-10.86,-46.17:99 +chr1 950272 rs4970392 G C 3.67 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=405.25;QD=17.62;SB=-227.38 GT:AD:DP:GL:GQ 0/1:10,13:21:-50.14,-6.33,-36.47:99 +chr1 951690 rs3121556 G A 175.37 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=59.49;MQ0=0;OQ=541.95;QD=12.04;SB=-261.27 GT:AD:DP:GL:GQ 0/1:25,20:39:-69.24,-11.76,-65.32:99 +chr1 952469 rs4970393 G A 53.25 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=4.24;MQ=58.80;MQ0=0;OQ=631.93;QD=18.06;SB=-331.90 GT:AD:DP:GL:GQ 0/1:14,21:33:-76.42,-9.95,-42.13:99 +chr1 952754 rs4970394 C T 113.27 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=59.23;MQ0=0;OQ=488.22;QD=16.27;SB=-210.21 GT:AD:DP:GL:GQ 0/1:14,15:29:-60.84,-8.74,-49.96:99 +chr1 953112 rs2710870 C T 198.18 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.50;MQ=60.00;MQ0=0;OQ=692.82;QD=14.74;SB=-280.19 GT:AD:DP:GL:GQ 0/1:24,23:46:-86.43,-13.86,-83.87:99 +chr1 953580 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=16;HaplotypeScore=1.95;MQ=42.79;MQ0=0;OQ=89.92;QD=8.17;SB=-0.97 GT:AD:DP:GL:GQ 0/1:7,4:8:-14.69,-2.41,-16.44:99 +chr1 953584 rs2465127 T C 0.45 PASS AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=3;HaplotypeScore=3.77;MQ=52.61;MQ0=0;OQ=94.29;QD=7.86;SB=-65.34 GT:AD:DP:GL:GQ 0/1:4,8:9:-15.43,-2.71,-16.16:99 +chr1 954093 . G A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=9.68;MQ=33.26;MQ0=5;OQ=209.72;QD=5.67;SB=-3.99 GT:AD:DP:GL:GQ 0/1:21,12:15:-28.78,-4.52,-24.72:99 +chr1 954161 rs61766303 C G 18.49 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=31.02;MQ0=1;OQ=184.53;QD=5.27;SB=-0.98 GT:AD:DP:GL:GQ 0/1:19,16:16:-26.57,-4.83,-37.31:99 +chr1 954252 rs4970397 C T 103.23 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=32.94;MQ0=3;OQ=204.52;QD=7.57;SB=-35.64 GT:AD:DP:GL:GQ 0/1:17,10:18:-29.16,-5.43,-34.74:99 +chr1 954703 rs4970343 T C 2.35 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=6.47;MQ=58.52;MQ0=0;OQ=457.55;QD=14.30;SB=-98.71 GT:AD:DP:GL:GQ 0/1:14,18:30:-58.08,-9.04,-50.50:99 +chr1 954711 rs4970344 A T 37.45 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.43;MQ0=0;OQ=626.99;QD=19.00;SB=-168.81 GT:AD:DP:GL:GQ 0/1:12,21:33:-75.92,-9.94,-45.13:99 +chr1 954872 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=20.43;MQ=48.78;MQ0=1;OQ=116.04;QD=3.14;SB=-52.28 GT:AD:DP:GL:GQ 0/1:25,12:25:-22.42,-7.54,-71.63:99 +chr1 955038 rs28373660 A G 250.76 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=55.30;MQ0=0;OQ=611.00;QD=13.28;SB=-229.46 GT:AD:DP:GL:GQ 0/1:20,26:39:-76.13,-11.75,-66.91:99 +chr1 955106 . A G 23.39 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=10.05;MQ=39.47;MQ0=7;QD=0.46;SB=-5.58 GT:AD:DP:GL:GQ 0/1:38,13:31:-14.97,-9.35,-98.23:56.21 +chr1 955141 rs28433148 T C 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.04;HRun=0;HaplotypeScore=16.86;MQ=40.85;MQ0=6;OQ=407.46;QD=7.41;SB=-215.36 GT:AD:DP:GL:GQ 0/1:25,28:41:-56.09,-12.06,-84.28:99 +chr1 955386 rs4970404 A G 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.02;HRun=0;HaplotypeScore=18.83;MQ=42.69;MQ0=11;OQ=218.68;QD=3.58;SB=-113.62 GT:AD:DP:GL:GQ 0/1:39,21:33:-35.11,-9.95,-82.73:99 +chr1 955467 rs4970345 C T 151.03 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=44.49;MQ0=2;OQ=398.93;QD=9.73;SB=-192.19 GT:AD:DP:GL:GQ 0/1:19,21:26:-51.01,-7.84,-42.93:99 +chr1 955802 rs4970398 A T 97.51 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=47.03;MQ0=2;OQ=550.07;QD=10.19;SB=-184.73 GT:AD:DP:GL:GQ 0/1:27,27:47:-72.45,-14.16,-100.00:99 +chr1 955812 rs4970399 A G 52.54 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.02;HRun=0;HaplotypeScore=3.69;MQ=45.58;MQ0=2;OQ=418.21;QD=7.47;SB=-156.96 GT:AD:DP:GL:GQ 0/1:27,28:43:-57.78,-12.67,-88.06:99 +chr1 955927 . T C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.47;MQ=51.74;MQ0=5;OQ=79.40;QD=1.80;SB=-44.68 GT:AD:DP:GL:GQ 0/1:30,14:34:-21.47,-10.25,-106.58:99 +chr1 955942 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=21.62;MQ=50.59;MQ0=7;OQ=96.72;QD=1.97;SB=-71.62 GT:AD:DP:GL:GQ 0/1:29,17:31:-22.31,-9.35,-90.50:99 +chr1 956010 . A G 17.59 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=45.86;MQ0=9;QD=0.35;SB=1.17 GT:AD:DP:GL:GQ 0/1:36,13:34:-15.29,-10.25,-111.87:50.35 +chr1 957521 rs4970349 C T 109.68 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.54;MQ=59.65;MQ0=0;OQ=696.48;QD=12.90;SB=-243.23 GT:AD:DP:GL:GQ 0/1:30,24:51:-88.30,-15.37,-100.68:99 +chr1 960023 . C T 7.39 PASS AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=53.50;MQ0=0;OQ=70.28;QD=5.86;SB=-0.98 GT:AD:DP:GL:GQ 0/1:7,5:10:-13.33,-3.02,-17.80:99 +chr1 960078 rs9442364 G C 190.47 PASS AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=59.38;QD=8.48;SB=-32.42 GT:AD:DP:GL:GQ 0/1:3,4:6:-11.04,-1.82,-11.54:92.22 +chr1 961087 rs2799055 A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=6;HaplotypeScore=0.98;MQ=59.32;MQ0=0;OQ=442.07;QD=13.00;SB=-186.63 GT:AD:DP:GL:GQ 0/1:16,18:32:-57.14,-9.65,-55.82:99 +chr1 961230 rs2710883 T C 342.64 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=662.38;QD=14.09;SB=-345.94 GT:AD:DP:GL:GQ 0/1:23,24:47:-83.68,-14.16,-90.90:99 +chr1 961997 rs3121575 C T 135.78 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=582.22;QD=15.32;SB=-286.19 GT:AD:DP:GL:GQ 0/1:17,20:35:-72.05,-10.55,-56.30:99 +chr1 962043 rs4970350 G A 118.77 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=762.03;QD=19.05;SB=-359.38 GT:AD:DP:GL:GQ 0/1:16,24:38:-90.95,-11.46,-47.96:99 +chr1 963199 rs2488993 A G 276.26 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=691.22;QD=14.71;SB=-269.95 GT:AD:DP:GL:GQ 0/1:22,25:46:-86.26,-13.86,-87.86:99 +chr1 963240 rs2465129 G A 277.94 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.66;MQ=58.44;MQ0=0;OQ=598.48;QD=15.35;SB=-309.81 GT:AD:DP:GL:GQ 0/1:19,20:36:-73.98,-10.85,-56.47:99 +chr1 963321 rs2465130 C T 51.96 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=517.87;QD=11.26;SB=-211.85 GT:AD:DP:GL:GQ 0/1:28,18:43:-68.02,-12.95,-92.79:99 +chr1 963531 rs2488994 A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=4;HaplotypeScore=7.50;MQ=58.37;MQ0=0;OQ=421.46;QD=9.80;SB=-94.66 GT:AD:DP:GL:GQ 0/1:26,17:40:-57.48,-12.05,-93.15:99 +chr1 964043 rs3121577 G T 194.69 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=59.29;MQ0=0;OQ=740.60;QD=11.39;SB=-370.98 GT:AD:DP:GL:GQ 0/1:36,29:64:-96.63,-19.29,-128.48:99 +chr1 964062 rs2465131 C T 262.80 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.28;MQ0=0;OQ=941.69;QD=14.71;SB=-361.86 GT:AD:DP:GL:GQ 0/1:34,30:62:-116.13,-18.68,-116.79:99 +chr1 964088 rs2488995 A G 204.47 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=60.00;MQ0=0;OQ=709.06;QD=12.66;SB=-311.29 GT:AD:DP:GL:GQ 0/1:29,27:55:-90.77,-16.58,-108.13:99 +chr1 964159 rs2488996 A G 168.04 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=59.09;MQ0=0;OQ=732.05;QD=15.91;SB=-365.63 GT:AD:DP:GL:GQ 0/1:18,28:43:-89.45,-12.96,-67.34:99 +chr1 964218 rs2488997 G A 8.67 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.51;MQ=58.80;MQ0=0;OQ=657.04;QD=18.77;SB=-348.46 GT:AD:DP:GL:GQ 0/1:15,20:35:-79.53,-10.55,-53.54:99 +chr1 964219 rs2465132 T C 152.74 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=58.80;MQ0=0;OQ=438.83;QD=12.54;SB=-221.28 GT:AD:DP:GL:GQ 0/1:15,20:33:-57.12,-9.95,-56.00:99 +chr1 964357 rs2465133 G T 31.32 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=5.89;MQ=58.66;MQ0=0;OQ=971.31;QD=14.72;SB=-505.87 GT:AD:DP:GL:GQ 0/1:30,36:62:-119.10,-18.68,-97.98:99 +chr1 964433 rs2465134 T G 140.23 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.32;MQ=58.54;MQ0=0;OQ=578.70;QD=12.58;SB=-251.93 GT:AD:DP:GL:GQ 0/1:22,23:38:-72.60,-11.45,-62.23:99 +chr1 964525 rs2465135 G T 124.08 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=58.59;MQ0=0;OQ=621.72;QD=18.84;SB=-320.48 GT:AD:DP:GL:GQ 0/1:13,20:32:-75.10,-9.64,-38.41:99 +chr1 964757 rs3121578 C T 344.84 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.81;MQ0=0;OQ=283.06;QD=10.11;SB=-156.67 GT:AD:DP:GL:GQ 0/1:18,10:26:-39.43,-7.84,-52.76:99 +chr1 964996 rs3121579 T A 109.73 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.40;MQ0=0;OQ=475.63;QD=15.34;SB=-146.82 GT:AD:DP:GL:GQ 0/1:15,16:30:-59.88,-9.04,-53.03:99 +chr1 965565 rs9331224 A G 58.24 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=1.21;MQ=58.67;MQ0=0;OQ=414.04;QD=11.83;SB=-233.27 GT:AD:DP:GL:GQ 0/1:19,16:32:-54.33,-9.64,-64.60:99 +chr1 967066 rs3121552 G C 40.51 LowQual AC=1;AF=0.50;AN=2;DB;DP=5;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=8.10;SB=-43.44 GT:AD:DP:GL:GQ 0/1:3,2:4:-8.54,-1.21,-8.39:71.79 +chr1 967193 rs2799066 T C 15.85 LowQual AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.05;MQ0=0;QD=1.98;SB=-24.63 GT:AD:DP:GL:GQ 0/1:6,2:8:-7.27,-2.41,-22.53:48.57 +chr1 967433 rs2710876 G A 2.15 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=7.34;MQ=57.29;MQ0=0;OQ=207.99;QD=8.00;SB=-101.60 GT:AD:DP:GL:GQ 0/1:14,12:21:-30.42,-6.34,-38.59:99 +chr1 967643 rs2710875 C T 1.07 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=57.25;MQ0=0;OQ=665.34;QD=21.46;SB=-289.34 GT:AD:DP:GL:GQ 0/1:11,20:28:-78.26,-8.44,-23.82:99 +chr1 970323 rs3128097 G A 1.18 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=9.72;MQ=59.47;MQ0=0;OQ=926.21;QD=16.84;SB=-308.84 GT:AD:DP:GL:GQ 0/1:24,31:51:-111.27,-15.36,-80.98:99 +chr1 970950 rs3128098 A G 264.56 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=57.28;MQ0=0;OQ=593.17;QD=14.83;SB=-270.38 GT:AD:DP:GL:GQ 0/1:15,24:36:-73.46,-10.85,-50.98:99 +chr1 971794 rs2465128 A G 68.21 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=60.00;MQ0=0;OQ=206.80;QD=7.66;SB=-83.65 GT:AD:DP:GL:GQ 0/1:13,14:23:-30.90,-6.93,-51.94:99 +chr1 972307 rs3128099 A G 0.33 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=7.82;MQ=57.77;MQ0=0;OQ=622.11;QD=14.81;SB=-282.64 GT:AD:DP:GL:GQ 0/1:15,25:37:-76.65,-11.15,-58.34:99 +chr1 972325 rs3128100 T C 8.29 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=4.33;MQ=57.56;MQ0=0;OQ=1298.64;QD=27.06;SB=-459.21 GT:AD:DP:GL:GQ 1/1:0,48:42:-133.49,-12.67,-0.04:99 +chr1 972376 rs3128101 T C 10.73 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=5.66;MQ=56.76;MQ0=0;OQ=571.56;QD=13.94;SB=-141.55 GT:AD:DP:GL:GQ 0/1:15,25:36:-73.37,-12.93,-53.37:99 +chr1 972804 rs3128102 T C 4.22 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=3.75;MQ=59.50;MQ0=0;OQ=547.08;QD=11.89;SB=-200.60 GT:AD:DP:GL:GQ 0/1:23,23:37:-69.14,-11.15,-71.89:99 +chr1 972857 rs10267 T C 1.79 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.51;MQ=58.63;MQ0=0;OQ=633.32;QD=18.63;SB=-175.96 GT:AD:DP:GL:GQ 0/1:12,21:33:-76.56,-9.94,-48.12:99 +chr1 974010 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=20;HaplotypeScore=11.22;MQ=50.83;MQ0=0;OQ=57.83;QD=3.04;SB=2.03 GT:AD:DP:GL:GQ 0/1:15,4:17:-14.19,-5.12,-41.74:90.67 +chr1 974165 rs9442391 T C 32.20 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=57.07;MQ0=0;OQ=302.47;QD=11.63;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,13:22:-40.16,-6.63,-43.34:99 +chr1 975129 rs2275813 C T 11.79 PASS AC=1;AF=0.50;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.16;MQ0=0;OQ=102.58;QD=20.52;SB=-45.66 GT:AD:DP:GL:GQ 0/1:1,4:5:-15.04,-1.51,-2.70:11.90 +chr1 975309 rs2275812 G T 1.40 PASS AC=1;AF=0.50;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=7.77;MQ=59.16;MQ0=0;OQ=108.56;QD=9.87;SB=-36.92 GT:AD:DP:GL:GQ 0/1:5,6:10:-17.15,-3.01,-16.77:99 +chr1 975312 rs56255212 G A 0.19 PASS AC=1;AF=0.50;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=7.96;MQ=57.00;MQ0=0;OQ=248.84;QD=22.62;SB=-118.97 GT:AD:DP:GL:GQ 0/1:2,9:10:-31.18,-3.01,-6.57:35.54 +chr1 976306 rs2710887 C T 180.42 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=498.86;QD=13.13;SB=-206.20 GT:AD:DP:GL:GQ 0/1:21,17:37:-64.33,-11.16,-66.50:99 +chr1 977063 rs9803031 C T 254.02 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=585.89;QD=18.90;SB=-309.86 GT:AD:DP:GL:GQ 0/1:13,18:30:-70.92,-9.05,-35.55:99 +chr1 977533 rs13303287 T G 495.76 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=796.56;QD=13.73;SB=-424.70 GT:AD:DP:GL:GQ 0/1:25,33:58:-100.42,-17.48,-92.24:99 +chr1 978366 rs2799071 A T 261.84 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=849.34;QD=16.33;SB=-440.60 GT:AD:DP:GL:GQ 0/1:23,29:48:-102.68,-14.47,-71.41:99 +chr1 978795 rs2710871 G C 22.28 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.83;MQ=58.33;MQ0=0;OQ=743.65;QD=17.71;SB=-370.12 GT:AD:DP:GL:GQ 0/1:18,24:36:-88.51,-10.86,-57.89:99 +chr1 980143 rs4275402 C T 40.06 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=58.13;MQ0=0;OQ=896.64;QD=35.87;SB=-438.31 GT:AD:DP:GL:GQ 1/1:0,25:24:-93.26,-7.23,-0.01:72.23 +chr1 980380 rs2710872 C T 78.16 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=549.92;QD=18.33;SB=-189.29 GT:AD:DP:GL:GQ 0/1:12,18:27:-66.42,-8.14,-30.90:99 +chr1 980636 rs2799072 C T 101.12 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.00;MQ0=0;OQ=1104.80;QD=20.09;SB=-396.92 GT:AD:DP:GL:GQ 0/1:22,33:54:-130.03,-16.27,-75.12:99 +chr1 980669 rs2799073 G A 136.86 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=60.00;MQ0=0;OQ=1001.06;QD=20.02;SB=-407.16 GT:AD:DP:GL:GQ 0/1:17,32:47:-117.55,-14.17,-57.43:99 +chr1 980847 rs8014 G A 99.13 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=656.29;QD=17.27;SB=-261.26 GT:AD:DP:GL:GQ 0/1:18,20:38:-80.37,-11.45,-56.60:99 +chr1 981587 rs3121562 C T 350.10 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.79;MQ0=0;OQ=354.87;QD=13.14;SB=-164.15 GT:AD:DP:GL:GQ 0/1:12,15:25:-46.32,-7.55,-37.60:99 +chr1 981840 rs4970400 G A 115.33 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=38.45;MQ=54.81;MQ0=0;QD=3.04;SB=-51.02 GT:AD:DP:GL:GQ 0/1:30,8:33:-24.78,-9.96,-81.20:99 +chr1 981844 rs13303259 A G 138.38 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=33.28;MQ=55.32;MQ0=0;QD=3.29;SB=-90.63 GT:AD:DP:GL:GQ 0/1:32,10:37:-28.28,-11.16,-110.43:99 +chr1 981845 rs2710885 T C 325.46 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=29.31;MQ=55.32;MQ0=0;QD=7.75;SB=-95.70 GT:AD:DP:GL:GQ 0/1:24,18:34:-46.08,-10.25,-78.60:99 +chr1 981905 rs3121564 C T 503.25 Indel AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=56.07;MQ0=0;QD=13.24;SB=-230.23 GT:AD:DP:GL:GQ 0/1:19,19:34:-63.86,-10.25,-57.54:99 +chr1 981947 rs2710886 T C 139.57 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=57.30;MQ0=0;OQ=454.51;QD=9.88;SB=-191.43 GT:AD:DP:GL:GQ 0/1:25,21:45:-62.31,-13.57,-94.53:99 +chr1 981957 rs2799074 T C 39.32 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=57.39;MQ0=0;OQ=362.93;QD=6.48;SB=-127.51 GT:AD:DP:GL:GQ 0/1:32,23:44:-52.84,-13.27,-101.58:99 +chr1 982190 rs2245754 C T 115.77 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.93;MQ=56.87;MQ0=0;OQ=667.97;QD=12.60;SB=-322.42 GT:AD:DP:GL:GQ 0/1:29,24:49:-84.84,-14.76,-98.05:99 +chr1 982682 rs9331226 G A 139.28 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=47.23;MQ0=0;OQ=1563.99;QD=20.85;SB=-791.90 GT:AD:DP:GL:GQ 0/1:29,46:74:-181.97,-22.29,-107.08:99 +chr1 983223 rs13303240 C A 201.17 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.32;MQ0=0;OQ=838.66;QD=15.82;SB=-290.67 GT:AD:DP:GL:GQ 0/1:25,28:52:-102.82,-15.67,-74.49:99 +chr1 984254 rs2488991 G T 204.10 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=58.59;MQ0=0;OQ=458.34;QD=13.89;SB=-201.49 GT:AD:DP:GL:GQ 0/1:13,19:30:-58.16,-9.04,-45.43:99 +chr1 985344 rs9442393 T G 429.35 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=599.53;QD=14.99;SB=-298.50 GT:AD:DP:GL:GQ 0/1:18,22:39:-74.98,-11.75,-60.16:99 +chr1 987271 rs28397086 T C 29.44 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.90;MQ0=0;OQ=513.69;QD=32.11;SB=-117.05 GT:AD:DP:GL:GQ 1/1:0,16:15:-54.96,-4.52,-0.01:45.13 +chr1 988258 rs7526076 A G 181.81 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.56;MQ0=0;OQ=852.42;QD=16.08;SB=-332.31 GT:AD:DP:GL:GQ 0/1:24,29:52:-104.19,-15.67,-91.85:99 +chr1 988445 rs3813194 G C 229.28 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.48;MQ0=0;OQ=676.17;QD=16.90;SB=-324.02 GT:AD:DP:GL:GQ 0/1:19,21:38:-82.36,-11.46,-78.97:99 +chr1 990019 rs11584349 C T 5.80 PASS AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=221.74;QD=18.48;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,7:12:-29.08,-3.62,-14.98:99 +chr1 991040 rs4970401 G C 199.01 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1348.36;QD=21.75;SB=-452.37 GT:AD:DP:GL:GQ 0/1:27,35:61:-156.51,-18.39,-101.07:99 +chr1 992297 rs11260596 C T 126.12 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.11;MQ0=0;OQ=235.14;QD=11.76;SB=-75.09 GT:AD:DP:GL:GQ 0/1:10,10:18:-32.23,-5.43,-30.14:99 +chr1 992795 rs4246502 C G 1.88 PASS AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.20;MQ0=0;OQ=331.32;QD=25.49;SB=-10.00 GT:AD:DP:GL:GQ 0/1:3,10:12:-40.03,-3.62,-11.85:82.27 +chr1 992916 rs4074992 C T 64.57 PASS AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.96;MQ0=0;OQ=236.09;QD=13.12;SB=-45.65 GT:AD:DP:GL:GQ 0/1:9,9:18:-32.32,-5.43,-28.25:99 +chr1 993492 rs4075116 C T 510.01 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=697.41;QD=15.16;SB=-277.76 GT:AD:DP:GL:GQ 0/1:23,23:43:-85.98,-12.96,-73.34:99 +chr1 994820 rs4073176 G A 10.79 PASS AC=1;AF=0.50;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=141.42;QD=15.71;SB=-0.98 GT:AD:DP:GL:GQ 0/1:4,5:9:-20.14,-2.71,-13.80:99 +chr1 994843 rs4073177 G A 1.13 PASS AC=1;AF=0.50;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=225.74;QD=20.52;SB=-3.99 GT:AD:DP:GL:GQ 0/1:4,7:11:-29.17,-3.31,-13.13:98.16 +chr1 995932 rs55918415 G A 129.98 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=57.98;MQ0=1;OQ=500.10;QD=13.89;SB=-124.09 GT:AD:DP:GL:GQ 0/1:20,16:33:-63.24,-9.94,-54.88:99 +chr1 996086 rs9442394 G A 160.48 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=2.17;MQ=59.51;MQ0=0;OQ=685.95;QD=14.59;SB=-304.81 GT:AD:DP:GL:GQ 0/1:25,22:45:-85.44,-13.56,-78.07:99 +chr1 996853 rs4326571 G A 22.99 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.32;MQ=58.90;MQ0=0;OQ=529.40;QD=13.93;SB=-35.65 GT:AD:DP:GL:GQ 0/1:21,17:38:-67.68,-11.45,-66.25:99 +chr1 999097 rs9442366 T C 69.15 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.30;MQ0=0;OQ=217.52;QD=6.59;SB=-81.95 GT:AD:DP:GL:GQ 0/1:21,12:31:-34.38,-9.34,-81.07:99 +chr1 999304 . G A 28.33 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=57.94;MQ0=0;OQ=327.19;QD=9.62;SB=-182.19 GT:AD:DP:GL:GQ 0/1:21,13:31:-45.35,-9.34,-65.26:99 +chr1 999341 rs9442367 G C 25.99 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=2;HaplotypeScore=0.81;MQ=58.59;MQ0=0;OQ=590.30;QD=17.89;SB=-256.14 GT:AD:DP:GL:GQ 0/1:14,19:30:-71.37,-9.06,-48.75:99 +chr1 1000580 rs9442368 C T 47.69 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=4.96;MQ=54.71;MQ0=0;OQ=650.78;QD=15.49;SB=-262.79 GT:AD:DP:GL:GQ 0/1:21,21:39:-80.11,-11.75,-60.91:99 +chr1 1000958 rs11810785 A G 695.93 Indel AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=6;HaplotypeScore=2.96;MQ=54.24;MQ0=1;QD=26.77;SB=-339.63 GT:AD:DP:GL:GQ 1/1:0,26:21:-73.19,-6.33,-0.01:63.17 +chr1 1001394 . T C 34.95 LowQual AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=41.30;MQ0=1;QD=3.88;SB=-6.99 GT:AD:DP:GL:GQ 0/1:6,3:8:-9.19,-2.41,-20.53:67.78 +chr1 1001500 . A T 20.13 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=16.78;MQ0=8;QD=0.81;SB=-10.00 GT:AD:DP:GL:GQ 0/1:19,5:9:-8.01,-2.72,-22.07:52.92 +chr1 1002064 . G C 10.08 LowQual AC=1;AF=0.50;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.77;MQ0=0;QD=5.04;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,1:1:-4.25,-0.30,-0.00:1.76 +chr1 1002464 . A T 1.23 PASS AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=18.46;MQ0=3;OQ=57.47;QD=3.59;SB=-37.37 GT:AD:DP:GL:GQ 0/1:8,7:4:-10.24,-1.21,-3.80:25.95 +chr1 1002488 . A T 34.11 LowQual AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=7.23;MQ=19.96;MQ0=3;QD=2.27;SB=-4.00 GT:AD:DP:GL:GQ 0/1:9,6:4:-7.90,-1.21,-5.60:43.89 +chr1 1002494 . A T 35.11 LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=4.75;MQ=19.72;MQ0=3;QD=2.51;SB=-7.00 GT:AD:DP:GL:GQ 0/1:7,7:3:-7.70,-0.90,-3.30:23.95 +chr1 1002516 . G A 46.02 LowQual AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=18.44;MQ0=1;QD=4.60;SB=-10.00 GT:AD:DP:GL:GQ 1/1:5,5:2:-8.01,-0.60,-0.00:6.02 +chr1 1002856 . T G 12.29 PASS AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.33;MQ0=1;OQ=106.33;QD=5.32;SB=-21.95 GT:AD:DP:GL:GQ 0/1:10,10:13:-17.84,-3.92,-27.80:99 +chr1 1003100 . C T 26.46 LowQual AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=39.70;MQ0=0;QD=2.65;SB=-3.99 GT:AD:DP:GL:GQ 0/1:8,2:6:-7.74,-1.81,-13.13:59.28 +chr1 1003243 . G C 4.11 PASS AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.94;MQ=27.95;MQ0=9;OQ=330.47;QD=13.77;SB=-94.94 GT:AD:DP:GL:GQ 1/1:14,10:9:-36.64,-2.72,-0.01:27.09 +chr1 1003514 . C A 42.25 LowQual AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.30;MQ0=1;QD=7.04;SB=-46.39 GT:AD:DP:GL:GQ 1/1:0,6:2:-7.63,-0.60,-0.00:6.02 +chr1 1003557 . T A 0.08 PASS AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=5.02;MQ=17.13;MQ0=14;OQ=71.49;QD=2.98;SB=-43.38 GT:AD:DP:GL:GQ 0/1:21,3:4:-11.64,-1.20,-3.64:24.35 +chr1 1003864 . G C 10.99 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=9.87;MQ=5.60;MQ0=15;QD=0.58;SB=-10.00 GT:AD:DP:GL:GQ 0/1:17,2:1:-4.35,-0.30,-0.00:1.76 +chr1 1004168 . A T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=12.18;MQ=19.95;MQ0=11;OQ=53.86;QD=2.56;SB=-37.95 GT:AD:DP:GL:GQ 0/1:14,6:6:-10.48,-1.81,-11.22:86.70 +chr1 1004254 . G C 33.05 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=6.90;MQ=13.09;MQ0=11;QD=1.32;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,12:4:-7.80,-1.21,-8.59:65.89 +chr1 1004313 . G C 21.04 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=11.38;MQ0=14;QD=0.84;SB=-3.98 GT:AD:DP:GL:GQ 0/1:23,2:6:-7.19,-1.81,-17.58:53.84 +chr1 1004699 rs12401605 A G 193.45 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=54.82;MQ0=0;OQ=256.92;QD=8.56;SB=-154.32 GT:AD:DP:GL:GQ 0/1:17,12:28:-37.42,-8.44,-63.53:99 +chr1 1004727 rs12411041 T A 29.53 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=54.35;MQ0=0;OQ=225.92;QD=6.11;SB=-72.06 GT:AD:DP:GL:GQ 0/1:25,11:32:-35.52,-9.65,-76.83:99 +chr1 1004989 rs36027499 A G 65.38 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=54.55;MQ0=0;OQ=184.41;QD=7.38;SB=-109.60 GT:AD:DP:GL:GQ 0/1:16,9:24:-28.96,-7.24,-58.60:99 +chr1 1005120 rs9442369 A G 5.28 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.36;MQ0=0;OQ=146.76;QD=4.08;SB=-64.75 GT:AD:DP:GL:GQ 0/1:26,10:34:-28.21,-10.25,-99.59:99 +chr1 1005414 rs9442370 C T 185.20 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.23;MQ0=0;OQ=413.23;QD=13.77;SB=-165.25 GT:AD:DP:GL:GQ 0/1:14,16:26:-52.45,-7.84,-38.57:99 +chr1 1005680 rs12746483 G A 50.56 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=2.06;MQ=55.16;MQ0=0;OQ=462.98;QD=16.54;SB=-241.55 GT:AD:DP:GL:GQ 0/1:13,15:28:-58.02,-8.44,-44.58:99 +chr1 1007033 rs3766193 C G 206.38 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=57.65;MQ0=0;OQ=606.89;QD=15.97;SB=-241.40 GT:AD:DP:GL:GQ 0/1:19,19:36:-74.82,-10.85,-77.35:99 +chr1 1007060 rs3766192 C T 263.39 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=59.03;MQ0=0;OQ=740.51;QD=17.22;SB=-335.87 GT:AD:DP:GL:GQ 0/1:19,24:42:-90.01,-12.67,-54.97:99 +chr1 1007204 rs1133647 G T 220.81 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.63;MQ0=0;OQ=352.30;QD=10.36;SB=-144.83 GT:AD:DP:GL:GQ 0/1:20,14:34:-48.76,-10.25,-68.42:99 +chr1 1008007 rs9442395 T C 79.76 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.17;MQ=58.20;MQ0=0;OQ=515.12;QD=11.71;SB=-260.59 GT:AD:DP:GL:GQ 0/1:23,21:43:-67.76,-12.96,-87.04:99 +chr1 1008425 rs9442371 C T 263.64 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=58.95;MQ0=0;OQ=629.69;QD=14.31;SB=-217.52 GT:AD:DP:GL:GQ 0/1:24,20:39:-78.01,-11.76,-59.01:99 +chr1 1008567 rs9442372 A G 252.74 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.72;MQ=58.97;MQ0=0;OQ=538.45;QD=11.97;SB=-254.34 GT:AD:DP:GL:GQ 0/1:20,24:42:-69.79,-12.66,-79.04:99 +chr1 1009038 rs2298215 C G 217.10 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=60.00;MQ0=0;OQ=687.91;QD=14.95;SB=-237.07 GT:AD:DP:GL:GQ 0/1:26,20:46:-85.94,-13.87,-107.64:99 +chr1 1009043 rs9442396 T C 432.81 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=537.22;QD=11.94;SB=-291.59 GT:AD:DP:GL:GQ 0/1:24,21:42:-69.65,-12.65,-93.39:99 +chr1 1010269 rs9442397 T C 3.22 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.96;MQ=59.38;MQ0=0;OQ=202.19;QD=5.46;SB=-53.82 GT:AD:DP:GL:GQ 0/1:25,12:35:-34.05,-10.54,-100.39:99 +chr1 1011278 rs3737728 A G 36.30 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=58.01;MQ0=0;OQ=401.40;QD=7.72;SB=-209.34 GT:AD:DP:GL:GQ 0/1:32,20:49:-58.20,-14.77,-121.11:99 +chr1 1011558 rs9442398 A G 416.42 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.92;MQ0=0;OQ=544.78;QD=12.67;SB=-280.28 GT:AD:DP:GL:GQ 0/1:17,25:38:-69.23,-11.47,-56.30:99 +chr1 1011900 rs6701114 C T 240.77 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=59.30;MQ0=0;OQ=587.87;QD=17.81;SB=-314.84 GT:AD:DP:GL:GQ 0/1:13,20:30:-71.11,-9.04,-40.79:99 +chr1 1013307 rs9442399 C G 25.25 PASS AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=338.37;QD=37.60;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:9:-37.42,-2.71,-0.00:27.09 +chr1 1015133 . C T 6.55 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.91;MQ=59.48;MQ0=0;OQ=504.60;QD=11.47;SB=-145.62 GT:AD:DP:GL:GQ 0/1:26,18:38:-65.20,-11.46,-67.24:99 +chr1 1015164 rs9442400 T C 212.54 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.61;MQ0=0;OQ=1416.80;QD=29.52;SB=-594.18 GT:AD:DP:GL:GQ 1/1:0,48:47:-145.32,-14.18,-0.06:99 +chr1 1016570 rs4074137 C A 81.77 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=60.00;MQ0=0;OQ=196.23;QD=6.33;SB=-112.43 GT:AD:DP:GL:GQ 0/1:22,9:30:-31.95,-9.04,-69.97:99 +chr1 1016664 rs4562563 T A 69.49 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=58.99;MQ0=0;OQ=428.33;QD=18.62;SB=-222.84 GT:AD:DP:GL:GQ 0/1:8,15:23:-53.05,-6.93,-28.44:99 +chr1 1021403 rs9651273 A G 292.85 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=648.57;QD=9.40;SB=-308.20 GT:AD:DP:GL:GQ 0/1:44,25:69:-88.92,-20.78,-180.93:99 +chr1 1022047 rs9651272 A G 123.66 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=59.58;MQ0=0;OQ=389.06;QD=8.84;SB=-195.60 GT:AD:DP:GL:GQ 0/1:25,19:42:-54.85,-12.66,-100.05:99 +chr1 1023862 rs4970353 C T 10.88 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=971.03;QD=16.18;SB=-472.48 GT:AD:DP:GL:GQ 0/1:30,30:59:-118.16,-17.77,-101.63:99 +chr1 1025668 rs12759295 G A 84.62 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=59.60;MQ0=0;OQ=2089.51;QD=36.03;SB=-522.67 GT:AD:DP:GL:GQ 1/1:0,58:54:-212.56,-16.27,-0.02:99 +chr1 1026680 rs61766341 T C 205.76 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=959.29;QD=13.51;SB=-415.84 GT:AD:DP:GL:GQ 0/1:32,39:68:-119.71,-20.50,-125.74:99 +chr1 1026910 rs12134754 C T 210.31 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.33;MQ0=0;OQ=1080.76;QD=17.43;SB=-366.87 GT:AD:DP:GL:GQ 0/1:30,32:60:-129.44,-18.08,-89.78:99 +chr1 1027893 . T A 15.04 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=20;HaplotypeScore=5.87;MQ=44.25;MQ0=4;QD=0.40;SB=32.13 GT:AD:DP:GL:GQ 0/1:33,5:23:-11.70,-6.93,-76.52:47.73 +chr1 1037844 rs11584392 G A 163.44 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.82;MQ0=0;OQ=608.74;QD=14.16;SB=-241.74 GT:AD:DP:GL:GQ 0/1:22,21:40:-76.22,-12.06,-65.82:99 +chr1 1043248 rs4970408 C T 441.42 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.36;MQ0=0;OQ=945.52;QD=17.51;SB=-425.94 GT:AD:DP:GL:GQ 0/1:25,29:54:-114.11,-16.27,-86.23:99 +chr1 1050037 rs7548798 C T 114.73 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=3.36;MQ=58.61;MQ0=0;OQ=733.89;QD=15.61;SB=-330.30 GT:AD:DP:GL:GQ 0/1:24,23:47:-90.84,-14.17,-83.86:99 +chr1 1050038 rs7556082 T C 10.07 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=4;HaplotypeScore=2.36;MQ=58.61;MQ0=0;OQ=528.95;QD=11.25;SB=-283.60 GT:AD:DP:GL:GQ 0/1:24,23:46:-70.05,-13.87,-95.38:99 +chr1 1050218 rs12567855 G C 18.84 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=1.10;MQ=59.48;MQ0=0;OQ=549.12;QD=15.25;SB=-150.55 GT:AD:DP:GL:GQ 0/1:19,17:33:-68.15,-9.95,-68.62:99 +chr1 1050923 . C G 38.31 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=7.12;MQ=59.57;MQ0=0;QD=0.71;SB=62.24 GT:AD:DP:GL:GQ 0/1:40,14:36:-17.98,-10.86,-134.66:71.15 +chr1 1051029 rs11807848 T C 153.72 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.10;MQ=60.00;MQ0=0;OQ=328.64;QD=9.39;SB=-171.94 GT:AD:DP:GL:GQ 0/1:21,14:34:-46.39,-10.24,-82.90:99 +chr1 1051657 rs34530354 A G 139.07 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.25;MQ0=0;OQ=341.50;QD=11.02;SB=-128.73 GT:AD:DP:GL:GQ 0/1:17,14:30:-46.47,-9.04,-63.98:99 +chr1 1051711 rs35207507 A G 157.75 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=57.36;MQ0=0;OQ=232.59;QD=9.30;SB=-75.78 GT:AD:DP:GL:GQ 0/1:12,13:22:-33.17,-6.63,-47.34:99 +chr1 1051888 rs9329411 A G 8.12 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=3;HaplotypeScore=0.32;MQ=58.95;MQ0=0;OQ=307.14;QD=13.96;SB=-152.31 GT:AD:DP:GL:GQ 0/1:10,12:20:-40.02,-6.03,-35.33:99 +chr1 1052501 rs9442373 C A 218.78 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.03;MQ0=0;OQ=1229.67;QD=18.35;SB=-293.35 GT:AD:DP:GL:GQ 0/1:29,38:65:-145.84,-19.58,-78.11:99 +chr1 1052907 rs7545801 A G 1.69 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=2.49;MQ=60.00;MQ0=0;OQ=935.67;QD=29.24;SB=-247.57 GT:AD:DP:GL:GQ 1/1:0,32:30:-97.17,-9.04,-0.02:90.21 +chr1 1053104 rs4970413 G T 111.15 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.50;MQ=59.42;MQ0=0;OQ=637.82;QD=15.95;SB=-209.62 GT:AD:DP:GL:GQ 0/1:16,24:36:-77.92,-10.85,-38.08:99 +chr1 1053355 rs55945496 G A 154.74 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=58.97;MQ0=0;OQ=692.26;QD=15.38;SB=-240.56 GT:AD:DP:GL:GQ 0/1:24,21:40:-84.57,-12.06,-60.15:99 +chr1 1054398 rs6682475 G C 62.97 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=3.35;MQ=57.20;MQ0=0;OQ=522.88;QD=16.34;SB=-284.57 GT:AD:DP:GL:GQ 0/1:16,16:32:-65.22,-9.65,-67.94:99 +chr1 1054533 rs7547403 C G 0.36 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=4;HaplotypeScore=0.79;MQ=59.42;MQ0=0;OQ=1637.77;QD=40.94;SB=-672.45 GT:AD:DP:GL:GQ 1/1:0,40:39:-167.38,-11.75,-0.02:99 +chr1 1054665 rs2298216 T C 152.44 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=59.60;MQ0=0;OQ=1938.74;QD=34.01;SB=-772.11 GT:AD:DP:GL:GQ 1/1:0,57:57:-197.48,-17.17,-0.02:99 +chr1 1055159 rs4072537 T C 138.47 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.50;MQ0=0;OQ=1817.15;QD=30.80;SB=-665.83 GT:AD:DP:GL:GQ 1/1:0,59:56:-185.34,-16.89,-0.04:99 +chr1 1055460 rs9442357 C A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.04;HRun=20;HaplotypeScore=17.31;MQ=48.11;MQ0=2;OQ=1123.16;QD=23.90;SB=-311.46 GT:AD:DP:GL:GQ 1/1:9,36:37:-122.62,-11.15,-6.72:44.32 +chr1 1056122 rs4072496 G C 273.90 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=828.08;QD=31.85;SB=-146.57 GT:AD:DP:GL:GQ 1/1:0,26:22:-86.41,-6.64,-0.02:66.21 +chr1 1056145 rs10907181 A G 65.29 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=60.00;MQ0=0;OQ=849.61;QD=28.32;SB=-350.43 GT:AD:DP:GL:GQ 1/1:0,30:29:-88.58,-8.75,-0.04:87.15 +chr1 1056266 rs10907182 T C 152.84 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.47;MQ0=0;OQ=1343.61;QD=29.86;SB=-493.15 GT:AD:DP:GL:GQ 1/1:0,45:43:-137.99,-12.97,-0.04:99 +chr1 1056679 . A G 17.68 PASS AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.92;MQ0=0;OQ=622.64;QD=23.06;SB=-77.91 GT:AD:DP:GL:GQ 1/1:0,27:19:-65.86,-5.72,-0.01:57.16 +chr1 1056682 rs7513297 A G 4.15 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=33.92;MQ0=0;OQ=613.60;QD=22.73;SB=-73.89 GT:AD:DP:GL:GQ 1/1:0,27:19:-64.96,-5.73,-0.01:57.15 +chr1 1056691 rs7553878 C G 182.98 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=38.04;MQ0=0;OQ=986.57;QD=30.83;SB=-182.68 GT:AD:DP:GL:GQ 1/1:0,32:25:-102.26,-7.54,-0.01:75.24 +chr1 1056809 rs7513404 A G 1483.16 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=11.12;MQ=36.69;MQ0=3;QD=26.02;SB=-571.97 GT:AD:DP:GL:GQ 1/1:2,55:47:-151.94,-14.18,-0.04:99 +chr1 1056815 rs7513405 A G 1422.20 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=12.03;MQ=35.94;MQ0=3;QD=26.83;SB=-591.02 GT:AD:DP:GL:GQ 1/1:4,49:44:-145.84,-13.27,-0.03:99 +chr1 1056816 rs7516160 T C 1466.09 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=12.03;MQ=36.53;MQ0=3;QD=27.15;SB=-727.28 GT:AD:DP:GL:GQ 1/1:3,50:47:-150.24,-14.18,-0.04:99 +chr1 1057725 rs9442374 T G 13.34 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=58.50;MQ0=0;OQ=951.55;QD=30.70;SB=-471.37 GT:AD:DP:GL:GQ 1/1:0,31:29:-98.75,-8.74,-0.01:87.23 +chr1 1057728 rs9442358 A C 4.18 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=0.48;MQ=58.50;MQ0=0;OQ=931.22;QD=30.04;SB=-418.04 GT:AD:DP:GL:GQ 1/1:1,30:28:-96.72,-8.44,-0.02:84.22 +chr1 1059288 rs9442375 C A 11.97 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=37.62;MQ0=0;OQ=1307.51;QD=33.53;SB=-359.86 GT:AD:DP:GL:GQ 1/1:0,39:37:-134.35,-11.15,-0.01:99 +chr1 1059306 rs9442376 G A 317.82 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=30.41;MQ0=0;OQ=1189.43;QD=32.15;SB=-404.66 GT:AD:DP:GL:GQ 1/1:0,37:31:-122.54,-9.34,-0.01:93.30 +chr1 1059314 rs9442377 G A 1.90 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=4.82;MQ=29.14;MQ0=0;OQ=1298.78;QD=30.92;SB=-496.01 GT:AD:DP:GL:GQ 1/1:0,42:35:-133.48,-10.55,-0.02:99 +chr1 1059991 rs9442378 T G 44.61 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.34;MQ0=0;OQ=1111.12;QD=31.75;SB=-500.92 GT:AD:DP:GL:GQ 1/1:0,35:33:-114.71,-9.94,-0.02:99 +chr1 1060304 rs9442379 C T 128.73 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1793.65;QD=37.37;SB=-715.98 GT:AD:DP:GL:GQ 1/1:0,48:46:-182.96,-13.86,-0.01:99 +chr1 1060981 rs10907183 G C 289 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.17;MQ=58.88;MQ0=0;OQ=1986.90;QD=34.26;SB=-998.16 GT:AD:DP:GL:GQ 1/1:0,58:51:-202.32,-15.40,-0.05:99 +chr1 1061055 rs6604971 T C 165.65 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=59.35;MQ0=0;OQ=1959.28;QD=30.61;SB=-872.00 GT:AD:DP:GL:GQ 1/1:0,64:62:-199.57,-18.70,-0.06:99 +chr1 1062361 rs9442360 G C 41.74 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.77;MQ0=0;QD=13.91;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:2:-7.58,-0.60,-0.00:6.02 +chr1 1063812 . C A 39.60 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=20;HaplotypeScore=10.99;MQ=49.89;MQ0=1;QD=0.94;SB=53.19 GT:AD:DP:GL:GQ 0/1:34,7:30:-16.28,-9.04,-89.71:72.44 +chr1 1064433 . T C 21.13 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=43.11;MQ0=1;QD=1.11;SB=5.04 GT:AD:DP:GL:GQ 0/1:14,5:14:-9.62,-4.23,-37.37:53.93 +chr1 1064508 . A G 48.32 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=5;HaplotypeScore=5.11;MQ=25.52;MQ0=20;QD=0.93;SB=-10.00 GT:AD:DP:GL:GQ 0/1:42,6:27:-16.25,-8.14,-83.13:81.15 +chr1 1064534 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=5.91;MQ=22.24;MQ0=19;OQ=77.81;QD=1.62;SB=-10.00 GT:AD:DP:GL:GQ 0/1:26,22:23:-17.99,-6.93,-63.10:99 +chr1 1064544 . G A 18.70 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=9.26;MQ=23.84;MQ0=13;QD=0.45;SB=-10.00 GT:AD:DP:GL:GQ 0/1:39,3:23:-12.08,-6.93,-67.67:51.47 +chr1 1064666 . G A 28.24 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=17.49;MQ0=7;QD=1.34;SB=-10.00 GT:AD:DP:GL:GQ 0/1:19,2:4:-7.31,-1.21,-6.24:50.32 +chr1 1064676 . G A 32.25 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=15.31;MQ0=8;QD=1.61;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,4:3:-7.41,-0.90,-3.57:26.65 +chr1 1064678 . A G 13.68 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=15.31;MQ0=8;QD=0.68;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,5:3:-5.54,-0.90,-4.06:31.54 +chr1 1065083 . T G 0.75 PASS AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=13.28;MQ0=6;OQ=72.14;QD=8.02;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,7:3:-10.70,-0.90,-0.00:9.03 +chr1 1065545 . A T 15.58 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=6.82;MQ=15.84;MQ0=10;QD=0.78;SB=-20.32 GT:AD:DP:GL:GQ 0/1:16,4:8:-7.24,-2.41,-23.49:48.29 +chr1 1065754 . T G 10.50 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=26.23;MQ0=5;QD=0.50;SB=-7.00 GT:AD:DP:GL:GQ 0/1:10,11:9:-7.00,-2.71,-25.01:42.93 +chr1 1065788 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=4;HaplotypeScore=1.91;MQ=35.15;MQ0=3;OQ=426.85;QD=16.42;SB=-65.33 GT:AD:DP:GL:GQ 0/1:10,16:20:-52.00,-6.03,-21.27:99 +chr1 1065876 rs34294086 G T 14.09 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.05;MQ=16.68;MQ0=19;QD=0.25;SB=-0.98 GT:AD:DP:GL:GQ 0/1:47,10:18:-10.10,-5.43,-46.58:46.75 +chr1 1065896 rs34976191 A G 3.15 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=5.11;MQ=25.24;MQ0=16;OQ=221.06;QD=5.02;SB=-47.30 GT:AD:DP:GL:GQ 0/1:32,12:17:-30.51,-5.13,-29.81:99 +chr1 1065898 rs35853231 G A 14.06 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=25.42;MQ0=15;OQ=228.24;QD=5.43;SB=-22.49 GT:AD:DP:GL:GQ 0/1:33,9:15:-30.63,-4.52,-21.87:99 +chr1 1066927 rs4970357 C A 263.23 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=704.25;QD=32.01;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,22:21:-74.02,-6.32,-0.01:63.19 +chr1 1067825 rs55750860 C T 23.40 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.51;MQ=58.95;MQ0=0;OQ=1494.41;QD=37.36;SB=-613.01 GT:AD:DP:GL:GQ 1/1:0,40:39:-153.04,-11.75,-0.01:99 +chr1 1070149 rs1539638 G A 498.18 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1278.23;QD=37.59;SB=-657.67 GT:AD:DP:GL:GQ 1/1:0,34:33:-131.42,-9.94,-0.01:99 +chr1 1070766 . C G 0.10 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=47.59;MQ0=0;OQ=113.71;QD=2.58;SB=-2.32 GT:AD:DP:GL:GQ 0/1:34,9:39:-26.42,-11.76,-133.80:99 +chr1 1070768 . C T 0.13 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=46.93;MQ0=0;OQ=115.95;QD=2.64;SB=-32.19 GT:AD:DP:GL:GQ 0/1:34,10:38:-26.33,-11.45,-104.66:99 +chr1 1070788 rs1539637 G C 8.38 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=2.86;MQ=44.98;MQ0=0;OQ=574.54;QD=14.73;SB=-154.58 GT:AD:DP:GL:GQ 0/1:22,17:37:-71.91,-11.17,-77.14:99 +chr1 1070790 rs4512588 T C 118.97 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.33;MQ=44.52;MQ0=0;OQ=439.51;QD=11.57;SB=-120.73 GT:AD:DP:GL:GQ 0/1:20,18:36:-58.08,-10.85,-73.14:99 +chr1 1070804 . T C 317.73 Indel AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=43.50;MQ0=0;QD=8.83;SB=-125.65 GT:AD:DP:GL:GQ 0/1:20,16:34:-45.31,-10.25,-78.50:99 +chr1 1070810 . T C 59.59 Indel AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=42.56;MQ0=0;QD=1.92;SB=-21.88 GT:AD:DP:GL:GQ 0/1:21,10:26:-17.08,-7.83,-82.36:92.43 +chr1 1070825 . C T 12.15 LowQual AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=46.99;MQ0=0;QD=0.45;SB=-5.49 GT:AD:DP:GL:GQ 0/1:24,3:26:-12.31,-7.84,-75.55:44.71 +chr1 1070828 . C T 17.92 LowQual AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=46.99;MQ0=0;QD=0.66;SB=-11.45 GT:AD:DP:GL:GQ 0/1:24,3:24:-12.30,-7.23,-73.32:50.69 +chr1 1074807 . T G 14.10 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=4;HaplotypeScore=1.72;MQ=58.59;MQ0=0;QD=0.43;SB=59.21 GT:AD:DP:GL:GQ 0/1:24,8:27:-12.81,-8.13,-82.30:46.77 +chr1 1075432 . C T 38.87 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=57.97;MQ0=0;OQ=818.81;QD=17.80;SB=-345.86 GT:AD:DP:GL:GQ 0/1:20,26:46:-99.04,-13.88,-63.69:99 +chr1 1077546 rs9442380 T C 202.60 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=2295.26;QD=29.81;SB=-1162.13 GT:AD:DP:GL:GQ 1/1:0,76:73:-233.18,-22.02,-0.07:99 +chr1 1079125 rs4970358 A G 12.32 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=5.70;MQ=59.35;MQ0=0;OQ=2374.58;QD=33.44;SB=-995.95 GT:AD:DP:GL:GQ 1/1:0,69:68:-244.00,-23.26,-2.96:99 +chr1 1079873 rs9442361 C A 5.87 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=1.89;MQ=53.07;MQ0=0;OQ=1204.88;QD=33.47;SB=-532.76 GT:AD:DP:GL:GQ 1/1:0,36:34:-124.08,-10.24,-0.01:99 +chr1 1080440 rs6604972 A G 531.63 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=1807.70;QD=30.64;SB=-735.76 GT:AD:DP:GL:GQ 1/1:0,59:56:-184.40,-16.89,-0.04:99 +chr1 1082462 rs56863140 G C 99.95 PASS AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=146.93;QD=24.49;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,6:5:-18.26,-1.52,-0.01:15.05 +chr1 1084348 rs4970360 C T 64.65 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.36;MQ=58.41;MQ0=0;OQ=1613.83;QD=36.68;SB=-777.04 GT:AD:DP:GL:GQ 1/1:0,44:42:-164.99,-12.66,-0.02:99 +chr1 1084535 rs4970361 A C 88.25 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=58.78;MQ0=1;OQ=1424.16;QD=32.37;SB=-688.05 GT:AD:DP:GL:GQ 1/1:1,43:41:-146.01,-12.35,-0.01:99 +chr1 1084601 rs4970362 A G 229.75 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.71;MQ=59.53;MQ0=0;OQ=1464.98;QD=29.90;SB=-668.84 GT:AD:DP:GL:GQ 1/1:0,49:47:-150.13,-14.18,-0.04:99 +chr1 1084842 rs7538773 G A 9.80 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.13;MQ0=0;OQ=1279.59;QD=36.56;SB=-199.76 GT:AD:DP:GL:GQ 1/1:0,33:33:-131.55,-9.94,-0.01:99 +chr1 1085246 rs6604973 G A 85.72 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.42;MQ0=0;OQ=1511.71;QD=37.79;SB=-646.86 GT:AD:DP:GL:GQ 1/1:0,40:38:-154.76,-11.45,-0.01:99 +chr1 1085482 rs4970419 C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=7;HaplotypeScore=2.24;MQ=59.45;MQ0=0;OQ=1670.84;QD=39.78;SB=-828.31 GT:AD:DP:GL:GQ 1/1:0,42:40:-170.69,-12.06,-0.02:99 +chr1 1085874 rs9442381 C G 314.67 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.11;MQ0=0;OQ=1195.39;QD=38.56;SB=-412.65 GT:AD:DP:GL:GQ 1/1:0,31:28:-123.13,-8.44,-0.01:84.28 +chr1 1086061 rs9442382 C T 139.37 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=990.01;QD=38.08;SB=-164.21 GT:AD:DP:GL:GQ 1/1:0,26:26:-102.60,-7.84,-0.01:78.25 +chr1 1086771 rs1539636 T C 148.49 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=60.00;MQ0=0;OQ=1262.30;QD=33.22;SB=-642.89 GT:AD:DP:GL:GQ 1/1:0,38:37:-129.83,-11.15,-0.02:99 +chr1 1086955 rs1539635 G A 48.48 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.31;MQ=56.37;MQ0=0;OQ=1687.66;QD=35.91;SB=-612.00 GT:AD:DP:GL:GQ 1/1:0,47:43:-172.36,-12.95,-0.01:99 +chr1 1086963 rs1539634 C T 83.45 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.95;MQ0=0;OQ=1761.33;QD=36.69;SB=-642.86 GT:AD:DP:GL:GQ 1/1:0,48:45:-179.73,-13.56,-0.02:99 +chr1 1087150 rs9442384 T C 36.04 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=59.81;MQ0=0;OQ=1429.90;QD=29.79;SB=-636.25 GT:AD:DP:GL:GQ 1/1:0,48:46:-146.63,-13.88,-0.05:99 +chr1 1087198 rs9442385 T G 89.37 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=57.84;MQ0=0;OQ=1240.37;QD=26.39;SB=-556.87 GT:AD:DP:GL:GQ 1/1:0,47:40:-127.66,-12.06,-0.04:99 +chr1 1087800 rs1891907 A G 2.98 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=57.36;MQ0=0;OQ=810.89;QD=32.44;SB=-193.80 GT:AD:DP:GL:GQ 1/1:0,25:24:-84.68,-7.23,-0.01:72.21 +chr1 1088284 rs12135382 C T 198.45 PASS AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=312.05;QD=28.37;SB=-50.56 GT:AD:DP:GL:GQ 1/1:0,11:9:-34.79,-2.71,-0.00:27.09 +chr1 1088577 rs4379629 C G 8.91 PASS AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=217.53;QD=24.17;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:7:-25.35,-2.12,-0.02:21.06 +chr1 1089205 rs9660710 A C 62.17 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=60.00;MQ0=0;OQ=1253.07;QD=26.66;SB=-477.88 GT:AD:DP:GL:GQ 1/1:0,47:40:-128.93,-12.06,-0.03:99 +chr1 1090080 rs1891905 C T 107.83 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=58.89;MQ0=0;OQ=1593.75;QD=37.95;SB=-678.31 GT:AD:DP:GL:GQ 1/1:0,42:41:-162.97,-12.35,-0.01:99 +chr1 1090182 rs1891904 C A 413.02 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=739.19;QD=30.80;SB=-375.45 GT:AD:DP:GL:GQ 1/1:0,24:22:-77.51,-6.63,-0.01:66.17 +chr1 1090866 rs7549819 C T 73.60 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=59.25;MQ0=0;OQ=998.72;QD=32.22;SB=-450.59 GT:AD:DP:GL:GQ 1/1:1,30:27:-103.47,-8.14,-0.02:81.25 +chr1 1091932 rs9442386 A G 1.23 PASS AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=172.84;QD=21.61;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:7:-20.87,-2.12,-0.01:21.04 +chr1 1093405 rs7518873 T C 57.10 PASS AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.77;MQ0=0;OQ=646.68;QD=30.79;SB=-268.71 GT:AD:DP:GL:GQ 1/1:0,21:20:-68.26,-6.03,-0.01:60.16 +chr1 1093821 rs7521584 T G 116.26 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.95;MQ0=0;OQ=1316.49;QD=29.92;SB=-587.88 GT:AD:DP:GL:GQ 1/1:0,44:43:-135.27,-12.96,-0.04:99 +chr1 1095101 rs9442362 T C 65.07 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.90;MQ=60.00;MQ0=0;OQ=375.39;QD=7.99;SB=-207.86 GT:AD:DP:GL:GQ 0/1:27,20:44:-54.09,-13.27,-100.76:99 +chr1 1095924 rs6656236 G A 130.43 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=57.77;MQ0=0;OQ=609.61;QD=16.04;SB=-273.30 GT:AD:DP:GL:GQ 0/1:18,20:34:-74.49,-10.25,-50.31:99 +chr1 1096647 rs4442317 T C 203.56 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=59.13;MQ0=0;OQ=506.89;QD=10.56;SB=-244.47 GT:AD:DP:GL:GQ 0/1:29,19:48:-68.44,-14.47,-111.87:99 +chr1 1114401 rs11577350 G A 483.74 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1009.34;QD=13.28;SB=-463.05 GT:AD:DP:GL:GQ 0/1:45,31:75:-126.83,-22.61,-139.35:99 +chr1 1114613 rs6702156 T C 467.81 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=978.73;QD=12.23;SB=-374.99 GT:AD:DP:GL:GQ 0/1:42,38:78:-124.66,-23.50,-162.90:99 +chr1 1127805 . C T 17.93 LowQual AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.76;MQ=47.96;MQ0=1;QD=0.48;SB=-4.44 GT:AD:DP:GL:GQ 0/1:29,6:21:-11.40,-6.33,-63.23:50.69 +chr1 1133298 rs55945303 G A 59.18 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=925.55;QD=21.52;SB=-252.58 GT:AD:DP:GL:GQ 0/1:14,29:40:-107.89,-12.05,-42.24:99 +chr1 1139524 rs35878953 C T 131.94 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=58.24;MQ0=0;OQ=799.98;QD=18.60;SB=-423.99 GT:AD:DP:GL:GQ 0/1:17,25:37:-94.44,-11.16,-36.66:99 +chr1 1148494 rs6603781 A G 136.52 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.05;MQ0=0;OQ=1330.48;QD=27.15;SB=-433.29 GT:AD:DP:GL:GQ 1/1:0,49:42:-136.66,-12.66,-0.03:99 +chr1 1149380 rs6702268 T C 227.72 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.80;MQ0=0;OQ=961.17;QD=27.46;SB=-122.75 GT:AD:DP:GL:GQ 1/1:0,35:31:-99.73,-9.35,-0.03:93.18 +chr1 1152189 rs4970423 A G 15.48 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=59.39;MQ0=0;OQ=1088.52;QD=28.65;SB=-378.40 GT:AD:DP:GL:GQ 1/1:0,38:34:-112.46,-10.25,-0.02:99 +chr1 1161280 rs6603782 C T 102.99 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=59.00;MQ0=0;OQ=708.75;QD=16.88;SB=-201.20 GT:AD:DP:GL:GQ 0/1:20,22:40:-86.21,-12.05,-64.42:99 +chr1 1162770 rs715643 C T 309.12 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.45;MQ=57.65;MQ0=0;OQ=561.34;QD=14.77;SB=-301.32 GT:AD:DP:GL:GQ 0/1:18,19:36:-70.27,-10.85,-55.47:99 +chr1 1171665 . C T 4.62 PASS AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.39;MQ0=0;OQ=105.76;QD=11.75;SB=-6.99 GT:AD:DP:GL:GQ 0/1:5,4:9:-16.57,-2.71,-16.65:99 +chr1 1178813 . G C 27.28 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=10.95;MQ=55.60;MQ0=0;QD=0.43;SB=74.28 GT:AD:DP:GL:GQ 0/1:46,17:41:-18.38,-12.37,-155.87:60.10 +chr1 1182131 . G A 44.09 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.04;HRun=20;HaplotypeScore=11.11;MQ=50.33;MQ0=0;QD=0.85;SB=65.22 GT:AD:DP:GL:GQ 0/1:38,12:42:-20.05,-12.36,-125.30:76.92 +chr1 1183574 . T C 30.78 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=5;HaplotypeScore=13.00;MQ=56.93;MQ0=0;QD=0.83;SB=23.10 GT:AD:DP:GL:GQ 0/1:22,15:21:-12.69,-6.33,-67.62:63.61 +chr1 1186726 rs6659787 T C 444.24 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1920.21;QD=33.11;SB=-425.81 GT:AD:DP:GL:GQ 1/1:0,58:55:-195.63,-16.57,-0.02:99 +chr1 1194535 . A G 16.67 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=6.08;MQ=52.52;MQ0=1;QD=0.32;SB=29.11 GT:AD:DP:GL:GQ 0/1:42,10:39:-16.70,-11.76,-128.34:49.41 +chr1 1204684 rs34258594 C T 26.14 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=41.53;MQ0=1;OQ=534.60;QD=15.27;SB=-99.92 GT:AD:DP:GL:GQ 0/1:16,19:32:-66.39,-9.65,-50.26:99 +chr1 1206810 . C A 15.67 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=59.17;MQ0=0;QD=0.56;SB=17.05 GT:AD:DP:GL:GQ 0/1:19,7:21:-11.17,-6.33,-52.97:48.38 +chr1 1212553 . C T 5.74 PASS AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=5.06;MQ=57.97;MQ0=0;OQ=298.13;QD=12.96;SB=-173.70 GT:AD:DP:GL:GQ 0/1:12,11:19:-38.83,-5.73,-27.23:99 +chr1 1213523 . A T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=15.57;MQ=33.50;MQ0=4;OQ=59.03;QD=3.28;SB=2.04 GT:AD:DP:GL:GQ 0/1:9,9:9:-11.90,-2.71,-23.47:91.86 +chr1 1213617 . C T 7.11 PASS AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=3.14;MQ=18.72;MQ0=10;OQ=134.34;QD=6.72;SB=-10.00 GT:AD:DP:GL:GQ 1/1:5,15:4:-16.97,-1.20,-0.00:12.04 +chr1 1213622 . T C 11.33 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=3.30;MQ=19.74;MQ0=10;QD=0.49;SB=-3.98 GT:AD:DP:GL:GQ 0/1:20,3:7:-6.49,-2.11,-18.92:43.83 +chr1 1213635 . C T 23.33 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=18.06;MQ0=13;QD=0.75;SB=-33.62 GT:AD:DP:GL:GQ 0/1:24,7:9:-8.33,-2.71,-24.32:56.15 +chr1 1213653 . C T 47.94 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=17.89;MQ0=21;QD=1.00;SB=-23.48 GT:AD:DP:GL:GQ 0/1:37,11:13:-11.99,-3.92,-35.04:80.78 +chr1 1213671 . C T 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=22.77;MQ0=22;OQ=90.19;QD=1.80;SB=-17.46 GT:AD:DP:GL:GQ 0/1:28,22:20:-18.33,-6.03,-51.67:99 +chr1 1213694 . T C 39.97 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=2;HaplotypeScore=8.39;MQ=23.73;MQ0=21;QD=0.73;SB=-15.88 GT:AD:DP:GL:GQ 0/1:51,4:21:-13.61,-6.33,-64.53:72.80 +chr1 1213750 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=7.03;MQ=25.74;MQ0=11;OQ=59.44;QD=1.56;SB=-49.23 GT:AD:DP:GL:GQ 0/1:22,16:17:-14.35,-5.12,-45.82:92.28 +chr1 1213763 . C T 47.85 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.61;MQ0=8;QD=1.65;SB=-29.61 GT:AD:DP:GL:GQ 0/1:21,8:13:-11.99,-3.92,-33.55:80.68 +chr1 1213781 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=3.20;MQ=28.82;MQ0=7;OQ=70.59;QD=2.82;SB=-20.63 GT:AD:DP:GL:GQ 0/1:21,4:13:-14.26,-3.92,-34.86:99 +chr1 1213884 . C T 18.32 PASS AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=20.52;MQ0=9;OQ=123.88;QD=9.53;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,11:4:-15.92,-1.20,-0.00:12.04 +chr1 1213994 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=2;HaplotypeScore=2.99;MQ=9.42;MQ0=22;OQ=67.77;QD=1.94;SB=-42.68 GT:AD:DP:GL:GQ 0/1:31,4:4:-11.26,-1.21,-2.97:17.61 +chr1 1214386 . C T 18.53 PASS AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=12.80;MQ0=7;OQ=79.89;QD=6.15;SB=-52.67 GT:AD:DP:GL:GQ 1/1:3,10:3:-11.48,-0.90,-0.00:9.03 +chr1 1214538 . C T 13.99 PASS AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.76;MQ0=3;OQ=222.41;QD=22.24;SB=-119.99 GT:AD:DP:GL:GQ 1/1:1,9:7:-25.82,-2.11,-0.00:21.06 +chr1 1214556 . C T 78.88 PASS AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.62;MQ0=3;OQ=125.22;QD=13.91;SB=-42.55 GT:AD:DP:GL:GQ 1/1:2,7:4:-16.06,-1.21,-0.00:12.04 +chr1 1214569 . C T 4.09 PASS AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=21.21;MQ0=3;OQ=121.10;QD=17.30;SB=-81.10 GT:AD:DP:GL:GQ 1/1:3,4:4:-15.65,-1.21,-0.00:12.04 +chr1 1214849 . T C 10.83 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=11.01;MQ0=15;QD=0.39;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,8:6:-6.14,-1.81,-16.12:43.30 +chr1 1214919 . A T 0.53 PASS AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=20.32;MQ0=10;OQ=98.85;QD=4.94;SB=-69.74 GT:AD:DP:GL:GQ 0/1:10,9:7:-15.28,-2.11,-10.80:86.87 +chr1 1215102 . A T 1.26 PASS AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.90;MQ=20.59;MQ0=9;OQ=98.25;QD=4.91;SB=-47.98 GT:AD:DP:GL:GQ 0/1:4,16:7:-15.22,-2.11,-12.20:99 +chr1 1215147 . T C 24.78 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=2;HaplotypeScore=5.19;MQ=18.98;MQ0=32;QD=0.28;SB=-36.82 GT:AD:DP:GL:GQ 0/1:83,7:38:-17.21,-11.45,-127.57:57.61 +chr1 1215165 . C T 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=3.30;MQ=20.48;MQ0=21;OQ=101.26;QD=1.35;SB=26.10 GT:AD:DP:GL:GQ 0/1:48,27:30:-22.45,-9.04,-79.18:99 +chr1 1215324 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=4.60;MQ=26.05;MQ0=19;OQ=186.49;QD=2.49;SB=8.19 GT:AD:DP:GL:GQ 0/1:60,15:45:-35.50,-13.57,-130.76:99 +chr1 1227467 rs2296475 T C 67.24 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=59.44;MQ0=0;OQ=1380.81;QD=33.68;SB=-616.59 GT:AD:DP:GL:GQ 1/1:0,40:39:-141.68,-11.75,-0.01:99 +chr1 1227692 rs11586188 G A 13.68 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=2.73;MQ=60.00;MQ0=0;OQ=456.88;QD=14.74;SB=-204.92 GT:AD:DP:GL:GQ 0/1:15,16:30:-58.02,-9.04,-49.24:99 +chr1 1228900 . T C 25.48 LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=4;HaplotypeScore=1.75;MQ=56.48;MQ0=0;QD=0.75;SB=-20.62 GT:AD:DP:GL:GQ 0/1:26,7:28:-14.27,-8.44,-89.93:58.30 +chr1 1229202 rs11260584 T G 37.45 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=976.99;QD=27.91;SB=-499.87 GT:AD:DP:GL:GQ 1/1:0,35:32:-101.31,-9.64,-0.03:96.16 +chr1 1229816 rs10399878 A G 473.23 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1102.82;QD=26.90;SB=-522.83 GT:AD:DP:GL:GQ 1/1:0,41:37:-113.91,-11.17,-0.05:99 +chr1 1231392 rs1536168 A G 97.21 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.82;MQ0=0;OQ=1395.06;QD=27.90;SB=-606.94 GT:AD:DP:GL:GQ 1/1:0,50:45:-143.13,-13.57,-0.04:99 +chr1 1231663 rs3737720 A G 139.66 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.21;MQ=58.81;MQ0=0;OQ=1690.11;QD=30.73;SB=-679.26 GT:AD:DP:GL:GQ 1/1:0,55:50:-172.62,-15.06,-0.03:99 +chr1 1231766 rs3737719 C G 2.42 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=1.43;MQ=58.78;MQ0=0;OQ=1400.23;QD=36.85;SB=-370.18 GT:AD:DP:GL:GQ 1/1:0,38:34:-143.63,-10.26,-0.03:99 +chr1 1232078 rs4970431 A G 216.41 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1612.70;QD=32.91;SB=-685.61 GT:AD:DP:GL:GQ 1/1:0,49:46:-164.87,-13.86,-0.01:99 +chr1 1232570 rs2274262 A G 6.01 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=2.33;MQ=58.39;MQ0=0;OQ=927.22;QD=31.97;SB=-261.82 GT:AD:DP:GL:GQ 1/1:0,28:29:-99.47,-11.27,-3.16:81.12 +chr1 1232846 rs2887285 G A 7.05 PASS AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=60.00;MQ0=0;OQ=156.17;QD=26.03;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,5:5:-19.18,-1.51,-0.00:15.05 +chr1 1233759 rs61766198 C T 47.25 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=23.62;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-8.13,-0.60,-0.00:6.02 +chr1 1235231 rs11590283 G A 557.67 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1461.68;QD=36.54;SB=-745.00 GT:AD:DP:GL:GQ 1/1:1,39:37:-149.76,-11.15,-0.01:99 +chr1 1235867 rs2296474 A G 712.67 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.51;MQ0=0;OQ=1812.39;QD=34.20;SB=-908.32 GT:AD:DP:GL:GQ 1/1:0,53:53:-184.85,-15.97,-0.02:99 +chr1 1237357 rs12103 T C 207.29 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=647.94;QD=29.45;SB=-286.45 GT:AD:DP:GL:GQ 1/1:0,22:21:-68.40,-6.33,-0.02:63.15 +chr1 1237452 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=10;HaplotypeScore=2.81;MQ=58.76;MQ0=0;OQ=54.80;QD=4.98;SB=-3.98 GT:AD:DP:GL:GQ 0/1:7,4:6:-10.58,-1.82,-11.64:87.64 +chr1 1239050 rs12142199 G A 66.55 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=1.62;MQ=58.97;MQ0=0;OQ=2440.21;QD=38.73;SB=-1144.03 GT:AD:DP:GL:GQ 1/1:1,62:62:-247.62,-18.68,-0.02:99 +chr1 1239352 . C G 26.31 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=58.82;MQ0=0;OQ=1214.59;QD=20.59;SB=-515.28 GT:AD:DP:GL:GQ 0/1:25,34:56:-141.62,-16.88,-95.25:99 +chr1 1242263 rs55998830 C T 160.41 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=57.24;MQ0=0;OQ=503.69;QD=12.29;SB=-134.60 GT:AD:DP:GL:GQ 0/1:23,18:39:-65.41,-11.76,-71.08:99 +chr1 1243999 rs4970432 G A 36.99 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=58.63;MQ0=0;OQ=2692.59;QD=39.60;SB=-1179.08 GT:AD:DP:GL:GQ 1/1:0,68:67:-272.86,-20.18,-0.01:99 +chr1 1244299 rs1886773 A G 203.79 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.11;MQ0=0;OQ=1463.44;QD=28.14;SB=-748.56 GT:AD:DP:GL:GQ 1/1:0,52:48:-149.98,-14.48,-0.05:99 +chr1 1244306 rs1886772 G A 170.95 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=58.89;MQ0=0;OQ=2428.21;QD=38.54;SB=-1150.05 GT:AD:DP:GL:GQ 1/1:0,63:62:-246.42,-18.68,-0.02:99 +chr1 1244704 rs10907179 C G 226.16 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=2474.22;QD=40.56;SB=-1116.55 GT:AD:DP:GL:GQ 1/1:0,61:58:-251.03,-17.48,-0.03:99 +chr1 1245150 rs10449892 C T 372.09 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1031.28;QD=35.56;SB=-512.17 GT:AD:DP:GL:GQ 1/1:0,29:28:-106.73,-8.44,-0.02:84.26 +chr1 1247456 rs1810745 A G 110.17 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=54.75;MQ0=0;OQ=1043.28;QD=28.20;SB=-313.49 GT:AD:DP:GL:GQ 1/1:0,37:33:-107.94,-9.95,-0.02:99 +chr1 1256339 rs28704486 A G 29.57 PASS AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=16.01;MQ0=0;OQ=60.16;QD=4.63;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,13:3:-9.51,-0.90,-0.00:9.02 +chr1 1258710 rs307378 T G 2.23 PASS AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=76.83;QD=25.61;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:3:-11.17,-0.90,-0.00:9.03 +chr1 1259417 rs307377 T C 101.96 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=21.92;MQ0=3;OQ=105.39;QD=15.06;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:4:-14.07,-1.20,-0.00:12.04 +chr1 1260192 rs188647 A G 29.27 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=14.64;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-6.34,-0.60,-0.00:6.01 +chr1 1260222 rs307374 T C 0.04 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=63.98;QD=21.33;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:3:-9.89,-0.91,-0.00:9.02 +chr1 1262360 rs307372 A G 1.31 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.52;MQ=35.06;MQ0=0;OQ=290.20;QD=24.18;SB=-151.34 GT:AD:DP:GL:GQ 1/1:0,12:11:-32.62,-3.32,-0.02:33.05 +chr1 1262979 rs307371 A G 118.35 PASS AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.17;MQ0=0;OQ=96.93;QD=24.23;SB=-72.91 GT:AD:DP:GL:GQ 1/1:0,4:4:-13.23,-1.21,-0.00:12.03 +chr1 1263141 rs307370 A G 373.13 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.14;MQ0=0;OQ=479.19;QD=34.23;SB=-188.41 GT:AD:DP:GL:GQ 1/1:0,14:14:-51.51,-4.22,-0.00:42.13 +chr1 1265154 rs11582808 G A 10.31 PASS AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=44.52;MQ0=0;OQ=273.35;QD=19.53;SB=-116.97 GT:AD:DP:GL:GQ 0/1:5,9:13:-34.54,-3.92,-12.73:88.15 +chr1 1266341 rs307364 T G 24.11 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.44;MQ=22.99;MQ0=5;OQ=64.81;QD=5.40;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,10:3:-9.97,-0.90,-0.00:9.02 +chr1 1267396 rs17854636 T C 111.78 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=34.81;MQ0=1;OQ=372.39;QD=23.27;SB=-142.72 GT:AD:DP:GL:GQ 1/1:0,16:13:-40.84,-3.92,-0.02:39.08 +chr1 1268100 rs307361 T C 193.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.78;MQ0=3;OQ=449.98;QD=25.00;SB=-194.71 GT:AD:DP:GL:GQ 1/1:0,18:15:-48.59,-4.52,-0.01:45.11 +chr1 1268888 rs307360 A G 2.79 PASS AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=29.77;MQ0=0;OQ=268.28;QD=26.83;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:9:-30.42,-2.71,-0.01:27.07 +chr1 1270382 rs307358 T C 22.61 PASS AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=83.45;QD=20.86;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,4:4:-11.88,-1.21,-0.01:12.02 +chr1 1276604 . G C 27.05 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.66;MQ=11.97;MQ0=10;QD=1.29;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,12:4:-7.20,-1.21,-7.49:59.88 +chr1 1276657 rs35104845 C T 49.02 PASS AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=0;HaplotypeScore=2.90;MQ=23.40;MQ0=3;OQ=76.78;QD=6.98;SB=-10.00 GT:AD:DP:GL:GQ 1/1:5,5:3:-11.17,-0.90,-0.00:9.03 +chr1 1276684 rs61766214 G C 3.73 PASS AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=32.46;MQ0=2;OQ=374.70;QD=28.82;SB=-82.81 GT:AD:DP:GL:GQ 1/1:1,12:10:-41.06,-3.02,-0.01:30.10 +chr1 1276760 rs34380086 G C 256.91 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.61;MQ0=0;OQ=915.51;QD=35.21;SB=-194.53 GT:AD:DP:GL:GQ 1/1:0,26:24:-95.15,-7.24,-0.02:72.23 +chr1 1276990 rs56165241 G A 0.14 PASS AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=23.71;MQ0=1;OQ=124.88;QD=20.81;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,6:4:-16.02,-1.20,-0.00:12.04 +chr1 1278208 rs13249 A G 0.03 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=4;HaplotypeScore=0.79;MQ=29.00;MQ0=0;OQ=519.51;QD=34.63;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:15:-55.54,-4.52,-0.01:45.13 +chr1 1278334 rs3766183 C T 70.79 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=12.77;MQ0=25;OQ=129.88;QD=4.48;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,29:4:-16.52,-1.20,-0.00:12.04 +chr1 1279774 rs4970365 G A 205.12 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=37.02;MQ0=1;OQ=413.00;QD=27.53;SB=-81.33 GT:AD:DP:GL:GQ 1/1:0,15:12:-44.89,-3.62,-0.01:36.11 +chr1 1283627 rs34841888 G C 242.04 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=17.25;MQ0=18;OQ=165.64;QD=7.20;SB=-87.83 GT:AD:DP:GL:GQ 1/1:0,23:5:-20.13,-1.51,-0.00:15.05 +chr1 1284791 rs2649608 A G 15.70 PASS AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=325.53;QD=25.04;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,13:12:-36.15,-3.62,-0.02:36.07 +chr1 1285186 rs34389364 G A 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=44.84;MQ0=0;OQ=775.48;QD=28.72;SB=-269.63 GT:AD:DP:GL:GQ 1/1:0,25:23:-81.16,-6.94,-0.03:69.18 +chr1 1285266 rs34876581 T C 166.99 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=42.89;MQ0=0;OQ=1629.47;QD=31.95;SB=-823.96 GT:AD:DP:GL:GQ 1/1:0,51:47:-166.55,-14.16,-0.02:99 +chr1 1285545 rs61766236 A G 14.70 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=53.58;MQ0=0;OQ=756.88;QD=26.10;SB=-99.85 GT:AD:DP:GL:GQ 1/1:0,29:25:-79.29,-7.54,-0.02:75.15 +chr1 1285750 . T C 31.55 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=14.50;MQ0=6;QD=3.94;SB=-38.95 GT:AD:DP:GL:GQ 1/1:0,8:2:-6.56,-0.60,-0.00:6.01 +chr1 1286016 rs2765027 T G 82.17 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=481.12;QD=30.07;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,16:16:-51.71,-4.82,-0.01:48.07 +chr1 1286554 rs2765025 C G 315.48 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.90;MQ0=0;OQ=1204.51;QD=36.50;SB=-193.69 GT:AD:DP:GL:GQ 1/1:0,33:29:-124.04,-8.74,-0.01:87.29 +chr1 1286681 rs2765024 C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=715.35;QD=35.77;SB=-192.69 GT:AD:DP:GL:GQ 1/1:0,20:18:-75.13,-5.42,-0.01:54.18 +chr1 1286922 rs35056373 G A 454.44 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.41;MQ0=1;OQ=1368.71;QD=34.22;SB=-459.59 GT:AD:DP:GL:GQ 1/1:0,40:36:-140.48,-10.85,-0.02:99 +chr1 1287079 rs2649611 A G 142 PASS AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.17;MQ0=0;OQ=99.93;QD=24.98;SB=-76.36 GT:AD:DP:GL:GQ 1/1:0,4:4:-13.53,-1.21,-0.00:12.03 +chr1 1287285 rs2765021 C T 19.52 PASS AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=27.13;MQ0=1;OQ=211.29;QD=26.41;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:6:-24.70,-1.81,-0.00:18.06 +chr1 1287346 . G A 32.26 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.41;MQ=19.54;MQ0=6;QD=3.23;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,5:4:-7.72,-1.21,-5.84:46.31 +chr1 1287498 rs34896744 G A 28.51 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=522.90;QD=37.35;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,14:14:-55.88,-4.22,-0.00:42.14 +chr1 1288153 . C T 10.16 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=6.84;MQ0=17;QD=0.56;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,3:1:-4.26,-0.30,-0.00:1.76 +chr1 1288274 rs4970439 C T 158.39 PASS AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.76;MQ0=1;OQ=198.94;QD=24.87;SB=-120.99 GT:AD:DP:GL:GQ 1/1:0,8:6:-23.47,-1.81,-0.00:18.06 +chr1 1288396 rs9700464 T G 39.49 LowQual AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.48;MQ0=3;QD=7.90;SB=-46.01 GT:AD:DP:GL:GQ 1/1:0,5:2:-7.36,-0.60,-0.00:6.02 +chr1 1288400 rs2477784 C T 45.25 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.37;MQ0=1;QD=15.08;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:2:-7.93,-0.60,-0.00:6.02 +chr1 1288965 . T C 42.83 LowQual AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=3;HaplotypeScore=1.16;MQ=15.81;MQ0=3;QD=8.57;SB=-10.00 GT:AD:DP:GL:GQ 1/1:3,2:2:-7.69,-0.60,-0.00:6.02 +chr1 1288989 . G A 32 LowQual AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.68;MQ0=2;QD=8.00;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,2:2:-6.61,-0.60,-0.00:6.01 +chr1 1288993 . G A 39.02 LowQual AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.68;MQ0=2;QD=9.75;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,2:2:-7.31,-0.60,-0.00:6.02 +chr1 1289038 . G A 46.02 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=8.33;MQ0=16;QD=2.56;SB=-10.00 GT:AD:DP:GL:GQ 1/1:16,2:2:-8.01,-0.60,-0.00:6.02 +chr1 1289229 rs28368296 C T 48.25 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=16.08;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,2:2:-8.23,-0.60,-0.00:6.02 +chr1 1292190 . A C 28.74 DPFilter;HARD_TO_VALIDATE;Indel;LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=31.67;MQ=32.93;MQ0=5;QD=1.44;SB=2.03 GT:AD:DP:GL:GQ 0/1:14,6:12:-9.77,-3.62,-33.18:61.57 +chr1 1292271 rs61766242 A G 18.08 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=30.84;MQ0=4;OQ=1066.32;QD=26.66;SB=-193.80 GT:AD:DP:GL:GQ 1/1:0,40:32:-110.23,-9.64,-0.01:96.27 +chr1 1292418 rs3104610 C T 418.78 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=45.84;MQ0=1;OQ=2220.73;QD=38.96;SB=-760.52 GT:AD:DP:GL:GQ 1/1:0,57:55:-225.67,-16.57,-0.01:99 +chr1 1297501 rs2649597 T C 2.48 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.11;MQ0=4;OQ=360.28;QD=22.52;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,16:12:-39.62,-3.62,-0.01:36.08 +chr1 1298491 rs2477775 A G 32.28 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=16.14;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-6.64,-0.60,-0.00:6.02 +chr1 1298734 rs2649595 A T 1.65 PASS AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.11;MQ0=1;OQ=88.08;QD=22.02;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,4:3:-12.30,-0.90,-0.00:9.03 +chr1 1300531 rs2242398 A C 250.70 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.82;MQ0=0;OQ=470.94;QD=31.40;SB=-111.01 GT:AD:DP:GL:GQ 1/1:0,15:15:-50.69,-4.52,-0.01:45.12 +chr1 1300838 rs2649594 C T 51.73 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.25;MQ0=5;OQ=315.14;QD=22.51;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,14:9:-35.10,-2.71,-0.01:27.08 +chr1 1300941 rs2649592 G T 12.43 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.29;MQ0=5;OQ=256.28;QD=18.31;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,14:8:-29.21,-2.41,-0.00:24.07 +chr1 1302674 rs34582295 C T 6.04 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=3.06;MQ=25.59;MQ0=11;OQ=374.66;QD=16.29;SB=-144.64 GT:AD:DP:GL:GQ 1/1:0,23:11:-41.06,-3.32,-0.01:33.10 +chr1 1303447 rs11489820 G C 2.99 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=7.53;MQ0=41;OQ=125.53;QD=2.73;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,46:4:-16.09,-1.21,-0.00:12.04 +chr1 1304035 rs2477777 C T 175.22 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=34.74;MQ0=4;OQ=578.49;QD=28.92;SB=-248.33 GT:AD:DP:GL:GQ 1/1:0,20:15:-61.44,-4.52,-0.00:45.15 +chr1 1304333 rs2313135 T G 34.29 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.98;MQ0=4;QD=4.90;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,2:3:-7.61,-0.90,-3.34:24.36 +chr1 1304907 rs2368566 G A 186.02 PASS AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.16;MQ0=0;OQ=83.01;QD=27.67;SB=-45.55 GT:AD:DP:GL:GQ 1/1:0,3:3:-11.79,-0.90,-0.00:9.03 +chr1 1305206 rs2368565 G A 178.76 PASS AC=2;AF=1.00;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=123.88;QD=30.97;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,4:4:-15.92,-1.20,-0.00:12.04 +chr1 1305756 rs2454652 C T 47.02 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=23.51;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-8.11,-0.60,-0.00:6.02 +chr1 1306033 rs2649587 G A 6.56 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=34.70;MQ0=1;OQ=503.12;QD=31.45;SB=-129.67 GT:AD:DP:GL:GQ 1/1:0,16:14:-53.90,-4.22,-0.01:42.13 +chr1 1306331 rs2649586 A G 0.26 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=29.00;MQ0=0;OQ=293.94;QD=24.50;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,11:10:-32.98,-3.01,-0.01:30.07 +chr1 1307502 . C G 13.29 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=4.50;MQ0=24;QD=0.49;SB=-10.00 GT:AD:DP:GL:GQ 0/1:26,1:1:-4.59,-0.30,-0.00:1.76 +chr1 1307925 . G C 0.13 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=13.45;MQ0=29;OQ=83.85;QD=1.78;SB=-0.97 GT:AD:DP:GL:GQ 0/1:38,9:8:-14.08,-2.41,-22.17:99 +chr1 1307979 . T C 42.83 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=7.67;MQ0=16;QD=2.38;SB=-10.00 GT:AD:DP:GL:GQ 1/1:13,5:2:-7.69,-0.60,-0.00:6.02 +chr1 1308095 . C G 10.99 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.17;HRun=1;HaplotypeScore=14.74;MQ=6.41;MQ0=25;QD=0.38;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,4:1:-4.35,-0.30,-0.00:1.76 +chr1 1321841 . G T 47.94 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=20;HaplotypeScore=6.03;MQ=23.98;MQ0=9;QD=1.65;SB=-0.97 GT:AD:DP:GL:GQ 0/1:18,11:6:-9.89,-1.81,-11.27:80.77 +chr1 1323299 rs1240743 C A 6.63 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=38.33;MQ0=6;OQ=144.07;QD=3.27;SB=50.03 GT:AD:DP:GL:GQ 0/1:30,14:36:-28.54,-10.85,-84.17:99 +chr1 1332475 rs2275915 G C 24.94 PASS AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=31.54;MQ0=6;OQ=92.26;QD=5.77;SB=-43.44 GT:AD:DP:GL:GQ 0/1:8,8:10:-15.53,-3.02,-24.58:99 +chr1 1346911 . G A 0.08 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=8.57;MQ=40.33;MQ0=2;OQ=331.50;QD=8.72;SB=-7.00 GT:AD:DP:GL:GQ 0/1:22,16:33:-46.38,-9.94,-72.87:99 +chr1 1349702 . C A 0.66 PASS AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=5.78;MQ=19.45;MQ0=7;OQ=297.18;QD=9.29;SB=-141.76 GT:AD:DP:GL:GQ 0/1:14,17:13:-36.92,-3.92,-7.86:39.43 +chr1 1352746 rs58304223 G C 14.25 LowQual AC=1;AF=0.50;AN=2;DB;DP=1;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=14.25;SB=-10.00 GT:AD:DP:GL:GQ 0/1:0,1:1:-4.69,-0.30,-0.00:1.76 +chr1 1353363 . G T 42.81 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=37.00;MQ0=0;QD=21.40;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-7.69,-0.60,-0.00:6.02 +chr1 1355197 rs1781138 A G 15.22 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=39.89;MQ0=3;OQ=305.23;QD=16.96;SB=-38.95 GT:AD:DP:GL:GQ 1/1:0,18:10:-34.11,-3.01,-0.00:30.08 +chr1 1358462 rs1240703 A C 0.99 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=3;HaplotypeScore=0.32;MQ=21.92;MQ0=3;OQ=100.91;QD=14.42;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:4:-13.63,-1.21,-0.00:12.03 +chr1 1358648 . C G 24.94 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=3;HaplotypeScore=2.70;MQ=19.30;MQ0=6;QD=1.19;SB=5.05 GT:AD:DP:GL:GQ 0/1:13,8:7:-7.89,-2.11,-21.96:57.76 +chr1 1377530 rs1781144 C G 16.31 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=20.51;MQ0=10;OQ=394.74;QD=19.74;SB=-103.85 GT:AD:DP:GL:GQ 1/1:0,20:10:-43.06,-3.01,-0.00:30.10 +chr1 1380491 . G A 10.40 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=6;HaplotypeScore=29.42;MQ=36.22;MQ0=8;QD=0.18;SB=26.07 GT:AD:DP:GL:GQ 0/1:33,26:17:-9.41,-5.13,-45.72:42.82 +chr1 1390605 rs1240723 T C 30.71 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.36;MQ=30.70;MQ0=2;OQ=239.92;QD=7.06;SB=-41.82 GT:AD:DP:GL:GQ 0/1:20,14:26:-35.12,-7.84,-56.30:99 +chr1 1390829 . C T 33.01 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=3;HaplotypeScore=8.88;MQ=28.73;MQ0=9;QD=1.00;SB=26.10 GT:AD:DP:GL:GQ 0/1:27,6:18:-12.01,-5.42,-52.81:65.84 +chr1 1394381 . T G 40.77 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=20.66;MQ0=17;QD=0.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:31,13:12:-10.98,-3.61,-30.75:73.61 +chr1 1398226 . C T 36.49 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=10.21;MQ0=21;QD=1.46;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,13:3:-7.84,-0.90,-3.10:21.92 +chr1 1410500 rs35871802 C T 116.85 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.49;MQ0=17;OQ=181.39;QD=6.05;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,18:11:-24.74,-3.31,-17.34:99 +chr1 1413144 . G A 12.73 PASS AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=22.29;MQ0=2;OQ=489.12;QD=14.82;SB=-131.14 GT:AD:DP:GL:GQ 0/1:17,16:30:-61.25,-9.05,-41.87:99 +chr1 1414249 . G C 31.95 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=2;HaplotypeScore=6.60;MQ=15.28;MQ0=13;QD=1.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:18,6:4:-7.69,-1.21,-7.60:63.89 +chr1 1423959 rs1781141 T G 30.05 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=21.23;MQ0=4;QD=1.58;SB=5.04 GT:AD:DP:GL:GQ 0/1:13,6:14:-10.50,-4.22,-40.36:62.88 +chr1 1424829 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=20;HaplotypeScore=5.78;MQ=28.83;MQ0=9;OQ=77.31;QD=1.98;SB=59.13 GT:AD:DP:GL:GQ 0/1:32,7:28:-19.45,-8.44,-75.28:99 +chr1 1424855 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=20;HaplotypeScore=4.13;MQ=29.08;MQ0=4;OQ=54.78;QD=1.96;SB=29.12 GT:AD:DP:GL:GQ 0/1:21,7:17:-13.88,-5.12,-48.25:87.62 +chr1 1425922 rs28755011 C T 122.75 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=53.56;MQ0=1;OQ=756.68;QD=16.45;SB=-222.92 GT:AD:DP:GL:GQ 0/1:21,25:43:-91.92,-12.96,-62.88:99 +chr1 1430132 rs3104609 A G 485.47 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=42.69;MQ0=1;OQ=1088.71;QD=31.11;SB=-534.36 GT:AD:DP:GL:GQ 1/1:0,35:33:-112.47,-9.94,-0.02:99 +chr1 1447936 rs3118507 A G 40.78 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=47.98;MQ0=0;OQ=209.16;QD=6.97;SB=-124.72 GT:AD:DP:GL:GQ 0/1:20,10:26:-32.03,-7.83,-67.04:99 +chr1 1450120 rs6603789 G C 0.59 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=28.41;MQ0=9;OQ=784.91;QD=23.09;SB=-55.93 GT:AD:DP:GL:GQ 1/1:6,28:20:-82.08,-6.03,-0.01:60.20 +chr1 1450953 rs3128345 A G 6.78 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=8.00;MQ=58.21;MQ0=0;OQ=533.48;QD=10.67;SB=-234.27 GT:AD:DP:GL:GQ 0/1:28,22:48:-71.10,-14.47,-106.23:99 +chr1 1457784 . T A 85.12 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.74;MQ0=0;OQ=950.58;QD=15.09;SB=-335.63 GT:AD:DP:GL:GQ 0/1:32,31:63:-117.32,-18.98,-122.45:99 +chr1 1458041 rs6694994 T C 138.18 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=49.26;MQ0=0;OQ=499.68;QD=12.19;SB=-117.64 GT:AD:DP:GL:GQ 0/1:20,21:38:-64.71,-11.46,-68.00:99 +chr1 1459409 rs3128344 G A 558.61 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.45;MQ0=0;OQ=1638.56;QD=37.24;SB=-778.68 GT:AD:DP:GL:GQ 1/1:0,43:42:-167.45,-12.65,-0.01:99 +chr1 1461502 . A C 42.07 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=2;HaplotypeScore=1.74;MQ=57.05;MQ0=0;QD=2.63;SB=14.06 GT:AD:DP:GL:GQ 0/1:8,8:12:-11.11,-3.62,-27.42:74.90 +chr1 1461910 rs3118505 C T 45.13 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.75;MQ=58.35;MQ0=0;OQ=649.92;QD=17.57;SB=-339.91 GT:AD:DP:GL:GQ 0/1:17,20:34:-78.52,-10.25,-48.35:99 +chr1 1462403 rs1571148 T G 289.59 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=414.06;QD=9.41;SB=-126.87 GT:AD:DP:GL:GQ 0/1:27,17:41:-57.04,-12.35,-89.89:99 +chr1 1462736 rs4259576 T A 334.86 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.42;MQ=60.00;MQ0=0;OQ=380.45;QD=11.19;SB=-195.57 GT:AD:DP:GL:GQ 0/1:20,14:33:-51.27,-9.94,-69.97:99 +chr1 1464030 rs1571149 A G 400.49 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=649.88;QD=11.01;SB=-311.08 GT:AD:DP:GL:GQ 0/1:30,29:55:-84.85,-16.58,-112.84:99 +chr1 1464167 rs1571150 C A 91.13 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.52;MQ0=0;OQ=665.06;QD=17.05;SB=-221.93 GT:AD:DP:GL:GQ 0/1:16,23:39:-81.54,-11.75,-55.47:99 +chr1 1464327 rs56239289 T C 341.41 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=731.44;QD=11.99;SB=-372.97 GT:AD:DP:GL:GQ 0/1:31,30:58:-93.91,-17.48,-117.75:99 +chr1 1464734 rs9439465 G C 86.71 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=410.54;QD=15.21;SB=-187.22 GT:AD:DP:GL:GQ 0/1:13,14:25:-51.89,-7.55,-46.69:99 +chr1 1468557 rs55694463 C G 72.40 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.11;MQ0=0;OQ=367.44;QD=14.13;SB=-116.67 GT:AD:DP:GL:GQ 0/1:13,13:22:-46.66,-6.63,-46.00:99 +chr1 1468920 rs61777888 A T 11.23 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=40.58;MQ0=0;QD=1.12;SB=2.00 GT:AD:DP:GL:GQ 0/1:8,2:6:-6.19,-1.81,-11.86:43.73 +chr1 1471211 rs3766177 T C 144.43 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=59.42;MQ0=0;OQ=424.79;QD=8.50;SB=-61.74 GT:AD:DP:GL:GQ 0/1:28,22:46:-59.63,-13.86,-111.57:99 +chr1 1472873 rs7517401 G A 289.79 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.75;MQ=59.55;MQ0=0;OQ=742.89;QD=14.57;SB=-367.87 GT:AD:DP:GL:GQ 0/1:27,24:48:-92.05,-14.47,-78.97:99 +chr1 1474833 rs7515814 C G 227.61 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.23;MQ0=0;OQ=1418.95;QD=20.87;SB=-692.35 GT:AD:DP:GL:GQ 0/1:30,38:67:-165.38,-20.20,-121.41:99 +chr1 1476697 rs3128342 C A 175.56 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=1.77;MQ=59.37;MQ0=0;OQ=1038.77;QD=15.74;SB=-518.96 GT:AD:DP:GL:GQ 0/1:32,34:66:-127.04,-19.88,-111.54:99 +chr1 1478935 rs3930748 A G 131.03 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=57.35;MQ0=0;OQ=678.62;QD=14.44;SB=-210.49 GT:AD:DP:GL:GQ 0/1:18,29:41:-83.51,-12.36,-58.93:99 +chr1 1479484 rs11590038 T C 187.36 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=60.00;MQ0=0;OQ=498.05;QD=12.45;SB=-267.61 GT:AD:DP:GL:GQ 0/1:17,23:38:-64.56,-11.47,-62.93:99 +chr1 1479489 rs11588893 C T 162.61 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=60.00;MQ0=0;OQ=580.48;QD=15.69;SB=-263.76 GT:AD:DP:GL:GQ 0/1:17,20:34:-71.58,-10.25,-50.12:99 +chr1 1479533 rs7531530 C T 220.27 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.91;MQ=59.18;MQ0=1;OQ=444.32;QD=12.01;SB=-149.64 GT:AD:DP:GL:GQ 0/1:19,18:31:-57.07,-9.35,-49.87:99 +chr1 1479791 rs7366884 T C 122.14 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=816.32;QD=13.61;SB=-418.23 GT:AD:DP:GL:GQ 0/1:30,30:57:-102.08,-17.17,-116.37:99 +chr1 1479937 rs7366635 A G 20.12 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.12;MQ=59.07;MQ0=0;OQ=292.89;QD=6.51;SB=-136.53 GT:AD:DP:GL:GQ 0/1:30,15:42:-45.23,-12.66,-112.08:99 +chr1 1480024 rs3753332 A G 36.05 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=1.31;MQ=59.44;MQ0=0;OQ=490.38;QD=11.96;SB=-170.97 GT:AD:DP:GL:GQ 0/1:21,20:37:-63.47,-11.15,-78.00:99 +chr1 1480095 rs3753331 T C 462.82 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=783.79;QD=15.07;SB=-339.35 GT:AD:DP:GL:GQ 0/1:24,28:51:-97.03,-15.37,-89.70:99 +chr1 1480422 rs3820075 A G 268.84 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=768.88;QD=14.24;SB=-360.10 GT:AD:DP:GL:GQ 0/1:23,31:53:-96.15,-15.98,-92.13:99 +chr1 1480490 rs3753330 T A 237.50 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.22;MQ0=0;OQ=615.93;QD=11.41;SB=-300.65 GT:AD:DP:GL:GQ 0/1:28,26:50:-79.94,-15.07,-101.11:99 +chr1 1480556 . C T 26.64 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=59.59;MQ0=0;OQ=854.85;QD=18.58;SB=-376.92 GT:AD:DP:GL:GQ 0/1:20,26:44:-102.04,-13.27,-56.58:99 +chr1 1481114 rs12048706 T C 201.19 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=57.91;MQ0=0;OQ=878.58;QD=11.87;SB=-292.17 GT:AD:DP:GL:GQ 0/1:36,38:70:-112.24,-21.10,-138.24:99 +chr1 1484218 rs3118509 T C 19.29 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1926.74;QD=28.76;SB=-881.49 GT:AD:DP:GL:GQ 1/1:0,67:60:-196.31,-18.09,-0.05:99 +chr1 1484946 rs6667347 G C 188.55 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.64;MQ0=0;OQ=1104.15;QD=17.25;SB=-384.86 GT:AD:DP:GL:GQ 0/1:33,31:63:-132.69,-18.99,-142.09:99 +chr1 1485056 rs3118508 A G 123.40 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.54;MQ0=0;OQ=1673.18;QD=28.36;SB=-768.59 GT:AD:DP:GL:GQ 1/1:0,59:54:-170.96,-16.29,-0.05:99 +chr1 1486871 rs3766170 T C 6.17 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=1.66;MQ=57.15;MQ0=0;OQ=440.82;QD=8.82;SB=-192.43 GT:AD:DP:GL:GQ 0/1:28,22:46:-61.23,-13.87,-105.72:99 +chr1 1488802 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=20;HaplotypeScore=27.79;MQ=52.29;MQ0=1;OQ=57.57;QD=0.82;SB=89.30 GT:AD:DP:GL:GQ 0/1:49,20:48:-23.51,-14.47,-151.88:90.40 +chr1 1489161 rs9439468 A G 111.48 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.15;MQ=56.25;MQ0=0;OQ=911.03;QD=16.56;SB=-250.50 GT:AD:DP:GL:GQ 0/1:21,34:50:-109.45,-15.06,-75.57:99 +chr1 1490804 rs6603791 A G 440.61 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=55.41;MQ0=0;OQ=778.85;QD=12.98;SB=-348.06 GT:AD:DP:GL:GQ 0/1:28,32:58:-98.65,-17.48,-110.76:99 +chr1 1490867 . C G 0.31 PASS AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=53.32;MQ0=0;OQ=206.00;QD=2.71;SB=-32.07 GT:AD:DP:GL:GQ 0/1:64,12:75:-46.49,-22.61,-271.24:99 +chr1 1490871 . A G 0.08 PASS AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.61;MQ=53.82;MQ0=0;OQ=220.05;QD=2.75;SB=-14.75 GT:AD:DP:GL:GQ 0/1:66,14:78:-48.79,-23.50,-263.73:99 +chr1 1490927 rs6656541 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=23.59;MQ=53.32;MQ0=0;OQ=1558.39;QD=20.51;SB=-788.78 GT:AD:DP:GL:GQ 0/1:23,53:74:-181.42,-22.29,-76.04:99 +chr1 1490930 rs12730242 C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=22.45;MQ=53.65;MQ0=0;OQ=417.53;QD=5.49;SB=-224.35 GT:AD:DP:GL:GQ 0/1:55,21:70:-66.13,-21.09,-238.86:99 +chr1 1490948 rs12742689 T C 0.19 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=53.98;MQ0=0;OQ=96.30;QD=1.23;SB=-34.35 GT:AD:DP:GL:GQ 0/1:66,12:72:-34.61,-21.70,-240.60:99 +chr1 1490950 rs12730248 C T 0.53 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=54.06;MQ0=0;OQ=172.01;QD=2.18;SB=-98.81 GT:AD:DP:GL:GQ 0/1:67,11:73:-45.59,-25.10,-225.19:99 +chr1 1491329 rs7543799 G A 29 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=5.33;MQ=58.37;MQ0=0;OQ=592.32;QD=13.16;SB=-320.34 GT:AD:DP:GL:GQ 0/1:24,21:38:-73.97,-11.45,-67.99:99 +chr1 1492958 rs7367692 G A 226.72 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=59.16;MQ0=0;OQ=759.07;QD=13.80;SB=-311.80 GT:AD:DP:GL:GQ 0/1:31,24:51:-94.56,-15.37,-89.99:99 +chr1 1492962 rs7364711 A C 163.84 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=59.20;MQ0=0;OQ=581.10;QD=10.02;SB=-270.86 GT:AD:DP:GL:GQ 0/1:35,23:56:-78.26,-16.87,-122.50:99 +chr1 1493671 rs11578409 C G 251.66 PASS AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=59.04;MQ0=0;OQ=1371.84;QD=13.45;SB=-443.87 GT:AD:DP:GL:GQ 0/1:57,45:96:-169.40,-28.93,-244.12:99 +chr1 1493791 rs7550471 G A 6.65 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=5.83;MQ=58.91;MQ0=0;OQ=1272.31;QD=21.21;SB=-593.09 GT:AD:DP:GL:GQ 0/1:20,38:56:-150.16,-19.64,-65.04:99 +chr1 1494423 rs7552586 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=6;HaplotypeScore=3.99;MQ=59.04;MQ0=0;OQ=1025.73;QD=12.36;SB=-469.22 GT:AD:DP:GL:GQ 0/1:45,38:80:-129.96,-24.11,-158.72:99 +chr1 1494904 rs6603792 T C 342.81 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=427.21;QD=9.94;SB=-158.94 GT:AD:DP:GL:GQ 0/1:24,19:43:-58.97,-12.96,-97.93:99 +chr1 1495118 rs6603793 C T 185.94 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.74;MQ0=0;OQ=1162.21;QD=15.92;SB=-407.71 GT:AD:DP:GL:GQ 0/1:38,35:73:-141.49,-21.99,-140.54:99 +chr1 1495830 rs7548959 C T 131.47 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=58.74;MQ0=0;OQ=1025.47;QD=14.65;SB=-444.99 GT:AD:DP:GL:GQ 0/1:38,32:69:-126.64,-20.81,-114.78:99 +chr1 1495898 rs7540231 G A 67.32 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=2;HaplotypeScore=1.75;MQ=58.44;MQ0=0;OQ=3508.72;QD=37.73;SB=-1621.33 GT:AD:DP:GL:GQ 1/1:0,92:90:-349.87,-27.12,-0.03:99 +chr1 1497229 rs9439469 G A 187.99 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.17;MQ0=0;OQ=210.39;QD=8.42;SB=-10.00 GT:AD:DP:GL:GQ 0/1:17,8:25:-31.85,-7.53,-57.26:99 +chr1 1497775 rs61774865 A C 52.62 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=53.97;MQ0=0;OQ=260.15;QD=7.88;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,13:31:-38.64,-9.34,-70.58:99 +chr1 1498322 rs9439473 A G 18.83 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=3.82;MQ=56.11;MQ0=0;OQ=610.76;QD=13.57;SB=-249.32 GT:AD:DP:GL:GQ 0/1:21,24:44:-77.63,-13.27,-79.03:99 +chr1 1498506 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=5;HaplotypeScore=2.45;MQ=50.85;MQ0=0;OQ=161.89;QD=3.37;SB=24.24 GT:AD:DP:GL:GQ 0/1:38,10:40:-31.52,-12.05,-112.23:99 +chr1 1498508 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=15;HaplotypeScore=1.82;MQ=51.05;MQ0=0;OQ=196.72;QD=4.01;SB=27.81 GT:AD:DP:GL:GQ 0/1:38,11:41:-35.31,-12.36,-104.62:99 +chr1 1498897 rs7520996 T C 291.45 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=56.74;MQ0=0;OQ=1344.56;QD=17.46;SB=-662.63 GT:AD:DP:GL:GQ 0/1:31,46:75:-160.33,-22.59,-123.58:99 +chr1 1499019 rs7518083 A G 453.47 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.97;MQ0=0;OQ=1144.84;QD=14.49;SB=-308.25 GT:AD:DP:GL:GQ 0/1:39,40:76:-140.66,-22.89,-155.49:99 +chr1 1499688 rs6666293 A G 47.16 LowQual AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=1.90;MQ=53.03;MQ0=0;QD=6.74;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,3:5:-9.51,-1.51,-8.01:65.07 +chr1 1500664 rs7519837 C T 335.96 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=543.75;QD=13.59;SB=-294.78 GT:AD:DP:GL:GQ 0/1:21,19:39:-69.41,-11.75,-74.55:99 +chr1 1500967 rs7556282 G C 209.02 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=56.81;MQ0=0;OQ=874.72;QD=17.85;SB=-362.79 GT:AD:DP:GL:GQ 0/1:21,27:44:-104.04,-13.28,-69.73:99 +chr1 1501107 rs4590622 G A 74.70 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.06;MQ=35.43;MQ0=2;OQ=406.87;QD=8.30;SB=-78.55 GT:AD:DP:GL:GQ 0/1:30,19:38:-55.43,-11.46,-75.84:99 +chr1 1501178 rs4618908 T C 437.65 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.31;MQ0=1;OQ=645.96;QD=14.68;SB=-291.48 GT:AD:DP:GL:GQ 0/1:19,25:40:-79.93,-12.05,-65.32:99 +chr1 1504046 . C T 7.57 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=59.17;MQ0=0;OQ=1022.24;QD=18.25;SB=-279.21 GT:AD:DP:GL:GQ 0/1:26,30:52:-121.18,-15.67,-71.09:99 +chr1 1504960 rs9331751 T A 36.07 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=4.88;MQ=56.51;MQ0=1;OQ=1100.76;QD=14.11;SB=-360.40 GT:AD:DP:GL:GQ 0/1:39,39:73:-135.35,-21.99,-132.17:99 +chr1 1506133 rs9442407 C T 139.40 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=35.12;MQ0=12;OQ=825.82;QD=11.16;SB=-394.16 GT:AD:DP:GL:GQ 0/1:42,32:54:-102.14,-16.28,-92.88:99 +chr1 1509564 rs9442406 T C 136.95 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=56.80;MQ0=0;OQ=711.41;QD=13.42;SB=-198.20 GT:AD:DP:GL:GQ 0/1:27,26:51:-89.79,-15.37,-103.56:99 +chr1 1510588 rs28788874 C T 634.33 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.10;MQ0=1;OQ=2154.00;QD=35.90;SB=-1071.35 GT:AD:DP:GL:GQ 1/1:0,60:56:-219.01,-16.88,-0.03:99 +chr1 1510832 rs6666084 A G 27.92 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=29.16;MQ0=1;OQ=863.94;QD=22.15;SB=-357.32 GT:AD:DP:GL:GQ 1/1:0,34:29:-93.05,-11.63,-3.07:85.61 +chr1 1511143 rs6679999 C T 270.78 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.32;MQ0=0;OQ=967.03;QD=37.19;SB=-287.88 GT:AD:DP:GL:GQ 1/1:0,26:25:-100.30,-7.53,-0.01:75.24 +chr1 1511216 . T A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.79;MQ=40.83;MQ0=0;OQ=921.95;QD=25.61;SB=-124.48 GT:AD:DP:GL:GQ 0/1:7,29:35:-106.02,-10.55,-27.02:99 +chr1 1511668 rs4648786 A G 87.12 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=58.14;MQ0=0;OQ=1843.13;QD=31.78;SB=-498.18 GT:AD:DP:GL:GQ 1/1:0,58:57:-187.94,-17.18,-0.05:99 +chr1 1511869 rs4648787 C T 29.58 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.56;MQ=56.20;MQ0=1;OQ=2155.57;QD=37.82;SB=-1079.94 GT:AD:DP:GL:GQ 1/1:1,56:55:-219.17,-16.58,-0.02:99 +chr1 1511922 rs4648612 C T 25.92 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=42.53;MQ0=1;OQ=1102.46;QD=35.56;SB=-299.68 GT:AD:DP:GL:GQ 1/1:1,30:28:-113.84,-8.43,-0.01:84.28 +chr1 1512199 rs4648613 T C 554.79 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.33;MQ0=0;OQ=1584.81;QD=33.02;SB=-688.28 GT:AD:DP:GL:GQ 1/1:0,48:45:-162.08,-13.55,-0.01:99 +chr1 1512230 rs28809773 G A 465.17 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=52.87;MQ0=0;OQ=1755.99;QD=36.58;SB=-748.51 GT:AD:DP:GL:GQ 1/1:0,48:45:-179.20,-13.56,-0.01:99 +chr1 1512325 . G A 85.65 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=55.47;MQ0=0;OQ=776.49;QD=14.65;SB=-378.86 GT:AD:DP:GL:GQ 0/1:28,24:51:-96.30,-15.37,-89.39:99 +chr1 1512595 rs4366263 A G 19.23 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=3.13;MQ=56.40;MQ0=0;OQ=1310.46;QD=34.49;SB=-610.36 GT:AD:DP:GL:GQ 1/1:0,38:38:-134.64,-11.45,-0.01:99 +chr1 1512656 rs28778974 C T 131.47 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=49.50;MQ0=1;OQ=1426.66;QD=34.80;SB=-730.49 GT:AD:DP:GL:GQ 1/1:1,40:37:-146.26,-11.15,-0.01:99 +chr1 1512790 rs61774869 C T 40.58 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=48.67;MQ0=1;OQ=1682.46;QD=36.58;SB=-840.63 GT:AD:DP:GL:GQ 1/1:2,44:43:-171.84,-12.95,-0.01:99 +chr1 1513302 rs9725077 G A 148.03 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=48.17;MQ0=1;OQ=1464.10;QD=34.05;SB=-687.33 GT:AD:DP:GL:GQ 1/1:1,42:38:-150.01,-11.45,-0.01:99 +chr1 1514300 rs9442423 T C 34.69 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.59;MQ0=0;OQ=266.23;QD=6.83;SB=-0.97 GT:AD:DP:GL:GQ 0/1:24,15:34:-40.16,-10.25,-85.89:99 +chr1 1514394 . C T 901.86 Indel AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.65;MQ0=0;QD=14.78;SB=-128.11 GT:AD:DP:GL:GQ 0/1:33,28:59:-111.26,-17.79,-98.57:99 +chr1 1514734 rs9442403 A G 0.24 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=12.23;MQ=53.49;MQ0=0;OQ=367.70;QD=7.99;SB=-54.31 GT:AD:DP:GL:GQ 0/1:25,19:37:-51.21,-11.16,-85.57:99 +chr1 1514861 . A T 164.64 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.34;MQ0=0;OQ=646.82;QD=13.76;SB=-331.07 GT:AD:DP:GL:GQ 0/1:25,22:46:-81.82,-13.86,-91.60:99 +chr1 1515925 rs6681422 T C 152.90 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=56.53;MQ0=0;OQ=534.97;QD=11.15;SB=-174.52 GT:AD:DP:GL:GQ 0/1:23,25:43:-69.74,-12.96,-84.05:99 +chr1 1516662 rs12735276 A G 21.98 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.05;MQ=57.32;MQ0=1;OQ=2133.75;QD=30.05;SB=-1092.47 GT:AD:DP:GL:GQ 1/1:2,69:66:-217.02,-19.91,-0.06:99 +chr1 1516946 rs10157140 T C 503.19 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.65;MQ0=0;OQ=1116.09;QD=14.69;SB=-475.23 GT:AD:DP:GL:GQ 0/1:37,39:76:-137.79,-22.90,-145.96:99 +chr1 1517815 . T C 151.98 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.19;MQ0=0;OQ=718.93;QD=11.41;SB=-330.87 GT:AD:DP:GL:GQ 0/1:32,31:61:-93.57,-18.39,-126.83:99 +chr1 1518089 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=19;HaplotypeScore=19.37;MQ=53.15;MQ0=1;OQ=397.54;QD=5.76;SB=50.30 GT:AD:DP:GL:GQ 0/1:45,23:60:-60.81,-17.78,-147.22:99 +chr1 1518109 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=82;Dels=0.01;HRun=19;HaplotypeScore=9.39;MQ=51.76;MQ0=1;OQ=216.06;QD=2.63;SB=62.19 GT:AD:DP:GL:GQ 0/1:54,27:58:-42.07,-17.18,-142.92:99 +chr1 1518112 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=77;Dels=0.01;HRun=4;HaplotypeScore=9.55;MQ=51.62;MQ0=1;OQ=92.02;QD=1.20;SB=65.18 GT:AD:DP:GL:GQ 0/1:56,20:51:-27.56,-15.07,-144.06:99 +chr1 1518863 rs12725297 G C 139.44 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=58.84;MQ0=0;OQ=1568.02;QD=18.67;SB=-365.83 GT:AD:DP:GL:GQ 0/1:39,45:81:-184.49,-24.41,-167.76:99 +chr1 1518975 rs12725449 G C 178.35 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.97;MQ0=0;OQ=2276.77;QD=38.59;SB=-1002.01 GT:AD:DP:GL:GQ 1/1:0,59:56:-231.29,-16.89,-0.03:99 +chr1 1519320 rs28566709 T C 64.56 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.25;MQ=59.59;MQ0=0;OQ=477.78;QD=8.53;SB=-190.61 GT:AD:DP:GL:GQ 0/1:33,23:51:-66.44,-15.38,-114.90:99 +chr1 1519374 rs28662991 T C 77.77 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=59.56;MQ0=0;OQ=635.95;QD=12.23;SB=-285.60 GT:AD:DP:GL:GQ 0/1:29,23:51:-82.25,-15.37,-108.55:99 +chr1 1519813 rs28503881 A G 211.45 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.02;MQ0=0;OQ=531.98;QD=8.58;SB=-234.91 GT:AD:DP:GL:GQ 0/1:35,27:58:-73.97,-17.49,-134.84:99 +chr1 1519842 rs4648788 T C 59.76 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=56.83;MQ0=0;OQ=1829.71;QD=27.72;SB=-554.05 GT:AD:DP:GL:GQ 1/1:0,66:57:-186.60,-17.18,-0.04:99 +chr1 1519857 . G C 3.15 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=5.53;MQ=56.98;MQ0=0;OQ=985.46;QD=15.64;SB=-338.06 GT:AD:DP:GL:GQ 0/1:28,35:57:-119.03,-17.20,-116.72:99 +chr1 1519861 rs28689700 C G 213.40 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=56.88;MQ0=0;OQ=841.97;QD=13.80;SB=-287.94 GT:AD:DP:GL:GQ 0/1:30,31:57:-104.69,-17.21,-125.41:99 +chr1 1520060 rs4648789 A C 15.22 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=4;HaplotypeScore=1.27;MQ=50.71;MQ0=0;OQ=838.47;QD=14.46;SB=-329.82 GT:AD:DP:GL:GQ 0/1:26,32:54:-103.41,-16.28,-79.25:99 +chr1 1520063 rs4648790 C T 336.83 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=51.65;MQ0=0;OQ=926.60;QD=15.19;SB=-418.36 GT:AD:DP:GL:GQ 0/1:30,31:60:-114.03,-18.08,-107.59:99 +chr1 1520195 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=113;Dels=0.02;HRun=0;HaplotypeScore=46.04;MQ=50.13;MQ0=3;OQ=55.61;QD=0.49;SB=110.40 GT:AD:DP:GL:GQ 0/1:96,14:92:-36.27,-27.42,-356.52:88.45 +chr1 1520222 . G A 94.09 SnpCluster AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=77.51;MQ=46.35;MQ0=0;QD=0.80;SB=-48.89 GT:AD:DP:GL:GQ 0/1:102,15:106:-44.62,-31.93,-348.40:99 +chr1 1520225 . G C 344.68 SnpCluster AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=69.75;MQ=44.94;MQ0=0;QD=2.92;SB=-153.13 GT:AD:DP:GL:GQ 0/1:100,18:110:-70.90,-33.15,-412.65:99 +chr1 1520229 . C G 412.05 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=94.26;MQ=43.35;MQ0=0;QD=3.41;SB=-151.44 GT:AD:DP:GL:GQ 0/1:103,18:106:-76.44,-31.95,-372.75:99 +chr1 1520237 . G C 91.10 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=128;Dels=0.05;HRun=0;HaplotypeScore=131.86;MQ=42.98;MQ0=0;QD=0.71;SB=13.51 GT:AD:DP:GL:GQ 0/1:106,16:113:-45.55,-33.15,-430.26:99 +chr1 1520238 rs61774873 T A 718.56 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.05;HRun=0;HaplotypeScore=125.70;MQ=43.01;MQ0=0;QD=5.75;SB=-75.62 GT:AD:DP:GL:GQ 0/1:71,41:100:-122.71,-47.57,-247.49:99 +chr1 1520243 . C G 225.05 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=118.32;MQ=42.36;MQ0=0;QD=1.77;SB=107.39 GT:AD:DP:GL:GQ 0/1:107,20:111:-59.26,-33.47,-404.28:99 +chr1 1520250 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=130;Dels=0.03;HRun=1;HaplotypeScore=70.65;MQ=43.20;MQ0=0;OQ=629.57;QD=4.84;SB=-297.59 GT:AD:DP:GL:GQ 0/1:85,37:107:-98.49,-32.25,-308.33:99 +chr1 1520281 rs61774874 G C 511.99 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=95.68;MQ=43.19;MQ0=0;QD=4.13;SB=-246.08 GT:AD:DP:GL:GQ 0/1:99,25:103:-85.52,-31.04,-362.79:99 +chr1 1520285 . G C 387.17 SnpCluster AC=1;AF=0.50;AN=2;DP=119;Dels=0.01;HRun=0;HaplotypeScore=65.61;MQ=43.42;MQ0=0;QD=3.25;SB=-155.15 GT:AD:DP:GL:GQ 0/1:98,20:100:-71.84,-29.84,-355.29:99 +chr1 1520289 rs62642589 C G 93.31 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.01;HRun=0;HaplotypeScore=35.98;MQ=43.17;MQ0=0;QD=0.77;SB=134.48 GT:AD:DP:GL:GQ 0/1:107,13:109:-45.17,-32.56,-411.19:99 +chr1 1520331 rs28654137 C G 48.96 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.01;HRun=0;HaplotypeScore=27.98;MQ=47.63;MQ0=0;QD=0.60;SB=18.43 GT:AD:DP:GL:GQ 0/1:72,9:75:-30.78,-22.60,-290.44:81.79 +chr1 1520344 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=73;Dels=0.01;HRun=0;HaplotypeScore=35.55;MQ=46.62;MQ0=0;OQ=147.13;QD=2.02;SB=-55.25 GT:AD:DP:GL:GQ 0/1:57,14:62:-36.39,-18.39,-179.58:99 +chr1 1520377 . C G 26.02 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=20.54;MQ=46.26;MQ0=1;QD=0.42;SB=59.22 GT:AD:DP:GL:GQ 0/1:52,10:48:-20.35,-14.47,-182.03:58.84 +chr1 1520381 rs28593368 C G 11.70 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=9.32;MQ=47.21;MQ0=1;QD=0.18;SB=37.38 GT:AD:DP:GL:GQ 0/1:58,8:56:-21.30,-16.87,-217.45:44.23 +chr1 1520469 rs11488585 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.01;HRun=0;HaplotypeScore=36.86;MQ=43.53;MQ0=4;OQ=2355.10;QD=23.55;SB=-1049.66 GT:AD:DP:GL:GQ 0/1:35,63:89:-265.31,-26.51,-115.33:99 +chr1 1520498 . G A 0.22 PASS AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=42.41;MQ0=4;OQ=313.12;QD=3.48;SB=-164.48 GT:AD:DP:GL:GQ 0/1:71,19:76:-57.51,-22.91,-206.14:99 +chr1 1520609 . G C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=16.97;MQ=45.11;MQ0=1;OQ=1017.74;QD=9.51;SB=-327.71 GT:AD:DP:GL:GQ 0/1:72,34:94:-133.38,-28.32,-275.79:99 +chr1 1520627 . T C 0.10 PASS AC=2;AF=1.00;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=10.65;MQ=46.29;MQ0=2;OQ=3224.03;QD=30.42;SB=-1396.99 GT:AD:DP:GL:GQ 1/1:0,101:93:-329.81,-30.68,-3.83:99 +chr1 1520757 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=47.64;MQ0=6;OQ=89.81;QD=0.88;SB=110.39 GT:AD:DP:GL:GQ 0/1:91,11:89:-39.08,-26.81,-310.80:99 +chr1 1520774 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=99;Dels=0.01;HRun=0;HaplotypeScore=56.31;MQ=48.08;MQ0=6;OQ=62.24;QD=0.63;SB=110.34 GT:AD:DP:GL:GQ 0/1:89,9:83:-34.23,-24.72,-231.51:95.08 +chr1 1520787 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=96;Dels=0.04;HRun=0;HaplotypeScore=27.20;MQ=49.95;MQ0=4;OQ=173.92;QD=1.81;SB=77.51 GT:AD:DP:GL:GQ 0/1:78,14:87:-45.69,-25.01,-305.10:99 +chr1 1520821 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=37.97;MQ=51.43;MQ0=1;OQ=216.93;QD=2.55;SB=101.36 GT:AD:DP:GL:GQ 0/1:69,16:80:-49.07,-24.10,-269.00:99 +chr1 1520848 . G A 0.20 PASS AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=50.21;MQ0=2;OQ=302.35;QD=3.44;SB=74.15 GT:AD:DP:GL:GQ 0/1:72,16:76:-56.43,-22.92,-203.92:99 +chr1 1520892 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=1;HaplotypeScore=71.05;MQ=51.39;MQ0=2;OQ=950.76;QD=9.51;SB=-387.75 GT:AD:DP:GL:GQ 0/1:63,37:86:-124.27,-25.91,-211.22:99 +chr1 1520953 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=74;Dels=0.01;HRun=0;HaplotypeScore=47.85;MQ=52.80;MQ0=2;OQ=265.98;QD=3.59;SB=-146.32 GT:AD:DP:GL:GQ 0/1:59,14:61:-47.97,-18.09,-205.99:99 +chr1 1520957 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=21.78;MQ=53.36;MQ0=2;OQ=105.70;QD=1.55;SB=-47.11 GT:AD:DP:GL:GQ 0/1:59,9:55:-30.43,-16.57,-209.84:99 +chr1 1520979 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=45.80;MQ=49.11;MQ0=2;OQ=234.58;QD=3.72;SB=-118.04 GT:AD:DP:GL:GQ 0/1:53,10:50:-41.81,-15.07,-172.68:99 +chr1 1521029 . C G 208.12 Indel AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=31.42;MQ=47.45;MQ0=1;QD=3.20;SB=-33.62 GT:AD:DP:GL:GQ 0/1:53,12:61:-42.48,-18.38,-218.36:99 +chr1 1521111 . C G 34.71 LowQual AC=1;AF=0.50;AN=2;DP=75;Dels=0.05;HRun=0;HaplotypeScore=51.94;MQ=49.50;MQ0=5;QD=0.46;SB=-34.07 GT:AD:DP:GL:GQ 0/1:62,9:60:-24.84,-18.09,-231.30:67.54 +chr1 1521139 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=19.29;MQ=49.73;MQ0=4;OQ=471.32;QD=8.42;SB=-237.06 GT:AD:DP:GL:GQ 0/1:38,18:43:-63.38,-12.96,-121.81:99 +chr1 1521149 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=50;Dels=0.04;HRun=0;HaplotypeScore=25.97;MQ=51.25;MQ0=5;OQ=94.80;QD=1.90;SB=0.71 GT:AD:DP:GL:GQ 0/1:42,6:42:-25.43,-12.66,-151.77:99 +chr1 1521416 . G A 908.87 Indel AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=49.66;MQ0=7;QD=12.12;SB=-403.37 GT:AD:DP:GL:GQ 0/1:47,28:66:-114.05,-19.88,-141.06:99 +chr1 1521692 . G A 0.94 PASS AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=9.14;MQ=58.40;MQ0=0;OQ=1252.37;QD=15.27;SB=-600.00 GT:AD:DP:GL:GQ 0/1:41,41:79:-152.32,-23.80,-150.35:99 +chr1 1521772 rs36210710 A G 0.25 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=15.96;MQ=57.04;MQ0=1;OQ=875.12;QD=13.46;SB=-359.37 GT:AD:DP:GL:GQ 0/1:32,33:57:-107.96,-17.17,-110.70:99 +chr1 1522125 rs28569178 A G 2.98 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=5.24;MQ=53.41;MQ0=0;OQ=1519.29;QD=31.65;SB=-783.99 GT:AD:DP:GL:GQ 1/1:0,48:43:-155.53,-12.95,-0.01:99 +chr1 1522142 rs35051391 A C 34.82 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=4.14;MQ=53.19;MQ0=0;OQ=509.94;QD=11.86;SB=-251.92 GT:AD:DP:GL:GQ 0/1:20,23:38:-65.73,-11.45,-61.61:99 +chr1 1522705 . C T 4.71 PASS AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=50.65;MQ0=0;OQ=133.19;QD=16.65;SB=-79.09 GT:AD:DP:GL:GQ 0/1:3,5:8:-19.01,-2.41,-10.59:81.80 +chr1 1524477 rs11552172 T C 56.64 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.17;MQ0=0;OQ=436.12;QD=15.58;SB=-113.68 GT:AD:DP:GL:GQ 0/1:12,16:28:-55.34,-8.44,-45.31:99 +chr1 1527039 rs4075469 A C 248.77 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.34;MQ0=0;OQ=696.22;QD=16.58;SB=-340.88 GT:AD:DP:GL:GQ 0/1:16,26:40:-84.95,-12.05,-59.28:99 +chr1 1527300 rs7554569 C T 296.92 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=424.42;QD=8.16;SB=-236.55 GT:AD:DP:GL:GQ 0/1:35,17:46:-59.60,-13.87,-96.44:99 +chr1 1527750 . C A 254.99 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=986.18;QD=16.71;SB=-374.21 GT:AD:DP:GL:GQ 0/1:26,33:55:-118.47,-16.57,-69.65:99 +chr1 1527909 . G A 103.61 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.52;MQ0=0;OQ=783.03;QD=16.31;SB=-358.36 GT:AD:DP:GL:GQ 0/1:23,25:47:-95.76,-14.17,-71.60:99 +chr1 1528300 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=10.61;MQ=58.05;MQ0=0;OQ=286.83;QD=5.98;SB=62.19 GT:AD:DP:GL:GQ 0/1:26,22:41:-44.32,-12.35,-90.74:99 +chr1 1529232 rs6656591 T C 65.49 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.39;MQ=56.33;MQ0=0;OQ=1005.79;QD=17.65;SB=-491.70 GT:AD:DP:GL:GQ 0/1:23,34:55:-120.43,-16.57,-83.35:99 +chr1 1529445 rs6691649 G A 161.84 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.46;MQ0=0;OQ=1057.94;QD=19.59;SB=-480.07 GT:AD:DP:GL:GQ 0/1:20,34:51:-124.45,-15.37,-67.92:99 +chr1 1529817 rs4075275 G C 15.87 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=2.13;MQ=58.35;MQ0=0;OQ=1607.65;QD=30.92;SB=-720.33 GT:AD:DP:GL:GQ 1/1:0,52:40:-164.38,-12.07,-0.03:99 +chr1 1530590 . C T 27.41 PASS AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=55.36;MQ0=0;OQ=363.07;QD=13.45;SB=-133.59 GT:AD:DP:GL:GQ 0/1:14,13:26:-47.43,-7.84,-42.81:99 +chr1 1530910 . G C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=6.92;MQ=37.58;MQ0=2;OQ=79.86;QD=5.32;SB=-10.00 GT:AD:DP:GL:GQ 0/1:7,8:5:-12.78,-1.51,-7.90:63.88 +chr1 1530912 . C G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=2;HaplotypeScore=4.15;MQ=38.11;MQ0=2;OQ=71.50;QD=5.11;SB=-6.99 GT:AD:DP:GL:GQ 0/1:4,10:6:-12.24,-1.81,-12.03:99 +chr1 1530952 . G C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=8.79;MQ=42.16;MQ0=2;OQ=53.35;QD=3.33;SB=-39.44 GT:AD:DP:GL:GQ 0/1:11,5:9:-11.33,-2.71,-25.48:86.19 +chr1 1530975 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=5.18;MQ=46.58;MQ0=0;OQ=57.06;QD=3.57;SB=5.04 GT:AD:DP:GL:GQ 0/1:12,4:12:-12.60,-3.61,-32.43:89.90 +chr1 1531008 . C G 10.82 LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=2;HaplotypeScore=6.64;MQ=46.16;MQ0=1;QD=0.52;SB=-26.85 GT:AD:DP:GL:GQ 0/1:16,5:11:-7.66,-3.33,-32.36:43.28 +chr1 1531060 . A C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=9.36;MQ=36.61;MQ0=1;OQ=116.93;QD=7.31;SB=-3.99 GT:AD:DP:GL:GQ 0/1:5,10:9:-17.69,-2.71,-12.57:98.57 +chr1 1531096 . C T 31.46 LowQual AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=8.94;MQ=35.04;MQ0=1;QD=3.15;SB=-6.99 GT:AD:DP:GL:GQ 0/1:5,5:4:-7.64,-1.21,-6.67:54.60 +chr1 1531214 . C T 12.58 LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=48.08;MQ0=0;QD=0.90;SB=-28.53 GT:AD:DP:GL:GQ 0/1:11,2:10:-7.53,-3.02,-23.43:45.17 +chr1 1531255 . G A 2.13 PASS AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=54.60;MQ0=0;OQ=208.62;QD=17.39;SB=-121.64 GT:AD:DP:GL:GQ 0/1:2,10:8:-26.44,-2.41,-2.60:1.87 +chr1 1531316 . A T 48.17 LowQual AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=48.85;MQ0=0;QD=2.01;SB=-30.94 GT:AD:DP:GL:GQ 0/1:15,8:14:-12.32,-4.22,-35.65:81.01 +chr1 1531334 . C T 13.43 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=45.60;MQ0=1;QD=0.56;SB=5.01 GT:AD:DP:GL:GQ 0/1:15,7:11:-7.93,-3.32,-25.96:46.07 +chr1 1531359 . G A 17.07 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=4.20;MQ=46.76;MQ0=1;QD=0.74;SB=11.04 GT:AD:DP:GL:GQ 0/1:19,4:19:-10.71,-5.73,-55.15:49.82 +chr1 1531380 . C G 42.65 LowQual AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=3;HaplotypeScore=7.66;MQ=46.38;MQ0=2;QD=1.42;SB=-45.68 GT:AD:DP:GL:GQ 0/1:23,7:24:-14.78,-7.24,-85.75:75.49 +chr1 1531419 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=2;HaplotypeScore=5.63;MQ=45.92;MQ0=1;OQ=63.73;QD=3.03;SB=23.10 GT:AD:DP:GL:GQ 0/1:16,5:18:-15.09,-5.43,-50.86:96.57 +chr1 1531527 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=2;HaplotypeScore=3.70;MQ=32.41;MQ0=1;OQ=75.08;QD=3.75;SB=-44.95 GT:AD:DP:GL:GQ 0/1:9,10:9:-13.51,-2.71,-17.78:99 +chr1 1531545 . G C 27.47 LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=8.08;MQ=36.24;MQ0=1;QD=1.37;SB=-32.85 GT:AD:DP:GL:GQ 0/1:18,2:9:-8.74,-2.71,-27.23:60.30 +chr1 1531547 . C G 25.49 LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=2;HaplotypeScore=8.42;MQ=36.81;MQ0=1;QD=1.34;SB=-27.40 GT:AD:DP:GL:GQ 0/1:14,5:6:-7.64,-1.81,-15.17:58.31 +chr1 1532873 rs9442420 T C 73.52 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.50;MQ0=0;OQ=1279.49;QD=27.81;SB=-597.57 GT:AD:DP:GL:GQ 1/1:0,46:41:-131.57,-12.37,-0.04:99 +chr1 1533487 rs61774903 T C 6.43 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=59.07;MQ0=0;OQ=267.71;QD=10.71;SB=-22.90 GT:AD:DP:GL:GQ 0/1:12,13:23:-36.99,-6.93,-45.73:99 +chr1 1533846 . C A 150.54 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=607.30;QD=13.20;SB=-294.38 GT:AD:DP:GL:GQ 0/1:23,23:45:-77.57,-13.56,-81.22:99 +chr1 1534313 . G A 286.31 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.20;MQ0=0;OQ=679.07;QD=15.09;SB=-355.53 GT:AD:DP:GL:GQ 0/1:22,23:43:-84.16,-12.97,-66.20:99 +chr1 1535152 rs6671612 G T 108.66 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=2.91;MQ=57.71;MQ0=0;OQ=838.64;QD=11.98;SB=-304.64 GT:AD:DP:GL:GQ 0/1:41,29:64:-106.43,-19.29,-110.69:99 +chr1 1536167 rs11492279 C T 248.42 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=60.00;MQ0=0;OQ=1040.79;QD=15.31;SB=-440.43 GT:AD:DP:GL:GQ 0/1:36,32:64:-126.65,-19.29,-102.67:99 +chr1 1536812 rs4612573 T C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.03;HRun=1;HaplotypeScore=39.15;MQ=49.08;MQ0=0;OQ=1478.03;QD=23.09;SB=-556.56 GT:AD:DP:GL:GQ 1/1:5,57:50:-162.89,-15.07,-11.50:35.64 +chr1 1537429 rs4369171 A G 1.14 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=7.54;MQ=57.32;MQ0=0;OQ=2121.87;QD=33.68;SB=-744.31 GT:AD:DP:GL:GQ 1/1:0,62:59:-215.79,-17.77,-0.02:99 +chr1 1537803 . G T 52.70 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=13;HaplotypeScore=28.28;MQ=58.09;MQ0=1;QD=0.71;SB=63.90 GT:AD:DP:GL:GQ 0/1:60,13:55:-25.14,-16.58,-155.96:85.54 +chr1 1537805 . T C 135.64 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=41.12;MQ=58.24;MQ0=1;QD=2.02;SB=15.89 GT:AD:DP:GL:GQ 0/1:57,10:56:-33.73,-16.88,-176.73:99 +chr1 1538333 . A G 136.38 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=58.86;MQ0=0;OQ=748.93;QD=13.87;SB=-356.58 GT:AD:DP:GL:GQ 0/1:27,27:53:-94.15,-15.98,-99.69:99 +chr1 1538565 rs9442431 T C 829.64 Indel AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=7.58;MQ=50.06;MQ0=1;QD=21.83;SB=-151.73 GT:AD:DP:GL:GQ 1/1:0,37:28:-86.58,-8.45,-0.03:84.18 +chr1 1538664 rs9442430 T C 1.04 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.01;HRun=1;HaplotypeScore=8.39;MQ=59.12;MQ0=0;OQ=2182.53;QD=31.63;SB=-555.08 GT:AD:DP:GL:GQ 1/1:0,68:67:-221.88,-20.20,-0.05:99 +chr1 1539012 rs34501155 C T 24.47 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=0.10;MQ=59.44;MQ0=0;OQ=1523.49;QD=20.31;SB=-698.38 GT:AD:DP:GL:GQ 0/1:29,46:74:-177.93,-22.30,-104.96:99 +chr1 1539217 rs12066 G A 112.48 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2269.66;QD=38.47;SB=-1077.37 GT:AD:DP:GL:GQ 1/1:0,59:57:-230.57,-17.17,-0.02:99 +chr1 1539583 . C T 13.58 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.17;MQ=59.69;MQ0=0;OQ=849.58;QD=14.16;SB=-408.41 GT:AD:DP:GL:GQ 0/1:34,26:60:-106.31,-18.07,-125.62:99 +chr1 1540565 rs4648611 A G 1.07 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=2;HaplotypeScore=4.13;MQ=58.95;MQ0=0;OQ=632.46;QD=28.75;SB=-329.75 GT:AD:DP:GL:GQ 1/1:0,22:20:-66.85,-6.03,-0.02:60.13 +chr1 1541790 rs7418389 T C 9.16 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=644.37;QD=28.02;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,23:21:-68.04,-6.33,-0.01:63.14 +chr1 1542618 rs6604985 T C 187.42 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.49;MQ0=0;OQ=2789.66;QD=34.02;SB=-860.05 GT:AD:DP:GL:GQ 1/1:0,82:81:-282.58,-24.40,-0.03:99 +chr1 1543361 rs28546565 G A 262.71 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.46;MQ0=0;OQ=627.76;QD=14.60;SB=-285.20 GT:AD:DP:GL:GQ 0/1:20,23:40:-78.11,-12.05,-70.94:99 +chr1 1543456 rs28623434 C G 8.50 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=2.93;MQ=59.20;MQ0=0;OQ=2332.23;QD=40.21;SB=-1030.14 GT:AD:DP:GL:GQ 1/1:0,58:55:-236.83,-16.57,-0.02:99 +chr1 1543533 rs9442410 G C 82.06 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=2713.47;QD=43.07;SB=-1108.14 GT:AD:DP:GL:GQ 1/1:0,63:62:-274.95,-18.68,-0.02:99 +chr1 1544225 rs9442425 G A 33.58 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.11;MQ=59.22;MQ0=0;OQ=1855.01;QD=38.65;SB=-869.17 GT:AD:DP:GL:GQ 1/1:0,48:47:-189.10,-14.16,-0.01:99 +chr1 1545229 rs9329576 T C 4.58 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=60.00;MQ0=0;OQ=1266.55;QD=28.15;SB=-625.18 GT:AD:DP:GL:GQ 1/1:0,45:39:-130.27,-11.76,-0.03:99 +chr1 1545852 rs7543265 G A 8.95 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=6.32;MQ=58.20;MQ0=0;OQ=611.29;QD=15.67;SB=-238.27 GT:AD:DP:GL:GQ 0/1:17,20:35:-74.97,-10.56,-46.23:99 +chr1 1546595 rs34983251 G A 45.65 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=59.23;MQ0=0;OQ=349.98;QD=11.67;SB=-133.57 GT:AD:DP:GL:GQ 0/1:16,14:26:-46.12,-7.83,-51.50:99 +chr1 1547538 rs28710339 G C 59.83 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=3.45;MQ=58.50;MQ0=0;OQ=866.08;QD=15.47;SB=-347.43 GT:AD:DP:GL:GQ 0/1:31,25:53:-105.89,-16.00,-107.63:99 +chr1 1547753 . C T 52.88 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.60;MQ0=0;OQ=1139.64;QD=19.99;SB=-512.06 GT:AD:DP:GL:GQ 0/1:22,35:54:-133.53,-16.28,-63.46:99 +chr1 1548655 rs12755088 T C 97.70 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=439.27;QD=24.40;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,18:16:-47.54,-4.84,-0.03:48.08 +chr1 1548983 . C G 40.73 LowQual AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=5;HaplotypeScore=1.58;MQ=47.12;MQ0=0;QD=6.79;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,5:2:-7.48,-0.61,-0.00:6.02 +chr1 1549329 rs28617190 G A 97.62 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.74;MQ=57.37;MQ0=0;OQ=547.08;QD=16.09;SB=-253.53 GT:AD:DP:GL:GQ 0/1:16,18:32:-67.63,-9.64,-54.05:99 +chr1 1549834 rs12748433 C T 442.94 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.23;MQ0=0;OQ=1400.65;QD=37.86;SB=-569.32 GT:AD:DP:GL:GQ 1/1:0,37:36:-143.66,-10.85,-0.01:99 +chr1 1549963 rs28441650 G A 319.81 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.05;MQ0=0;OQ=739.99;QD=15.10;SB=-342.91 GT:AD:DP:GL:GQ 0/1:25,24:48:-91.75,-14.47,-81.34:99 +chr1 1551048 . G A 13.72 PASS AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=55.20;MQ0=0;OQ=331.40;QD=13.81;SB=-96.94 GT:AD:DP:GL:GQ 0/1:12,12:21:-42.75,-6.33,-33.17:99 +chr1 1551194 . G A 9.75 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=59.45;MQ0=0;OQ=497.08;QD=14.62;SB=-108.95 GT:AD:DP:GL:GQ 0/1:18,16:33:-62.94,-9.95,-55.65:99 +chr1 1552758 rs12735861 C T 11.10 PASS AC=1;AF=0.50;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=56.58;MQ0=0;OQ=143.44;QD=15.94;SB=-6.99 GT:AD:DP:GL:GQ 0/1:3,6:8:-20.04,-2.41,-9.16:67.50 +chr1 1553652 . C A 57.28 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=59.52;MQ0=0;OQ=736.76;QD=15.35;SB=-347.43 GT:AD:DP:GL:GQ 0/1:23,25:44:-90.22,-13.26,-60.84:99 +chr1 1554057 rs3935032 C T 0.35 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=59.31;MQ0=0;OQ=580.92;QD=21.52;SB=-104.60 GT:AD:DP:GL:GQ 0/1:9,18:26:-69.21,-7.83,-32.29:99 +chr1 1555931 rs28730454 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=7;HaplotypeScore=0.32;MQ=55.21;MQ0=0;OQ=59.16;QD=11.83;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:3:-9.41,-0.90,-0.00:9.02 +chr1 1556023 rs28464684 T C 13.91 PASS AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=73.72;QD=24.57;SB=-40.68 GT:AD:DP:GL:GQ 1/1:0,3:3:-10.86,-0.90,-0.00:9.03 +chr1 1556952 rs28451771 T C 12.66 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=601.05;QD=31.63;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,19:19:-63.70,-5.72,-0.01:57.14 +chr1 1561503 rs61774909 G T 0.68 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=9.65;MQ0=29;OQ=78.96;QD=2.47;SB=-10.00 GT:AD:DP:GL:GQ 1/1:16,16:3:-11.38,-0.90,-0.00:9.03 +chr1 1563882 rs61774911 A G 1.20 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=39.06;MQ0=5;OQ=124.38;QD=2.76;SB=-85.66 GT:AD:DP:GL:GQ 0/1:34,10:35:-26.27,-10.55,-104.24:99 +chr1 1563939 rs9442413 G A 8.49 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=40.26;MQ0=2;OQ=315.22;QD=4.50;SB=-153.56 GT:AD:DP:GL:GQ 0/1:51,19:59:-52.60,-17.79,-143.72:99 +chr1 1564183 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=20;HaplotypeScore=14.98;MQ=46.49;MQ0=5;OQ=64.66;QD=1.80;SB=35.13 GT:AD:DP:GL:GQ 0/1:31,5:28:-18.18,-8.44,-79.86:97.49 +chr1 1564572 rs28401288 T G 29.42 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=41.92;MQ0=1;OQ=1158.48;QD=27.58;SB=-476.97 GT:AD:DP:GL:GQ 1/1:0,42:35:-119.45,-10.55,-0.02:99 +chr1 1565479 rs28394074 T C 98.76 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=12.86;MQ0=16;OQ=207.25;QD=7.68;SB=-36.94 GT:AD:DP:GL:GQ 1/1:0,27:7:-24.31,-2.11,-0.00:21.06 +chr1 1565699 . C G 5.41 PASS AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=1;HaplotypeScore=2.34;MQ=26.47;MQ0=10;OQ=657.44;QD=8.65;SB=-346.42 GT:AD:DP:GL:GQ 0/1:55,21:62:-87.73,-18.71,-164.80:99 +chr1 1566499 rs3765908 G A 18.31 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.75;MQ=37.81;MQ0=3;OQ=1730.84;QD=29.34;SB=-752.15 GT:AD:DP:GL:GQ 1/1:8,51:54:-192.27,-16.27,-15.84:4.30 +chr1 1566866 rs3819995 C T 33.13 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=17.30;MQ0=34;OQ=418.63;QD=7.34;SB=-10.00 GT:AD:DP:GL:GQ 0/1:21,36:18:-50.57,-5.43,-18.99:99 +chr1 1567043 rs1137001 C T 0.22 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=9.65;MQ0=38;OQ=66.77;QD=1.34;SB=-10.00 GT:AD:DP:GL:GQ 0/1:35,15:6:-11.77,-1.81,-10.91:90.99 +chr1 1569585 rs61774912 C T 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=8.98;MQ=13.84;MQ0=43;OQ=132.92;QD=1.51;SB=-3.99 GT:AD:DP:GL:GQ 0/1:64,24:26:-24.41,-7.83,-74.67:99 +chr1 1569917 rs6688326 C A 0.25 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=26.34;MQ0=26;OQ=227.69;QD=3.04;SB=-87.75 GT:AD:DP:GL:GQ 0/1:58,17:44:-39.31,-13.26,-117.30:99 +chr1 1570601 rs4648767 T A 243.47 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=24.85;MQ0=18;OQ=1006.84;QD=11.57;SB=-380.53 GT:AD:DP:GL:GQ 0/1:42,45:58:-121.45,-17.48,-87.58:99 +chr1 1570928 . G C 0.90 PASS AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=0;HaplotypeScore=3.62;MQ=32.27;MQ0=14;OQ=845.01;QD=5.52;SB=-333.79 GT:AD:DP:GL:GQ 0/1:113,40:123:-124.85,-37.07,-408.45:99 +chr1 1570959 . C T 0.27 PASS AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=2;HaplotypeScore=4.89;MQ=34.90;MQ0=12;OQ=2272.40;QD=13.77;SB=-727.55 GT:AD:DP:GL:GQ 0/1:85,80:144:-273.90,-43.38,-268.43:99 +chr1 1571421 rs61774913 C T 442.63 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.06;MQ0=31;OQ=744.27;QD=14.31;SB=-218.78 GT:AD:DP:GL:GQ 1/1:0,52:19:-78.02,-5.72,-0.00:57.19 +chr1 1571449 rs61774914 T C 385.68 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=19.48;MQ0=37;OQ=993.50;QD=14.19;SB=-324.14 GT:AD:DP:GL:GQ 1/1:0,70:28:-102.94,-8.43,-0.01:84.26 +chr1 1571467 . G A 0.11 PASS AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=5.46;MQ=31.83;MQ0=25;OQ=330.51;QD=3.76;SB=-146.19 GT:AD:DP:GL:GQ 0/1:69,19:55:-52.91,-16.58,-135.58:99 +chr1 1571576 . A C 50.03 PASS AC=2;AF=1.00;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=35.58;MQ0=13;OQ=1974.59;QD=21.23;SB=-847.56 GT:AD:DP:GL:GQ 1/1:0,61:79:-282.59,-90.56,-81.54:90.13 +chr1 1571744 rs61774916 T C 0.32 PASS AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=43.65;MQ0=18;OQ=618.53;QD=4.99;SB=-195.46 GT:AD:DP:GL:GQ 0/1:91,33:103:-96.17,-31.03,-294.76:99 +chr1 1571789 rs61774917 G T 99.17 PASS AC=1;AF=0.50;AN=2;DB;DP=114;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=40.38;MQ0=17;OQ=858.73;QD=7.53;SB=-166.41 GT:AD:DP:GL:GQ 0/1:66,48:94:-117.47,-28.31,-223.12:99 +chr1 1571821 rs4279785 T C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=33.09;MQ0=22;OQ=74.70;QD=0.60;SB=13.40 GT:AD:DP:GL:GQ 0/1:103,22:85:-36.35,-25.60,-306.33:99 +chr1 1571969 rs4648753 T C 252.37 PASS AC=2;AF=1.00;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.21;MQ0=23;OQ=2308.47;QD=23.08;SB=-928.73 GT:AD:DP:GL:GQ 1/1:1,99:73:-234.50,-22.02,-0.07:99 +chr1 1572065 rs61774918 C T 271.62 PASS AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=40.98;MQ0=5;OQ=1993.46;QD=16.08;SB=-715.20 GT:AD:DP:GL:GQ 0/1:57,67:116:-237.58,-34.95,-201.11:99 +chr1 1572318 rs61774919 G A 28.59 PASS AC=1;AF=0.50;AN=2;DB;DP=173;Dels=0.00;HRun=0;HaplotypeScore=4.27;MQ=26.57;MQ0=15;OQ=1639.76;QD=9.48;SB=-550.56 GT:AD:DP:GL:GQ 0/1:104,69:121:-203.75,-36.49,-222.67:99 +chr1 1572479 . T C 0.14 PASS AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=45.14;MQ0=0;OQ=1750.04;QD=12.24;SB=-888.87 GT:AD:DP:GL:GQ 0/1:83,60:141:-220.76,-42.47,-332.08:99 +chr1 1572504 . T C 0.71 PASS AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=42.33;MQ0=3;OQ=1049.29;QD=7.72;SB=-546.16 GT:AD:DP:GL:GQ 0/1:84,52:129:-147.09,-38.88,-337.66:99 +chr1 1572657 rs4648754 C A 97.80 PASS AC=2;AF=1.00;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=39.40;MQ0=0;OQ=4131.60;QD=35.01;SB=-1448.13 GT:AD:DP:GL:GQ 1/1:1,117:114:-412.16,-34.34,-0.04:99 +chr1 1572704 rs61774920 A G 0.40 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=29.04;MQ0=13;OQ=131.71;QD=1.78;SB=23.25 GT:AD:DP:GL:GQ 0/1:54,20:56:-33.33,-16.87,-184.69:99 +chr1 1572707 rs61774921 G T 0.96 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=28.52;MQ0=13;OQ=177.56;QD=2.50;SB=-37.61 GT:AD:DP:GL:GQ 0/1:52,19:55:-37.61,-16.57,-159.55:99 +chr1 1572743 rs3820000 G C 38.18 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.84;MQ0=19;OQ=650.68;QD=7.75;SB=38.16 GT:AD:DP:GL:GQ 0/1:50,34:58:-85.85,-17.49,-156.24:99 +chr1 1572824 rs3820001 G C 184.22 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=41.82;MQ0=4;OQ=1359.68;QD=17.43;SB=-597.25 GT:AD:DP:GL:GQ 0/1:31,47:67:-159.47,-20.22,-110.10:99 +chr1 1572866 rs61776849 C T 39.28 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=4.48;MQ=49.73;MQ0=0;OQ=1155.72;QD=12.70;SB=-351.36 GT:AD:DP:GL:GQ 0/1:50,41:84:-144.17,-25.32,-161.47:99 +chr1 1572951 . A G 0.08 PASS AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=47.33;MQ0=7;OQ=238.29;QD=2.91;SB=26.27 GT:AD:DP:GL:GQ 0/1:60,22:73:-49.11,-21.99,-235.06:99 +chr1 1573358 rs61774952 T C 32.21 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=47.33;MQ0=8;QD=0.37;SB=67.42 GT:AD:DP:GL:GQ 0/1:70,16:71:-27.89,-21.39,-252.84:65.04 +chr1 1573532 . C T 35.47 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=10.41;MQ0=15;QD=1.97;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,3:3:-7.73,-0.90,-3.80:28.93 +chr1 1573550 . T C 24.36 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=33.97;MQ0=17;QD=0.72;SB=-17.89 GT:AD:DP:GL:GQ 0/1:23,11:14:-9.94,-4.22,-42.08:57.18 +chr1 1573618 . C T 2.54 PASS AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=5.35;MQ=45.15;MQ0=15;OQ=814.16;QD=7.75;SB=-232.64 GT:AD:DP:GL:GQ 0/1:66,38:82:-109.43,-24.73,-173.93:99 +chr1 1573625 . G A 3.56 PASS AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=45.17;MQ0=14;OQ=654.74;QD=6.18;SB=-207.09 GT:AD:DP:GL:GQ 0/1:70,36:84:-94.09,-25.34,-189.03:99 +chr1 1573865 rs6691927 A G 0.48 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=13.93;MQ=47.63;MQ0=8;OQ=1026.45;QD=17.40;SB=-411.69 GT:AD:DP:GL:GQ 0/1:13,46:46:-119.80,-13.87,-37.07:99 +chr1 1573965 rs28525262 G A 126.85 PASS AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=48.13;MQ0=7;OQ=3091.70;QD=33.97;SB=-1505.87 GT:AD:DP:GL:GQ 1/1:7,83:80:-316.25,-24.10,-3.49:99 +chr1 1573980 rs4648756 G C 18.18 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=4.39;MQ=47.15;MQ0=6;OQ=3392.36;QD=38.99;SB=-1642.01 GT:AD:DP:GL:GQ 1/1:0,87:79:-338.24,-23.81,-0.03:99 +chr1 1574055 rs4648606 G A 59.73 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=37.73;MQ0=7;OQ=2424.32;QD=33.21;SB=-1231.00 GT:AD:DP:GL:GQ 1/1:0,72:61:-246.03,-18.38,-0.02:99 +chr1 1574081 rs4648607 T C 84.11 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=40.76;MQ0=4;OQ=2240.23;QD=31.55;SB=-1072.45 GT:AD:DP:GL:GQ 1/1:0,71:63:-227.63,-18.98,-0.02:99 +chr1 1574087 rs4648757 G C 98.21 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=43.14;MQ0=1;OQ=2791.35;QD=39.31;SB=-1268.99 GT:AD:DP:GL:GQ 1/1:0,71:65:-282.74,-19.59,-0.02:99 +chr1 1574123 . A C 149.77 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=169.77;MQ=39.72;MQ0=1;QD=1.63;SB=83.29 GT:AD:DP:GL:GQ 0/1:79,13:73:-40.25,-21.99,-225.95:99 +chr1 1574124 . A G 50.98 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=170.51;MQ=39.99;MQ0=1;QD=0.55;SB=86.31 GT:AD:DP:GL:GQ 0/1:80,13:72:-30.08,-21.70,-250.90:83.81 +chr1 1574131 . A G 472.59 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=2;HaplotypeScore=66.93;MQ=41.08;MQ0=1;QD=5.25;SB=86.31 GT:AD:DP:GL:GQ 0/1:61,29:78:-74.04,-23.50,-234.93:99 +chr1 1574135 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=78.57;MQ=41.20;MQ0=1;OQ=155.65;QD=1.75;SB=86.32 GT:AD:DP:GL:GQ 0/1:76,13:71:-40.23,-21.39,-240.65:99 +chr1 1574143 . A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=43.74;MQ0=1;OQ=78.06;QD=1.07;SB=89.31 GT:AD:DP:GL:GQ 0/1:60,13:65:-30.68,-19.59,-219.52:99 +chr1 1574152 . C T 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=43.30;MQ0=0;OQ=130.78;QD=1.92;SB=41.52 GT:AD:DP:GL:GQ 0/1:58,10:59:-34.15,-17.79,-160.93:99 +chr1 1574339 . T A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=12.88;MQ=42.39;MQ0=0;OQ=429.14;QD=5.50;SB=104.35 GT:AD:DP:GL:GQ 0/1:59,19:76:-69.09,-22.90,-217.44:99 +chr1 1574367 rs12749208 C T 7.96 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=36.29;MQ0=0;OQ=733.94;QD=10.48;SB=80.18 GT:AD:DP:GL:GQ 0/1:43,27:66:-96.58,-19.90,-132.61:99 +chr1 1574398 rs12756960 A G 17.43 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=34.26;MQ0=0;QD=0.28;SB=39.57 GT:AD:DP:GL:GQ 0/1:29,33:32:-14.67,-9.65,-103.72:50.18 +chr1 1574404 rs12756961 A T 204.46 Indel AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=35.46;MQ0=0;QD=3.01;SB=-19.65 GT:AD:DP:GL:GQ 0/1:32,36:41:-36.08,-12.35,-112.04:99 +chr1 1574410 rs12749336 C G 884.89 Indel AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=10.32;MQ=35.72;MQ0=0;QD=12.82;SB=-17.81 GT:AD:DP:GL:GQ 0/1:40,29:35:-102.33,-10.56,-39.37:99 +chr1 1574434 rs61774954 A C 428.65 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=8.25;MQ=34.95;MQ0=1;QD=6.30;SB=56.20 GT:AD:DP:GL:GQ 0/1:39,29:57:-63.32,-17.18,-124.62:99 +chr1 1574437 rs61774955 A C 431.78 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=7.93;MQ=34.95;MQ0=1;QD=6.35;SB=56.19 GT:AD:DP:GL:GQ 0/1:38,30:51:-61.82,-15.36,-118.50:99 +chr1 1574456 rs12749364 C A 1380.74 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=20.46;MQ=37.20;MQ0=1;QD=17.26;SB=-577.01 GT:AD:DP:GL:GQ 1/1:30,50:46:-152.08,-13.86,-10.42:34.36 +chr1 1574458 . G C 45.27 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=79;Dels=0.01;HRun=0;HaplotypeScore=10.44;MQ=37.76;MQ0=1;QD=0.57;SB=71.27 GT:AD:DP:GL:GQ 0/1:52,26:51:-22.87,-15.06,-200.14:78.10 +chr1 1574459 . G A 19.52 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=78;Dels=0.01;HRun=1;HaplotypeScore=9.38;MQ=37.85;MQ0=1;QD=0.25;SB=68.24 GT:AD:DP:GL:GQ 0/1:50,27:51:-20.29,-15.06,-165.60:52.31 +chr1 1574490 . C T 446.32 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=13.97;MQ=40.46;MQ0=1;QD=6.11;SB=62.20 GT:AD:DP:GL:GQ 0/1:48,25:59:-65.69,-17.77,-151.07:99 +chr1 1574491 . A G 363.54 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=40.79;MQ0=1;QD=4.91;SB=65.24 GT:AD:DP:GL:GQ 0/1:48,26:58:-57.11,-17.48,-164.32:99 +chr1 1574495 . G A 435.54 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=16.96;MQ=40.97;MQ0=1;QD=5.73;SB=65.16 GT:AD:DP:GL:GQ 0/1:50,26:61:-65.23,-18.39,-146.68:99 +chr1 1574611 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=41.66;MQ0=2;OQ=80.08;QD=1.13;SB=68.24 GT:AD:DP:GL:GQ 0/1:54,17:60:-29.38,-18.09,-195.87:99 +chr1 1574622 . G A 0.30 PASS AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=40.91;MQ0=2;OQ=251.34;QD=3.44;SB=59.11 GT:AD:DP:GL:GQ 0/1:55,18:61:-46.81,-18.39,-160.50:99 +chr1 1574627 . C T 0.19 PASS AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=42.21;MQ0=2;OQ=221.98;QD=2.88;SB=74.24 GT:AD:DP:GL:GQ 0/1:61,16:67:-45.68,-20.20,-184.31:99 +chr1 1574705 rs12753686 C T 533.95 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=47.26;MQ0=1;OQ=2577.15;QD=38.46;SB=-1301.71 GT:AD:DP:GL:GQ 1/1:1,66:64:-261.31,-19.28,-0.01:99 +chr1 1574781 rs12753729 C T 0.96 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=7.51;MQ=55.74;MQ0=0;OQ=2039.46;QD=37.77;SB=-910.24 GT:AD:DP:GL:GQ 1/1:1,53:52:-207.55,-15.67,-0.02:99 +chr1 1575120 rs4648758 A G 435.58 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.79;MQ0=0;OQ=1070.30;QD=28.93;SB=-511.19 GT:AD:DP:GL:GQ 1/1:0,37:35:-110.65,-10.56,-0.04:99 +chr1 1575210 rs4648760 T C 43.48 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=63.90;MQ0=0;OQ=1693.31;QD=34.56;SB=-784.12 GT:AD:DP:GL:GQ 1/1:0,49:49:-172.94,-14.76,-0.02:99 +chr1 1575251 rs4648761 A G 5.46 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.80;MQ0=0;OQ=1436.67;QD=28.17;SB=-671.85 GT:AD:DP:GL:GQ 1/1:0,51:45:-147.29,-13.57,-0.04:99 +chr1 1575460 rs7531938 A G 536.50 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.20;MQ0=0;OQ=2059.81;QD=30.29;SB=-875.65 GT:AD:DP:GL:GQ 1/1:0,68:66:-209.63,-19.91,-0.06:99 +chr1 1575505 rs3936009 G T 209.53 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=57.75;MQ0=0;OQ=2310.00;QD=35.54;SB=-1127.37 GT:AD:DP:GL:GQ 1/1:0,65:65:-234.60,-19.58,-0.02:99 +chr1 1576615 rs11486023 T C 106.32 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.19;MQ0=0;OQ=1526.39;QD=31.15;SB=-484.14 GT:AD:DP:GL:GQ 1/1:0,49:47:-156.26,-14.17,-0.04:99 +chr1 1577178 rs4648762 A G 161.07 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=54.74;MQ0=0;OQ=2251.82;QD=30.85;SB=-761.70 GT:AD:DP:GL:GQ 1/1:0,72:69:-228.82,-20.80,-0.05:99 +chr1 1578533 rs61774958 G A 209.68 PASS AC=1;AF=0.50;AN=2;DB;DP=136;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.20;MQ0=11;OQ=1051.54;QD=7.73;SB=-56.39 GT:AD:DP:GL:GQ 0/1:86,50:122:-145.19,-36.75,-299.83:99 +chr1 1578580 rs61774959 G A 15.52 PASS AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=42.73;MQ0=4;OQ=297.29;QD=2.89;SB=-52.85 GT:AD:DP:GL:GQ 0/1:73,30:83:-58.01,-25.00,-251.41:99 +chr1 1578600 rs61776760 C T 0.35 PASS AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=43.98;MQ0=2;OQ=158.49;QD=1.69;SB=-47.28 GT:AD:DP:GL:GQ 0/1:69,25:74:-41.42,-22.29,-233.46:99 +chr1 1579194 rs28530622 C G 155.54 PASS AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.72;MQ0=1;OQ=430.39;QD=33.11;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,13:10:-46.62,-3.01,-0.00:30.10 +chr1 1579428 rs61776762 A G 153.73 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.52;MQ0=1;OQ=97.37;QD=13.91;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:4:-13.27,-1.21,-0.00:12.02 +chr1 1580015 rs11486024 G A 46.74 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=22.93;MQ0=7;OQ=160.84;QD=5.96;SB=11.04 GT:AD:DP:GL:GQ 0/1:15,12:15:-23.90,-4.53,-24.75:99 +chr1 1580190 rs7547516 A G 298.92 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.87;MQ0=6;OQ=291.00;QD=13.23;SB=-79.37 GT:AD:DP:GL:GQ 1/1:0,22:11:-32.70,-3.32,-0.02:33.05 +chr1 1580389 rs9329573 G C 27.04 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=38.23;MQ0=0;OQ=1419.74;QD=36.40;SB=-378.04 GT:AD:DP:GL:GQ 1/1:0,39:37:-145.59,-11.17,-0.03:99 +chr1 1580438 rs9661285 G A 38.22 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=39.42;MQ0=4;OQ=1274.78;QD=31.87;SB=-484.63 GT:AD:DP:GL:GQ 1/1:2,38:33:-131.07,-9.94,-0.01:99 +chr1 1580544 rs9661500 G A 46.95 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=56.47;MQ0=0;OQ=1331.19;QD=35.03;SB=-445.09 GT:AD:DP:GL:GQ 1/1:0,38:35:-136.72,-10.55,-0.02:99 +chr1 1581642 . C T 0.06 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.20;MQ=10.78;MQ0=31;OQ=96.64;QD=2.06;SB=-42.54 GT:AD:DP:GL:GQ 0/1:28,19:6:-14.76,-1.81,-6.20:43.86 +chr1 1581652 rs61776763 A G 3.75 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=2.07;MQ=12.19;MQ0=23;OQ=234.90;QD=5.87;SB=-48.96 GT:AD:DP:GL:GQ 1/1:0,40:8:-27.08,-2.41,-0.00:24.06 +chr1 1581732 . C T 10.55 PASS AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.72;MQ0=12;OQ=388.23;QD=16.18;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,24:11:-42.41,-3.31,-0.00:33.10 +chr1 1581758 rs61776764 C G 0.40 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=4.17;MQ=24.63;MQ0=12;OQ=1218.98;QD=26.50;SB=-184.87 GT:AD:DP:GL:GQ 1/1:2,44:29:-125.50,-8.74,-0.02:87.29 +chr1 1582007 rs28625763 T C 180.58 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.96;MQ0=0;OQ=1011.19;QD=29.74;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,34:31:-104.72,-9.34,-0.02:93.23 +chr1 1582130 rs4648770 T G 609.06 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.32;MQ0=0;OQ=2027.74;QD=33.24;SB=-1018.12 GT:AD:DP:GL:GQ 1/1:1,60:58:-206.38,-17.47,-0.02:99 +chr1 1582744 rs4648774 A C 3.99 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=4.26;MQ=37.79;MQ0=0;OQ=1971.73;QD=29.87;SB=-941.08 GT:AD:DP:GL:GQ 1/1:1,65:56:-200.78,-16.87,-0.02:99 +chr1 1582886 rs1062088 G C 0.12 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=28.33;MQ0=1;OQ=872.58;QD=39.66;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,22:20:-90.85,-6.03,-0.01:60.20 +chr1 1584178 rs1061892 C T 196.43 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=53.48;MQ0=0;OQ=3220.76;QD=38.34;SB=-1363.82 GT:AD:DP:GL:GQ 1/1:0,84:80:-325.67,-24.10,-0.02:99 +chr1 1584256 rs6659270 T A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=6;HaplotypeScore=1.24;MQ=50.39;MQ0=3;OQ=904.07;QD=12.05;SB=-396.42 GT:AD:DP:GL:GQ 0/1:40,35:71:-115.08,-21.39,-150.96:99 +chr1 1584361 rs7416520 C T 137.41 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.09;MQ0=1;OQ=651.60;QD=13.86;SB=-179.69 GT:AD:DP:GL:GQ 0/1:25,22:41:-80.80,-12.36,-66.61:99 +chr1 1585061 rs4307513 A G 66.26 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=51.44;MQ0=9;OQ=1311.89;QD=23.85;SB=-662.93 GT:AD:DP:GL:GQ 1/1:0,55:42:-134.81,-12.67,-0.04:99 +chr1 1585263 rs4313339 A G 2.76 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=25.65;MQ0=5;OQ=594.23;QD=25.84;SB=-123.88 GT:AD:DP:GL:GQ 1/1:0,23:18:-63.01,-5.42,-0.01:54.15 +chr1 1585730 rs4443835 C A 38.28 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=31.44;MQ0=8;OQ=878.16;QD=23.73;SB=-366.86 GT:AD:DP:GL:GQ 1/1:0,37:25:-91.41,-7.53,-0.01:75.22 +chr1 1586059 rs1109644 C T 45.13 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=26.30;MQ0=10;OQ=1336.40;QD=26.73;SB=-334.34 GT:AD:DP:GL:GQ 1/1:3,47:35:-137.24,-10.55,-0.01:99 +chr1 1586167 rs1109645 G A 15.01 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=25.64;MQ0=10;OQ=920.81;QD=25.58;SB=-127.66 GT:AD:DP:GL:GQ 1/1:5,31:24:-95.67,-7.23,-0.01:72.23 +chr1 1586837 rs4074020 C T 96.36 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.56;MQ0=0;OQ=1972.50;QD=37.93;SB=-886.69 GT:AD:DP:GL:GQ 1/1:0,52:51:-200.86,-15.37,-0.02:99 +chr1 1588296 . A C 37.76 DPFilter;Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=44.22;MQ0=1;QD=2.36;SB=20.08 GT:AD:DP:GL:GQ 0/1:12,4:13:-10.98,-3.92,-35.85:70.59 +chr1 1588297 . C T 55.71 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=2;HaplotypeScore=3.93;MQ=44.22;MQ0=1;QD=3.48;SB=17.08 GT:AD:DP:GL:GQ 0/1:12,4:12:-12.47,-3.61,-34.17:88.55 +chr1 1588300 . G T 70.59 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=2;HaplotypeScore=3.93;MQ=44.22;MQ0=1;QD=4.41;SB=-0.98 GT:AD:DP:GL:GQ 0/1:12,4:13:-14.26,-3.92,-32.75:99 +chr1 1588313 . A G 0.48 PASS AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=34.54;MQ0=0;OQ=106.39;QD=17.73;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,6:4:-14.17,-1.20,-0.00:12.04 +chr1 1588430 . A C 41.05 HARD_TO_VALIDATE;LowQual;SnpCluster AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=1;HaplotypeScore=7.96;MQ=16.51;MQ0=4;QD=5.86;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,5:2:-7.51,-0.60,-0.00:6.02 +chr1 1588435 . G A 88.13 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=17.24;MQ0=5;QD=8.81;SB=-10.00 GT:AD:DP:GL:GQ 1/1:5,5:3:-12.30,-0.90,-0.00:9.03 +chr1 1588436 . C T 85.79 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=17.47;MQ0=5;QD=9.53;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,5:3:-12.07,-0.90,-0.00:9.03 +chr1 1588443 . T A 229.32 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=32.72;MQ0=5;QD=15.29;SB=-115.17 GT:AD:DP:GL:GQ 1/1:5,10:7:-26.51,-2.11,-0.00:21.07 +chr1 1589024 rs6604981 A G 620.61 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.22;MQ0=0;OQ=1995.26;QD=35.00;SB=-949.98 GT:AD:DP:GL:GQ 1/1:0,57:56:-203.13,-16.87,-0.02:99 +chr1 1589224 rs6662227 A G 24.79 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=48.28;MQ0=4;OQ=837.14;QD=23.92;SB=-301.43 GT:AD:DP:GL:GQ 1/1:0,35:27:-87.33,-8.14,-0.03:81.18 +chr1 1589250 . A G 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=3.35;MQ=44.60;MQ0=6;OQ=197.93;QD=4.95;SB=-12.85 GT:AD:DP:GL:GQ 0/1:24,16:34:-33.32,-10.25,-92.46:99 +chr1 1589410 rs12725286 C T 1.49 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=10.99;MQ=39.64;MQ0=8;OQ=1191.02;QD=13.38;SB=-569.58 GT:AD:DP:GL:GQ 0/1:50,39:71:-143.77,-21.38,-134.51:99 +chr1 1589675 rs12729295 C T 309.36 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.48;MQ0=3;OQ=671.60;QD=8.72;SB=-350.30 GT:AD:DP:GL:GQ 0/1:53,24:68:-90.94,-20.50,-145.90:99 +chr1 1589751 rs2072923 A G 247.26 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=29.67;MQ0=6;OQ=1186.35;QD=17.98;SB=-547.83 GT:AD:DP:GL:GQ 0/1:14,52:56:-138.81,-16.89,-48.69:99 +chr1 1589844 . C T 0.07 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=10.53;MQ=52.48;MQ0=3;OQ=898.69;QD=17.28;SB=-297.81 GT:AD:DP:GL:GQ 0/1:24,28:47:-107.32,-14.16,-70.31:99 +chr1 1589914 . C G 0.11 PASS AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=2;HaplotypeScore=0.33;MQ=46.80;MQ0=0;OQ=573.53;QD=6.52;SB=39.39 GT:AD:DP:GL:GQ 0/1:67,21:88:-87.20,-26.56,-264.39:99 +chr1 1589924 . G A 1.33 PASS AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=0.49;MQ=46.92;MQ0=0;OQ=633.71;QD=6.67;SB=49.65 GT:AD:DP:GL:GQ 0/1:70,25:92:-94.37,-27.71,-247.48:99 +chr1 1590019 . C G 30.30 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=49.37;MQ0=3;OQ=641.05;QD=9.29;SB=-314.06 GT:AD:DP:GL:GQ 0/1:47,21:64:-90.20,-22.81,-187.56:99 +chr1 1590023 . C T 0.46 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=8.72;MQ=48.76;MQ0=3;OQ=551.31;QD=8.89;SB=-275.75 GT:AD:DP:GL:GQ 0/1:40,22:54:-74.68,-16.27,-125.00:99 +chr1 1590878 . G A 29.06 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=58.63;MQ0=0;OQ=418.19;QD=12.30;SB=-160.22 GT:AD:DP:GL:GQ 0/1:18,16:32:-54.75,-9.64,-59.96:99 +chr1 1590915 . G A 47.89 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.20;MQ0=0;OQ=322.06;QD=8.26;SB=-141.18 GT:AD:DP:GL:GQ 0/1:27,12:38:-46.95,-11.46,-84.40:99 +chr1 1592399 rs4648609 G C 54.97 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=906.62;QD=20.60;SB=-310.97 GT:AD:DP:GL:GQ 0/1:19,25:42:-106.61,-12.66,-75.02:99 +chr1 1592450 rs4233029 C T 90.67 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.31;MQ=60.00;MQ0=0;OQ=849.63;QD=19.76;SB=-437.98 GT:AD:DP:GL:GQ 0/1:15,28:37:-99.40,-11.15,-39.71:99 +chr1 1592650 rs4639697 G T 61.57 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.87;MQ=58.92;MQ0=0;OQ=2757.17;QD=35.35;SB=-1369.99 GT:AD:DP:GL:GQ 1/1:1,77:76:-279.32,-22.89,-0.02:99 +chr1 1593099 rs11523819 G A 285.98 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.60;MQ0=0;OQ=1010.41;QD=14.43;SB=-280.29 GT:AD:DP:GL:GQ 0/1:39,31:68:-124.83,-20.51,-114.09:99 +chr1 1593297 rs6699975 G T 40.53 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.04;MQ=58.42;MQ0=0;OQ=872.27;QD=15.58;SB=-424.16 GT:AD:DP:GL:GQ 0/1:24,32:48:-104.97,-14.46,-59.27:99 +chr1 1594362 rs36048328 G A 212.33 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=53.76;MQ0=0;OQ=936.15;QD=14.86;SB=-437.40 GT:AD:DP:GL:GQ 0/1:33,30:61:-115.28,-18.38,-109.00:99 +chr1 1595120 rs12736155 A C 482.21 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=48.94;MQ0=1;OQ=857.21;QD=13.61;SB=-454.19 GT:AD:DP:GL:GQ 0/1:31,32:60:-107.08,-18.07,-108.87:99 +chr1 1595458 . A G 4.92 PASS AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=5.30;MQ=27.16;MQ0=16;OQ=685.03;QD=9.01;SB=-336.52 GT:AD:DP:GL:GQ 0/1:42,34:52:-87.45,-15.67,-106.28:99 +chr1 1595935 . C A 13.79 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=13;HaplotypeScore=5.11;MQ=47.25;MQ0=0;QD=0.27;SB=44.14 GT:AD:DP:GL:GQ 0/1:44,8:42:-17.30,-12.66,-119.04:46.44 +chr1 1596150 rs28678861 G C 0.01 FDRtranche2.00to10.00 AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=6;HaplotypeScore=0.16;MQ=35.71;MQ0=1;OQ=1428.28;QD=37.59;SB=-739.75 GT:AD:DP:GL:GQ 1/1:0,38:34:-146.42,-10.25,-0.01:99 +chr1 1596170 rs61776786 G A 218.03 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.46;MQ=33.82;MQ0=1;OQ=367.66;QD=11.86;SB=-172.25 GT:AD:DP:GL:GQ 0/1:17,14:26:-47.89,-7.84,-41.82:99 +chr1 1596393 . A G 1.96 PASS AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=2;HaplotypeScore=1.79;MQ=38.63;MQ0=2;OQ=223.84;QD=8.95;SB=-123.74 GT:AD:DP:GL:GQ 0/1:13,12:22:-32.30,-6.64,-46.25:99 +chr1 1596434 rs61776787 A G 239.06 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=27.74;MQ0=11;OQ=461.68;QD=12.82;SB=-213.08 GT:AD:DP:GL:GQ 1/1:0,36:16:-49.77,-4.83,-0.02:48.10 +chr1 1598092 rs61776790 C T 85.65 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=16.88;MQ0=18;OQ=268.46;QD=6.88;SB=-142.62 GT:AD:DP:GL:GQ 0/1:27,12:20:-36.16,-6.04,-33.65:99 +chr1 1599022 rs12724172 T G 248.35 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=48.86;MQ0=1;OQ=792.00;QD=12.00;SB=-236.82 GT:AD:DP:GL:GQ 0/1:30,36:59:-100.27,-17.78,-99.33:99 +chr1 1599028 rs12757736 A T 344.72 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=49.16;MQ0=1;OQ=842.96;QD=13.82;SB=-342.44 GT:AD:DP:GL:GQ 0/1:27,34:53:-103.55,-15.97,-87.26:99 +chr1 1600387 rs7544851 T C 182.79 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=59.17;MQ0=0;OQ=618.77;QD=11.05;SB=-250.34 GT:AD:DP:GL:GQ 0/1:28,28:48:-79.63,-14.47,-94.46:99 +chr1 1601295 rs6700884 A G 128.62 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=57.79;MQ0=0;OQ=747.49;QD=15.90;SB=-253.32 GT:AD:DP:GL:GQ 0/1:21,26:46:-91.89,-13.86,-83.83:99 +chr1 1601516 rs6695303 T C 234.37 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.59;MQ=57.63;MQ0=0;OQ=837.86;QD=14.45;SB=-344.58 GT:AD:DP:GL:GQ 0/1:27,31:54:-103.34,-16.27,-95.10:99 +chr1 1601858 rs4074196 A G 175.78 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=56.26;MQ0=0;OQ=386.06;QD=8.39;SB=-209.64 GT:AD:DP:GL:GQ 0/1:26,20:39:-53.65,-11.76,-84.70:99 +chr1 1601974 rs4074197 C T 305.80 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=818.07;QD=17.41;SB=-411.47 GT:AD:DP:GL:GQ 0/1:22,25:46:-98.95,-13.86,-71.35:99 +chr1 1602466 rs4074198 G A 258.82 PASS AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.07;MQ0=0;OQ=1998.12;QD=19.98;SB=-732.09 GT:AD:DP:GL:GQ 0/1:43,57:99:-232.92,-29.82,-143.69:99 +chr1 1602672 rs4076580 T G 4.32 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=6.99;MQ=58.71;MQ0=0;OQ=379.11;QD=10.53;SB=-115.90 GT:AD:DP:GL:GQ 0/1:20,16:35:-51.74,-10.54,-71.19:99 +chr1 1603230 . C A 105.90 PASS AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.30;MQ0=0;OQ=439.60;QD=13.32;SB=-227.94 GT:AD:DP:GL:GQ 0/1:17,16:31:-56.59,-9.34,-45.91:99 +chr1 1605211 rs7520934 A C 437.30 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=732.80;QD=12.42;SB=-285.83 GT:AD:DP:GL:GQ 0/1:28,31:56:-93.43,-16.87,-99.80:99 +chr1 1605568 rs28774670 T C 204.99 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.50;MQ0=0;OQ=582.27;QD=9.87;SB=-203.22 GT:AD:DP:GL:GQ 0/1:33,26:57:-78.69,-17.18,-127.49:99 +chr1 1605610 rs28435953 G C 130.21 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=58.73;MQ0=0;OQ=779.25;QD=14.17;SB=-322.40 GT:AD:DP:GL:GQ 0/1:29,26:52:-96.88,-15.68,-122.76:99 +chr1 1605921 rs28464677 G A 40.24 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=6.09;MQ=58.05;MQ0=1;OQ=855.32;QD=14.50;SB=-377.37 GT:AD:DP:GL:GQ 0/1:31,28:56:-105.70,-16.88,-92.60:99 +chr1 1606119 rs61776792 G C 0.17 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=15.64;MQ=49.02;MQ0=1;OQ=469.22;QD=9.02;SB=-238.10 GT:AD:DP:GL:GQ 0/1:28,21:33:-60.17,-9.96,-72.09:99 +chr1 1606735 . G A 20.16 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=18;HaplotypeScore=5.53;MQ=52.51;MQ0=0;QD=0.29;SB=62.21 GT:AD:DP:GL:GQ 0/1:55,14:41:-17.65,-12.36,-123.60:52.96 +chr1 1607449 rs28736713 T G 133.05 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.99;MQ=58.63;MQ0=0;OQ=1023.89;QD=16.00;SB=-507.80 GT:AD:DP:GL:GQ 0/1:29,35:64:-124.95,-19.28,-105.76:99 +chr1 1607623 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=18;HaplotypeScore=7.66;MQ=51.83;MQ0=1;OQ=52.14;QD=1.00;SB=0.53 GT:AD:DP:GL:GQ 0/1:41,11:37:-19.66,-11.16,-103.64:84.98 +chr1 1608184 rs28367203 T C 304.04 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.41;MQ0=0;OQ=680.60;QD=12.15;SB=-333.30 GT:AD:DP:GL:GQ 0/1:31,25:55:-87.91,-16.57,-127.27:99 +chr1 1608363 rs28463291 C T 163.50 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1453.08;QD=22.02;SB=-689.01 GT:AD:DP:GL:GQ 0/1:22,44:66:-168.48,-19.89,-77.76:99 +chr1 1608455 rs28366981 A G 89.05 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=57.97;MQ0=0;OQ=661.92;QD=12.98;SB=-317.10 GT:AD:DP:GL:GQ 0/1:21,30:45:-83.04,-13.57,-76.52:99 +chr1 1608461 rs28561498 G T 18.93 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=3.73;MQ=57.75;MQ0=0;OQ=745.42;QD=16.20;SB=-317.33 GT:AD:DP:GL:GQ 0/1:20,26:44:-91.08,-13.26,-59.03:99 +chr1 1608538 rs28541555 T G 156.62 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=57.89;MQ0=0;OQ=606.69;QD=12.91;SB=-204.78 GT:AD:DP:GL:GQ 0/1:20,27:44:-77.21,-13.26,-75.77:99 +chr1 1608823 rs4648780 T C 124.64 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.99;MQ0=0;OQ=1965.86;QD=28.49;SB=-779.58 GT:AD:DP:GL:GQ 1/1:0,69:63:-200.23,-19.00,-0.06:99 +chr1 1608945 rs7524863 G A 246.35 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=57.51;MQ0=0;OQ=796.58;QD=15.03;SB=-348.35 GT:AD:DP:GL:GQ 0/1:28,25:52:-98.61,-15.67,-100.29:99 +chr1 1609404 rs28487995 G A 270.45 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=56.05;MQ0=0;OQ=943.08;QD=14.97;SB=-428.82 GT:AD:DP:GL:GQ 0/1:34,29:58:-115.07,-17.48,-93.42:99 +chr1 1609630 rs9442411 T C 340.52 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.02;MQ0=2;OQ=562.05;QD=9.37;SB=-254.95 GT:AD:DP:GL:GQ 0/1:29,31:53:-75.47,-15.98,-117.16:99 +chr1 1609711 rs61776794 G C 177 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=50.27;MQ0=2;OQ=557.29;QD=11.15;SB=-303.13 GT:AD:DP:GL:GQ 0/1:25,25:40:-71.08,-12.07,-91.96:99 +chr1 1609833 . C T 8.33 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=46.17;MQ0=4;OQ=546.56;QD=9.42;SB=-24.96 GT:AD:DP:GL:GQ 0/1:34,24:50:-73.01,-15.07,-102.31:99 +chr1 1609872 . T A 2.74 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=43.11;MQ0=2;OQ=308.49;QD=7.17;SB=35.14 GT:AD:DP:GL:GQ 0/1:26,17:38:-45.58,-11.45,-97.07:99 +chr1 1609888 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=6.91;MQ=43.11;MQ0=0;OQ=145.44;QD=3.93;SB=26.10 GT:AD:DP:GL:GQ 0/1:23,14:31:-27.18,-9.35,-84.75:99 +chr1 1609946 . A G 0.35 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=42.17;MQ0=4;OQ=138.81;QD=3.39;SB=-12.69 GT:AD:DP:GL:GQ 0/1:29,12:37:-28.31,-11.14,-120.75:99 +chr1 1610085 rs61776797 A G 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=1.23;MQ=52.83;MQ0=0;OQ=168.50;QD=4.32;SB=29.12 GT:AD:DP:GL:GQ 0/1:29,10:36:-30.98,-10.85,-111.33:99 +chr1 1610720 rs3737622 A G 151.65 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=52.83;MQ0=0;OQ=742.56;QD=16.14;SB=-328.41 GT:AD:DP:GL:GQ 0/1:21,25:45:-91.09,-13.55,-80.03:99 +chr1 1610745 rs3737623 C T 272.53 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=54.47;MQ0=0;OQ=1103.20;QD=18.09;SB=-448.99 GT:AD:DP:GL:GQ 0/1:28,33:59:-131.40,-17.79,-81.29:99 +chr1 1610764 rs3737624 G A 559.02 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.35;MQ0=0;OQ=1181.67;QD=16.88;SB=-410.16 GT:AD:DP:GL:GQ 0/1:34,36:69:-142.24,-20.78,-119.02:99 +chr1 1612040 . T A 0.13 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=1.10;MQ=42.64;MQ0=1;OQ=306.88;QD=6.39;SB=17.08 GT:AD:DP:GL:GQ 0/1:34,14:39:-45.73,-11.76,-89.73:99 +chr1 1612676 rs1855706 C T 48.38 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=4.57;MQ=18.63;MQ0=42;OQ=747.37;QD=8.59;SB=-370.40 GT:AD:DP:GL:GQ 0/1:52,35:41:-90.38,-12.36,-60.67:99 +chr1 1612716 rs61776798 T C 0.25 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=7.54;MQ0=54;OQ=87.83;QD=1.39;SB=-10.00 GT:AD:DP:GL:GQ 0/1:40,23:6:-13.87,-1.81,-8.21:64.05 +chr1 1613585 rs7542306 C A 20.92 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=15.32;MQ0=21;QD=0.67;SB=-10.00 GT:AD:DP:GL:GQ 0/1:18,13:6:-7.18,-1.81,-14.53:53.72 +chr1 1614256 rs368915 T G 26.47 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=20.52;MQ0=9;QD=2.04;SB=-32.98 GT:AD:DP:GL:GQ 1/1:0,13:2:-6.06,-0.60,-0.00:6 +chr1 1614726 rs4648651 G A 96.84 PASS AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.04;MQ0=5;OQ=94.30;QD=5.55;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,5:9:-15.42,-2.71,-17.14:99 +chr1 1615466 rs35947799 G A 107.06 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=52.41;MQ0=0;OQ=601.60;QD=18.23;SB=-258.27 GT:AD:DP:GL:GQ 0/1:13,20:32:-73.09,-9.64,-46.27:99 +chr1 1616758 rs28587348 A G 239 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=22.66;MQ0=5;OQ=648.18;QD=9.53;SB=-227.25 GT:AD:DP:GL:GQ 0/1:39,28:59:-88.06,-19.96,-129.14:99 +chr1 1617046 rs1932228 C T 15.28 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=15.02;MQ0=16;OQ=210.38;QD=4.29;SB=-111.61 GT:AD:DP:GL:GQ 0/1:30,19:14:-28.54,-4.22,-22.09:99 +chr1 1617416 rs61776801 G A 266.02 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=37.27;MQ0=15;OQ=982.95;QD=15.60;SB=-353.39 GT:AD:DP:GL:GQ 0/1:28,35:47:-115.75,-14.17,-56.63:99 +chr1 1617665 rs601141 A C 373.76 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=54.30;MQ0=0;OQ=987.22;QD=15.19;SB=-461.24 GT:AD:DP:GL:GQ 0/1:31,34:63:-120.98,-18.98,-104.99:99 +chr1 1618057 rs61776802 A G 60.56 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=53.96;MQ0=1;OQ=690.37;QD=9.86;SB=-238.28 GT:AD:DP:GL:GQ 0/1:36,33:62:-91.01,-18.69,-134.09:99 +chr1 1618313 rs61776803 G T 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=3;HaplotypeScore=2.46;MQ=39.85;MQ0=11;OQ=285.62;QD=3.97;SB=-133.03 GT:AD:DP:GL:GQ 0/1:51,21:59:-49.62,-17.77,-159.76:99 +chr1 1618571 rs12081891 G A 12.44 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=28.69;MQ0=14;OQ=348.19;QD=5.36;SB=-177.80 GT:AD:DP:GL:GQ 0/1:47,18:38:-49.56,-11.46,-83.32:99 +chr1 1618766 rs61776804 G A 86.02 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=43.94;MQ0=0;OQ=732.16;QD=19.27;SB=-352.49 GT:AD:DP:GL:GQ 0/1:16,22:37:-87.65,-11.15,-51.61:99 +chr1 1619321 rs4648621 G A 136.25 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=27.57;MQ0=5;OQ=508.21;QD=13.37;SB=-144.61 GT:AD:DP:GL:GQ 0/1:18,20:30:-63.15,-9.04,-45.60:99 +chr1 1619347 rs34716550 T C 0.89 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=6.10;MQ=29.73;MQ0=3;OQ=380.00;QD=9.05;SB=-24.63 GT:AD:DP:GL:GQ 0/1:23,19:33:-51.24,-9.95,-72.01:99 +chr1 1624864 rs874516 T C 339.91 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=46.52;MQ0=1;OQ=784.43;QD=15.38;SB=-383.28 GT:AD:DP:GL:GQ 0/1:22,29:49:-96.49,-14.76,-89.37:99 +chr1 1625479 rs2076329 T C 1.54 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=3.63;MQ=58.85;MQ0=0;OQ=346.77;QD=7.08;SB=-173.37 GT:AD:DP:GL:GQ 0/1:30,19:42:-50.63,-12.67,-103.10:99 +chr1 1625609 rs1136997 C A 28.98 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.88;MQ=49.57;MQ0=0;OQ=129.32;QD=4.62;SB=-74.73 GT:AD:DP:GL:GQ 0/1:19,9:24:-23.45,-7.23,-57.11:99 +chr1 1625904 rs1059822 G A 133.74 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=49.02;MQ0=1;OQ=290.88;QD=7.65;SB=-88.57 GT:AD:DP:GL:GQ 0/1:22,16:33:-42.33,-9.95,-69.30:99 +chr1 1626134 rs2179381 C T 246.87 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=42.93;MQ0=0;OQ=354.22;QD=9.84;SB=-190.16 GT:AD:DP:GL:GQ 0/1:22,14:30:-47.74,-9.04,-64.17:99 +chr1 1626190 . G A 71.25 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=48.48;MQ0=0;OQ=619.32;QD=15.48;SB=-321.82 GT:AD:DP:GL:GQ 0/1:21,19:40:-77.26,-12.05,-77.19:99 +chr1 1627098 rs61774911 A G 6.01 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.86;MQ0=3;OQ=57.73;QD=2.14;SB=17.07 GT:AD:DP:GL:GQ 0/1:19,8:19:-14.79,-5.73,-53.94:90.57 +chr1 1627115 rs9439480 A G 25.79 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=40.42;MQ0=0;QD=1.07;SB=26.10 GT:AD:DP:GL:GQ 0/1:18,5:21:-12.19,-6.33,-66.21:58.62 +chr1 1627865 rs17162876 G C 61.32 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=50.90;MQ0=0;OQ=596.59;QD=13.56;SB=-287.98 GT:AD:DP:GL:GQ 0/1:25,19:41:-75.32,-12.38,-88.05:99 +chr1 1628397 . C T 6.47 PASS AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=17.03;MQ0=21;OQ=258.72;QD=7.19;SB=-86.31 GT:AD:DP:GL:GQ 0/1:19,17:11:-32.47,-3.31,-10.93:76.22 +chr1 1628516 . G A 0.42 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=23.14;MQ0=15;OQ=161.97;QD=3.60;SB=-32.64 GT:AD:DP:GL:GQ 0/1:32,13:24:-26.72,-7.23,-54.65:99 +chr1 1629661 . T C 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=34.50;MQ0=9;OQ=82.09;QD=2.22;SB=-48.26 GT:AD:DP:GL:GQ 0/1:21,16:24:-18.73,-7.24,-70.81:99 +chr1 1631887 rs61776845 C T 226.45 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.12;MQ0=0;OQ=487.31;QD=34.81;SB=-143.63 GT:AD:DP:GL:GQ 1/1:0,14:14:-52.32,-4.22,-0.01:42.13 +chr1 1633129 rs6688326 C A 4.88 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=11.56;MQ0=25;OQ=150.41;QD=4.30;SB=-10.00 GT:AD:DP:GL:GQ 0/1:25,10:8:-20.73,-2.41,-7.32:49.07 +chr1 1634432 rs2143105 A G 2.04 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=3.86;MQ=24.63;MQ0=4;OQ=286.53;QD=16.85;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,17:11:-32.26,-3.33,-0.02:33.05 +chr1 1634696 rs2179382 G A 8.71 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=32.34;MQ0=16;OQ=279.13;QD=3.58;SB=-95.45 GT:AD:DP:GL:GQ 0/1:61,16:59:-48.98,-17.78,-155.91:99 +chr1 1634768 rs2179383 C T 205.44 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=11.72;MQ0=13;OQ=127.00;QD=6.35;SB=-51.67 GT:AD:DP:GL:GQ 1/1:0,20:4:-16.23,-1.20,-0.00:12.04 +chr1 1634910 . C T 73.11 PASS AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=12.98;MQ0=22;OQ=295.97;QD=9.25;SB=-135.01 GT:AD:DP:GL:GQ 1/1:0,32:8:-33.18,-2.41,-0.00:24.08 +chr1 1634953 . C T 62.81 PASS AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=17.86;MQ0=18;OQ=384.85;QD=13.27;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,29:10:-42.07,-3.01,-0.00:30.10 +chr1 1634973 . T C 4.22 PASS AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.05;MQ0=18;OQ=118.84;QD=3.71;SB=-10.00 GT:AD:DP:GL:GQ 0/1:22,10:13:-19.08,-3.92,-33.24:99 +chr1 1634975 . C T 14.66 PASS AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=19.05;MQ0=18;OQ=504.84;QD=15.78;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,32:13:-54.07,-3.92,-0.00:39.13 +chr1 1635050 rs4279785 T C 293.02 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.94;MQ0=12;OQ=364.98;QD=8.90;SB=-161.33 GT:AD:DP:GL:GQ 0/1:23,18:28:-48.21,-8.43,-62.26:99 +chr1 1635547 rs61774919 G A 162.09 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=14.59;MQ0=11;OQ=173.64;QD=7.55;SB=-50.56 GT:AD:DP:GL:GQ 1/1:6,17:5:-20.92,-1.51,-0.00:15.05 +chr1 1635860 rs3819996 T C 34.28 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=13.67;MQ0=7;QD=3.81;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:2:-6.84,-0.60,-0.00:6.02 +chr1 1635866 rs3819997 A G 27.83 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.50;MQ0=6;QD=3.48;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:2:-6.19,-0.60,-0.00:6.01 +chr1 1635934 rs3819998 A G 17.88 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=5.04;MQ=31.93;MQ0=9;OQ=462.29;QD=12.84;SB=-95.99 GT:AD:DP:GL:GQ 0/1:9,27:21:-55.85,-6.34,-11.59:52.52 +chr1 1635937 rs3819999 G T 0.54 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=5.04;MQ=31.93;MQ0=9;OQ=663.10;QD=18.42;SB=-104.11 GT:AD:DP:GL:GQ 0/1:9,26:24:-76.82,-7.23,-11.28:40.49 +chr1 1635973 rs3820000 G C 54.40 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.49;MQ0=15;OQ=883.63;QD=21.55;SB=-127.19 GT:AD:DP:GL:GQ 1/1:8,33:25:-95.91,-7.54,-3.96:35.78 +chr1 1636091 rs3820002 T C 108.62 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.55;MQ0=2;OQ=418.10;QD=27.87;SB=-161.84 GT:AD:DP:GL:GQ 1/1:0,15:13:-45.40,-3.92,-0.01:39.10 +chr1 1636096 rs61776849 C T 171.23 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.06;MQ0=2;OQ=513.34;QD=30.20;SB=-178.68 GT:AD:DP:GL:GQ 1/1:0,17:14:-54.92,-4.22,-0.01:42.13 +chr1 1636231 rs61776850 G T 45.78 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=2.84;MQ=41.85;MQ0=7;OQ=641.89;QD=13.95;SB=-342.30 GT:AD:DP:GL:GQ 0/1:20,26:39:-79.22,-11.75,-58.73:99 +chr1 1636287 rs61776851 T G 219.44 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=36.80;MQ0=8;OQ=1107.10;QD=20.13;SB=-508.74 GT:AD:DP:GL:GQ 1/1:4,51:37:-114.34,-11.16,-0.05:99 +chr1 1636310 rs3820004 G A 84.02 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=34.50;MQ0=11;OQ=1585.10;QD=27.33;SB=-811.33 GT:AD:DP:GL:GQ 1/1:6,52:41:-162.11,-12.35,-0.01:99 +chr1 1636434 rs56030177 T C 84.71 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=28.90;MQ0=10;OQ=1324.64;QD=27.60;SB=-500.48 GT:AD:DP:GL:GQ 1/1:0,48:38:-136.06,-11.45,-0.01:99 +chr1 1636517 rs760926 T C 66.97 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=26.90;MQ0=7;OQ=976.98;QD=25.05;SB=-384.56 GT:AD:DP:GL:GQ 1/1:1,38:28:-101.29,-8.43,-0.01:84.25 +chr1 1636649 rs760927 T C 127.83 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.47;MQ0=5;OQ=898.10;QD=25.66;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,35:25:-93.41,-7.53,-0.01:75.22 +chr1 1636735 . C G 66.44 PASS AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=39.28;MQ0=9;OQ=1254.01;QD=12.80;SB=-309.31 GT:AD:DP:GL:GQ 0/1:56,42:83:-153.70,-25.01,-208.71:99 +chr1 1636777 . C T 31.32 PASS AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=38.96;MQ0=9;OQ=1301.14;QD=13.41;SB=-647.75 GT:AD:DP:GL:GQ 0/1:49,48:84:-158.72,-25.32,-141.36:99 +chr1 1636840 rs61776853 A C 1.58 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=0.97;MQ=31.48;MQ0=5;OQ=997.06;QD=27.70;SB=-256.95 GT:AD:DP:GL:GQ 1/1:0,36:30:-103.31,-9.04,-0.02:90.22 +chr1 1636845 rs61776854 C T 13.28 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=31.12;MQ0=5;OQ=595.02;QD=17.50;SB=-27.62 GT:AD:DP:GL:GQ 0/1:11,23:28:-71.23,-8.44,-30.58:99 +chr1 1636852 rs35642458 G A 71.80 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.10;MQ0=4;OQ=612.21;QD=24.49;SB=-39.52 GT:AD:DP:GL:GQ 0/1:3,22:20:-70.53,-6.02,-10.71:46.85 +chr1 1637044 rs61073446 G A 19.06 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=5.47;MQ=48.10;MQ0=1;OQ=604.36;QD=8.06;SB=-316.73 GT:AD:DP:GL:GQ 0/1:54,21:68:-84.21,-20.50,-156.95:99 +chr1 1637060 . G C 0.16 PASS AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=3.23;MQ=46.92;MQ0=1;OQ=770.35;QD=8.37;SB=83.29 GT:AD:DP:GL:GQ 0/1:66,26:89:-107.18,-26.86,-257.87:99 +chr1 1637092 . A G 13.80 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=45.24;MQ0=3;OQ=524.47;QD=7.09;SB=62.24 GT:AD:DP:GL:GQ 0/1:50,24:71:-77.11,-21.38,-201.71:99 +chr1 1637137 rs4437818 C T 70.80 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.48;MQ=37.21;MQ0=3;OQ=419.91;QD=7.63;SB=-236.03 GT:AD:DP:GL:GQ 0/1:38,17:49:-60.03,-14.76,-127.40:99 +chr1 1637159 rs760928 C T 610.42 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.78;MQ0=3;OQ=1773.57;QD=35.47;SB=-891.67 GT:AD:DP:GL:GQ 1/1:0,50:45:-180.95,-13.56,-0.01:99 +chr1 1637161 rs760929 G A 499.31 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=39.49;MQ0=3;OQ=1819.83;QD=36.40;SB=-852.64 GT:AD:DP:GL:GQ 1/1:0,50:45:-185.58,-13.55,-0.01:99 +chr1 1637349 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=12.15;MQ=53.21;MQ0=0;OQ=258.06;QD=3.04;SB=74.27 GT:AD:DP:GL:GQ 0/1:68,17:73:-51.13,-22.04,-238.97:99 +chr1 1637350 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=13.99;MQ=53.21;MQ0=0;OQ=156.60;QD=1.84;SB=74.27 GT:AD:DP:GL:GQ 0/1:68,16:78:-42.44,-23.50,-258.99:99 +chr1 1637384 rs760930 C T 155.40 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.38;MQ0=0;OQ=2369.71;QD=38.22;SB=-867.02 GT:AD:DP:GL:GQ 1/1:0,62:60:-240.58,-18.08,-0.02:99 +chr1 1637388 rs760931 G C 174.43 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=56.72;MQ0=0;OQ=2115.79;QD=36.48;SB=-781.25 GT:AD:DP:GL:GQ 1/1:0,58:53:-215.20,-15.99,-0.03:99 +chr1 1637546 rs56081394 A C 94.23 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=52.34;MQ0=0;OQ=2774.94;QD=32.65;SB=-1180.71 GT:AD:DP:GL:GQ 1/1:0,85:81:-281.12,-24.40,-0.04:99 +chr1 1637613 . C T 21.89 LowQual AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=50.67;MQ0=0;QD=0.27;SB=-29.39 GT:AD:DP:GL:GQ 0/1:68,12:72:-27.16,-21.69,-231.62:54.70 +chr1 1637638 . C G 0.51 PASS AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=4.82;MQ=47.75;MQ0=0;OQ=459.74;QD=4.84;SB=-189.88 GT:AD:DP:GL:GQ 0/1:65,30:83:-74.29,-25.03,-272.64:99 +chr1 1637674 . T C 96.11 PASS AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.42;MQ0=0;OQ=794.87;QD=7.87;SB=-336.87 GT:AD:DP:GL:GQ 0/1:55,46:82:-107.47,-24.70,-217.72:99 +chr1 1637731 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=47.58;MQ0=0;OQ=197.23;QD=2.38;SB=-124.83 GT:AD:DP:GL:GQ 0/1:61,22:74:-45.30,-22.29,-250.27:99 +chr1 1637788 rs1883424 A G 452.02 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.70;MQ0=0;OQ=1180.37;QD=13.26;SB=-539.57 GT:AD:DP:GL:GQ 0/1:48,41:89:-148.13,-26.81,-196.69:99 +chr1 1637887 rs61776857 T C 8.97 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=37.62;MQ0=3;OQ=1207.11;QD=23.21;SB=-211.69 GT:AD:DP:GL:GQ 1/1:2,49:41:-124.35,-12.38,-0.05:99 +chr1 1638000 . G C 4.04 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=49.72;MQ0=1;OQ=363.96;QD=6.17;SB=-28.72 GT:AD:DP:GL:GQ 0/1:37,21:48:-56.87,-17.19,-155.52:99 +chr1 1638008 . G C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=51.97;MQ0=1;OQ=62.73;QD=1.08;SB=29.80 GT:AD:DP:GL:GQ 0/1:41,17:44:-22.82,-13.26,-168.23:95.57 +chr1 1638068 rs61776858 C T 414.28 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.78;MQ0=0;OQ=1645.34;QD=38.26;SB=-705.35 GT:AD:DP:GL:GQ 1/1:1,42:42:-168.13,-12.65,-0.01:99 +chr1 1638095 rs28722732 A C 115.66 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=48.13;MQ0=1;OQ=1285.24;QD=32.95;SB=-522.05 GT:AD:DP:GL:GQ 1/1:1,38:38:-132.12,-11.45,-0.02:99 +chr1 1638236 . G A 17.91 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=2;HaplotypeScore=8.77;MQ=38.97;MQ0=0;QD=0.34;SB=23.08 GT:AD:DP:GL:GQ 0/1:43,6:25:-15.81,-10.75,-74.55:50.67 +chr1 1638252 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=56.73;MQ=41.68;MQ0=0;OQ=220.25;QD=3.86;SB=17.08 GT:AD:DP:GL:GQ 0/1:43,13:37:-36.47,-11.16,-97.19:99 +chr1 1638265 rs28669101 A G 1.73 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=5.08;MQ=44.94;MQ0=1;OQ=1841.80;QD=27.49;SB=-530.20 GT:AD:DP:GL:GQ 1/1:1,66:52:-187.79,-15.67,-0.02:99 +chr1 1638282 . T C 372.16 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=2;HaplotypeScore=20.32;MQ=48.81;MQ0=1;QD=5.64;SB=53.20 GT:AD:DP:GL:GQ 0/1:48,18:62:-59.18,-18.68,-176.85:99 +chr1 1638285 . G A 362.16 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=22.88;MQ=49.05;MQ0=1;QD=5.57;SB=50.16 GT:AD:DP:GL:GQ 0/1:45,17:60:-57.59,-18.09,-158.00:99 +chr1 1638291 . G T 350.74 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=36.28;MQ=47.79;MQ0=1;QD=5.48;SB=47.16 GT:AD:DP:GL:GQ 0/1:46,17:57:-55.53,-17.18,-142.31:99 +chr1 1638353 . T C 4.41 PASS AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=49.10;MQ0=0;OQ=579.45;QD=7.24;SB=-118.38 GT:AD:DP:GL:GQ 0/1:52,28:75:-83.82,-22.59,-209.22:99 +chr1 1638397 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.02;HRun=4;HaplotypeScore=13.77;MQ=49.39;MQ0=0;OQ=1251.99;QD=12.16;SB=-214.10 GT:AD:DP:GL:GQ 0/1:54,47:95:-156.50,-28.02,-195.84:99 +chr1 1638484 rs61776859 C A 0.46 PASS AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=1;HaplotypeScore=3.66;MQ=44.01;MQ0=0;OQ=2573.54;QD=19.06;SB=-1062.18 GT:AD:DP:GL:GQ 0/1:54,81:126:-298.59,-37.95,-167.48:99 +chr1 1638485 . A G 2.65 PASS AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=44.20;MQ0=0;OQ=954.08;QD=7.07;SB=27.40 GT:AD:DP:GL:GQ 0/1:81,54:124:-136.06,-37.37,-329.92:99 +chr1 1638496 . A C 4.42 PASS AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=43.37;MQ0=0;OQ=1281.45;QD=9.42;SB=-10.58 GT:AD:DP:GL:GQ 0/1:80,56:126:-169.38,-37.95,-296.59:99 +chr1 1638502 . T C 3.56 PASS AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=44.49;MQ0=0;OQ=1373.44;QD=10.25;SB=-79.40 GT:AD:DP:GL:GQ 0/1:76,58:123:-177.67,-37.05,-300.79:99 +chr1 1638544 . C T 171.39 PASS AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=48.39;MQ0=0;OQ=1993.39;QD=14.44;SB=-439.97 GT:AD:DP:GL:GQ 0/1:62,76:123:-239.68,-37.06,-213.30:99 +chr1 1638628 . C T 21.95 PASS AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=49.90;MQ0=0;OQ=1604.78;QD=15.14;SB=-725.65 GT:AD:DP:GL:GQ 0/1:52,53:100:-193.90,-30.14,-170.77:99 +chr1 1638640 . A C 22.88 PASS AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=47.54;MQ0=0;OQ=1027.76;QD=10.18;SB=-470.68 GT:AD:DP:GL:GQ 0/1:56,45:93:-134.07,-28.01,-207.58:99 +chr1 1638645 . G C 1.18 PASS AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=6.44;MQ=47.94;MQ0=0;OQ=1189.28;QD=12.14;SB=-604.90 GT:AD:DP:GL:GQ 0/1:56,42:91:-149.63,-27.42,-247.05:99 +chr1 1638691 rs61777460 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.00;HRun=1;HaplotypeScore=70.95;MQ=45.55;MQ0=0;OQ=1598.01;QD=14.14;SB=-702.52 GT:AD:DP:GL:GQ 0/1:53,60:107:-195.32,-32.23,-214.62:99 +chr1 1638728 . T A 0.06 PASS AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=48.71;MQ0=0;OQ=2481.89;QD=16.22;SB=-1020.86 GT:AD:DP:GL:GQ 0/1:71,82:150:-296.65,-45.18,-270.24:99 +chr1 1638806 rs909824 T C 0.61 PASS AC=1;AF=0.50;AN=2;DB;DP=154;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=50.30;MQ0=0;OQ=2209.99;QD=14.35;SB=-996.92 GT:AD:DP:GL:GQ 0/1:79,75:150:-269.47,-45.19,-301.46:99 +chr1 1638825 rs61777461 C T 0.09 PASS AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.00;HRun=1;HaplotypeScore=2.68;MQ=50.48;MQ0=0;OQ=2137.82;QD=14.95;SB=-1070.06 GT:AD:DP:GL:GQ 0/1:71,72:135:-257.74,-40.67,-255.42:99 +chr1 1638946 . C T 467.64 SnpCluster AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=32.37;MQ=43.71;MQ0=5;QD=7.19;SB=-205.68 GT:AD:DP:GL:GQ 0/1:44,21:47:-64.21,-14.16,-108.79:99 +chr1 1638954 . T C 736.34 SnpCluster AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=21.87;MQ=42.89;MQ0=5;QD=12.70;SB=-358.18 GT:AD:DP:GL:GQ 0/1:23,35:42:-89.58,-12.66,-57.09:99 +chr1 1638955 . G A 193.46 SnpCluster AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=28.88;MQ=42.53;MQ0=5;QD=3.39;SB=-66.48 GT:AD:DP:GL:GQ 0/1:44,13:42:-35.29,-12.66,-112.58:99 +chr1 1638965 rs61777464 A G 0.09 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=17.05;MQ=41.40;MQ0=5;OQ=280.02;QD=5.83;SB=-138.25 GT:AD:DP:GL:GQ 0/1:30,18:32:-40.93,-9.64,-84.27:99 +chr1 1638997 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=41.45;MQ0=4;OQ=154.17;QD=3.08;SB=35.12 GT:AD:DP:GL:GQ 0/1:37,12:37:-29.85,-11.15,-98.68:99 +chr1 1639030 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=25.29;MQ=40.65;MQ0=7;OQ=247.09;QD=2.75;SB=50.20 GT:AD:DP:GL:GQ 0/1:68,21:63:-46.97,-18.98,-193.46:99 +chr1 1639109 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=25.12;MQ=46.53;MQ0=4;OQ=115.22;QD=1.05;SB=83.25 GT:AD:DP:GL:GQ 0/1:96,13:84:-40.14,-25.34,-234.06:99 +chr1 1639113 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=24.12;MQ=46.66;MQ0=4;OQ=396.71;QD=3.64;SB=8.10 GT:AD:DP:GL:GQ 0/1:82,27:87:-69.20,-26.24,-219.98:99 +chr1 1639145 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=1;HaplotypeScore=44.81;MQ=46.42;MQ0=3;OQ=230.67;QD=1.94;SB=-28.38 GT:AD:DP:GL:GQ 0/1:92,27:94:-54.66,-28.31,-297.41:99 +chr1 1639152 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=23.68;MQ=46.30;MQ0=1;OQ=1088.67;QD=9.07;SB=-62.94 GT:AD:DP:GL:GQ 0/1:69,50:95:-140.79,-28.64,-195.69:99 +chr1 1639166 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=19.38;MQ=46.56;MQ0=1;OQ=479.08;QD=3.89;SB=-121.97 GT:AD:DP:GL:GQ 0/1:92,31:101:-81.65,-30.45,-258.17:99 +chr1 1639203 . C T 59.61 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=106;Dels=0.01;HRun=4;HaplotypeScore=28.93;MQ=49.66;MQ0=0;QD=0.56;SB=37.04 GT:AD:DP:GL:GQ 0/1:84,20:85:-34.85,-25.61,-268.94:92.45 +chr1 1639204 . A G 88.80 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=34.26;MQ=50.07;MQ0=0;QD=0.81;SB=122.42 GT:AD:DP:GL:GQ 0/1:87,23:90:-39.28,-27.11,-316.10:99 +chr1 1639210 . T G 106.61 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=1;HaplotypeScore=109.94;MQ=48.22;MQ0=0;QD=0.90;SB=107.36 GT:AD:DP:GL:GQ 0/1:99,20:91:-41.35,-27.41,-290.49:99 +chr1 1639221 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=51.18;MQ=48.34;MQ0=0;OQ=110.59;QD=0.87;SB=-36.37 GT:AD:DP:GL:GQ 0/1:109,18:89:-41.16,-26.82,-305.73:99 +chr1 1639227 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=3;HaplotypeScore=53.65;MQ=47.85;MQ0=2;OQ=61.26;QD=0.48;SB=63.76 GT:AD:DP:GL:GQ 0/1:90,38:88:-35.92,-26.51,-284.90:94.09 +chr1 1639237 . A T 220.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=2;HaplotypeScore=39.50;MQ=47.38;MQ0=3;QD=1.53;SB=98.34 GT:AD:DP:GL:GQ 0/1:108,36:102:-56.01,-30.73,-323.39:99 +chr1 1639238 . T C 363.43 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=40.62;MQ=46.99;MQ0=4;QD=2.51;SB=-35.37 GT:AD:DP:GL:GQ 0/1:115,29:91:-67.04,-27.41,-296.52:99 +chr1 1639239 . T G 307.74 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=40.46;MQ=46.55;MQ0=5;QD=2.08;SB=5.35 GT:AD:DP:GL:GQ 0/1:110,36:106:-65.98,-31.93,-325.39:99 +chr1 1639244 . C G 433.01 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=0;HaplotypeScore=72.81;MQ=46.68;MQ0=6;QD=2.87;SB=-83.32 GT:AD:DP:GL:GQ 0/1:112,37:109:-82.29,-35.70,-402.49:99 +chr1 1639252 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=2;HaplotypeScore=45.12;MQ=45.10;MQ0=7;OQ=932.16;QD=6.13;SB=-397.36 GT:AD:DP:GL:GQ 0/1:117,33:103:-127.53,-31.03,-261.51:99 +chr1 1639301 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=21.56;MQ=40.71;MQ0=20;OQ=622.52;QD=6.35;SB=-215.64 GT:AD:DP:GL:GQ 0/1:52,46:51:-80.90,-15.37,-137.71:99 +chr1 1639318 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=38.28;MQ=34.31;MQ0=28;OQ=125.27;QD=1.35;SB=-14.91 GT:AD:DP:GL:GQ 0/1:76,17:35:-26.35,-10.54,-101.55:99 +chr1 1639325 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=5.46;MQ=33.52;MQ0=28;OQ=116.93;QD=1.38;SB=23.07 GT:AD:DP:GL:GQ 0/1:73,12:33:-24.93,-9.95,-86.29:99 +chr1 1639374 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=1;HaplotypeScore=20.02;MQ=34.37;MQ0=20;OQ=192.31;QD=2.19;SB=-88.00 GT:AD:DP:GL:GQ 0/1:73,15:45:-36.07,-13.55,-128.18:99 +chr1 1639407 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=42.54;MQ0=9;OQ=114.05;QD=1.02;SB=-8.75 GT:AD:DP:GL:GQ 0/1:85,19:71:-46.36,-31.67,-236.26:99 +chr1 1639417 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=4;HaplotypeScore=17.30;MQ=43.78;MQ0=5;OQ=74.87;QD=0.61;SB=-8.76 GT:AD:DP:GL:GQ 0/1:106,16:83:-35.80,-25.03,-240.05:99 +chr1 1639441 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=3;HaplotypeScore=5.23;MQ=45.90;MQ0=8;OQ=109.77;QD=0.77;SB=-10.15 GT:AD:DP:GL:GQ 0/1:120,22:103:-45.28,-31.02,-334.31:99 +chr1 1639479 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=26.42;MQ=48.72;MQ0=12;OQ=76.35;QD=0.64;SB=70.54 GT:AD:DP:GL:GQ 0/1:100,20:90:-38.04,-27.12,-310.60:99 +chr1 1639492 . C T 15.20 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=3;HaplotypeScore=52.40;MQ=48.82;MQ0=15;QD=0.14;SB=67.73 GT:AD:DP:GL:GQ 0/1:90,22:79:-28.59,-23.80,-254.17:47.90 +chr1 1639499 rs36141200 G A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=107;Dels=0.01;HRun=0;HaplotypeScore=32.74;MQ=48.53;MQ0=15;OQ=2982.80;QD=27.88;SB=-1344.29 GT:AD:DP:GL:GQ 1/1:0,106:74:-301.88,-22.29,-0.02:99 +chr1 1639600 rs36135823 C T 0.07 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=3;HaplotypeScore=14.31;MQ=43.93;MQ0=12;OQ=2247.07;QD=26.44;SB=-416.38 GT:AD:DP:GL:GQ 1/1:10,75:60:-232.21,-18.08,-3.91:99 +chr1 1639610 rs34963151 A T 0.17 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=15.64;MQ=43.34;MQ0=11;OQ=1936.12;QD=25.14;SB=-344.48 GT:AD:DP:GL:GQ 1/1:5,72:55:-200.25,-16.56,-3.05:99 +chr1 1639612 rs36137888 T G 0.67 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=11.64;MQ=43.34;MQ0=11;OQ=1831.08;QD=23.78;SB=-311.74 GT:AD:DP:GL:GQ 1/1:2,72:55:-190.04,-16.56,-3.35:99 +chr1 1639702 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=0;HaplotypeScore=34.54;MQ=35.32;MQ0=37;OQ=98.37;QD=0.75;SB=39.28 GT:AD:DP:GL:GQ 0/1:59,72:53:-29.08,-15.96,-156.59:99 +chr1 1639726 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=70.45;MQ=36.36;MQ0=39;OQ=52.18;QD=0.37;SB=48.69 GT:AD:DP:GL:GQ 0/1:67,74:65:-28.09,-19.58,-201.69:85.02 +chr1 1639861 . C T 25.55 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=57.75;MQ=41.48;MQ0=14;QD=0.18;SB=-23.37 GT:AD:DP:GL:GQ 0/1:90,50:90:-32.98,-27.15,-260.27:58.37 +chr1 1639867 . C T 19.37 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=3;HaplotypeScore=75.47;MQ=41.18;MQ0=14;QD=0.14;SB=-17.32 GT:AD:DP:GL:GQ 0/1:97,46:92:-32.93,-27.71,-303.81:52.16 +chr1 1639892 rs61777469 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.04;HRun=2;HaplotypeScore=74.14;MQ=41.98;MQ0=12;OQ=2469.47;QD=18.43;SB=-1178.56 GT:AD:DP:GL:GQ 0/1:25,104:86:-276.13,-25.90,-32.75:68.49 +chr1 1639893 rs61777470 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.00;HRun=0;HaplotypeScore=137.24;MQ=41.98;MQ0=12;OQ=2615.52;QD=19.52;SB=-1204.51 GT:AD:DP:GL:GQ 0/1:44,90:89:-291.64,-26.81,-37.18:99 +chr1 1639911 . G A 14.93 LowQual AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=0;HaplotypeScore=26.42;MQ=45.76;MQ0=10;QD=0.13;SB=-12.75 GT:AD:DP:GL:GQ 0/1:81,37:78:-28.28,-23.52,-231.19:47.63 +chr1 1639962 rs61777471 C T 260.52 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.09;MQ0=1;OQ=1805.36;QD=37.61;SB=-829.34 GT:AD:DP:GL:GQ 1/1:0,48:47:-184.14,-14.16,-0.02:99 +chr1 1640060 rs1969650 A C 38.33 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=47.36;MQ0=0;OQ=1283.12;QD=25.66;SB=-659.19 GT:AD:DP:GL:GQ 1/1:0,50:43:-131.95,-12.97,-0.05:99 +chr1 1640123 rs1967676 G T 619.20 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.68;MQ0=0;OQ=2013.64;QD=35.33;SB=-938.04 GT:AD:DP:GL:GQ 1/1:0,57:55:-204.96,-16.56,-0.01:99 +chr1 1640270 rs1967677 T C 0.01 FDRtranche2.00to10.00 AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=23.68;MQ=51.29;MQ0=1;OQ=2260.88;QD=25.69;SB=-1076.20 GT:AD:DP:GL:GQ 1/1:7,81:78:-241.90,-23.52,-12.23:99 +chr1 1640284 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=21.65;MQ=49.80;MQ0=1;OQ=283.77;QD=2.56;SB=107.23 GT:AD:DP:GL:GQ 0/1:95,16:94:-60.00,-28.34,-253.49:99 +chr1 1640321 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=250.42;MQ=48.13;MQ0=0;OQ=561.76;QD=3.98;SB=122.35 GT:AD:DP:GL:GQ 0/1:98,27:119:-99.13,-39.67,-333.17:99 +chr1 1640332 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=158;Dels=0.00;HRun=0;HaplotypeScore=133.26;MQ=46.63;MQ0=0;OQ=950.96;QD=6.02;SB=119.36 GT:AD:DP:GL:GQ 0/1:94,64:124:-135.74,-37.36,-315.76:99 +chr1 1640347 . T C 550.46 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=23.57;MQ=45.32;MQ0=0;QD=3.72;SB=95.35 GT:AD:DP:GL:GQ 0/1:118,30:114:-92.67,-34.34,-350.75:99 +chr1 1640368 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=1;HaplotypeScore=38.96;MQ=45.47;MQ0=0;OQ=414.73;QD=2.94;SB=65.22 GT:AD:DP:GL:GQ 0/1:119,22:108:-77.29,-32.53,-317.79:99 +chr1 1640378 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=4;HaplotypeScore=21.61;MQ=45.56;MQ0=0;OQ=227.10;QD=1.77;SB=59.14 GT:AD:DP:GL:GQ 0/1:110,18:98:-55.53,-29.53,-284.49:99 +chr1 1640389 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=23.69;MQ=45.00;MQ0=0;OQ=372.62;QD=3.11;SB=38.14 GT:AD:DP:GL:GQ 0/1:83,37:73:-62.56,-22.01,-186.44:99 +chr1 1640393 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=31.49;MQ=46.43;MQ0=0;OQ=193.70;QD=1.67;SB=47.18 GT:AD:DP:GL:GQ 0/1:63,52:78:-46.16,-23.50,-255.92:99 +chr1 1640402 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=3;HaplotypeScore=44.61;MQ=47.57;MQ0=0;OQ=589.53;QD=5.51;SB=47.18 GT:AD:DP:GL:GQ 0/1:71,36:90:-89.34,-27.11,-243.28:99 +chr1 1640405 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=32.67;MQ=47.67;MQ0=0;OQ=576.56;QD=5.54;SB=44.17 GT:AD:DP:GL:GQ 0/1:79,25:85:-86.54,-25.60,-227.82:99 +chr1 1640428 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=12.31;MQ=51.68;MQ0=0;OQ=687.66;QD=7.47;SB=59.21 GT:AD:DP:GL:GQ 0/1:63,29:86:-97.95,-25.90,-226.28:99 +chr1 1640435 . T C 0.39 PASS AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=52.41;MQ0=0;OQ=479.95;QD=4.95;SB=65.24 GT:AD:DP:GL:GQ 0/1:69,28:91:-78.69,-27.41,-274.97:99 +chr1 1640479 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=10.56;MQ=53.01;MQ0=0;OQ=125.57;QD=1.23;SB=55.33 GT:AD:DP:GL:GQ 0/1:77,25:89:-42.65,-26.81,-277.44:99 +chr1 1640500 . C A 40.46 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=1;HaplotypeScore=5.00;MQ=52.43;MQ0=0;QD=0.42;SB=79.01 GT:AD:DP:GL:GQ 0/1:71,25:78:-30.82,-23.49,-254.06:73.30 +chr1 1640502 . T G 39.38 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=52.41;MQ0=0;QD=0.40;SB=58.40 GT:AD:DP:GL:GQ 0/1:73,26:82:-31.92,-24.69,-274.53:72.21 +chr1 1640517 . C G 1.85 PASS AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.82;MQ0=0;OQ=540.14;QD=4.54;SB=-210.84 GT:AD:DP:GL:GQ 0/1:81,38:99:-87.13,-29.83,-340.31:99 +chr1 1640647 rs17845218 T C 5.93 PASS AC=1;AF=0.50;AN=2;DB;DP=139;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=46.16;MQ0=1;OQ=829.41;QD=5.97;SB=-392.09 GT:AD:DP:GL:GQ 0/1:85,54:124:-123.60,-37.37,-339.83:99 +chr1 1640657 rs1059830 A G 689.07 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=136;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=46.01;MQ0=1;QD=5.07;SB=-273.97 GT:AD:DP:GL:GQ 0/1:84,52:114:-106.55,-34.36,-315.05:99 +chr1 1640661 rs1137004 T C 924.56 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=137;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=45.08;MQ0=1;QD=6.75;SB=-478.80 GT:AD:DP:GL:GQ 0/1:82,55:116:-130.68,-34.94,-330.64:99 +chr1 1640667 rs3200657 T C 2206.14 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=133;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=43.98;MQ0=1;QD=16.59;SB=-708.39 GT:AD:DP:GL:GQ 0/1:59,73:112:-259.82,-35.92,-162.90:99 +chr1 1640692 . A G 15.57 PASS AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=41.55;MQ0=0;OQ=1129.49;QD=8.89;SB=-491.78 GT:AD:DP:GL:GQ 0/1:59,68:99:-146.06,-29.83,-231.81:99 +chr1 1640705 rs1059831 G A 307.80 PASS AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=41.79;MQ0=0;OQ=1854.51;QD=15.72;SB=-686.99 GT:AD:DP:GL:GQ 0/1:63,55:86:-214.65,-25.92,-105.31:99 +chr1 1640780 rs36191908 G A 2.57 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=50.84;MQ0=0;OQ=222.00;QD=2.52;SB=-69.38 GT:AD:DP:GL:GQ 0/1:66,22:78:-49.00,-23.51,-215.31:99 +chr1 1640799 . G A 26.24 LowQual AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=54.16;MQ0=0;QD=0.29;SB=-18.77 GT:AD:DP:GL:GQ 0/1:79,12:87:-32.13,-26.22,-265.70:59.07 +chr1 1640856 . T C 1.18 PASS AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=51.06;MQ0=0;OQ=537.04;QD=4.84;SB=42.60 GT:AD:DP:GL:GQ 0/1:73,38:93:-85.00,-28.02,-284.38:99 +chr1 1640863 . G A 0.15 PASS AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=2;HaplotypeScore=0.93;MQ=50.41;MQ0=0;OQ=682.37;QD=6.20;SB=40.52 GT:AD:DP:GL:GQ 0/1:69,41:93:-99.55,-28.03,-223.44:99 +chr1 1640907 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=91;Dels=0.01;HRun=2;HaplotypeScore=10.49;MQ=48.20;MQ0=0;OQ=731.52;QD=8.04;SB=71.23 GT:AD:DP:GL:GQ 0/1:53,37:73:-98.42,-21.99,-174.07:99 +chr1 1640923 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=64.78;MQ=43.84;MQ0=1;OQ=272.78;QD=3.17;SB=56.20 GT:AD:DP:GL:GQ 0/1:67,19:80:-54.67,-24.11,-250.01:99 +chr1 1640931 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=98.55;MQ=40.13;MQ0=1;OQ=147.14;QD=2.16;SB=38.15 GT:AD:DP:GL:GQ 0/1:57,11:64:-37.28,-19.28,-217.64:99 +chr1 1640986 . A C 0.64 PASS AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=43.40;MQ0=0;OQ=371.72;QD=5.81;SB=77.22 GT:AD:DP:GL:GQ 0/1:47,17:62:-59.13,-18.68,-158.05:99 +chr1 1640996 . C T 0.49 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=45.56;MQ0=0;OQ=291.78;QD=4.63;SB=80.17 GT:AD:DP:GL:GQ 0/1:49,14:56:-49.34,-16.88,-145.60:99 +chr1 1641016 . C T 53.74 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=51.28;MQ0=0;QD=0.87;SB=74.21 GT:AD:DP:GL:GQ 0/1:47,15:50:-23.72,-15.06,-152.06:86.58 +chr1 1641017 . A G 257.15 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=51.43;MQ0=0;QD=4.08;SB=80.28 GT:AD:DP:GL:GQ 0/1:48,15:61:-47.39,-18.39,-179.46:99 +chr1 1641026 . C T 369.95 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=52.99;MQ0=0;QD=5.97;SB=74.25 GT:AD:DP:GL:GQ 0/1:47,15:60:-58.35,-18.07,-168.55:99 +chr1 1641040 . G C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=51.94;MQ0=0;OQ=253.54;QD=4.23;SB=74.26 GT:AD:DP:GL:GQ 0/1:44,15:55:-45.26,-16.62,-168.61:99 +chr1 1641126 rs12137617 A G 24.87 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.12;MQ=54.87;MQ0=0;OQ=1275.18;QD=31.10;SB=-536.43 GT:AD:DP:GL:GQ 1/1:0,41:37:-131.12,-11.15,-0.02:99 +chr1 1641482 rs11260627 C T 34.89 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=55.33;MQ0=0;OQ=1435.98;QD=36.82;SB=-496.00 GT:AD:DP:GL:GQ 1/1:0,39:37:-147.19,-11.15,-0.01:99 +chr1 1641491 rs12135951 T G 20.84 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=56.50;MQ0=0;OQ=197.57;QD=5.20;SB=-66.56 GT:AD:DP:GL:GQ 0/1:25,13:35:-33.59,-10.55,-90.46:99 +chr1 1641587 rs12044811 G A 0.08 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=15.92;MQ=55.20;MQ0=1;OQ=1462.24;QD=35.66;SB=-578.76 GT:AD:DP:GL:GQ 1/1:1,40:37:-149.82,-11.15,-0.01:99 +chr1 1641608 rs12044814 G C 398.84 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.85;MQ0=0;OQ=998.26;QD=30.25;SB=-358.22 GT:AD:DP:GL:GQ 1/1:1,32:26:-103.43,-7.84,-0.02:78.25 +chr1 1641675 rs4648768 T C 52.50 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=49.39;MQ0=0;OQ=640.24;QD=18.29;SB=-205.57 GT:AD:DP:GL:GQ 1/1:0,32:21:-67.63,-6.34,-0.02:63.13 +chr1 1641761 rs4648772 T C 503.17 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=1369.78;QD=30.44;SB=-625.00 GT:AD:DP:GL:GQ 1/1:0,45:43:-140.60,-12.97,-0.03:99 +chr1 1641771 rs4648773 C A 18.84 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=2.41;MQ=54.78;MQ0=0;OQ=1559.28;QD=33.90;SB=-751.90 GT:AD:DP:GL:GQ 1/1:0,46:44:-159.53,-13.25,-0.02:99 +chr1 1641797 rs4648775 G A 91.99 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=54.06;MQ0=0;OQ=1591.86;QD=36.18;SB=-734.99 GT:AD:DP:GL:GQ 1/1:0,44:41:-162.79,-12.35,-0.01:99 +chr1 1641822 rs4648776 G A 529.47 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.06;MQ0=0;OQ=1730.65;QD=38.46;SB=-774.66 GT:AD:DP:GL:GQ 1/1:0,45:44:-176.66,-13.26,-0.01:99 +chr1 1642086 rs4648777 A G 238.91 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.56;MQ0=1;OQ=1172.89;QD=24.44;SB=-406.15 GT:AD:DP:GL:GQ 1/1:1,47:39:-120.92,-11.77,-0.04:99 +chr1 1642864 rs36039898 T C 113.78 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.55;MQ0=0;OQ=2211.83;QD=36.26;SB=-727.29 GT:AD:DP:GL:GQ 1/1:0,61:61:-224.79,-18.37,-0.02:99 +chr1 1642888 rs16825265 C T 105.46 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=54.90;MQ0=0;OQ=2464.17;QD=40.40;SB=-985.30 GT:AD:DP:GL:GQ 1/1:0,61:61:-250.01,-18.37,-0.01:99 +chr1 1643163 rs35548050 T C 620.20 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.02;MQ0=0;OQ=2383.87;QD=34.06;SB=-1115.83 GT:AD:DP:GL:GQ 1/1:0,70:67:-241.99,-20.18,-0.02:99 +chr1 1643221 rs2206307 C T 629.97 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.40;MQ0=0;OQ=2196.71;QD=34.87;SB=-1116.03 GT:AD:DP:GL:GQ 1/1:0,63:57:-223.28,-17.18,-0.02:99 +chr1 1643274 rs2206308 C T 615.08 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.68;MQ0=0;OQ=2077.20;QD=37.77;SB=-1010.04 GT:AD:DP:GL:GQ 1/1:0,55:53:-211.32,-15.97,-0.02:99 +chr1 1643659 rs2223485 C T 454.72 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.70;MQ0=1;OQ=1724.40;QD=36.69;SB=-535.21 GT:AD:DP:GL:GQ 1/1:0,47:43:-176.03,-12.95,-0.01:99 +chr1 1643745 rs61777493 C A 268.51 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=53.15;MQ0=3;OQ=2449.58;QD=34.50;SB=-1240.29 GT:AD:DP:GL:GQ 1/1:3,68:66:-248.56,-19.87,-0.01:99 +chr1 1643867 . A T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=19.40;MQ0=14;OQ=84.98;QD=3.04;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,15:12:-15.40,-3.61,-30.71:99 +chr1 1643873 . C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=27;Dels=0.41;HRun=0;HaplotypeScore=83.92;MQ=18.34;MQ0=14;OQ=350.65;QD=12.99;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:10:-42.29,-6.54,-3.64:28.97 +chr1 1643898 rs61777494 G A 157 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.17;MQ0=2;OQ=461.81;QD=27.17;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,16:12:-49.77,-3.61,-0.00:36.12 +chr1 1643918 rs61777495 C T 757.85 Indel AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.37;MQ0=1;QD=31.58;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,23:19:-79.37,-5.72,-0.00:57.19 +chr1 1643924 . A T 950.73 Indel AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.62;MQ0=1;QD=30.67;SB=-180.94 GT:AD:DP:GL:GQ 1/1:1,30:26:-98.67,-7.83,-0.01:78.24 +chr1 1644591 rs61777496 G A 138.94 PASS AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.34;MQ0=0;OQ=130.88;QD=26.18;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:4:-16.62,-1.20,-0.00:12.04 +chr1 1644813 rs2056977 A G 170.73 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.65;MQ0=9;OQ=292.06;QD=7.69;SB=-147.83 GT:AD:DP:GL:GQ 1/1:7,31:10:-32.80,-3.01,-0.01:30.08 +chr1 1645334 rs11486024 G A 35.89 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=22.46;MQ0=10;OQ=345.89;QD=5.67;SB=32.11 GT:AD:DP:GL:GQ 0/1:46,15:32:-47.52,-9.65,-66.64:99 +chr1 1645788 rs28649027 G C 26.17 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=53.44;MQ0=0;OQ=593.92;QD=15.23;SB=-280.31 GT:AD:DP:GL:GQ 0/1:20,19:36:-73.54,-10.87,-73.49:99 +chr1 1646881 rs61777497 T C 0.39 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=11.68;MQ0=43;OQ=71.62;QD=1.23;SB=-32.65 GT:AD:DP:GL:GQ 0/1:40,18:10:-13.46,-3.01,-23.67:99 +chr1 1646928 . C T 0.40 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=15.38;MQ0=21;OQ=97.42;QD=2.87;SB=-39.65 GT:AD:DP:GL:GQ 0/1:20,14:7:-15.13,-2.11,-10.71:85.98 +chr1 1646938 rs61776763 A G 17.48 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=2.10;MQ=17.28;MQ0=15;OQ=266.90;QD=8.34;SB=-88.98 GT:AD:DP:GL:GQ 1/1:0,32:9:-30.28,-2.71,-0.01:27.04 +chr1 1646996 rs4648783 T C 206.37 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=31.62;MQ0=1;OQ=494.82;QD=9.00;SB=-214.36 GT:AD:DP:GL:GQ 0/1:25,30:43:-65.73,-12.96,-90.44:99 +chr1 1647044 rs4648784 C G 2.96 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=1.82;MQ=32.49;MQ0=8;OQ=1818.45;QD=23.93;SB=-827.04 GT:AD:DP:GL:GQ 0/1:14,62:58:-202.62,-17.49,-37.52:99 +chr1 1647352 rs9439501 G C 210.43 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=45.38;MQ0=4;OQ=1643.24;QD=34.96;SB=-614.99 GT:AD:DP:GL:GQ 1/1:0,47:39:-167.92,-11.75,-0.01:99 +chr1 1647425 rs11576302 G A 125.25 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=52.45;MQ0=0;OQ=868.24;QD=17.72;SB=-259.77 GT:AD:DP:GL:GQ 0/1:23,26:49:-104.87,-14.76,-83.38:99 +chr1 1647461 rs11589282 T C 44.46 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=0.94;MQ=51.71;MQ0=1;OQ=1927.78;QD=33.24;SB=-715.12 GT:AD:DP:GL:GQ 1/1:0,58:56:-196.39,-16.87,-0.02:99 +chr1 1648203 rs4648785 T C 8.14 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=39.29;MQ0=4;OQ=1376.56;QD=30.59;SB=-396.50 GT:AD:DP:GL:GQ 1/1:0,45:38:-141.25,-11.44,-0.01:99 +chr1 1648805 rs1062057 T C 6.42 PASS AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=1;HaplotypeScore=3.69;MQ=25.80;MQ0=25;OQ=1469.54;QD=13.86;SB=-734.60 GT:AD:DP:GL:GQ 0/1:45,61:78:-173.74,-23.50,-116.68:99 +chr1 1649970 rs1801781 C A 600.71 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.53;MQ0=0;OQ=2075.47;QD=36.41;SB=-874.83 GT:AD:DP:GL:GQ 1/1:0,57:57:-211.15,-17.17,-0.01:99 +chr1 1650495 rs2377220 T G 497.64 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.20;MQ0=1;OQ=1908.80;QD=31.81;SB=-547.03 GT:AD:DP:GL:GQ 1/1:0,60:54:-194.48,-16.27,-0.02:99 +chr1 1650579 . G C 24.29 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=9.52;MQ=48.11;MQ0=12;QD=0.34;SB=80.30 GT:AD:DP:GL:GQ 0/1:60,12:43:-18.68,-12.97,-167.36:57.11 +chr1 1650586 rs28662997 T C 0.09 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=7.30;MQ=48.54;MQ0=13;OQ=175.02;QD=2.22;SB=-47.44 GT:AD:DP:GL:GQ 0/1:53,26:60:-38.86,-18.08,-194.29:99 +chr1 1650595 rs1061883 T C 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=49.38;MQ0=13;OQ=60.20;QD=0.69;SB=-8.74 GT:AD:DP:GL:GQ 0/1:58,29:65:-28.90,-19.59,-216.78:93.04 +chr1 1651158 rs1546882 A G 91.08 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=1.86;MQ=36.24;MQ0=1;OQ=1126.99;QD=14.09;SB=-474.67 GT:AD:DP:GL:GQ 0/1:32,48:73:-138.00,-22.01,-116.79:99 +chr1 1651704 rs61777505 G C 26.06 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.62;MQ=32.64;MQ0=2;OQ=1226.35;QD=32.27;SB=-479.52 GT:AD:DP:GL:GQ 1/1:4,34:33:-134.22,-9.95,-8.01:19.39 +chr1 1652175 . C G 107.65 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.31;MQ0=18;OQ=446.15;QD=8.42;SB=-112.32 GT:AD:DP:GL:GQ 0/1:32,21:35:-58.45,-10.56,-85.98:99 +chr1 1652288 rs2281171 A G 55.47 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.68;MQ=47.07;MQ0=0;OQ=1046.84;QD=33.77;SB=-483.46 GT:AD:DP:GL:GQ 1/1:0,31:31:-108.28,-9.34,-0.01:93.26 +chr1 1652674 rs61777506 T C 260.73 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.10;MQ0=0;OQ=1515.24;QD=32.94;SB=-289.56 GT:AD:DP:GL:GQ 1/1:0,46:45:-155.13,-13.56,-0.02:99 +chr1 1652697 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=17;HaplotypeScore=26.60;MQ=53.41;MQ0=0;OQ=216.45;QD=3.80;SB=47.16 GT:AD:DP:GL:GQ 0/1:42,15:40:-36.99,-12.06,-92.34:99 +chr1 1652700 . G A 48.19 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=2;HaplotypeScore=19.75;MQ=52.95;MQ0=0;QD=0.96;SB=53.18 GT:AD:DP:GL:GQ 0/1:40,10:33:-18.05,-9.95,-95.61:81.03 +chr1 1652755 rs61777507 A G 615.92 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=1969.12;QD=34.55;SB=-927.86 GT:AD:DP:GL:GQ 1/1:0,57:57:-200.52,-17.17,-0.03:99 +chr1 1653262 rs34298494 A C 3.15 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=4.92;MQ=57.93;MQ0=0;OQ=1820.14;QD=28.89;SB=-933.22 GT:AD:DP:GL:GQ 1/1:0,63:59:-185.65,-17.78,-0.05:99 +chr1 1653465 . A G 0.67 PASS AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.82;MQ=58.69;MQ0=0;OQ=1218.77;QD=28.34;SB=-585.02 GT:AD:DP:GL:GQ 1/1:0,43:39:-125.50,-11.76,-0.03:99 +chr1 1653691 rs3817856 C T 262.98 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.21;MQ0=0;OQ=2006.29;QD=37.85;SB=-990.80 GT:AD:DP:GL:GQ 1/1:0,53:51:-204.23,-15.37,-0.02:99 +chr1 1653879 rs2294488 T C 118.63 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=52.10;MQ0=0;OQ=1419.75;QD=28.40;SB=-681.96 GT:AD:DP:GL:GQ 1/1:0,49:45:-145.60,-13.57,-0.04:99 +chr1 1653984 rs2294489 T C 14.56 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=58.58;MQ0=0;OQ=1353.88;QD=31.49;SB=-691.09 GT:AD:DP:GL:GQ 1/1:0,43:40:-138.99,-12.05,-0.02:99 +chr1 1655431 rs61777508 T G 492.95 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.47;MQ0=3;OQ=2585.92;QD=31.92;SB=-532.88 GT:AD:DP:GL:GQ 1/1:0,81:75:-262.21,-22.59,-0.04:99 +chr1 1655473 rs4648764 A G 513.83 PASS AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.46;MQ0=4;OQ=2874.97;QD=29.64;SB=-827.61 GT:AD:DP:GL:GQ 1/1:1,96:86:-291.13,-25.92,-0.05:99 +chr1 1655600 rs2281176 T C 43.16 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=43.78;MQ0=0;OQ=2374.61;QD=30.44;SB=-588.04 GT:AD:DP:GL:GQ 1/1:0,78:71:-241.09,-21.40,-0.04:99 +chr1 1655607 rs2281177 T C 16.19 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=43.12;MQ0=0;OQ=1801.45;QD=22.24;SB=-550.84 GT:AD:DP:GL:GQ 0/1:17,64:75:-206.03,-22.60,-57.34:99 +chr1 1656111 . G A 19.94 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=24.98;MQ0=9;OQ=1269.10;QD=20.14;SB=-363.89 GT:AD:DP:GL:GQ 0/1:20,43:51:-145.56,-15.37,-46.93:99 +chr1 1656198 rs2072924 G A 130.85 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=29.23;MQ0=3;OQ=1510.31;QD=34.33;SB=-636.84 GT:AD:DP:GL:GQ 1/1:0,44:39:-154.63,-11.75,-0.02:99 +chr1 1656202 rs2072925 A G 35.86 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=31.20;MQ0=3;OQ=1130.90;QD=24.58;SB=-545.87 GT:AD:DP:GL:GQ 1/1:0,46:37:-116.71,-11.16,-0.04:99 +chr1 1656475 rs2076325 C T 114.33 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=50.53;MQ0=0;OQ=1787.32;QD=37.24;SB=-867.16 GT:AD:DP:GL:GQ 1/1:0,48:46:-182.33,-13.86,-0.01:99 +chr1 1657113 rs1474648 T C 589.09 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.20;MQ0=0;OQ=2447.49;QD=32.63;SB=-1145.82 GT:AD:DP:GL:GQ 1/1:0,75:68:-248.35,-20.48,-0.02:99 +chr1 1657231 rs1474649 A G 31.11 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=49.42;MQ0=0;OQ=1497.15;QD=33.27;SB=-642.31 GT:AD:DP:GL:GQ 1/1:0,45:43:-153.31,-12.95,-0.02:99 +chr1 1657279 rs2377208 A C 135.92 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=44.04;MQ0=1;OQ=1645.48;QD=30.47;SB=-668.23 GT:AD:DP:GL:GQ 1/1:0,54:48:-168.15,-14.46,-0.02:99 +chr1 1658028 rs28718827 G T 1.42 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=10.14;MQ=51.62;MQ0=0;OQ=1872.10;QD=31.73;SB=-828.68 GT:AD:DP:GL:GQ 1/1:2,57:55:-190.82,-16.57,-0.03:99 +chr1 1658119 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.03;HRun=18;HaplotypeScore=24.79;MQ=51.46;MQ0=0;OQ=102.87;QD=1.49;SB=-23.99 GT:AD:DP:GL:GQ 0/1:55,12:49:-28.05,-14.47,-131.71:99 +chr1 1658135 rs2889577 A G 0.64 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=15.54;MQ=53.86;MQ0=0;OQ=1611.78;QD=21.78;SB=-529.45 GT:AD:DP:GL:GQ 1/1:8,66:53:-172.54,-15.98,-7.77:82.05 +chr1 1658803 rs28537345 A C 60.48 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.02;HRun=1;HaplotypeScore=0.16;MQ=51.80;MQ0=0;OQ=1884.76;QD=31.95;SB=-820.50 GT:AD:DP:GL:GQ 1/1:0,58:56:-192.08,-16.57,-0.02:99 +chr1 1659088 rs11485870 T C 2.06 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=5.25;MQ=48.74;MQ0=0;OQ=1314.03;QD=25.77;SB=-582.00 GT:AD:DP:GL:GQ 1/1:2,49:46:-142.54,-13.87,-7.55:63.21 +chr1 1659426 rs9442408 C T 56.19 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=38.94;MQ0=1;OQ=469.40;QD=7.96;SB=-62.79 GT:AD:DP:GL:GQ 0/1:41,18:57:-67.39,-17.17,-141.22:99 +chr1 1659594 rs61777512 G T 329.49 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.52;MQ0=1;OQ=761.00;QD=27.18;SB=-349.52 GT:AD:DP:GL:GQ 1/1:2,26:23:-79.70,-6.93,-0.01:69.17 +chr1 1659896 . C A 16.91 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=18.32;MQ0=25;OQ=324.85;QD=7.55;SB=-33.35 GT:AD:DP:GL:GQ 0/1:14,29:14:-39.99,-4.22,-11.38:71.59 +chr1 1659905 . C T 19.49 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=18.62;MQ0=24;OQ=356.25;QD=8.28;SB=-31.52 GT:AD:DP:GL:GQ 0/1:14,29:15:-43.43,-4.52,-12.58:80.58 +chr1 1661214 rs2005995 G A 408.17 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=11.78;MQ0=23;OQ=327.72;QD=9.93;SB=-165.22 GT:AD:DP:GL:GQ 1/1:16,17:9:-36.36,-2.71,-0.00:27.09 +chr1 1661590 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.96;MQ=36.56;MQ0=3;OQ=54.36;QD=1.05;SB=68.26 GT:AD:DP:GL:GQ 0/1:38,14:35:-19.28,-10.56,-129.90:87.20 +chr1 1661642 rs4648793 C T 457.64 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.04;MQ0=0;OQ=1470.76;QD=37.71;SB=-587.27 GT:AD:DP:GL:GQ 1/1:0,39:38:-150.68,-11.45,-0.01:99 +chr1 1661726 rs7364986 A T 4.25 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=5.15;MQ=47.34;MQ0=1;OQ=2656.76;QD=33.63;SB=-1106.52 GT:AD:DP:GL:GQ 1/1:0,79:72:-269.28,-21.69,-0.02:99 +chr1 1662002 . C T 0.16 PASS AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=5.72;MQ=52.52;MQ0=1;OQ=1857.08;QD=37.14;SB=-705.36 GT:AD:DP:GL:GQ 1/1:0,50:47:-189.31,-14.16,-0.02:99 +chr1 1662772 . C T 43.11 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=50.80;MQ0=2;QD=0.70;SB=83.20 GT:AD:DP:GL:GQ 0/1:53,9:53:-23.58,-15.98,-150.38:75.94 +chr1 1663032 . T C 46.58 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=53.54;MQ0=2;QD=0.93;SB=38.12 GT:AD:DP:GL:GQ 0/1:38,9:34:-18.20,-10.26,-102.10:79.41 +chr1 1663379 rs35790103 T C 8.23 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=-0.24;MQ=57.22;MQ0=0;OQ=1409.71;QD=33.56;SB=-634.30 GT:AD:DP:GL:GQ 1/1:0,42:41:-144.58,-12.35,-0.02:99 +chr1 1663767 rs35678883 G C 8.07 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=2.38;MQ=50.72;MQ0=2;OQ=2425.38;QD=39.12;SB=-647.42 GT:AD:DP:GL:GQ 1/1:0,62:56:-246.15,-16.88,-0.03:99 +chr1 1663886 rs36050429 G C 377.70 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.29;MQ0=3;OQ=1259.11;QD=34.03;SB=-328.71 GT:AD:DP:GL:GQ 1/1:0,37:30:-129.51,-9.04,-0.01:90.30 +chr1 1664767 . G C 282.90 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.97;MQ0=0;OQ=606.08;QD=13.77;SB=-320.01 GT:AD:DP:GL:GQ 0/1:24,20:40:-75.96,-12.06,-88.71:99 +chr1 1664855 . A G 129.97 Indel AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=9.28;MQ=43.11;MQ0=1;QD=4.06;SB=-24.89 GT:AD:DP:GL:GQ 0/1:24,8:26:-24.12,-7.84,-71.93:99 +chr1 1664856 . G A 433.28 Indel AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=12;HaplotypeScore=9.83;MQ=42.77;MQ0=1;QD=12.74;SB=-25.59 GT:AD:DP:GL:GQ 0/1:18,16:29:-55.35,-8.74,-47.19:99 +chr1 1665027 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=13;HaplotypeScore=3.74;MQ=53.18;MQ0=0;OQ=78.07;QD=1.28;SB=0.76 GT:AD:DP:GL:GQ 0/1:47,14:45:-24.65,-13.56,-131.48:99 +chr1 1665395 . C T 17.70 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.53;MQ=22.06;MQ0=30;QD=0.34;SB=14.07 GT:AD:DP:GL:GQ 0/1:42,10:21:-11.37,-6.32,-66.25:50.46 +chr1 1667416 rs16824474 G C 10.38 LowQual AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=47.86;MQ0=3;QD=0.61;SB=-0.97 GT:AD:DP:GL:GQ 0/1:12,5:14:-8.50,-4.22,-50.97:42.79 +chr1 1670869 . G C 14.33 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=45.06;MQ0=4;QD=0.19;SB=74.28 GT:AD:DP:GL:GQ 0/1:64,12:62:-23.39,-18.69,-239.55:47 +chr1 1670881 . G C 19.24 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=4.38;MQ=42.81;MQ0=4;QD=0.27;SB=74.28 GT:AD:DP:GL:GQ 0/1:59,12:59:-22.99,-17.79,-226.11:52.02 +chr1 1670904 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=38.22;MQ0=4;OQ=63.86;QD=0.91;SB=56.13 GT:AD:DP:GL:GQ 0/1:50,20:51:-25.06,-15.39,-141.72:96.69 +chr1 1670928 . G A 848.58 HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=30.83;MQ0=10;QD=13.91;SB=-297.25 GT:AD:DP:GL:GQ 0/1:30,31:35:-98.68,-10.54,-33.99:99 +chr1 1670936 . G T 255.10 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=3;HaplotypeScore=4.00;MQ=28.80;MQ0=12;QD=3.99;SB=20.07 GT:AD:DP:GL:GQ 0/1:33,31:36:-39.64,-10.84,-86.07:99 +chr1 1671525 rs35301881 C T 26.84 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=43.35;MQ0=4;OQ=980.88;QD=30.65;SB=-483.00 GT:AD:DP:GL:GQ 1/1:4,28:26:-101.68,-7.83,-0.01:78.25 +chr1 1672234 rs4648812 G A 127.32 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=26.23;MQ0=1;OQ=275.04;QD=7.86;SB=-150.63 GT:AD:DP:GL:GQ 0/1:24,11:30:-39.83,-9.05,-63.69:99 +chr1 1673187 rs14390 C T 78.82 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=730.68;QD=36.53;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,20:19:-76.66,-5.72,-0.00:57.19 +chr1 1673425 rs12588 G A 34.78 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=30.14;MQ0=16;OQ=466.02;QD=6.66;SB=-83.01 GT:AD:DP:GL:GQ 0/1:47,23:47:-64.06,-14.17,-100.00:99 +chr1 1675073 rs2072928 C G 44.21 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.71;MQ=59.55;MQ0=0;OQ=1934.62;QD=37.93;SB=-835.43 GT:AD:DP:GL:GQ 1/1:0,51:47:-197.07,-14.17,-0.02:99 +chr1 1675900 rs4751 G T 24.68 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=1.42;MQ=59.65;MQ0=0;OQ=1889.22;QD=34.99;SB=-617.91 GT:AD:DP:GL:GQ 1/1:0,54:52:-192.52,-15.66,-0.02:99 +chr1 1676803 rs2072929 T C 69.29 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=1256.22;QD=28.55;SB=-491.53 GT:AD:DP:GL:GQ 1/1:0,44:41:-129.26,-12.37,-0.05:99 +chr1 1676822 rs2076327 C T 34.01 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=58.97;MQ0=0;OQ=1637.49;QD=36.39;SB=-774.03 GT:AD:DP:GL:GQ 1/1:0,45:43:-167.35,-12.96,-0.02:99 +chr1 1677485 rs34306661 T C 77.88 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=60.00;MQ0=0;OQ=1787.88;QD=27.94;SB=-566.94 GT:AD:DP:GL:GQ 1/1:0,64:57:-182.43,-17.19,-0.05:99 +chr1 1677651 . C T 157.32 PASS AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=1381.04;QD=20.92;SB=-549.37 GT:AD:DP:GL:GQ 0/1:23,43:64:-160.68,-19.29,-80.55:99 +chr1 1677956 . C T 7.81 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=59.68;MQ0=0;OQ=1209.30;QD=20.50;SB=-531.10 GT:AD:DP:GL:GQ 0/1:22,37:56:-141.09,-16.88,-73.03:99 +chr1 1678052 rs2281173 A G 576.86 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1215.40;QD=30.39;SB=-536.99 GT:AD:DP:GL:GQ 1/1:0,40:39:-125.17,-11.77,-0.04:99 +chr1 1678329 rs4648623 C G 0.20 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=58.16;MQ0=0;OQ=844.68;QD=36.73;SB=-124.74 GT:AD:DP:GL:GQ 1/1:0,23:22:-88.07,-6.64,-0.02:66.21 +chr1 1678373 rs4648624 G T 1.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=58.84;MQ0=0;OQ=639.15;QD=31.96;SB=-120.84 GT:AD:DP:GL:GQ 1/1:0,20:19:-67.51,-5.72,-0.01:57.16 +chr1 1679024 rs2235536 C T 173.64 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.47;MQ0=0;OQ=2302.66;QD=39.70;SB=-1126.49 GT:AD:DP:GL:GQ 1/1:0,58:58:-233.87,-17.47,-0.02:99 +chr1 1679622 rs2235537 T C 108.22 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=59.56;MQ0=0;OQ=1772.95;QD=33.45;SB=-589.32 GT:AD:DP:GL:GQ 1/1:0,53:52:-180.90,-15.67,-0.02:99 +chr1 1681624 . G A 66.45 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=58.28;MQ0=0;OQ=379.97;QD=10.00;SB=-141.64 GT:AD:DP:GL:GQ 0/1:24,13:33:-51.23,-9.94,-69.72:99 +chr1 1682181 rs1107910 T C 610.89 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=1733.17;QD=30.41;SB=-652.94 GT:AD:DP:GL:GQ 1/1:0,57:55:-176.95,-16.58,-0.05:99 +chr1 1683963 rs2011384 A G 3.98 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=4.20;MQ=58.55;MQ0=0;OQ=1546.21;QD=34.36;SB=-525.21 GT:AD:DP:GL:GQ 1/1:0,45:43:-158.22,-12.95,-0.01:99 +chr1 1684111 . C T 6.27 PASS AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=0;HaplotypeScore=5.81;MQ=58.90;MQ0=0;OQ=1337.84;QD=16.12;SB=-601.14 GT:AD:DP:GL:GQ 0/1:40,41:79:-160.90,-23.83,-119.77:99 +chr1 1685322 rs4648629 C A 210.40 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.13;MQ0=0;OQ=2599.96;QD=34.67;SB=-1123.97 GT:AD:DP:GL:GQ 1/1:0,75:71:-263.60,-21.38,-0.02:99 +chr1 1685434 rs876029 G T 83.73 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1202.21;QD=31.64;SB=-492.27 GT:AD:DP:GL:GQ 1/1:0,38:36:-123.83,-10.85,-0.02:99 +chr1 1685691 rs63093560 C T 514.92 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=1899.13;QD=37.98;SB=-713.35 GT:AD:DP:GL:GQ 1/1:0,50:49:-193.52,-14.77,-0.02:99 +chr1 1686194 rs35270315 A C 13.33 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=3.38;MQ=58.28;MQ0=0;OQ=2324.40;QD=30.19;SB=-1042.79 GT:AD:DP:GL:GQ 1/1:0,77:73:-236.08,-22.00,-0.06:99 +chr1 1686519 . A G 162.43 PASS AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1839.98;QD=29.21;SB=-784.98 GT:AD:DP:GL:GQ 1/1:0,63:60:-187.66,-18.11,-0.08:99 +chr1 1687967 rs35086222 C T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=6;HaplotypeScore=6.25;MQ=58.18;MQ0=0;OQ=2341.51;QD=37.77;SB=-1078.61 GT:AD:DP:GL:GQ 1/1:1,61:60:-237.76,-18.08,-0.02:99 +chr1 1688667 rs4648826 C G 14.69 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=58.62;MQ0=0;OQ=2540.02;QD=41.64;SB=-864.78 GT:AD:DP:GL:GQ 1/1:0,61:58:-257.61,-17.48,-0.02:99 +chr1 1689061 rs4648827 C A 174 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2030.67;QD=34.42;SB=-1001.13 GT:AD:DP:GL:GQ 1/1:1,58:58:-206.68,-17.47,-0.02:99 +chr1 1692374 rs6658139 T C 285.34 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.82;MQ0=0;OQ=1093.26;QD=29.55;SB=-273.03 GT:AD:DP:GL:GQ 0/1:3,34:37:-123.62,-11.15,-11.29:1.44 +chr1 1694514 rs61774982 C A 248.31 PASS AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.73;MQ0=0;OQ=726.51;QD=34.60;SB=-285.07 GT:AD:DP:GL:GQ 1/1:0,21:21:-76.24,-6.33,-0.01:63.18 +chr1 1695016 . T A 11.74 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=37;Dels=0.03;HRun=0;HaplotypeScore=27.67;MQ=32.06;MQ0=0;QD=0.32;SB=-25.92 GT:AD:DP:GL:GQ 0/1:10,26:10:-7.44,-3.01,-29.53:44.28 +chr1 1695024 . T A 13.63 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=9.62;MQ=29.68;MQ0=0;QD=0.39;SB=-25.92 GT:AD:DP:GL:GQ 0/1:9,26:10:-7.64,-3.01,-29.53:46.28 +chr1 1695026 . T A 81.80 SnpCluster AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=32.06;MQ0=0;QD=2.21;SB=-59.89 GT:AD:DP:GL:GQ 0/1:8,29:12:-15.08,-3.61,-28.63:99 +chr1 1695028 . T A 128.81 SnpCluster AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.66;MQ=32.06;MQ0=0;QD=3.48;SB=-77.75 GT:AD:DP:GL:GQ 0/1:7,30:9:-18.88,-2.71,-13.92:99 +chr1 1695464 rs61774983 A G 565.11 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.28;MQ0=0;OQ=1675.23;QD=34.19;SB=-712.27 GT:AD:DP:GL:GQ 1/1:0,49:49:-171.13,-14.76,-0.02:99 +chr1 1695607 rs6603809 G A 610.11 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.73;MQ0=0;OQ=1827.34;QD=36.55;SB=-919.23 GT:AD:DP:GL:GQ 1/1:0,50:48:-186.34,-14.47,-0.02:99 +chr1 1695633 rs6603810 A G 70.23 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.63;MQ0=1;OQ=1141.91;QD=27.85;SB=-557.89 GT:AD:DP:GL:GQ 1/1:0,41:37:-117.81,-11.16,-0.04:99 +chr1 1695996 rs6603811 T C 513.06 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1134.00;QD=29.08;SB=-433.18 GT:AD:DP:GL:GQ 1/1:0,39:37:-117.03,-11.17,-0.04:99 +chr1 1696020 rs7531583 A G 565.84 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1293.98;QD=28.76;SB=-649.94 GT:AD:DP:GL:GQ 1/1:0,45:43:-133.03,-12.97,-0.04:99 +chr1 1697600 rs12041925 T G 3.96 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=58.61;MQ0=0;OQ=1724.62;QD=29.73;SB=-619.85 GT:AD:DP:GL:GQ 1/1:0,58:53:-176.09,-15.97,-0.04:99 +chr1 1702090 rs10907194 C T 0.75 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=5.73;MQ=57.94;MQ0=0;OQ=1197.78;QD=35.23;SB=-529.68 GT:AD:DP:GL:GQ 1/1:1,33:31:-123.37,-9.34,-0.01:93.30 +chr1 1703208 rs10907195 C T 76.64 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.55;MQ0=0;OQ=1814.27;QD=37.80;SB=-686.40 GT:AD:DP:GL:GQ 1/1:0,48:45:-185.02,-13.55,-0.01:99 +chr1 1703574 rs454577 T G 67.40 PASS AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=652.72;QD=31.08;SB=-294.53 GT:AD:DP:GL:GQ 1/1:0,21:20:-68.87,-6.03,-0.01:60.16 +chr1 1703729 rs7534617 T G 38.29 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=59.38;MQ0=0;OQ=1200.11;QD=32.44;SB=-519.95 GT:AD:DP:GL:GQ 1/1:0,37:36:-123.61,-10.85,-0.02:99 +chr1 1704871 rs742359 C A 251.57 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.49;MQ0=0;OQ=1398.04;QD=31.07;SB=-698.80 GT:AD:DP:GL:GQ 1/1:0,45:41:-143.41,-12.36,-0.02:99 +chr1 1706848 . G A 26.61 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=3.11;MQ=59.44;MQ0=0;QD=0.65;SB=62.22 GT:AD:DP:GL:GQ 0/1:33,8:34:-16.19,-10.25,-103.26:59.43 +chr1 1709327 . C A 45.07 LowQual AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=18;HaplotypeScore=15.97;MQ=51.18;MQ0=0;QD=1.07;SB=-1.26 GT:AD:DP:GL:GQ 0/1:34,8:30:-16.83,-9.04,-86.61:77.90 +chr1 1710980 . G C 20.70 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=53.66;MQ0=1;QD=0.48;SB=38.15 GT:AD:DP:GL:GQ 0/1:38,5:37:-16.51,-11.16,-138.32:53.50 +chr1 1712688 rs3737627 G A 389.56 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1534.00;QD=37.41;SB=-461.61 GT:AD:DP:GL:GQ 1/1:0,41:41:-157.01,-12.36,-0.03:99 +chr1 1715121 rs7545812 A G 362.56 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=2055.38;QD=33.69;SB=-1042.38 GT:AD:DP:GL:GQ 1/1:0,61:58:-209.15,-17.47,-0.02:99 +chr1 1715620 rs6690956 C T 11.88 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=5.08;MQ=58.81;MQ0=0;OQ=2937.89;QD=37.67;SB=-1197.36 GT:AD:DP:GL:GQ 1/1:0,77:75:-297.40,-22.60,-0.03:99 +chr1 1716741 . G A 184.26 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=52.39;MQ0=0;OQ=1148.50;QD=16.18;SB=-579.64 GT:AD:DP:GL:GQ 0/1:37,34:69:-138.94,-20.80,-109.67:99 +chr1 1718547 rs6603794 C G 73.37 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.81;MQ=57.85;MQ0=0;OQ=2921.36;QD=42.96;SB=-1363.94 GT:AD:DP:GL:GQ 1/1:0,68:67:-295.74,-20.18,-0.02:99 +chr1 1722071 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=84;Dels=0.01;HRun=18;HaplotypeScore=24.45;MQ=58.30;MQ0=0;OQ=60.55;QD=0.72;SB=155.39 GT:AD:DP:GL:GQ 0/1:70,13:70:-30.14,-20.80,-197.36:93.38 +chr1 1724830 rs12077553 C T 351.52 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.34;MQ0=0;OQ=2450.74;QD=39.53;SB=-952.27 GT:AD:DP:GL:GQ 1/1:0,62:62:-248.68,-18.68,-0.02:99 +chr1 1726513 rs12134783 T G 35.44 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=59.11;MQ0=0;OQ=1936.28;QD=28.47;SB=-959.69 GT:AD:DP:GL:GQ 1/1:0,68:64:-197.28,-19.30,-0.07:99 +chr1 1726715 rs11260613 A G 12.97 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=55.98;MQ0=0;OQ=727.27;QD=23.46;SB=-220.64 GT:AD:DP:GL:GQ 1/1:0,31:24:-76.34,-7.24,-0.02:72.14 +chr1 1728231 rs11585349 C T 444.74 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.78;MQ0=0;OQ=853.44;QD=13.13;SB=-325.29 GT:AD:DP:GL:GQ 0/1:37,28:63:-107.61,-18.98,-131.07:99 +chr1 1728793 . C A 11.24 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=87;Dels=0.01;HRun=20;HaplotypeScore=12.66;MQ=49.01;MQ0=7;QD=0.13;SB=83.42 GT:AD:DP:GL:GQ 0/1:67,19:60:-22.45,-18.07,-182.40:43.74 +chr1 1731385 rs12407008 A G 570.73 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=1462.68;QD=34.02;SB=-730.24 GT:AD:DP:GL:GQ 1/1:0,43:43:-149.87,-12.95,-0.02:99 +chr1 1733337 rs4648725 G C 64.92 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=54.96;MQ0=0;OQ=2515.07;QD=40.57;SB=-1047.66 GT:AD:DP:GL:GQ 1/1:0,62:59:-255.12,-17.78,-0.02:99 +chr1 1733967 rs6603795 T C 231.72 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.62;MQ0=0;OQ=1265.69;QD=28.77;SB=-184.41 GT:AD:DP:GL:GQ 1/1:0,44:42:-130.20,-12.68,-0.05:99 +chr1 1736016 rs12408690 A G 634.80 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1961.02;QD=35.02;SB=-638.31 GT:AD:DP:GL:GQ 1/1:0,56:56:-199.70,-16.87,-0.02:99 +chr1 1736120 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=20;HaplotypeScore=11.72;MQ=42.99;MQ0=2;OQ=648.30;QD=8.64;SB=8.14 GT:AD:DP:GL:GQ 0/1:44,31:58:-85.60,-17.49,-115.79:99 +chr1 1737932 . A T 32.39 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=5;HaplotypeScore=48.11;MQ=56.04;MQ0=0;QD=0.40;SB=116.40 GT:AD:DP:GL:GQ 0/1:65,15:66:-26.41,-19.89,-217.38:65.23 +chr1 1737943 . C T 27.67 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=20;HaplotypeScore=10.01;MQ=51.69;MQ0=1;QD=0.36;SB=101.33 GT:AD:DP:GL:GQ 0/1:61,16:52:-21.72,-15.67,-162.40:60.50 +chr1 1739272 . T G 33.88 PASS AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=58.21;MQ0=0;OQ=1071.30;QD=13.56;SB=-555.72 GT:AD:DP:GL:GQ 0/1:40,39:77:-133.61,-23.19,-145.75:99 +chr1 1741546 rs12140085 T C 459.98 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.38;MQ0=0;OQ=960.01;QD=14.12;SB=-398.30 GT:AD:DP:GL:GQ 0/1:32,36:66:-119.17,-19.88,-129.12:99 +chr1 1741636 rs11260615 A G 471.98 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.06;MQ0=1;OQ=1308.14;QD=29.07;SB=-638.27 GT:AD:DP:GL:GQ 1/1:1,44:42:-134.44,-12.67,-0.04:99 +chr1 1742815 rs4648726 C T 274.47 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=3089.56;QD=40.12;SB=-1427.40 GT:AD:DP:GL:GQ 1/1:0,77:77:-312.56,-23.19,-0.02:99 +chr1 1743224 rs7542340 T C 171.92 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=3;HaplotypeScore=-0.06;MQ=58.50;MQ0=0;OQ=2101.69;QD=35.62;SB=-1028.76 GT:AD:DP:GL:GQ 1/1:0,59:59:-213.77,-17.77,-0.02:99 +chr1 1744541 . G A 32.03 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=61;Dels=0.03;HRun=20;HaplotypeScore=23.82;MQ=51.57;MQ0=1;QD=0.53;SB=71.26 GT:AD:DP:GL:GQ 0/1:45,13:49:-20.64,-14.16,-151.56:64.87 +chr1 1748886 rs9786963 T C 652.35 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1920.23;QD=32.55;SB=-686.89 GT:AD:DP:GL:GQ 1/1:0,59:59:-195.65,-17.79,-0.04:99 +chr1 1748914 rs10907187 G A 586.04 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2397.92;QD=36.89;SB=-817.09 GT:AD:DP:GL:GQ 1/1:0,65:65:-243.43,-19.61,-0.05:99 +chr1 1750849 rs12568603 A C 141.73 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=1462.88;QD=34.02;SB=-618.64 GT:AD:DP:GL:GQ 1/1:0,43:43:-149.89,-12.95,-0.02:99 +chr1 1751196 rs1999704 A C 13.93 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=2.14;MQ=56.69;MQ0=1;OQ=2047.05;QD=32.49;SB=-593.04 GT:AD:DP:GL:GQ 1/1:1,62:59:-208.31,-17.77,-0.02:99 +chr1 1751865 rs11260616 A T 0.13 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=6;HaplotypeScore=1.13;MQ=59.11;MQ0=0;OQ=1852.12;QD=35.62;SB=-771.53 GT:AD:DP:GL:GQ 1/1:0,52:52:-188.82,-15.67,-0.02:99 +chr1 1751874 rs7553640 T C 711.95 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1893.02;QD=35.06;SB=-889.04 GT:AD:DP:GL:GQ 1/1:0,54:53:-192.90,-15.97,-0.02:99 +chr1 1752558 rs6603796 T C 171.81 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.20;MQ0=0;OQ=1646.02;QD=32.27;SB=-583.16 GT:AD:DP:GL:GQ 1/1:0,51:48:-168.22,-14.47,-0.03:99 +chr1 1755443 rs6603797 T C 720.20 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=2694.93;QD=35.46;SB=-935.73 GT:AD:DP:GL:GQ 1/1:0,76:74:-273.10,-22.29,-0.02:99 +chr1 1755954 rs6663586 A C 220.63 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.45;MQ0=0;OQ=1370.69;QD=32.64;SB=-604.02 GT:AD:DP:GL:GQ 1/1:0,42:40:-140.67,-12.05,-0.02:99 +chr1 1756219 rs6603798 A G 29.08 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=55.51;MQ0=2;OQ=1475.64;QD=28.38;SB=-669.92 GT:AD:DP:GL:GQ 1/1:2,50:47:-151.19,-14.18,-0.04:99 +chr1 1757221 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=20;HaplotypeScore=10.23;MQ=53.30;MQ0=1;OQ=618.88;QD=9.67;SB=31.58 GT:AD:DP:GL:GQ 0/1:38,25:58:-82.66,-17.49,-122.37:99 +chr1 1758520 rs10752417 C G 0.14 PASS AC=2;AF=1.00;AN=2;DB;DP=106;Dels=0.00;HRun=1;HaplotypeScore=5.58;MQ=57.83;MQ0=0;OQ=4550.45;QD=42.93;SB=-2086.29 GT:AD:DP:GL:GQ 1/1:0,106:103:-454.04,-31.03,-0.03:99 +chr1 1758754 rs10907188 C T 32.55 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=58.85;MQ0=1;OQ=2558.37;QD=38.18;SB=-882.18 GT:AD:DP:GL:GQ 1/1:1,66:64:-259.44,-19.28,-0.02:99 +chr1 1759918 rs6603799 T C 1.47 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=10.20;MQ=56.09;MQ0=0;OQ=1988.53;QD=33.14;SB=-981.94 GT:AD:DP:GL:GQ 1/1:1,59:56:-202.45,-16.87,-0.02:99 +chr1 1760648 rs6657357 C G 301.74 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.38;MQ0=0;OQ=2954.84;QD=38.37;SB=-1347.06 GT:AD:DP:GL:GQ 1/1:0,77:74:-299.12,-22.32,-0.05:99 +chr1 1760649 rs6665287 T A 112.70 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.39;MQ0=0;OQ=2934.49;QD=37.15;SB=-1492.41 GT:AD:DP:GL:GQ 1/1:0,79:78:-297.05,-23.49,-0.02:99 +chr1 1762348 rs6603800 T G 88.85 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=59.54;MQ0=0;OQ=1401.85;QD=28.04;SB=-481.90 GT:AD:DP:GL:GQ 1/1:0,50:43:-143.80,-12.96,-0.03:99 +chr1 1762595 rs10907189 T C 215.16 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.73;MQ0=1;OQ=2558.08;QD=35.53;SB=-1178.50 GT:AD:DP:GL:GQ 1/1:1,71:71:-259.41,-21.39,-0.02:99 +chr1 1763512 rs11260618 A G 251.61 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=34.24;MQ0=0;OQ=1296.92;QD=19.36;SB=-537.23 GT:AD:DP:GL:GQ 1/1:0,67:42:-133.32,-12.67,-0.05:99 +chr1 1763520 rs11260619 C G 204.70 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=32.31;MQ0=0;OQ=1789.21;QD=27.11;SB=-722.93 GT:AD:DP:GL:GQ 1/1:0,66:41:-182.52,-12.35,-0.01:99 +chr1 1763525 rs11260620 T C 490.04 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.33;MQ0=0;OQ=1197.40;QD=18.42;SB=-469.25 GT:AD:DP:GL:GQ 1/1:0,65:37:-123.35,-11.15,-0.02:99 +chr1 1763536 rs11260621 T C 53.91 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=32.77;MQ0=1;OQ=1342.11;QD=19.74;SB=-614.98 GT:AD:DP:GL:GQ 1/1:1,67:42:-137.83,-12.66,-0.03:99 +chr1 1763632 rs10907190 G A 500.76 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=2342.36;QD=38.40;SB=-955.26 GT:AD:DP:GL:GQ 1/1:0,61:60:-237.85,-18.08,-0.03:99 +chr1 1765035 rs11260622 A G 3.08 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=4.83;MQ=58.68;MQ0=1;OQ=1949.34;QD=28.25;SB=-876.43 GT:AD:DP:GL:GQ 1/1:0,68:61:-198.58,-18.40,-0.06:99 +chr1 1766129 rs4648727 C A 222.67 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.39;MQ0=0;OQ=2474.83;QD=35.87;SB=-1254.46 GT:AD:DP:GL:GQ 1/1:0,69:68:-251.09,-20.48,-0.02:99 +chr1 1768896 rs6692959 T C 606.28 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=2761.38;QD=31.74;SB=-1372.68 GT:AD:DP:GL:GQ 1/1:0,87:87:-279.80,-26.24,-0.08:99 +chr1 1769657 . A T 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=45;Dels=0.02;HRun=0;HaplotypeScore=8.89;MQ=56.00;MQ0=1;OQ=229.76;QD=5.11;SB=-125.76 GT:AD:DP:GL:GQ 0/1:24,18:27:-34.10,-7.84,-57.21:99 +chr1 1770738 rs6603801 T C 614.13 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1986.61;QD=34.85;SB=-910.02 GT:AD:DP:GL:GQ 1/1:0,57:57:-202.27,-17.17,-0.02:99 +chr1 1771205 rs6664578 G A 696.21 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=3186.74;QD=38.39;SB=-1518.58 GT:AD:DP:GL:GQ 1/1:0,83:81:-322.28,-24.40,-0.02:99 +chr1 1772480 rs12066667 C T 200.36 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.77;MQ0=0;OQ=1986.28;QD=37.48;SB=-1001.85 GT:AD:DP:GL:GQ 1/1:0,53:51:-202.23,-15.37,-0.02:99 +chr1 1773061 rs12402876 G A 282.08 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.70;MQ0=0;OQ=2522.68;QD=37.10;SB=-929.21 GT:AD:DP:GL:GQ 1/1:0,68:65:-255.88,-19.59,-0.03:99 +chr1 1773444 rs7526236 G A 531.06 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=1822.31;QD=37.96;SB=-748.50 GT:AD:DP:GL:GQ 1/1:0,48:47:-185.83,-14.16,-0.02:99 +chr1 1782409 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=18;HaplotypeScore=10.25;MQ=50.63;MQ0=2;OQ=451.92;QD=7.66;SB=-97.66 GT:AD:DP:GL:GQ 0/1:39,20:52:-64.14,-15.67,-118.24:99 +chr1 1782428 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=65;Dels=0.02;HRun=18;HaplotypeScore=18.34;MQ=52.25;MQ0=1;OQ=88.42;QD=1.36;SB=56.19 GT:AD:DP:GL:GQ 0/1:56,8:49:-26.89,-14.77,-145.13:99 +chr1 1782863 rs1889678 A G 536.70 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.83;MQ0=0;OQ=1352.43;QD=28.18;SB=-598.57 GT:AD:DP:GL:GQ 1/1:0,48:43:-138.86,-12.97,-0.04:99 +chr1 1782931 rs12076620 A G 575.25 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1635.06;QD=34.79;SB=-754.18 GT:AD:DP:GL:GQ 1/1:0,47:46:-167.10,-13.85,-0.01:99 +chr1 1782971 rs10907192 A G 594.85 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1599.36;QD=34.03;SB=-532.43 GT:AD:DP:GL:GQ 1/1:0,47:46:-163.54,-13.86,-0.02:99 +chr1 1783646 rs7511905 A C 266.52 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1582.35;QD=31.65;SB=-751.07 GT:AD:DP:GL:GQ 1/1:0,50:47:-161.84,-14.16,-0.02:99 +chr1 1785347 rs6660452 A C 506.81 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.51;MQ0=0;OQ=1748.60;QD=30.15;SB=-666.84 GT:AD:DP:GL:GQ 1/1:0,58:55:-178.49,-16.58,-0.04:99 +chr1 1785613 . C A 22.53 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=20;HaplotypeScore=2.54;MQ=46.56;MQ0=0;QD=0.48;SB=89.31 GT:AD:DP:GL:GQ 0/1:40,7:41:-17.88,-12.35,-133.39:55.34 +chr1 1785636 rs6697311 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.01;HRun=20;HaplotypeScore=31.36;MQ=43.36;MQ0=1;OQ=989.12;QD=9.79;SB=-44.45 GT:AD:DP:GL:GQ 0/1:50,49:75:-124.51,-22.31,-136.94:99 +chr1 1785639 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=98;Dels=0.01;HRun=4;HaplotypeScore=41.45;MQ=42.87;MQ0=1;OQ=381.85;QD=3.90;SB=86.26 GT:AD:DP:GL:GQ 0/1:59,38:65:-60.76,-19.29,-163.75:99 +chr1 1785649 rs12036384 C T 5.26 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=10.21;MQ=50.24;MQ0=1;OQ=2105.43;QD=30.96;SB=-932.26 GT:AD:DP:GL:GQ 1/1:2,63:54:-214.14,-16.27,-0.02:99 +chr1 1786577 rs12134553 A C 2.61 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=7.76;MQ=57.97;MQ0=1;OQ=1915.32;QD=26.98;SB=-959.05 GT:AD:DP:GL:GQ 1/1:3,68:63:-201.59,-18.99,-6.48:99 +chr1 1787250 rs6670246 T A 192 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=2864.46;QD=33.70;SB=-1257.90 GT:AD:DP:GL:GQ 1/1:2,83:84:-296.95,-25.31,-6.91:99 +chr1 1789560 rs4648591 T C 58.31 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=47.68;MQ0=0;OQ=1563.80;QD=30.66;SB=-605.93 GT:AD:DP:GL:GQ 1/1:0,51:49:-160.01,-14.78,-0.04:99 +chr1 1789813 rs7516995 T C 114.34 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.57;MQ0=0;OQ=1801.38;QD=30.53;SB=-555.03 GT:AD:DP:GL:GQ 1/1:0,59:55:-183.76,-16.58,-0.04:99 +chr1 1790511 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=20;HaplotypeScore=40.13;MQ=50.15;MQ0=2;OQ=70.47;QD=0.70;SB=149.46 GT:AD:DP:GL:GQ 0/1:69,28:73:-32.03,-21.69,-222.30:99 +chr1 1790894 rs4648592 G A 598.36 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.49;MQ0=0;OQ=2599.64;QD=38.23;SB=-928.70 GT:AD:DP:GL:GQ 1/1:0,68:65:-263.57,-19.58,-0.02:99 +chr1 1792032 rs6666068 A G 457.40 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2160.60;QD=28.43;SB=-673.85 GT:AD:DP:GL:GQ 1/1:0,76:67:-219.70,-20.20,-0.05:99 +chr1 1794162 rs3855951 C T 52.04 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=2.26;MQ=59.71;MQ0=0;OQ=3179.43;QD=39.74;SB=-1555.57 GT:AD:DP:GL:GQ 1/1:0,80:79:-321.55,-23.80,-0.02:99 +chr1 1795251 rs10907193 G A 266.85 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=60.00;MQ0=0;OQ=1860.92;QD=32.65;SB=-731.44 GT:AD:DP:GL:GQ 1/1:0,56:50:-189.71,-15.08,-0.03:99 +chr1 1796166 rs10399762 A G 54.56 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=58.73;MQ0=0;OQ=1409.98;QD=25.64;SB=-484.50 GT:AD:DP:GL:GQ 1/1:0,55:46:-144.64,-13.88,-0.05:99 +chr1 1798609 . A T 162.96 SnpCluster AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=74.10;MQ=46.50;MQ0=2;QD=4.29;SB=-81.05 GT:AD:DP:GL:GQ 0/1:27,11:32:-29.22,-9.64,-87.24:99 +chr1 1798611 . A T 632.57 SnpCluster AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=43.92;MQ=46.08;MQ0=2;QD=17.10;SB=-306.76 GT:AD:DP:GL:GQ 0/1:10,25:30:-75.58,-9.04,-33.08:99 +chr1 1798613 rs57488553 A T 825.28 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=35.29;MQ=45.64;MQ0=2;QD=22.92;SB=-393.55 GT:AD:DP:GL:GQ 0/1:7,29:31:-95.15,-9.34,-18.41:90.67 +chr1 1798615 rs58263709 A T 846.29 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=33.82;MQ=45.64;MQ0=2;QD=23.51;SB=-402.56 GT:AD:DP:GL:GQ 0/1:6,30:30:-96.95,-9.04,-14.67:56.29 +chr1 1799369 rs11260624 C T 198.24 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.40;MQ0=0;OQ=2735.01;QD=39.07;SB=-1363.94 GT:AD:DP:GL:GQ 1/1:0,69:70:-279.86,-23.72,-2.77:99 +chr1 1799950 rs7525092 C T 160.98 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=59.72;MQ0=0;OQ=3051.79;QD=36.77;SB=-1420.35 GT:AD:DP:GL:GQ 1/1:0,83:79:-308.79,-23.80,-0.03:99 +chr1 1800981 rs12133865 G A 87.68 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=56.12;MQ0=0;OQ=1844.69;QD=38.43;SB=-730.97 GT:AD:DP:GL:GQ 1/1:0,48:48:-188.07,-14.47,-0.02:99 +chr1 1802311 . A G 78.46 Indel AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=3;HaplotypeScore=2.28;MQ=57.45;MQ0=0;QD=1.09;SB=-6.51 GT:AD:DP:GL:GQ 0/1:62,10:70:-32.22,-21.09,-246.49:99 +chr1 1802688 rs6670776 G A 560.73 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=2301.44;QD=40.38;SB=-996.99 GT:AD:DP:GL:GQ 1/1:0,57:57:-233.74,-17.17,-0.01:99 +chr1 1805482 rs12138152 G A 76.26 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.49;MQ0=0;OQ=2306.96;QD=39.10;SB=-1138.66 GT:AD:DP:GL:GQ 1/1:0,59:59:-234.30,-17.78,-0.02:99 +chr1 1807030 rs10796396 G A 291.66 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.36;MQ0=0;OQ=1090.79;QD=38.96;SB=-403.67 GT:AD:DP:GL:GQ 1/1:0,28:28:-112.67,-8.43,-0.01:84.28 +chr1 1809238 rs6603804 T C 659.20 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2030.11;QD=33.84;SB=-689.61 GT:AD:DP:GL:GQ 1/1:0,60:59:-206.62,-17.78,-0.03:99 +chr1 1809966 rs28608797 A C 520.78 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.00;MQ0=0;OQ=1235.99;QD=32.53;SB=-595.06 GT:AD:DP:GL:GQ 1/1:1,37:36:-127.20,-10.84,-0.01:99 +chr1 1813782 rs6688000 A G 233.16 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=58.61;MQ0=0;OQ=1439.33;QD=30.62;SB=-681.87 GT:AD:DP:GL:GQ 1/1:0,46:46:-147.56,-13.87,-0.04:99 +chr1 1818624 rs12045595 G A 59.58 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.53;MQ0=0;OQ=1836.38;QD=37.48;SB=-594.97 GT:AD:DP:GL:GQ 1/1:0,49:48:-187.24,-14.46,-0.02:99 +chr1 1821118 rs6603808 A G 79.87 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=60.00;MQ0=0;OQ=1052.30;QD=28.44;SB=-413.55 GT:AD:DP:GL:GQ 1/1:0,37:31:-108.83,-9.34,-0.01:93.27 +chr1 1822217 rs941531 G A 113.99 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=58.68;MQ0=0;OQ=2643.63;QD=39.46;SB=-1073.33 GT:AD:DP:GL:GQ 1/1:0,67:66:-267.97,-19.88,-0.02:99 +chr1 1822410 . A G 49.96 LowQual AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;QD=0.89;SB=-35.78 GT:AD:DP:GL:GQ 0/1:49,7:55:-24.85,-16.57,-195.12:82.80 +chr1 1822442 rs4996032 G A 113.94 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.02;HRun=2;HaplotypeScore=1.09;MQ=59.55;MQ0=0;OQ=884.12;QD=14.03;SB=-419.83 GT:AD:DP:GL:GQ 0/1:35,27:62:-110.37,-18.67,-127.42:99 +chr1 1822448 rs4996031 A G 133.35 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.02;MQ=59.08;MQ0=1;OQ=897.87;QD=14.03;SB=-423.51 GT:AD:DP:GL:GQ 0/1:31,33:61:-111.45,-18.38,-115.75:99 +chr1 1823355 rs10454464 G A 100.58 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=57.95;MQ0=0;OQ=1113.42;QD=34.79;SB=-534.62 GT:AD:DP:GL:GQ 1/1:0,31:31:-117.34,-11.71,-2.42:92.95 +chr1 1824608 rs4648731 A G 30.88 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=54.33;MQ0=0;OQ=891.08;QD=28.74;SB=-233.75 GT:AD:DP:GL:GQ 1/1:0,31:26:-92.71,-7.84,-0.01:78.21 +chr1 1824902 rs11260625 G A 47.11 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=46.58;MQ0=0;OQ=814.82;QD=27.16;SB=-295.36 GT:AD:DP:GL:GQ 1/1:0,25:22:-85.08,-6.64,-0.02:66.19 +chr1 1824916 rs11260626 C T 92.97 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=48.72;MQ0=0;OQ=1289.62;QD=36.85;SB=-588.96 GT:AD:DP:GL:GQ 1/1:0,35:34:-132.56,-10.25,-0.01:99 +chr1 1825136 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=16;HaplotypeScore=8.80;MQ=56.14;MQ0=0;OQ=163.77;QD=3.72;SB=41.15 GT:AD:DP:GL:GQ 0/1:27,17:32:-29.31,-9.65,-83.86:99 +chr1 1826546 rs2748989 C G 308.42 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.60;MQ0=0;OQ=2438.44;QD=41.33;SB=-736.72 GT:AD:DP:GL:GQ 1/1:0,59:58:-247.45,-17.48,-0.02:99 +chr1 1827738 rs4648732 C T 470.86 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=1741.59;QD=38.70;SB=-666.40 GT:AD:DP:GL:GQ 1/1:0,45:44:-177.75,-13.25,-0.01:99 +chr1 1828376 rs2377037 C A 189.26 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=1605.71;QD=33.45;SB=-826.68 GT:AD:DP:GL:GQ 1/1:1,47:46:-164.17,-13.86,-0.02:99 +chr1 1828498 rs28672079 A G 314.26 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=1270.30;QD=29.54;SB=-594.88 GT:AD:DP:GL:GQ 1/1:0,43:41:-130.66,-12.37,-0.05:99 +chr1 1829551 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=17.55;MQ=56.35;MQ0=0;OQ=57.59;QD=1.48;SB=26.11 GT:AD:DP:GL:GQ 0/1:19,19:17:-14.19,-5.14,-50.87:90.43 +chr1 1829898 rs2474461 T C 40.50 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=579.60;QD=34.09;SB=-105.03 GT:AD:DP:GL:GQ 1/1:0,17:17:-61.55,-5.12,-0.01:51.14 +chr1 1830536 rs28384316 G T 112.96 PASS AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=125.10;QD=25.02;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:5:-16.07,-1.51,-0.01:15.03 +chr1 1832651 . A G 0.32 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=742.60;QD=18.11;SB=-247.32 GT:AD:DP:GL:GQ 0/1:17,24:40:-89.59,-12.05,-62.50:99 +chr1 1834219 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=20;HaplotypeScore=9.36;MQ=53.72;MQ0=0;OQ=93.63;QD=2.46;SB=11.06 GT:AD:DP:GL:GQ 0/1:25,13:25:-20.18,-7.53,-63.71:99 +chr1 1834282 . T C 14.27 PASS AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=417.56;QD=26.10;SB=-221.65 GT:AD:DP:GL:GQ 1/1:0,16:14:-45.35,-4.22,-0.01:42.10 +chr1 1834553 rs28842562 C T 275.34 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.51;MQ0=1;OQ=892.93;QD=34.34;SB=-192.75 GT:AD:DP:GL:GQ 1/1:0,26:23:-92.88,-6.93,-0.01:69.22 +chr1 1836321 rs41306992 C T 57.34 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.24;MQ0=0;OQ=2100.54;QD=38.19;SB=-756.01 GT:AD:DP:GL:GQ 1/1:0,55:53:-213.65,-15.97,-0.01:99 +chr1 1836442 rs2748987 A G 431.11 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=1604.85;QD=34.15;SB=-631.28 GT:AD:DP:GL:GQ 1/1:0,47:47:-164.09,-14.16,-0.02:99 +chr1 1838594 rs941532 A G 20.25 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=58.71;MQ0=0;OQ=477.15;QD=26.51;SB=-129.69 GT:AD:DP:GL:GQ 1/1:0,18:17:-51.32,-5.13,-0.02:51.08 +chr1 1839996 rs2295364 C T 1.07 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.59;MQ0=0;OQ=1245.14;QD=37.73;SB=-117.65 GT:AD:DP:GL:GQ 1/1:0,33:32:-128.11,-9.64,-0.01:96.31 +chr1 1841796 rs2474458 C A 22.03 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=3.16;MQ=58.78;MQ0=0;OQ=1243.51;QD=32.72;SB=-630.04 GT:AD:DP:GL:GQ 1/1:0,38:36:-127.95,-10.85,-0.01:99 +chr1 1842344 rs28508199 A G 34.17 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=58.67;MQ0=0;OQ=1404.62;QD=28.67;SB=-672.87 GT:AD:DP:GL:GQ 1/1:0,49:45:-144.09,-13.57,-0.04:99 +chr1 1843148 rs1884454 G T 340.59 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=56.74;MQ0=0;OQ=831.99;QD=14.34;SB=-322.02 GT:AD:DP:GL:GQ 0/1:28,30:55:-103.05,-16.57,-95.32:99 +chr1 1844181 rs2250833 A G 20.17 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=995.90;QD=27.66;SB=-313.46 GT:AD:DP:GL:GQ 1/1:0,36:31:-103.20,-9.35,-0.02:93.22 +chr1 1845310 rs28423370 A G 170.66 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=608.06;QD=32.00;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,19:19:-64.40,-5.72,-0.01:57.14 +chr1 1845407 . C A 46.94 LowQual AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=55.21;MQ0=0;QD=9.39;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,3:5:-9.49,-1.51,-6.80:52.97 +chr1 1845958 rs752965 C T 17.19 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.17;MQ0=0;OQ=985.76;QD=35.21;SB=-88.34 GT:AD:DP:GL:GQ 1/1:0,28:26:-102.17,-7.83,-0.01:78.25 +chr1 1846560 rs2092922 C T 67.91 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.95;MQ0=0;OQ=1561.86;QD=36.32;SB=-529.71 GT:AD:DP:GL:GQ 1/1:0,43:41:-159.79,-12.36,-0.02:99 +chr1 1848991 rs4648734 C T 0.80 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=7.13;MQ=58.00;MQ0=0;OQ=1973.99;QD=36.56;SB=-772.04 GT:AD:DP:GL:GQ 1/1:0,53:53:-203.45,-18.19,-2.47:99 +chr1 1849418 rs28670388 T C 0.23 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=3;HaplotypeScore=7.22;MQ=55.28;MQ0=2;OQ=1025.15;QD=29.29;SB=-496.47 GT:AD:DP:GL:GQ 1/1:3,32:30:-106.11,-9.04,-0.01:90.24 +chr1 1850605 rs28685049 C T 18.19 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=778.38;QD=38.92;SB=-47.56 GT:AD:DP:GL:GQ 1/1:0,20:20:-81.43,-6.03,-0.01:60.20 +chr1 1850678 . T A 0.69 PASS AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=41.96;MQ0=0;OQ=61.03;QD=6.78;SB=5.04 GT:AD:DP:GL:GQ 0/1:6,3:9:-12.10,-2.71,-21.43:93.87 +chr1 1850683 . G A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=10.93;MQ=35.14;MQ0=0;OQ=63.11;QD=9.02;SB=-3.99 GT:AD:DP:GL:GQ 0/1:4,3:6:-11.40,-1.81,-10.53:87.27 +chr1 1851012 rs55825112 G A 257.30 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.15;MQ0=0;OQ=1284.14;QD=38.91;SB=-355.97 GT:AD:DP:GL:GQ 1/1:0,33:33:-132.01,-9.94,-0.01:99 +chr1 1852535 rs2474449 C T 115.82 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=42.11;MQ0=1;OQ=2050.54;QD=37.28;SB=-856.64 GT:AD:DP:GL:GQ 1/1:1,54:53:-211.75,-15.96,-3.11:99 +chr1 1852731 . T A 22.37 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=63;Dels=0.05;HRun=20;HaplotypeScore=13.90;MQ=48.22;MQ0=0;QD=0.36;SB=16.21 GT:AD:DP:GL:GQ 0/1:42,18:40:-16.96,-11.45,-121.97:55.18 +chr1 1852818 rs4648595 A G 3.40 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.78;MQ=50.34;MQ0=1;OQ=917.27;QD=25.48;SB=-127.78 GT:AD:DP:GL:GQ 1/1:1,35:28:-95.33,-8.44,-0.02:84.22 +chr1 1853042 . C A 10.89 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=20;HaplotypeScore=9.56;MQ=49.02;MQ0=4;QD=0.19;SB=86.27 GT:AD:DP:GL:GQ 0/1:51,7:42:-16.99,-12.66,-132.54:43.35 +chr1 1853068 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=2;HaplotypeScore=13.43;MQ=48.98;MQ0=4;OQ=94.12;QD=1.00;SB=104.36 GT:AD:DP:GL:GQ 0/1:70,24:65:-32.29,-19.60,-195.03:99 +chr1 1853265 rs60147457 T C 26.01 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=56.17;MQ0=0;OQ=1299.21;QD=28.24;SB=-640.40 GT:AD:DP:GL:GQ 1/1:1,45:44:-136.91,-13.28,-3.40:98.74 +chr1 1855559 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=1.77;MQ=58.15;MQ0=0;OQ=143.93;QD=1.87;SB=17.18 GT:AD:DP:GL:GQ 0/1:67,10:76:-40.57,-22.90,-237.26:99 +chr1 1855612 rs2748968 C T 224.03 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=53.49;MQ0=2;OQ=1207.94;QD=15.10;SB=-597.02 GT:AD:DP:GL:GQ 0/1:40,40:73:-146.08,-22.00,-120.30:99 +chr1 1855646 . T C 0.93 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=9.48;MQ=53.45;MQ0=2;OQ=1049.44;QD=14.78;SB=-537.98 GT:AD:DP:GL:GQ 0/1:31,40:66:-128.11,-19.89,-114.90:99 +chr1 1855674 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=15.63;MQ=50.86;MQ0=1;OQ=126.19;QD=2.25;SB=-24.71 GT:AD:DP:GL:GQ 0/1:49,7:53:-31.88,-15.98,-189.82:99 +chr1 1855675 . A G 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=14.63;MQ=50.86;MQ0=1;OQ=886.43;QD=15.83;SB=-281.60 GT:AD:DP:GL:GQ 0/1:21,35:52:-107.60,-15.67,-76.26:99 +chr1 1856033 rs34454803 C G 2.87 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=4.56;MQ=48.03;MQ0=9;OQ=1928.44;QD=26.78;SB=-825.04 GT:AD:DP:GL:GQ 1/1:9,62:49:-203.74,-17.80,-7.31:99 +chr1 1856195 rs61775027 C T 136.98 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=55.46;MQ0=1;OQ=2158.57;QD=29.98;SB=-1089.45 GT:AD:DP:GL:GQ 1/1:8,64:59:-222.77,-17.79,-3.33:99 +chr1 1856465 rs34793596 C G 37.34 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.87;MQ=54.29;MQ0=1;OQ=3153.75;QD=39.92;SB=-1439.03 GT:AD:DP:GL:GQ 1/1:3,76:75:-323.13,-22.60,-4.17:99 +chr1 1856473 rs35531706 C G 44.13 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=2.23;MQ=55.29;MQ0=1;OQ=2974.48;QD=40.20;SB=-1193.83 GT:AD:DP:GL:GQ 1/1:1,73:71:-301.06,-21.40,-0.03:99 +chr1 1858345 rs28658236 G A 98.82 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=1111.27;QD=16.34;SB=-403.37 GT:AD:DP:GL:GQ 0/1:35,33:68:-134.91,-20.49,-114.02:99 +chr1 1859106 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=2;HaplotypeScore=6.59;MQ=57.30;MQ0=0;OQ=100.83;QD=1.80;SB=56.18 GT:AD:DP:GL:GQ 0/1:31,25:39:-25.12,-11.75,-106.73:99 +chr1 1859766 rs28592294 C T 2.76 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=5.60;MQ=57.03;MQ0=0;OQ=2783.58;QD=37.62;SB=-907.72 GT:AD:DP:GL:GQ 1/1:1,72:73:-285.26,-22.00,-3.32:99 +chr1 1860070 rs2803323 G A 91.89 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=58.89;MQ0=0;OQ=1564.69;QD=37.25;SB=-659.28 GT:AD:DP:GL:GQ 1/1:0,42:41:-160.07,-12.36,-0.02:99 +chr1 1861277 rs2803324 T C 62.39 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=848.26;QD=30.30;SB=-320.13 GT:AD:DP:GL:GQ 1/1:0,28:28:-88.44,-8.45,-0.03:84.18 +chr1 1863485 rs12758705 G A 595.32 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2263.21;QD=38.36;SB=-926.70 GT:AD:DP:GL:GQ 1/1:0,59:57:-229.92,-17.17,-0.01:99 +chr1 1864441 rs2803329 A G 280.82 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1008.85;QD=27.27;SB=-491.17 GT:AD:DP:GL:GQ 1/1:0,37:33:-104.50,-9.95,-0.03:99 +chr1 1864697 rs2803330 A G 60.11 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=756.37;QD=30.25;SB=-313.68 GT:AD:DP:GL:GQ 1/1:0,25:22:-79.23,-6.63,-0.01:66.20 +chr1 1865005 rs2803331 C T 233.79 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=58.84;MQ0=0;OQ=1354.55;QD=33.86;SB=-668.39 GT:AD:DP:GL:GQ 1/1:0,37:37:-139.06,-11.16,-0.02:99 +chr1 1865127 rs2262190 A G 525.82 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=948.06;QD=30.58;SB=-404.33 GT:AD:DP:GL:GQ 1/1:0,31:30:-98.41,-9.05,-0.02:90.22 +chr1 1867098 rs2748978 T G 544.45 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.39;MQ0=0;OQ=1416.47;QD=34.55;SB=-657.23 GT:AD:DP:GL:GQ 1/1:0,41:41:-145.24,-12.35,-0.01:99 +chr1 1867212 rs2803339 T C 83.30 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=54.90;MQ0=0;OQ=1104.15;QD=27.60;SB=-492.17 GT:AD:DP:GL:GQ 1/1:1,39:37:-114.04,-11.17,-0.04:99 +chr1 1868944 rs2490543 C T 282.58 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=58.05;MQ0=0;OQ=849.11;QD=14.15;SB=-315.86 GT:AD:DP:GL:GQ 0/1:33,27:55:-104.77,-16.57,-95.97:99 +chr1 1868947 rs28573337 G A 161.30 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=57.95;MQ0=0;OQ=983.65;QD=17.26;SB=-292.79 GT:AD:DP:GL:GQ 0/1:26,31:55:-118.23,-16.58,-80.47:99 +chr1 1869420 rs28498068 T G 172.46 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=56.75;MQ0=0;OQ=395.95;QD=11.31;SB=-182.88 GT:AD:DP:GL:GQ 0/1:18,17:34:-53.12,-10.25,-61.66:99 +chr1 1869908 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=14;HaplotypeScore=14.65;MQ=46.99;MQ0=0;OQ=127.58;QD=2.90;SB=11.06 GT:AD:DP:GL:GQ 0/1:29,15:29:-24.78,-8.74,-71.11:99 +chr1 1870211 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=105;Dels=0.02;HRun=2;HaplotypeScore=156.21;MQ=37.45;MQ0=0;OQ=89.02;QD=0.85;SB=-10.74 GT:AD:DP:GL:GQ 0/1:91,12:93:-39.61,-27.42,-314.70:99 +chr1 1870216 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.13;HRun=3;HaplotypeScore=129.57;MQ=35.88;MQ0=0;OQ=216.82;QD=2.28;SB=-71.49 GT:AD:DP:GL:GQ 0/1:69,14:77:-47.26,-22.30,-241.64:99 +chr1 1870237 . C T 350.17 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=136.82;MQ=33.84;MQ0=0;QD=4.38;SB=-96.57 GT:AD:DP:GL:GQ 0/1:64,16:68:-58.79,-20.48,-197.51:99 +chr1 1870241 . T C 795.72 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=2;HaplotypeScore=105.65;MQ=33.28;MQ0=0;QD=10.33;SB=-171.98 GT:AD:DP:GL:GQ 0/1:49,28:68:-103.35,-20.49,-158.12:99 +chr1 1870246 . T C 783.37 SnpCluster AC=1;AF=0.50;AN=2;DP=75;Dels=0.01;HRun=3;HaplotypeScore=106.17;MQ=32.28;MQ0=0;QD=10.44;SB=-190.65 GT:AD:DP:GL:GQ 0/1:44,29:65:-101.22,-19.60,-139.10:99 +chr1 1870249 rs28490251 C T 536.49 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=65.25;MQ=33.25;MQ0=0;QD=8.01;SB=-19.48 GT:AD:DP:GL:GQ 0/1:45,22:60:-75.01,-18.07,-158.51:99 +chr1 1870263 . T C 67.37 SnpCluster AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=2;HaplotypeScore=102.33;MQ=35.77;MQ0=0;QD=1.07;SB=-0.98 GT:AD:DP:GL:GQ 0/1:55,8:53:-25.99,-15.97,-184.95:99 +chr1 1870272 . C T 96.33 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=2;HaplotypeScore=53.42;MQ=40.73;MQ0=0;QD=1.55;SB=5.03 GT:AD:DP:GL:GQ 0/1:52,10:55:-29.48,-16.57,-180.28:99 +chr1 1870273 . T C 72.37 SnpCluster AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=2;HaplotypeScore=53.42;MQ=40.73;MQ0=0;QD=1.17;SB=-0.98 GT:AD:DP:GL:GQ 0/1:55,7:53:-26.49,-15.97,-188.35:99 +chr1 1870281 . C T 187.69 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=96.79;MQ=44.56;MQ0=0;QD=3.24;SB=5.04 GT:AD:DP:GL:GQ 0/1:46,12:51:-37.41,-15.36,-160.10:99 +chr1 1870294 . T C 11.65 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=47.97;MQ0=0;QD=0.19;SB=8.05 GT:AD:DP:GL:GQ 0/1:55,6:59:-22.20,-17.78,-213.89:44.18 +chr1 1870405 . C A 16.24 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=38.44;MQ0=0;OQ=457.23;QD=8.97;SB=-4.29 GT:AD:DP:GL:GQ 0/1:33,18:50:-64.07,-15.06,-117.59:99 +chr1 1870410 . T C 0.86 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=38.95;MQ0=0;OQ=422.51;QD=8.80;SB=-31.25 GT:AD:DP:GL:GQ 0/1:31,17:47:-59.69,-14.16,-126.57:99 +chr1 1870428 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=20.35;MQ=41.74;MQ0=0;OQ=75.20;QD=2.15;SB=23.10 GT:AD:DP:GL:GQ 0/1:27,8:31:-20.14,-9.34,-96.20:99 +chr1 1870432 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=16.08;MQ=42.82;MQ0=0;OQ=52.58;QD=1.81;SB=29.11 GT:AD:DP:GL:GQ 0/1:24,5:28:-16.98,-8.43,-86.35:85.42 +chr1 1870446 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=25;Dels=0.04;HRun=2;HaplotypeScore=17.65;MQ=47.45;MQ0=0;OQ=105.58;QD=4.22;SB=-62.85 GT:AD:DP:GL:GQ 0/1:18,6:24:-20.77,-6.93,-68.32:99 +chr1 1871370 rs2490541 C A 191.01 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.38;MQ0=1;OQ=2594.06;QD=33.69;SB=-1155.38 GT:AD:DP:GL:GQ 1/1:0,76:73:-263.01,-21.99,-0.02:99 +chr1 1872147 rs2490540 A G 201.87 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.87;MQ0=0;OQ=2121.33;QD=34.22;SB=-1028.42 GT:AD:DP:GL:GQ 1/1:0,62:60:-215.74,-18.07,-0.02:99 +chr1 1872797 rs28754760 C T 596.04 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.63;MQ0=0;OQ=2762.82;QD=40.63;SB=-1367.30 GT:AD:DP:GL:GQ 1/1:0,68:68:-279.88,-20.48,-0.01:99 +chr1 1872809 rs2490564 A G 614.38 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=2664.00;QD=34.60;SB=-1257.66 GT:AD:DP:GL:GQ 1/1:0,77:76:-270.02,-22.89,-0.03:99 +chr1 1872820 rs2490563 C A 537.89 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.73;MQ0=0;OQ=2673.37;QD=36.62;SB=-1103.59 GT:AD:DP:GL:GQ 1/1:0,73:73:-270.94,-21.99,-0.02:99 +chr1 1872941 rs28505085 C T 182.42 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.70;MQ0=0;OQ=3049.13;QD=40.12;SB=-1406.71 GT:AD:DP:GL:GQ 1/1:0,76:76:-308.51,-22.89,-0.02:99 +chr1 1873219 rs2490562 A G 659.58 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=2029.90;QD=31.23;SB=-828.58 GT:AD:DP:GL:GQ 1/1:0,65:64:-206.63,-19.30,-0.05:99 +chr1 1874915 rs2474455 C T 626.28 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2935.86;QD=37.64;SB=-1349.01 GT:AD:DP:GL:GQ 1/1:0,78:74:-297.19,-22.29,-0.02:99 +chr1 1876080 rs4648738 C T 622.15 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.86;MQ0=0;OQ=2172.76;QD=36.21;SB=-969.30 GT:AD:DP:GL:GQ 1/1:0,60:56:-220.88,-16.87,-0.02:99 +chr1 1876082 rs2803287 T G 577.20 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.86;MQ0=0;OQ=1927.37;QD=32.12;SB=-839.09 GT:AD:DP:GL:GQ 1/1:0,60:56:-196.35,-16.87,-0.02:99 +chr1 1876206 . G A 152.24 Indel AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=32.79;MQ=48.52;MQ0=0;QD=4.91;SB=-65.27 GT:AD:DP:GL:GQ 0/1:20,7:27:-34.54,-16.03,-70.20:99 +chr1 1876245 rs2803286 T C 61.43 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=51.77;MQ0=0;OQ=999.35;QD=27.76;SB=-355.43 GT:AD:DP:GL:GQ 1/1:0,36:34:-103.57,-10.26,-0.05:99 +chr1 1876361 rs2748976 C A 113.55 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=45.22;MQ0=0;OQ=179.32;QD=6.90;SB=-106.45 GT:AD:DP:GL:GQ 0/1:18,8:25:-28.75,-7.53,-52.51:99 +chr1 1876371 . C A 48.69 LowQual AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=43.76;MQ0=0;QD=2.03;SB=-50.67 GT:AD:DP:GL:GQ 0/1:20,4:23:-15.08,-6.93,-60.82:81.52 +chr1 1876379 rs2748975 C A 111.71 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=47.73;MQ0=0;OQ=820.31;QD=34.18;SB=-360.86 GT:AD:DP:GL:GQ 1/1:0,24:23:-85.62,-6.93,-0.01:69.21 +chr1 1876719 rs3795290 C T 341.91 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.08;MQ0=0;OQ=1064.55;QD=38.02;SB=-422.06 GT:AD:DP:GL:GQ 1/1:0,28:28:-110.05,-8.44,-0.01:84.27 +chr1 1876879 rs28548017 A G 12.14 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=3.36;MQ=59.09;MQ0=0;OQ=1547.11;QD=33.63;SB=-748.91 GT:AD:DP:GL:GQ 1/1:0,45:45:-158.32,-13.56,-0.02:99 +chr1 1877105 rs28575980 G A 126.28 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=58.88;MQ0=0;OQ=2123.64;QD=39.33;SB=-940.36 GT:AD:DP:GL:GQ 1/1:0,54:54:-215.96,-16.27,-0.02:99 +chr1 1878053 rs3820011 C A 596.21 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1358.01;QD=33.95;SB=-534.23 GT:AD:DP:GL:GQ 1/1:0,40:39:-139.40,-11.75,-0.01:99 +chr1 1878190 rs28535696 C T 4.02 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=5.27;MQ=59.60;MQ0=0;OQ=1961.78;QD=33.82;SB=-651.37 GT:AD:DP:GL:GQ 1/1:0,56:52:-199.79,-15.68,-0.03:99 +chr1 1878229 rs2803285 A G 106.12 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=1952.57;QD=31.49;SB=-789.62 GT:AD:DP:GL:GQ 1/1:0,62:61:-198.90,-18.40,-0.05:99 +chr1 1878313 rs28549710 G A 560.24 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1883.77;QD=38.44;SB=-852.64 GT:AD:DP:GL:GQ 1/1:0,49:48:-191.98,-14.46,-0.02:99 +chr1 1878885 rs2748974 A G 5.77 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=58.15;MQ0=0;OQ=1276.90;QD=26.60;SB=-511.07 GT:AD:DP:GL:GQ 1/1:1,47:40:-131.31,-12.06,-0.03:99 +chr1 1878935 rs941533 C T 78.39 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.81;MQ0=0;OQ=1331.51;QD=34.14;SB=-642.34 GT:AD:DP:GL:GQ 1/1:0,39:35:-136.75,-10.55,-0.02:99 +chr1 1879652 rs2748973 A T 145.27 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1566.33;QD=34.81;SB=-658.70 GT:AD:DP:GL:GQ 1/1:0,44:44:-160.23,-13.26,-0.02:99 +chr1 1881908 rs2803292 G C 343.50 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1280.73;QD=16.85;SB=-445.74 GT:AD:DP:GL:GQ 0/1:41,35:73:-153.35,-22.00,-166.87:99 +chr1 1882185 rs2803291 T C 583.24 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1616.58;QD=28.87;SB=-749.95 GT:AD:DP:GL:GQ 1/1:0,56:52:-165.29,-15.68,-0.05:99 +chr1 1883521 rs9777849 T C 52.56 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=58.55;MQ0=0;OQ=2600.99;QD=33.78;SB=-793.15 GT:AD:DP:GL:GQ 1/1:0,77:75:-263.71,-22.59,-0.03:99 +chr1 1883775 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=18;HaplotypeScore=34.55;MQ=54.67;MQ0=0;OQ=115.46;QD=1.72;SB=60.06 GT:AD:DP:GL:GQ 0/1:50,15:53:-37.44,-22.61,-153.19:99 +chr1 1884144 rs4648739 T C 265.60 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=56.66;MQ0=0;OQ=1089.11;QD=12.10;SB=-234.30 GT:AD:DP:GL:GQ 0/1:41,48:84:-137.52,-25.33,-160.93:99 +chr1 1884622 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=7.50;MQ=53.07;MQ0=0;OQ=108.82;QD=2.02;SB=71.24 GT:AD:DP:GL:GQ 0/1:31,23:39:-25.91,-11.75,-106.64:99 +chr1 1884705 rs9697615 G A 136.68 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=58.71;MQ0=0;OQ=608.41;QD=12.94;SB=-170.23 GT:AD:DP:GL:GQ 0/1:24,22:44:-77.39,-13.26,-79.80:99 +chr1 1884754 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=43.50;MQ=52.44;MQ0=1;OQ=107.17;QD=1.76;SB=65.22 GT:AD:DP:GL:GQ 0/1:47,13:52:-29.66,-15.66,-164.16:99 +chr1 1884755 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=20;HaplotypeScore=45.92;MQ=52.41;MQ0=1;OQ=326.78;QD=5.11;SB=65.23 GT:AD:DP:GL:GQ 0/1:48,16:59:-53.73,-17.77,-157.95:99 +chr1 1884837 rs35817970 T C 556.60 Indel AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=55.91;MQ0=0;QD=10.91;SB=-219.26 GT:AD:DP:GL:GQ 0/1:29,21:48:-73.41,-14.46,-106.68:99 +chr1 1885037 rs7523728 C T 495.93 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.35;MQ0=0;OQ=754.75;QD=13.98;SB=-403.19 GT:AD:DP:GL:GQ 0/1:30,24:50:-93.83,-15.07,-88.75:99 +chr1 1885400 rs28561741 A G 4.33 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=59.52;MQ0=0;OQ=350.23;QD=7.30;SB=-137.55 GT:AD:DP:GL:GQ 0/1:31,17:46:-52.17,-13.87,-117.69:99 +chr1 1885962 rs13302978 G A 113.63 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.25;MQ=53.12;MQ0=0;OQ=689.28;QD=12.53;SB=-222.75 GT:AD:DP:GL:GQ 0/1:26,26:49:-87.00,-14.79,-79.84:99 +chr1 1886045 rs13303324 T C 252.63 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.41;MQ0=0;OQ=434.96;QD=11.15;SB=-181.59 GT:AD:DP:GL:GQ 0/1:18,21:37:-57.94,-11.16,-71.83:99 +chr1 1886083 rs13303202 C T 406.23 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=730.31;QD=16.98;SB=-346.33 GT:AD:DP:GL:GQ 0/1:21,22:43:-89.27,-12.95,-73.96:99 +chr1 1886300 rs16824585 G A 23.99 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=56.05;MQ0=0;OQ=933.53;QD=20.75;SB=-382.89 GT:AD:DP:GL:GQ 0/1:18,27:45:-110.19,-13.56,-62.00:99 +chr1 1886413 rs28625839 C T 106.43 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.20;MQ0=0;OQ=181.47;QD=6.98;SB=-69.07 GT:AD:DP:GL:GQ 0/1:17,9:21:-27.77,-6.34,-42.14:99 +chr1 1887329 rs28523363 A G 314.68 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=60.00;MQ0=0;OQ=843.98;QD=13.40;SB=-333.92 GT:AD:DP:GL:GQ 0/1:32,31:62:-106.36,-18.68,-128.89:99 +chr1 1887451 rs4648599 C T 245.43 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=58.01;MQ0=0;OQ=690.92;QD=14.70;SB=-275.28 GT:AD:DP:GL:GQ 0/1:24,23:44:-85.64,-13.26,-73.07:99 +chr1 1887613 rs4648600 C G 12.90 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=4.38;MQ=58.99;MQ0=0;OQ=734.25;QD=15.96;SB=-239.38 GT:AD:DP:GL:GQ 0/1:23,23:42:-89.37,-12.66,-89.33:99 +chr1 1887905 rs28712827 G A 21.15 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=6.31;MQ=57.89;MQ0=0;OQ=502.21;QD=13.22;SB=-250.22 GT:AD:DP:GL:GQ 0/1:20,17:35:-64.07,-10.57,-52.53:99 +chr1 1888209 rs28414188 C T 21.14 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=59.03;MQ0=0;OQ=593.85;QD=13.81;SB=-128.12 GT:AD:DP:GL:GQ 0/1:24,19:42:-75.32,-12.65,-82.23:99 +chr1 1888229 rs28629936 G A 50.03 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.95;MQ0=0;OQ=708.17;QD=17.70;SB=-204.21 GT:AD:DP:GL:GQ 0/1:19,21:39:-85.85,-11.75,-58.81:99 +chr1 1888545 rs17715950 T C 188.94 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=392.93;QD=12.68;SB=-143.27 GT:AD:DP:GL:GQ 0/1:16,15:29:-51.31,-8.74,-58.30:99 +chr1 1888637 rs34506333 G C 174.46 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.80;MQ=57.85;MQ0=0;OQ=1081.48;QD=18.97;SB=-492.64 GT:AD:DP:GL:GQ 0/1:26,30:56:-128.32,-16.89,-103.04:99 +chr1 1888639 rs35698161 C A 246.37 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.80;MQ=57.81;MQ0=0;OQ=901.53;QD=16.10;SB=-413.05 GT:AD:DP:GL:GQ 0/1:26,30:56:-110.30,-16.87,-89.43:99 +chr1 1888688 rs34824947 T C 245.62 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.71;MQ0=0;OQ=584.90;QD=12.44;SB=-198.60 GT:AD:DP:GL:GQ 0/1:25,22:46:-75.63,-13.86,-99.35:99 +chr1 1888695 rs34586002 C A 280.09 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.48;MQ0=0;OQ=561.20;QD=12.75;SB=-230.89 GT:AD:DP:GL:GQ 0/1:24,20:42:-72.05,-12.65,-79.10:99 +chr1 1888719 rs35031992 G A 261.38 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=534.91;QD=11.38;SB=-199.88 GT:AD:DP:GL:GQ 0/1:28,19:46:-70.65,-13.87,-88.35:99 +chr1 1888794 rs35186797 T C 29.82 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.78;MQ=57.65;MQ0=0;OQ=525.33;QD=10.94;SB=-267.94 GT:AD:DP:GL:GQ 0/1:23,25:43:-68.78,-12.96,-87.05:99 +chr1 1888798 rs13303138 G A 173.43 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=57.75;MQ0=0;OQ=779.95;QD=15.60;SB=-266.18 GT:AD:DP:GL:GQ 0/1:24,26:46:-95.14,-13.87,-72.15:99 +chr1 1888835 rs34940616 G A 9.86 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.88;MQ0=0;OQ=741.91;QD=23.93;SB=-335.86 GT:AD:DP:GL:GQ 0/1:9,22:29:-86.21,-8.74,-25.83:99 +chr1 1889024 rs17778128 G C 179.10 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=57.35;MQ0=0;OQ=668.72;QD=10.79;SB=-360.78 GT:AD:DP:GL:GQ 0/1:38,24:59:-87.94,-17.79,-162.55:99 +chr1 1889139 rs61775058 A T 458.44 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.25;MQ0=0;OQ=787.44;QD=13.58;SB=-299.67 GT:AD:DP:GL:GQ 0/1:31,27:58:-99.50,-17.47,-121.67:99 +chr1 1889179 rs61775059 T C 275.84 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.27;MQ0=0;OQ=765.16;QD=11.42;SB=-328.14 GT:AD:DP:GL:GQ 0/1:35,32:66:-99.69,-19.89,-140.70:99 +chr1 1889260 rs13303007 G A 42.33 Indel;LowQual AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=6.98;MQ=52.93;MQ0=0;QD=0.73;SB=-30.38 GT:AD:DP:GL:GQ 0/1:52,6:58:-24.99,-17.47,-182.54:75.16 +chr1 1889721 rs4648601 C T 94.28 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=56.35;MQ0=0;OQ=530.41;QD=10.20;SB=-77.51 GT:AD:DP:GL:GQ 0/1:33,19:47:-70.50,-14.17,-95.11:99 +chr1 1890092 rs16824588 T C 13.33 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=57.02;MQ0=0;OQ=150.77;QD=3.97;SB=-54.71 GT:AD:DP:GL:GQ 0/1:26,12:35:-28.91,-10.55,-104.30:99 +chr1 1890192 rs55709963 A G 31.87 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=56.20;MQ0=0;OQ=293.66;QD=11.75;SB=-65.87 GT:AD:DP:GL:GQ 0/1:12,13:24:-39.88,-7.23,-45.12:99 +chr1 1890199 rs56126097 A G 24.29 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=55.86;MQ0=0;OQ=270.97;QD=11.78;SB=-47.83 GT:AD:DP:GL:GQ 0/1:11,12:22:-37.01,-6.63,-43.67:99 +chr1 1890235 rs55676322 G A 36.70 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.45;MQ0=0;QD=2.82;SB=-3.98 GT:AD:DP:GL:GQ 0/1:10,3:12:-10.57,-3.62,-30.38:69.54 +chr1 1890236 . C T 56.05 SnpCluster AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.03;MQ0=0;QD=4.00;SB=-3.98 GT:AD:DP:GL:GQ 0/1:11,3:13:-12.81,-3.92,-36.41:88.89 +chr1 1890241 rs55784504 G A 37.70 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=53.95;MQ0=0;QD=2.36;SB=-0.97 GT:AD:DP:GL:GQ 0/1:13,3:15:-11.57,-4.52,-40.91:70.54 +chr1 1890268 rs61776961 A G 12.56 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=53.61;MQ0=0;QD=0.66;SB=-31.93 GT:AD:DP:GL:GQ 0/1:15,4:17:-9.64,-5.12,-56.10:45.15 +chr1 1890270 rs61776962 C T 67.49 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=53.03;MQ0=0;QD=3.21;SB=-45.25 GT:AD:DP:GL:GQ 0/1:16,5:19:-15.77,-5.74,-45.89:99 +chr1 1890274 rs61776963 T C 59.17 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=2;HaplotypeScore=2.43;MQ=51.33;MQ0=0;QD=2.96;SB=-53.70 GT:AD:DP:GL:GQ 0/1:14,6:19:-14.93,-5.73,-56.51:92.01 +chr1 1890292 rs61776964 T G 172.84 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=50.53;MQ0=0;OQ=263.44;QD=9.08;SB=-95.94 GT:AD:DP:GL:GQ 0/1:17,12:28:-38.07,-8.44,-56.66:99 +chr1 1890305 rs61776965 C T 161.45 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=50.32;MQ0=0;OQ=365.34;QD=11.79;SB=-175.70 GT:AD:DP:GL:GQ 0/1:18,13:27:-47.95,-8.13,-56.49:99 +chr1 1890314 rs6681749 A G 143.47 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=50.65;MQ0=0;OQ=306.18;QD=9.57;SB=-129.77 GT:AD:DP:GL:GQ 0/1:17,15:29:-42.64,-8.74,-64.98:99 +chr1 1890507 . T C 42.73 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=3.92;MQ=54.77;MQ0=0;QD=1.86;SB=14.07 GT:AD:DP:GL:GQ 0/1:16,7:17:-12.68,-5.13,-48.62:75.57 +chr1 1890548 . A T 8.30 PASS AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=60.00;MQ0=0;OQ=79.81;QD=7.98;SB=-57.71 GT:AD:DP:GL:GQ 0/1:6,4:10:-14.28,-3.01,-22.53:99 +chr1 1890778 rs28707401 G A 84.90 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.74;MQ=58.33;MQ0=0;OQ=401.02;QD=14.32;SB=-129.13 GT:AD:DP:GL:GQ 0/1:13,14:24:-53.53,-10.14,-35.22:99 +chr1 1892326 . A C 112.36 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.24;MQ0=0;OQ=852.28;QD=15.50;SB=-429.85 GT:AD:DP:GL:GQ 0/1:26,29:52:-104.18,-15.67,-81.22:99 +chr1 1892422 rs7367171 A G 220.04 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.60;MQ0=0;OQ=514.17;QD=9.02;SB=-267.96 GT:AD:DP:GL:GQ 0/1:32,25:54:-70.98,-16.28,-126.05:99 +chr1 1892426 rs7367879 G A 251.13 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=59.60;MQ0=0;OQ=832.91;QD=14.36;SB=-352.38 GT:AD:DP:GL:GQ 0/1:32,26:52:-102.26,-15.68,-81.39:99 +chr1 1892733 rs7366028 C T 234.62 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.35;MQ0=0;OQ=1086.69;QD=15.31;SB=-535.37 GT:AD:DP:GL:GQ 0/1:36,35:67:-132.15,-20.20,-106.68:99 +chr1 1893163 rs4648603 C T 25.39 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=59.48;MQ0=0;OQ=261.75;QD=5.95;SB=-111.10 GT:AD:DP:GL:GQ 0/1:32,12:41:-41.83,-12.38,-90.87:99 +chr1 1893572 rs13303201 C A 360.69 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.58;MQ0=0;OQ=726.40;QD=15.46;SB=-340.06 GT:AD:DP:GL:GQ 0/1:22,25:44:-89.18,-13.26,-62.88:99 +chr1 1895166 rs56313717 C A 171.85 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=635.59;QD=15.13;SB=-197.47 GT:AD:DP:GL:GQ 0/1:18,24:41:-79.20,-12.35,-61.36:99 +chr1 1897772 rs7528894 C T 135.70 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=58.63;MQ0=0;OQ=607.52;QD=11.91;SB=-152.65 GT:AD:DP:GL:GQ 0/1:30,21:44:-77.30,-13.26,-84.20:99 +chr1 1897865 rs7536087 T C 25.44 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=54.74;MQ0=0;OQ=378.78;QD=5.83;SB=-147.48 GT:AD:DP:GL:GQ 0/1:38,27:56:-58.05,-16.88,-148.17:99 +chr1 1897872 rs28588807 T C 29.81 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=53.22;MQ0=0;OQ=367.97;QD=6.24;SB=-166.50 GT:AD:DP:GL:GQ 0/1:36,23:50:-55.16,-15.08,-127.98:99 +chr1 1897899 rs4388640 C T 188.74 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=52.25;MQ0=0;OQ=499.97;QD=8.20;SB=-247.55 GT:AD:DP:GL:GQ 0/1:39,22:51:-68.65,-15.37,-112.84:99 +chr1 1897945 rs28410799 A G 3.16 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.71;MQ=54.36;MQ0=0;OQ=341.23;QD=5.59;SB=-142.90 GT:AD:DP:GL:GQ 0/1:39,21:52:-53.08,-15.68,-138.70:99 +chr1 1897960 rs28789409 G T 236.91 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=55.27;MQ0=0;OQ=569.89;QD=9.19;SB=-286.60 GT:AD:DP:GL:GQ 0/1:38,24:59:-78.04,-17.77,-137.70:99 +chr1 1898245 rs13303203 C T 367.31 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.47;MQ0=0;OQ=546.46;QD=10.31;SB=-185.87 GT:AD:DP:GL:GQ 0/1:33,20:47:-72.10,-14.17,-90.13:99 +chr1 1898289 rs28545809 T C 170.68 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=55.94;MQ0=0;OQ=320.54;QD=7.82;SB=-173.95 GT:AD:DP:GL:GQ 0/1:24,16:37:-46.49,-11.16,-87.43:99 +chr1 1898563 rs4233027 C G 427.81 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.18;MQ0=0;OQ=977.32;QD=15.27;SB=-297.92 GT:AD:DP:GL:GQ 0/1:36,28:63:-120.00,-18.99,-153.02:99 +chr1 1899064 rs35953639 A G 134.17 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.58;MQ=58.52;MQ0=0;OQ=901.65;QD=15.82;SB=-439.15 GT:AD:DP:GL:GQ 0/1:25,32:55:-110.02,-16.57,-94.81:99 +chr1 1899178 rs61776976 G A 36.91 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=59.15;MQ0=0;OQ=1106.44;QD=22.13;SB=-371.92 GT:AD:DP:GL:GQ 0/1:16,34:48:-128.39,-14.47,-53.19:99 +chr1 1899305 rs55863117 A G 206.03 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.24;MQ0=0;OQ=872.61;QD=14.31;SB=-340.17 GT:AD:DP:GL:GQ 0/1:25,35:57:-107.73,-17.18,-95.38:99 +chr1 1899354 rs28716654 C T 202.23 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=59.30;MQ0=0;OQ=1176.35;QD=17.82;SB=-612.15 GT:AD:DP:GL:GQ 0/1:31,35:62:-139.59,-18.67,-102.07:99 +chr1 1899413 rs28680595 T A 360.31 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.29;MQ0=0;OQ=1036.44;QD=15.95;SB=-464.88 GT:AD:DP:GL:GQ 0/1:30,35:63:-125.91,-18.98,-108.28:99 +chr1 1899561 rs28613404 C T 21.64 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=5.89;MQ=58.07;MQ0=0;OQ=742.01;QD=16.13;SB=-312.34 GT:AD:DP:GL:GQ 0/1:20,25:42:-90.15,-12.66,-60.03:99 +chr1 1899593 rs28491083 G T 384.56 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=572.46;QD=14.31;SB=-222.49 GT:AD:DP:GL:GQ 0/1:17,23:37:-71.67,-11.14,-60.73:99 +chr1 1899703 rs28433557 C T 153.68 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.28;MQ0=0;OQ=695.04;QD=16.55;SB=-241.74 GT:AD:DP:GL:GQ 0/1:19,23:39:-84.54,-11.75,-59.04:99 +chr1 1899714 rs28448395 G A 59.92 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=57.87;MQ0=0;OQ=975.55;QD=21.68;SB=-411.21 GT:AD:DP:GL:GQ 0/1:16,29:43:-113.79,-12.96,-49.10:99 +chr1 1899728 rs28539219 G A 22.10 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=58.50;MQ0=0;OQ=1039.92;QD=21.66;SB=-531.16 GT:AD:DP:GL:GQ 0/1:16,32:45:-120.83,-13.56,-54.90:99 +chr1 1899861 rs28468541 C G 2.92 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=9.03;MQ=56.76;MQ0=0;OQ=898.89;QD=17.63;SB=-410.04 GT:AD:DP:GL:GQ 0/1:24,26:48:-107.64,-14.46,-99.37:99 +chr1 1899872 rs28588737 T C 12.45 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=3.04;MQ=57.56;MQ0=0;OQ=448.65;QD=9.35;SB=-239.28 GT:AD:DP:GL:GQ 0/1:25,23:43:-61.11,-12.96,-97.10:99 +chr1 1899946 rs28645949 G T 144.20 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=60.00;MQ0=0;OQ=332.80;QD=10.40;SB=-155.69 GT:AD:DP:GL:GQ 0/1:19,13:30:-45.61,-9.04,-50.81:99 +chr1 1900096 rs28651716 T C 225.12 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=54.90;MQ0=0;OQ=686.40;QD=12.71;SB=-338.36 GT:AD:DP:GL:GQ 0/1:28,26:53:-87.90,-15.97,-105.41:99 +chr1 1900231 rs28642304 G A 31.56 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=5.35;MQ=52.67;MQ0=2;OQ=686.17;QD=14.00;SB=-341.85 GT:AD:DP:GL:GQ 0/1:25,24:43:-84.86,-12.96,-72.07:99 +chr1 1900342 . C G 14.82 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=12.94;MQ=53.14;MQ0=2;QD=0.37;SB=26.12 GT:AD:DP:GL:GQ 0/1:35,5:34:-15.00,-10.25,-129.63:47.51 +chr1 1900344 . T C 47.56 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=13.10;MQ=54.07;MQ0=2;QD=1.16;SB=26.11 GT:AD:DP:GL:GQ 0/1:32,9:34:-18.29,-10.25,-109.75:80.39 +chr1 1900366 . T C 19.64 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=56.14;MQ0=0;QD=0.48;SB=17.08 GT:AD:DP:GL:GQ 0/1:34,7:35:-15.79,-10.55,-116.81:52.43 +chr1 1900466 rs7550407 A G 75.71 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=45.89;MQ0=2;OQ=380.59;QD=19.03;SB=-189.68 GT:AD:DP:GL:GQ 1/1:0,20:13:-41.66,-3.92,-0.01:39.09 +chr1 1900518 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=10.99;MQ=35.59;MQ0=6;OQ=55.62;QD=1.29;SB=-13.87 GT:AD:DP:GL:GQ 0/1:29,14:19:-14.57,-5.73,-56.56:88.46 +chr1 1900571 . C T 45.32 LowQual AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=19.95;MQ=36.93;MQ0=3;QD=0.91;SB=-24.62 GT:AD:DP:GL:GQ 0/1:41,9:25:-15.36,-7.54,-65.46:78.16 +chr1 1900816 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=6.83;MQ=47.18;MQ0=2;OQ=71.50;QD=1.79;SB=-42.78 GT:AD:DP:GL:GQ 0/1:30,10:31:-19.78,-9.34,-96.64:99 +chr1 1900861 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=8.07;MQ=42.04;MQ0=5;OQ=136.19;QD=2.67;SB=-39.59 GT:AD:DP:GL:GQ 0/1:31,18:36:-30.43,-13.53,-101.33:99 +chr1 1900880 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=21.93;MQ=42.64;MQ0=5;OQ=81.77;QD=1.99;SB=26.03 GT:AD:DP:GL:GQ 0/1:32,9:28:-19.91,-8.45,-71.11:99 +chr1 1900981 . G A 32.02 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=14.77;MQ=47.97;MQ0=0;QD=1.07;SB=20.08 GT:AD:DP:GL:GQ 0/1:27,3:20:-12.51,-6.03,-56.06:64.85 +chr1 1900982 . C T 11.94 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=14.77;MQ=47.50;MQ0=0;QD=0.41;SB=35.07 GT:AD:DP:GL:GQ 0/1:26,3:25:-11.99,-7.54,-69.22:44.49 +chr1 1900987 . C G 179.53 SnpCluster AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=15.25;MQ=49.14;MQ0=0;QD=5.79;SB=-106.68 GT:AD:DP:GL:GQ 0/1:23,8:22:-27.88,-6.64,-59.47:99 +chr1 1901007 . A G 17.82 PASS AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=50.60;MQ0=0;OQ=269.42;QD=8.42;SB=-129.64 GT:AD:DP:GL:GQ 0/1:19,13:29:-38.97,-8.74,-66.56:99 +chr1 1901025 . T C 1.37 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=50.85;MQ0=0;OQ=146.63;QD=3.67;SB=-63.91 GT:AD:DP:GL:GQ 0/1:26,13:31:-27.31,-9.36,-79.17:99 +chr1 1901036 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=7.09;MQ=51.49;MQ0=1;OQ=87.37;QD=1.99;SB=-8.61 GT:AD:DP:GL:GQ 0/1:38,6:38:-23.49,-11.46,-98.15:99 +chr1 1901053 . T C 11.36 LowQual AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=52.41;MQ0=1;QD=0.25;SB=-25.22 GT:AD:DP:GL:GQ 0/1:37,8:38:-15.84,-11.45,-126.44:43.87 +chr1 1901418 rs28645431 C T 0.52 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=3.95;MQ=41.39;MQ0=1;OQ=172.22;QD=4.53;SB=-89.91 GT:AD:DP:GL:GQ 0/1:29,9:21:-26.84,-6.33,-42.67:99 +chr1 1901574 rs13303001 G A 41.49 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=7.68;MQ=10.86;MQ0=15;QD=1.66;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,5:3:-8.34,-0.90,-3.10:21.92 +chr1 1901637 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=16.41;MQ=17.84;MQ0=13;OQ=157.79;QD=2.87;SB=-10.00 GT:AD:DP:GL:GQ 0/1:44,10:26:-26.90,-7.83,-65.70:99 +chr1 1901664 . G A 34.02 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.20;MQ=18.33;MQ0=14;QD=0.67;SB=-10.00 GT:AD:DP:GL:GQ 0/1:42,9:17:-11.81,-5.13,-50.35:66.86 +chr1 1901668 . G A 0.06 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.04;MQ=18.51;MQ0=13;OQ=99.32;QD=2.03;SB=-7.00 GT:AD:DP:GL:GQ 0/1:40,9:16:-18.04,-4.83,-38.64:99 +chr1 1901732 rs13303290 T C 12.82 LowQual AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.55;MQ0=0;QD=0.64;SB=-24.62 GT:AD:DP:GL:GQ 0/1:15,5:16:-9.37,-4.82,-51.21:45.43 +chr1 1901798 rs4648740 A G 153 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=48.72;MQ0=0;OQ=495.24;QD=14.15;SB=-240.44 GT:AD:DP:GL:GQ 0/1:16,19:34:-63.06,-10.25,-57.72:99 +chr1 1901828 rs4648741 T A 223.12 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=49.47;MQ0=0;OQ=518.42;QD=14.01;SB=-218.56 GT:AD:DP:GL:GQ 0/1:16,21:33:-65.07,-9.94,-58.68:99 +chr1 1902252 rs35209771 G A 29.20 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.72;MQ=59.38;MQ0=0;OQ=570.39;QD=15.42;SB=-188.28 GT:AD:DP:GL:GQ 0/1:17,20:31:-69.66,-9.34,-43.55:99 +chr1 1902361 rs35032062 A G 8.53 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=1.19;MQ=56.62;MQ0=0;OQ=288.56;QD=9.31;SB=-81.77 GT:AD:DP:GL:GQ 0/1:15,16:27:-40.29,-8.15,-49.29:99 +chr1 1902443 rs4648742 T G 2.74 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=3;HaplotypeScore=1.88;MQ=52.64;MQ0=0;OQ=307.57;QD=13.98;SB=-102.98 GT:AD:DP:GL:GQ 0/1:8,14:19:-39.76,-5.72,-27.07:99 +chr1 1902590 rs34957887 A G 5.37 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=54.60;MQ0=0;OQ=111.21;QD=3.83;SB=-42.82 GT:AD:DP:GL:GQ 0/1:21,8:27:-22.55,-8.14,-76.38:99 +chr1 1902594 rs34699657 T C 6.89 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=55.30;MQ0=0;OQ=114.19;QD=4.08;SB=-28.64 GT:AD:DP:GL:GQ 0/1:19,9:26:-22.55,-7.85,-71.28:99 +chr1 1902618 rs13302917 G C 80.21 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=55.30;MQ0=0;OQ=235.26;QD=8.40;SB=8.06 GT:AD:DP:GL:GQ 0/1:18,10:26:-34.65,-7.84,-76.52:99 +chr1 1902752 . G A 16.41 LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=23.04;MQ0=3;QD=0.82;SB=-30.52 GT:AD:DP:GL:GQ 0/1:17,3:9:-7.63,-2.71,-23.66:49.15 +chr1 1902780 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=12.84;MQ=20.15;MQ0=3;OQ=68.78;QD=3.62;SB=-7.00 GT:AD:DP:GL:GQ 0/1:14,5:6:-11.97,-1.81,-9.13:73.25 +chr1 1902787 . G A 0.55 PASS AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=20.15;MQ0=3;OQ=103.65;QD=5.46;SB=-46.55 GT:AD:DP:GL:GQ 0/1:13,6:5:-15.16,-1.51,-3.80:22.92 +chr1 1902803 . A G 0.43 PASS AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=19.89;MQ0=3;OQ=59.98;QD=3.75;SB=-6.99 GT:AD:DP:GL:GQ 0/1:11,5:6:-11.09,-1.81,-11.69:92.82 +chr1 1902817 . T C 41.42 LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=9.95;MQ=22.02;MQ0=2;QD=2.96;SB=-35.94 GT:AD:DP:GL:GQ 0/1:9,4:6:-9.23,-1.81,-11.87:74.25 +chr1 1902835 rs61776983 A C 26.37 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=1.55;MQ=20.97;MQ0=2;OQ=78.83;QD=5.63;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,12:3:-11.37,-0.90,-0.00:9.03 +chr1 1903052 . G A 0.07 PASS AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=10.18;MQ=21.19;MQ0=5;OQ=185.24;QD=7.12;SB=-114.97 GT:AD:DP:GL:GQ 0/1:13,13:10:-24.83,-3.02,-9.74:67.23 +chr1 1903096 . C T 19.36 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=27.09;MQ=29.12;MQ0=4;QD=0.84;SB=-32.50 GT:AD:DP:GL:GQ 0/1:20,3:10:-8.23,-3.01,-26.23:52.14 +chr1 1903103 . G A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=11.25;MQ=32.31;MQ0=4;OQ=203.36;QD=8.13;SB=-108.63 GT:AD:DP:GL:GQ 0/1:11,14:13:-27.54,-3.92,-21.98:99 +chr1 1903122 . G A 1.51 PASS AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=5.86;MQ=37.50;MQ0=2;OQ=277.72;QD=11.11;SB=-116.63 GT:AD:DP:GL:GQ 0/1:11,14:14:-35.28,-4.22,-14.88:99 +chr1 1903133 . C T 26.70 DPFilter;HARD_TO_VALIDATE;Indel;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=14.79;MQ=33.51;MQ0=4;QD=0.92;SB=2.00 GT:AD:DP:GL:GQ 0/1:25,3:16:-10.78,-4.83,-41.60:59.53 +chr1 1903194 . G A 0.17 PASS AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=22.60;MQ0=6;OQ=59.87;QD=3.15;SB=-29.63 GT:AD:DP:GL:GQ 0/1:15,4:8:-11.68,-2.41,-15.55:92.71 +chr1 1903256 rs56273126 A C 0.43 PASS AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=9.88;MQ=34.34;MQ0=2;OQ=157.91;QD=8.77;SB=-43.00 GT:AD:DP:GL:GQ 0/1:8,10:11:-22.39,-3.31,-17.60:99 +chr1 1903263 rs56067355 C T 0.21 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=9.27;MQ=35.40;MQ0=1;OQ=103.77;QD=4.72;SB=-3.99 GT:AD:DP:GL:GQ 0/1:16,6:17:-18.78,-5.12,-41.68:99 +chr1 1903283 . G A 8.07 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.95;MQ=39.68;MQ0=0;OQ=372.77;QD=10.96;SB=-73.09 GT:AD:DP:GL:GQ 0/1:17,16:22:-47.20,-6.63,-29.71:99 +chr1 1903404 . C T 39.84 LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=6.15;MQ=48.13;MQ0=1;QD=1.73;SB=-35.65 GT:AD:DP:GL:GQ 0/1:19,4:16:-12.09,-4.83,-40.40:72.68 +chr1 1903423 rs58434854 A G 0.71 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=7.95;MQ=46.73;MQ0=3;OQ=182.58;QD=6.30;SB=-71.95 GT:AD:DP:GL:GQ 0/1:18,11:23:-28.48,-6.94,-51.85:99 +chr1 1903439 rs58923167 C T 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=17.53;MQ=42.29;MQ0=6;OQ=136.42;QD=4.01;SB=-25.62 GT:AD:DP:GL:GQ 0/1:26,8:22:-23.56,-6.63,-53.26:99 +chr1 1903440 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=17.53;MQ=42.29;MQ0=6;OQ=187.84;QD=5.52;SB=-110.54 GT:AD:DP:GL:GQ 0/1:26,8:23:-29.00,-6.94,-48.31:99 +chr1 1903458 rs55879512 A G 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=7.35;MQ=44.38;MQ0=5;OQ=75.85;QD=1.85;SB=-63.75 GT:AD:DP:GL:GQ 0/1:26,14:24:-18.11,-7.24,-65.52:99 +chr1 1903493 . G A 1.04 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=47.31;MQ0=2;OQ=168.07;QD=4.31;SB=-57.28 GT:AD:DP:GL:GQ 0/1:31,8:25:-27.63,-7.54,-58.38:99 +chr1 1903509 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=11.62;MQ=39.25;MQ0=5;OQ=92.69;QD=2.73;SB=5.04 GT:AD:DP:GL:GQ 0/1:25,9:18:-17.98,-5.43,-46.46:99 +chr1 1903540 . G A 33.23 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=27.81;MQ=22.93;MQ0=9;QD=1.15;SB=-3.98 GT:AD:DP:GL:GQ 0/1:26,3:5:-8.11,-1.51,-11.06:66.06 +chr1 1903547 . T A 34.51 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=29.76;MQ=15.81;MQ0=9;QD=1.33;SB=-42.38 GT:AD:DP:GL:GQ 0/1:19,6:3:-7.64,-0.90,-3.64:27.36 +chr1 1903587 rs4648605 C T 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=14.50;MQ=19.08;MQ0=11;OQ=79.27;QD=1.98;SB=-3.99 GT:AD:DP:GL:GQ 0/1:27,13:10:-14.23,-3.02,-19.87:99 +chr1 1904125 rs4648745 T C 247.21 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.25;MQ0=0;OQ=694.34;QD=11.20;SB=-245.29 GT:AD:DP:GL:GQ 0/1:33,29:61:-91.10,-18.39,-129.32:99 +chr1 1904347 rs4648746 A G 176.14 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.39;MQ0=0;OQ=338.48;QD=8.91;SB=-150.90 GT:AD:DP:GL:GQ 0/1:21,17:36:-47.98,-10.85,-82.55:99 +chr1 1904465 rs28737396 A T 328.52 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=1094.85;QD=18.56;SB=-354.42 GT:AD:DP:GL:GQ 0/1:24,35:59:-130.54,-17.77,-93.43:99 +chr1 1904806 rs61776990 C T 103.75 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=56.91;MQ0=0;OQ=639.60;QD=17.29;SB=-221.92 GT:AD:DP:GL:GQ 0/1:15,22:35:-77.80,-10.56,-46.60:99 +chr1 1905885 rs4648747 G A 213.38 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=54.80;MQ0=0;OQ=758.00;QD=15.16;SB=-295.79 GT:AD:DP:GL:GQ 0/1:26,24:49:-93.85,-14.76,-88.23:99 +chr1 1905894 rs13303091 C T 219.74 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=53.79;MQ0=0;OQ=656.87;QD=13.14;SB=-261.28 GT:AD:DP:GL:GQ 0/1:27,22:45:-82.54,-13.57,-75.64:99 +chr1 1905900 rs13302998 T C 119.27 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=54.88;MQ0=0;OQ=405.99;QD=8.83;SB=-193.60 GT:AD:DP:GL:GQ 0/1:27,19:44:-57.15,-13.26,-102.12:99 +chr1 1906158 rs13302999 C T 171.25 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=58.63;MQ0=0;OQ=813.49;QD=15.95;SB=-262.17 GT:AD:DP:GL:GQ 0/1:25,26:49:-99.40,-14.77,-77.74:99 +chr1 1906389 rs3795284 C T 21.30 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=2.33;MQ=60.00;MQ0=0;OQ=758.20;QD=14.04;SB=-278.28 GT:AD:DP:GL:GQ 0/1:28,26:52:-94.77,-15.67,-93.68:99 +chr1 1906447 rs3795283 G T 377.61 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=60.00;MQ0=0;OQ=998.45;QD=16.37;SB=-378.14 GT:AD:DP:GL:GQ 0/1:26,35:60:-121.20,-18.07,-93.96:99 +chr1 1906750 rs3795280 C T 425.49 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=568.99;QD=13.55;SB=-250.75 GT:AD:DP:GL:GQ 0/1:24,18:42:-72.83,-12.65,-87.72:99 +chr1 1906918 rs34331632 A G 117.25 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=58.45;MQ0=0;OQ=396.71;QD=8.82;SB=-212.27 GT:AD:DP:GL:GQ 0/1:26,19:41:-55.32,-12.36,-92.05:99 +chr1 1907309 rs34567059 T G 9.37 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=3;HaplotypeScore=0.99;MQ=59.28;MQ0=0;OQ=266.80;QD=8.34;SB=-138.72 GT:AD:DP:GL:GQ 0/1:18,13:26:-37.80,-7.84,-51.38:99 +chr1 1907332 rs13303173 G A 219.11 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=59.50;MQ0=0;OQ=402.42;QD=8.75;SB=-215.71 GT:AD:DP:GL:GQ 0/1:30,16:41:-55.89,-12.37,-85.41:99 +chr1 1907475 rs13302992 A T 11.71 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=5.57;MQ=54.24;MQ0=0;OQ=373.16;QD=8.88;SB=-86.42 GT:AD:DP:GL:GQ 0/1:20,21:33:-50.55,-9.95,-63.90:99 +chr1 1907510 rs13302993 T C 10.65 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=3.38;MQ=53.93;MQ0=0;OQ=691.42;QD=12.35;SB=-327.29 GT:AD:DP:GL:GQ 0/1:24,32:51:-87.80,-15.38,-95.79:99 +chr1 1907689 rs4648748 T G 25.50 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.34;MQ=60.00;MQ0=0;OQ=189.73;QD=5.93;SB=-95.86 GT:AD:DP:GL:GQ 0/1:21,11:31:-31.60,-9.34,-75.09:99 +chr1 1907731 rs4648749 T A 88.57 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=58.55;MQ0=0;OQ=1056.82;QD=33.03;SB=-482.74 GT:AD:DP:GL:GQ 1/1:0,32:31:-109.29,-9.34,-0.02:93.25 +chr1 1907768 rs4648750 A C 41.15 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=58.69;MQ0=0;OQ=501.71;QD=15.68;SB=-178.91 GT:AD:DP:GL:GQ 0/1:13,18:31:-62.79,-9.34,-46.86:99 +chr1 1908051 rs4233028 A G 0.83 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=11.36;MQ=58.24;MQ0=0;OQ=590.53;QD=10.36;SB=-318.09 GT:AD:DP:GL:GQ 0/1:28,29:51:-77.71,-15.37,-108.19:99 +chr1 1908348 rs4350140 A G 295.92 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=483.27;QD=11.51;SB=-249.48 GT:AD:DP:GL:GQ 0/1:22,19:40:-63.66,-12.05,-87.28:99 +chr1 1908395 rs4535948 A T 243.05 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=561.16;QD=14.03;SB=-291.34 GT:AD:DP:GL:GQ 0/1:20,20:38:-70.85,-11.45,-68.83:99 +chr1 1908444 rs4603072 C T 95.97 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.91;MQ=59.00;MQ0=0;OQ=825.49;QD=16.19;SB=-274.16 GT:AD:DP:GL:GQ 0/1:24,27:46:-99.69,-13.86,-72.18:99 +chr1 1908455 rs4466593 G A 154 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.00;MQ0=0;OQ=749.94;QD=14.70;SB=-209.69 GT:AD:DP:GL:GQ 0/1:25,26:47:-92.45,-14.17,-73.64:99 +chr1 1910822 rs13303020 T C 316 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.07;MQ0=0;OQ=856.90;QD=15.30;SB=-348.06 GT:AD:DP:GL:GQ 0/1:22,34:54:-105.26,-16.29,-79.82:99 +chr1 1912163 rs13303195 C T 281.64 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.42;MQ0=0;OQ=1071.80;QD=15.76;SB=-460.45 GT:AD:DP:GL:GQ 0/1:35,33:67:-130.66,-20.19,-113.97:99 +chr1 1912512 rs13303233 T C 59.35 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=5.24;MQ=56.21;MQ0=1;OQ=632.02;QD=12.15;SB=-238.92 GT:AD:DP:GL:GQ 0/1:24,28:49:-81.26,-14.77,-90.12:99 +chr1 1912694 rs6605075 T C 195.05 PASS AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.81;MQ0=0;OQ=3518.98;QD=36.28;SB=-1667.64 GT:AD:DP:GL:GQ 1/1:0,97:97:-350.90,-29.22,-0.04:99 +chr1 1912989 rs13303332 A G 477.80 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.92;MQ0=0;OQ=1063.77;QD=12.66;SB=-392.88 GT:AD:DP:GL:GQ 0/1:42,42:74:-131.95,-22.29,-145.18:99 +chr1 1913060 rs13303315 T C 275.58 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=55.32;MQ0=0;OQ=932.62;QD=13.14;SB=-432.88 GT:AD:DP:GL:GQ 0/1:32,39:67:-116.74,-20.20,-124.71:99 +chr1 1913077 rs7529662 A G 28.09 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=51.94;MQ0=0;OQ=415.73;QD=6.60;SB=-158.33 GT:AD:DP:GL:GQ 0/1:37,26:55:-61.45,-16.59,-136.84:99 +chr1 1913121 rs6605076 G A 18.01 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=2.95;MQ=38.45;MQ0=0;OQ=1375.58;QD=22.55;SB=-647.86 GT:AD:DP:GL:GQ 1/1:0,60:36:-143.81,-13.38,-2.67:99 +chr1 1913134 rs6662056 C T 90.11 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=31.19;MQ0=0;OQ=470.14;QD=8.11;SB=-253.79 GT:AD:DP:GL:GQ 0/1:33,25:32:-59.95,-9.65,-52.35:99 +chr1 1913140 rs6605077 T C 265.58 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=26.77;MQ0=0;OQ=931.68;QD=17.25;SB=-415.14 GT:AD:DP:GL:GQ 1/1:0,54:27:-96.76,-8.13,-0.01:81.23 +chr1 1913166 rs6605078 A G 225.40 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=29.40;MQ0=0;OQ=379.61;QD=9.73;SB=-193.70 GT:AD:DP:GL:GQ 1/1:0,39:13:-41.56,-3.92,-0.01:39.09 +chr1 1913525 rs13303140 A G 349.47 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.90;MQ0=0;OQ=337.35;QD=9.92;SB=-170.51 GT:AD:DP:GL:GQ 0/1:16,18:26:-44.86,-7.84,-45.87:99 +chr1 1913541 rs6675865 A G 238.98 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=54.81;MQ0=0;OQ=476.22;QD=12.53;SB=-203.64 GT:AD:DP:GL:GQ 0/1:19,19:32:-60.55,-9.64,-59.13:99 +chr1 1914266 rs35822535 A G 10.16 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.48;MQ=52.01;MQ0=0;OQ=172.60;QD=5.57;SB=-106.80 GT:AD:DP:GL:GQ 0/1:17,12:25:-30.72,-10.17,-62.92:99 +chr1 1914406 rs28674034 C A 137.53 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=56.09;MQ0=0;OQ=479.30;QD=11.15;SB=-93.09 GT:AD:DP:GL:GQ 0/1:24,19:37:-62.36,-11.14,-73.40:99 +chr1 1914407 . C G 17.06 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.38;MQ=56.18;MQ0=0;OQ=578.11;QD=13.14;SB=-126.71 GT:AD:DP:GL:GQ 0/1:24,20:35:-71.66,-10.56,-69.93:99 +chr1 1914645 rs58504758 G A 76.95 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=56.31;MQ0=0;OQ=649.38;QD=14.43;SB=-87.56 GT:AD:DP:GL:GQ 0/1:23,22:44:-81.48,-13.26,-81.33:99 +chr1 1914669 rs57460771 C G 59.99 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=52.90;MQ0=0;OQ=635.24;QD=15.88;SB=-152.79 GT:AD:DP:GL:GQ 0/1:17,23:37:-77.97,-11.16,-71.80:99 +chr1 1915019 rs5021356 C T 38.12 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=38.83;MQ0=0;OQ=299.26;QD=5.16;SB=-51.25 GT:AD:DP:GL:GQ 0/1:26,32:29:-41.96,-8.75,-54.57:99 +chr1 1915025 rs5021357 C T 0.49 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=37.79;MQ0=0;OQ=104.46;QD=1.66;SB=-36.16 GT:AD:DP:GL:GQ 0/1:31,32:32:-23.37,-9.64,-89.65:99 +chr1 1915153 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=18.97;MQ=41.21;MQ0=1;OQ=317.64;QD=7.56;SB=-31.63 GT:AD:DP:GL:GQ 0/1:23,16:24:-42.29,-7.24,-39.07:99 +chr1 1915186 rs2377036 C A 0.52 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.46;MQ=38.80;MQ0=2;OQ=789.31;QD=23.22;SB=-127.84 GT:AD:DP:GL:GQ 1/1:3,31:25:-82.54,-7.54,-0.02:75.13 +chr1 1915197 . C T 2.41 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=35.96;MQ0=2;OQ=151.83;QD=4.34;SB=2.02 GT:AD:DP:GL:GQ 0/1:24,11:24:-25.70,-7.23,-56.48:99 +chr1 1915324 rs2889540 C T 459.53 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.97;MQ0=0;OQ=2370.24;QD=35.38;SB=-497.01 GT:AD:DP:GL:GQ 1/1:1,66:63:-240.64,-18.99,-0.03:99 +chr1 1915581 rs6691182 G A 155.40 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=58.09;MQ0=0;OQ=1565.00;QD=18.20;SB=-799.86 GT:AD:DP:GL:GQ 0/1:40,46:84:-185.10,-25.32,-125.47:99 +chr1 1915947 rs6661597 T C 434.36 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=753.37;QD=11.59;SB=-273.59 GT:AD:DP:GL:GQ 0/1:32,33:62:-97.31,-18.69,-126.97:99 +chr1 1915962 rs6675751 G C 346.68 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1124.09;QD=17.56;SB=-315.97 GT:AD:DP:GL:GQ 0/1:34,30:64:-134.99,-19.30,-134.99:99 +chr1 1916138 rs6667687 A T 24.65 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=5.93;MQ=59.44;MQ0=0;OQ=1046.27;QD=14.14;SB=-543.64 GT:AD:DP:GL:GQ 0/1:37,36:71:-129.30,-21.39,-135.06:99 +chr1 1917124 rs13302991 A G 77.08 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=48.19;MQ0=0;OQ=664.15;QD=15.09;SB=-132.68 GT:AD:DP:GL:GQ 0/1:17,27:41:-82.05,-12.36,-62.14:99 +chr1 1918235 rs58325500 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.01;HRun=15;HaplotypeScore=12.28;MQ=47.41;MQ0=2;OQ=54.80;QD=0.68;SB=8.48 GT:AD:DP:GL:GQ 0/1:66,14:56:-25.35,-16.59,-150.42:87.64 +chr1 1918448 rs28827857 G A 289.35 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=57.61;MQ0=0;OQ=1091.40;QD=15.82;SB=-363.89 GT:AD:DP:GL:GQ 0/1:36,33:66:-132.32,-19.90,-105.59:99 +chr1 1918459 rs28770275 C T 156.31 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.33;MQ0=0;OQ=990.70;QD=15.98;SB=-272.19 GT:AD:DP:GL:GQ 0/1:31,31:62:-121.04,-18.69,-98.12:99 +chr1 1919267 rs6672175 T C 222.23 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.35;MQ=59.22;MQ0=0;OQ=1139.84;QD=14.61;SB=-513.90 GT:AD:DP:GL:GQ 0/1:38,40:77:-140.46,-23.19,-152.92:99 +chr1 1919526 rs7532409 A G 229.15 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.27;MQ0=0;OQ=832.47;QD=13.21;SB=-385.03 GT:AD:DP:GL:GQ 0/1:26,37:58:-104.01,-17.48,-104.69:99 +chr1 1919694 rs7532529 A C 228.41 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=57.10;MQ0=0;OQ=714.32;QD=14.58;SB=-265.84 GT:AD:DP:GL:GQ 0/1:24,25:47:-88.87,-14.15,-84.13:99 +chr1 1919719 rs7527169 T C 335.23 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.16;MQ0=0;OQ=729.87;QD=16.59;SB=-259.34 GT:AD:DP:GL:GQ 0/1:16,28:43:-89.23,-12.96,-64.51:99 +chr1 1919737 rs7520124 C A 233.30 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.52;MQ0=0;OQ=916.99;QD=20.84;SB=-414.85 GT:AD:DP:GL:GQ 0/1:15,29:44:-108.24,-13.26,-45.66:99 +chr1 1919954 rs7542825 G A 154.86 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=58.01;MQ0=0;OQ=805.39;QD=15.79;SB=-224.54 GT:AD:DP:GL:GQ 0/1:26,25:50:-98.90,-15.08,-78.21:99 +chr1 1920251 rs6605079 C G 333.78 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=1146.24;QD=15.08;SB=-200.61 GT:AD:DP:GL:GQ 0/1:45,31:76:-140.81,-22.90,-188.17:99 +chr1 1920372 rs6605080 A G 234.56 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=57.79;MQ0=0;OQ=682.29;QD=12.87;SB=-281.00 GT:AD:DP:GL:GQ 0/1:25,28:47:-85.67,-14.16,-99.05:99 +chr1 1920614 rs6605081 C T 426.14 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=58.39;MQ0=0;OQ=1403.83;QD=17.12;SB=-667.29 GT:AD:DP:GL:GQ 0/1:39,43:80:-167.77,-24.10,-135.75:99 +chr1 1920665 rs6605082 G C 238.27 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=58.49;MQ0=0;OQ=1324.95;QD=16.99;SB=-669.29 GT:AD:DP:GL:GQ 0/1:42,36:76:-158.70,-22.92,-158.25:99 +chr1 1920803 rs13303035 C T 159 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=59.45;MQ0=0;OQ=1062.14;QD=13.98;SB=-530.37 GT:AD:DP:GL:GQ 0/1:41,35:73:-131.51,-22.01,-125.50:99 +chr1 1920841 rs13303352 T C 445.18 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.82;MQ0=0;OQ=837.48;QD=11.63;SB=-306.06 GT:AD:DP:GL:GQ 0/1:38,34:70:-108.13,-21.10,-146.79:99 +chr1 1921055 rs13303031 G T 88.89 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=58.92;MQ0=0;OQ=786.34;QD=15.12;SB=-342.30 GT:AD:DP:GL:GQ 0/1:26,26:52:-97.58,-15.66,-91.48:99 +chr1 1921356 rs6685055 A G 17.33 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=2.97;MQ=59.49;MQ0=0;OQ=448.41;QD=9.96;SB=-237.28 GT:AD:DP:GL:GQ 0/1:26,19:44:-61.39,-13.26,-100.60:99 +chr1 1921389 rs6679335 T G 83.14 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=1.67;MQ=59.13;MQ0=0;OQ=685.03;QD=12.93;SB=-353.06 GT:AD:DP:GL:GQ 0/1:29,24:52:-87.45,-15.66,-100.08:99 +chr1 1922327 rs28588769 G A 183.28 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.89;MQ0=1;OQ=778.96;QD=15.58;SB=-259.18 GT:AD:DP:GL:GQ 0/1:25,25:47:-95.35,-14.17,-73.16:99 +chr1 1922868 rs2376808 G A 157.54 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.34;MQ0=0;OQ=723.69;QD=10.34;SB=-347.08 GT:AD:DP:GL:GQ 0/1:45,25:64:-94.96,-19.30,-123.08:99 +chr1 1922895 rs2376807 G A 266.63 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=58.98;MQ0=0;OQ=1217.48;QD=13.99;SB=-488.00 GT:AD:DP:GL:GQ 0/1:49,38:84:-150.33,-25.30,-168.79:99 +chr1 1923727 rs4434797 T C 63.04 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.46;MQ0=0;OQ=1150.76;QD=28.77;SB=-542.44 GT:AD:DP:GL:GQ 1/1:1,39:35:-118.68,-10.55,-0.02:99 +chr1 1923976 rs2376806 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=7;HaplotypeScore=3.79;MQ=59.30;MQ0=0;OQ=886.58;QD=14.78;SB=-242.95 GT:AD:DP:GL:GQ 0/1:31,29:60:-110.01,-18.07,-107.98:99 +chr1 1924507 rs6682175 C G 459.83 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1286.38;QD=16.93;SB=-654.00 GT:AD:DP:GL:GQ 0/1:39,37:74:-154.22,-22.30,-163.90:99 +chr1 1925440 . A C 17.47 PASS AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=54.31;MQ0=0;OQ=233.12;QD=9.71;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,12:20:-32.62,-6.03,-38.03:99 +chr1 1925994 rs13303219 G A 173.92 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.24;MQ0=0;OQ=2130.07;QD=38.04;SB=-927.23 GT:AD:DP:GL:GQ 1/1:0,56:55:-216.61,-16.57,-0.02:99 +chr1 1927245 . C A 6.32 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=50.81;MQ0=0;OQ=1490.54;QD=26.15;SB=-627.15 GT:AD:DP:GL:GQ 0/1:11,46:54:-168.60,-16.27,-27.03:99 +chr1 1929194 . G A 93.04 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=54.76;MQ0=0;OQ=934.74;QD=16.40;SB=-478.51 GT:AD:DP:GL:GQ 0/1:29,28:56:-113.63,-16.87,-101.37:99 +chr1 1929934 . G A 0.59 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=6.95;MQ=58.36;MQ0=1;OQ=902.25;QD=19.20;SB=-435.95 GT:AD:DP:GL:GQ 0/1:20,27:46:-107.37,-13.86,-69.60:99 +chr1 1931518 rs6605072 C T 176.76 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.65;MQ0=0;OQ=1960.94;QD=37.71;SB=-913.32 GT:AD:DP:GL:GQ 1/1:0,52:51:-199.70,-15.37,-0.02:99 +chr1 1931688 rs13303071 T C 1556.10 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.24;MQ0=0;QD=27.79;SB=-792.66 GT:AD:DP:GL:GQ 1/1:0,56:50:-159.24,-15.08,-0.05:99 +chr1 1931693 . A G 1848.16 SnpCluster AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.03;MQ0=0;QD=33.60;SB=-934.96 GT:AD:DP:GL:GQ 1/1:0,55:53:-188.42,-15.97,-0.02:99 +chr1 1931694 . T A 1917.61 SnpCluster AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=49.24;MQ0=0;QD=35.51;SB=-952.61 GT:AD:DP:GL:GQ 1/1:0,54:52:-195.36,-15.66,-0.02:99 +chr1 1931789 rs6656398 G A 540.24 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.77;MQ0=0;OQ=2040.90;QD=38.51;SB=-804.04 GT:AD:DP:GL:GQ 1/1:0,53:51:-207.69,-15.36,-0.01:99 +chr1 1931893 rs13303124 C A 616.35 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.54;MQ0=0;OQ=2901.26;QD=36.72;SB=-1390.14 GT:AD:DP:GL:GQ 1/1:0,79:79:-293.73,-23.79,-0.02:99 +chr1 1933151 rs6672254 C T 447.19 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1292.37;QD=33.14;SB=-431.53 GT:AD:DP:GL:GQ 1/1:0,39:34:-132.84,-10.25,-0.02:99 +chr1 1933961 rs6605073 C G 112.88 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=54.93;MQ0=0;OQ=3433.93;QD=42.39;SB=-1558.19 GT:AD:DP:GL:GQ 1/1:0,81:81:-342.39,-24.42,-0.04:99 +chr1 1936451 rs13303016 G A 86.32 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=58.88;MQ0=0;OQ=2221.58;QD=38.30;SB=-691.42 GT:AD:DP:GL:GQ 1/1:0,56:56:-225.76,-16.87,-0.02:99 +chr1 1936669 rs4648752 C T 217.65 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=2508.96;QD=37.45;SB=-1210.99 GT:AD:DP:GL:GQ 1/1:0,67:64:-254.50,-19.28,-0.02:99 +chr1 1937615 rs2376804 C A 568.58 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.26;MQ0=0;OQ=1581.66;QD=34.38;SB=-723.87 GT:AD:DP:GL:GQ 1/1:0,46:45:-161.77,-13.56,-0.02:99 +chr1 1938260 rs13303344 C A 671.62 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=1865.08;QD=33.91;SB=-728.87 GT:AD:DP:GL:GQ 1/1:0,55:54:-190.12,-16.27,-0.02:99 +chr1 1938665 rs4481796 T C 1.68 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=7.00;MQ=59.19;MQ0=0;OQ=1999.82;QD=33.90;SB=-790.00 GT:AD:DP:GL:GQ 1/1:1,58:55:-203.58,-16.56,-0.01:99 +chr1 1939404 rs3121818 G T 55.95 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.13;MQ=57.70;MQ0=0;OQ=2038.83;QD=32.88;SB=-977.56 GT:AD:DP:GL:GQ 1/1:1,61:60:-210.75,-18.07,-3.28:99 +chr1 1940481 rs28603108 G A 85.60 PASS AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=244.10;QD=30.51;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:7:-27.99,-2.11,-0.00:21.07 +chr1 1941687 rs3121819 A G 228.42 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2020.01;QD=32.58;SB=-994.40 GT:AD:DP:GL:GQ 1/1:0,62:62:-205.63,-18.69,-0.05:99 +chr1 1942465 rs28502222 T C 371.08 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=1719.40;QD=30.16;SB=-855.54 GT:AD:DP:GL:GQ 1/1:0,57:54:-175.57,-16.29,-0.05:99 +chr1 1942470 rs28407473 T C 563.92 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1937.81;QD=31.25;SB=-894.53 GT:AD:DP:GL:GQ 1/1:0,62:60:-197.41,-18.09,-0.05:99 +chr1 1942642 rs3128318 C A 368.40 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1363.24;QD=34.95;SB=-493.39 GT:AD:DP:GL:GQ 1/1:0,39:38:-139.92,-11.45,-0.01:99 +chr1 1943112 rs3128321 T C 309.66 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.60;MQ0=0;OQ=865.40;QD=28.85;SB=-224.64 GT:AD:DP:GL:GQ 1/1:0,30:27:-90.14,-8.14,-0.02:81.21 +chr1 1943436 rs28595482 G A 148.08 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.62;MQ0=0;OQ=1902.67;QD=38.83;SB=-885.18 GT:AD:DP:GL:GQ 1/1:0,49:48:-193.87,-14.46,-0.01:99 +chr1 1943672 rs4648614 C T 198.11 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.32;MQ0=0;OQ=2028.99;QD=36.89;SB=-959.37 GT:AD:DP:GL:GQ 1/1:0,55:53:-206.51,-15.97,-0.03:99 +chr1 1944296 rs3128322 G A 216.26 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=59.01;MQ0=0;OQ=2427.18;QD=36.78;SB=-1173.08 GT:AD:DP:GL:GQ 1/1:0,65:64:-246.33,-19.29,-0.03:99 +chr1 1944940 rs3128323 G A 20.33 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=59.13;MQ0=0;OQ=1516.55;QD=28.61;SB=-577.76 GT:AD:DP:GL:GQ 1/1:0,53:41:-155.26,-12.36,-0.02:99 +chr1 1945844 rs2889475 C T 626.28 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=2161.84;QD=35.44;SB=-988.03 GT:AD:DP:GL:GQ 1/1:0,61:56:-219.79,-16.87,-0.02:99 +chr1 1946222 rs2376805 G A 202.65 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.86;MQ0=0;OQ=2273.19;QD=37.27;SB=-1064.36 GT:AD:DP:GL:GQ 1/1:0,61:58:-230.92,-17.47,-0.02:99 +chr1 1946897 rs2229110 T C 11.35 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=58.29;MQ0=0;OQ=1169.00;QD=28.51;SB=-410.54 GT:AD:DP:GL:GQ 1/1:1,40:35:-120.50,-10.54,-0.02:99 +chr1 1947159 rs3820007 C T 19.86 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=59.17;MQ0=0;OQ=557.21;QD=19.90;SB=-159.09 GT:AD:DP:GL:GQ 1/1:0,24:17:-62.02,-7.79,-2.71:50.81 +chr1 1949121 rs28574670 A G 500.63 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1666.55;QD=35.46;SB=-850.35 GT:AD:DP:GL:GQ 1/1:0,47:47:-170.25,-14.16,-0.02:99 +chr1 1949838 rs28409373 C T 14.57 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.07;MQ0=0;OQ=1034.54;QD=34.48;SB=-177.68 GT:AD:DP:GL:GQ 1/1:0,30:29:-107.06,-8.75,-0.02:87.26 +chr1 1950786 rs28581504 T C 332.55 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.64;MQ0=0;OQ=1013.22;QD=32.68;SB=-423.78 GT:AD:DP:GL:GQ 1/1:0,31:30:-104.92,-9.04,-0.02:90.23 +chr1 1953035 rs13302932 A G 11.68 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.55;MQ=60.00;MQ0=0;OQ=905.11;QD=24.46;SB=-434.83 GT:AD:DP:GL:GQ 1/1:0,37:30:-94.12,-9.05,-0.03:90.20 +chr1 1953275 rs17715203 A G 438.40 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1126.75;QD=30.45;SB=-438.29 GT:AD:DP:GL:GQ 1/1:0,37:35:-116.28,-10.55,-0.02:99 +chr1 1955750 . G C 30.56 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=3;HaplotypeScore=5.70;MQ=42.68;MQ0=2;QD=0.27;SB=83.98 GT:AD:DP:GL:GQ 0/1:64,50:68:-26.83,-20.49,-269.17:63.39 +chr1 1955789 . C G 28.79 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=3.29;MQ=41.60;MQ0=2;QD=0.26;SB=62.45 GT:AD:DP:GL:GQ 0/1:60,50:64:-25.45,-19.29,-247.08:61.62 +chr1 1956476 rs3128311 A G 7.52 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=2.79;MQ=58.13;MQ0=0;OQ=1189.30;QD=33.98;SB=-560.89 GT:AD:DP:GL:GQ 1/1:0,35:34:-122.53,-10.24,-0.01:99 +chr1 1956519 rs3128312 A G 0.03 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=5;HaplotypeScore=2.16;MQ=57.85;MQ0=0;OQ=1010.92;QD=30.63;SB=-251.77 GT:AD:DP:GL:GQ 1/1:0,33:30:-104.69,-9.04,-0.02:90.25 +chr1 1956874 . G A 318.30 PASS AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1884.66;QD=38.46;SB=-687.34 GT:AD:DP:GL:GQ 1/1:0,49:48:-192.06,-14.46,-0.01:99 +chr1 1957814 rs2376803 C T 3.63 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=59.46;MQ0=0;OQ=1636.24;QD=38.05;SB=-662.40 GT:AD:DP:GL:GQ 1/1:0,43:42:-167.22,-12.65,-0.01:99 +chr1 1958691 rs9442614 A G 93.39 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.19;MQ0=0;OQ=1548.19;QD=27.16;SB=-690.61 GT:AD:DP:GL:GQ 1/1:0,57:50:-158.45,-15.08,-0.05:99 +chr1 1958819 rs13303086 G A 42.72 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.38;MQ0=0;OQ=1355.91;QD=36.65;SB=-559.75 GT:AD:DP:GL:GQ 1/1:0,37:35:-139.19,-10.54,-0.01:99 +chr1 1961249 rs3121820 G C 348.51 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.98;MQ0=0;OQ=1964.71;QD=40.10;SB=-703.68 GT:AD:DP:GL:GQ 1/1:0,49:48:-200.08,-14.47,-0.02:99 +chr1 1964088 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=20;HaplotypeScore=27.35;MQ=45.54;MQ0=0;OQ=216.77;QD=4.93;SB=-12.47 GT:AD:DP:GL:GQ 0/1:28,16:30:-34.00,-9.04,-73.59:99 +chr1 1966711 rs28394674 G T 70.40 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.59;MQ=58.47;MQ0=0;OQ=2068.09;QD=33.90;SB=-496.39 GT:AD:DP:GL:GQ 1/1:0,60:58:-210.42,-17.47,-0.02:99 +chr1 1974087 rs3128319 C T 215.82 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=59.66;MQ0=0;OQ=974.85;QD=17.72;SB=-353.37 GT:AD:DP:GL:GQ 0/1:25,30:52:-116.43,-15.67,-87.00:99 +chr1 1974552 rs3121826 A G 92.93 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.67;MQ0=0;OQ=1020.08;QD=29.15;SB=-506.02 GT:AD:DP:GL:GQ 1/1:0,35:33:-105.63,-9.96,-0.04:99 +chr1 1974671 rs3121827 G T 491.82 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.58;MQ0=0;OQ=1710.64;QD=34.91;SB=-820.86 GT:AD:DP:GL:GQ 1/1:0,49:48:-174.66,-14.46,-0.02:99 +chr1 1975030 rs35020387 G A 113.28 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=1769.06;QD=36.10;SB=-889.65 GT:AD:DP:GL:GQ 1/1:0,49:46:-180.51,-13.86,-0.02:99 +chr1 1982066 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=56.20;MQ0=0;OQ=60.60;QD=2.42;SB=35.14 GT:AD:DP:GL:GQ 0/1:18,7:19:-15.09,-5.75,-56.99:93.44 +chr1 1982837 rs17777295 G T 2.34 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=4.79;MQ=57.88;MQ0=0;OQ=1411.52;QD=35.29;SB=-620.56 GT:AD:DP:GL:GQ 1/1:0,40:39:-144.75,-11.75,-0.01:99 +chr1 1987331 rs56136180 A G 202.47 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=1.52;MQ=55.14;MQ0=0;OQ=1346.89;QD=15.85;SB=-685.93 GT:AD:DP:GL:GQ 0/1:38,47:81:-162.37,-24.40,-147.70:99 +chr1 1989540 rs28479788 G A 186.47 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=58.66;MQ0=0;OQ=851.87;QD=16.38;SB=-358.89 GT:AD:DP:GL:GQ 0/1:25,27:48:-102.94,-14.47,-69.44:99 +chr1 1995600 rs2459986 T C 313.08 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.14;MQ0=0;OQ=733.38;QD=27.16;SB=-310.12 GT:AD:DP:GL:GQ 1/1:0,27:25:-76.96,-7.55,-0.03:75.14 +chr1 1996588 rs2678943 T C 52.85 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.08;MQ0=0;OQ=1052.54;QD=26.99;SB=-491.16 GT:AD:DP:GL:GQ 1/1:0,38:34:-108.87,-10.26,-0.03:99 +chr1 1997534 rs2803307 A G 10.35 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.74;MQ=59.13;MQ0=0;OQ=1580.39;QD=29.82;SB=-788.60 GT:AD:DP:GL:GQ 1/1:0,53:50:-161.67,-15.08,-0.05:99 +chr1 1999411 . C T 1.67 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=5.65;MQ=58.95;MQ0=0;OQ=1145.66;QD=18.48;SB=-378.12 GT:AD:DP:GL:GQ 0/1:25,36:58:-135.32,-17.47,-87.50:99 +chr1 2004056 rs28436686 G A 119.72 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=59.61;MQ0=0;OQ=2326.78;QD=39.44;SB=-1079.37 GT:AD:DP:GL:GQ 1/1:0,59:59:-236.28,-17.77,-0.01:99 +chr1 2014367 rs9729600 T C 414.10 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=1723.74;QD=27.36;SB=-655.55 GT:AD:DP:GL:GQ 1/1:0,63:57:-176.03,-17.20,-0.07:99 +chr1 2015467 rs61775405 G A 154 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=57.06;MQ0=0;OQ=444.57;QD=10.84;SB=-245.22 GT:AD:DP:GL:GQ 0/1:23,18:37:-58.92,-11.18,-62.94:99 +chr1 2015957 . T A 20.13 LowQual AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.77;MQ0=3;QD=0.75;SB=-6.99 GT:AD:DP:GL:GQ 0/1:17,10:5:-6.80,-1.51,-8.98:52.92 +chr1 2015991 . G T 43.95 LowQual AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=23.36;MQ0=2;QD=1.19;SB=-6.99 GT:AD:DP:GL:GQ 0/1:34,3:8:-10.09,-2.41,-13.96:76.78 +chr1 2017284 rs12123775 G A 100.24 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=256.85;QD=11.17;SB=-34.51 GT:AD:DP:GL:GQ 0/1:14,9:22:-35.60,-6.63,-46.44:99 +chr1 2019252 rs3128329 T C 18.82 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.93;MQ=58.39;MQ0=0;OQ=1634.16;QD=29.71;SB=-754.64 GT:AD:DP:GL:GQ 1/1:0,55:52:-167.05,-15.69,-0.05:99 +chr1 2019320 . T G 18.93 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=4;HaplotypeScore=7.98;MQ=58.04;MQ0=0;QD=0.34;SB=68.22 GT:AD:DP:GL:GQ 0/1:29,26:34:-15.41,-10.24,-102.90:51.71 +chr1 2019693 . T G 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=51.54;MQ0=0;OQ=164.91;QD=4.34;SB=47.17 GT:AD:DP:GL:GQ 0/1:19,19:29:-28.51,-8.74,-68.55:99 +chr1 2023899 rs7521371 A G 276.27 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.14;MQ0=0;OQ=762.93;QD=15.26;SB=-284.46 GT:AD:DP:GL:GQ 0/1:23,27:49:-94.34,-14.76,-92.20:99 +chr1 2025239 rs10910029 A G 201.72 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.60;MQ0=0;OQ=1376.71;QD=29.29;SB=-649.94 GT:AD:DP:GL:GQ 1/1:0,47:44:-141.29,-13.27,-0.04:99 +chr1 2025544 rs10910030 C T 525.81 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1279.25;QD=36.55;SB=-479.12 GT:AD:DP:GL:GQ 1/1:0,35:34:-131.53,-10.25,-0.02:99 +chr1 2025659 rs10752741 G A 653.38 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2163.55;QD=37.96;SB=-800.07 GT:AD:DP:GL:GQ 1/1:0,57:55:-219.96,-16.57,-0.02:99 +chr1 2025837 rs10752742 G T 4.06 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=6.39;MQ=58.92;MQ0=0;OQ=1340.29;QD=31.17;SB=-640.07 GT:AD:DP:GL:GQ 1/1:0,43:38:-137.63,-11.45,-0.01:99 +chr1 2026123 rs10797413 G A 219.84 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.78;MQ0=0;OQ=1381.00;QD=36.34;SB=-700.35 GT:AD:DP:GL:GQ 1/1:0,38:36:-141.70,-10.85,-0.01:99 +chr1 2026457 rs3128332 G T 494.54 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=1536.71;QD=35.74;SB=-400.25 GT:AD:DP:GL:GQ 1/1:0,43:42:-157.27,-12.65,-0.01:99 +chr1 2027806 . A G 242.28 HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=33.01;MQ0=5;QD=9.69;SB=-135.79 GT:AD:DP:GL:GQ 0/1:9,16:13:-31.43,-3.92,-15.54:99 +chr1 2027817 . A G 86.37 HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=28.31;MQ0=5;QD=5.08;SB=-66.32 GT:AD:DP:GL:GQ 0/1:7,10:8:-14.33,-2.41,-15.43:99 +chr1 2027825 rs7364595 T C 235.65 PASS AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.06;MQ0=5;OQ=93.65;QD=7.80;SB=-40.95 GT:AD:DP:GL:GQ 1/1:0,12:4:-12.90,-1.21,-0.00:12.03 +chr1 2027884 . A G 40.99 LowQual AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=37.48;MQ0=2;QD=4.10;SB=-10.00 GT:AD:DP:GL:GQ 0/1:3,7:4:-8.59,-1.21,-3.37:21.64 +chr1 2027902 . C T 0.78 PASS AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=45.01;MQ0=2;OQ=55.77;QD=3.49;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,3:11:-12.18,-3.32,-23.75:88.60 +chr1 2027903 . A G 47.94 LowQual AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=45.01;MQ0=2;QD=3.00;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,4:11:-11.39,-3.31,-30.54:80.77 +chr1 2027922 rs61775410 A G 254.38 Indel AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=52.34;MQ0=2;QD=12.11;SB=-40.68 GT:AD:DP:GL:GQ 0/1:8,13:15:-33.24,-4.52,-21.40:99 +chr1 2027961 rs12745429 G A 0.31 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=3.42;MQ=51.66;MQ0=4;OQ=50.47;QD=1.58;SB=-46.03 GT:AD:DP:GL:GQ 0/1:27,5:21:-14.67,-6.34,-51.74:83.30 +chr1 2027962 rs12723086 T C 0.38 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=3.42;MQ=51.66;MQ0=4;OQ=55.89;QD=1.75;SB=-41.82 GT:AD:DP:GL:GQ 0/1:25,7:25:-16.41,-7.54,-72.40:88.73 +chr1 2027980 . A G 0.42 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=49.52;MQ0=4;OQ=96.12;QD=2.75;SB=-41.28 GT:AD:DP:GL:GQ 0/1:27,8:28:-21.34,-8.45,-80.79:99 +chr1 2027991 . A G 34.81 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.55;MQ=51.01;MQ0=3;OQ=431.23;QD=9.58;SB=-194.62 GT:AD:DP:GL:GQ 0/1:24,21:36:-57.25,-10.85,-78.85:99 +chr1 2028038 rs7349084 A G 0.09 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=50.77;MQ0=1;OQ=115.20;QD=1.99;SB=-64.54 GT:AD:DP:GL:GQ 0/1:47,10:48:-29.27,-14.47,-151.97:99 +chr1 2028049 rs12133181 A G 36.56 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=65.95;MQ=50.10;MQ0=2;QD=0.48;SB=17.41 GT:AD:DP:GL:GQ 0/1:60,12:63:-25.92,-18.99,-218.94:69.39 +chr1 2028057 rs7514664 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=1;HaplotypeScore=92.07;MQ=50.08;MQ0=4;OQ=1734.98;QD=17.53;SB=-712.36 GT:AD:DP:GL:GQ 0/1:13,84:69:-197.59,-20.81,-27.48:66.63 +chr1 2028096 rs7349113 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=144;Dels=0.00;HRun=1;HaplotypeScore=338.66;MQ=50.60;MQ0=2;OQ=249.31;QD=1.73;SB=17.40 GT:AD:DP:GL:GQ 0/1:107,21:99:-60.23,-32.01,-282.27:99 +chr1 2028116 rs61775411 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=130;Dels=0.00;HRun=1;HaplotypeScore=156.17;MQ=50.22;MQ0=2;OQ=1368.71;QD=10.53;SB=-489.55 GT:AD:DP:GL:GQ 0/1:47,78:82:-164.90,-24.74,-105.56:99 +chr1 2028135 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=77.77;MQ=49.84;MQ0=2;OQ=170.97;QD=2.04;SB=-24.42 GT:AD:DP:GL:GQ 0/1:67,11:63:-39.37,-18.98,-181.92:99 +chr1 2028136 rs12080420 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=76.98;MQ=49.85;MQ0=2;OQ=157.43;QD=1.94;SB=-74.46 GT:AD:DP:GL:GQ 0/1:62,16:61:-37.41,-18.38,-198.10:99 +chr1 2028154 rs3753241 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=33.73;MQ=52.95;MQ0=1;OQ=379.95;QD=7.31;SB=-7.96 GT:AD:DP:GL:GQ 0/1:34,16:44:-54.55,-13.27,-93.77:99 +chr1 2028522 rs3128334 G A 30.30 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=59.44;MQ0=0;OQ=1539.70;QD=37.55;SB=-534.21 GT:AD:DP:GL:GQ 1/1:0,39:39:-157.57,-11.75,-0.01:99 +chr1 2028753 rs908744 G A 89.13 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.73;MQ=58.80;MQ0=0;OQ=1922.45;QD=33.15;SB=-549.87 GT:AD:DP:GL:GQ 1/1:0,58:52:-195.86,-15.68,-0.03:99 +chr1 2029096 rs1040231 G T 78.45 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.23;MQ=58.48;MQ0=0;OQ=1527.94;QD=33.22;SB=-620.05 GT:AD:DP:GL:GQ 1/1:1,45:45:-156.40,-13.56,-0.02:99 +chr1 2029381 rs16824792 G T 92.11 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.28;MQ0=0;OQ=1106.74;QD=34.59;SB=-441.64 GT:AD:DP:GL:GQ 1/1:0,32:31:-114.27,-9.34,-0.01:93.28 +chr1 2029579 rs1878752 G A 107.74 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.58;MQ0=0;OQ=1364.65;QD=36.88;SB=-510.18 GT:AD:DP:GL:GQ 1/1:0,37:36:-140.06,-10.85,-0.01:99 +chr1 2029956 rs6666117 T C 57.04 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=967.27;QD=27.64;SB=-467.25 GT:AD:DP:GL:GQ 1/1:0,35:31:-100.34,-9.35,-0.03:93.22 +chr1 2030248 rs6683011 G A 365.12 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.46;MQ0=0;OQ=938.15;QD=36.08;SB=-369.99 GT:AD:DP:GL:GQ 1/1:0,26:24:-97.41,-7.23,-0.01:72.24 +chr1 2030623 rs4648805 G A 629.77 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=1690.17;QD=38.41;SB=-769.01 GT:AD:DP:GL:GQ 1/1:0,44:44:-172.62,-13.26,-0.02:99 +chr1 2030637 rs4648806 C T 94.85 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=56.04;MQ0=0;OQ=1691.52;QD=35.24;SB=-723.01 GT:AD:DP:GL:GQ 1/1:0,48:44:-172.75,-13.26,-0.02:99 +chr1 2030645 rs6674878 A G 54.62 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=55.66;MQ0=0;OQ=1170.82;QD=26.61;SB=-567.76 GT:AD:DP:GL:GQ 1/1:0,44:39:-120.72,-11.78,-0.06:99 +chr1 2030758 rs4648807 T C 223.06 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=59.17;MQ0=0;OQ=1628.83;QD=29.09;SB=-733.30 GT:AD:DP:GL:GQ 1/1:0,56:52:-166.52,-15.69,-0.05:99 +chr1 2030796 rs4648808 T C 215.31 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.65;MQ0=0;OQ=1868.75;QD=28.75;SB=-846.52 GT:AD:DP:GL:GQ 1/1:0,65:59:-190.51,-17.80,-0.05:99 +chr1 2031015 rs10910046 C T 236.58 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.92;MQ0=0;OQ=619.66;QD=30.98;SB=-276.86 GT:AD:DP:GL:GQ 1/1:0,20:17:-65.56,-5.12,-0.01:51.16 +chr1 2031321 rs12059660 C T 236.90 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.27;MQ0=0;OQ=1048.92;QD=38.85;SB=-437.08 GT:AD:DP:GL:GQ 1/1:0,27:27:-108.48,-8.13,-0.01:81.26 +chr1 2032403 rs11584491 A G 58.20 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=59.38;MQ0=0;OQ=893.06;QD=29.77;SB=-424.80 GT:AD:DP:GL:GQ 1/1:0,30:30:-92.92,-9.05,-0.03:90.18 +chr1 2032854 rs3128336 C G 73.49 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=59.29;MQ0=0;OQ=1394.69;QD=35.76;SB=-622.82 GT:AD:DP:GL:GQ 1/1:0,39:35:-143.08,-10.56,-0.03:99 +chr1 2033844 rs3107141 C T 92.22 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.37;MQ=59.25;MQ0=0;OQ=2275.40;QD=36.70;SB=-1025.90 GT:AD:DP:GL:GQ 1/1:0,62:59:-231.15,-17.78,-0.02:99 +chr1 2033897 rs925905 T C 149.67 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.07;MQ0=0;OQ=2152.92;QD=34.17;SB=-821.32 GT:AD:DP:GL:GQ 1/1:0,63:61:-218.90,-18.38,-0.02:99 +chr1 2033914 rs925906 A C 279.99 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.02;HRun=0;HaplotypeScore=0.48;MQ=59.34;MQ0=0;OQ=1986.91;QD=33.12;SB=-865.63 GT:AD:DP:GL:GQ 1/1:0,59:59:-202.29,-17.47,-0.02:99 +chr1 2034402 rs3107142 T C 2.70 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=862.83;QD=28.76;SB=-292.45 GT:AD:DP:GL:GQ 1/1:0,30:25:-89.88,-7.54,-0.02:75.20 +chr1 2035025 rs1467217 G A 101.18 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=58.81;MQ0=0;OQ=1215.26;QD=31.16;SB=-472.57 GT:AD:DP:GL:GQ 1/1:2,37:32:-125.13,-9.65,-0.02:96.30 +chr1 2035232 rs3107143 G C 1383.32 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=3;HaplotypeScore=1.46;MQ=53.42;MQ0=0;QD=40.69;SB=-202.29 GT:AD:DP:GL:GQ 1/1:0,34:32:-141.93,-9.65,-0.01:96.32 +chr1 2035236 rs61775448 A G 957.24 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=52.98;MQ0=0;QD=29.91;SB=-159.74 GT:AD:DP:GL:GQ 1/1:0,32:29:-99.32,-8.74,-0.01:87.24 +chr1 2035240 rs3107144 C A 1108.98 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=53.21;MQ0=0;QD=33.61;SB=-288.09 GT:AD:DP:GL:GQ 1/1:0,33:31:-114.49,-9.34,-0.01:93.28 +chr1 2035742 rs3128337 A G 495.13 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.14;MQ0=0;OQ=2084.14;QD=30.20;SB=-613.59 GT:AD:DP:GL:GQ 1/1:0,69:67:-212.07,-20.22,-0.07:99 +chr1 2036646 rs3128338 G A 633.58 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2283.85;QD=36.84;SB=-1084.46 GT:AD:DP:GL:GQ 1/1:0,61:60:-232.00,-18.09,-0.03:99 +chr1 2036798 rs3128339 G T 418.21 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.44;MQ0=0;OQ=1615.06;QD=33.65;SB=-604.54 GT:AD:DP:GL:GQ 1/1:0,48:46:-165.11,-13.86,-0.02:99 +chr1 2037356 rs3128340 C G 20.94 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=1.21;MQ=59.34;MQ0=0;OQ=2469.41;QD=39.20;SB=-820.16 GT:AD:DP:GL:GQ 1/1:0,63:62:-250.56,-18.70,-0.04:99 +chr1 2037407 rs3107145 G A 220.34 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.05;MQ0=0;OQ=2392.58;QD=37.38;SB=-1173.71 GT:AD:DP:GL:GQ 1/1:0,64:62:-242.87,-18.68,-0.02:99 +chr1 2037444 rs3107146 T C 445.88 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=1708.25;QD=30.50;SB=-576.98 GT:AD:DP:GL:GQ 1/1:0,56:53:-174.45,-15.98,-0.04:99 +chr1 2038589 rs3107147 G A 179.13 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.78;MQ0=0;OQ=3375.92;QD=40.19;SB=-1379.05 GT:AD:DP:GL:GQ 1/1:0,83:83:-336.59,-25.00,-0.02:99 +chr1 2039293 . A T 534.23 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=3;HaplotypeScore=26.93;MQ=46.16;MQ0=1;QD=5.40;SB=50.36 GT:AD:DP:GL:GQ 0/1:64,35:82:-81.41,-24.70,-228.25:99 +chr1 2039297 . C T 849.12 Indel AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=16;HaplotypeScore=37.86;MQ=45.71;MQ0=2;QD=8.01;SB=-44.28 GT:AD:DP:GL:GQ 0/1:72,34:90:-115.31,-27.11,-215.41:99 +chr1 2039368 rs3128290 G T 199.82 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=57.68;MQ0=0;OQ=1893.89;QD=32.65;SB=-943.62 GT:AD:DP:GL:GQ 1/1:0,58:54:-193.00,-16.27,-0.02:99 +chr1 2039459 rs3107148 T C 580.43 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1837.96;QD=36.04;SB=-792.00 GT:AD:DP:GL:GQ 1/1:0,51:51:-187.40,-15.36,-0.01:99 +chr1 2040055 rs3107149 A T 0.64 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=7.05;MQ=47.19;MQ0=2;OQ=1180.60;QD=26.83;SB=-338.84 GT:AD:DP:GL:GQ 1/1:1,43:33:-121.66,-9.94,-0.01:99 +chr1 2040785 rs3107150 T A 621.62 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.05;MQ0=0;OQ=2606.94;QD=34.76;SB=-964.53 GT:AD:DP:GL:GQ 1/1:0,75:72:-264.30,-21.69,-0.03:99 +chr1 2041373 rs3107151 T G 405.29 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.29;MQ0=0;OQ=1384.90;QD=30.11;SB=-485.99 GT:AD:DP:GL:GQ 1/1:0,46:41:-142.10,-12.35,-0.02:99 +chr1 2042357 rs3107152 T C 727.24 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2187.52;QD=34.72;SB=-1010.74 GT:AD:DP:GL:GQ 1/1:0,63:62:-222.36,-18.68,-0.02:99 +chr1 2042782 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.57;MQ=44.83;MQ0=0;OQ=64.06;QD=1.26;SB=2.03 GT:AD:DP:GL:GQ 0/1:44,7:48:-24.15,-14.46,-148.69:96.90 +chr1 2042814 . C G 7.67 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.26;MQ=39.19;MQ0=0;OQ=415.49;QD=7.69;SB=-85.80 GT:AD:DP:GL:GQ 0/1:38,16:51:-60.21,-15.38,-162.70:99 +chr1 2042818 . A G 548.88 SnpCluster AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=3.40;MQ=38.13;MQ0=0;QD=9.15;SB=-238.62 GT:AD:DP:GL:GQ 0/1:35,25:55:-74.74,-16.57,-136.02:99 +chr1 2042827 rs56946456 C T 974.86 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=37.16;MQ0=0;QD=15.23;SB=-13.45 GT:AD:DP:GL:GQ 0/1:33,30:59:-118.54,-17.77,-108.89:99 +chr1 2042828 rs59510407 A G 718.63 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=2.75;MQ=36.52;MQ0=0;QD=11.98;SB=-10.84 GT:AD:DP:GL:GQ 0/1:33,26:56:-92.01,-16.87,-122.40:99 +chr1 2042846 rs58866862 A G 74.49 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=35.77;MQ0=0;QD=1.16;SB=32.14 GT:AD:DP:GL:GQ 0/1:43,21:44:-23.99,-13.25,-151.62:99 +chr1 2042857 rs61526019 C T 19.11 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=37.11;MQ0=1;QD=0.30;SB=35.13 GT:AD:DP:GL:GQ 0/1:49,15:46:-19.05,-13.86,-151.53:51.90 +chr1 2042876 . G T 13.23 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=1;HaplotypeScore=9.69;MQ=38.17;MQ0=2;QD=0.18;SB=41.11 GT:AD:DP:GL:GQ 0/1:58,9:53:-20.55,-15.96,-167.03:45.86 +chr1 2042878 . T C 0.10 PASS AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=11.69;MQ=38.38;MQ0=2;OQ=1187.23;QD=16.96;SB=-479.73 GT:AD:DP:GL:GQ 0/1:15,55:50:-137.09,-15.08,-24.25:91.67 +chr1 2042931 . A G 53.02 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=15.54;MQ=37.98;MQ0=2;QD=0.69;SB=20.09 GT:AD:DP:GL:GQ 0/1:67,10:63:-27.57,-18.98,-213.37:85.85 +chr1 2042932 . C T 144.76 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=10.55;MQ=37.98;MQ0=2;QD=1.88;SB=20.04 GT:AD:DP:GL:GQ 0/1:64,13:62:-36.47,-18.71,-162.72:99 +chr1 2042933 rs61775451 A G 2056.36 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=7.24;MQ=37.41;MQ0=2;QD=27.79;SB=-304.45 GT:AD:DP:GL:GQ 1/1:0,74:61:-209.25,-18.38,-0.03:99 +chr1 2042939 rs61775452 A G 1556.23 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=44.30;MQ=35.88;MQ0=3;QD=19.21;SB=-241.65 GT:AD:DP:GL:GQ 0/1:26,55:67:-179.09,-20.18,-61.01:99 +chr1 2042967 . G A 494.62 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=42.03;MQ=31.07;MQ0=2;QD=5.75;SB=-10.00 GT:AD:DP:GL:GQ 0/1:65,21:57:-69.92,-17.17,-132.17:99 +chr1 2042968 . T C 324.84 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=41.51;MQ=30.57;MQ0=2;QD=3.82;SB=-7.00 GT:AD:DP:GL:GQ 0/1:68,17:56:-52.65,-16.88,-157.62:99 +chr1 2042975 . G A 918.15 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=43.08;MQ=30.97;MQ0=1;QD=11.92;SB=-7.00 GT:AD:DP:GL:GQ 0/1:43,34:50:-110.16,-15.06,-77.95:99 +chr1 2042993 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=37.83;MQ=26.92;MQ0=1;OQ=262.34;QD=4.60;SB=-10.00 GT:AD:DP:GL:GQ 0/1:38,19:39:-41.26,-11.74,-103.99:99 +chr1 2043003 . A G 593.68 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=39;Dels=0.03;HRun=0;HaplotypeScore=30.47;MQ=26.18;MQ0=1;QD=15.22;SB=-10.00 GT:AD:DP:GL:GQ 0/1:16,22:23:-69.27,-6.63,-8.02:13.91 +chr1 2043004 . C T 763.57 Indel;SnpCluster AC=2;AF=1.00;AN=2;DP=36;Dels=0.06;HRun=0;HaplotypeScore=22.21;MQ=26.52;MQ0=1;QD=21.21;SB=-10.00 GT:AD:DP:GL:GQ 1/1:3,31:22:-82.94,-6.33,-3.00:33.26 +chr1 2043011 . A G 85.38 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=13.94;MQ=26.97;MQ0=0;QD=3.28;SB=-10.00 GT:AD:DP:GL:GQ 0/1:19,7:20:-17.84,-6.02,-61.94:99 +chr1 2043025 . C T 0.23 PASS AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=7.88;MQ=23.26;MQ0=0;OQ=89.13;QD=11.14;SB=-10.00 GT:AD:DP:GL:GQ 1/1:3,5:3:-12.40,-0.90,-0.00:9.03 +chr1 2043058 . C T 0.16 PASS AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=7.97;MQ=18.94;MQ0=5;OQ=124.33;QD=12.43;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,6:4:-15.97,-1.21,-0.00:12.04 +chr1 2043061 . C T 0.16 PASS AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=9.08;MQ=17.30;MQ0=6;OQ=117.32;QD=9.78;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,8:4:-15.27,-1.21,-0.00:12.04 +chr1 2043097 . C T 1.40 PASS AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=4.78;MQ=17.14;MQ0=7;OQ=117.84;QD=7.86;SB=-10.00 GT:AD:DP:GL:GQ 0/1:11,4:5:-16.57,-1.51,-3.10:15.90 +chr1 2043134 rs62641630 A G 85.81 Indel AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=34.82;MQ=24.20;MQ0=2;QD=5.36;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,7:9:-14.57,-2.71,-19.58:99 +chr1 2043141 . T G 143.26 Indel AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=21.33;MQ0=2;QD=11.94;SB=-10.00 GT:AD:DP:GL:GQ 1/1:3,9:5:-17.89,-1.51,-0.00:15.05 +chr1 2043178 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=18.82;MQ=19.76;MQ0=6;OQ=129.40;QD=2.70;SB=-10.00 GT:AD:DP:GL:GQ 0/1:34,14:15:-20.75,-4.53,-30.16:99 +chr1 2043181 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=18.51;MQ=19.26;MQ0=7;OQ=70.77;QD=1.31;SB=-10.00 GT:AD:DP:GL:GQ 0/1:41,12:15:-14.88,-4.52,-41.18:99 +chr1 2043199 . T C 326.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=71.39;MQ=18.51;MQ0=9;QD=3.23;SB=5.04 GT:AD:DP:GL:GQ 0/1:73,28:19:-41.66,-5.73,-27.12:99 +chr1 2043200 . G T 127.31 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=1;HaplotypeScore=109.06;MQ=18.45;MQ0=9;QD=1.24;SB=5.04 GT:AD:DP:GL:GQ 0/1:88,15:19:-21.74,-5.72,-47.36:99 +chr1 2043203 . A G 195.43 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=1;HaplotypeScore=58.32;MQ=18.15;MQ0=10;QD=1.74;SB=5.04 GT:AD:DP:GL:GQ 0/1:95,17:20:-28.85,-6.02,-47.43:99 +chr1 2043227 rs61775455 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=139;Dels=0.00;HRun=1;HaplotypeScore=26.18;MQ=17.76;MQ0=15;OQ=512.67;QD=3.69;SB=-282.20 GT:AD:DP:GL:GQ 0/1:22,117:18:-59.98,-5.43,-16.39:99 +chr1 2043250 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=40.25;MQ=18.52;MQ0=5;OQ=52.10;QD=0.80;SB=5.03 GT:AD:DP:GL:GQ 0/1:47,18:9:-11.21,-2.71,-18.54:84.93 +chr1 2043253 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=69.74;MQ=17.96;MQ0=6;OQ=126.28;QD=2.18;SB=-31.52 GT:AD:DP:GL:GQ 0/1:37,20:7:-18.02,-2.11,-6.74:46.31 +chr1 2043286 . C T 29.35 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=15.82;MQ=16.30;MQ0=5;QD=1.47;SB=-39.54 GT:AD:DP:GL:GQ 0/1:10,10:4:-7.42,-1.21,-6.19:49.87 +chr1 2043289 . C T 29.39 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=12.80;MQ=15.14;MQ0=5;QD=1.73;SB=-36.53 GT:AD:DP:GL:GQ 0/1:8,8:3:-7.13,-0.91,-2.70:17.92 +chr1 2043333 . T G 28.03 LowQual AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=18.60;MQ0=2;QD=4.00;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:2:-6.21,-0.60,-0.00:6.01 +chr1 2043370 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=30.96;MQ=17.94;MQ0=3;OQ=266.78;QD=3.51;SB=-158.18 GT:AD:DP:GL:GQ 0/1:20,55:9:-32.59,-2.71,-3.10:3.86 +chr1 2043387 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=305.93;MQ=17.79;MQ0=4;OQ=61.76;QD=0.60;SB=5.03 GT:AD:DP:GL:GQ 0/1:70,33:9:-12.17,-2.71,-18.55:94.59 +chr1 2043399 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=80.07;MQ=17.30;MQ0=8;OQ=50.40;QD=0.46;SB=-41.37 GT:AD:DP:GL:GQ 0/1:77,30:6:-10.13,-1.81,-8.76:69.51 +chr1 2043410 . G A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=62.95;MQ=16.84;MQ0=8;OQ=120.99;QD=1.22;SB=-42.66 GT:AD:DP:GL:GQ 1/1:14,85:4:-15.63,-1.21,-0.00:12.04 +chr1 2043421 . C T 40.51 LowQual AC=1;AF=0.50;AN=2;DP=97;Dels=0.01;HRun=0;HaplotypeScore=78.29;MQ=16.56;MQ0=9;QD=0.42;SB=-7.00 GT:AD:DP:GL:GQ 0/1:75,21:3:-8.24,-0.90,-2.77:18.65 +chr1 2043428 . G A 73.75 Indel AC=2;AF=1.00;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=65.46;MQ=16.72;MQ0=6;QD=0.88;SB=-10.00 GT:AD:DP:GL:GQ 1/1:16,68:3:-10.87,-0.91,-0.00:9.02 +chr1 2043438 . G A 70.80 Indel AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=64.65;MQ=17.33;MQ0=2;QD=1.00;SB=-10.00 GT:AD:DP:GL:GQ 0/1:44,27:4:-11.57,-1.20,-3.47:22.64 +chr1 2043560 . G C 29.95 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=54.01;MQ=17.20;MQ0=4;QD=0.86;SB=-10.00 GT:AD:DP:GL:GQ 0/1:29,6:4:-7.49,-1.21,-7.00:57.86 +chr1 2043565 . C T 49.25 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=47.09;MQ=17.14;MQ0=4;QD=1.37;SB=-10.00 GT:AD:DP:GL:GQ 1/1:19,17:2:-8.33,-0.60,-0.00:6.02 +chr1 2043572 . G A 46.02 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=33.86;MQ=16.62;MQ0=6;QD=1.18;SB=-10.00 GT:AD:DP:GL:GQ 1/1:22,17:2:-8.01,-0.60,-0.00:6.02 +chr1 2043583 . C T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=32.32;MQ=16.61;MQ0=6;OQ=173.76;QD=4.57;SB=-10.00 GT:AD:DP:GL:GQ 1/1:16,22:5:-20.94,-1.51,-0.00:15.05 +chr1 2043590 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=28.82;MQ=16.31;MQ0=5;OQ=78.84;QD=2.39;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,18:4:-12.37,-1.20,-2.87:16.64 +chr1 2043797 . C T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=30.70;MQ=15.39;MQ0=12;OQ=90.55;QD=2.66;SB=-10.00 GT:AD:DP:GL:GQ 1/1:10,21:4:-15.80,-4.21,-3.24:9.74 +chr1 2043818 . T C 79 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=39.74;MQ=12.98;MQ0=29;QD=1.39;SB=-10.00 GT:AD:DP:GL:GQ 1/1:42,15:3:-11.39,-0.90,-0.00:9.03 +chr1 2043819 . G T 74.28 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=66.63;MQ=12.86;MQ0=30;QD=1.28;SB=-10.00 GT:AD:DP:GL:GQ 1/1:43,15:3:-10.92,-0.90,-0.00:9.03 +chr1 2043822 . G A 85.78 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=66.31;MQ=12.73;MQ0=32;QD=1.41;SB=-10.00 GT:AD:DP:GL:GQ 1/1:35,26:3:-12.07,-0.90,-0.00:9.03 +chr1 2043840 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=53.86;MQ=13.17;MQ0=31;OQ=75.78;QD=1.28;SB=-3.99 GT:AD:DP:GL:GQ 0/1:33,26:5:-12.37,-1.51,-6.39:48.86 +chr1 2043865 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=29.69;MQ=17.30;MQ0=6;OQ=56.87;QD=2.19;SB=-30.92 GT:AD:DP:GL:GQ 0/1:19,7:4:-10.17,-1.21,-3.00:17.97 +chr1 2043873 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=65.88;MQ=20.81;MQ0=0;OQ=78.81;QD=5.63;SB=-7.00 GT:AD:DP:GL:GQ 0/1:7,7:4:-12.37,-1.21,-3.20:19.92 +chr1 2044254 . A G 32.28 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;HRun=1;HaplotypeScore=4.00;MQ=14.52;MQ0=7;QD=1.90;SB=-10.00 GT:AD:DP:GL:GQ 1/1:8,9:2:-6.64,-0.60,-0.00:6.02 +chr1 2044261 . G T 34.69 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=14.97;MQ0=6;QD=2.17;SB=-10.00 GT:AD:DP:GL:GQ 1/1:8,8:2:-6.88,-0.60,-0.00:6.02 +chr1 2045053 . A G 0.05 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=13.98;MQ=19.49;MQ0=2;OQ=141.20;QD=10.86;SB=-10.00 GT:AD:DP:GL:GQ 1/1:5,8:5:-17.68,-1.51,-0.00:15.04 +chr1 2045060 . G T 46.93 LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=16.54;MQ=19.21;MQ0=2;QD=3.35;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,5:5:-9.49,-1.51,-6.61:50.97 +chr1 2045064 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=17.54;MQ=18.55;MQ0=3;OQ=51.75;QD=3.45;SB=-10.00 GT:AD:DP:GL:GQ 0/1:6,9:5:-9.97,-1.51,-6.44:49.32 +chr1 2045454 . C T 0.01 FDRtranche2.00to10.00 AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=19.88;MQ=20.43;MQ0=9;OQ=198.28;QD=7.34;SB=-10.00 GT:AD:DP:GL:GQ 1/1:7,20:6:-23.40,-1.81,-0.00:18.06 +chr1 2045469 . C T 0.06 PASS AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=12.29;MQ=20.17;MQ0=11;OQ=284.41;QD=8.89;SB=-48.56 GT:AD:DP:GL:GQ 1/1:9,23:8:-32.02,-2.41,-0.00:24.08 +chr1 2045505 . C T 28.68 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=18.97;MQ=24.13;MQ0=5;QD=0.54;SB=11.04 GT:AD:DP:GL:GQ 0/1:44,9:20:-12.18,-6.03,-54.06:61.51 +chr1 2045518 . C G 738.24 SnpCluster AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=15.01;MQ=25.23;MQ0=2;QD=13.67;SB=-291.20 GT:AD:DP:GL:GQ 0/1:10,44:25:-84.64,-7.53,-25.69:99 +chr1 2045519 . G A 107.30 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=14.97;MQ=25.69;MQ0=2;QD=1.95;SB=11.06 GT:AD:DP:GL:GQ 0/1:46,9:22:-20.64,-6.63,-60.44:99 +chr1 2045523 rs61775456 C T 1156.65 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=31.40;MQ=26.13;MQ0=1;QD=21.03;SB=-340.35 GT:AD:DP:GL:GQ 1/1:5,50:30:-119.26,-9.04,-0.01:90.29 +chr1 2045530 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=38.81;MQ=25.91;MQ0=2;OQ=314.66;QD=4.56;SB=14.05 GT:AD:DP:GL:GQ 0/1:30,39:21:-41.08,-6.33,-36.84:99 +chr1 2045541 rs61775457 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=85.67;MQ=25.28;MQ0=4;OQ=1042.79;QD=14.28;SB=-111.96 GT:AD:DP:GL:GQ 0/1:30,43:36:-118.41,-10.85,-17.33:64.79 +chr1 2045548 rs61775458 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=80.30;MQ=24.94;MQ0=7;OQ=952.67;QD=11.48;SB=11.05 GT:AD:DP:GL:GQ 0/1:35,48:39:-110.31,-11.76,-31.30:99 +chr1 2045552 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=3;HaplotypeScore=82.09;MQ=25.54;MQ0=10;OQ=109.35;QD=1.09;SB=14.08 GT:AD:DP:GL:GQ 0/1:83,17:53:-30.20,-15.98,-173.43:99 +chr1 2045562 rs61775459 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=44.83;MQ=25.87;MQ0=15;OQ=1085.84;QD=10.54;SB=-112.96 GT:AD:DP:GL:GQ 0/1:18,82:44:-125.15,-13.28,-24.49:99 +chr1 2045577 rs61776561 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=71.26;MQ=25.93;MQ0=17;OQ=471.38;QD=4.36;SB=-66.29 GT:AD:DP:GL:GQ 0/1:83,25:48:-64.89,-14.47,-100.62:99 +chr1 2045590 rs61776562 C G 1122.80 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=71.62;MQ=27.29;MQ0=12;QD=12.62;SB=-466.47 GT:AD:DP:GL:GQ 0/1:38,51:51:-130.94,-15.38,-82.60:99 +chr1 2045591 . G A 91.87 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=67.28;MQ=27.29;MQ0=12;QD=1.03;SB=20.08 GT:AD:DP:GL:GQ 0/1:68,21:39:-24.23,-11.76,-108.70:99 +chr1 2045595 rs61776563 C T 1533.88 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=45.58;MQ=27.30;MQ0=11;QD=17.43;SB=-260.54 GT:AD:DP:GL:GQ 1/1:9,79:49:-170.95,-14.77,-14.14:6.27 +chr1 2045606 . A G 34.51 DPFilter;HARD_TO_VALIDATE;Indel;LowQual AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=3;HaplotypeScore=43.22;MQ=27.00;MQ0=12;QD=0.42;SB=23.11 GT:AD:DP:GL:GQ 0/1:76,7:41:-19.11,-12.37,-129.33:67.35 +chr1 2045616 . T C 78.88 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=250.84;MQ=27.16;MQ0=10;QD=1.21;SB=21.87 GT:AD:DP:GL:GQ 0/1:53,10:39:-22.94,-11.77,-110.81:99 +chr1 2045620 rs61776564 G A 378.54 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=91.32;MQ=25.99;MQ0=10;QD=7.14;SB=2.03 GT:AD:DP:GL:GQ 0/1:31,22:26:-48.98,-7.84,-44.75:99 +chr1 2045631 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=20.68;MQ=23.69;MQ0=10;OQ=345.67;QD=8.43;SB=-190.29 GT:AD:DP:GL:GQ 0/1:16,25:18:-43.28,-5.43,-21.54:99 +chr1 2045638 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=35.28;MQ=23.82;MQ0=10;OQ=167.44;QD=4.29;SB=-58.06 GT:AD:DP:GL:GQ 0/1:24,15:14:-24.25,-4.23,-24.00:99 +chr1 2045652 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=49.08;MQ=21.77;MQ0=9;OQ=173.85;QD=5.43;SB=-84.31 GT:AD:DP:GL:GQ 0/1:13,19:7:-22.76,-2.11,-3.10:9.89 +chr1 2045656 . G A 40.26 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=55.88;MQ=22.32;MQ0=8;QD=1.34;SB=-10.00 GT:AD:DP:GL:GQ 0/1:16,14:3:-8.21,-0.90,-3.07:21.65 +chr1 2045667 . C T 56.78 SnpCluster AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=27.04;MQ=25.03;MQ0=2;QD=2.18;SB=-3.99 GT:AD:DP:GL:GQ 0/1:9,17:7:-11.07,-2.11,-11.53:89.62 +chr1 2045670 . C T 22.25 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=24.25;MQ=25.19;MQ0=1;QD=0.93;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,19:3:-6.41,-0.91,-3.37:24.66 +chr1 2045674 . G A 38.46 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=35.09;MQ=29.74;MQ0=1;QD=1.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,15:4:-8.34,-1.21,-6.59:53.87 +chr1 2045688 rs61776565 C T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=37.51;MQ=32.86;MQ0=0;OQ=472.91;QD=12.78;SB=-219.35 GT:AD:DP:GL:GQ 1/1:8,29:13:-50.88,-3.92,-0.00:39.13 +chr1 2045716 rs11589827 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=37.92;MQ=32.79;MQ0=0;OQ=1051.52;QD=19.47;SB=-363.54 GT:AD:DP:GL:GQ 0/1:22,32:36:-119.28,-10.85,-21.22:99 +chr1 2045975 rs56260599 A G 8.24 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=2.17;MQ=48.30;MQ0=0;OQ=1370.04;QD=29.78;SB=-550.86 GT:AD:DP:GL:GQ 1/1:0,45:39:-140.61,-11.75,-0.02:99 +chr1 2047610 rs3107154 A C 149.56 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.43;MQ0=0;OQ=1416.93;QD=32.20;SB=-509.01 GT:AD:DP:GL:GQ 1/1:0,44:41:-145.30,-12.35,-0.02:99 +chr1 2047883 rs3128291 A G 544.70 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1311.92;QD=28.52;SB=-584.18 GT:AD:DP:GL:GQ 1/1:0,46:44:-134.83,-13.28,-0.06:99 +chr1 2050384 rs3107155 T C 5.04 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=1.93;MQ=59.45;MQ0=0;OQ=1167.72;QD=27.80;SB=-528.96 GT:AD:DP:GL:GQ 1/1:0,42:38:-120.40,-11.47,-0.04:99 +chr1 2050490 rs3107156 T C 249.61 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=60.00;MQ0=0;OQ=2021.38;QD=30.17;SB=-957.45 GT:AD:DP:GL:GQ 1/1:0,67:63:-205.77,-19.00,-0.05:99 +chr1 2050592 rs10797427 C T 209.13 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=2020.11;QD=36.73;SB=-999.03 GT:AD:DP:GL:GQ 1/1:0,54:53:-205.62,-15.97,-0.03:99 +chr1 2051236 rs6603815 T C 200 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.85;MQ0=0;OQ=2560.21;QD=35.07;SB=-874.04 GT:AD:DP:GL:GQ 1/1:0,73:73:-259.63,-21.99,-0.03:99 +chr1 2051829 rs3107157 T C 631.33 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=1661.55;QD=30.21;SB=-807.71 GT:AD:DP:GL:GQ 1/1:0,55:52:-169.78,-15.68,-0.04:99 +chr1 2053024 rs2222217 G A 330.52 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=1814.00;QD=39.43;SB=-879.02 GT:AD:DP:GL:GQ 1/1:0,46:46:-185.00,-13.86,-0.01:99 +chr1 2055199 rs3128293 A G 0.17 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=4;HaplotypeScore=2.50;MQ=57.87;MQ0=0;OQ=714.48;QD=32.48;SB=-354.81 GT:AD:DP:GL:GQ 1/1:0,22:21:-75.04,-6.33,-0.01:63.18 +chr1 2055203 rs3128294 G C 31.92 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=2.50;MQ=59.11;MQ0=0;OQ=958.73;QD=36.87;SB=-480.55 GT:AD:DP:GL:GQ 1/1:0,26:24:-99.47,-7.24,-0.01:72.23 +chr1 2056850 rs55958603 C T 1.19 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=3.45;MQ=57.77;MQ0=0;OQ=633.04;QD=15.07;SB=-129.09 GT:AD:DP:GL:GQ 0/1:21,21:38:-78.03,-11.45,-68.95:99 +chr1 2058340 rs3128295 C T 135.04 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=57.98;MQ0=0;OQ=1478.85;QD=33.61;SB=-754.65 GT:AD:DP:GL:GQ 1/1:0,43:39:-151.49,-11.75,-0.02:99 +chr1 2058766 rs3128296 G T 62.70 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=59.52;MQ0=0;OQ=1387.47;QD=35.58;SB=-366.86 GT:AD:DP:GL:GQ 1/1:0,39:38:-142.34,-11.45,-0.01:99 +chr1 2060181 rs411021 T C 39.97 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.62;MQ0=0;OQ=1893.37;QD=29.58;SB=-877.01 GT:AD:DP:GL:GQ 1/1:0,64:60:-192.98,-18.10,-0.06:99 +chr1 2061200 rs424079 C A 282.41 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.70;MQ0=0;OQ=2061.38;QD=33.25;SB=-816.15 GT:AD:DP:GL:GQ 1/1:2,60:59:-209.75,-17.78,-0.03:99 +chr1 2061416 rs436045 A G 341.67 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1852.88;QD=31.95;SB=-463.52 GT:AD:DP:GL:GQ 1/1:0,58:55:-188.90,-16.57,-0.02:99 +chr1 2061625 rs364677 A G 92.05 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=57.88;MQ0=0;OQ=1754.29;QD=33.10;SB=-829.10 GT:AD:DP:GL:GQ 1/1:0,53:50:-179.03,-15.06,-0.02:99 +chr1 2062860 rs2945573 A G 10.32 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=3.09;MQ=53.50;MQ0=0;OQ=1269.78;QD=34.32;SB=-473.51 GT:AD:DP:GL:GQ 1/1:0,37:36:-130.57,-10.84,-0.01:99 +chr1 2063413 rs643076 A G 32.55 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=23.27;MQ0=4;QD=3.26;SB=-41.68 GT:AD:DP:GL:GQ 1/1:0,9:2:-6.66,-0.60,-0.00:6.02 +chr1 2063477 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=1;HaplotypeScore=9.72;MQ=34.90;MQ0=16;OQ=82.45;QD=1.04;SB=5.04 GT:AD:DP:GL:GQ 0/1:72,7:47:-25.69,-14.16,-141.31:99 +chr1 2063706 rs56038539 T C 3.16 PASS AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=41.37;MQ0=1;OQ=139.38;QD=19.91;SB=-78.92 GT:AD:DP:GL:GQ 1/1:0,7:5:-17.50,-1.51,-0.00:15.04 +chr1 2068664 . C T 1.14 PASS AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=1;HaplotypeScore=4.59;MQ=58.77;MQ0=0;OQ=1604.59;QD=18.44;SB=-789.85 GT:AD:DP:GL:GQ 0/1:40,47:84:-189.05,-25.30,-139.35:99 +chr1 2076421 rs2459983 A G 9.14 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=6.88;MQ=57.31;MQ0=0;OQ=556.13;QD=9.43;SB=-262.92 GT:AD:DP:GL:GQ 0/1:36,23:54:-75.17,-16.28,-123.64:99 +chr1 2080370 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=7.10;MQ=51.87;MQ0=1;OQ=83.25;QD=1.63;SB=68.25 GT:AD:DP:GL:GQ 0/1:34,17:35:-22.19,-10.58,-111.66:99 +chr1 2084392 rs12132341 G A 174.47 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=59.31;MQ0=0;OQ=863.52;QD=15.99;SB=-268.13 GT:AD:DP:GL:GQ 0/1:26,28:52:-105.30,-15.67,-88.61:99 +chr1 2089742 rs12137653 G A 181.23 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=58.90;MQ0=0;OQ=1123.18;QD=19.04;SB=-544.82 GT:AD:DP:GL:GQ 0/1:23,36:56:-132.48,-16.88,-70.24:99 +chr1 2096700 rs12135175 T C 69.07 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=484.58;QD=34.61;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,14:14:-52.05,-4.22,-0.00:42.13 +chr1 2096756 rs12135178 T C 1.47 PASS AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=63.69;QD=21.23;SB=-45.69 GT:AD:DP:GL:GQ 1/1:0,3:3:-9.86,-0.91,-0.00:9.02 +chr1 2097150 . G T 29.88 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=2;HaplotypeScore=4.60;MQ=59.01;MQ0=0;QD=1.57;SB=20.09 GT:AD:DP:GL:GQ 0/1:12,7:13:-10.19,-3.92,-36.97:62.71 +chr1 2103132 . T G 33.73 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=2;HaplotypeScore=13.23;MQ=58.26;MQ0=0;QD=0.50;SB=77.26 GT:AD:DP:GL:GQ 0/1:40,27:45:-20.22,-13.56,-132.60:66.56 +chr1 2103519 . T G 34.88 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=24.16;MQ=56.69;MQ0=0;QD=0.66;SB=65.20 GT:AD:DP:GL:GQ 0/1:32,21:34:-17.01,-10.24,-99.26:67.71 +chr1 2110321 rs12145923 A C 0.48 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=12.44;MQ=52.00;MQ0=0;OQ=558.55;QD=9.01;SB=-276.83 GT:AD:DP:GL:GQ 0/1:36,25:56:-76.01,-16.87,-110.27:99 +chr1 2119788 . T C 18.51 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=3;HaplotypeScore=2.86;MQ=58.76;MQ0=0;QD=0.33;SB=56.21 GT:AD:DP:GL:GQ 0/1:41,15:42:-17.79,-12.66,-139.27:51.28 +chr1 2129255 . C G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=12.54;MQ=53.09;MQ0=0;OQ=134.48;QD=3.96;SB=-44.78 GT:AD:DP:GL:GQ 0/1:28,6:25:-24.27,-7.54,-83.09:99 +chr1 2130727 . C A 3.24 PASS AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=883.89;QD=21.05;SB=-232.51 GT:AD:DP:GL:GQ 0/1:13,29:42:-104.32,-12.65,-47.37:99 +chr1 2133967 rs2503715 A G 158.02 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=295.10;QD=12.30;SB=-168.37 GT:AD:DP:GL:GQ 0/1:13,11:24:-40.02,-7.23,-52.87:99 +chr1 2146787 . G T 26.55 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=20;HaplotypeScore=12.86;MQ=49.19;MQ0=1;QD=0.48;SB=62.22 GT:AD:DP:GL:GQ 0/1:43,12:38:-17.39,-11.45,-117.88:59.38 +chr1 2157661 . T G 18.80 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=2;HaplotypeScore=22.82;MQ=58.47;MQ0=0;QD=0.32;SB=110.33 GT:AD:DP:GL:GQ 0/1:45,13:50:-20.22,-15.06,-154.85:51.58 +chr1 2158219 . G A 102.84 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=58.11;MQ0=0;OQ=732.58;QD=15.59;SB=-362.51 GT:AD:DP:GL:GQ 0/1:23,24:45:-90.10,-13.56,-76.34:99 +chr1 2159397 . G A 168.87 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=557.34;QD=13.59;SB=-169.24 GT:AD:DP:GL:GQ 0/1:23,18:39:-70.77,-11.75,-72.68:99 +chr1 2162698 rs55996607 T A 417.68 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=618.41;QD=12.13;SB=-230.72 GT:AD:DP:GL:GQ 0/1:28,23:50:-80.19,-15.06,-104.77:99 +chr1 2164572 rs263525 T C 240.22 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=58.19;MQ0=0;OQ=1470.94;QD=30.02;SB=-709.84 GT:AD:DP:GL:GQ 1/1:0,49:48:-150.72,-14.48,-0.04:99 +chr1 2166877 rs4648817 C T 227.81 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=42.45;MQ0=0;OQ=888.81;QD=15.06;SB=-258.26 GT:AD:DP:GL:GQ 0/1:29,28:53:-108.14,-15.97,-85.30:99 +chr1 2167087 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=78;Dels=0.03;HRun=20;HaplotypeScore=33.19;MQ=45.08;MQ0=3;OQ=60.74;QD=0.78;SB=86.28 GT:AD:DP:GL:GQ 0/1:57,18:48:-23.51,-14.16,-146.86:93.57 +chr1 2172859 rs55827021 G A 215.80 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=60.00;MQ0=0;OQ=711.82;QD=15.47;SB=-343.87 GT:AD:DP:GL:GQ 0/1:21,25:42:-87.13,-12.66,-66.29:99 +chr1 2181828 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=5;HaplotypeScore=57.83;MQ=51.68;MQ0=2;OQ=160.28;QD=2.32;SB=74.25 GT:AD:DP:GL:GQ 0/1:46,21:51:-34.38,-15.07,-143.28:99 +chr1 2181834 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=20;HaplotypeScore=10.75;MQ=49.92;MQ0=3;OQ=651.07;QD=8.57;SB=86.24 GT:AD:DP:GL:GQ 0/1:47,28:67:-88.59,-20.20,-142.58:99 +chr1 2190201 rs4648625 G T 81.26 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.89;MQ=59.03;MQ0=0;OQ=1500.00;QD=34.88;SB=-738.07 GT:AD:DP:GL:GQ 1/1:0,43:43:-153.60,-12.95,-0.02:99 +chr1 2194650 rs4648819 G A 133.33 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=743.48;QD=16.52;SB=-314.80 GT:AD:DP:GL:GQ 0/1:22,23:44:-90.89,-13.26,-76.95:99 +chr1 2200056 rs55778641 A C 21.64 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.74;MQ=60.00;MQ0=0;OQ=608.53;QD=12.95;SB=-87.63 GT:AD:DP:GL:GQ 0/1:21,26:44:-77.39,-13.25,-77.32:99 +chr1 2201955 . C T 11.73 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=16.61;MQ=30.48;MQ0=8;QD=0.49;SB=-3.98 GT:AD:DP:GL:GQ 0/1:18,6:8:-6.84,-2.41,-19.02:44.27 +chr1 2202003 . A G 11.74 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=1;HaplotypeScore=7.13;MQ=18.21;MQ0=12;QD=0.30;SB=-3.98 GT:AD:DP:GL:GQ 0/1:31,8:9:-7.14,-2.71,-26.71:44.28 +chr1 2202019 . C A 24.05 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=18.13;MQ0=6;QD=1.05;SB=-6.99 GT:AD:DP:GL:GQ 0/1:15,8:6:-7.50,-1.81,-11.06:56.87 +chr1 2202047 . A G 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=10.59;MQ=18.96;MQ0=8;OQ=148.17;QD=5.93;SB=-3.98 GT:AD:DP:GL:GQ 0/1:17,8:9:-20.81,-2.71,-12.59:98.81 +chr1 2202060 . C T 1.87 PASS AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=16.70;MQ0=15;OQ=178.09;QD=5.94;SB=-4.00 GT:AD:DP:GL:GQ 0/1:17,12:9:-23.81,-2.71,-8.44:57.22 +chr1 2202081 . C T 18.49 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=39;Dels=0.03;HRun=0;HaplotypeScore=43.99;MQ=16.84;MQ0=21;QD=0.47;SB=-6.99 GT:AD:DP:GL:GQ 0/1:31,7:8:-7.54,-2.41,-18.75:51.27 +chr1 2202085 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=40;Dels=0.03;HRun=0;HaplotypeScore=35.15;MQ=14.59;MQ0=24;OQ=74.01;QD=1.85;SB=-48.55 GT:AD:DP:GL:GQ 0/1:30,9:6:-12.50,-1.81,-8.79:69.79 +chr1 2202103 . C T 23.47 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=12.67;MQ=15.94;MQ0=20;QD=0.57;SB=-6.99 GT:AD:DP:GL:GQ 0/1:31,9:7:-7.74,-2.11,-15.15:56.28 +chr1 2202167 . C A 13.22 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=11.12;MQ=8.91;MQ0=36;QD=0.22;SB=-10.00 GT:AD:DP:GL:GQ 0/1:51,9:4:-5.79,-1.21,-5.41:41.98 +chr1 2202296 . C A 18.94 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=1;HaplotypeScore=9.91;MQ=10.32;MQ0=37;QD=0.39;SB=-10.00 GT:AD:DP:GL:GQ 0/1:36,13:6:-6.98,-1.81,-13.53:51.72 +chr1 2202348 . A G 10.17 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=23.55;MQ=13.35;MQ0=40;QD=0.15;SB=-25.65 GT:AD:DP:GL:GQ 0/1:57,8:7:-6.37,-2.11,-18.82:42.57 +chr1 2202364 . C T 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=20.33;MQ0=13;OQ=62.56;QD=1.49;SB=-32.09 GT:AD:DP:GL:GQ 0/1:34,6:7:-15.23,-5.69,-14.13:84.42 +chr1 2202391 . A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=5.05;MQ=22.23;MQ0=9;OQ=175.98;QD=4.09;SB=-54.84 GT:AD:DP:GL:GQ 0/1:26,17:18:-26.30,-5.42,-41.13:99 +chr1 2202434 . A G 21.78 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=15.47;MQ=13.87;MQ0=17;QD=0.81;SB=-34.93 GT:AD:DP:GL:GQ 0/1:19,8:5:-6.97,-1.51,-11.89:54.59 +chr1 2202602 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=59.56;MQ=10.62;MQ0=43;OQ=145.43;QD=2.24;SB=-6.99 GT:AD:DP:GL:GQ 0/1:30,35:7:-19.94,-2.11,-6.77:46.57 +chr1 2202632 . G T 82.62 HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=11.21;MQ0=49;QD=1.18;SB=-10.00 GT:AD:DP:GL:GQ 0/1:61,9:9:-14.26,-2.71,-18.59:99 +chr1 2202667 . A C 16.33 DPFilter;HARD_TO_VALIDATE;Indel;LowQual AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=25.34;MQ=10.07;MQ0=49;QD=0.22;SB=8.05 GT:AD:DP:GL:GQ 0/1:64,9:8:-7.32,-2.41,-22.67:49.06 +chr1 2202682 . G A 36.23 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=78.01;MQ=9.70;MQ0=44;QD=0.48;SB=-3.98 GT:AD:DP:GL:GQ 0/1:63,12:4:-8.11,-1.20,-7.39:61.88 +chr1 2202686 . G A 35.24 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=79.87;MQ=9.88;MQ0=42;QD=0.50;SB=-3.99 GT:AD:DP:GL:GQ 0/1:59,12:4:-8.01,-1.21,-5.99:47.86 +chr1 2202707 . C T 38.48 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=10.09;MQ=9.21;MQ0=26;QD=0.82;SB=-10.00 GT:AD:DP:GL:GQ 0/1:44,3:4:-8.34,-1.21,-5.59:43.85 +chr1 2202728 . T C 26.83 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=9.84;MQ=8.94;MQ0=16;QD=1.07;SB=-10.00 GT:AD:DP:GL:GQ 1/1:12,12:2:-6.09,-0.60,-0.00:6.01 +chr1 2202823 . G A 38.25 LowQual AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=5.28;MQ=19.51;MQ0=2;QD=3.82;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,8:3:-8.01,-0.90,-3.57:26.65 +chr1 2203054 . A C 12.92 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=9.60;MQ0=26;QD=0.31;SB=-27.98 GT:AD:DP:GL:GQ 0/1:36,6:4:-5.76,-1.21,-6.84:45.53 +chr1 2203334 . C T 27.36 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=7.10;MQ=12.34;MQ0=21;QD=0.94;SB=-37.65 GT:AD:DP:GL:GQ 0/1:21,8:4:-7.23,-1.21,-5.77:45.59 +chr1 2203377 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=20.17;MQ=13.03;MQ0=22;OQ=140.31;QD=3.79;SB=-42.53 GT:AD:DP:GL:GQ 0/1:23,14:7:-19.42,-2.11,-7.14:50.30 +chr1 2203636 . C T 0.06 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=18.31;MQ0=12;OQ=75.25;QD=2.03;SB=-3.99 GT:AD:DP:GL:GQ 0/1:28,9:19:-16.53,-5.73,-47.88:99 +chr1 2203679 rs2643914 C T 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=6.14;MQ=18.30;MQ0=12;OQ=93.96;QD=1.92;SB=-63.48 GT:AD:DP:GL:GQ 0/1:36,12:24:-19.91,-7.23,-64.90:99 +chr1 2203718 rs2645079 T C 32.47 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.98;MQ0=8;OQ=123.75;QD=3.75;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,20:15:-20.18,-4.52,-29.86:99 +chr1 2203765 rs12117574 T C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=5.02;MQ=32.99;MQ0=11;OQ=133.28;QD=2.18;SB=-88.55 GT:AD:DP:GL:GQ 0/1:50,11:38:-28.07,-11.46,-111.19:99 +chr1 2204009 . C G 47.74 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=47.05;MQ0=0;OQ=366.61;QD=8.94;SB=-120.51 GT:AD:DP:GL:GQ 0/1:27,14:39:-51.71,-11.77,-108.96:99 +chr1 2206228 rs4648821 T G 261.20 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.19;MQ0=0;OQ=657.01;QD=12.63;SB=-349.05 GT:AD:DP:GL:GQ 0/1:29,23:51:-84.34,-15.36,-102.93:99 +chr1 2206251 rs6689315 A G 495.75 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=794.59;QD=13.94;SB=-403.30 GT:AD:DP:GL:GQ 0/1:29,28:56:-99.61,-16.87,-113.15:99 +chr1 2206925 rs61759158 G A 51.82 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=54.01;MQ0=0;OQ=371.96;QD=12.40;SB=-7.00 GT:AD:DP:GL:GQ 0/1:17,13:28:-48.92,-8.45,-48.51:99 +chr1 2207673 . G C 46.34 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=3;HaplotypeScore=11.90;MQ=55.68;MQ0=0;QD=1.03;SB=71.27 GT:AD:DP:GL:GQ 0/1:33,12:36:-18.77,-10.85,-141.59:79.18 +chr1 2207894 . C T 62.11 PASS AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=60.00;MQ0=0;OQ=1408.04;QD=16.96;SB=-562.41 GT:AD:DP:GL:GQ 0/1:38,45:79:-167.91,-23.82,-117.96:99 +chr1 2208688 rs10910049 G T 213.58 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=47.61;MQ0=2;OQ=399.96;QD=8.89;SB=-196.49 GT:AD:DP:GL:GQ 0/1:28,17:40:-55.33,-12.05,-79.33:99 +chr1 2208825 rs6691983 C T 81.79 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.59;MQ=52.03;MQ0=1;OQ=657.40;QD=17.30;SB=-233.73 GT:AD:DP:GL:GQ 0/1:18,20:35:-79.57,-10.55,-49.20:99 +chr1 2208828 rs6682474 G A 54.35 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=53.40;MQ0=1;OQ=696.36;QD=18.33;SB=-278.18 GT:AD:DP:GL:GQ 0/1:17,21:37:-84.07,-11.15,-57.35:99 +chr1 2209299 rs56051051 T G 55.14 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=58.49;MQ0=0;OQ=442.31;QD=9.41;SB=-244.75 GT:AD:DP:GL:GQ 0/1:22,25:42:-60.17,-12.66,-79.16:99 +chr1 2209740 rs17372827 A C 232.76 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=877.78;QD=13.10;SB=-279.93 GT:AD:DP:GL:GQ 0/1:36,31:66:-110.94,-19.88,-129.70:99 +chr1 2209930 rs4648823 T A 295.53 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=59.11;MQ0=0;OQ=697.00;QD=13.40;SB=-278.32 GT:AD:DP:GL:GQ 0/1:27,24:50:-88.05,-15.06,-97.62:99 +chr1 2210285 rs2643884 T C 4 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=5.32;MQ=58.60;MQ0=0;OQ=1465.33;QD=29.31;SB=-698.59 GT:AD:DP:GL:GQ 1/1:0,50:47:-150.17,-14.18,-0.05:99 +chr1 2210377 rs1039065 A C 393.22 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.65;MQ0=0;OQ=1107.46;QD=29.14;SB=-383.86 GT:AD:DP:GL:GQ 1/1:0,38:36:-114.37,-10.85,-0.04:99 +chr1 2210509 rs2017143 C T 306.58 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.15;MQ0=0;OQ=1280.02;QD=38.79;SB=-395.53 GT:AD:DP:GL:GQ 1/1:0,33:33:-131.60,-9.94,-0.01:99 +chr1 2211082 rs2643885 A C 289.56 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.73;MQ0=0;OQ=1017.95;QD=35.10;SB=-113.02 GT:AD:DP:GL:GQ 1/1:0,29:29:-105.39,-8.74,-0.01:87.26 +chr1 2211133 rs2843166 C A 247.56 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.20;MQ0=0;OQ=767.67;QD=31.99;SB=-111.83 GT:AD:DP:GL:GQ 1/1:0,24:23:-80.36,-6.93,-0.01:69.19 +chr1 2211394 rs903924 A G 577.26 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1710.61;QD=33.54;SB=-819.09 GT:AD:DP:GL:GQ 1/1:0,51:49:-174.66,-14.76,-0.02:99 +chr1 2211494 rs903923 G C 2.57 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=5.22;MQ=56.20;MQ0=0;OQ=1828.69;QD=36.57;SB=-846.47 GT:AD:DP:GL:GQ 1/1:0,50:45:-186.48,-13.57,-0.02:99 +chr1 2211496 rs903922 A T 57.75 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.95;MQ=56.42;MQ0=0;OQ=1691.54;QD=31.92;SB=-801.63 GT:AD:DP:GL:GQ 1/1:0,53:49:-172.77,-14.77,-0.03:99 +chr1 2211936 rs903921 G A 86.49 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=57.20;MQ0=0;OQ=1373.97;QD=32.71;SB=-609.72 GT:AD:DP:GL:GQ 1/1:1,40:39:-143.60,-11.76,-2.62:91.42 +chr1 2212420 rs903920 A G 98.07 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.39;MQ0=0;OQ=1274.47;QD=33.54;SB=-555.35 GT:AD:DP:GL:GQ 1/1:0,38:37:-131.05,-11.15,-0.02:99 +chr1 2212443 rs903919 T C 439.40 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=897.63;QD=27.20;SB=-373.47 GT:AD:DP:GL:GQ 1/1:0,33:30:-93.38,-9.05,-0.03:90.19 +chr1 2212983 rs2172900 T C 377 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1306.72;QD=32.67;SB=-161.75 GT:AD:DP:GL:GQ 1/1:0,40:40:-134.28,-12.05,-0.02:99 +chr1 2213118 rs2132303 T C 18.89 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.55;MQ0=0;OQ=1347.55;QD=32.08;SB=-116.87 GT:AD:DP:GL:GQ 1/1:0,41:39:-138.35,-11.75,-0.01:99 +chr1 2214142 rs903617 A G 32.99 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.29;MQ=58.97;MQ0=0;OQ=1261.61;QD=28.04;SB=-567.89 GT:AD:DP:GL:GQ 1/1:0,45:41:-129.80,-12.38,-0.05:99 +chr1 2214469 rs2643886 T G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=5;HaplotypeScore=4.66;MQ=57.70;MQ0=0;OQ=1258.31;QD=26.77;SB=-451.03 GT:AD:DP:GL:GQ 1/1:1,46:38:-129.44,-11.45,-0.02:99 +chr1 2214505 rs2645091 A G 160.46 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.58;MQ0=0;OQ=1430.84;QD=31.11;SB=-424.25 GT:AD:DP:GL:GQ 1/1:0,46:44:-146.70,-13.26,-0.03:99 +chr1 2214736 rs10910050 A C 929.01 Indel AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=9;HaplotypeScore=4.06;MQ=59.20;MQ0=0;QD=27.32;SB=-435.82 GT:AD:DP:GL:GQ 1/1:1,33:28:-96.50,-8.43,-0.01:84.23 +chr1 2215144 rs1532385 G A 183.41 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=59.56;MQ0=0;OQ=1969.69;QD=37.88;SB=-987.83 GT:AD:DP:GL:GQ 1/1:1,51:50:-200.57,-15.06,-0.01:99 +chr1 2216193 rs903918 T A 121.47 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=60.00;MQ0=0;OQ=1515.17;QD=34.44;SB=-696.39 GT:AD:DP:GL:GQ 1/1:0,44:41:-155.11,-12.35,-0.01:99 +chr1 2216414 . T G 45.79 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=2;HaplotypeScore=10.58;MQ=58.61;MQ0=0;QD=0.68;SB=86.26 GT:AD:DP:GL:GQ 0/1:37,30:42:-20.52,-12.66,-118.85:78.63 +chr1 2217282 rs2843163 C T 190.11 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=4.18;MQ=57.17;MQ0=0;OQ=844.33;QD=16.89;SB=-357.35 GT:AD:DP:GL:GQ 0/1:22,28:45:-101.28,-13.56,-64.72:99 +chr1 2217535 rs56117572 A C 228.37 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=59.71;MQ0=0;OQ=819.93;QD=12.61;SB=-293.99 GT:AD:DP:GL:GQ 0/1:33,32:61:-103.65,-18.38,-105.35:99 +chr1 2219307 rs2643888 A G 69.82 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=2.64;MQ=59.39;MQ0=0;OQ=1301.49;QD=34.25;SB=-624.24 GT:AD:DP:GL:GQ 1/1:0,38:38:-133.76,-11.45,-0.02:99 +chr1 2219413 rs2843161 C T 101.78 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=1668.32;QD=37.92;SB=-845.15 GT:AD:DP:GL:GQ 1/1:0,44:43:-170.43,-12.96,-0.01:99 +chr1 2219777 . C T 48.76 PASS AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.44;MQ=59.45;MQ0=0;OQ=599.56;QD=14.28;SB=-283.32 GT:AD:DP:GL:GQ 0/1:19,21:37:-74.40,-11.16,-63.66:99 +chr1 2220425 rs56341331 C G 57.44 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.43;MQ=59.52;MQ0=0;OQ=468.59;QD=12.02;SB=-132.55 GT:AD:DP:GL:GQ 0/1:23,16:35:-60.70,-10.56,-79.04:99 +chr1 2221427 rs1809823 G T 87.22 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.54;MQ0=0;OQ=673.61;QD=16.43;SB=-228.53 GT:AD:DP:GL:GQ 0/1:18,23:40:-82.70,-12.05,-57.34:99 +chr1 2221826 rs55710545 G C 290.21 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.48;MQ0=0;OQ=503.65;QD=11.45;SB=-276.95 GT:AD:DP:GL:GQ 0/1:26,18:42:-66.31,-12.67,-107.95:99 +chr1 2223172 rs903618 A G 139.54 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1447.93;QD=30.17;SB=-664.81 GT:AD:DP:GL:GQ 1/1:0,48:47:-148.43,-14.18,-0.05:99 +chr1 2224111 rs1496555 A G 103.05 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=57.88;MQ0=0;OQ=1360.32;QD=32.39;SB=-504.48 GT:AD:DP:GL:GQ 1/1:0,42:39:-139.63,-11.75,-0.01:99 +chr1 2224763 rs2256178 C T 433.01 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=665.60;QD=16.23;SB=-342.52 GT:AD:DP:GL:GQ 0/1:20,21:41:-82.21,-12.37,-61.19:99 +chr1 2225516 rs11577387 G A 98.98 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=58.87;MQ0=0;OQ=626.11;QD=16.92;SB=-209.93 GT:AD:DP:GL:GQ 0/1:17,20:32:-75.54,-9.65,-40.72:99 +chr1 2226199 rs4648825 T C 63.68 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=3.65;MQ=59.17;MQ0=0;OQ=999.95;QD=17.24;SB=-492.13 GT:AD:DP:GL:GQ 0/1:22,36:55:-119.85,-16.57,-85.50:99 +chr1 2226557 rs2643904 A G 112.25 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=59.50;MQ0=0;OQ=1489.85;QD=32.39;SB=-771.11 GT:AD:DP:GL:GQ 1/1:0,46:44:-152.59,-13.26,-0.02:99 +chr1 2226618 rs2843158 G C 77.30 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=1399.75;QD=34.99;SB=-297.26 GT:AD:DP:GL:GQ 1/1:0,40:37:-143.60,-11.18,-0.04:99 +chr1 2227108 rs11580302 A G 15.25 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.17;MQ=58.99;MQ0=0;OQ=1313.96;QD=28.56;SB=-483.14 GT:AD:DP:GL:GQ 1/1:0,46:42:-135.02,-12.67,-0.04:99 +chr1 2228420 . T C 34.45 PASS AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.20;MQ0=0;OQ=345.13;QD=11.90;SB=-158.70 GT:AD:DP:GL:GQ 0/1:16,13:29:-46.53,-8.74,-63.45:99 +chr1 2229866 rs2173049 T C 234.22 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.01;MQ0=0;OQ=1791.17;QD=29.36;SB=-845.65 GT:AD:DP:GL:GQ 1/1:0,60:57:-182.75,-17.19,-0.05:99 +chr1 2230243 rs2843157 C T 3.13 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=5.43;MQ=58.16;MQ0=0;OQ=293.03;QD=7.71;SB=-52.03 GT:AD:DP:GL:GQ 0/1:21,15:25:-40.13,-7.54,-43.56:99 +chr1 2233378 rs2843156 C T 2.48 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.97;MQ0=0;OQ=1676.83;QD=39.00;SB=-476.64 GT:AD:DP:GL:GQ 1/1:0,43:42:-171.28,-12.65,-0.01:99 +chr1 2234765 rs2843154 C T 245.28 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.42;MQ0=0;OQ=364.59;QD=11.39;SB=-94.60 GT:AD:DP:GL:GQ 0/1:19,13:29:-48.48,-8.74,-59.24:99 +chr1 2235081 rs2843153 C T 158.69 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.00;MQ0=0;OQ=1550.87;QD=36.93;SB=-657.38 GT:AD:DP:GL:GQ 1/1:0,42:40:-158.69,-12.05,-0.01:99 +chr1 2235299 rs2643902 T C 83.90 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=58.80;MQ0=0;OQ=1694.87;QD=26.90;SB=-805.69 GT:AD:DP:GL:GQ 1/1:0,63:54:-173.12,-16.28,-0.05:99 +chr1 2235430 rs2843152 C G 36.95 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=1353.71;QD=36.59;SB=-455.86 GT:AD:DP:GL:GQ 1/1:0,37:35:-138.99,-10.57,-0.03:99 +chr1 2235493 rs2843151 C T 341.97 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=1519.57;QD=37.99;SB=-552.74 GT:AD:DP:GL:GQ 1/1:0,40:39:-155.55,-11.75,-0.01:99 +chr1 2237259 rs2643903 T C 68.22 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.78;MQ0=0;OQ=1099.17;QD=28.93;SB=-371.38 GT:AD:DP:GL:GQ 1/1:0,38:35:-113.53,-10.55,-0.03:99 +chr1 2237347 rs2645076 A G 8.05 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=892.74;QD=27.90;SB=-347.40 GT:AD:DP:GL:GQ 1/1:0,32:29:-92.89,-8.75,-0.03:87.17 +chr1 2237604 rs2843150 G C 105.40 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.39;MQ0=0;OQ=929.83;QD=32.06;SB=-483.10 GT:AD:DP:GL:GQ 1/1:0,29:23:-96.58,-6.93,-0.01:69.23 +chr1 2237845 rs2643905 T C 349.37 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1229.58;QD=32.36;SB=-467.52 GT:AD:DP:GL:GQ 1/1:0,38:37:-126.56,-11.15,-0.02:99 +chr1 2238243 rs60565777 G T 1452.57 Indel AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.48;MQ0=0;QD=34.58;SB=-671.66 GT:AD:DP:GL:GQ 1/1:0,42:42:-148.86,-12.66,-0.02:99 +chr1 2238484 rs12035836 A C 189.10 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.53;MQ0=0;OQ=471.85;QD=11.80;SB=-205.81 GT:AD:DP:GL:GQ 0/1:20,20:36:-61.31,-10.85,-64.85:99 +chr1 2239096 rs2645077 G A 27.69 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=1.28;MQ=59.32;MQ0=0;OQ=1136.46;QD=33.43;SB=-382.99 GT:AD:DP:GL:GQ 1/1:0,33:31:-117.25,-9.35,-0.02:93.28 +chr1 2241682 . G A 17.89 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=57.94;MQ0=0;OQ=417.19;QD=12.27;SB=-164.16 GT:AD:DP:GL:GQ 0/1:17,17:31:-54.36,-9.35,-49.53:99 +chr1 2243754 rs56393204 G A 58.20 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=58.84;MQ0=0;OQ=282.27;QD=14.11;SB=-81.31 GT:AD:DP:GL:GQ 0/1:7,11:14:-35.73,-4.22,-15.87:99 +chr1 2244770 rs2645075 T C 149.18 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.02;MQ0=0;OQ=1276.49;QD=27.75;SB=-655.75 GT:AD:DP:GL:GQ 1/1:0,46:42:-131.28,-12.68,-0.05:99 +chr1 2245871 rs2645074 A G 281.10 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.11;MQ0=0;OQ=516.48;QD=10.99;SB=-220.38 GT:AD:DP:GL:GQ 0/1:24,23:43:-67.90,-12.97,-87.14:99 +chr1 2246105 rs2843148 A T 522.32 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.70;MQ0=0;OQ=1342.05;QD=33.55;SB=-593.22 GT:AD:DP:GL:GQ 1/1:0,40:36:-137.80,-10.84,-0.01:99 +chr1 2246150 . C T 22.21 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=51.90;MQ0=0;OQ=477.24;QD=15.39;SB=-219.23 GT:AD:DP:GL:GQ 0/1:15,16:26:-58.85,-7.84,-34.36:99 +chr1 2246331 . T A 1.20 PASS AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=56.18;MQ0=0;OQ=642.82;QD=20.09;SB=-121.93 GT:AD:DP:GL:GQ 0/1:11,21:32:-77.21,-9.64,-40.89:99 +chr1 2246422 . C T 17.03 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=2;HaplotypeScore=46.69;MQ=32.60;MQ0=2;QD=0.46;SB=17.08 GT:AD:DP:GL:GQ 0/1:33,4:25:-12.51,-7.53,-79.77:49.78 +chr1 2246424 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=2;HaplotypeScore=54.85;MQ=32.43;MQ0=2;OQ=173.30;QD=4.56;SB=-18.60 GT:AD:DP:GL:GQ 0/1:26,12:25:-28.15,-7.53,-68.25:99 +chr1 2246439 rs9725291 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=64.95;MQ=33.89;MQ0=1;OQ=86.92;QD=2.12;SB=-39.19 GT:AD:DP:GL:GQ 0/1:33,8:25:-19.51,-7.53,-71.60:99 +chr1 2246445 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=48.09;MQ=35.48;MQ0=0;OQ=216.97;QD=4.82;SB=-10.56 GT:AD:DP:GL:GQ 0/1:34,11:29:-33.72,-8.74,-70.74:99 +chr1 2246456 . C T 34.43 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=27.71;MQ=37.83;MQ0=0;QD=0.69;SB=1.58 GT:AD:DP:GL:GQ 0/1:43,7:33:-16.67,-9.94,-103.65:67.27 +chr1 2246469 . T C 28.75 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=49;Dels=0.02;HRun=2;HaplotypeScore=77.34;MQ=40.72;MQ0=0;QD=0.59;SB=44.16 GT:AD:DP:GL:GQ 0/1:38,10:28:-14.30,-8.14,-89.44:61.58 +chr1 2246471 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=2;HaplotypeScore=72.35;MQ=42.43;MQ0=0;OQ=76.08;QD=1.58;SB=-6.17 GT:AD:DP:GL:GQ 0/1:36,12:29:-19.64,-8.74,-87.84:99 +chr1 2246484 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=2;HaplotypeScore=51.65;MQ=47.04;MQ0=0;OQ=81.71;QD=2.15;SB=50.19 GT:AD:DP:GL:GQ 0/1:29,8:26:-19.29,-7.83,-83.08:99 +chr1 2246793 . G A 5.64 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=55.18;MQ0=1;OQ=1074.55;QD=18.53;SB=-560.61 GT:AD:DP:GL:GQ 0/1:23,35:54:-127.01,-16.27,-81.39:99 +chr1 2247067 rs35006635 C A 47.20 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.81;MQ0=0;OQ=1074.59;QD=21.07;SB=-429.40 GT:AD:DP:GL:GQ 1/1:0,28:51:-197.40,-96.91,-86.36:99 +chr1 2247213 rs12566205 C T 241.62 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=57.90;MQ0=0;OQ=759.24;QD=13.09;SB=-368.12 GT:AD:DP:GL:GQ 0/1:33,25:57:-96.39,-17.18,-106.07:99 +chr1 2247351 rs2643892 C T 241.87 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=665.97;QD=19.59;SB=-340.91 GT:AD:DP:GL:GQ 0/1:14,20:33:-79.82,-9.94,-42.88:99 +chr1 2247555 rs10910051 G A 197.02 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=4.80;MQ=58.86;MQ0=0;OQ=1049.52;QD=16.15;SB=-447.98 GT:AD:DP:GL:GQ 0/1:31,34:61:-126.63,-18.39,-90.57:99 +chr1 2247587 rs2643893 C T 300.53 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=58.44;MQ0=0;OQ=2112.94;QD=35.22;SB=-1052.32 GT:AD:DP:GL:GQ 1/1:0,60:56:-214.91,-16.88,-0.03:99 +chr1 2247723 rs2645092 C T 700.02 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=2085.22;QD=38.62;SB=-998.04 GT:AD:DP:GL:GQ 1/1:0,54:53:-212.12,-15.97,-0.01:99 +chr1 2247791 rs2645093 G A 189.38 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=60.00;MQ0=0;OQ=700.42;QD=15.92;SB=-289.76 GT:AD:DP:GL:GQ 0/1:22,22:42:-85.99,-12.66,-67.45:99 +chr1 2248183 rs2643894 C T 135.91 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=57.95;MQ0=0;OQ=1940.09;QD=35.27;SB=-797.32 GT:AD:DP:GL:GQ 1/1:0,55:52:-197.62,-15.67,-0.03:99 +chr1 2248333 rs2643895 G A 408.80 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2697.00;QD=39.09;SB=-1222.14 GT:AD:DP:GL:GQ 1/1:0,69:68:-273.30,-20.48,-0.02:99 +chr1 2248552 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.80;MQ=51.38;MQ0=0;OQ=50.72;QD=0.83;SB=23.47 GT:AD:DP:GL:GQ 0/1:53,7:56:-28.20,-19.84,-214.64:83.56 +chr1 2248554 . G A 35.21 LowQual AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=3;HaplotypeScore=5.80;MQ=51.10;MQ0=0;QD=0.57;SB=-8.06 GT:AD:DP:GL:GQ 0/1:56,6:58:-24.27,-17.47,-188.51:68.04 +chr1 2248658 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=56.92;MQ0=0;OQ=60.63;QD=0.88;SB=6.91 GT:AD:DP:GL:GQ 0/1:61,8:68:-29.84,-20.49,-240.21:93.47 +chr1 2249886 . C T 54.96 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=60.00;MQ0=0;OQ=750.55;QD=14.72;SB=-348.88 GT:AD:DP:GL:GQ 0/1:25,26:44:-91.61,-13.27,-61.40:99 +chr1 2249910 rs2645063 G A 24.12 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=5.82;MQ=59.50;MQ0=0;OQ=758.18;QD=16.48;SB=-336.52 GT:AD:DP:GL:GQ 0/1:22,24:45:-92.67,-13.57,-67.35:99 +chr1 2250405 rs2645064 G A 151.63 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.71;MQ0=0;OQ=569.60;QD=15.82;SB=-242.53 GT:AD:DP:GL:GQ 0/1:16,20:34:-70.49,-10.25,-54.37:99 +chr1 2251037 rs35273536 C T 60.30 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.05;MQ=58.82;MQ0=0;OQ=1072.47;QD=18.18;SB=-334.93 GT:AD:DP:GL:GQ 0/1:24,34:52:-128.89,-18.36,-63.36:99 +chr1 2253264 . T C 16.56 Indel;LowQual AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=51.77;MQ0=0;QD=2.76;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,2:6:-6.74,-1.81,-16.62:49.30 +chr1 2253282 . C G 16.92 PASS AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=51.16;MQ0=0;OQ=118.58;QD=9.88;SB=-10.00 GT:AD:DP:GL:GQ 0/1:6,6:11:-18.46,-3.32,-24.69:99 +chr1 2253362 rs12752072 T C 172.88 PASS AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=253.44;QD=12.07;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,11:21:-34.96,-6.33,-38.76:99 +chr1 2254886 rs2645066 G A 78.79 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=5.62;MQ=59.17;MQ0=0;OQ=893.72;QD=15.96;SB=-436.47 GT:AD:DP:GL:GQ 0/1:25,31:52:-108.33,-15.67,-85.72:99 +chr1 2255036 rs2645067 T C 87.26 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.60;MQ0=0;OQ=995.78;QD=33.19;SB=-523.42 GT:AD:DP:GL:GQ 1/1:0,30:29:-103.17,-8.74,-0.01:87.25 +chr1 2255079 rs2643898 C T 28.85 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=59.03;MQ0=0;OQ=590.58;QD=13.73;SB=-262.25 GT:AD:DP:GL:GQ 0/1:23,20:42:-75.01,-12.66,-72.41:99 +chr1 2255654 rs7546567 G A 132.53 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.73;MQ0=0;OQ=454.68;QD=13.78;SB=-126.36 GT:AD:DP:GL:GQ 0/1:16,16:32:-61.47,-12.72,-52.76:99 +chr1 2255829 rs2843146 T G 0.05 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=441.34;QD=27.58;SB=-113.02 GT:AD:DP:GL:GQ 1/1:0,16:14:-47.73,-4.22,-0.01:42.10 +chr1 2255938 rs2643899 T C 18.62 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=58.69;MQ0=0;OQ=756.05;QD=23.63;SB=-323.76 GT:AD:DP:GL:GQ 1/1:0,32:26:-79.22,-7.85,-0.03:78.14 +chr1 2256793 rs903905 C T 99.15 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=58.29;MQ0=0;OQ=354.28;QD=16.10;SB=-192.21 GT:AD:DP:GL:GQ 0/1:10,12:21:-45.05,-6.33,-27.84:99 +chr1 2258430 rs12091632 A G 318.94 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=1030.69;QD=30.31;SB=-507.55 GT:AD:DP:GL:GQ 1/1:0,34:33:-106.69,-9.95,-0.03:99 +chr1 2258440 rs12085675 G A 96.71 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.39;MQ0=0;OQ=1318.84;QD=34.71;SB=-520.68 GT:AD:DP:GL:GQ 1/1:0,37:35:-135.49,-10.55,-0.02:99 +chr1 2258510 rs28394874 C G 5.91 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=4.06;MQ=57.77;MQ0=0;OQ=783.94;QD=18.67;SB=-330.90 GT:AD:DP:GL:GQ 0/1:17,25:36:-92.55,-10.88,-48.65:99 +chr1 2258528 rs35986070 A G 102.16 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.27;MQ0=0;OQ=457.65;QD=16.95;SB=-106.83 GT:AD:DP:GL:GQ 0/1:11,16:27:-57.18,-8.13,-41.35:99 +chr1 2258538 rs2645069 T C 177.52 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.13;MQ0=0;OQ=677.36;QD=27.09;SB=-198.05 GT:AD:DP:GL:GQ 1/1:0,25:23:-71.35,-6.94,-0.03:69.14 +chr1 2258598 rs2645070 A G 16.76 PASS AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.00;MQ0=0;OQ=322.02;QD=18.94;SB=-156.34 GT:AD:DP:GL:GQ 0/1:4,13:17:-40.61,-5.13,-15.36:99 +chr1 2258651 rs2843145 A G 4.44 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=3;HaplotypeScore=2.01;MQ=59.14;MQ0=0;OQ=426.64;QD=15.80;SB=-196.02 GT:AD:DP:GL:GQ 0/1:8,19:23:-52.88,-6.93,-31.12:99 +chr1 2258910 . A G 4.11 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.17;MQ=58.13;MQ0=0;OQ=457.98;QD=13.09;SB=-246.31 GT:AD:DP:GL:GQ 0/1:17,18:33:-59.02,-9.94,-70.06:99 +chr1 2259759 rs2036085 T C 103.79 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=626.01;QD=14.56;SB=-172.51 GT:AD:DP:GL:GQ 0/1:16,27:40:-77.94,-12.06,-63.91:99 +chr1 2259869 rs12734736 C T 347.07 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=60.00;MQ0=0;OQ=965.34;QD=16.64;SB=-492.13 GT:AD:DP:GL:GQ 0/1:29,29:54:-116.09,-16.28,-80.58:99 +chr1 2259958 rs2843142 A G 263.06 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.46;MQ=59.76;MQ0=0;OQ=1095.49;QD=13.87;SB=-502.48 GT:AD:DP:GL:GQ 0/1:40,39:78:-136.33,-23.50,-157.46:99 +chr1 2261724 rs2843141 C T 591.96 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1956.29;QD=36.91;SB=-863.62 GT:AD:DP:GL:GQ 1/1:0,53:52:-199.24,-15.68,-0.03:99 +chr1 2262086 rs1472318 C T 44.42 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=57.36;MQ0=0;OQ=484.27;QD=19.37;SB=-215.23 GT:AD:DP:GL:GQ 0/1:8,16:22:-58.34,-6.63,-21.67:99 +chr1 2262763 rs2843139 A G 28.96 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=58.77;MQ0=0;OQ=1612.91;QD=30.43;SB=-829.43 GT:AD:DP:GL:GQ 1/1:0,53:52:-164.94,-15.69,-0.06:99 +chr1 2262883 . G A 16 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=49.61;MQ0=5;QD=0.44;SB=-17.46 GT:AD:DP:GL:GQ 0/1:28,8:25:-12.42,-7.54,-69.64:48.73 +chr1 2263004 rs12730050 A G 0.31 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=14.25;MQ=55.46;MQ0=1;OQ=1032.60;QD=11.35;SB=-477.87 GT:AD:DP:GL:GQ 0/1:51,40:84:-131.86,-25.32,-172.18:99 +chr1 2263146 rs2843138 T C 3.27 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.02;HRun=0;HaplotypeScore=5.34;MQ=54.41;MQ0=0;OQ=1335.96;QD=29.04;SB=-625.83 GT:AD:DP:GL:GQ 1/1:0,44:44:-137.23,-12.97,-0.04:99 +chr1 2263291 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=4;HaplotypeScore=15.31;MQ=57.02;MQ0=0;OQ=65.39;QD=1.72;SB=65.25 GT:AD:DP:GL:GQ 0/1:31,7:33:-19.78,-9.96,-120.76:98.22 +chr1 2263292 . A G 14.86 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=57.52;MQ0=0;QD=0.41;SB=62.21 GT:AD:DP:GL:GQ 0/1:29,6:31:-14.10,-9.35,-99.44:47.55 +chr1 2263765 rs1472319 T C 33.65 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.68;MQ=59.72;MQ0=0;OQ=1846.27;QD=27.56;SB=-842.46 GT:AD:DP:GL:GQ 1/1:0,67:60:-188.28,-18.10,-0.07:99 +chr1 2264170 rs12735747 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=4;HaplotypeScore=15.88;MQ=53.27;MQ0=1;OQ=600.98;QD=16.24;SB=-322.72 GT:AD:DP:GL:GQ 0/1:17,20:33:-73.32,-9.94,-46.93:99 +chr1 2264171 rs12740557 T A 0.25 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=15.88;MQ=53.27;MQ0=1;OQ=596.15;QD=16.11;SB=-294.37 GT:AD:DP:GL:GQ 0/1:17,20:33:-72.84,-9.94,-48.77:99 +chr1 2264298 rs61288374 A G 10.67 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=4.66;MQ=58.45;MQ0=0;OQ=219.39;QD=7.31;SB=-3.98 GT:AD:DP:GL:GQ 0/1:16,13:26:-33.06,-7.84,-58.70:99 +chr1 2264816 rs4648828 G A 38.81 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.55;MQ=58.44;MQ0=0;OQ=661.80;QD=16.97;SB=-286.79 GT:AD:DP:GL:GQ 0/1:17,22:36:-80.32,-10.86,-47.76:99 +chr1 2264998 rs4648829 C T 229.79 PASS AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.45;MQ0=0;OQ=171.83;QD=11.46;SB=-76.07 GT:AD:DP:GL:GQ 0/1:9,6:13:-24.38,-3.92,-22.89:99 +chr1 2265236 rs4648830 T G 6.90 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.55;MQ0=0;OQ=452.22;QD=28.26;SB=-174.97 GT:AD:DP:GL:GQ 1/1:0,16:15:-48.82,-4.52,-0.01:45.09 +chr1 2265809 rs2643909 C G 56 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=57.02;MQ0=0;OQ=1592.56;QD=34.62;SB=-562.49 GT:AD:DP:GL:GQ 1/1:0,46:39:-162.87,-11.76,-0.03:99 +chr1 2265882 . G A 8.69 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.87;MQ0=0;OQ=753.33;QD=18.37;SB=-247.76 GT:AD:DP:GL:GQ 0/1:17,24:37:-89.77,-11.15,-48.26:99 +chr1 2265933 . T C 0.10 PASS AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=3;HaplotypeScore=2.25;MQ=58.59;MQ0=0;OQ=218.96;QD=6.64;SB=-11.87 GT:AD:DP:GL:GQ 0/1:21,12:30:-34.22,-9.04,-78.51:99 +chr1 2266056 rs11589063 C A 17.26 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=3.57;MQ=58.25;MQ0=0;OQ=453.86;QD=11.35;SB=-250.27 GT:AD:DP:GL:GQ 0/1:23,17:40:-60.72,-12.05,-77.71:99 +chr1 2266060 rs2843137 T A 278.60 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=57.66;MQ0=0;OQ=421.83;QD=10.55;SB=-226.71 GT:AD:DP:GL:GQ 0/1:23,17:37:-56.61,-11.15,-79.80:99 +chr1 2266231 rs11589451 C A 57.46 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=5.26;MQ=58.41;MQ0=0;OQ=597.75;QD=10.67;SB=-255.49 GT:AD:DP:GL:GQ 0/1:32,24:50:-78.13,-15.07,-90.69:99 +chr1 2266279 rs11590175 A G 185.77 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.15;MQ0=0;OQ=537.72;QD=10.97;SB=-262.22 GT:AD:DP:GL:GQ 0/1:22,25:41:-69.42,-12.37,-72.12:99 +chr1 2266621 . G A 34.89 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=3.35;MQ=59.21;MQ0=0;OQ=474.72;QD=13.56;SB=-211.70 GT:AD:DP:GL:GQ 0/1:17,18:29:-59.50,-8.75,-41.35:99 +chr1 2267026 . G A 47.30 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.99;MQ0=0;OQ=613.73;QD=16.59;SB=-254.78 GT:AD:DP:GL:GQ 0/1:17,20:34:-74.91,-10.25,-50.44:99 +chr1 2267073 . T C 188.99 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.75;MQ0=0;OQ=394.61;QD=9.87;SB=-211.55 GT:AD:DP:GL:GQ 0/1:22,18:38:-54.20,-11.45,-84.44:99 +chr1 2267410 rs61762093 G C 176.11 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.35;MQ=56.22;MQ0=0;OQ=747.58;QD=15.26;SB=-308.18 GT:AD:DP:GL:GQ 0/1:27,22:44:-91.30,-13.26,-97.18:99 +chr1 2267687 rs2843134 G A 624.83 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=2217.24;QD=36.95;SB=-1015.91 GT:AD:DP:GL:GQ 1/1:0,60:58:-225.33,-17.48,-0.02:99 +chr1 2267975 rs12409523 G C 1.77 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=5.47;MQ=59.03;MQ0=0;OQ=822.23;QD=17.13;SB=-209.63 GT:AD:DP:GL:GQ 0/1:24,24:46:-99.39,-13.88,-93.78:99 +chr1 2268100 rs2132595 C T 240.52 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.35;MQ0=0;OQ=844.37;QD=16.56;SB=-387.19 GT:AD:DP:GL:GQ 0/1:23,28:47:-101.89,-14.17,-71.24:99 +chr1 2268508 rs2843133 A G 0.07 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=4;HaplotypeScore=2.38;MQ=57.65;MQ0=0;OQ=995.04;QD=26.19;SB=-340.62 GT:AD:DP:GL:GQ 1/1:0,38:30:-103.10,-9.04,-0.01:90.24 +chr1 2268841 rs2643910 C T 6.12 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=58.25;MQ0=0;OQ=784.65;QD=19.62;SB=-334.39 GT:AD:DP:GL:GQ 0/1:16,24:39:-93.50,-11.75,-52.91:99 +chr1 2269677 rs56030548 C T 80.69 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=57.12;MQ0=0;OQ=443.83;QD=15.85;SB=-131.12 GT:AD:DP:GL:GQ 0/1:13,15:27:-55.80,-8.14,-42.23:99 +chr1 2269999 rs35941092 C T 0.23 PASS AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=8.68;MQ=48.71;MQ0=0;OQ=64.58;QD=4.61;SB=-21.48 GT:AD:DP:GL:GQ 0/1:10,4:14:-13.97,-4.23,-30.76:97.42 +chr1 2270100 . T A 5.69 PASS AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=56.04;MQ0=0;OQ=92.13;QD=5.12;SB=-47.85 GT:AD:DP:GL:GQ 0/1:13,5:18:-17.92,-5.42,-46.07:99 +chr1 2270283 rs2645072 A C 0.37 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=56.22;MQ0=0;OQ=963.23;QD=33.21;SB=-173.01 GT:AD:DP:GL:GQ 1/1:0,29:28:-99.92,-8.44,-0.01:84.24 +chr1 2270521 rs2055204 G A 60.41 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=3.82;MQ=59.66;MQ0=0;OQ=983.74;QD=17.89;SB=-468.43 GT:AD:DP:GL:GQ 0/1:22,33:52:-117.32,-15.67,-79.90:99 +chr1 2271586 rs7527871 A C 436.10 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=784.91;QD=12.08;SB=-319.01 GT:AD:DP:GL:GQ 0/1:36,29:64:-101.05,-19.28,-130.62:99 +chr1 2271838 rs1039063 T G 2.04 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=5;HaplotypeScore=1.22;MQ=60.00;MQ0=0;OQ=495.93;QD=11.27;SB=-259.90 GT:AD:DP:GL:GQ 0/1:22,22:41:-65.23,-12.35,-74.62:99 +chr1 2271995 rs10910053 G A 269.15 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=60.00;MQ0=0;OQ=928.57;QD=18.95;SB=-437.81 GT:AD:DP:GL:GQ 0/1:20,29:47:-110.30,-14.16,-67.66:99 +chr1 2272064 . G A 22.07 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.67;MQ=59.48;MQ0=0;OQ=676.05;QD=15.36;SB=-356.51 GT:AD:DP:GL:GQ 0/1:22,22:42:-83.55,-12.66,-69.45:99 +chr1 2272233 . C T 4.84 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=3.42;MQ=59.14;MQ0=0;OQ=912.77;QD=16.90;SB=-354.47 GT:AD:DP:GL:GQ 0/1:26,28:53:-110.53,-15.96,-92.85:99 +chr1 2272335 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=2.06;MQ=56.98;MQ0=0;OQ=124.90;QD=3.20;SB=56.19 GT:AD:DP:GL:GQ 0/1:24,15:32:-25.41,-9.64,-85.35:99 +chr1 2272540 rs2279704 C T 249.66 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=59.55;MQ0=0;OQ=742.26;QD=14.55;SB=-245.76 GT:AD:DP:GL:GQ 0/1:25,25:47:-91.67,-14.16,-87.05:99 +chr1 2272636 rs2254874 G C 9.15 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=3.74;MQ=56.62;MQ0=0;OQ=1562.16;QD=37.19;SB=-628.86 GT:AD:DP:GL:GQ 1/1:0,42:38:-159.82,-11.46,-0.02:99 +chr1 2272850 rs2036082 C T 429.96 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=669.32;QD=14.55;SB=-278.20 GT:AD:DP:GL:GQ 0/1:25,21:46:-84.08,-13.87,-81.55:99 +chr1 2273702 rs2643912 G T 414.73 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=338.96;QD=15.41;SB=-195.57 GT:AD:DP:GL:GQ 0/1:9,13:21:-43.50,-6.33,-31.88:99 +chr1 2273756 rs2840528 A G 171.15 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.44;MQ0=0;OQ=666.96;QD=16.27;SB=-294.48 GT:AD:DP:GL:GQ 0/1:18,23:41:-82.33,-12.35,-70.40:99 +chr1 2273863 rs2645082 T C 3.28 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=2.08;MQ=58.41;MQ0=0;OQ=1044.33;QD=23.73;SB=-369.45 GT:AD:DP:GL:GQ 1/1:0,44:35:-108.06,-10.56,-0.04:99 +chr1 2274055 rs3795272 T C 1.91 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=3;HaplotypeScore=4.58;MQ=58.20;MQ0=0;OQ=382.95;QD=8.15;SB=-128.51 GT:AD:DP:GL:GQ 0/1:28,19:44:-54.84,-13.26,-106.89:99 +chr1 2274346 rs12049067 C T 357.23 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=57.77;MQ0=0;OQ=508.21;QD=12.71;SB=-252.25 GT:AD:DP:GL:GQ 0/1:22,18:38:-65.56,-11.45,-75.12:99 +chr1 2274758 rs2840529 T G 24.15 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.63;MQ=59.39;MQ0=0;OQ=311.73;QD=8.20;SB=-145.73 GT:AD:DP:GL:GQ 0/1:25,13:34:-44.70,-10.25,-72.81:99 +chr1 2275042 rs2036083 A T 221.53 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.71;MQ=59.63;MQ0=0;OQ=509.88;QD=10.20;SB=-241.63 GT:AD:DP:GL:GQ 0/1:29,21:43:-67.22,-12.95,-90.87:99 +chr1 2275274 rs2843129 G A 298.24 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.43;MQ0=0;OQ=2821.79;QD=38.65;SB=-1326.28 GT:AD:DP:GL:GQ 1/1:0,73:71:-285.78,-21.39,-0.02:99 +chr1 2276807 rs1039100 A G 434.33 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1195.19;QD=31.45;SB=-467.43 GT:AD:DP:GL:GQ 1/1:0,38:36:-123.12,-10.85,-0.02:99 +chr1 2277377 rs2645083 T C 625.87 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=1448.36;QD=34.48;SB=-607.22 GT:AD:DP:GL:GQ 1/1:0,42:42:-148.44,-12.65,-0.02:99 +chr1 2277394 rs11577374 C T 128.24 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=58.95;MQ0=0;OQ=767.18;QD=17.44;SB=-322.88 GT:AD:DP:GL:GQ 0/1:20,24:40:-92.06,-12.06,-52.10:99 +chr1 2277476 rs2645085 T C 300.52 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.58;MQ0=0;OQ=627.13;QD=11.40;SB=-216.37 GT:AD:DP:GL:GQ 0/1:27,28:51:-81.37,-15.38,-100.48:99 +chr1 2277708 rs16825067 G C 15.92 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=58.92;MQ0=0;OQ=727.07;QD=18.64;SB=-379.89 GT:AD:DP:GL:GQ 0/1:17,22:37:-87.14,-11.15,-70.33:99 +chr1 2278607 rs2645086 T C 275.36 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.11;MQ0=0;OQ=269.17;QD=10.35;SB=-101.72 GT:AD:DP:GL:GQ 0/1:13,13:25:-37.74,-7.54,-47.79:99 +chr1 2279110 rs903912 C G 0.92 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=12.20;MQ=57.42;MQ0=0;OQ=679.10;QD=12.81;SB=-356.81 GT:AD:DP:GL:GQ 0/1:28,25:46:-85.06,-13.87,-109.25:99 +chr1 2279111 rs903913 T C 0.56 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.02;HRun=1;HaplotypeScore=12.09;MQ=57.42;MQ0=0;OQ=643.89;QD=12.15;SB=-297.64 GT:AD:DP:GL:GQ 0/1:27,25:52:-83.04,-15.37,-108.03:99 +chr1 2279181 rs903914 G A 327.01 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=59.27;MQ0=0;OQ=1113.86;QD=17.68;SB=-571.62 GT:AD:DP:GL:GQ 0/1:30,33:61:-133.06,-18.39,-88.20:99 +chr1 2280148 rs2840544 T C 12.55 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=59.49;MQ0=0;OQ=176.15;QD=3.91;SB=-95.61 GT:AD:DP:GL:GQ 0/1:34,11:43:-33.87,-12.97,-121.04:99 +chr1 2280520 rs2645088 T C 494.99 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=961.96;QD=28.29;SB=-437.29 GT:AD:DP:GL:GQ 1/1:0,34:31:-99.81,-9.35,-0.03:93.20 +chr1 2280750 rs2840543 C T 201 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.69;MQ0=0;OQ=2174.81;QD=36.25;SB=-926.73 GT:AD:DP:GL:GQ 1/1:0,60:56:-221.09,-16.88,-0.02:99 +chr1 2280771 rs2645089 G A 262.49 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=676.44;QD=13.53;SB=-331.88 GT:AD:DP:GL:GQ 0/1:29,21:47:-85.09,-14.16,-84.51:99 +chr1 2281127 rs6424093 A G 144.23 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.16;MQ0=0;OQ=492.45;QD=11.73;SB=-156.68 GT:AD:DP:GL:GQ 0/1:23,19:40:-64.58,-12.05,-85.73:99 +chr1 2281540 rs2840542 T C 309.75 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=56.56;MQ0=0;OQ=2607.54;QD=33.86;SB=-1074.11 GT:AD:DP:GL:GQ 1/1:0,77:73:-264.36,-21.99,-0.02:99 +chr1 2282015 rs2840541 T C 311.98 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=585.20;QD=9.75;SB=-280.12 GT:AD:DP:GL:GQ 0/1:36,24:60:-79.89,-18.08,-145.26:99 +chr1 2282269 rs2645090 T C 432.32 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=613.50;QD=9.16;SB=-290.16 GT:AD:DP:GL:GQ 0/1:38,29:64:-83.92,-19.29,-153.60:99 +chr1 2283026 rs2250799 G A 138.76 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.62;MQ0=0;OQ=1864.73;QD=38.06;SB=-791.54 GT:AD:DP:GL:GQ 1/1:0,49:48:-190.08,-14.47,-0.02:99 +chr1 2284017 rs10797420 G A 1.04 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=10.89;MQ=55.69;MQ0=1;OQ=1110.47;QD=17.63;SB=-493.05 GT:AD:DP:GL:GQ 0/1:28,34:55:-130.90,-16.57,-82.96:99 +chr1 2284704 rs55873848 C T 485.15 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.27;MQ0=0;OQ=939.68;QD=16.78;SB=-471.48 GT:AD:DP:GL:GQ 0/1:26,30:53:-113.22,-15.97,-82.15:99 +chr1 2284890 rs7530501 T G 19.05 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=5.02;MQ=57.51;MQ0=0;OQ=731.65;QD=13.80;SB=-124.84 GT:AD:DP:GL:GQ 0/1:25,28:51:-91.81,-15.36,-86.72:99 +chr1 2285068 rs57840322 G A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=6;HaplotypeScore=29.71;MQ=39.31;MQ0=0;OQ=1533.11;QD=35.65;SB=-660.69 GT:AD:DP:GL:GQ 1/1:0,43:40:-156.91,-12.05,-0.01:99 +chr1 2285112 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=42;Dels=0.05;HRun=7;HaplotypeScore=20.40;MQ=45.44;MQ0=0;OQ=661.72;QD=15.76;SB=-259.95 GT:AD:DP:GL:GQ 0/1:19,21:41:-81.21,-11.75,-63.70:99 +chr1 2285126 rs6682345 A T 200.65 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.08;MQ0=0;OQ=1898.67;QD=35.16;SB=-880.24 GT:AD:DP:GL:GQ 1/1:1,53:53:-197.20,-15.96,-3.75:99 +chr1 2285128 rs6682346 A T 359.27 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.28;MQ0=0;OQ=737.49;QD=13.41;SB=-376.75 GT:AD:DP:GL:GQ 0/1:30,25:55:-93.60,-16.56,-117.95:99 +chr1 2285638 rs10910055 A C 76.19 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=3.44;MQ=49.97;MQ0=2;OQ=838.51;QD=11.65;SB=-398.65 GT:AD:DP:GL:GQ 0/1:39,33:60:-105.20,-18.07,-117.50:99 +chr1 2285783 rs12026746 C T 166.61 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=27.98;MQ=27.61;MQ0=1;QD=3.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:32,15:30:-28.99,-9.05,-73.71:99 +chr1 2285784 . A G 712.90 SnpCluster AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=27.98;MQ=27.61;MQ0=1;QD=15.17;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,34:30:-83.61,-9.04,-20.49:99 +chr1 2285789 . T C 107.62 SnpCluster AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=51.95;MQ=27.67;MQ0=1;QD=2.20;SB=-10.00 GT:AD:DP:GL:GQ 0/1:37,12:31:-23.38,-9.34,-102.78:99 +chr1 2285797 . C T 99.87 SnpCluster AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=37.97;MQ=27.29;MQ0=3;QD=1.72;SB=-6.99 GT:AD:DP:GL:GQ 0/1:46,12:38:-24.73,-11.46,-107.35:99 +chr1 2285798 rs6685453 A G 587.05 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=37.13;MQ=27.02;MQ0=4;QD=10.12;SB=-34.94 GT:AD:DP:GL:GQ 0/1:35,23:38:-73.44,-11.45,-64.40:99 +chr1 2285805 rs2840539 G A 1277.62 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=29.98;MQ=27.32;MQ0=3;QD=21.65;SB=-159.63 GT:AD:DP:GL:GQ 0/1:13,46:41:-143.39,-12.35,-21.42:90.69 +chr1 2285956 rs7539098 A T 36.30 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=32.84;MQ0=4;OQ=256.31;QD=4.93;SB=-97.36 GT:AD:DP:GL:GQ 0/1:30,22:31:-38.25,-9.34,-84.38:99 +chr1 2285957 rs7539099 A T 39.69 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=32.84;MQ0=4;OQ=262.32;QD=5.04;SB=-99.37 GT:AD:DP:GL:GQ 0/1:29,23:31:-38.85,-9.34,-83.38:99 +chr1 2286519 rs12029098 A G 0.14 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=10.29;MQ=20.58;MQ0=25;OQ=214.67;QD=3.41;SB=-10.00 GT:AD:DP:GL:GQ 0/1:52,10:32:-34.39,-9.64,-87.93:99 +chr1 2286535 rs10910056 C T 41.85 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=18.11;MQ0=29;OQ=264.94;QD=4.49;SB=-10.00 GT:AD:DP:GL:GQ 0/1:49,10:24:-37.01,-7.23,-58.35:99 +chr1 2286632 rs12062221 G A 163.59 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.73;MQ0=23;OQ=318.86;QD=6.13;SB=-122.97 GT:AD:DP:GL:GQ 0/1:37,15:21:-41.50,-6.33,-38.58:99 +chr1 2286682 rs10910057 T C 259.25 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=21.36;MQ0=18;OQ=880.98;QD=17.98;SB=-392.60 GT:AD:DP:GL:GQ 1/1:18,31:25:-91.69,-7.53,-0.01:75.23 +chr1 2287320 rs7366927 T C 67.59 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=20.66;MQ0=24;OQ=467.32;QD=6.97;SB=-192.02 GT:AD:DP:GL:GQ 0/1:40,27:33:-59.96,-9.95,-57.33:99 +chr1 2287795 rs10910058 A T 108.02 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.68;MQ0=0;OQ=672.40;QD=13.18;SB=-131.84 GT:AD:DP:GL:GQ 0/1:26,25:50:-85.58,-15.06,-97.61:99 +chr1 2287854 rs10910059 G C 295.33 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.70;MQ0=0;OQ=1098.70;QD=16.90;SB=-242.39 GT:AD:DP:GL:GQ 0/1:34,31:65:-132.74,-19.58,-150.89:99 +chr1 2288115 rs4648834 A G 229.51 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=58.69;MQ0=0;OQ=974.25;QD=11.88;SB=-367.23 GT:AD:DP:GL:GQ 0/1:45,37:80:-124.81,-24.10,-176.65:99 +chr1 2288354 rs55960350 C A 363.99 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=56.19;MQ0=0;OQ=926.53;QD=15.44;SB=-445.49 GT:AD:DP:GL:GQ 0/1:29,31:60:-114.01,-18.07,-107.19:99 +chr1 2288496 rs10453826 G A 57.25 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1349.11;QD=17.75;SB=-668.70 GT:AD:DP:GL:GQ 0/1:36,39:75:-160.78,-22.59,-131.92:99 +chr1 2288624 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.02;HRun=18;HaplotypeScore=24.48;MQ=54.73;MQ0=1;OQ=401.02;QD=6.57;SB=-41.45 GT:AD:DP:GL:GQ 0/1:43,17:55:-59.67,-16.28,-122.97:99 +chr1 2288630 rs28792725 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.02;HRun=6;HaplotypeScore=25.44;MQ=54.48;MQ0=1;OQ=211.43;QD=3.92;SB=68.22 GT:AD:DP:GL:GQ 0/1:42,11:47:-38.29,-13.87,-121.95:99 +chr1 2288943 rs6704200 G A 186.62 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.03;MQ0=0;OQ=2659.42;QD=39.69;SB=-1189.57 GT:AD:DP:GL:GQ 1/1:0,67:67:-269.55,-20.19,-0.02:99 +chr1 2289098 rs12069579 C T 14.78 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=4;HaplotypeScore=1.46;MQ=57.20;MQ0=1;OQ=865.75;QD=14.43;SB=-343.49 GT:AD:DP:GL:GQ 0/1:32,28:57:-107.04,-17.18,-97.55:99 +chr1 2289170 rs12069588 C T 455.09 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=1016.01;QD=15.88;SB=-357.83 GT:AD:DP:GL:GQ 0/1:33,31:64:-124.17,-19.28,-114.93:99 +chr1 2289171 rs12071572 A G 466.33 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=819.05;QD=12.80;SB=-318.26 GT:AD:DP:GL:GQ 0/1:33,31:63:-104.18,-18.99,-126.28:99 +chr1 2289487 rs7545940 T C 276.29 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=59.67;MQ0=0;OQ=618.09;QD=11.04;SB=-316.36 GT:AD:DP:GL:GQ 0/1:32,24:55:-81.66,-16.57,-127.86:99 +chr1 2289511 rs2840538 T C 82.58 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.41;MQ=59.24;MQ0=0;OQ=1874.35;QD=34.08;SB=-939.34 GT:AD:DP:GL:GQ 1/1:0,55:54:-191.04,-16.27,-0.02:99 +chr1 2289772 rs7546224 T C 223.24 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.97;MQ0=0;OQ=650.32;QD=11.02;SB=-248.17 GT:AD:DP:GL:GQ 0/1:33,26:58:-85.80,-17.48,-124.44:99 +chr1 2290017 rs12070927 C A 51.76 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=59.12;MQ0=0;OQ=1316.41;QD=19.08;SB=-657.73 GT:AD:DP:GL:GQ 0/1:26,43:67:-155.11,-20.18,-89.64:99 +chr1 2290238 rs7514750 G C 5.37 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=1.63;MQ=56.12;MQ0=0;OQ=999.16;QD=16.93;SB=-161.14 GT:AD:DP:GL:GQ 0/1:29,30:55:-119.78,-16.58,-120.03:99 +chr1 2290509 rs7542190 C T 358.30 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.38;MQ0=0;OQ=592.85;QD=11.62;SB=-156.20 GT:AD:DP:GL:GQ 0/1:31,20:49:-77.34,-14.77,-99.87:99 +chr1 2290635 rs7554609 A G 100.55 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.39;MQ=57.81;MQ0=0;OQ=439.50;QD=11.27;SB=-190.14 GT:AD:DP:GL:GQ 0/1:19,19:37:-60.47,-13.23,-75.89:99 +chr1 2290654 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=20;HaplotypeScore=28.09;MQ=53.25;MQ0=0;OQ=241.28;QD=4.02;SB=92.32 GT:AD:DP:GL:GQ 0/1:44,16:53:-43.38,-15.97,-152.46:99 +chr1 2290675 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=20;HaplotypeScore=29.22;MQ=49.62;MQ0=0;OQ=64.81;QD=0.94;SB=71.20 GT:AD:DP:GL:GQ 0/1:52,14:46:-23.33,-13.56,-132.10:97.65 +chr1 2291469 rs2840535 G T 504.16 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=896.75;QD=14.95;SB=-459.55 GT:AD:DP:GL:GQ 0/1:30,30:59:-110.74,-17.78,-88.69:99 +chr1 2291551 rs6665546 G A 392.04 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1434.00;QD=17.70;SB=-726.06 GT:AD:DP:GL:GQ 0/1:39,42:81:-171.09,-24.41,-128.82:99 +chr1 2292331 rs2453567 C T 202.13 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=54.48;MQ0=0;OQ=1114.28;QD=17.14;SB=-425.43 GT:AD:DP:GL:GQ 0/1:31,34:60:-132.80,-18.08,-88.05:99 +chr1 2292376 rs2453566 T C 254.25 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=52.46;MQ0=0;OQ=498.58;QD=10.18;SB=-208.48 GT:AD:DP:GL:GQ 0/1:22,27:40:-65.21,-12.06,-74.69:99 +chr1 2293426 rs2840534 A G 74.94 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=4.04;MQ=59.63;MQ0=0;OQ=998.53;QD=16.11;SB=-332.38 GT:AD:DP:GL:GQ 0/1:27,35:61:-121.51,-18.38,-106.86:99 +chr1 2297776 rs2843165 A C 120.65 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=714.07;QD=14.28;SB=-105.81 GT:AD:DP:GL:GQ 0/1:23,27:49:-89.45,-14.76,-84.29:99 +chr1 2298377 rs2843162 C G 368.81 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=490.57;QD=15.82;SB=-257.11 GT:AD:DP:GL:GQ 0/1:17,14:31:-61.68,-9.34,-73.31:99 +chr1 2298942 rs2843160 T G 117.23 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=5.47;MQ=59.17;MQ0=0;OQ=634.08;QD=11.32;SB=-278.70 GT:AD:DP:GL:GQ 0/1:27,29:53:-82.67,-15.98,-90.35:99 +chr1 2302255 rs2643908 C T 314.36 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.55;MQ0=0;OQ=684.01;QD=13.41;SB=-309.40 GT:AD:DP:GL:GQ 0/1:26,25:46:-85.54,-13.86,-88.50:99 +chr1 2303400 rs2843132 A G 8.40 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=3.40;MQ=59.58;MQ0=0;OQ=438.03;QD=9.96;SB=-158.56 GT:AD:DP:GL:GQ 0/1:24,20:38:-58.54,-11.45,-84.41:99 +chr1 2304179 rs2643901 T C 196.35 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.98;MQ=59.45;MQ0=0;OQ=721.33;QD=17.17;SB=-281.01 GT:AD:DP:GL:GQ 0/1:15,26:39:-87.17,-11.75,-56.36:99 +chr1 2305298 rs2645060 G A 178.67 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=60.00;MQ0=0;OQ=1082.92;QD=18.05;SB=-486.00 GT:AD:DP:GL:GQ 0/1:25,35:57:-128.76,-17.18,-76.49:99 +chr1 2305540 rs2843128 A G 194.82 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=59.59;MQ0=0;OQ=482.38;QD=10.49;SB=-248.93 GT:AD:DP:GL:GQ 0/1:24,22:42:-64.18,-12.66,-86.34:99 +chr1 2305577 rs2843127 A G 547.43 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.15;MQ0=0;OQ=527.20;QD=11.98;SB=-284.59 GT:AD:DP:GL:GQ 0/1:25,19:44:-69.26,-13.26,-98.42:99 +chr1 2306175 rs2843126 A G 188.97 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=58.39;MQ0=0;OQ=344.67;QD=9.07;SB=-143.56 GT:AD:DP:GL:GQ 0/1:18,19:33:-47.70,-9.95,-71.62:99 +chr1 2306848 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=13;HaplotypeScore=4.17;MQ=55.00;MQ0=0;OQ=100.30;QD=4.18;SB=17.09 GT:AD:DP:GL:GQ 0/1:17,7:16:-18.14,-4.82,-46.21:99 +chr1 2309288 rs903903 A G 560.94 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1265.25;QD=17.33;SB=-657.78 GT:AD:DP:GL:GQ 0/1:28,45:70:-150.90,-21.10,-100.41:99 +chr1 2309390 rs2645061 G T 558.68 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=773.84;QD=12.28;SB=-380.71 GT:AD:DP:GL:GQ 0/1:36,27:63:-99.64,-18.97,-129.32:99 +chr1 2310428 . G A 99.95 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=70;Dels=0.04;HRun=15;HaplotypeScore=39.00;MQ=46.05;MQ0=0;QD=1.43;SB=52.68 GT:AD:DP:GL:GQ 0/1:53,14:55:-29.56,-16.28,-149.90:99 +chr1 2313868 rs2840533 C T 252.17 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=59.24;MQ0=0;OQ=794.28;QD=14.44;SB=-234.49 GT:AD:DP:GL:GQ 0/1:29,26:54:-98.98,-16.27,-105.03:99 +chr1 2314319 . A G 42.45 LowQual AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=50.37;MQ0=0;QD=0.63;SB=-7.70 GT:AD:DP:GL:GQ 0/1:58,9:63:-26.51,-18.98,-220.77:75.28 +chr1 2314326 . A G 0.25 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=50.58;MQ0=0;OQ=173.32;QD=2.44;SB=-79.68 GT:AD:DP:GL:GQ 0/1:59,12:69:-41.40,-20.79,-226.63:99 +chr1 2314333 rs41315342 C T 21.24 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=49.96;MQ0=0;OQ=309.71;QD=4.62;SB=-180.11 GT:AD:DP:GL:GQ 0/1:53,14:62:-52.95,-18.70,-157.19:99 +chr1 2315408 . G A 4.80 PASS AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=3.55;MQ=59.13;MQ0=0;OQ=1258.74;QD=16.78;SB=-356.05 GT:AD:DP:GL:GQ 0/1:37,38:74:-151.46,-22.30,-126.73:99 +chr1 2315869 rs1123571 G A 390.91 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.65;MQ0=0;OQ=976.67;QD=13.95;SB=-457.41 GT:AD:DP:GL:GQ 0/1:38,32:64:-120.23,-19.28,-120.05:99 +chr1 2316672 rs903911 A G 4.65 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=4.83;MQ=58.81;MQ0=0;OQ=646.68;QD=16.58;SB=-230.30 GT:AD:DP:GL:GQ 0/1:16,22:38:-79.40,-11.45,-61.89:99 +chr1 2317675 rs2840532 C T 230.75 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.63;MQ0=0;OQ=2453.68;QD=38.95;SB=-993.83 GT:AD:DP:GL:GQ 1/1:0,63:62:-248.97,-18.68,-0.02:99 +chr1 2318574 rs2645081 A G 8.21 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=6.83;MQ=58.95;MQ0=0;OQ=2467.67;QD=30.85;SB=-995.94 GT:AD:DP:GL:GQ 1/1:0,79:71:-250.38,-21.39,-0.03:99 +chr1 2319521 rs6698680 A G 273.51 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.27;MQ0=0;OQ=618.22;QD=12.12;SB=-195.44 GT:AD:DP:GL:GQ 0/1:27,24:49:-79.88,-14.77,-98.83:99 +chr1 2319668 rs3001344 A G 117.65 PASS AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.27;MQ0=0;OQ=3223.06;QD=35.42;SB=-1436.46 GT:AD:DP:GL:GQ 1/1:0,91:90:-325.91,-27.11,-0.03:99 +chr1 2319862 rs6698978 A G 270.88 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=53.38;MQ0=0;OQ=935.78;QD=15.60;SB=-478.67 GT:AD:DP:GL:GQ 0/1:27,33:58:-114.34,-17.47,-100.10:99 +chr1 2319876 rs6685829 C T 18.19 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=6.10;MQ=50.59;MQ0=0;OQ=722.12;QD=12.24;SB=-192.86 GT:AD:DP:GL:GQ 0/1:35,24:57:-92.67,-17.18,-109.45:99 +chr1 2320050 rs6693447 T G 274.62 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.41;MQ0=0;OQ=1099.08;QD=15.48;SB=-483.82 GT:AD:DP:GL:GQ 0/1:33,38:70:-134.27,-21.08,-119.27:99 +chr1 2321898 rs55912310 A G 16.38 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=6.30;MQ=59.22;MQ0=0;OQ=1063.46;QD=13.63;SB=-443.56 GT:AD:DP:GL:GQ 0/1:40,38:76:-132.53,-22.90,-155.79:99 +chr1 2322251 rs12037485 C T 255.22 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=54.76;MQ0=0;OQ=603.45;QD=12.57;SB=-317.81 GT:AD:DP:GL:GQ 0/1:27,21:45:-77.19,-13.56,-84.03:99 +chr1 2322525 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=3;HaplotypeScore=18.90;MQ=37.53;MQ0=0;OQ=105.39;QD=3.90;SB=-31.65 GT:AD:DP:GL:GQ 0/1:20,7:25:-21.36,-7.54,-75.64:99 +chr1 2322526 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=17.62;MQ=38.02;MQ0=0;OQ=76.24;QD=2.63;SB=-0.98 GT:AD:DP:GL:GQ 0/1:23,6:24:-18.14,-7.23,-69.35:99 +chr1 2322566 . C T 184.67 Indel AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=7.93;MQ=44.33;MQ0=0;QD=9.72;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,7:16:-26.58,-4.82,-31.47:99 +chr1 2322586 . T C 43.94 LowQual AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=2;HaplotypeScore=6.02;MQ=50.39;MQ0=0;QD=3.38;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,4:11:-10.99,-3.32,-30.04:76.77 +chr1 2322650 . T C 18.09 LowQual AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=2;HaplotypeScore=5.99;MQ=43.00;MQ0=0;QD=3.01;SB=-3.98 GT:AD:DP:GL:GQ 0/1:4,2:6:-6.89,-1.81,-15.35:50.86 +chr1 2322668 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=1;HaplotypeScore=16.47;MQ=36.20;MQ0=0;OQ=99.28;QD=6.62;SB=-3.98 GT:AD:DP:GL:GQ 0/1:11,4:11:-16.52,-3.31,-24.94:99 +chr1 2322705 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=18.95;MQ=39.10;MQ0=0;OQ=127.82;QD=7.99;SB=-6.99 GT:AD:DP:GL:GQ 0/1:11,5:12:-19.68,-3.62,-24.01:99 +chr1 2322711 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=2;HaplotypeScore=13.96;MQ=44.08;MQ0=0;OQ=161.06;QD=8.05;SB=-38.94 GT:AD:DP:GL:GQ 0/1:13,7:16:-24.21,-4.82,-34.51:99 +chr1 2322848 rs3001337 T C 21.54 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.78;MQ0=0;OQ=436.82;QD=19.86;SB=-71.91 GT:AD:DP:GL:GQ 1/1:0,22:15:-47.28,-4.52,-0.02:45.08 +chr1 2322891 rs3001336 G A 52.42 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.61;MQ=57.77;MQ0=0;OQ=1380.55;QD=34.51;SB=-210.77 GT:AD:DP:GL:GQ 1/1:0,39:36:-141.66,-10.85,-0.02:99 +chr1 2324121 . G T 2.67 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=60.00;MQ0=0;OQ=1012.17;QD=19.85;SB=-217.60 GT:AD:DP:GL:GQ 0/1:19,32:51:-119.87,-15.37,-54.76:99 +chr1 2324716 rs41315648 C T 55.76 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=58.50;MQ0=0;OQ=419.39;QD=13.53;SB=-59.02 GT:AD:DP:GL:GQ 0/1:17,14:29:-53.97,-8.74,-50.19:99 +chr1 2325536 rs1129333 A G 283.63 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=1733.67;QD=33.99;SB=-802.65 GT:AD:DP:GL:GQ 1/1:0,51:50:-176.97,-15.06,-0.02:99 +chr1 2327137 rs11586985 C T 102.53 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=429.81;QD=12.28;SB=-139.15 GT:AD:DP:GL:GQ 0/1:21,14:35:-56.82,-10.56,-64.66:99 +chr1 2327397 rs2494426 C G 233.81 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=927.58;QD=37.10;SB=-342.73 GT:AD:DP:GL:GQ 1/1:0,25:23:-96.36,-6.94,-0.02:69.23 +chr1 2327420 rs55746053 G A 222.42 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.19;MQ0=0;OQ=251.55;QD=10.94;SB=-144.16 GT:AD:DP:GL:GQ 0/1:13,10:21:-34.77,-6.33,-37.00:99 +chr1 2327986 rs3795269 C A 81.57 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.48;MQ=59.11;MQ0=0;OQ=721.54;QD=13.88;SB=-337.19 GT:AD:DP:GL:GQ 0/1:25,27:47:-89.60,-14.16,-76.64:99 +chr1 2328429 rs2494427 T C 699.34 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1614.58;QD=34.35;SB=-832.33 GT:AD:DP:GL:GQ 1/1:0,47:46:-165.06,-13.86,-0.02:99 +chr1 2328739 rs6671420 G A 245.45 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=58.64;MQ0=0;OQ=433.47;QD=13.98;SB=-240.76 GT:AD:DP:GL:GQ 0/1:16,15:30:-55.68,-9.05,-50.08:99 +chr1 2328934 rs2494428 C T 252.86 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=2537.82;QD=38.45;SB=-908.73 GT:AD:DP:GL:GQ 1/1:0,66:65:-257.39,-19.59,-0.03:99 +chr1 2328975 rs2494599 T C 150.34 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=60.00;MQ0=0;OQ=1601.93;QD=34.08;SB=-647.90 GT:AD:DP:GL:GQ 1/1:0,47:46:-163.80,-13.86,-0.02:99 +chr1 2328999 rs6671730 G A 141.04 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=617.02;QD=15.43;SB=-196.85 GT:AD:DP:GL:GQ 0/1:20,20:39:-76.74,-11.75,-69.55:99 +chr1 2329255 rs2494429 A G 318.55 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=347.51;QD=11.21;SB=-114.76 GT:AD:DP:GL:GQ 0/1:16,15:29:-46.78,-8.74,-56.84:99 +chr1 2329287 rs4648634 C T 185.49 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.86;MQ=59.06;MQ0=0;OQ=270.55;QD=13.53;SB=-158.18 GT:AD:DP:GL:GQ 0/1:11,9:17:-35.47,-5.13,-24.67:99 +chr1 2329933 . C G 22.59 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=58.67;MQ0=0;OQ=614.01;QD=12.53;SB=-287.97 GT:AD:DP:GL:GQ 0/1:22,27:40:-76.76,-12.08,-83.82:99 +chr1 2330060 rs2494598 T C 290.44 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=58.95;MQ0=0;OQ=481.10;QD=12.03;SB=-246.32 GT:AD:DP:GL:GQ 0/1:19,21:39:-63.16,-11.76,-72.17:99 +chr1 2332427 . C T 0.21 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=10.66;MQ=58.03;MQ0=0;OQ=1034.47;QD=16.96;SB=-503.70 GT:AD:DP:GL:GQ 0/1:28,33:58:-124.21,-17.48,-97.70:99 +chr1 2333054 rs2494597 T C 55.95 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.48;MQ0=0;OQ=1376.62;QD=31.29;SB=-454.42 GT:AD:DP:GL:GQ 1/1:0,44:41:-141.27,-12.35,-0.02:99 +chr1 2334551 rs2494595 A G 104.16 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=58.99;MQ0=0;OQ=304.12;QD=13.22;SB=-164.34 GT:AD:DP:GL:GQ 0/1:12,11:22:-40.32,-6.63,-44.91:99 +chr1 2334785 rs9424320 T C 95.96 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.20;MQ0=0;OQ=385.94;QD=13.31;SB=-75.78 GT:AD:DP:GL:GQ 0/1:11,17:25:-49.42,-7.54,-38.41:99 +chr1 2335959 rs7556447 C G 349.75 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=56.82;MQ0=0;OQ=713.10;QD=13.71;SB=-329.23 GT:AD:DP:GL:GQ 0/1:30,22:47:-88.76,-14.16,-115.39:99 +chr1 2336342 rs4648839 T C 24.11 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=49.60;MQ0=0;OQ=479.90;QD=20.87;SB=-161.36 GT:AD:DP:GL:GQ 1/1:1,22:17:-51.60,-5.13,-0.02:51.09 +chr1 2336383 rs10910065 G C 120.25 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=52.63;MQ0=0;OQ=649.76;QD=18.05;SB=-286.56 GT:AD:DP:GL:GQ 0/1:17,19:34:-78.51,-10.25,-66.28:99 +chr1 2336384 rs10910066 T C 189.89 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=52.63;MQ0=0;OQ=539.82;QD=14.99;SB=-236.31 GT:AD:DP:GL:GQ 0/1:17,19:36:-68.12,-10.85,-65.37:99 +chr1 2336612 . G A 111.33 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=53.01;MQ0=0;OQ=620.89;QD=13.80;SB=-302.81 GT:AD:DP:GL:GQ 0/1:24,21:40:-77.43,-12.05,-71.03:99 +chr1 2337326 rs12746918 C T 6.83 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=7.69;MQ=54.86;MQ0=0;OQ=484.18;QD=9.68;SB=-259.25 GT:AD:DP:GL:GQ 0/1:29,21:42:-64.36,-12.66,-87.95:99 +chr1 2337359 . C T 7.61 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=4.85;MQ=55.32;MQ0=0;OQ=435.73;QD=9.68;SB=-169.11 GT:AD:DP:GL:GQ 0/1:27,17:41:-59.22,-12.37,-82.09:99 +chr1 2337436 . G T 34.30 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=57.73;MQ0=0;OQ=368.11;QD=11.87;SB=-146.62 GT:AD:DP:GL:GQ 0/1:16,15:30:-49.13,-9.04,-55.91:99 +chr1 2337592 rs12184328 G A 0.69 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=8.46;MQ=57.94;MQ0=0;OQ=510.09;QD=15.00;SB=-111.95 GT:AD:DP:GL:GQ 0/1:17,16:33:-64.24,-9.94,-57.68:99 +chr1 2337900 rs10910068 T C 14.61 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=3;HaplotypeScore=1.32;MQ=56.47;MQ0=0;OQ=310.27;QD=9.13;SB=-165.49 GT:AD:DP:GL:GQ 0/1:15,19:29:-43.06,-8.75,-59.62:99 +chr1 2339629 rs2494432 G A 402.74 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.15;MQ0=0;OQ=824.63;QD=16.83;SB=-334.87 GT:AD:DP:GL:GQ 0/1:23,26:44:-99.01,-13.26,-63.50:99 +chr1 2339896 . C T 167.28 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=715.32;QD=13.50;SB=-333.31 GT:AD:DP:GL:GQ 0/1:31,22:52:-90.49,-15.68,-97.09:99 +chr1 2340772 rs10910070 G A 197.79 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=60.00;MQ0=0;OQ=631.24;QD=14.35;SB=-260.25 GT:AD:DP:GL:GQ 0/1:23,21:43:-79.37,-12.96,-74.56:99 +chr1 2340956 rs11577147 A G 10.98 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=289.51;QD=8.77;SB=-78.79 GT:AD:DP:GL:GQ 0/1:19,14:32:-41.88,-9.65,-72.03:99 +chr1 2341435 rs11590507 G A 0.61 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=5.72;MQ=57.66;MQ0=0;OQ=472.75;QD=15.76;SB=-44.54 GT:AD:DP:GL:GQ 0/1:14,15:29:-59.30,-8.74,-51.63:99 +chr1 2341559 rs3935659 T C 7.79 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=3.23;MQ=59.25;MQ0=0;OQ=287.36;QD=11.49;SB=-29.91 GT:AD:DP:GL:GQ 0/1:13,12:25:-39.55,-7.53,-50.79:99 +chr1 2341739 rs3935660 C T 165.26 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=58.09;MQ0=0;OQ=670.17;QD=13.68;SB=-195.21 GT:AD:DP:GL:GQ 0/1:27,21:42:-82.97,-12.67,-64.00:99 +chr1 2342006 rs12731309 C T 203.63 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=58.88;MQ0=0;OQ=846.80;QD=15.68;SB=-399.13 GT:AD:DP:GL:GQ 0/1:28,26:51:-103.32,-15.36,-93.02:99 +chr1 2342252 . A T 13.40 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=20.03;MQ=56.40;MQ0=0;QD=0.29;SB=20.83 GT:AD:DP:GL:GQ 0/1:37,6:32:-14.24,-9.64,-106.31:46.04 +chr1 2342253 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=16;HaplotypeScore=7.92;MQ=56.40;MQ0=0;OQ=132.41;QD=2.82;SB=14.63 GT:AD:DP:GL:GQ 0/1:39,8:37:-27.67,-11.15,-101.20:99 +chr1 2342945 rs10910071 A G 300.82 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=58.83;MQ0=0;OQ=1016.43;QD=13.20;SB=-494.01 GT:AD:DP:GL:GQ 0/1:41,36:76:-127.82,-22.90,-155.86:99 +chr1 2343155 rs12143389 C T 127 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=58.70;MQ0=1;OQ=925.95;QD=15.69;SB=-402.44 GT:AD:DP:GL:GQ 0/1:31,28:58:-113.35,-17.47,-107.32:99 +chr1 2343729 rs35799953 G T 69.33 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.02;MQ0=0;OQ=852.19;QD=13.75;SB=-419.16 GT:AD:DP:GL:GQ 0/1:33,29:62:-107.18,-18.68,-104.15:99 +chr1 2343876 rs34574702 C T 503.31 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1119.07;QD=15.54;SB=-507.56 GT:AD:DP:GL:GQ 0/1:37,35:71:-136.60,-21.41,-114.39:99 +chr1 2344230 rs12022832 T C 209.47 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=1.97;MQ=58.42;MQ0=0;OQ=1122.84;QD=12.62;SB=-438.76 GT:AD:DP:GL:GQ 0/1:44,45:86:-141.48,-25.92,-179.52:99 +chr1 2344260 rs12096965 C T 229.98 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.88;MQ0=0;OQ=1606.93;QD=18.26;SB=-801.37 GT:AD:DP:GL:GQ 0/1:41,47:83:-188.99,-25.01,-117.57:99 +chr1 2344423 rs12097032 C T 484.25 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=986.20;QD=13.33;SB=-465.97 GT:AD:DP:GL:GQ 0/1:43,31:74:-124.19,-22.29,-159.47:99 +chr1 2344746 rs10797421 G A 65.48 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.32;MQ0=1;OQ=3166.01;QD=39.09;SB=-1482.03 GT:AD:DP:GL:GQ 1/1:0,81:79:-320.20,-23.80,-0.02:99 +chr1 2345260 . A G 75.95 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=59.23;MQ0=0;OQ=680.86;QD=11.35;SB=-282.57 GT:AD:DP:GL:GQ 0/1:36,24:58:-88.84,-17.47,-139.70:99 +chr1 2346437 rs4648840 A G 47.43 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.94;MQ0=0;OQ=537.49;QD=18.53;SB=-194.00 GT:AD:DP:GL:GQ 0/1:11,18:29:-65.77,-8.74,-43.90:99 +chr1 2346772 rs2494433 G A 58.11 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=56.91;MQ0=0;OQ=1163.67;QD=17.63;SB=-493.51 GT:AD:DP:GL:GQ 0/1:29,36:61:-138.03,-18.37,-99.55:99 +chr1 2347335 rs2494434 T C 559.97 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.75;MQ0=0;OQ=1472.38;QD=29.45;SB=-544.87 GT:AD:DP:GL:GQ 1/1:0,50:48:-150.87,-14.48,-0.05:99 +chr1 2347933 rs2494588 C T 188.87 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=57.48;MQ0=0;OQ=702.34;QD=16.33;SB=-327.35 GT:AD:DP:GL:GQ 0/1:19,24:41:-85.88,-12.36,-61.93:99 +chr1 2348381 rs55852252 G A 9.22 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=6.28;MQ=58.74;MQ0=0;OQ=406.10;QD=10.98;SB=-128.60 GT:AD:DP:GL:GQ 0/1:20,16:33:-53.85,-9.96,-60.26:99 +chr1 2348618 rs2494587 C T 128.74 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=58.45;MQ0=0;OQ=376.88;QD=12.56;SB=-173.14 GT:AD:DP:GL:GQ 0/1:17,13:28:-49.41,-8.44,-50.72:99 +chr1 2348708 rs12116913 G C 294.62 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=640.63;QD=17.31;SB=-259.09 GT:AD:DP:GL:GQ 0/1:14,23:34:-77.61,-10.26,-60.10:99 +chr1 2349777 rs2494436 T C 163.31 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=59.34;MQ0=0;OQ=309.46;QD=8.84;SB=-92.69 GT:AD:DP:GL:GQ 0/1:19,16:32:-43.87,-9.64,-70.50:99 +chr1 2349800 rs7515934 C T 251.15 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=58.83;MQ0=0;OQ=424.25;QD=11.78;SB=-175.26 GT:AD:DP:GL:GQ 0/1:19,17:28:-54.15,-8.45,-42.69:99 +chr1 2350992 rs10910075 C T 473.62 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=647.50;QD=14.08;SB=-334.47 GT:AD:DP:GL:GQ 0/1:24,22:45:-81.60,-13.57,-79.99:99 +chr1 2351241 . T G 21.83 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=2;HaplotypeScore=2.69;MQ=59.58;MQ0=0;QD=0.40;SB=68.21 GT:AD:DP:GL:GQ 0/1:36,19:40:-17.52,-12.05,-117.29:54.64 +chr1 2351880 rs4531246 G T 25.70 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=6.77;MQ=57.66;MQ0=0;OQ=504.52;QD=12.61;SB=-172.18 GT:AD:DP:GL:GQ 0/1:16,23:33:-63.68,-9.95,-50.73:99 +chr1 2352624 rs10797424 A T 924.88 Indel AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.64;MQ=59.45;MQ0=0;QD=16.52;SB=-353.59 GT:AD:DP:GL:GQ 0/1:25,31:52:-111.44,-15.67,-81.17:99 +chr1 2352687 rs2494641 C T 290.78 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=59.48;MQ0=0;OQ=558.90;QD=11.89;SB=-269.24 GT:AD:DP:GL:GQ 0/1:28,19:43:-72.14,-12.96,-80.82:99 +chr1 2353187 rs2494640 G C 26.97 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=4.41;MQ=59.56;MQ0=0;OQ=532.94;QD=10.25;SB=-240.06 GT:AD:DP:GL:GQ 0/1:33,18:51:-71.97,-15.39,-132.20:99 +chr1 2361858 rs12756220 T C 1.74 PASS AC=1;AF=0.50;AN=2;DB;DP=140;Dels=0.00;HRun=2;HaplotypeScore=7.14;MQ=34.26;MQ0=3;OQ=1721.38;QD=12.30;SB=-137.87 GT:AD:DP:GL:GQ 0/1:41,97:98:-204.99,-29.57,-118.98:99 +chr1 2361893 rs34648463 T G 24.56 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=3.90;MQ=42.90;MQ0=5;OQ=1167.25;QD=12.83;SB=-195.79 GT:AD:DP:GL:GQ 0/1:32,58:69:-140.80,-20.79,-99.18:99 +chr1 2361936 rs28669301 A C 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=18.37;MQ=47.88;MQ0=0;OQ=797.11;QD=9.96;SB=-212.34 GT:AD:DP:GL:GQ 0/1:30,48:65:-102.59,-19.60,-99.90:99 +chr1 2361993 rs2494638 G C 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=3.02;MQ=48.10;MQ0=3;OQ=294.71;QD=3.68;SB=53.21 GT:AD:DP:GL:GQ 0/1:57,23:60:-50.84,-18.09,-206.36:99 +chr1 2363043 . G A 28.79 PASS AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.42;MQ=59.14;MQ0=0;OQ=346.36;QD=12.83;SB=-157.68 GT:AD:DP:GL:GQ 0/1:14,13:24:-45.16,-7.24,-42.35:99 +chr1 2380627 . C G 34.70 LowQual AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=57.50;MQ0=0;QD=0.48;SB=-30.39 GT:AD:DP:GL:GQ 0/1:66,6:63:-25.74,-18.99,-243.93:67.54 +chr1 2380700 rs28508164 T C 2.51 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.08;MQ0=1;OQ=73.76;QD=1.76;SB=-56.90 GT:AD:DP:GL:GQ 0/1:36,6:33:-20.60,-9.94,-107.88:99 +chr1 2380723 . G C 46.32 LowQual AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=2;HaplotypeScore=2.29;MQ=49.69;MQ0=1;QD=2.72;SB=-23.39 GT:AD:DP:GL:GQ 0/1:12,5:11:-11.23,-3.32,-34.81:79.16 +chr1 2380725 . C T 43.06 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=4.03;MQ=49.69;MQ0=1;QD=2.53;SB=5.04 GT:AD:DP:GL:GQ 0/1:12,5:11:-10.90,-3.32,-27.83:75.90 +chr1 2380739 . G C 31.92 LowQual AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=2;HaplotypeScore=1.16;MQ=44.53;MQ0=1;QD=1.88;SB=-3.98 GT:AD:DP:GL:GQ 0/1:10,7:9:-9.19,-2.71,-29.02:64.75 +chr1 2380741 . C T 23.47 LowQual AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=43.38;MQ0=1;QD=1.47;SB=-3.99 GT:AD:DP:GL:GQ 0/1:10,6:8:-8.04,-2.42,-18.12:56.29 +chr1 2380787 . C G 11.87 PASS AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=3.66;MQ=41.08;MQ0=2;OQ=228.10;QD=9.12;SB=-107.32 GT:AD:DP:GL:GQ 0/1:13,12:14:-30.31,-4.22,-31.36:99 +chr1 2380789 . T C 0.06 PASS AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=2;HaplotypeScore=3.66;MQ=41.08;MQ0=2;OQ=146.59;QD=5.86;SB=-69.76 GT:AD:DP:GL:GQ 0/1:13,12:14:-22.16,-4.22,-27.36:99 +chr1 2380812 . C T 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=1;HaplotypeScore=13.92;MQ=46.38;MQ0=1;OQ=329.40;QD=9.98;SB=-91.91 GT:AD:DP:GL:GQ 0/1:15,18:19:-41.95,-5.73,-28.82:99 +chr1 2380819 . C G 37.83 LowQual AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=9.81;MQ=46.57;MQ0=1;QD=1.08;SB=-27.83 GT:AD:DP:GL:GQ 0/1:27,8:18:-12.49,-5.42,-65.92:70.67 +chr1 2382567 . A G 10.80 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=573.70;QD=14.34;SB=-186.56 GT:AD:DP:GL:GQ 0/1:16,24:36:-71.50,-10.85,-55.65:99 +chr1 2390539 rs56368227 C T 147.22 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=58.63;MQ0=0;OQ=772.55;QD=15.15;SB=-231.31 GT:AD:DP:GL:GQ 0/1:25,25:47:-96.89,-16.35,-71.90:99 +chr1 2391510 rs942818 T C 169.46 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=1503.43;QD=30.07;SB=-692.23 GT:AD:DP:GL:GQ 1/1:0,50:44:-153.95,-13.26,-0.02:99 +chr1 2393714 rs10910080 G A 120.05 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=2.52;MQ=58.38;MQ0=0;OQ=343.05;QD=13.19;SB=-140.60 GT:AD:DP:GL:GQ 0/1:13,13:24:-44.83,-7.24,-36.59:99 +chr1 2394116 rs2494626 C T 263.72 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=58.95;MQ0=0;OQ=492.85;QD=12.32;SB=-207.19 GT:AD:DP:GL:GQ 0/1:23,17:37:-63.72,-11.16,-67.50:99 +chr1 2398521 rs1536155 A G 7.46 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=3;HaplotypeScore=2.26;MQ=58.44;MQ0=0;OQ=280.60;QD=10.39;SB=-38.80 GT:AD:DP:GL:GQ 0/1:14,13:25:-38.88,-7.54,-51.71:99 +chr1 2399136 rs12049628 A G 275.01 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=58.16;MQ0=0;OQ=457.42;QD=9.94;SB=-243.30 GT:AD:DP:GL:GQ 0/1:24,22:43:-61.98,-12.96,-96.02:99 +chr1 2399220 rs59417818 G A 58.40 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=60.00;MQ0=0;OQ=406.26;QD=15.63;SB=-103.61 GT:AD:DP:GL:GQ 0/1:12,13:24:-51.14,-7.23,-38.48:99 +chr1 2399752 rs12727342 A G 0.92 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=4.77;MQ=57.40;MQ0=0;OQ=225.70;QD=6.10;SB=-108.60 GT:AD:DP:GL:GQ 0/1:20,17:31:-35.20,-9.35,-75.95:99 +chr1 2399993 . G C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.11;MQ=57.31;MQ0=0;OQ=125.38;QD=3.58;SB=53.21 GT:AD:DP:GL:GQ 0/1:25,10:27:-23.96,-8.14,-94.75:99 +chr1 2400649 rs11799501 C T 116.65 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=4.89;MQ=60.00;MQ0=0;OQ=748.36;QD=14.39;SB=-393.78 GT:AD:DP:GL:GQ 0/1:28,24:51:-93.50,-15.38,-86.98:99 +chr1 2401311 rs10797428 A G 76.46 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=59.53;MQ0=0;OQ=638.41;QD=15.96;SB=-314.23 GT:AD:DP:GL:GQ 0/1:15,25:38:-78.58,-11.46,-54.60:99 +chr1 2402139 rs4648638 A T 283.51 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.43;MQ0=0;OQ=382.69;QD=11.60;SB=-121.80 GT:AD:DP:GL:GQ 0/1:19,14:31:-50.89,-9.34,-63.99:99 +chr1 2403494 rs942817 G C 329.65 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=58.68;MQ0=0;OQ=865.92;QD=18.82;SB=-441.92 GT:AD:DP:GL:GQ 0/1:21,25:43:-102.83,-12.96,-79.86:99 +chr1 2404788 rs4995304 G A 54.16 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=55.45;MQ0=0;OQ=801.00;QD=19.54;SB=-282.18 GT:AD:DP:GL:GQ 0/1:16,24:39:-95.13,-11.75,-53.28:99 +chr1 2405062 . T G 6.04 PASS AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=55.86;MQ0=0;OQ=164.49;QD=7.15;SB=2.04 GT:AD:DP:GL:GQ 0/1:15,8:23:-26.66,-6.93,-55.71:99 +chr1 2405078 . C T 5.98 PASS AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=52.76;MQ0=0;OQ=151.99;QD=6.61;SB=-0.99 GT:AD:DP:GL:GQ 0/1:16,7:20:-24.51,-6.03,-50.27:99 +chr1 2405106 . G T 34.21 LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=4.38;MQ=49.04;MQ0=0;QD=1.63;SB=-10.00 GT:AD:DP:GL:GQ 0/1:16,5:14:-10.92,-4.22,-37.23:67.05 +chr1 2405179 . T G 0.09 PASS AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=3;HaplotypeScore=3.52;MQ=52.14;MQ0=0;OQ=147.78;QD=8.21;SB=-98.66 GT:AD:DP:GL:GQ 0/1:11,7:13:-21.98,-3.92,-24.09:99 +chr1 2405189 . T C 0.04 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;HRun=3;HaplotypeScore=5.56;MQ=47.05;MQ0=0;OQ=344.28;QD=18.12;SB=-173.40 GT:AD:DP:GL:GQ 1/1:0,19:11:-38.02,-3.32,-0.01:33.08 +chr1 2405210 . C A 0.76 PASS AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=2.86;MQ=39.01;MQ0=0;OQ=86.77;QD=6.20;SB=-60.75 GT:AD:DP:GL:GQ 0/1:10,4:8:-14.37,-2.41,-11.67:92.61 +chr1 2405220 . G C 0.99 PASS AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=39.01;MQ0=0;OQ=62.38;QD=4.46;SB=-40.43 GT:AD:DP:GL:GQ 0/1:10,4:7:-11.64,-2.12,-15.93:95.21 +chr1 2405254 . T C 25.50 LowQual AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=3;HaplotypeScore=1.85;MQ=37.93;MQ0=1;QD=3.64;SB=-6.99 GT:AD:DP:GL:GQ 0/1:3,4:4:-7.04,-1.21,-6.92:57.17 +chr1 2405275 . C A 10.07 PASS AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=32.15;MQ0=1;OQ=98.76;QD=10.97;SB=-39.94 GT:AD:DP:GL:GQ 1/1:5,4:4:-13.41,-1.21,-0.00:12.03 +chr1 2405285 . G C 5.32 PASS AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=37.51;MQ0=1;OQ=185.89;QD=12.39;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,7:7:-23.98,-2.11,-4.50:23.85 +chr1 2405307 . G C 0.94 PASS AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=44.11;MQ0=0;OQ=225.33;QD=17.33;SB=-6.99 GT:AD:DP:GL:GQ 0/1:5,8:9:-28.53,-2.71,-8.94:62.30 +chr1 2405357 rs61763948 T C 6.42 PASS AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=58.63;MQ0=0;OQ=296.15;QD=17.42;SB=-3.98 GT:AD:DP:GL:GQ 0/1:4,13:16:-37.72,-4.82,-15.46:99 +chr1 2406217 rs4648639 G A 225.22 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=51.38;MQ0=0;OQ=834.51;QD=18.14;SB=-265.24 GT:AD:DP:GL:GQ 0/1:20,26:45:-100.29,-13.55,-72.00:99 +chr1 2407818 rs4648640 G A 162.08 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.42;MQ=59.09;MQ0=0;OQ=709.86;QD=15.43;SB=-272.15 GT:AD:DP:GL:GQ 0/1:23,23:44:-87.53,-13.26,-76.87:99 +chr1 2408795 rs10910082 C T 122.37 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.49;MQ0=0;OQ=319.86;QD=7.11;SB=-107.45 GT:AD:DP:GL:GQ 0/1:33,12:44:-48.52,-13.25,-117.65:99 +chr1 2410450 rs10752744 T C 140.49 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=60.00;MQ0=0;OQ=499.26;QD=10.62;SB=-158.91 GT:AD:DP:GL:GQ 0/1:28,19:47:-67.37,-14.16,-113.54:99 +chr1 2410773 rs6668720 A G 120.35 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=58.84;MQ0=0;OQ=320.90;QD=8.02;SB=-52.83 GT:AD:DP:GL:GQ 0/1:24,16:36:-46.22,-10.85,-86.61:99 +chr1 2412474 rs2477699 G A 360.42 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.60;MQ0=0;OQ=676.25;QD=13.52;SB=-318.34 GT:AD:DP:GL:GQ 0/1:25,25:46:-84.77,-13.86,-87.14:99 +chr1 2413426 rs3001349 C G 122.02 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=59.07;MQ0=0;OQ=984.04;QD=19.68;SB=-507.27 GT:AD:DP:GL:GQ 0/1:22,28:50:-116.76,-15.07,-93.45:99 +chr1 2414277 rs2477701 T C 471.99 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=1313.31;QD=32.03;SB=-482.12 GT:AD:DP:GL:GQ 1/1:0,41:41:-134.95,-12.36,-0.03:99 +chr1 2414754 rs2477702 T C 257.38 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=58.58;MQ0=0;OQ=407.32;QD=11.31;SB=-181.54 GT:AD:DP:GL:GQ 0/1:18,17:33:-53.96,-9.95,-62.99:99 +chr1 2415234 . G A 52.54 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.50;MQ=58.25;MQ0=0;OQ=558.86;QD=13.97;SB=-294.85 GT:AD:DP:GL:GQ 0/1:20,20:36:-70.03,-10.86,-54.36:99 +chr1 2415852 rs2477703 C T 47.65 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=7.69;MQ=58.80;MQ0=0;OQ=763.15;QD=13.16;SB=-352.50 GT:AD:DP:GL:GQ 0/1:34,24:57:-96.78,-17.18,-104.35:99 +chr1 2416626 rs3001347 A G 166.06 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=58.74;MQ0=0;OQ=303.26;QD=8.20;SB=-170.50 GT:AD:DP:GL:GQ 0/1:20,17:33:-43.56,-9.95,-71.18:99 +chr1 2417572 rs3762444 C T 276.23 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=447.88;QD=14.93;SB=-199.90 GT:AD:DP:GL:GQ 0/1:15,15:29:-56.82,-8.74,-44.39:99 +chr1 2418734 rs2477706 T C 40.91 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=58.67;MQ0=0;OQ=224.99;QD=6.43;SB=-131.52 GT:AD:DP:GL:GQ 0/1:20,15:30:-34.83,-9.05,-71.11:99 +chr1 2422191 rs4648641 C A 142.70 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.65;MQ0=0;OQ=139.36;QD=6.33;SB=-88.78 GT:AD:DP:GL:GQ 0/1:13,9:20:-23.25,-6.03,-44.88:99 +chr1 2422622 rs4648642 G A 142.31 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=59.39;MQ0=0;OQ=411.20;QD=10.82;SB=-172.27 GT:AD:DP:GL:GQ 0/1:23,15:36:-55.26,-10.86,-70.83:99 +chr1 2422899 . G A 37.84 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.45;MQ0=0;OQ=458.87;QD=13.50;SB=-199.87 GT:AD:DP:GL:GQ 0/1:18,16:31:-58.52,-9.34,-51.58:99 +chr1 2423328 . G A 53.96 PASS AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=296.62;QD=12.90;SB=-35.64 GT:AD:DP:GL:GQ 0/1:13,10:22:-39.58,-6.63,-40.93:99 +chr1 2423754 rs55874156 G A 35.47 LowQual AC=1;AF=0.50;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=5.91;SB=-7.00 GT:AD:DP:GL:GQ 0/1:3,3:5:-8.34,-1.51,-8.96:68.30 +chr1 2423760 rs12736998 C T 230.21 PASS AC=1;AF=0.50;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=70.89;QD=11.81;SB=-46.66 GT:AD:DP:GL:GQ 0/1:3,3:6:-12.18,-1.81,-9.71:78.98 +chr1 2424604 rs3814298 C T 190.56 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=60.00;MQ0=0;OQ=798.59;QD=18.57;SB=-384.92 GT:AD:DP:GL:GQ 0/1:19,24:41:-95.50,-12.36,-53.02:99 +chr1 2428628 rs12725663 C T 86.80 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=59.46;MQ0=0;OQ=892.70;QD=20.76;SB=-466.01 GT:AD:DP:GL:GQ 0/1:16,27:41:-104.92,-12.36,-47.45:99 +chr1 2429459 rs2494621 C A 2.75 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=3;HaplotypeScore=1.26;MQ=59.48;MQ0=0;OQ=889.11;QD=20.21;SB=-361.22 GT:AD:DP:GL:GQ 0/1:15,29:43:-105.15,-12.95,-49.46:99 +chr1 2429541 rs4648559 C T 370.29 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=862.47;QD=17.60;SB=-340.86 GT:AD:DP:GL:GQ 0/1:22,27:49:-104.31,-14.78,-68.65:99 +chr1 2429545 rs3791180 G C 362.92 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=669.25;QD=13.12;SB=-329.42 GT:AD:DP:GL:GQ 0/1:24,27:45:-83.79,-13.58,-96.76:99 +chr1 2434274 rs7535528 G A 398.69 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=57.41;MQ0=0;OQ=974.09;QD=16.23;SB=-447.47 GT:AD:DP:GL:GQ 0/1:29,31:55:-117.28,-16.58,-80.59:99 +chr1 2440170 rs56168662 G C 440.84 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=641.06;QD=13.94;SB=-291.00 GT:AD:DP:GL:GQ 0/1:24,22:44:-80.67,-13.28,-95.39:99 +chr1 2442429 rs2985862 T C 118.89 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=58.11;MQ0=0;OQ=446.59;QD=12.07;SB=-57.29 GT:AD:DP:GL:GQ 0/1:20,17:36:-58.79,-10.85,-82.58:99 +chr1 2442985 . C G 26.50 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=2.73;MQ=57.66;MQ0=0;QD=0.66;SB=53.21 GT:AD:DP:GL:GQ 0/1:27,13:28:-14.38,-8.45,-107.19:59.33 +chr1 2443996 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=42.41;MQ=51.42;MQ0=0;OQ=532.54;QD=4.29;SB=-103.57 GT:AD:DP:GL:GQ 0/1:93,31:115:-91.18,-34.64,-325.86:99 +chr1 2444008 rs12757829 A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=24.89;MQ=51.04;MQ0=0;OQ=890.38;QD=6.31;SB=-413.05 GT:AD:DP:GL:GQ 0/1:89,52:127:-130.59,-38.27,-352.78:99 +chr1 2444025 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=0;HaplotypeScore=101.62;MQ=51.11;MQ0=0;OQ=575.04;QD=3.76;SB=-161.02 GT:AD:DP:GL:GQ 0/1:119,34:145:-104.47,-43.68,-467.68:99 +chr1 2444046 rs11582708 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.00;HRun=3;HaplotypeScore=36.45;MQ=48.57;MQ0=0;OQ=119.48;QD=0.71;SB=230.81 GT:AD:DP:GL:GQ 0/1:152,17:154:-61.64,-46.41,-606.32:99 +chr1 2444064 rs11583446 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=165;Dels=0.00;HRun=0;HaplotypeScore=21.72;MQ=47.52;MQ0=0;OQ=2894.91;QD=17.54;SB=-1278.77 GT:AD:DP:GL:GQ 0/1:56,109:148:-337.38,-44.60,-196.45:99 +chr1 2444078 rs2494629 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=179;Dels=0.00;HRun=0;HaplotypeScore=85.91;MQ=46.23;MQ0=1;OQ=3166.59;QD=17.69;SB=-903.91 GT:AD:DP:GL:GQ 0/1:79,100:143:-363.06,-43.11,-245.67:99 +chr1 2444084 rs11583448 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=183;Dels=0.00;HRun=0;HaplotypeScore=146.19;MQ=45.66;MQ0=1;OQ=1337.56;QD=7.31;SB=32.08 GT:AD:DP:GL:GQ 0/1:128,54:167:-187.36,-50.32,-447.47:99 +chr1 2444090 rs11582711 C T 0.69 PASS AC=1;AF=0.50;AN=2;DB;DP=184;Dels=0.00;HRun=1;HaplotypeScore=9.96;MQ=45.23;MQ0=1;OQ=1767.35;QD=9.61;SB=-110.22 GT:AD:DP:GL:GQ 0/1:119,64:165:-229.73,-49.72,-378.76:99 +chr1 2444114 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=1;HaplotypeScore=224.24;MQ=44.82;MQ0=1;OQ=1189.56;QD=7.12;SB=-484.53 GT:AD:DP:GL:GQ 0/1:105,62:153:-168.35,-46.11,-399.99:99 +chr1 2444123 rs60947977 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=164;Dels=0.00;HRun=1;HaplotypeScore=187.19;MQ=44.56;MQ0=1;OQ=222.03;QD=1.35;SB=140.46 GT:AD:DP:GL:GQ 0/1:146,18:145:-69.17,-43.68,-451.95:99 +chr1 2444144 rs12735280 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.00;HRun=0;HaplotypeScore=41.21;MQ=45.78;MQ0=2;OQ=126.97;QD=0.80;SB=158.55 GT:AD:DP:GL:GQ 0/1:146,13:126:-53.98,-38.00,-474.20:99 +chr1 2444156 rs61763952 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.00;HRun=1;HaplotypeScore=50.63;MQ=44.65;MQ0=2;OQ=841.78;QD=5.89;SB=-177.38 GT:AD:DP:GL:GQ 0/1:107,36:119:-123.33,-35.87,-307.59:99 +chr1 2444175 . A G 1992.57 SnpCluster AC=1;AF=0.50;AN=2;DP=119;Dels=0.00;HRun=1;HaplotypeScore=57.72;MQ=43.73;MQ0=1;QD=16.74;SB=-969.28 GT:AD:DP:GL:GQ 0/1:46,73:107:-234.78,-32.23,-167.74:99 +chr1 2444179 . C T 733.69 SnpCluster AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=1;HaplotypeScore=94.68;MQ=43.15;MQ0=1;QD=6.79;SB=-249.70 GT:AD:DP:GL:GQ 0/1:79,29:94:-104.98,-28.32,-236.84:99 +chr1 2444180 . T C 74.50 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=102.88;MQ=43.30;MQ0=1;QD=0.72;SB=40.74 GT:AD:DP:GL:GQ 0/1:89,15:92:-38.46,-27.73,-318.94:99 +chr1 2444188 . C T 230.63 SnpCluster AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=1;HaplotypeScore=69.58;MQ=42.94;MQ0=1;QD=2.33;SB=-68.96 GT:AD:DP:GL:GQ 0/1:80,18:83:-51.35,-25.01,-254.74:99 +chr1 2444203 rs12723596 A G 0.31 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=13.04;MQ=41.89;MQ0=1;OQ=932.46;QD=10.25;SB=-166.34 GT:AD:DP:GL:GQ 0/1:48,43:72:-118.23,-21.70,-146.57:99 +chr1 2444214 . T G 33.51 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=90.11;MQ=41.94;MQ0=0;QD=0.39;SB=20.19 GT:AD:DP:GL:GQ 0/1:75,10:71:-28.02,-21.39,-222.83:66.35 +chr1 2444236 rs3001351 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=1;HaplotypeScore=44.56;MQ=42.21;MQ0=1;OQ=1478.32;QD=13.82;SB=-341.03 GT:AD:DP:GL:GQ 0/1:32,75:79:-174.93,-23.81,-103.79:99 +chr1 2444239 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=57.18;MQ=42.22;MQ0=1;OQ=253.01;QD=2.32;SB=-45.72 GT:AD:DP:GL:GQ 0/1:94,15:81:-52.98,-24.40,-242.61:99 +chr1 2444569 rs2494625 T C 30.67 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.30;MQ0=0;OQ=234.27;QD=7.10;SB=-122.64 GT:AD:DP:GL:GQ 0/1:20,13:30:-35.75,-9.04,-76.61:99 +chr1 2445722 rs12131236 C T 283.83 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=971.15;QD=13.87;SB=-406.34 GT:AD:DP:GL:GQ 0/1:39,31:69:-121.19,-20.79,-133.37:99 +chr1 2446063 rs3122922 A G 422.66 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.95;MQ0=0;OQ=840.10;QD=14.48;SB=-338.93 GT:AD:DP:GL:GQ 0/1:28,30:57:-104.46,-17.17,-113.53:99 +chr1 2452678 rs2494603 T C 117.86 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.28;MQ0=0;OQ=471.49;QD=14.73;SB=-130.66 GT:AD:DP:GL:GQ 0/1:12,20:28:-58.88,-8.44,-38.02:99 +chr1 2452695 rs10910087 A G 48.63 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=58.97;MQ0=0;OQ=650.54;QD=14.46;SB=-235.28 GT:AD:DP:GL:GQ 0/1:22,23:45:-81.90,-13.56,-89.06:99 +chr1 2453274 rs11583602 G A 37.53 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=1048.89;QD=19.42;SB=-532.12 GT:AD:DP:GL:GQ 0/1:23,31:52:-123.83,-15.66,-80.52:99 +chr1 2453609 rs4648645 G T 421.56 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=634.41;QD=13.22;SB=-255.25 GT:AD:DP:GL:GQ 0/1:25,23:48:-81.19,-14.46,-89.13:99 +chr1 2453905 rs6694195 G A 6.21 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=641.00;QD=22.10;SB=-187.27 GT:AD:DP:GL:GQ 0/1:9,20:26:-75.22,-7.83,-25.34:99 +chr1 2454427 rs12406506 G T 168.99 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.39;MQ0=0;OQ=384.63;QD=10.12;SB=-161.15 GT:AD:DP:GL:GQ 0/1:22,16:36:-52.59,-10.85,-75.30:99 +chr1 2454955 rs11585747 C T 158.41 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.68;MQ0=0;OQ=442.85;QD=9.63;SB=-209.92 GT:AD:DP:GL:GQ 0/1:30,16:43:-60.53,-12.97,-87.57:99 +chr1 2455004 rs9803764 C T 21.92 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=718.09;QD=21.76;SB=-255.79 GT:AD:DP:GL:GQ 0/1:12,21:31:-84.43,-9.34,-35.39:99 +chr1 2455189 rs11584295 G A 326.39 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.30;MQ0=0;OQ=897.10;QD=14.95;SB=-369.89 GT:AD:DP:GL:GQ 0/1:30,30:57:-110.18,-17.19,-92.60:99 +chr1 2455531 rs4648561 T C 59.57 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.71;MQ=60.00;MQ0=0;OQ=506.09;QD=9.04;SB=-221.92 GT:AD:DP:GL:GQ 0/1:28,28:51:-69.27,-15.38,-110.78:99 +chr1 2455652 rs3001339 C T 0.17 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=4;HaplotypeScore=3.44;MQ=59.16;MQ0=0;OQ=1028.71;QD=18.70;SB=-294.19 GT:AD:DP:GL:GQ 0/1:22,32:53:-122.12,-15.97,-77.91:99 +chr1 2455772 rs6661956 C T 143.28 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=537.50;QD=14.93;SB=-189.16 GT:AD:DP:GL:GQ 0/1:19,17:35:-67.58,-10.55,-58.49:99 +chr1 2455810 rs2494605 A G 6.95 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=3.59;MQ=59.41;MQ0=0;OQ=1343.57;QD=34.45;SB=-641.25 GT:AD:DP:GL:GQ 1/1:0,39:38:-137.96,-11.45,-0.01:99 +chr1 2456285 rs2985860 T G 0.20 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=9.84;MQ=58.13;MQ0=0;OQ=394.22;QD=7.88;SB=-79.96 GT:AD:DP:GL:GQ 0/1:20,30:34:-52.96,-10.25,-63.38:99 +chr1 2456493 rs2494606 A G 522.55 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=1382.51;QD=30.72;SB=-394.30 GT:AD:DP:GL:GQ 1/1:0,45:44:-141.87,-13.27,-0.04:99 +chr1 2460535 . T C 626.63 Indel AC=1;AF=0.50;AN=2;DP=47;Dels=0.04;HRun=0;HaplotypeScore=9.81;MQ=45.54;MQ0=0;QD=13.33;SB=-234.30 GT:AD:DP:GL:GQ 0/1:22,23:45:-78.90,-12.95,-84.01:99 +chr1 2460708 rs12042279 G A 153.95 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=58.99;MQ0=0;OQ=696.74;QD=15.15;SB=-237.53 GT:AD:DP:GL:GQ 0/1:24,22:46:-86.83,-13.87,-76.84:99 +chr1 2461941 rs1886731 T C 87.33 PASS AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=203.62;QD=14.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,9:14:-27.87,-4.22,-19.55:99 +chr1 2462004 rs4487972 G C 44.05 PASS AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=1.24;MQ=56.62;MQ0=0;OQ=71.85;QD=10.26;SB=-10.00 GT:AD:DP:GL:GQ 0/1:3,4:6:-12.28,-1.81,-12.84:99 +chr1 2464065 rs942824 T C 72.36 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=59.36;MQ0=0;OQ=370.87;QD=10.30;SB=-61.73 GT:AD:DP:GL:GQ 0/1:20,16:34:-50.61,-10.24,-77.88:99 +chr1 2465072 rs10797429 G C 201.07 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=57.71;MQ0=0;OQ=487.96;QD=13.19;SB=-257.25 GT:AD:DP:GL:GQ 0/1:21,16:34:-62.33,-10.25,-80.32:99 +chr1 2465334 rs55929178 C T 11.28 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=4.63;MQ=56.91;MQ0=0;OQ=721.66;QD=14.73;SB=-233.74 GT:AD:DP:GL:GQ 0/1:26,23:43:-88.40,-12.95,-74.05:99 +chr1 2467218 rs12097268 T A 23.21 PASS AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=190.70;QD=11.22;SB=-35.94 GT:AD:DP:GL:GQ 0/1:9,8:17:-27.48,-5.13,-30.96:99 +chr1 2468371 rs2477678 T A 119.20 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=60.00;MQ0=0;OQ=463.47;QD=13.24;SB=-147.88 GT:AD:DP:GL:GQ 0/1:17,17:32:-59.27,-9.64,-59.80:99 +chr1 2469843 rs1974044 A G 45.39 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=3.40;MQ=59.34;MQ0=0;OQ=371.34;QD=10.61;SB=-193.60 GT:AD:DP:GL:GQ 0/1:21,14:32:-50.06,-9.64,-71.49:99 +chr1 2471303 . C T 62.24 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=41.42;MQ0=6;OQ=776.47;QD=14.38;SB=-282.22 GT:AD:DP:GL:GQ 0/1:29,25:42:-93.59,-12.66,-60.88:99 +chr1 2472781 rs2147905 T C 210.38 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=57.08;MQ0=0;OQ=779.17;QD=15.90;SB=-258.93 GT:AD:DP:GL:GQ 0/1:21,26:47:-95.36,-14.16,-80.25:99 +chr1 2473130 rs3748825 T C 24.77 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=50.53;MQ0=0;OQ=489.49;QD=14.40;SB=-174.97 GT:AD:DP:GL:GQ 0/1:17,17:34:-62.48,-10.24,-67.15:99 +chr1 2473158 rs2985858 C G 170.01 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=52.63;MQ0=0;OQ=759.64;QD=17.67;SB=-375.14 GT:AD:DP:GL:GQ 0/1:22,21:42:-91.90,-12.65,-91.93:99 +chr1 2474608 rs4449972 T C 1.07 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=17.16;MQ0=14;OQ=59.70;QD=2.60;SB=-42.68 GT:AD:DP:GL:GQ 0/1:13,10:7:-11.36,-2.11,-16.47:92.53 +chr1 2474629 rs2764846 G T 13.02 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=13.44;MQ0=12;OQ=72.28;QD=4.25;SB=-10.00 GT:AD:DP:GL:GQ 1/1:7,10:3:-10.72,-0.90,-0.00:9.03 +chr1 2474959 rs10910088 A G 3.08 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=22.58;MQ0=15;OQ=106.75;QD=3.44;SB=-10.00 GT:AD:DP:GL:GQ 0/1:16,14:12:-17.58,-3.63,-21.51:99 +chr1 2475164 rs2182176 C T 397.56 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=48.51;MQ0=0;OQ=552.02;QD=13.14;SB=-223.69 GT:AD:DP:GL:GQ 0/1:24,18:39:-70.24,-11.76,-69.97:99 +chr1 2475556 rs1555791 C G 11.33 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=2.88;MQ=58.58;MQ0=0;OQ=550.02;QD=11.96;SB=-241.08 GT:AD:DP:GL:GQ 0/1:27,19:40:-70.37,-12.08,-87.80:99 +chr1 2475800 rs10910089 C A 3.66 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=9.04;MQ=58.28;MQ0=0;OQ=671.47;QD=13.70;SB=-238.39 GT:AD:DP:GL:GQ 0/1:23,26:46:-84.29,-13.86,-77.00:99 +chr1 2476366 rs61054170 G A 7.02 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=6.03;MQ=57.64;MQ0=0;OQ=224.60;QD=8.64;SB=-97.61 GT:AD:DP:GL:GQ 0/1:16,10:23:-32.68,-6.93,-48.70:99 +chr1 2476391 rs2495365 T C 262.15 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=56.62;MQ0=0;OQ=373.37;QD=12.04;SB=-190.59 GT:AD:DP:GL:GQ 0/1:16,15:29:-49.36,-8.74,-57.56:99 +chr1 2476740 rs11577783 T C 207.60 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=58.69;MQ0=0;OQ=459.72;QD=9.19;SB=-194.29 GT:AD:DP:GL:GQ 0/1:30,20:49:-64.03,-14.78,-111.22:99 +chr1 2476777 rs7550231 C T 162.70 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.21;MQ0=0;OQ=483.70;QD=13.44;SB=-69.05 GT:AD:DP:GL:GQ 0/1:20,15:32:-61.30,-9.65,-52.93:99 +chr1 2477765 rs7515633 T C 23.90 PASS AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=58.71;MQ0=0;OQ=253.35;QD=14.07;SB=-51.83 GT:AD:DP:GL:GQ 0/1:8,10:18:-34.04,-5.43,-30.81:99 +chr1 2477769 rs7544646 G C 297.66 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=6.07;MQ=56.04;MQ0=0;QD=16.54;SB=-32.86 GT:AD:DP:GL:GQ 0/1:9,9:14:-37.27,-4.22,-20.23:99 +chr1 2477776 . G C 10.29 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=1;HaplotypeScore=18.19;MQ=56.92;MQ0=0;QD=0.45;SB=20.10 GT:AD:DP:GL:GQ 0/1:13,10:13:-8.19,-3.92,-49.87:42.70 +chr1 2477778 . A C 172 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=2;HaplotypeScore=22.60;MQ=57.66;MQ0=0;QD=5.73;SB=23.08 GT:AD:DP:GL:GQ 0/1:12,18:21:-26.81,-6.33,-40.53:99 +chr1 2477836 rs2843396 C G 11.98 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=3.04;MQ=59.36;MQ0=0;OQ=1290.53;QD=35.85;SB=-556.54 GT:AD:DP:GL:GQ 1/1:0,36:34:-132.68,-10.27,-0.04:99 +chr1 2478204 rs10910090 G A 182.29 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.53;MQ0=0;OQ=449.68;QD=11.24;SB=-202.69 GT:AD:DP:GL:GQ 0/1:23,17:38:-59.71,-11.46,-71.62:99 +chr1 2479633 rs8725 C T 49.19 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.46;MQ=59.51;MQ0=0;OQ=577.64;QD=12.29;SB=-219.70 GT:AD:DP:GL:GQ 0/1:27,20:42:-73.71,-12.66,-80.51:99 +chr1 2480088 rs2234167 C T 215.09 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=60.00;MQ0=0;OQ=519.75;QD=13.33;SB=-131.13 GT:AD:DP:GL:GQ 0/1:22,17:38:-66.72,-11.46,-63.96:99 +chr1 2481753 rs11573988 C A 159.02 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.54;MQ0=0;OQ=542.33;QD=13.23;SB=-158.65 GT:AD:DP:GL:GQ 0/1:20,21:37:-68.66,-11.14,-62.61:99 +chr1 2483213 rs2234161 G A 326.82 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.71;MQ0=0;OQ=435.68;QD=12.10;SB=-173.67 GT:AD:DP:GL:GQ 0/1:20,16:32:-56.50,-9.65,-56.89:99 +chr1 2483476 rs2281852 G T 352.55 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.50;MQ0=0;OQ=604.05;QD=13.13;SB=-299.46 GT:AD:DP:GL:GQ 0/1:23,23:43:-76.65,-12.96,-66.34:99 +chr1 2483520 rs2257763 G T 186.21 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.87;MQ=58.41;MQ0=0;OQ=599.64;QD=13.63;SB=-190.60 GT:AD:DP:GL:GQ 0/1:21,23:41:-75.60,-12.36,-64.98:99 +chr1 2485488 rs2495366 C T 214.98 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.54;MQ0=0;OQ=410.34;QD=10.01;SB=-177.87 GT:AD:DP:GL:GQ 0/1:24,17:33:-54.27,-9.95,-57.69:99 +chr1 2485810 rs1886730 A G 395.82 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=201.47;QD=10.07;SB=-95.61 GT:AD:DP:GL:GQ 0/1:11,9:20:-29.46,-6.03,-42.35:99 +chr1 2486265 rs4870 T C 17.43 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=53.94;MQ0=0;OQ=133.00;QD=5.54;SB=-10.85 GT:AD:DP:GL:GQ 0/1:16,8:22:-23.21,-6.63,-59.96:99 +chr1 2486652 rs2227313 A G 323.64 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=361.41;QD=9.04;SB=-171.95 GT:AD:DP:GL:GQ 0/1:24,16:39:-51.18,-11.76,-90.45:99 +chr1 2486755 rs2227312 G T 192.71 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.51;MQ0=0;OQ=435.37;QD=11.46;SB=-199.58 GT:AD:DP:GL:GQ 0/1:21,17:35:-57.36,-10.54,-70.01:99 +chr1 2489670 rs4449972 A G 6.05 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=14.84;MQ0=21;OQ=104.96;QD=3.09;SB=-10.00 GT:AD:DP:GL:GQ 0/1:18,15:5:-15.28,-1.51,-4.27:27.62 +chr1 2489758 rs4385650 G C 16.53 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=2.00;MQ=35.98;MQ0=1;OQ=450.14;QD=15.00;SB=-208.64 GT:AD:DP:GL:GQ 0/1:17,13:27:-56.44,-8.15,-54.66:99 +chr1 2490753 rs4648647 G A 26.84 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=50.09;MQ0=0;OQ=371.65;QD=10.04;SB=-147.20 GT:AD:DP:GL:GQ 0/1:24,13:35:-51.00,-10.56,-68.63:99 +chr1 2490924 . G A 58.67 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=40.19;MQ0=3;OQ=773.22;QD=14.59;SB=-281.28 GT:AD:DP:GL:GQ 0/1:27,26:42:-93.26,-12.65,-67.56:99 +chr1 2491198 rs10797432 C T 12.45 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=7.73;MQ=51.44;MQ0=1;OQ=449.43;QD=8.48;SB=-221.51 GT:AD:DP:GL:GQ 0/1:35,17:47:-62.39,-14.17,-101.99:99 +chr1 2491376 rs10910092 A G 353.95 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.86;MQ0=0;OQ=953.50;QD=15.89;SB=-479.29 GT:AD:DP:GL:GQ 0/1:27,33:59:-116.41,-17.77,-105.03:99 +chr1 2491870 rs10797433 T C 399.98 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.09;MQ0=0;OQ=643.74;QD=13.99;SB=-281.26 GT:AD:DP:GL:GQ 0/1:20,26:45:-81.22,-13.56,-79.26:99 +chr1 2492640 rs6667605 C T 284.33 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=1076.76;QD=20.32;SB=-511.53 GT:AD:DP:GL:GQ 0/1:22,31:53:-126.92,-15.96,-81.92:99 +chr1 2492694 rs6672381 A G 59.10 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=2.96;MQ=59.67;MQ0=0;OQ=836.72;QD=14.68;SB=-261.21 GT:AD:DP:GL:GQ 0/1:25,31:56:-103.83,-16.88,-100.88:99 +chr1 2493042 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=3;HaplotypeScore=24.29;MQ=58.55;MQ0=0;OQ=229.07;QD=5.45;SB=41.17 GT:AD:DP:GL:GQ 0/1:24,18:31:-35.54,-9.35,-97.62:99 +chr1 2494094 rs6671426 C A 112.49 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=782.65;QD=13.98;SB=-297.63 GT:AD:DP:GL:GQ 0/1:30,26:56:-98.41,-16.86,-108.17:99 +chr1 2494223 rs28734787 T C 285.54 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.94;MQ=59.74;MQ0=0;OQ=1016.84;QD=14.32;SB=-488.08 GT:AD:DP:GL:GQ 0/1:37,34:71:-126.35,-21.38,-153.97:99 +chr1 2495573 rs10910093 C T 602.04 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1162.34;QD=15.92;SB=-466.49 GT:AD:DP:GL:GQ 0/1:38,35:73:-141.53,-22.01,-121.32:99 +chr1 2496089 rs55658746 T C 89.31 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=57.64;MQ0=0;OQ=790.54;QD=12.35;SB=-411.26 GT:AD:DP:GL:GQ 0/1:36,28:63:-101.32,-18.98,-139.07:99 +chr1 2496219 rs2477685 G T 165.82 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=55.91;MQ0=0;OQ=1646.89;QD=32.29;SB=-779.73 GT:AD:DP:GL:GQ 1/1:1,50:48:-168.30,-14.46,-0.02:99 +chr1 2496348 rs10910094 C T 138.18 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=47.91;MQ0=1;OQ=444.30;QD=9.66;SB=-141.63 GT:AD:DP:GL:GQ 0/1:26,19:40:-59.77,-12.06,-79.45:99 +chr1 2497303 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=4;HaplotypeScore=6.77;MQ=59.20;MQ0=0;OQ=63.06;QD=2.17;SB=17.06 GT:AD:DP:GL:GQ 0/1:13,16:15:-14.11,-4.52,-33.25:95.89 +chr1 2497798 rs10752745 A G 23.19 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=2.74;MQ=53.22;MQ0=0;OQ=566.34;QD=12.59;SB=-208.51 GT:AD:DP:GL:GQ 0/1:24,21:42:-72.57,-12.65,-89.49:99 +chr1 2498203 rs6675676 G C 138.01 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=30.17;MQ0=2;OQ=540.65;QD=15.02;SB=-227.70 GT:AD:DP:GL:GQ 0/1:18,18:32:-67.01,-9.66,-62.30:99 +chr1 2500615 rs10910095 G A 293.14 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=53.83;MQ0=0;OQ=619.40;QD=15.49;SB=-326.87 GT:AD:DP:GL:GQ 0/1:18,21:35:-75.77,-10.55,-51.15:99 +chr1 2501140 rs10797434 C T 359.97 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=59.72;MQ0=0;OQ=1006.21;QD=15.25;SB=-442.36 GT:AD:DP:GL:GQ 0/1:35,31:65:-123.49,-19.58,-121.16:99 +chr1 2501248 rs12129508 G A 509.24 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1099.72;QD=18.33;SB=-426.78 GT:AD:DP:GL:GQ 0/1:28,32:59:-131.03,-17.77,-95.59:99 +chr1 2502312 rs4648648 G A 10.75 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=5.67;MQ=56.86;MQ0=0;OQ=538.80;QD=17.96;SB=-254.77 GT:AD:DP:GL:GQ 0/1:13,17:27:-65.30,-8.13,-39.62:99 +chr1 2502510 rs4648649 T C 255.66 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.39;MQ0=0;OQ=590.46;QD=13.42;SB=-228.32 GT:AD:DP:GL:GQ 0/1:17,27:40:-74.40,-12.07,-60.31:99 +chr1 2502570 rs10910096 T C 112.48 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.22;MQ0=0;OQ=671.99;QD=19.20;SB=-218.66 GT:AD:DP:GL:GQ 0/1:13,22:35:-81.03,-10.54,-52.21:99 +chr1 2502755 . G A 190.59 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=20;HaplotypeScore=16.86;MQ=48.05;MQ0=1;QD=2.32;SB=89.22 GT:AD:DP:GL:GQ 0/1:62,20:60:-40.44,-18.10,-157.12:99 +chr1 2502759 . G A 95.63 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=4;HaplotypeScore=8.02;MQ=49.03;MQ0=1;QD=1.15;SB=92.21 GT:AD:DP:GL:GQ 0/1:62,21:60:-30.94,-18.09,-170.87:99 +chr1 2502764 . G A 61.94 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=4;HaplotypeScore=11.73;MQ=52.06;MQ0=1;QD=0.77;SB=101.27 GT:AD:DP:GL:GQ 0/1:64,16:66:-29.37,-19.89,-196.86:94.78 +chr1 2502769 . G A 36.83 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=4;HaplotypeScore=29.21;MQ=54.00;MQ0=1;QD=0.49;SB=101.32 GT:AD:DP:GL:GQ 0/1:66,9:67:-27.16,-20.19,-206.36:69.66 +chr1 2502915 rs4486391 A T 575.38 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=706.11;QD=12.61;SB=-348.36 GT:AD:DP:GL:GQ 0/1:31,25:55:-90.46,-16.56,-121.47:99 +chr1 2502965 rs735000 C T 134.95 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.41;MQ0=0;OQ=774.05;QD=19.85;SB=-347.38 GT:AD:DP:GL:GQ 0/1:16,23:37:-91.84,-11.15,-44.36:99 +chr1 2503076 rs734999 C T 284.99 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=51.96;MQ0=0;OQ=837.38;QD=13.51;SB=-164.65 GT:AD:DP:GL:GQ 0/1:35,27:61:-105.40,-18.37,-127.82:99 +chr1 2503492 rs2016175 C G 123.40 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=50.82;MQ0=0;OQ=1084.11;QD=19.71;SB=-398.00 GT:AD:DP:GL:GQ 0/1:24,31:54:-127.97,-16.28,-102.13:99 +chr1 2503538 rs2016366 A T 76.85 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=3.79;MQ=51.20;MQ0=0;OQ=1061.50;QD=16.33;SB=-509.95 GT:AD:DP:GL:GQ 0/1:31,34:63:-128.41,-18.98,-104.88:99 +chr1 2504435 rs2094074 C T 20.77 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=6.13;MQ=59.30;MQ0=0;OQ=1039.69;QD=17.04;SB=-426.84 GT:AD:DP:GL:GQ 0/1:29,32:61:-125.64,-18.39,-96.67:99 +chr1 2506299 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=15.52;MQ=57.83;MQ0=0;OQ=93.19;QD=2.39;SB=56.19 GT:AD:DP:GL:GQ 0/1:27,12:31:-21.95,-9.34,-90.63:99 +chr1 2511290 rs10910097 C T 251.37 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=59.70;MQ0=0;OQ=1148.10;QD=18.52;SB=-511.69 GT:AD:DP:GL:GQ 0/1:27,35:61:-136.47,-18.38,-99.00:99 +chr1 2512252 rs2296443 G A 195.68 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.53;MQ0=0;OQ=544.43;QD=13.61;SB=-235.74 GT:AD:DP:GL:GQ 0/1:18,22:33:-67.68,-9.95,-51.18:99 +chr1 2515036 . A C 42.97 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.51;MQ0=0;OQ=337.76;QD=7.68;SB=-183.81 GT:AD:DP:GL:GQ 0/1:27,17:42:-49.72,-12.66,-93.24:99 +chr1 2517538 rs2260976 A G 4.94 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.14;MQ=56.76;MQ0=0;OQ=1272.91;QD=31.05;SB=-372.36 GT:AD:DP:GL:GQ 1/1:0,41:39:-130.90,-11.76,-0.03:99 +chr1 2517993 rs2843401 T C 105.48 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=57.77;MQ0=0;OQ=962.33;QD=26.73;SB=-342.23 GT:AD:DP:GL:GQ 1/1:0,36:31:-99.85,-9.36,-0.04:93.19 +chr1 2518542 rs2843402 T C 221.44 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=60.00;MQ0=0;OQ=1968.59;QD=35.79;SB=-942.98 GT:AD:DP:GL:GQ 1/1:0,55:55:-200.46,-16.56,-0.01:99 +chr1 2518859 rs2764845 G T 123.68 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=60.00;MQ0=0;OQ=1822.58;QD=33.75;SB=-893.66 GT:AD:DP:GL:GQ 1/1:0,54:52:-185.86,-15.67,-0.02:99 +chr1 2518957 rs2843403 T C 21.95 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=1.02;MQ=56.17;MQ0=0;OQ=926.62;QD=29.89;SB=-317.56 GT:AD:DP:GL:GQ 1/1:0,31:28:-96.27,-8.44,-0.02:84.21 +chr1 2519052 rs2764842 A G 76.78 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1201.00;QD=30.79;SB=-460.21 GT:AD:DP:GL:GQ 1/1:0,39:38:-123.72,-11.46,-0.03:99 +chr1 2519220 rs2764841 G A 268.55 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=59.01;MQ0=0;OQ=1602.47;QD=34.10;SB=-756.02 GT:AD:DP:GL:GQ 1/1:0,46:43:-163.85,-12.96,-0.02:99 +chr1 2519297 rs2764840 C T 22.50 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=57.55;MQ0=0;OQ=1701.90;QD=37.00;SB=-691.34 GT:AD:DP:GL:GQ 1/1:0,46:43:-173.78,-12.95,-0.01:99 +chr1 2520418 rs2843404 T C 200.03 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.75;MQ0=0;OQ=2535.27;QD=33.80;SB=-857.06 GT:AD:DP:GL:GQ 1/1:0,75:73:-257.13,-21.99,-0.02:99 +chr1 2520554 rs2764848 G A 508.37 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2620.71;QD=40.32;SB=-1288.71 GT:AD:DP:GL:GQ 1/1:0,65:65:-265.67,-19.58,-0.01:99 +chr1 2521232 rs2985855 A C 625.35 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.53;MQ0=0;OQ=2344.13;QD=34.47;SB=-1125.14 GT:AD:DP:GL:GQ 1/1:0,68:67:-238.02,-20.18,-0.02:99 +chr1 2521327 rs6689711 T C 152.61 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.71;MQ0=0;OQ=2140.18;QD=32.93;SB=-405.31 GT:AD:DP:GL:GQ 1/1:0,65:64:-217.64,-19.29,-0.04:99 +chr1 2521365 rs6681973 C T 205.20 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1951.81;QD=38.27;SB=-716.95 GT:AD:DP:GL:GQ 1/1:0,51:50:-198.79,-15.07,-0.02:99 +chr1 2521374 rs6682043 C A 555.65 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1757.71;QD=35.87;SB=-715.96 GT:AD:DP:GL:GQ 1/1:0,49:49:-179.37,-14.76,-0.01:99 +chr1 2521839 . A G 1244.02 Indel AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.74;MQ0=0;QD=31.90;SB=-233.75 GT:AD:DP:GL:GQ 1/1:1,38:37:-132.07,-11.15,-4.08:70.65 +chr1 2522276 rs2985859 T C 630.86 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.35;MQ0=0;OQ=2205.91;QD=35.58;SB=-1051.93 GT:AD:DP:GL:GQ 1/1:0,62:62:-224.19,-18.67,-0.02:99 +chr1 2522366 rs3001837 G A 528.70 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.76;MQ0=0;OQ=2660.16;QD=39.12;SB=-1251.03 GT:AD:DP:GL:GQ 1/1:0,68:68:-269.62,-20.49,-0.02:99 +chr1 2522484 rs2985857 C T 472.23 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=3579.52;QD=41.62;SB=-1476.96 GT:AD:DP:GL:GQ 1/1:0,86:86:-356.95,-25.90,-0.02:99 +chr1 2522759 rs6424092 C A 529.01 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2798.98;QD=36.83;SB=-1322.91 GT:AD:DP:GL:GQ 1/1:0,76:75:-283.50,-22.58,-0.01:99 +chr1 2523213 . A C 18.95 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=2;HaplotypeScore=7.65;MQ=59.48;MQ0=0;QD=0.43;SB=47.15 GT:AD:DP:GL:GQ 0/1:27,17:32:-14.82,-9.65,-87.52:51.73 +chr1 2530333 . T C 29.61 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=7.38;MQ=54.61;MQ0=1;QD=0.64;SB=33.57 GT:AD:DP:GL:GQ 0/1:37,5:39:-21.30,-15.06,-133.42:62.44 +chr1 2530381 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=20.91;MQ=54.33;MQ0=2;OQ=131.02;QD=2.85;SB=56.21 GT:AD:DP:GL:GQ 0/1:39,7:40:-28.44,-12.05,-138.25:99 +chr1 2537888 rs4379628 A G 6.62 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=4.46;MQ=59.75;MQ0=0;OQ=2299.26;QD=31.07;SB=-964.39 GT:AD:DP:GL:GQ 1/1:0,74:72:-233.58,-21.72,-0.07:99 +chr1 2541362 . T C 301.82 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=1099.72;QD=15.94;SB=-567.63 GT:AD:DP:GL:GQ 0/1:31,38:67:-133.44,-20.18,-122.76:99 +chr1 2541645 rs12117343 C T 412.42 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.64;MQ0=0;OQ=1073.30;QD=16.77;SB=-513.05 GT:AD:DP:GL:GQ 0/1:32,32:63:-129.60,-18.99,-99.14:99 +chr1 2543980 rs61765771 T G 318.19 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=635.63;QD=14.45;SB=-332.88 GT:AD:DP:GL:GQ 0/1:20,24:43:-79.80,-12.95,-72.63:99 +chr1 2546847 . G A 17.21 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.27;MQ0=0;OQ=1072.92;QD=19.87;SB=-329.89 GT:AD:DP:GL:GQ 0/1:19,35:49:-125.34,-14.77,-58.33:99 +chr1 2547051 rs7523364 C T 194.54 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=55.15;MQ0=0;OQ=3310.62;QD=39.41;SB=-1353.31 GT:AD:DP:GL:GQ 1/1:0,84:83:-330.06,-25.01,-0.03:99 +chr1 2547391 rs6422657 C T 186.53 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=2783.42;QD=38.13;SB=-1334.38 GT:AD:DP:GL:GQ 1/1:1,71:72:-284.61,-21.69,-2.69:99 +chr1 2548168 rs6668149 A C 205.71 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.44;MQ0=0;OQ=2627.68;QD=35.04;SB=-1288.37 GT:AD:DP:GL:GQ 1/1:0,75:74:-266.37,-22.29,-0.02:99 +chr1 2548600 rs12748729 C T 627.69 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2890.24;QD=37.05;SB=-1331.37 GT:AD:DP:GL:GQ 1/1:0,78:77:-292.65,-23.21,-0.04:99 +chr1 2549449 rs12730932 T G 82.44 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.16;MQ0=0;OQ=1601.53;QD=32.03;SB=-737.35 GT:AD:DP:GL:GQ 1/1:0,50:47:-163.76,-14.16,-0.02:99 +chr1 2550595 rs4648657 A G 5.77 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.33;MQ0=0;OQ=350.17;QD=25.01;SB=-43.68 GT:AD:DP:GL:GQ 1/1:0,14:13:-38.62,-3.93,-0.02:39.06 +chr1 2550742 rs4648658 G A 10.42 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.23;MQ0=0;OQ=551.80;QD=32.46;SB=-125.66 GT:AD:DP:GL:GQ 1/1:0,17:15:-58.77,-4.52,-0.01:45.14 +chr1 2550763 rs4648659 T G 0.34 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=55.52;MQ0=0;OQ=309.18;QD=19.32;SB=-86.14 GT:AD:DP:GL:GQ 1/1:0,16:12:-34.52,-3.62,-0.02:36.01 +chr1 2551146 rs28532547 T G 110.03 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=53.21;MQ0=0;OQ=1059.23;QD=30.26;SB=-548.02 GT:AD:DP:GL:GQ 1/1:0,35:32:-109.53,-9.64,-0.02:96.26 +chr1 2552029 rs4648564 C T 0.99 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=7.47;MQ=58.85;MQ0=1;OQ=2625.23;QD=39.18;SB=-1028.39 GT:AD:DP:GL:GQ 1/1:1,66:66:-266.13,-19.88,-0.02:99 +chr1 2553110 rs12749591 G T 349.46 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=723.50;QD=32.89;SB=-266.61 GT:AD:DP:GL:GQ 1/1:0,22:22:-75.95,-6.63,-0.01:66.17 +chr1 2553270 . G T 45.57 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=10.71;MQ=58.27;MQ0=0;QD=1.69;SB=20.06 GT:AD:DP:GL:GQ 0/1:17,10:20:-13.87,-6.03,-50.95:78.40 +chr1 2554043 rs6698817 T C 9.96 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=887.43;QD=26.89;SB=-424.17 GT:AD:DP:GL:GQ 1/1:0,33:29:-92.36,-8.75,-0.03:87.20 +chr1 2554325 rs12752515 T C 17.47 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.11;MQ0=0;OQ=775.65;QD=29.83;SB=-403.34 GT:AD:DP:GL:GQ 1/1:0,26:25:-81.17,-7.54,-0.02:75.18 +chr1 2554665 rs12723864 A G 160.30 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=60.00;MQ0=0;OQ=414.17;QD=9.86;SB=-197.61 GT:AD:DP:GL:GQ 0/1:26,16:42:-57.35,-12.65,-104.43:99 +chr1 2555187 rs55649610 G T 258.93 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=951.34;QD=20.68;SB=-431.11 GT:AD:DP:GL:GQ 0/1:14,32:46:-112.28,-13.86,-47.81:99 +chr1 2555885 . C T 1.81 PASS AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=57.89;MQ0=0;OQ=690.84;QD=23.82;SB=-291.84 GT:AD:DP:GL:GQ 0/1:8,21:28:-80.81,-8.44,-25.16:99 +chr1 2556197 . T G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=11.22;MQ=54.79;MQ0=0;OQ=66.20;QD=3.31;SB=-59.09 GT:AD:DP:GL:GQ 0/1:16,4:14:-14.12,-4.22,-33.87:99 +chr1 2556342 rs6657378 T G 21.29 LowQual AC=1;AF=0.50;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=3.31;MQ=37.32;MQ0=0;QD=3.04;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,2:5:-6.92,-1.51,-9.22:54.10 +chr1 2556350 rs6671623 G A 0.26 PASS AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=6.12;MQ=40.03;MQ0=1;OQ=207.84;QD=25.98;SB=-95.34 GT:AD:DP:GL:GQ 1/1:1,7:6:-24.36,-1.81,-0.00:18.06 +chr1 2556357 rs6671625 G A 182.34 PASS AC=2;AF=1.00;AN=2;DB;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.68;MQ0=1;OQ=89.01;QD=14.84;SB=-50.56 GT:AD:DP:GL:GQ 1/1:1,5:3:-12.39,-0.90,-0.00:9.03 +chr1 2556483 rs61765773 C T 0.15 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=11.29;MQ=45.87;MQ0=1;OQ=153.35;QD=5.11;SB=26.06 GT:AD:DP:GL:GQ 0/1:23,7:20:-24.65,-6.03,-43.69:99 +chr1 2556797 rs61765774 G C 178.56 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.58;MQ0=0;OQ=587.02;QD=17.79;SB=-197.49 GT:AD:DP:GL:GQ 0/1:16,17:32:-71.63,-9.64,-64.58:99 +chr1 2557281 rs12756665 C T 187.45 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.25;MQ=59.28;MQ0=0;OQ=722.29;QD=11.29;SB=-327.75 GT:AD:DP:GL:GQ 0/1:40,24:64:-94.79,-19.28,-146.15:99 +chr1 2557351 rs12739597 A G 96.49 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.10;MQ0=0;OQ=470.82;QD=7.03;SB=-215.20 GT:AD:DP:GL:GQ 0/1:44,23:67:-70.56,-20.20,-177.79:99 +chr1 2557360 rs6666788 A G 33.09 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=2.28;MQ=59.11;MQ0=0;OQ=2385.56;QD=35.08;SB=-1067.87 GT:AD:DP:GL:GQ 1/1:0,68:67:-242.16,-20.18,-0.02:99 +chr1 2558285 rs4648661 T C 264.82 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=58.76;MQ0=0;OQ=708.13;QD=11.80;SB=-352.07 GT:AD:DP:GL:GQ 0/1:29,30:58:-91.59,-17.49,-110.76:99 +chr1 2559883 rs4648565 A G 68.89 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=1657.37;QD=34.53;SB=-734.30 GT:AD:DP:GL:GQ 1/1:0,48:47:-169.34,-14.16,-0.02:99 +chr1 2561683 rs28690427 A G 44.51 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.48;MQ0=0;OQ=1625.27;QD=33.17;SB=-564.36 GT:AD:DP:GL:GQ 1/1:0,49:47:-166.13,-14.16,-0.02:99 +chr1 2563059 rs4648662 A G 36.80 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=57.88;MQ0=0;OQ=986.78;QD=31.83;SB=-278.44 GT:AD:DP:GL:GQ 1/1:0,30:28:-102.27,-8.43,-0.01:84.25 +chr1 2563587 rs4648663 A C 432.35 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=1398.67;QD=33.30;SB=-656.05 GT:AD:DP:GL:GQ 1/1:0,42:41:-143.47,-12.35,-0.02:99 +chr1 2563763 rs12726651 C T 270.02 PASS AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.90;MQ0=0;OQ=164.81;QD=9.69;SB=-74.06 GT:AD:DP:GL:GQ 0/1:11,6:16:-24.59,-4.82,-34.68:99 +chr1 2563938 rs9970196 T C 22.23 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.81;MQ=59.28;MQ0=0;OQ=1014.31;QD=31.70;SB=-295.06 GT:AD:DP:GL:GQ 1/1:0,32:30:-105.04,-9.04,-0.02:90.22 +chr1 2566315 rs6604989 T C 18.73 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.60;MQ0=0;OQ=1647.45;QD=28.40;SB=-794.64 GT:AD:DP:GL:GQ 1/1:0,58:52:-168.38,-15.68,-0.05:99 +chr1 2568080 rs12744876 G T 183.89 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=58.84;MQ0=0;OQ=1106.09;QD=17.02;SB=-318.70 GT:AD:DP:GL:GQ 0/1:29,35:64:-133.17,-19.27,-104.78:99 +chr1 2571402 rs28611770 A G 632.64 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.32;MQ0=1;OQ=2534.42;QD=35.20;SB=-1124.79 GT:AD:DP:GL:GQ 1/1:0,72:70:-257.05,-21.08,-0.02:99 +chr1 2571473 . C T 26.42 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=54.51;MQ0=1;OQ=420.48;QD=8.58;SB=-192.15 GT:AD:DP:GL:GQ 0/1:33,16:41:-57.68,-12.35,-93.81:99 +chr1 2571476 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=3;HaplotypeScore=3.65;MQ=54.65;MQ0=1;OQ=290.92;QD=5.94;SB=-124.22 GT:AD:DP:GL:GQ 0/1:34,15:41:-44.73,-12.36,-110.26:99 +chr1 2571505 . C T 0.62 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=52.42;MQ0=0;OQ=231.01;QD=4.20;SB=-18.13 GT:AD:DP:GL:GQ 0/1:42,13:52:-42.05,-15.67,-144.47:99 +chr1 2571527 . A T 14.96 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.42;MQ=51.64;MQ0=0;OQ=434.87;QD=7.91;SB=-142.65 GT:AD:DP:GL:GQ 0/1:35,20:51:-62.14,-15.37,-122.01:99 +chr1 2572200 rs12732266 C G 51.91 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=5.49;MQ=58.04;MQ0=0;OQ=559.70;QD=11.91;SB=-261.11 GT:AD:DP:GL:GQ 0/1:26,21:41:-71.62,-12.36,-99.19:99 +chr1 2573315 rs12738064 C T 887.13 DPFilter;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=171.89;MQ=24.26;MQ0=9;QD=6.67;SB=-137.01 GT:AD:DP:GL:GQ 1/1:10,119:25:-96.41,-11.12,-4.11:70.06 +chr1 2573322 . T G 343.20 DPFilter;SnpCluster AC=2;AF=1.00;AN=2;DP=144;Dels=0.01;HRun=0;HaplotypeScore=333.45;MQ=22.10;MQ0=11;QD=2.38;SB=-10.00 GT:AD:DP:GL:GQ 1/1:29,104:11:-37.91,-3.31,-0.00:33.09 +chr1 2573323 . C G 95.88 DPFilter;SnpCluster AC=2;AF=1.00;AN=2;DP=144;Dels=0.01;HRun=1;HaplotypeScore=342.46;MQ=22.10;MQ0=11;QD=0.67;SB=-10.00 GT:AD:DP:GL:GQ 1/1:103,36:3:-13.08,-0.90,-0.00:9.03 +chr1 2573324 . G C 506.46 DPFilter;Indel;SnpCluster AC=2;AF=1.00;AN=2;DP=147;Dels=0.01;HRun=1;HaplotypeScore=339.64;MQ=22.28;MQ0=11;QD=3.45;SB=-10.00 GT:AD:DP:GL:GQ 1/1:15,116:14:-57.88,-7.75,-3.65:41.01 +chr1 2573329 rs12734173 G A 146.94 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=218;Dels=0.00;HRun=1;HaplotypeScore=513.41;MQ=21.01;MQ0=20;QD=0.67;SB=-10.00 GT:AD:DP:GL:GQ 0/1:132,84:24:-25.21,-7.23,-67.73:99 +chr1 2573338 . C G 83.26 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=710.09;MQ=20.03;MQ0=40;QD=0.29;SB=-0.97 GT:AD:DP:GL:GQ 0/1:254,26:38:-23.06,-11.45,-135.55:99 +chr1 2573342 . C A 213.70 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=322;Dels=0.00;HRun=1;HaplotypeScore=673.88;MQ=20.07;MQ0=46;QD=0.66;SB=1.99 GT:AD:DP:GL:GQ 0/1:277,45:41:-37.01,-12.35,-108.15:99 +chr1 2573345 . A C 1425.86 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=338;Dels=0.02;HRun=3;HaplotypeScore=632.90;MQ=20.26;MQ0=48;QD=4.22;SB=-172.79 GT:AD:DP:GL:GQ 0/1:132,186:90:-176.25,-30.38,-146.77:99 +chr1 2573350 . T C 293.04 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=399;Dels=0.00;HRun=0;HaplotypeScore=691.94;MQ=19.84;MQ0=54;QD=0.73;SB=44.71 GT:AD:DP:GL:GQ 0/1:277,71:78:-104.74,-72.15,-238.43:99 +chr1 2573354 . C A 62.42 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=432;Dels=0.00;HRun=1;HaplotypeScore=848.73;MQ=19.94;MQ0=56;QD=0.14;SB=50.16 GT:AD:DP:GL:GQ 0/1:379,40:51:-24.89,-15.36,-155.69:95.25 +chr1 2573358 . T C 129.61 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=457;Dels=0.00;HRun=1;HaplotypeScore=683.78;MQ=19.93;MQ0=58;QD=0.28;SB=-34.65 GT:AD:DP:GL:GQ 0/1:367,56:52:-42.68,-26.43,-169.09:99 +chr1 2573364 rs55738582 C G 575.47 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=473;Dels=0.00;HRun=1;HaplotypeScore=961.37;MQ=19.71;MQ0=62;QD=1.22;SB=-67.52 GT:AD:DP:GL:GQ 0/1:411,23:43:-73.79,-12.96,-105.12:99 +chr1 2573370 rs55790383 G A 775.08 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=470;Dels=0.00;HRun=1;HaplotypeScore=917.62;MQ=19.72;MQ0=61;QD=1.65;SB=-367.90 GT:AD:DP:GL:GQ 0/1:265,173:48:-98.76,-17.97,-89.48:99 +chr1 2573371 rs55657722 G C 3489.08 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=470;Dels=0.00;HRun=0;HaplotypeScore=944.58;MQ=19.72;MQ0=61;QD=7.42;SB=-1002.13 GT:AD:DP:GL:GQ 1/1:47,398:84:-347.91,-28.85,-3.68:99 +chr1 2573372 . A G 46.25 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=482;Dels=0.00;HRun=2;HaplotypeScore=999.26;MQ=19.79;MQ0=62;QD=0.10;SB=26.11 GT:AD:DP:GL:GQ 0/1:425,48:54:-24.18,-16.27,-184.96:79.08 +chr1 2573374 . C A 193.31 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=490;Dels=0.00;HRun=1;HaplotypeScore=979.59;MQ=19.99;MQ0=60;QD=0.39;SB=-75.64 GT:AD:DP:GL:GQ 0/1:438,45:65:-48.93,-26.32,-189.47:99 +chr1 2573382 . C A 261.06 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=502;Dels=0.01;HRun=1;HaplotypeScore=946.29;MQ=19.95;MQ0=64;QD=0.52;SB=17.04 GT:AD:DP:GL:GQ 0/1:391,72:71:-67.99,-38.60,-197.52:99 +chr1 2573383 . C G 55.13 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=502;Dels=0.00;HRun=0;HaplotypeScore=899.21;MQ=20.04;MQ0=63;QD=0.11;SB=37.79 GT:AD:DP:GL:GQ 0/1:438,33:65:-35.38,-26.59,-240.37:87.97 +chr1 2573385 . C A 145.75 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=503;Dels=0.00;HRun=0;HaplotypeScore=828.45;MQ=20.02;MQ0=64;QD=0.29;SB=-23.06 GT:AD:DP:GL:GQ 0/1:432,48:49:-35.99,-18.13,-141.74:99 +chr1 2573390 . T C 166.49 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=483;Dels=0.01;HRun=0;HaplotypeScore=660.44;MQ=20.15;MQ0=61;QD=0.34;SB=-43.82 GT:AD:DP:GL:GQ 0/1:342,96:43:-35.67,-15.74,-120.66:99 +chr1 2573404 rs56352113 A C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=412;Dels=0.00;HRun=1;HaplotypeScore=785.14;MQ=20.24;MQ0=50;OQ=1746.05;QD=4.24;SB=-272.76 GT:AD:DP:GL:GQ 1/1:48,316:72:-242.08,-66.55,-63.89:26.61 +chr1 2573410 rs12759490 A G 148.65 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DB;DP=383;Dels=0.00;HRun=0;HaplotypeScore=682.21;MQ=20.35;MQ0=44;QD=0.39;SB=-43.26 GT:AD:DP:GL:GQ 0/1:276,96:57:-35.34,-17.19,-178.84:99 +chr1 2573423 . C A 163.64 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=1;HaplotypeScore=927.03;MQ=21.34;MQ0=33;QD=0.58;SB=26.07 GT:AD:DP:GL:GQ 0/1:224,38:48:-34.11,-14.46,-128.40:99 +chr1 2573426 . C A 487.43 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=275;Dels=0.00;HRun=0;HaplotypeScore=598.86;MQ=21.74;MQ0=31;QD=1.77;SB=-144.61 GT:AD:DP:GL:GQ 0/1:229,39:67:-72.21,-20.18,-167.89:99 +chr1 2573431 . T A 55.01 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=244;Dels=0.00;HRun=0;HaplotypeScore=414.88;MQ=22.20;MQ0=23;QD=0.23;SB=-37.64 GT:AD:DP:GL:GQ 0/1:198,17:62:-42.64,-33.85,-190.83:87.85 +chr1 2573439 rs12738268 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=199;Dels=0.00;HRun=0;HaplotypeScore=197.41;MQ=23.56;MQ0=17;OQ=1379.28;QD=6.93;SB=-473.52 GT:AD:DP:GL:GQ 0/1:75,107:51:-156.58,-15.37,-36.65:99 +chr1 2573442 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=0;HaplotypeScore=181.20;MQ=23.67;MQ0=14;OQ=103.36;QD=0.53;SB=32.13 GT:AD:DP:GL:GQ 0/1:179,11:55:-39.39,-25.77,-162.27:99 +chr1 2573451 . A G 329.45 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=156;Dels=0.00;HRun=0;HaplotypeScore=168.85;MQ=25.71;MQ0=9;QD=2.11;SB=-36.23 GT:AD:DP:GL:GQ 0/1:80,76:54:-52.50,-16.27,-154.97:99 +chr1 2573454 rs55760918 C G 556.39 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=140;Dels=0.00;HRun=0;HaplotypeScore=206.74;MQ=26.90;MQ0=8;QD=3.97;SB=-52.80 GT:AD:DP:GL:GQ 0/1:46,88:51:-74.30,-15.38,-138.45:99 +chr1 2573455 rs56258540 A C 134.39 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=145;Dels=0.00;HRun=1;HaplotypeScore=218.70;MQ=26.73;MQ0=9;QD=0.93;SB=-34.89 GT:AD:DP:GL:GQ 0/1:91,52:51:-34.62,-17.90,-142.52:99 +chr1 2573485 rs55714819 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=241;Dels=0.00;HRun=1;HaplotypeScore=172.11;MQ=27.92;MQ0=9;OQ=766.38;QD=3.18;SB=-61.60 GT:AD:DP:GL:GQ 0/1:152,84:106:-115.24,-35.32,-271.38:99 +chr1 2573510 rs61765777 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=332;Dels=0.00;HRun=1;HaplotypeScore=336.11;MQ=27.14;MQ0=14;OQ=2271.13;QD=6.84;SB=-383.23 GT:AD:DP:GL:GQ 0/1:103,229:130:-269.56,-39.16,-232.28:99 +chr1 2573523 . C T 271.88 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=476;Dels=0.00;HRun=0;HaplotypeScore=388.59;MQ=26.03;MQ0=25;QD=0.57;SB=-54.44 GT:AD:DP:GL:GQ 0/1:421,51:171:-82.00,-51.53,-495.80:99 +chr1 2573524 . G A 673.59 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=489;Dels=0.00;HRun=0;HaplotypeScore=381.72;MQ=26.07;MQ0=26;QD=1.38;SB=-235.66 GT:AD:DP:GL:GQ 0/1:348,136:174:-123.14,-52.50,-452.42:99 +chr1 2573532 . A G 266.78 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=584;Dels=0.00;HRun=0;HaplotypeScore=454.81;MQ=26.29;MQ0=38;QD=0.46;SB=-50.09 GT:AD:DP:GL:GQ 0/1:462,118:225:-100.76,-70.80,-803.69:99 +chr1 2573533 . C T 518.62 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=590;Dels=0.00;HRun=0;HaplotypeScore=454.86;MQ=26.25;MQ0=38;QD=0.88;SB=-177.22 GT:AD:DP:GL:GQ 0/1:555,34:221:-123.94,-68.80,-639.87:99 +chr1 2573545 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=760;Dels=0.00;HRun=0;HaplotypeScore=554.01;MQ=25.28;MQ0=58;OQ=2752.41;QD=3.62;SB=-334.08 GT:AD:DP:GL:GQ 0/1:504,247:275:-368.19,-89.67,-758.94:99 +chr1 2573551 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=816;Dels=0.00;HRun=0;HaplotypeScore=706.82;MQ=24.77;MQ0=61;OQ=92.57;QD=0.11;SB=99.33 GT:AD:DP:GL:GQ 0/1:767,48:306:-104.74,-92.20,-1021.89:99 +chr1 2573560 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=935;Dels=0.00;HRun=0;HaplotypeScore=771.90;MQ=24.19;MQ0=82;OQ=1354.07;QD=1.45;SB=-436.68 GT:AD:DP:GL:GQ 0/1:723,199:339:-248.95,-110.26,-942.99:99 +chr1 2573563 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=967;Dels=0.00;HRun=0;HaplotypeScore=867.36;MQ=23.97;MQ0=86;OQ=1389.93;QD=1.44;SB=161.22 GT:AD:DP:GL:GQ 0/1:819,137:345:-262.46,-120.18,-962.42:99 +chr1 2573572 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1012;Dels=0.00;HRun=0;HaplotypeScore=731.51;MQ=23.62;MQ0=98;OQ=634.63;QD=0.63;SB=-79.47 GT:AD:DP:GL:GQ 0/1:773,210:334:-172.80,-106.05,-1139.69:99 +chr1 2573600 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=878;Dels=0.00;HRun=0;HaplotypeScore=653.71;MQ=23.12;MQ0=120;OQ=1122.68;QD=1.28;SB=-567.08 GT:AD:DP:GL:GQ 0/1:678,154:296:-246.10,-130.55,-807.07:99 +chr1 2573603 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=862;Dels=0.00;HRun=0;HaplotypeScore=618.67;MQ=23.10;MQ0=123;OQ=316.50;QD=0.37;SB=-169.71 GT:AD:DP:GL:GQ 0/1:783,67:305:-136.37,-101.44,-918.41:99 +chr1 2573643 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=406;Dels=0.00;HRun=0;HaplotypeScore=240.70;MQ=22.59;MQ0=105;OQ=101.01;QD=0.25;SB=40.47 GT:AD:DP:GL:GQ 0/1:341,64:133:-53.47,-40.09,-445.02:99 +chr1 2573645 . T G 27.32 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=393;Dels=0.00;HRun=0;HaplotypeScore=214.15;MQ=22.61;MQ0=102;QD=0.07;SB=22.12 GT:AD:DP:GL:GQ 0/1:333,60:125:-43.68,-37.67,-396.83:60.15 +chr1 2573659 rs28581291 G C 4615.63 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=333;Dels=0.00;HRun=1;HaplotypeScore=205.79;MQ=24.13;MQ0=78;QD=13.86;SB=-1212.00 GT:AD:DP:GL:GQ 0/1:35,294:132:-460.56,-39.52,-82.06:99 +chr1 2573662 . C T 559.05 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=354;Dels=0.00;HRun=0;HaplotypeScore=280.21;MQ=24.11;MQ0=79;QD=1.58;SB=-274.91 GT:AD:DP:GL:GQ 0/1:309,45:145:-102.89,-43.70,-398.94:99 +chr1 2573665 . C G 1510.34 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=408;Dels=0.00;HRun=0;HaplotypeScore=325.78;MQ=24.58;MQ0=76;QD=3.70;SB=-297.94 GT:AD:DP:GL:GQ 0/1:264,141:179:-211.73,-57.41,-536.45:99 +chr1 2573688 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=651;Dels=0.00;HRun=2;HaplotypeScore=395.85;MQ=24.99;MQ0=65;OQ=362.26;QD=0.56;SB=-155.57 GT:AD:DP:GL:GQ 0/1:581,65:307:-140.30,-100.79,-1081.14:99 +chr1 2573689 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=665;Dels=0.00;HRun=0;HaplotypeScore=525.06;MQ=24.91;MQ0=65;OQ=1827.67;QD=2.75;SB=-517.28 GT:AD:DP:GL:GQ 0/1:550,112:319:-282.15,-96.10,-903.12:99 +chr1 2573699 rs28514305 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=700;Dels=0.00;HRun=1;HaplotypeScore=627.89;MQ=25.13;MQ0=51;OQ=504.00;QD=0.72;SB=-50.28 GT:AD:DP:GL:GQ 0/1:553,135:325:-164.84,-111.15,-1100.31:99 +chr1 2573722 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=939;Dels=0.00;HRun=0;HaplotypeScore=511.14;MQ=24.55;MQ0=41;OQ=652.05;QD=0.69;SB=-156.78 GT:AD:DP:GL:GQ 0/1:833,100:448:-203.46,-134.97,-1376.56:99 +chr1 2573743 . C A 1376.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=920;Dels=0.01;HRun=1;HaplotypeScore=1049.31;MQ=24.03;MQ0=45;QD=1.50;SB=-654.94 GT:AD:DP:GL:GQ 0/1:771,125:393:-273.72,-132.79,-1119.66:99 +chr1 2573744 . C A 2246.36 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=920;Dels=0.00;HRun=0;HaplotypeScore=1100.48;MQ=24.05;MQ0=45;QD=2.44;SB=-774.39 GT:AD:DP:GL:GQ 0/1:696,198:389:-363.03,-135.11,-1033.83:99 +chr1 2573747 . C T 2541.21 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=900;Dels=0.00;HRun=0;HaplotypeScore=1014.50;MQ=23.93;MQ0=43;QD=2.82;SB=-593.64 GT:AD:DP:GL:GQ 0/1:671,157:361:-422.27,-164.86,-953.11:99 +chr1 2573753 . A T 936.20 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=863;Dels=0.00;HRun=0;HaplotypeScore=1289.29;MQ=23.50;MQ0=46;QD=1.08;SB=-444.50 GT:AD:DP:GL:GQ 0/1:735,98:311:-195.18,-98.28,-961.18:99 +chr1 2573759 . C T 306.11 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=786;Dels=0.00;HRun=0;HaplotypeScore=944.88;MQ=23.40;MQ0=46;QD=0.39;SB=80.59 GT:AD:DP:GL:GQ 0/1:568,186:262:-146.29,-112.39,-779.46:99 +chr1 2573762 . C T 1224.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=751;Dels=0.00;HRun=0;HaplotypeScore=1008.25;MQ=23.38;MQ0=43;QD=1.63;SB=32.31 GT:AD:DP:GL:GQ 0/1:549,181:260:-207.81,-82.08,-705.47:99 +chr1 2573768 . G A 69.35 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=690;Dels=0.00;HRun=0;HaplotypeScore=1128.47;MQ=23.25;MQ0=39;QD=0.10;SB=181.10 GT:AD:DP:GL:GQ 0/1:645,45:222:-77.09,-66.88,-732.33:99 +chr1 2573775 rs61765778 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=598;Dels=0.00;HRun=0;HaplotypeScore=829.09;MQ=23.11;MQ0=35;OQ=51.56;QD=0.09;SB=-51.39 GT:AD:DP:GL:GQ 0/1:411,178:176:-78.89,-70.45,-552.62:84.40 +chr1 2573784 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=482;Dels=0.00;HRun=0;HaplotypeScore=533.05;MQ=23.86;MQ0=35;OQ=97.06;QD=0.20;SB=-41.06 GT:AD:DP:GL:GQ 0/1:428,39:135:-57.53,-44.54,-428.93:99 +chr1 2573791 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=376;Dels=0.00;HRun=0;HaplotypeScore=279.62;MQ=25.08;MQ0=23;OQ=809.10;QD=2.15;SB=-122.99 GT:AD:DP:GL:GQ 0/1:249,119:103:-122.37,-38.18,-240.78:99 +chr1 2573803 rs61765779 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=238;Dels=0.00;HRun=0;HaplotypeScore=273.29;MQ=27.85;MQ0=11;OQ=738.52;QD=3.10;SB=-305.23 GT:AD:DP:GL:GQ 0/1:82,152:68:-97.64,-20.50,-141.62:99 +chr1 2573809 rs61765805 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=1;HaplotypeScore=207.51;MQ=30.86;MQ0=7;OQ=486.71;QD=2.85;SB=-123.47 GT:AD:DP:GL:GQ 0/1:47,107:55:-75.59,-23.64,-159.88:99 +chr1 2573825 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.04;HRun=2;HaplotypeScore=133.51;MQ=37.12;MQ0=1;OQ=152.18;QD=1.48;SB=68.24 GT:AD:DP:GL:GQ 0/1:42,51:50:-47.81,-29.31,-160.18:99 +chr1 2573831 rs55855140 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=126.91;MQ=39.65;MQ0=1;OQ=158.89;QD=1.62;SB=62.19 GT:AD:DP:GL:GQ 0/1:53,43:46:-39.96,-20.79,-124.08:99 +chr1 2573842 . A C 115.63 SnpCluster AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=142.04;MQ=40.93;MQ0=1;QD=1.17;SB=-71.86 GT:AD:DP:GL:GQ 0/1:45,45:51:-30.22,-15.37,-141.99:99 +chr1 2573846 rs61765806 C G 427.99 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.00;HRun=0;HaplotypeScore=158.02;MQ=39.65;MQ0=2;QD=3.34;SB=50.19 GT:AD:DP:GL:GQ 0/1:94,33:65:-65.70,-19.61,-201.59:99 +chr1 2573851 . G A 820.83 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=1;HaplotypeScore=122.19;MQ=40.52;MQ0=2;QD=5.86;SB=-152.15 GT:AD:DP:GL:GQ 0/1:66,72:74:-107.66,-22.30,-166.53:99 +chr1 2573859 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=126.84;MQ=40.41;MQ0=2;OQ=121.72;QD=0.77;SB=152.53 GT:AD:DP:GL:GQ 0/1:122,36:93:-43.49,-28.03,-346.24:99 +chr1 2573901 rs35515286 G C 550.86 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=206;Dels=0.00;HRun=0;HaplotypeScore=105.96;MQ=43.03;MQ0=1;QD=2.67;SB=237.50 GT:AD:DP:GL:GQ 0/1:135,63:142:-119.31,-60.94,-520.06:99 +chr1 2573904 . G C 824.37 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=3;HaplotypeScore=109.03;MQ=42.87;MQ0=2;QD=4.04;SB=193.35 GT:AD:DP:GL:GQ 0/1:129,71:137:-131.62,-45.90,-468.47:99 +chr1 2573907 . C T 232.33 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=234;Dels=0.00;HRun=0;HaplotypeScore=169.38;MQ=41.15;MQ0=2;QD=0.99;SB=246.29 GT:AD:DP:GL:GQ 0/1:198,35:151:-72.01,-45.49,-466.42:99 +chr1 2573937 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=313;Dels=0.00;HRun=2;HaplotypeScore=156.05;MQ=41.48;MQ0=6;OQ=610.21;QD=1.95;SB=184.28 GT:AD:DP:GL:GQ 0/1:179,131:178:-121.09,-56.78,-561.52:99 +chr1 2573955 rs4648664 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=309;Dels=0.01;HRun=0;HaplotypeScore=189.00;MQ=39.75;MQ0=9;OQ=5144.30;QD=16.65;SB=-1373.56 GT:AD:DP:GL:GQ 0/1:99,207:204:-513.43,-64.42,-219.84:99 +chr1 2573957 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=0;HaplotypeScore=210.03;MQ=39.51;MQ0=9;OQ=1411.76;QD=4.57;SB=186.52 GT:AD:DP:GL:GQ 0/1:164,144:192:-204.89,-60.43,-482.07:99 +chr1 2573977 rs36074084 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=329;Dels=0.14;HRun=3;HaplotypeScore=420.13;MQ=34.94;MQ0=9;OQ=1855.95;QD=5.64;SB=145.19 GT:AD:DP:GL:GQ 0/1:152,125:193:-244.66,-55.78,-561.08:99 +chr1 2573987 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=436;Dels=0.02;HRun=3;HaplotypeScore=523.62;MQ=29.87;MQ0=18;OQ=97.02;QD=0.22;SB=235.20 GT:AD:DP:GL:GQ 0/1:315,109:216:-76.87,-63.88,-657.84:99 +chr1 2574006 rs56001931 C A 193.50 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=578;Dels=0.00;HRun=0;HaplotypeScore=796.32;MQ=26.82;MQ0=27;QD=0.33;SB=-95.26 GT:AD:DP:GL:GQ 0/1:506,46:197:-84.56,-61.92,-620.37:99 +chr1 2574010 . G A 47.43 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=576;Dels=0.00;HRun=1;HaplotypeScore=936.31;MQ=26.86;MQ0=27;QD=0.08;SB=305.98 GT:AD:DP:GL:GQ 0/1:514,37:196:-70.15,-62.12,-641.00:80.27 +chr1 2574012 . G A 1112.09 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=567;Dels=0.00;HRun=1;HaplotypeScore=881.66;MQ=26.70;MQ0=27;QD=1.96;SB=173.94 GT:AD:DP:GL:GQ 0/1:337,218:205:-176.25,-61.76,-573.77:99 +chr1 2574013 rs35375421 G C 2739.83 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=556;Dels=0.00;HRun=0;HaplotypeScore=907.42;MQ=26.74;MQ0=27;QD=4.93;SB=-98.82 GT:AD:DP:GL:GQ 0/1:185,358:186:-340.69,-63.42,-477.87:99 +chr1 2574046 rs61765808 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=633;Dels=0.00;HRun=1;HaplotypeScore=769.62;MQ=25.77;MQ0=33;OQ=2369.47;QD=3.74;SB=-14.31 GT:AD:DP:GL:GQ 0/1:214,394:219:-332.81,-92.58,-459.77:99 +chr1 2574062 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=571;Dels=0.02;HRun=0;HaplotypeScore=1395.05;MQ=27.31;MQ0=25;OQ=270.74;QD=0.47;SB=9.21 GT:AD:DP:GL:GQ 0/1:393,159:156:-79.45,-49.09,-466.84:99 +chr1 2574081 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=574;Dels=0.00;HRun=0;HaplotypeScore=636.02;MQ=28.62;MQ0=23;OQ=102.79;QD=0.18;SB=258.30 GT:AD:DP:GL:GQ 0/1:339,178:156:-99.87,-86.31,-482.50:99 +chr1 2574099 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=481;Dels=0.01;HRun=2;HaplotypeScore=469.12;MQ=32.08;MQ0=15;OQ=332.15;QD=0.69;SB=-15.43 GT:AD:DP:GL:GQ 0/1:184,278:155:-88.85,-52.35,-456.19:99 +chr1 2574112 rs4648665 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=407;Dels=0.00;HRun=1;HaplotypeScore=376.40;MQ=32.86;MQ0=13;OQ=5520.38;QD=13.56;SB=-1708.96 GT:AD:DP:GL:GQ 1/1:7,385:151:-551.04,-45.49,-0.05:99 +chr1 2574233 rs6678571 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=482;Dels=0.00;HRun=0;HaplotypeScore=317.44;MQ=37.14;MQ0=103;OQ=51.18;QD=0.11;SB=33.13 GT:AD:DP:GL:GQ 0/1:400,76:222:-75.35,-66.94,-654.61:84.02 +chr1 2574280 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=411;Dels=0.00;HRun=0;HaplotypeScore=206.24;MQ=40.63;MQ0=25;OQ=702.83;QD=1.71;SB=165.25 GT:AD:DP:GL:GQ 0/1:262,145:248:-148.35,-74.78,-882.77:99 +chr1 2574370 rs56005609 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=224;Dels=0.00;HRun=0;HaplotypeScore=51.47;MQ=47.47;MQ0=12;OQ=160.10;QD=0.71;SB=-105.06 GT:AD:DP:GL:GQ 0/1:203,21:172:-71.19,-51.89,-483.26:99 +chr1 2574383 rs4648666 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=215;Dels=0.00;HRun=0;HaplotypeScore=154.22;MQ=48.52;MQ0=8;OQ=4531.65;QD=21.08;SB=-1293.59 GT:AD:DP:GL:GQ 0/1:45,169:169:-452.16,-50.92,-131.50:99 +chr1 2574398 rs4648667 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=297;Dels=0.00;HRun=0;HaplotypeScore=177.69;MQ=43.72;MQ0=17;OQ=1775.91;QD=5.98;SB=-869.96 GT:AD:DP:GL:GQ 0/1:211,86:190:-238.16,-57.29,-446.26:99 +chr1 2574435 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=784;Dels=0.00;HRun=0;HaplotypeScore=476.42;MQ=30.94;MQ0=61;OQ=552.66;QD=0.70;SB=-126.39 GT:AD:DP:GL:GQ 0/1:497,287:235:-129.39,-70.84,-631.70:99 +chr1 2574468 . A C 45.91 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=925;Dels=0.00;HRun=3;HaplotypeScore=499.34;MQ=30.78;MQ0=79;QD=0.05;SB=344.95 GT:AD:DP:GL:GQ 0/1:799,98:301:-105.40,-97.53,-960.73:78.74 +chr1 2574499 . C A 22.95 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=665;Dels=0.00;HRun=2;HaplotypeScore=681.86;MQ=36.15;MQ0=63;QD=0.03;SB=89.36 GT:AD:DP:GL:GQ 0/1:533,92:270:-145.98,-140.40,-853.73:55.76 +chr1 2574516 rs61765812 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=416;Dels=0.00;HRun=0;HaplotypeScore=217.32;MQ=43.57;MQ0=35;OQ=129.59;QD=0.31;SB=68.68 GT:AD:DP:GL:GQ 0/1:278,133:243:-89.48,-73.24,-851.13:99 +chr1 2574566 rs28558799 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=282;Dels=0.00;HRun=0;HaplotypeScore=119.44;MQ=43.46;MQ0=13;OQ=5625.16;QD=19.95;SB=-2459.11 GT:AD:DP:GL:GQ 0/1:49,230:200:-561.52,-60.25,-174.15:99 +chr1 2574594 rs56062029 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=452;Dels=0.00;HRun=2;HaplotypeScore=294.75;MQ=33.13;MQ0=30;OQ=1117.30;QD=2.47;SB=-453.09 GT:AD:DP:GL:GQ 0/1:369,56:211:-181.97,-66.96,-565.43:99 +chr1 2574621 rs57267388 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=571;Dels=0.00;HRun=0;HaplotypeScore=771.91;MQ=31.23;MQ0=33;OQ=342.14;QD=0.60;SB=-185.77 GT:AD:DP:GL:GQ 0/1:283,102:222:-153.52,-116.02,-729.22:99 +chr1 2574649 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=993;Dels=0.00;HRun=0;HaplotypeScore=693.61;MQ=28.27;MQ0=75;OQ=1079.32;QD=1.09;SB=-556.01 GT:AD:DP:GL:GQ 0/1:844,137:401:-235.64,-124.42,-1471.20:99 +chr1 2574659 . A C 29.66 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=980;Dels=0.00;HRun=3;HaplotypeScore=948.25;MQ=27.73;MQ0=79;QD=0.03;SB=242.38 GT:AD:DP:GL:GQ 0/1:842,123:385:-128.64,-122.39,-1217.71:62.50 +chr1 2574737 rs61765814 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=400;Dels=0.00;HRun=0;HaplotypeScore=203.09;MQ=41.26;MQ0=24;OQ=736.68;QD=1.84;SB=-0.60 GT:AD:DP:GL:GQ 0/1:202,185:205:-145.42,-68.47,-717.91:99 +chr1 2574757 rs61765815 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=370;Dels=0.00;HRun=0;HaplotypeScore=249.27;MQ=42.55;MQ0=25;OQ=384.28;QD=1.04;SB=73.46 GT:AD:DP:GL:GQ 0/1:205,136:201:-108.67,-66.96,-637.57:99 +chr1 2574806 rs61765816 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=433;Dels=0.00;HRun=0;HaplotypeScore=271.20;MQ=41.78;MQ0=23;OQ=447.69;QD=1.03;SB=-108.45 GT:AD:DP:GL:GQ 0/1:271,156:236:-119.20,-71.14,-762.60:99 +chr1 2574851 rs6691639 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=333;Dels=0.00;HRun=0;HaplotypeScore=216.92;MQ=45.13;MQ0=5;OQ=7151.39;QD=21.48;SB=-2958.67 GT:AD:DP:GL:GQ 0/1:25,306:212:-714.14,-63.86,-81.27:99 +chr1 2574904 rs6604990 T C 6413.62 DPFilter;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=427;Dels=0.06;HRun=3;HaplotypeScore=563.84;MQ=34.54;MQ0=9;QD=15.02;SB=-2045.14 GT:AD:DP:GL:GQ 1/1:119,272:189:-640.36,-56.34,-15.02:99 +chr1 2574911 . A C 149.58 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=456;Dels=0.00;HRun=3;HaplotypeScore=557.08;MQ=32.46;MQ0=11;QD=0.33;SB=-79.57 GT:AD:DP:GL:GQ 0/1:298,141:171:-69.76,-51.52,-530.42:99 +chr1 2574914 . A G 786.99 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=464;Dels=0.02;HRun=1;HaplotypeScore=590.68;MQ=31.99;MQ0=11;QD=1.70;SB=-166.87 GT:AD:DP:GL:GQ 0/1:189,264:184:-140.25,-58.27,-581.91:99 +chr1 2574924 rs61765818 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=562;Dels=0.00;HRun=1;HaplotypeScore=584.85;MQ=29.44;MQ0=16;OQ=664.13;QD=1.18;SB=-72.04 GT:AD:DP:GL:GQ 0/1:412,132:178:-126.09,-56.39,-566.98:99 +chr1 2574942 rs60506177 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=681;Dels=0.00;HRun=2;HaplotypeScore=1240.22;MQ=29.22;MQ0=28;OQ=4364.77;QD=6.41;SB=-1487.53 GT:AD:DP:GL:GQ 0/1:160,495:256:-435.48,-89.03,-503.32:99 +chr1 2574956 rs59191334 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=906;Dels=0.00;HRun=0;HaplotypeScore=851.71;MQ=29.72;MQ0=44;OQ=1149.69;QD=1.27;SB=-284.23 GT:AD:DP:GL:GQ 0/1:632,252:274:-200.91,-82.66,-713.01:99 +chr1 2574986 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=944;Dels=0.00;HRun=1;HaplotypeScore=1818.61;MQ=31.01;MQ0=59;OQ=1122.41;QD=1.19;SB=-398.32 GT:AD:DP:GL:GQ 0/1:745,146:351:-246.18,-130.65,-980.48:99 +chr1 2575019 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=719;Dels=0.00;HRun=0;HaplotypeScore=472.84;MQ=36.86;MQ0=62;OQ=2013.75;QD=2.80;SB=-548.67 GT:AD:DP:GL:GQ 0/1:509,205:351:-310.40,-105.75,-919.85:99 +chr1 2575034 rs61763547 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=646;Dels=0.00;HRun=1;HaplotypeScore=246.19;MQ=38.01;MQ0=57;OQ=1218.08;QD=1.89;SB=297.56 GT:AD:DP:GL:GQ 0/1:304,285:351:-300.74,-175.64,-1150.43:99 +chr1 2575068 . C G 824.18 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=841;Dels=0.00;HRun=0;HaplotypeScore=834.43;MQ=32.24;MQ0=93;QD=0.98;SB=69.34 GT:AD:DP:GL:GQ 0/1:592,151:395:-352.89,-267.19,-1451.52:99 +chr1 2575069 rs11510858 C A 2054.73 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=851;Dels=0.00;HRun=0;HaplotypeScore=833.69;MQ=32.03;MQ0=94;QD=2.41;SB=-732.04 GT:AD:DP:GL:GQ 0/1:701,130:386:-337.44,-128.68,-1037.66:99 +chr1 2575076 . C G 56.74 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=869;Dels=0.00;HRun=2;HaplotypeScore=716.58;MQ=31.37;MQ0=95;QD=0.07;SB=276.82 GT:AD:DP:GL:GQ 0/1:773,41:392:-146.00,-137.04,-1458.73:89.57 +chr1 2575191 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=619;Dels=0.01;HRun=3;HaplotypeScore=666.18;MQ=32.68;MQ0=22;OQ=1037.47;QD=1.68;SB=-98.59 GT:AD:DP:GL:GQ 0/1:385,224:265:-186.87,-79.84,-734.84:99 +chr1 2575196 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=669;Dels=0.00;HRun=0;HaplotypeScore=585.81;MQ=31.95;MQ0=25;OQ=410.40;QD=0.61;SB=138.71 GT:AD:DP:GL:GQ 0/1:518,139:278:-128.14,-83.81,-902.17:99 +chr1 2575224 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=936;Dels=0.00;HRun=0;HaplotypeScore=711.05;MQ=30.70;MQ0=52;OQ=206.48;QD=0.22;SB=16.18 GT:AD:DP:GL:GQ 0/1:817,101:399:-165.30,-141.37,-1545.34:99 +chr1 2575246 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=981;Dels=0.00;HRun=1;HaplotypeScore=733.47;MQ=31.11;MQ0=67;OQ=1892.73;QD=1.93;SB=-760.65 GT:AD:DP:GL:GQ 0/1:771,204:430:-322.12,-129.56,-1274.76:99 +chr1 2575261 rs6692051 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=945;Dels=0.00;HRun=3;HaplotypeScore=358.84;MQ=32.03;MQ0=68;OQ=2338.43;QD=2.47;SB=-661.83 GT:AD:DP:GL:GQ 0/1:802,142:427:-365.78,-128.65,-1131.84:99 +chr1 2575299 . G T 161.49 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=614;Dels=0.00;HRun=1;HaplotypeScore=591.39;MQ=37.63;MQ0=50;QD=0.26;SB=20.79 GT:AD:DP:GL:GQ 0/1:494,69:362:-227.05,-207.62,-1136.93:99 +chr1 2575300 rs61765821 T C 1192.57 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=603;Dels=0.00;HRun=0;HaplotypeScore=567.88;MQ=38.04;MQ0=47;QD=1.98;SB=-535.85 GT:AD:DP:GL:GQ 0/1:348,222:348:-246.80,-124.26,-1045.28:99 +chr1 2575308 . C A 283.33 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=591;Dels=0.00;HRun=1;HaplotypeScore=502.16;MQ=39.21;MQ0=53;QD=0.48;SB=90.50 GT:AD:DP:GL:GQ 0/1:465,102:356:-142.06,-110.45,-1099.38:99 +chr1 2575350 rs28411086 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=541;Dels=0.00;HRun=2;HaplotypeScore=281.76;MQ=38.20;MQ0=48;OQ=2021.31;QD=3.74;SB=-545.18 GT:AD:DP:GL:GQ 0/1:247,291:277:-288.88,-83.46,-673.01:99 +chr1 2575391 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=992;Dels=0.00;HRun=2;HaplotypeScore=510.05;MQ=30.36;MQ0=68;OQ=227.39;QD=0.23;SB=145.08 GT:AD:DP:GL:GQ 0/1:854,132:434:-160.44,-134.42,-1359.22:99 +chr1 2575398 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1075;Dels=0.00;HRun=0;HaplotypeScore=310.34;MQ=30.19;MQ0=65;OQ=528.27;QD=0.49;SB=20.12 GT:AD:DP:GL:GQ 0/1:895,162:479:-203.83,-147.72,-1593.06:99 +chr1 2575422 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1315;Dels=0.00;HRun=1;HaplotypeScore=628.02;MQ=29.05;MQ0=70;OQ=417.47;QD=0.32;SB=307.23 GT:AD:DP:GL:GQ 0/1:1146,168:592:-223.40,-178.37,-1814.12:99 +chr1 2575443 rs6678990 C G 1968.81 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=1397;Dels=0.00;HRun=0;HaplotypeScore=834.10;MQ=29.41;MQ0=63;QD=1.41;SB=-880.90 GT:AD:DP:GL:GQ 0/1:1263,104:657:-428.32,-228.16,-2407.74:99 +chr1 2575448 . C T 306.07 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=1347;Dels=0.00;HRun=0;HaplotypeScore=969.72;MQ=29.55;MQ0=58;QD=0.23;SB=98.85 GT:AD:DP:GL:GQ 0/1:1166,127:596:-237.42,-203.53,-1765.67:99 +chr1 2575453 . G A 633.22 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=1324;Dels=0.01;HRun=0;HaplotypeScore=1094.28;MQ=29.55;MQ0=52;QD=0.48;SB=22.83 GT:AD:DP:GL:GQ 0/1:1098,210:631:-255.45,-188.85,-1774.06:99 +chr1 2575459 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1275;Dels=0.00;HRun=1;HaplotypeScore=976.35;MQ=29.72;MQ0=48;OQ=260.30;QD=0.20;SB=456.22 GT:AD:DP:GL:GQ 0/1:1186,88:626:-217.90,-188.59,-2068.65:99 +chr1 2575467 . A T 1827.05 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=1257;Dels=0.00;HRun=0;HaplotypeScore=1002.71;MQ=30.06;MQ0=39;QD=1.45;SB=-471.84 GT:AD:DP:GL:GQ 0/1:1025,208:608:-372.29,-186.30,-1881.69:99 +chr1 2575472 . C A 9687.38 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=1255;Dels=0.00;HRun=1;HaplotypeScore=858.65;MQ=30.07;MQ0=41;QD=7.72;SB=-1503.87 GT:AD:DP:GL:GQ 0/1:729,316:639:-967.74,-542.07,-1662.70:99 +chr1 2575476 rs28479903 C T 328.26 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=1232;Dels=0.00;HRun=0;HaplotypeScore=989.29;MQ=30.12;MQ0=43;QD=0.27;SB=122.56 GT:AD:DP:GL:GQ 0/1:1040,174:572:-219.19,-183.08,-1716.97:99 +chr1 2575484 rs61765822 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=1214;Dels=0.00;HRun=0;HaplotypeScore=468.08;MQ=30.51;MQ0=43;OQ=1888.53;QD=1.56;SB=-874.96 GT:AD:DP:GL:GQ 0/1:984,212:602:-396.91,-204.77,-1679.64:99 +chr1 2575509 rs7367485 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=1003;Dels=0.00;HRun=3;HaplotypeScore=708.39;MQ=31.59;MQ0=44;OQ=1317.31;QD=1.31;SB=-683.17 GT:AD:DP:GL:GQ 0/1:599,311:447:-397.20,-262.18,-1298.11:99 +chr1 2575527 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=899;Dels=0.00;HRun=1;HaplotypeScore=616.46;MQ=32.40;MQ0=36;OQ=2129.63;QD=2.37;SB=-658.87 GT:AD:DP:GL:GQ 0/1:666,188:432:-362.76,-146.52,-1154.94:99 +chr1 2575536 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=816;Dels=0.00;HRun=1;HaplotypeScore=629.02;MQ=33.06;MQ0=36;OQ=245.82;QD=0.30;SB=187.48 GT:AD:DP:GL:GQ 0/1:660,150:389:-147.61,-119.74,-1232.57:99 +chr1 2575553 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=672;Dels=0.00;HRun=0;HaplotypeScore=869.01;MQ=35.62;MQ0=23;OQ=1048.35;QD=1.56;SB=44.73 GT:AD:DP:GL:GQ 0/1:542,123:340:-220.20,-112.08,-1057.17:99 +chr1 2575577 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=529;Dels=0.00;HRun=0;HaplotypeScore=616.14;MQ=41.10;MQ0=11;OQ=295.55;QD=0.56;SB=93.12 GT:AD:DP:GL:GQ 0/1:363,155:340:-135.27,-102.43,-1079.29:99 +chr1 2575583 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=497;Dels=0.00;HRun=0;HaplotypeScore=739.15;MQ=41.67;MQ0=9;OQ=177.97;QD=0.36;SB=340.79 GT:AD:DP:GL:GQ 0/1:426,63:314:-122.58,-101.50,-1218.09:99 +chr1 2575632 rs6686754 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=363;Dels=0.00;HRun=1;HaplotypeScore=439.13;MQ=46.08;MQ0=4;OQ=7215.73;QD=19.88;SB=-2967.87 GT:AD:DP:GL:GQ 0/1:59,294:248:-720.57,-74.71,-189.55:99 +chr1 2575661 rs28498367 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=482;Dels=0.00;HRun=0;HaplotypeScore=598.03;MQ=41.57;MQ0=4;OQ=4453.10;QD=9.24;SB=-977.05 GT:AD:DP:GL:GQ 0/1:194,269:275:-444.31,-82.91,-730.02:99 +chr1 2575692 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=647;Dels=0.00;HRun=1;HaplotypeScore=594.08;MQ=36.97;MQ0=17;OQ=2155.18;QD=3.33;SB=272.10 GT:AD:DP:GL:GQ 0/1:259,365:295:-329.81,-111.01,-802.38:99 +chr1 2575711 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=667;Dels=0.00;HRun=3;HaplotypeScore=1191.59;MQ=36.49;MQ0=18;OQ=1467.43;QD=2.20;SB=-170.23 GT:AD:DP:GL:GQ 0/1:245,407:245:-231.00,-80.98,-619.30:99 +chr1 2575718 . C T 91.63 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=668;Dels=0.07;HRun=0;HaplotypeScore=726.36;MQ=36.74;MQ0=18;QD=0.14;SB=390.06 GT:AD:DP:GL:GQ 0/1:453,157:278:-93.88,-81.43,-798.07:99 +chr1 2575725 . C T 321.62 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=662;Dels=0.00;HRun=1;HaplotypeScore=724.85;MQ=36.17;MQ0=17;QD=0.49;SB=411.17 GT:AD:DP:GL:GQ 0/1:600,56:323:-132.74,-97.29,-1057.81:99 +chr1 2575728 . A T 148.72 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=660;Dels=0.00;HRun=0;HaplotypeScore=737.53;MQ=36.50;MQ0=17;QD=0.23;SB=417.37 GT:AD:DP:GL:GQ 0/1:600,48:321:-114.85,-96.69,-1096.48:99 +chr1 2575731 . G A 128.25 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=638;Dels=0.00;HRun=1;HaplotypeScore=523.34;MQ=37.45;MQ0=16;QD=0.20;SB=259.66 GT:AD:DP:GL:GQ 0/1:525,83:335:-143.82,-127.71,-1107.68:99 +chr1 2575750 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=473;Dels=0.00;HRun=1;HaplotypeScore=339.24;MQ=40.86;MQ0=6;OQ=314.90;QD=0.67;SB=-156.95 GT:AD:DP:GL:GQ 0/1:417,42:281:-123.25,-88.47,-781.88:99 +chr1 2575766 rs6694964 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=418;Dels=0.00;HRun=0;HaplotypeScore=190.54;MQ=43.00;MQ0=6;OQ=9217.59;QD=22.05;SB=-3555.11 GT:AD:DP:GL:GQ 0/1:33,383:267:-920.76,-80.43,-83.85:34.20 +chr1 2575784 rs28583924 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=426;Dels=0.00;HRun=0;HaplotypeScore=272.61;MQ=42.95;MQ0=8;OQ=181.28;QD=0.43;SB=6.29 GT:AD:DP:GL:GQ 0/1:359,64:257:-98.92,-77.51,-960.45:99 +chr1 2575825 rs6689281 T C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=557;Dels=0.01;HRun=2;HaplotypeScore=469.61;MQ=35.81;MQ0=25;OQ=9475.08;QD=17.01;SB=-3650.18 GT:AD:DP:GL:GQ 1/1:3,541:282:-946.51,-86.27,-2.51:99 +chr1 2575851 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=634;Dels=0.00;HRun=0;HaplotypeScore=686.59;MQ=33.18;MQ0=30;OQ=77.00;QD=0.12;SB=-18.66 GT:AD:DP:GL:GQ 0/1:437,151:251:-86.73,-75.75,-723.32:99 +chr1 2575861 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=670;Dels=0.00;HRun=0;HaplotypeScore=1084.95;MQ=32.16;MQ0=34;OQ=174.30;QD=0.26;SB=144.01 GT:AD:DP:GL:GQ 0/1:448,201:255:-97.68,-76.97,-707.97:99 +chr1 2575918 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=659;Dels=0.00;HRun=0;HaplotypeScore=602.10;MQ=33.55;MQ0=33;OQ=1205.47;QD=1.83;SB=-331.68 GT:AD:DP:GL:GQ 0/1:520,139:294:-212.43,-88.60,-836.61:99 +chr1 2575963 rs61765824 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=414;Dels=0.00;HRun=0;HaplotypeScore=225.65;MQ=45.71;MQ0=16;OQ=175.37;QD=0.42;SB=-3.54 GT:AD:DP:GL:GQ 0/1:256,154:262:-99.81,-78.99,-882.64:99 +chr1 2576027 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=375;Dels=0.00;HRun=0;HaplotypeScore=441.20;MQ=41.08;MQ0=22;OQ=359.44;QD=0.96;SB=-25.38 GT:AD:DP:GL:GQ 0/1:347,27:212:-103.15,-63.92,-790.76:99 +chr1 2576035 rs55917765 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=384;Dels=0.02;HRun=4;HaplotypeScore=406.51;MQ=41.42;MQ0=19;OQ=289.17;QD=0.75;SB=-132.89 GT:AD:DP:GL:GQ 0/1:212,141:214:-106.50,-74.30,-717.21:99 +chr1 2576075 rs57994724 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=300;Dels=0.03;HRun=4;HaplotypeScore=363.80;MQ=42.84;MQ0=2;OQ=76.42;QD=0.25;SB=-28.60 GT:AD:DP:GL:GQ 0/1:192,90:162:-61.96,-51.03,-580.93:99 +chr1 2576111 rs58221160 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=281;Dels=0.00;HRun=1;HaplotypeScore=182.21;MQ=43.93;MQ0=7;OQ=597.72;QD=2.13;SB=-221.46 GT:AD:DP:GL:GQ 0/1:232,45:207:-125.42,-62.37,-596.71:99 +chr1 2576240 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1159;Dels=0.00;HRun=0;HaplotypeScore=623.69;MQ=25.02;MQ0=69;OQ=409.78;QD=0.35;SB=-223.95 GT:AD:DP:GL:GQ 0/1:968,178:369:-162.51,-118.25,-1426.92:99 +chr1 2576263 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1066;Dels=0.00;HRun=1;HaplotypeScore=622.37;MQ=26.52;MQ0=59;OQ=159.54;QD=0.15;SB=19.45 GT:AD:DP:GL:GQ 0/1:984,81:387:-135.82,-116.58,-1209.01:99 +chr1 2576333 . C G 40.07 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=1;HaplotypeScore=154.83;MQ=40.65;MQ0=29;QD=0.18;SB=-8.93 GT:AD:DP:GL:GQ 0/1:181,32:158:-64.21,-56.92,-644.64:72.91 +chr1 2576335 . C T 1221.15 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=0;HaplotypeScore=167.65;MQ=40.55;MQ0=30;QD=5.65;SB=-581.17 GT:AD:DP:GL:GQ 0/1:122,94:144:-168.83,-43.43,-331.79:99 +chr1 2576336 rs28676518 G A 1105.16 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=214;Dels=0.00;HRun=0;HaplotypeScore=205.71;MQ=40.45;MQ0=30;QD=5.16;SB=-168.80 GT:AD:DP:GL:GQ 0/1:170,44:143:-156.87,-43.08,-364.02:99 +chr1 2576346 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=74.98;MQ=40.01;MQ0=31;OQ=210.24;QD=1.17;SB=-126.34 GT:AD:DP:GL:GQ 0/1:138,41:111:-57.78,-33.47,-394.51:99 +chr1 2576366 rs61765835 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=158;Dels=0.00;HRun=0;HaplotypeScore=35.61;MQ=33.02;MQ0=57;OQ=96.35;QD=0.61;SB=-36.52 GT:AD:DP:GL:GQ 0/1:92,66:79:-36.73,-23.81,-255.03:99 +chr1 2576428 rs61765837 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=303;Dels=0.00;HRun=2;HaplotypeScore=260.74;MQ=16.89;MQ0=145;OQ=101.18;QD=0.33;SB=-66.11 GT:AD:DP:GL:GQ 0/1:155,144:52:-29.09,-15.69,-174.52:99 +chr1 2576448 rs61765838 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=595;Dels=0.00;HRun=0;HaplotypeScore=426.54;MQ=17.45;MQ0=199;OQ=372.66;QD=0.63;SB=-42.53 GT:AD:DP:GL:GQ 0/1:377,206:114:-74.98,-34.43,-280.80:99 +chr1 2576460 rs61765839 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=687;Dels=0.00;HRun=1;HaplotypeScore=471.75;MQ=17.40;MQ0=212;OQ=453.85;QD=0.66;SB=-3.98 GT:AD:DP:GL:GQ 0/1:511,164:138:-90.25,-41.59,-375.50:99 +chr1 2576472 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=774;Dels=0.03;HRun=1;HaplotypeScore=800.59;MQ=17.54;MQ0=228;OQ=234.98;QD=0.30;SB=-38.37 GT:AD:DP:GL:GQ 0/1:618,98:166:-76.78,-50.00,-493.07:99 +chr1 2576534 rs57105227 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=374;Dels=0.00;HRun=1;HaplotypeScore=347.91;MQ=18.87;MQ0=112;OQ=329.07;QD=0.88;SB=-154.80 GT:AD:DP:GL:GQ 0/1:156,198:111:-73.27,-37.08,-391.39:99 +chr1 2576577 rs4648668 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=122;Dels=0.00;HRun=1;HaplotypeScore=59.62;MQ=22.81;MQ0=26;OQ=851.22;QD=6.98;SB=10.08 GT:AD:DP:GL:GQ 0/1:55,66:69:-109.20,-20.79,-201.97:99 +chr1 2576600 rs4648566 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=1;HaplotypeScore=109.15;MQ=20.95;MQ0=39;OQ=455.68;QD=3.38;SB=83.24 GT:AD:DP:GL:GQ 0/1:105,30:52:-64.51,-15.66,-117.10:99 +chr1 2576616 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=178.18;MQ=20.10;MQ0=38;OQ=374.43;QD=2.62;SB=-39.54 GT:AD:DP:GL:GQ 0/1:116,27:44:-54.00,-13.27,-93.80:99 +chr1 2576848 rs61765840 G T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=22.44;MQ=39.05;MQ0=35;OQ=52.46;QD=0.37;SB=-15.32 GT:AD:DP:GL:GQ 0/1:129,12:77:-31.72,-23.19,-231.93:85.30 +chr1 2577010 rs4648671 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=239;Dels=0.00;HRun=0;HaplotypeScore=65.16;MQ=37.14;MQ0=12;OQ=5199.52;QD=21.76;SB=-2266.90 GT:AD:DP:GL:GQ 1/1:7,232:163:-518.95,-49.17,-3.73:99 +chr1 2577062 rs28507281 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=295;Dels=0.00;HRun=0;HaplotypeScore=78.67;MQ=40.58;MQ0=11;OQ=1143.65;QD=3.88;SB=-492.64 GT:AD:DP:GL:GQ 0/1:238,57:237:-189.11,-71.46,-605.04:99 +chr1 2577084 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=72.39;MQ=39.59;MQ0=17;OQ=519.07;QD=1.69;SB=-15.56 GT:AD:DP:GL:GQ 0/1:259,48:248:-129.89,-74.70,-751.71:99 +chr1 2577123 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=291;Dels=0.00;HRun=1;HaplotypeScore=84.53;MQ=39.37;MQ0=26;OQ=265.40;QD=0.91;SB=-39.23 GT:AD:DP:GL:GQ 0/1:250,41:219:-95.80,-65.98,-773.71:99 +chr1 2577397 rs58719822 G C 0.55 PASS AC=2;AF=1.00;AN=2;DB;DP=190;Dels=0.00;HRun=0;HaplotypeScore=14.16;MQ=39.42;MQ0=19;OQ=6097.98;QD=32.09;SB=-764.81 GT:AD:DP:GL:GQ 1/1:1,189:137:-608.80,-41.28,-0.05:99 +chr1 2577433 rs60264562 G C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=207;Dels=0.05;HRun=4;HaplotypeScore=105.46;MQ=35.87;MQ0=25;OQ=5113.11;QD=24.70;SB=-614.98 GT:AD:DP:GL:GQ 1/1:9,184:123:-510.31,-38.53,-16.18:99 +chr1 2577515 . A C 17.95 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=331;Dels=0.00;HRun=3;HaplotypeScore=311.11;MQ=35.94;MQ0=23;QD=0.05;SB=173.50 GT:AD:DP:GL:GQ 0/1:258,71:167:-55.40,-50.33,-521.31:50.72 +chr1 2577549 rs4648567 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=289;Dels=0.00;HRun=0;HaplotypeScore=107.18;MQ=38.40;MQ0=7;OQ=5448.91;QD=18.85;SB=-2125.98 GT:AD:DP:GL:GQ 1/1:24,231:174:-543.89,-82.79,-51.97:99 +chr1 2577655 . G C 44.44 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=2;HaplotypeScore=58.73;MQ=26.75;MQ0=23;QD=0.33;SB=26.12 GT:AD:DP:GL:GQ 0/1:116,10:43:-24.31,-16.59,-159.35:77.27 +chr1 2577671 rs58842912 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=128.81;MQ=16.71;MQ0=28;OQ=137.08;QD=1.46;SB=-35.94 GT:AD:DP:GL:GQ 0/1:63,25:12:-20.61,-3.62,-16.30:99 +chr1 2577677 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=3;HaplotypeScore=117.98;MQ=17.54;MQ0=28;OQ=281.66;QD=3.03;SB=-45.56 GT:AD:DP:GL:GQ 0/1:33,58:12:-35.06,-3.61,-7.69:40.79 +chr1 2577682 . T C 14.20 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=57.79;MQ=17.58;MQ0=34;QD=0.14;SB=-10.00 GT:AD:DP:GL:GQ 0/1:68,26:4:-5.89,-1.21,-7.84:46.86 +chr1 2577700 . T C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=167.08;MQ=18.58;MQ0=41;OQ=266.89;QD=2.36;SB=-10.00 GT:AD:DP:GL:GQ 1/1:35,36:10:-34.52,-6.65,-4.25:23.97 +chr1 2577709 . C T 15.40 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=131;Dels=0.00;HRun=0;HaplotypeScore=233.03;MQ=18.07;MQ0=48;QD=0.12;SB=-10.00 GT:AD:DP:GL:GQ 0/1:96,13:7:-9.83,-5.02,-17.83:48.10 +chr1 2577721 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=182;Dels=0.00;HRun=0;HaplotypeScore=74.87;MQ=18.10;MQ0=63;OQ=399.60;QD=2.20;SB=-10.00 GT:AD:DP:GL:GQ 0/1:147,35:41:-55.60,-12.35,-87.25:99 +chr1 2577722 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=54.78;MQ=18.15;MQ0=62;OQ=179.28;QD=0.99;SB=-10.00 GT:AD:DP:GL:GQ 0/1:160,20:38:-32.69,-11.48,-98.33:99 +chr1 2577735 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=37.61;MQ=17.86;MQ0=65;OQ=262.32;QD=1.37;SB=-10.00 GT:AD:DP:GL:GQ 0/1:173,18:55:-46.08,-16.57,-148.55:99 +chr1 2577740 rs61763463 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.00;HRun=1;HaplotypeScore=34.83;MQ=17.84;MQ0=63;OQ=1671.60;QD=8.99;SB=-10.00 GT:AD:DP:GL:GQ 0/1:52,133:54:-186.71,-16.27,-40.75:99 +chr1 2577765 . C A 125.78 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=41.35;MQ=16.77;MQ0=52;QD=0.87;SB=-10.00 GT:AD:DP:GL:GQ 0/1:91,53:26:-23.70,-7.84,-54.51:99 +chr1 2577769 . C T 71.72 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=43.82;MQ=16.10;MQ0=52;QD=0.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:87,47:21:-16.80,-6.34,-49.74:99 +chr1 2577770 . G C 89.65 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=1;HaplotypeScore=42.82;MQ=16.09;MQ0=52;QD=0.67;SB=-10.00 GT:AD:DP:GL:GQ 0/1:85,48:21:-18.58,-6.33,-66.40:99 +chr1 2577784 rs61761450 G C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=108;Dels=0.00;HRun=0;HaplotypeScore=93.26;MQ=15.12;MQ0=44;OQ=499.20;QD=4.62;SB=-10.00 GT:AD:DP:GL:GQ 1/1:36,72:12:-53.51,-3.62,-0.00:36.12 +chr1 2577796 rs28368363 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=154.23;MQ=14.20;MQ0=39;OQ=53.95;QD=0.56;SB=-10.00 GT:AD:DP:GL:GQ 0/1:68,23:5:-10.19,-1.51,-6.10:45.96 +chr1 2577799 rs61765844 A C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=4;HaplotypeScore=106.56;MQ=13.50;MQ0=38;OQ=136.44;QD=1.53;SB=-10.00 GT:AD:DP:GL:GQ 1/1:37,52:5:-17.20,-1.51,-0.00:15.04 +chr1 2577815 rs61761446 G A 0.11 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=16.91;MQ=12.99;MQ0=33;OQ=113.87;QD=2.19;SB=-10.00 GT:AD:DP:GL:GQ 1/1:30,21:4:-14.92,-1.21,-0.00:12.04 +chr1 2577825 . G A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=32.84;MQ=14.16;MQ0=28;OQ=149.17;QD=3.17;SB=-10.00 GT:AD:DP:GL:GQ 1/1:28,19:5:-18.48,-1.51,-0.00:15.04 +chr1 2577833 . C T 42.25 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=22.86;MQ=13.04;MQ0=28;QD=0.98;SB=-10.00 GT:AD:DP:GL:GQ 1/1:33,10:2:-7.63,-0.60,-0.00:6.02 +chr1 2577851 . G T 0.04 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=11.27;MQ=14.57;MQ0=20;OQ=148.54;QD=4.24;SB=-10.00 GT:AD:DP:GL:GQ 1/1:17,14:6:-18.43,-1.81,-0.01:18.02 +chr1 2577883 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=114.78;MQ=19.71;MQ0=31;OQ=87.78;QD=0.84;SB=-10.00 GT:AD:DP:GL:GQ 0/1:82,22:16:-16.89,-4.83,-35.06:99 +chr1 2577892 rs61761448 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=139.63;MQ=19.08;MQ0=41;OQ=358.39;QD=3.04;SB=-10.00 GT:AD:DP:GL:GQ 0/1:46,69:13:-43.04,-3.92,-5.80:18.77 +chr1 2577904 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=1;HaplotypeScore=169.18;MQ=18.99;MQ0=45;OQ=432.72;QD=3.38;SB=-10.00 GT:AD:DP:GL:GQ 0/1:56,72:16:-51.38,-4.83,-6.85:20.23 +chr1 2577913 . A G 43.14 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=228.63;MQ=18.89;MQ0=43;QD=0.37;SB=-10.00 GT:AD:DP:GL:GQ 0/1:102,14:7:-9.71,-2.11,-14.52:75.98 +chr1 2577923 . G A 12.44 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=0;HaplotypeScore=139.34;MQ=19.75;MQ0=38;QD=0.10;SB=-10.00 GT:AD:DP:GL:GQ 0/1:84,37:10:-7.51,-3.01,-26.55:45.02 +chr1 2577924 . T C 61.88 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=137.09;MQ=19.68;MQ0=38;QD=0.52;SB=-10.00 GT:AD:DP:GL:GQ 0/1:94,23:11:-12.79,-3.32,-26.27:94.71 +chr1 2577931 rs61763465 G C 371.46 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=106.32;MQ=19.54;MQ0=35;QD=3.50;SB=-10.00 GT:AD:DP:GL:GQ 1/1:30,75:9:-40.73,-2.71,-0.00:27.09 +chr1 2577945 rs61765845 G C 1059.87 HARD_TO_VALIDATE;Indel AC=2;AF=1.00;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=141.04;MQ=19.73;MQ0=38;QD=10.00;SB=-10.00 GT:AD:DP:GL:GQ 1/1:31,70:26:-113.65,-11.26,-4.08:71.85 +chr1 2577953 . A G 356.53 HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=136.50;MQ=18.50;MQ0=43;QD=3.64;SB=-10.00 GT:AD:DP:GL:GQ 0/1:78,20:16:-43.76,-4.82,-8.02:32 +chr1 2577977 . G A 20.69 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=16.21;MQ=15.79;MQ0=48;QD=0.27;SB=-10.00 GT:AD:DP:GL:GQ 0/1:72,5:20:-11.37,-6.02,-58.36:53.49 +chr1 2579397 rs61761374 C G 193.05 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=22.35;MQ0=6;OQ=1341.59;QD=14.91;SB=-551.47 GT:AD:DP:GL:GQ 0/1:44,46:77:-160.66,-23.22,-161.20:99 +chr1 2580726 . T G 35.92 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.11;MQ=5.25;MQ0=59;QD=0.59;SB=-10.00 GT:AD:DP:GL:GQ 1/1:58,2:2:-7.00,-0.60,-0.00:6.02 +chr1 2580768 . T C 36.28 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=5.74;MQ0=49;QD=0.71;SB=-10.00 GT:AD:DP:GL:GQ 1/1:46,5:2:-7.04,-0.60,-0.00:6.02 +chr1 2580784 rs11488598 T A 45.88 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=6.33;MQ0=40;QD=1.09;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,41:2:-8.00,-0.60,-0.00:6.02 +chr1 2581065 rs61761440 A C 33.92 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=9.03;MQ=10.33;MQ0=29;QD=0.71;SB=-10.00 GT:AD:DP:GL:GQ 1/1:28,20:2:-6.80,-0.60,-0.00:6.02 +chr1 2581076 . T A 42.69 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=11.35;MQ0=18;QD=1.33;SB=-10.00 GT:AD:DP:GL:GQ 1/1:16,15:2:-7.68,-0.60,-0.00:6.02 +chr1 2581088 . A C 35.92 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=15.32;MQ0=5;QD=3.27;SB=-10.00 GT:AD:DP:GL:GQ 1/1:3,8:2:-7.00,-0.60,-0.00:6.02 +chr1 2581203 . C G 46.77 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=12.99;MQ=10.81;MQ0=53;QD=0.69;SB=5.05 GT:AD:DP:GL:GQ 0/1:57,11:14:-12.18,-4.22,-47.55:79.61 +chr1 2581221 rs4648702 C A 0.09 PASS AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=1;HaplotypeScore=12.38;MQ=17.15;MQ0=42;OQ=109.22;QD=1.11;SB=-5.56 GT:AD:DP:GL:GQ 0/1:80,16:46:-28.07,-13.86,-128.22:99 +chr1 2581257 rs4648701 T A 0.08 PASS AC=2;AF=1.00;AN=2;DB;DP=134;Dels=0.00;HRun=0;HaplotypeScore=5.16;MQ=20.38;MQ0=25;OQ=3859.45;QD=28.80;SB=-1801.06 GT:AD:DP:GL:GQ 1/1:0,134:101:-384.94,-30.42,-0.03:99 +chr1 2587428 . A C 37.49 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=14.36;MQ0=8;QD=1.10;SB=-45.01 GT:AD:DP:GL:GQ 1/1:0,34:2:-7.16,-0.60,-0.00:6.02 +chr1 2593169 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=425;Dels=0.00;HRun=1;HaplotypeScore=105.62;MQ=17.46;MQ0=82;OQ=848.96;QD=2.00;SB=-332.82 GT:AD:DP:GL:GQ 0/1:365,60:163:-137.29,-49.11,-428.79:99 +chr1 2596443 . C T 41.24 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=12.40;MQ0=7;QD=3.75;SB=-10.00 GT:AD:DP:GL:GQ 1/1:7,4:2:-7.53,-0.60,-0.00:6.02 +chr1 2596445 . T G 36.05 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=2.31;MQ=11.87;MQ0=8;QD=3.00;SB=-10.00 GT:AD:DP:GL:GQ 1/1:5,7:2:-7.01,-0.60,-0.00:6.02 +chr1 2596476 . G A 46.02 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;HRun=1;HaplotypeScore=26.89;MQ=5.53;MQ0=56;QD=0.77;SB=-10.00 GT:AD:DP:GL:GQ 1/1:58,2:2:-8.01,-0.60,-0.00:6.02 +chr1 2596850 . G C 35.05 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=11.43;MQ0=28;QD=0.82;SB=-10.00 GT:AD:DP:GL:GQ 0/1:29,14:5:-8.30,-1.51,-13.08:67.88 +chr1 2596943 . C A 49.59 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=50.99;MQ=11.35;MQ0=54;QD=0.70;SB=-6.99 GT:AD:DP:GL:GQ 0/1:65,5:13:-12.16,-3.92,-30.66:82.43 +chr1 2597318 . T C 31.81 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=14.62;MQ=5.54;MQ0=70;QD=0.42;SB=-10.00 GT:AD:DP:GL:GQ 1/1:73,2:2:-6.59,-0.60,-0.00:6.01 +chr1 2598250 . T A 27.90 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=1;HaplotypeScore=2.24;MQ=16.56;MQ0=5;QD=1.27;SB=-0.98 GT:AD:DP:GL:GQ 0/1:19,3:5:-7.58,-1.51,-10.62:60.73 +chr1 2598257 . G T 12.16 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=15.61;MQ0=8;QD=0.55;SB=-0.98 GT:AD:DP:GL:GQ 0/1:19,3:5:-5.98,-1.51,-10.70:44.72 +chr1 2598656 . G A 10.26 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=1;HaplotypeScore=114.17;MQ=5.78;MQ0=152;QD=0.06;SB=-10.00 GT:AD:DP:GL:GQ 0/1:161,14:1:-4.27,-0.30,-0.00:1.76 +chr1 2598795 . G A 10.26 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=47.85;MQ=7.17;MQ0=69;QD=0.12;SB=-10.00 GT:AD:DP:GL:GQ 0/1:84,2:1:-4.27,-0.30,-0.00:1.76 +chr1 2598944 . A C 17.83 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=1;HaplotypeScore=67.67;MQ=10.48;MQ0=39;QD=0.27;SB=-25.99 GT:AD:DP:GL:GQ 0/1:48,17:3:-5.96,-0.91,-2.50:15.92 +chr1 2598946 . A G 34.06 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=82.40;MQ=11.36;MQ0=42;QD=0.46;SB=-10.00 GT:AD:DP:GL:GQ 0/1:70,4:3:-7.59,-0.90,-4.17:32.64 +chr1 2598950 . C A 54.26 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=105.52;MQ=12.29;MQ0=47;QD=0.53;SB=-3.99 GT:AD:DP:GL:GQ 0/1:94,7:7:-10.82,-2.11,-14.32:87.10 +chr1 2599001 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=31.75;MQ=12.68;MQ0=54;OQ=83.85;QD=0.63;SB=-3.99 GT:AD:DP:GL:GQ 0/1:91,33:10:-18.26,-6.59,-21.60:99 +chr1 2599015 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=2;HaplotypeScore=24.68;MQ=11.50;MQ0=72;OQ=64.97;QD=0.46;SB=-43.54 GT:AD:DP:GL:GQ 0/1:128,12:9:-12.49,-2.71,-23.15:97.80 +chr1 2599040 rs61761456 A T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=133;Dels=0.00;HRun=0;HaplotypeScore=87.15;MQ=9.23;MQ0=88;OQ=72.77;QD=0.55;SB=-10.00 GT:AD:DP:GL:GQ 1/1:81,14:5:-17.43,-7.71,-6.64:10.71 +chr1 2599044 rs61761457 T A 33.25 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=131;Dels=0.00;HRun=1;HaplotypeScore=64.29;MQ=9.30;MQ0=86;QD=0.25;SB=-10.00 GT:AD:DP:GL:GQ 0/1:104,11:6:-11.67,-5.06,-13.57:66.08 +chr1 2599198 . C T 23.45 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=16.24;MQ=14.99;MQ0=19;QD=0.50;SB=-3.99 GT:AD:DP:GL:GQ 0/1:29,18:5:-7.14,-1.51,-10.24:56.27 +chr1 2599218 . G A 105.55 HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=106.10;MQ=16.73;MQ0=11;QD=2.29;SB=-69.07 GT:AD:DP:GL:GQ 0/1:28,17:6:-15.65,-1.81,-6.14:43.30 +chr1 2599225 . C G 35.32 HARD_TO_VALIDATE;Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=82.64;MQ=16.87;MQ0=11;QD=0.78;SB=-10.88 GT:AD:DP:GL:GQ 0/1:36,6:7:-14.02,-7.20,-19.31:68.16 +chr1 2599228 . G A 323.86 HARD_TO_VALIDATE;Indel;SnpCluster AC=2;AF=1.00;AN=2;DP=46;Dels=0.04;HRun=0;HaplotypeScore=68.32;MQ=16.68;MQ0=12;QD=7.04;SB=-89.34 GT:AD:DP:GL:GQ 1/1:16,28:10:-35.98,-3.02,-0.01:30.08 +chr1 2599239 . T A 19.57 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=43.45;MQ=14.62;MQ0=19;QD=0.36;SB=-4.42 GT:AD:DP:GL:GQ 0/1:49,2:7:-12.49,-7.25,-17.00:52.36 +chr1 2599247 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=40.77;MQ=14.18;MQ0=20;OQ=70.13;QD=1.35;SB=-7.01 GT:AD:DP:GL:GQ 0/1:29,21:6:-12.11,-1.81,-8.56:67.52 +chr1 2599654 . G C 12.35 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=26.39;MQ=2.65;MQ0=119;QD=0.10;SB=-10.00 GT:AD:DP:GL:GQ 0/1:119,1:1:-4.49,-0.30,-0.00:1.76 +chr1 2601422 . A G 25.82 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=114;Dels=0.00;HRun=0;HaplotypeScore=10.71;MQ=4.09;MQ0=110;QD=0.23;SB=-10.00 GT:AD:DP:GL:GQ 1/1:99,14:2:-5.99,-0.60,-0.00:6.01 +chr1 2601437 . T C 35.28 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=12.99;MQ=3.79;MQ0=129;QD=0.27;SB=-10.00 GT:AD:DP:GL:GQ 1/1:103,30:2:-6.94,-0.60,-0.00:6.02 +chr1 2601504 . G A 41.24 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=19.74;MQ=3.30;MQ0=165;QD=0.25;SB=-10.00 GT:AD:DP:GL:GQ 1/1:158,9:2:-7.53,-0.60,-0.00:6.02 +chr1 2601515 . A C 43.05 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=155;Dels=0.00;HRun=2;HaplotypeScore=7.29;MQ=3.29;MQ0=153;QD=0.28;SB=-10.00 GT:AD:DP:GL:GQ 1/1:91,64:2:-7.71,-0.60,-0.00:6.02 +chr1 2601516 . G A 0.02 FDRtranche1.00to2.00 AC=2;AF=1.00;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=6.38;MQ=3.29;MQ0=153;OQ=51.25;QD=0.33;SB=-10.00 GT:AD:DP:GL:GQ 1/1:89,66:2:-8.53,-0.60,-0.00:6.02 +chr1 2601859 . G A 39.02 DPFilter;HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=20.82;MQ=4.64;MQ0=146;QD=0.24;SB=-10.00 GT:AD:DP:GL:GQ 1/1:150,13:2:-7.31,-0.60,-0.00:6.02 +chr1 2603248 rs11486046 A C 0.95 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=4;HaplotypeScore=1.14;MQ=19.37;MQ0=3;OQ=283.27;QD=11.33;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,23:9:-31.91,-2.71,-0.00:27.08 +chr1 2603587 . A G 31.28 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=24.46;MQ=5.10;MQ0=81;QD=0.34;SB=-10.00 GT:AD:DP:GL:GQ 1/1:74,19:2:-6.54,-0.60,-0.00:6.01 +chr1 2603630 . C T 0.04 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=4.88;MQ=7.26;MQ0=55;OQ=82.12;QD=1.35;SB=-10.00 GT:AD:DP:GL:GQ 1/1:51,10:3:-11.70,-0.90,-0.00:9.03 +chr1 2603684 . A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=23.79;MQ=8.35;MQ0=58;OQ=160.35;QD=2.36;SB=-10.00 GT:AD:DP:GL:GQ 1/1:55,13:6:-19.61,-1.81,-0.00:18.04 +chr1 2603850 . C G 10.08 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=0;HaplotypeScore=68.31;MQ=3.10;MQ0=215;QD=0.04;SB=-10.00 GT:AD:DP:GL:GQ 0/1:213,10:1:-4.25,-0.30,-0.00:1.76 +chr1 2604182 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=169;Dels=0.00;HRun=1;HaplotypeScore=49.21;MQ=7.86;MQ0=143;OQ=70.78;QD=0.42;SB=-10.00 GT:AD:DP:GL:GQ 0/1:162,7:11:-13.68,-3.31,-27.79:99 +chr1 2604202 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=174;Dels=0.00;HRun=0;HaplotypeScore=66.53;MQ=7.81;MQ0=146;OQ=55.73;QD=0.32;SB=-10.00 GT:AD:DP:GL:GQ 0/1:164,10:11:-12.17,-3.31,-27.45:88.56 +chr1 2604211 . C A 34.20 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=202;Dels=0.00;HRun=0;HaplotypeScore=110.16;MQ=8.09;MQ0=168;QD=0.17;SB=-10.00 GT:AD:DP:GL:GQ 0/1:190,11:14:-10.92,-4.22,-40.03:67.04 +chr1 2604257 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=82.11;MQ=12.16;MQ0=114;OQ=80.38;QD=0.46;SB=32.96 GT:AD:DP:GL:GQ 0/1:146,20:31:-22.91,-11.59,-89.29:99 +chr1 2604263 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=1;HaplotypeScore=133.02;MQ=12.71;MQ0=105;OQ=191.66;QD=1.14;SB=50.18 GT:AD:DP:GL:GQ 0/1:122,46:33:-32.40,-9.95,-88.01:99 +chr1 2604269 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=77.37;MQ=13.05;MQ0=90;OQ=192.77;QD=1.32;SB=17.43 GT:AD:DP:GL:GQ 0/1:70,69:33:-34.89,-12.33,-71.96:99 +chr1 2604305 . T A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=7.47;MQ=17.34;MQ0=29;OQ=55.74;QD=0.69;SB=74.25 GT:AD:DP:GL:GQ 0/1:58,22:37:-20.01,-11.15,-121.92:88.58 +chr1 2604310 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=4.63;MQ=18.11;MQ0=23;OQ=69.18;QD=0.93;SB=74.24 GT:AD:DP:GL:GQ 0/1:55,19:37:-21.34,-11.14,-111.00:99 +chr1 2604358 . C T 71.23 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=145.78;MQ=14.15;MQ0=44;QD=0.82;SB=11.06 GT:AD:DP:GL:GQ 0/1:71,13:12:-14.02,-3.62,-30.75:99 +chr1 2604359 . C A 74.64 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=131.89;MQ=14.13;MQ0=41;QD=0.91;SB=5.02 GT:AD:DP:GL:GQ 0/1:26,56:10:-13.76,-3.01,-18.66:99 +chr1 2604363 . G C 180.85 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=2;HaplotypeScore=137.79;MQ=13.57;MQ0=46;QD=2.10;SB=2.04 GT:AD:DP:GL:GQ 0/1:29,40:11:-24.68,-3.31,-21.48:99 +chr1 2604377 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=82.82;MQ=13.39;MQ0=50;OQ=54.76;QD=0.61;SB=-10.00 GT:AD:DP:GL:GQ 0/1:65,25:4:-9.97,-1.21,-3.57:23.65 +chr1 2604397 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=1;HaplotypeScore=150.87;MQ=13.17;MQ0=49;OQ=71.12;QD=0.83;SB=-10.00 GT:AD:DP:GL:GQ 0/1:47,38:4:-11.60,-1.21,-3.90:26.92 +chr1 2604403 . T C 38.45 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=82;Dels=0.00;HRun=2;HaplotypeScore=145.51;MQ=12.80;MQ0=46;QD=0.47;SB=-10.00 GT:AD:DP:GL:GQ 1/1:13,58:3:-10.84,-4.28,-3.54:7.45 +chr1 2604424 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=48.30;MQ=13.20;MQ0=33;OQ=76.83;QD=1.35;SB=-6.99 GT:AD:DP:GL:GQ 0/1:21,30:6:-12.78,-1.81,-6.73:49.16 +chr1 2604431 . C T 25.24 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=33.49;MQ=13.71;MQ0=25;QD=0.55;SB=-7.01 GT:AD:DP:GL:GQ 0/1:40,3:5:-7.32,-1.51,-9.43:58.07 +chr1 2604444 . G C 43.47 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=38.64;MQ=15.55;MQ0=13;QD=1.67;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,16:4:-12.26,-4.63,-7.13:24.99 +chr1 2604449 . G C 30.45 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=21;Dels=0.10;HRun=4;HaplotypeScore=30.98;MQ=14.63;MQ0=12;QD=1.45;SB=-10.00 GT:AD:DP:GL:GQ 0/1:6,6:4:-11.16,-4.83,-7.63:28 +chr1 2604508 . G C 0.07 PASS AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=11.01;MQ=14.95;MQ0=13;OQ=265.66;QD=7.81;SB=-10.00 GT:AD:DP:GL:GQ 1/1:9,25:7:-30.15,-2.11,-0.00:21.07 +chr1 2604516 . G T 0.07 PASS AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;HRun=1;HaplotypeScore=5.00;MQ=14.42;MQ0=18;OQ=191.90;QD=4.68;SB=-10.00 GT:AD:DP:GL:GQ 1/1:15,26:7:-22.77,-2.11,-0.00:21.05 +chr1 2604535 rs61763522 A G 0.35 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=9.63;MQ=11.76;MQ0=38;OQ=251.64;QD=3.87;SB=-10.00 GT:AD:DP:GL:GQ 1/1:12,53:8:-28.75,-2.41,-0.00:24.07 +chr1 2604555 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=35.24;MQ=12.18;MQ0=57;OQ=115.73;QD=1.24;SB=14.08 GT:AD:DP:GL:GQ 0/1:66,27:12:-18.47,-3.62,-35.84:99 +chr1 2604572 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=3;HaplotypeScore=50.74;MQ=13.39;MQ0=78;OQ=55.27;QD=0.40;SB=20.07 GT:AD:DP:GL:GQ 0/1:127,10:20:-14.84,-6.03,-56.38:88.11 +chr1 2604579 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=62.98;MQ=13.28;MQ0=75;OQ=144.76;QD=1.05;SB=20.08 GT:AD:DP:GL:GQ 0/1:125,13:18:-23.19,-5.43,-45.19:99 +chr1 2604585 rs61763523 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=140;Dels=0.00;HRun=1;HaplotypeScore=70.32;MQ=13.11;MQ0=76;OQ=158.49;QD=1.13;SB=-6.99 GT:AD:DP:GL:GQ 0/1:102,37:9:-21.84,-2.71,-10.97:82.64 +chr1 2604597 . A G 110.83 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=107.90;MQ=13.27;MQ0=78;QD=0.74;SB=8.05 GT:AD:DP:GL:GQ 0/1:135,14:14:-18.58,-4.22,-35.74:99 +chr1 2604601 . A C 218.40 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=111.25;MQ=13.41;MQ0=75;QD=1.51;SB=4.22 GT:AD:DP:GL:GQ 0/1:108,36:15:-33.23,-8.10,-26.51:99 +chr1 2604603 . T C 273.40 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=2;HaplotypeScore=107.87;MQ=13.23;MQ0=76;QD=1.89;SB=-75.88 GT:AD:DP:GL:GQ 0/1:65,76:14:-34.84,-4.22,-16.55:99 +chr1 2604631 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=169;Dels=0.00;HRun=1;HaplotypeScore=78.83;MQ=15.93;MQ0=66;OQ=130.30;QD=0.77;SB=-43.00 GT:AD:DP:GL:GQ 0/1:129,40:31:-25.65,-9.34,-87.13:99 +chr1 2604640 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=154;Dels=0.00;HRun=0;HaplotypeScore=101.27;MQ=16.99;MQ0=53;OQ=84.42;QD=0.55;SB=-10.00 GT:AD:DP:GL:GQ 0/1:93,61:34:-21.98,-10.25,-116.76:99 +chr1 2604659 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=114.19;MQ=17.85;MQ0=39;OQ=180.46;QD=1.31;SB=-10.00 GT:AD:DP:GL:GQ 0/1:106,32:34:-31.57,-10.24,-88.52:99 +chr1 2604673 rs7415296 T C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=120;Dels=0.00;HRun=1;HaplotypeScore=73.29;MQ=18.57;MQ0=29;OQ=1125.63;QD=9.38;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,107:33:-116.16,-9.94,-0.01:99 +chr1 2604706 rs6673862 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=39.35;MQ=23.53;MQ0=16;OQ=454.13;QD=4.83;SB=-3.99 GT:AD:DP:GL:GQ 0/1:51,43:41:-61.05,-12.35,-88.54:99 +chr1 2604709 rs6604993 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=41.02;MQ=25.10;MQ0=15;OQ=512.66;QD=5.40;SB=-34.93 GT:AD:DP:GL:GQ 0/1:48,47:45:-68.11,-13.56,-92.92:99 +chr1 2604721 rs61763524 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=115.04;MQ=25.76;MQ0=12;OQ=386.36;QD=4.15;SB=-44.44 GT:AD:DP:GL:GQ 0/1:49,44:40:-53.97,-12.05,-114.41:99 +chr1 2604728 rs61763525 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=150.75;MQ=27.24;MQ0=8;OQ=52.75;QD=0.62;SB=-10.00 GT:AD:DP:GL:GQ 0/1:49,22:37:-19.70,-11.14,-117.15:85.59 +chr1 2604813 rs6687492 A C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.04;HRun=2;HaplotypeScore=47.11;MQ=23.79;MQ0=20;OQ=1537.32;QD=16.53;SB=-154.02 GT:AD:DP:GL:GQ 1/1:2,87:44:-157.33,-12.95,-0.02:99 +chr1 2604848 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=9.77;MQ=17.69;MQ0=30;OQ=71.77;QD=1.30;SB=-10.00 GT:AD:DP:GL:GQ 0/1:37,18:14:-14.68,-4.22,-36.61:99 +chr1 2604864 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=28.67;MQ=16.02;MQ0=35;OQ=77.33;QD=1.17;SB=-10.00 GT:AD:DP:GL:GQ 0/1:62,4:12:-14.63,-3.61,-28.91:99 +chr1 2604867 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=23.02;MQ=16.18;MQ0=37;OQ=170.35;QD=2.43;SB=-10.00 GT:AD:DP:GL:GQ 0/1:59,11:15:-24.84,-4.52,-31.52:99 +chr1 2604879 . A G 48.78 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=25.49;MQ=18.59;MQ0=41;QD=0.57;SB=-6.99 GT:AD:DP:GL:GQ 0/1:79,7:20:-14.19,-6.03,-66.66:81.62 +chr1 2604892 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=1;HaplotypeScore=62.88;MQ=20.71;MQ0=36;OQ=145.34;QD=1.60;SB=-40.00 GT:AD:DP:GL:GQ 0/1:67,21:27:-25.95,-8.13,-71.88:99 +chr1 2604894 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.01;HRun=1;HaplotypeScore=55.68;MQ=20.44;MQ0=36;OQ=138.96;QD=1.49;SB=-41.95 GT:AD:DP:GL:GQ 0/1:67,21:26:-25.01,-7.83,-77.06:99 +chr1 2604912 rs61763528 T G 20.95 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=50.36;MQ=22.66;MQ0=25;QD=0.19;SB=-10.00 GT:AD:DP:GL:GQ 0/1:76,35:29:-14.11,-8.74,-95.07:53.75 +chr1 2604916 rs61763529 T G 194.85 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.00;HRun=0;HaplotypeScore=46.31;MQ=24.02;MQ0=23;QD=1.72;SB=-10.00 GT:AD:DP:GL:GQ 0/1:75,37:38:-34.21,-11.44,-107.06:99 +chr1 2604917 rs61763530 C G 1480.34 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=47.31;MQ=24.13;MQ0=22;QD=13.22;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,96:38:-168.50,-25.75,-16.88:88.75 +chr1 2604946 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=236;Dels=0.00;HRun=1;HaplotypeScore=63.84;MQ=27.71;MQ0=21;OQ=79.42;QD=0.34;SB=27.56 GT:AD:DP:GL:GQ 0/1:204,31:106:-43.16,-31.93,-335.49:99 +chr1 2604947 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=236;Dels=0.00;HRun=1;HaplotypeScore=57.70;MQ=27.78;MQ0=20;OQ=56.57;QD=0.24;SB=26.25 GT:AD:DP:GL:GQ 0/1:201,34:107:-41.17,-32.23,-378.22:89.40 +chr1 2604959 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=241;Dels=0.00;HRun=1;HaplotypeScore=113.45;MQ=29.01;MQ0=17;OQ=854.86;QD=3.55;SB=-18.43 GT:AD:DP:GL:GQ 0/1:165,75:109:-121.61,-32.84,-284.29:99 +chr1 2604960 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=123.76;MQ=29.06;MQ0=17;OQ=593.64;QD=2.47;SB=71.18 GT:AD:DP:GL:GQ 0/1:190,50:108:-95.18,-32.53,-286.72:99 +chr1 2604983 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=1;HaplotypeScore=495.52;MQ=29.66;MQ0=13;OQ=71.64;QD=0.32;SB=60.44 GT:AD:DP:GL:GQ 0/1:161,61:71:-31.89,-21.44,-242.50:99 +chr1 2604984 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=1;HaplotypeScore=666.90;MQ=29.67;MQ0=14;OQ=53.59;QD=0.24;SB=51.85 GT:AD:DP:GL:GQ 0/1:162,59:73:-33.13,-24.49,-250.82:86.43 +chr1 2604994 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=301;Dels=0.00;HRun=1;HaplotypeScore=445.50;MQ=27.33;MQ0=32;OQ=911.93;QD=3.03;SB=-289.52 GT:AD:DP:GL:GQ 0/1:244,47:103:-139.58,-45.10,-310.97:99 +chr1 2605000 . A G 39.90 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=313;Dels=0.00;HRun=0;HaplotypeScore=296.02;MQ=26.42;MQ0=37;QD=0.13;SB=95.30 GT:AD:DP:GL:GQ 0/1:236,73:110:-42.96,-35.69,-387.52:72.73 +chr1 2605008 . C A 80.14 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=1;HaplotypeScore=230.13;MQ=26.37;MQ0=45;QD=0.26;SB=104.26 GT:AD:DP:GL:GQ 0/1:278,18:127:-64.22,-52.92,-396.67:99 +chr1 2605010 . C A 77.92 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=1;HaplotypeScore=334.39;MQ=26.26;MQ0=46;QD=0.25;SB=101.18 GT:AD:DP:GL:GQ 0/1:276,18:125:-51.79,-40.71,-371.85:99 +chr1 2605026 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=292;Dels=0.00;HRun=0;HaplotypeScore=503.51;MQ=24.87;MQ0=63;OQ=127.24;QD=0.44;SB=-33.91 GT:AD:DP:GL:GQ 0/1:107,181:82:-40.71,-24.70,-242.51:99 +chr1 2605040 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=333;Dels=0.00;HRun=0;HaplotypeScore=585.35;MQ=23.26;MQ0=69;OQ=164.03;QD=0.49;SB=60.04 GT:AD:DP:GL:GQ 0/1:234,98:87:-48.89,-29.20,-293.13:99 +chr1 2605055 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=394;Dels=0.00;HRun=0;HaplotypeScore=493.35;MQ=22.62;MQ0=80;OQ=367.10;QD=0.93;SB=90.44 GT:AD:DP:GL:GQ 0/1:300,89:126:-77.94,-37.95,-375.51:99 +chr1 2605064 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=394;Dels=0.00;HRun=1;HaplotypeScore=562.83;MQ=22.35;MQ0=77;OQ=111.09;QD=0.28;SB=241.07 GT:AD:DP:GL:GQ 0/1:342,17:127:-65.55,-51.15,-483.41:99 +chr1 2605074 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=367;Dels=0.02;HRun=1;HaplotypeScore=550.64;MQ=22.20;MQ0=72;OQ=1826.16;QD=4.98;SB=11.30 GT:AD:DP:GL:GQ 0/1:140,136:125:-251.01,-65.11,-307.30:99 +chr1 2605078 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=360;Dels=0.00;HRun=1;HaplotypeScore=645.39;MQ=22.69;MQ0=67;OQ=145.82;QD=0.41;SB=80.26 GT:AD:DP:GL:GQ 0/1:281,25:108:-50.40,-32.54,-347.91:99 +chr1 2605087 rs9442451 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=302;Dels=0.00;HRun=1;HaplotypeScore=515.01;MQ=23.21;MQ0=61;OQ=1550.28;QD=5.13;SB=0.26 GT:AD:DP:GL:GQ 0/1:127,172:83:-183.36,-25.04,-152.30:99 +chr1 2605095 rs7411254 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=295;Dels=0.00;HRun=0;HaplotypeScore=864.08;MQ=22.89;MQ0=61;OQ=861.12;QD=2.92;SB=-439.01 GT:AD:DP:GL:GQ 0/1:231,62:100:-119.53,-30.13,-233.73:99 +chr1 2605099 rs61763531 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=268;Dels=0.03;HRun=1;HaplotypeScore=671.07;MQ=23.34;MQ0=56;OQ=331.54;QD=1.24;SB=62.18 GT:AD:DP:GL:GQ 0/1:101,158:88:-62.36,-25.93,-228.22:99 +chr1 2605116 rs61763532 G T 727.77 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=280;Dels=0.00;HRun=0;HaplotypeScore=340.71;MQ=26.06;MQ0=38;QD=2.60;SB=80.25 GT:AD:DP:GL:GQ 0/1:98,160:86:-122.32,-46.26,-192.83:99 +chr1 2605118 . G A 130.78 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=2;HaplotypeScore=353.34;MQ=26.07;MQ0=39;QD=0.45;SB=68.17 GT:AD:DP:GL:GQ 0/1:266,20:82:-41.07,-24.71,-249.92:99 +chr1 2605120 . A G 143.56 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=286;Dels=0.00;HRun=0;HaplotypeScore=391.53;MQ=26.07;MQ0=38;QD=0.50;SB=44.57 GT:AD:DP:GL:GQ 0/1:230,56:92:-45.37,-27.73,-305.63:99 +chr1 2605121 . C A 843.63 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=283;Dels=0.00;HRun=2;HaplotypeScore=384.52;MQ=26.08;MQ0=38;QD=2.98;SB=80.20 GT:AD:DP:GL:GQ 0/1:195,69:112:-123.96,-36.31,-258.00:99 +chr1 2605143 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=261;Dels=0.00;HRun=0;HaplotypeScore=165.80;MQ=26.36;MQ0=57;OQ=2061.60;QD=7.90;SB=82.92 GT:AD:DP:GL:GQ 0/1:135,121:131:-251.29,-41.84,-249.16:99 +chr1 2605152 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=276;Dels=0.00;HRun=0;HaplotypeScore=166.41;MQ=25.95;MQ0=68;OQ=1747.63;QD=6.33;SB=68.24 GT:AD:DP:GL:GQ 0/1:180,94:128:-216.61,-38.56,-254.69:99 +chr1 2605164 rs56278231 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=99.67;MQ=26.36;MQ0=65;OQ=2109.83;QD=7.59;SB=62.23 GT:AD:DP:GL:GQ 0/1:140,134:129:-253.13,-38.87,-210.06:99 +chr1 2605176 rs61763533 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=283;Dels=0.00;HRun=4;HaplotypeScore=192.72;MQ=26.37;MQ0=64;OQ=2285.97;QD=8.08;SB=50.20 GT:AD:DP:GL:GQ 0/1:155,126:135:-272.62,-40.74,-266.81:99 +chr1 2605179 rs7415101 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=293;Dels=0.00;HRun=0;HaplotypeScore=210.05;MQ=26.19;MQ0=65;OQ=1158.68;QD=3.95;SB=-384.91 GT:AD:DP:GL:GQ 0/1:236,57:97:-148.38,-29.23,-220.79:99 +chr1 2605208 . C A 465.30 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=269;Dels=0.00;HRun=1;HaplotypeScore=227.21;MQ=26.15;MQ0=63;QD=1.73;SB=32.07 GT:AD:DP:GL:GQ 0/1:153,116:69:-70.60,-20.78,-175.32:99 +chr1 2605210 . C A 482.33 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=1;HaplotypeScore=189.40;MQ=26.42;MQ0=62;QD=1.81;SB=32.08 GT:AD:DP:GL:GQ 0/1:149,115:67:-71.70,-20.18,-161.20:99 +chr1 2605214 rs61082664 T C 967.30 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=276;Dels=0.00;HRun=2;HaplotypeScore=127.28;MQ=27.64;MQ0=60;QD=3.50;SB=23.10 GT:AD:DP:GL:GQ 0/1:97,178:76:-122.91,-22.90,-161.42:99 +chr1 2605243 . G T 751.64 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=305;Dels=0.00;HRun=1;HaplotypeScore=253.27;MQ=31.30;MQ0=36;QD=2.46;SB=71.20 GT:AD:DP:GL:GQ 0/1:173,132:102:-109.18,-30.73,-247.59:99 +chr1 2605244 rs28455054 T C 853.34 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=304;Dels=0.00;HRun=0;HaplotypeScore=224.13;MQ=31.61;MQ0=34;QD=2.81;SB=-69.58 GT:AD:DP:GL:GQ 0/1:99,183:104:-137.17,-48.55,-265.91:99 +chr1 2605247 . C T 78.33 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=241.73;MQ=32.15;MQ0=30;QD=0.26;SB=92.28 GT:AD:DP:GL:GQ 0/1:261,44:108:-43.66,-32.54,-342.18:99 +chr1 2605252 . C A 302.63 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=316;Dels=0.00;HRun=1;HaplotypeScore=325.23;MQ=32.85;MQ0=33;QD=0.96;SB=113.24 GT:AD:DP:GL:GQ 0/1:197,119:109:-66.39,-32.84,-311.74:99 +chr1 2605255 rs55876897 A C 449.77 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=317;Dels=0.00;HRun=3;HaplotypeScore=260.93;MQ=33.01;MQ0=35;QD=1.42;SB=-150.70 GT:AD:DP:GL:GQ 0/1:239,77:117:-83.21,-34.95,-326.08:99 +chr1 2605259 rs56999649 T G 716.83 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=300;Dels=0.00;HRun=1;HaplotypeScore=227.19;MQ=34.47;MQ0=29;QD=2.39;SB=-184.23 GT:AD:DP:GL:GQ 0/1:116,182:121:-111.42,-36.45,-316.52:99 +chr1 2605264 rs4648676 C T 210.17 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=316;Dels=0.00;HRun=0;HaplotypeScore=557.56;MQ=35.06;MQ0=25;QD=0.67;SB=-21.82 GT:AD:DP:GL:GQ 0/1:289,24:136:-67.74,-43.44,-416.85:99 +chr1 2605334 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=408;Dels=0.00;HRun=4;HaplotypeScore=186.79;MQ=36.75;MQ0=7;OQ=1485.59;QD=3.64;SB=-538.59 GT:AD:DP:GL:GQ 0/1:275,118:294:-243.85,-92.01,-1014.23:99 +chr1 2605341 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=415;Dels=0.00;HRun=0;HaplotypeScore=229.92;MQ=36.33;MQ0=7;OQ=215.75;QD=0.52;SB=102.02 GT:AD:DP:GL:GQ 0/1:365,48:297:-114.34,-89.49,-957.91:99 +chr1 2605353 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=430;Dels=0.00;HRun=0;HaplotypeScore=200.04;MQ=35.29;MQ0=7;OQ=112.93;QD=0.26;SB=60.60 GT:AD:DP:GL:GQ 0/1:389,39:313:-108.94,-94.36,-1191.77:99 +chr1 2605354 rs4648678 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=435;Dels=0.00;HRun=0;HaplotypeScore=203.33;MQ=35.33;MQ0=8;OQ=1038.03;QD=2.39;SB=-273.03 GT:AD:DP:GL:GQ 0/1:373,60:307:-199.57,-92.49,-955.77:99 +chr1 2605374 rs61763535 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=451;Dels=0.00;HRun=4;HaplotypeScore=174.52;MQ=33.98;MQ0=15;OQ=1772.73;QD=3.93;SB=-155.11 GT:AD:DP:GL:GQ 0/1:257,185:286:-266.74,-86.18,-803.52:99 +chr1 2605416 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=641;Dels=0.00;HRun=0;HaplotypeScore=116.73;MQ=29.52;MQ0=38;OQ=101.05;QD=0.16;SB=-26.09 GT:AD:DP:GL:GQ 0/1:592,49:383:-128.76,-115.37,-1229.08:99 +chr1 2605473 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=505;Dels=0.00;HRun=1;HaplotypeScore=72.40;MQ=31.01;MQ0=19;OQ=529.76;QD=1.05;SB=-238.32 GT:AD:DP:GL:GQ 0/1:450,54:383:-171.63,-115.37,-1165.16:99 +chr1 2605495 rs56293461 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=486;Dels=0.00;HRun=0;HaplotypeScore=95.08;MQ=32.56;MQ0=15;OQ=821.52;QD=1.69;SB=-409.31 GT:AD:DP:GL:GQ 0/1:403,80:369:-196.58,-111.15,-1127.43:99 +chr1 2605529 rs28651038 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=428;Dels=0.00;HRun=0;HaplotypeScore=82.79;MQ=34.53;MQ0=16;OQ=2602.34;QD=6.08;SB=-653.43 GT:AD:DP:GL:GQ 0/1:288,123:298:-353.40,-89.88,-659.17:99 +chr1 2605657 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=389;Dels=0.01;HRun=3;HaplotypeScore=175.38;MQ=30.03;MQ0=70;OQ=99.64;QD=0.26;SB=74.25 GT:AD:DP:GL:GQ 0/1:326,61:215:-77.75,-64.51,-660.65:99 +chr1 2605686 . A C 325.50 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=398;Dels=0.00;HRun=0;HaplotypeScore=501.75;MQ=28.89;MQ0=57;QD=0.82;SB=95.28 GT:AD:DP:GL:GQ 0/1:281,115:207:-98.21,-62.38,-634.44:99 +chr1 2605688 . T C 330.54 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=397;Dels=0.00;HRun=2;HaplotypeScore=497.47;MQ=28.92;MQ0=57;QD=0.83;SB=65.64 GT:AD:DP:GL:GQ 0/1:226,152:200:-122.31,-85.97,-661.75:99 +chr1 2605695 rs55827558 C T 892.89 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=401;Dels=0.00;HRun=0;HaplotypeScore=534.98;MQ=29.24;MQ0=57;QD=2.23;SB=9.18 GT:AD:DP:GL:GQ 0/1:315,49:193:-153.53,-60.96,-575.72:99 +chr1 2605725 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=284;Dels=0.00;HRun=0;HaplotypeScore=360.95;MQ=32.85;MQ0=34;OQ=61.42;QD=0.22;SB=89.31 GT:AD:DP:GL:GQ 0/1:168,111:137:-50.75,-41.32,-529.65:94.25 +chr1 2605754 . C T 591.89 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=467.58;MQ=37.63;MQ0=15;QD=2.12;SB=140.37 GT:AD:DP:GL:GQ 0/1:235,40:127:-100.77,-38.29,-327.93:99 +chr1 2605755 . G A 525.10 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=436.48;MQ=37.79;MQ0=15;QD=1.94;SB=80.56 GT:AD:DP:GL:GQ 0/1:156,112:135:-96.50,-40.71,-357.83:99 +chr1 2605761 rs61763538 C G 1339.29 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=259;Dels=0.00;HRun=1;HaplotypeScore=254.24;MQ=38.34;MQ0=17;QD=5.17;SB=4.72 GT:AD:DP:GL:GQ 0/1:84,169:121:-173.69,-36.48,-327.29:99 +chr1 2605783 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=297;Dels=0.00;HRun=0;HaplotypeScore=293.73;MQ=35.79;MQ0=20;OQ=562.93;QD=1.90;SB=121.81 GT:AD:DP:GL:GQ 0/1:195,74:123:-135.97,-76.40,-335.89:99 +chr1 2605795 . G A 252.45 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=324;Dels=0.00;HRun=0;HaplotypeScore=499.11;MQ=34.45;MQ0=20;QD=0.78;SB=203.66 GT:AD:DP:GL:GQ 0/1:201,116:126:-66.49,-37.96,-390.94:99 +chr1 2605804 . C T 66.11 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=356;Dels=0.00;HRun=0;HaplotypeScore=268.83;MQ=34.41;MQ0=22;QD=0.19;SB=-31.15 GT:AD:DP:GL:GQ 0/1:312,39:152:-58.55,-48.66,-460.06:98.95 +chr1 2605805 . G A 2340.79 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=356;Dels=0.00;HRun=0;HaplotypeScore=224.04;MQ=34.36;MQ0=23;QD=6.58;SB=164.74 GT:AD:DP:GL:GQ 0/1:199,157:186:-293.46,-56.10,-343.74:99 +chr1 2605831 . C T 1118.55 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=295;Dels=0.00;HRun=0;HaplotypeScore=238.92;MQ=35.23;MQ0=23;QD=3.79;SB=174.98 GT:AD:DP:GL:GQ 0/1:220,69:156:-162.17,-47.03,-376.03:99 +chr1 2605834 . C T 954.45 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=236.05;MQ=35.80;MQ0=20;QD=3.42;SB=200.51 GT:AD:DP:GL:GQ 0/1:218,59:162:-147.54,-48.81,-432.29:99 +chr1 2605836 . T G 306.78 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=263;Dels=0.00;HRun=0;HaplotypeScore=206.04;MQ=36.89;MQ0=20;QD=1.17;SB=188.58 GT:AD:DP:GL:GQ 0/1:205,52:142:-88.13,-54.17,-440.06:99 +chr1 2605841 . A G 545.99 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=1;HaplotypeScore=155.67;MQ=38.58;MQ0=20;QD=2.35;SB=182.62 GT:AD:DP:GL:GQ 0/1:160,70:131:-97.35,-39.47,-411.37:99 +chr1 2605874 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=0;HaplotypeScore=124.99;MQ=42.37;MQ0=11;OQ=512.21;QD=2.21;SB=-14.46 GT:AD:DP:GL:GQ 0/1:155,74:147:-102.43,-47.93,-470.53:99 +chr1 2605886 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=108.30;MQ=44.38;MQ0=8;OQ=363.46;QD=1.81;SB=149.68 GT:AD:DP:GL:GQ 0/1:128,71:139:-81.51,-41.88,-451.45:99 +chr1 2605893 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=0;HaplotypeScore=120.52;MQ=42.83;MQ0=17;OQ=327.45;QD=1.66;SB=185.60 GT:AD:DP:GL:GQ 0/1:128,68:129:-77.12,-41.09,-417.50:99 +chr1 2605899 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=1;HaplotypeScore=109.97;MQ=40.67;MQ0=24;OQ=225.12;QD=1.10;SB=176.57 GT:AD:DP:GL:GQ 0/1:183,21:132:-65.55,-39.76,-408.38:99 +chr1 2605937 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=2;HaplotypeScore=54.75;MQ=35.12;MQ0=33;OQ=125.52;QD=0.63;SB=203.69 GT:AD:DP:GL:GQ 0/1:151,48:110:-48.99,-33.15,-378.43:99 +chr1 2605949 rs55869659 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=295;Dels=0.00;HRun=1;HaplotypeScore=266.34;MQ=30.03;MQ0=43;OQ=1589.71;QD=5.39;SB=-453.79 GT:AD:DP:GL:GQ 0/1:231,64:135:-202.93,-40.67,-294.60:99 +chr1 2605976 rs6683769 G C 6974.39 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=343;Dels=0.02;HRun=3;HaplotypeScore=423.51;MQ=29.44;MQ0=37;QD=20.33;SB=-2874.56 GT:AD:DP:GL:GQ 1/1:19,284:159:-696.44,-51.43,-8.07:99 +chr1 2605977 rs6661848 C T 1027.05 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=358;Dels=0.00;HRun=0;HaplotypeScore=456.32;MQ=29.31;MQ0=37;QD=2.87;SB=-210.09 GT:AD:DP:GL:GQ 0/1:307,50:125:-143.65,-37.67,-316.41:99 +chr1 2605979 . C A 1028.24 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=357;Dels=0.00;HRun=1;HaplotypeScore=354.37;MQ=29.31;MQ0=37;QD=2.88;SB=152.21 GT:AD:DP:GL:GQ 0/1:297,56:154:-152.50,-46.39,-400.06:99 +chr1 2605985 . A G 302.88 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=344;Dels=0.00;HRun=1;HaplotypeScore=327.75;MQ=29.96;MQ0=33;QD=0.88;SB=170.59 GT:AD:DP:GL:GQ 0/1:269,70:128:-72.14,-38.56,-425.79:99 +chr1 2606004 . C T 951.09 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=290;Dels=0.00;HRun=0;HaplotypeScore=672.95;MQ=32.63;MQ0=23;QD=3.28;SB=87.89 GT:AD:DP:GL:GQ 0/1:220,66:128:-136.98,-38.59,-302.88:99 +chr1 2606005 rs6683777 G A 1342.36 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=287;Dels=0.00;HRun=0;HaplotypeScore=631.13;MQ=33.21;MQ0=21;QD=4.68;SB=-76.00 GT:AD:DP:GL:GQ 0/1:85,177:126:-230.50,-92.98,-257.82:99 +chr1 2606006 rs57008511 G T 1549.99 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=289;Dels=0.00;HRun=0;HaplotypeScore=644.99;MQ=33.16;MQ0=21;QD=5.36;SB=-385.70 GT:AD:DP:GL:GQ 0/1:228,60:127:-196.55,-38.27,-243.78:99 +chr1 2606009 . A T 459 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=281;Dels=0.00;HRun=0;HaplotypeScore=430.52;MQ=33.69;MQ0=19;QD=1.63;SB=105.62 GT:AD:DP:GL:GQ 0/1:113,66:123:-152.84,-103.65,-371.87:99 +chr1 2606031 . C G 597.38 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=1;HaplotypeScore=164.77;MQ=37.58;MQ0=8;QD=2.69;SB=139.07 GT:AD:DP:GL:GQ 0/1:114,51:127:-143.77,-80.75,-412.83:99 +chr1 2606038 . C A 277.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=0;HaplotypeScore=107.00;MQ=38.94;MQ0=8;QD=1.28;SB=120.78 GT:AD:DP:GL:GQ 0/1:160,54:121:-67.44,-36.45,-363.09:99 +chr1 2606041 . G T 124.23 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=0;HaplotypeScore=125.82;MQ=39.98;MQ0=7;QD=0.60;SB=144.54 GT:AD:DP:GL:GQ 0/1:161,44:113:-49.75,-34.04,-340.70:99 +chr1 2606206 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=315;Dels=0.00;HRun=1;HaplotypeScore=256.44;MQ=28.06;MQ0=39;OQ=155.48;QD=0.49;SB=-29.90 GT:AD:DP:GL:GQ 0/1:209,63:107:-66.50,-47.67,-397.67:99 +chr1 2606217 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=250;Dels=0.00;HRun=3;HaplotypeScore=224.65;MQ=29.86;MQ0=28;OQ=458.20;QD=1.83;SB=-95.78 GT:AD:DP:GL:GQ 0/1:87,160:81:-76.54,-27.44,-208.99:99 +chr1 2606220 rs36162961 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=249;Dels=0.00;HRun=0;HaplotypeScore=180.31;MQ=29.93;MQ0=27;OQ=201.47;QD=0.81;SB=-7.21 GT:AD:DP:GL:GQ 0/1:213,32:103:-54.47,-31.04,-311.81:99 +chr1 2606247 rs6662065 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=58.65;MQ=36.60;MQ0=15;OQ=2337.23;QD=14.98;SB=-1097.47 GT:AD:DP:GL:GQ 0/1:41,86:97:-280.18,-43.17,-102.47:99 +chr1 2606279 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=1;HaplotypeScore=25.92;MQ=42.76;MQ0=2;OQ=312.76;QD=2.56;SB=-74.63 GT:AD:DP:GL:GQ 0/1:94,28:104:-65.90,-31.34,-343.27:99 +chr1 2606294 rs28562476 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=129;Dels=0.00;HRun=0;HaplotypeScore=45.48;MQ=41.64;MQ0=3;OQ=158.71;QD=1.23;SB=-91.27 GT:AD:DP:GL:GQ 0/1:99,30:98:-48.69,-29.54,-326.61:99 +chr1 2606300 rs6662172 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=148;Dels=0.00;HRun=1;HaplotypeScore=45.57;MQ=40.35;MQ0=4;OQ=2445.81;QD=16.53;SB=-1064.82 GT:AD:DP:GL:GQ 0/1:63,84:112:-281.60,-33.73,-119.13:99 +chr1 2606379 rs28410393 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=27.63;MQ=39.78;MQ0=6;OQ=368.46;QD=3.02;SB=6.71 GT:AD:DP:GL:GQ 0/1:95,26:92:-67.86,-27.73,-327.77:99 +chr1 2606380 rs28520729 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=27.50;MQ=39.82;MQ0=6;OQ=559.99;QD=4.71;SB=-194.85 GT:AD:DP:GL:GQ 0/1:94,25:96:-88.22,-28.94,-322.33:99 +chr1 2606465 rs28436923 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=147;Dels=0.00;HRun=0;HaplotypeScore=131.13;MQ=40.98;MQ0=13;OQ=2035.71;QD=13.85;SB=-905.49 GT:AD:DP:GL:GQ 0/1:80,64:81:-231.26,-24.41,-73.56:99 +chr1 2606518 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=218.01;MQ=25.24;MQ0=20;OQ=216.97;QD=1.17;SB=68.19 GT:AD:DP:GL:GQ 0/1:119,56:69:-45.78,-20.79,-195.94:99 +chr1 2606520 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=182;Dels=0.01;HRun=1;HaplotypeScore=197.55;MQ=24.90;MQ0=18;OQ=425.87;QD=2.34;SB=7.72 GT:AD:DP:GL:GQ 0/1:98,71:68:-66.40,-20.53,-203.96:99 +chr1 2606555 rs55641610 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=142;Dels=0.00;HRun=0;HaplotypeScore=86.83;MQ=22.44;MQ0=15;OQ=611.31;QD=4.31;SB=-217.67 GT:AD:DP:GL:GQ 0/1:66,72:64:-83.70,-19.29,-186.04:99 +chr1 2606567 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=1;HaplotypeScore=115.34;MQ=22.30;MQ0=19;OQ=114.64;QD=0.87;SB=-3.31 GT:AD:DP:GL:GQ 0/1:113,14:59:-32.52,-17.77,-180.72:99 +chr1 2606594 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=41.70;MQ=23.56;MQ0=16;OQ=75.03;QD=0.63;SB=28.48 GT:AD:DP:GL:GQ 0/1:83,36:66:-30.68,-19.89,-255.45:99 +chr1 2606643 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=21.80;MQ=30.64;MQ0=12;OQ=1721.23;QD=15.37;SB=-793.00 GT:AD:DP:GL:GQ 0/1:46,66:82:-200.11,-24.70,-94.60:99 +chr1 2606798 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=16.08;MQ=18.33;MQ0=33;OQ=155.22;QD=2.13;SB=-92.26 GT:AD:DP:GL:GQ 0/1:36,34:23:-29.36,-10.56,-75.52:99 +chr1 2607095 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=174;Dels=0.00;HRun=0;HaplotypeScore=115.98;MQ=20.76;MQ0=93;OQ=63.80;QD=0.37;SB=-35.41 GT:AD:DP:GL:GQ 0/1:164,10:54:-25.95,-16.29,-195.04:96.63 +chr1 2607127 rs28555663 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.00;HRun=0;HaplotypeScore=71.01;MQ=31.05;MQ0=18;OQ=1628.35;QD=13.57;SB=-397.76 GT:AD:DP:GL:GQ 0/1:27,60:78:-215.41,-49.30,-93.76:99 +chr1 2607162 rs61763542 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=215;Dels=0.00;HRun=1;HaplotypeScore=85.56;MQ=29.70;MQ0=30;OQ=368.13;QD=1.71;SB=-56.56 GT:AD:DP:GL:GQ 0/1:178,35:124:-77.45,-37.35,-360.47:99 +chr1 2607163 . G A 13.12 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=2;HaplotypeScore=87.56;MQ=29.61;MQ0=31;QD=0.06;SB=-11.83 GT:AD:DP:GL:GQ 0/1:187,28:129:-43.44,-38.86,-425.52:45.74 +chr1 2607204 . G C 43.54 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=196;Dels=0.00;HRun=0;HaplotypeScore=43.04;MQ=31.64;MQ0=30;QD=0.22;SB=-29.18 GT:AD:DP:GL:GQ 0/1:170,26:109:-40.50,-32.86,-424.67:76.37 +chr1 2607231 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=1;HaplotypeScore=72.77;MQ=31.17;MQ0=24;OQ=125.47;QD=0.87;SB=-42.71 GT:AD:DP:GL:GQ 0/1:125,19:75:-38.43,-22.60,-228.94:99 +chr1 2607242 rs61763545 G T 46.85 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=36.90;MQ=31.04;MQ0=29;QD=0.40;SB=43.89 GT:AD:DP:GL:GQ 0/1:84,30:54:-24.25,-16.28,-154.98:79.69 +chr1 2607298 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=68.12;MQ=14.41;MQ0=82;OQ=66.90;QD=0.45;SB=20.86 GT:AD:DP:GL:GQ 0/1:129,10:21:-19.87,-9.89,-58.18:99 +chr1 2607355 rs61765818 C T 12.91 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=56.37;MQ=16.61;MQ0=62;QD=0.11;SB=29.06 GT:AD:DP:GL:GQ 0/1:90,27:23:-11.49,-6.94,-61.93:45.51 +chr1 2607366 . A G 13.05 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=2;HaplotypeScore=34.50;MQ=17.10;MQ0=55;QD=0.12;SB=29.12 GT:AD:DP:GL:GQ 0/1:102,6:22:-11.19,-6.63,-75.23:45.67 +chr1 2607368 rs61763546 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=35.70;MQ=17.26;MQ0=53;OQ=303.93;QD=2.87;SB=-146.92 GT:AD:DP:GL:GQ 0/1:46,59:26:-41.51,-7.84,-47.60:99 +chr1 2607409 . G A 15.60 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=0;HaplotypeScore=56.89;MQ=28.46;MQ0=6;QD=0.24;SB=38.64 GT:AD:DP:GL:GQ 0/1:41,24:37:-15.99,-11.15,-106.07:48.31 +chr1 2607422 rs56133135 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=19.37;MQ=32.69;MQ0=0;OQ=693.38;QD=12.61;SB=2.03 GT:AD:DP:GL:GQ 0/1:26,28:39:-84.38,-11.76,-83.37:99 +chr1 2607465 rs61763547 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=40.98;MQ=25.86;MQ0=35;OQ=388.51;QD=4.63;SB=-36.91 GT:AD:DP:GL:GQ 0/1:60,23:42:-54.79,-12.65,-94.92:99 +chr1 2607520 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=176;Dels=0.00;HRun=1;HaplotypeScore=43.55;MQ=22.90;MQ0=79;OQ=121.23;QD=0.69;SB=8.68 GT:AD:DP:GL:GQ 0/1:158,14:67:-35.59,-20.18,-205.83:99 +chr1 2607562 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=147;Dels=0.00;HRun=0;HaplotypeScore=58.31;MQ=31.97;MQ0=28;OQ=222.37;QD=1.51;SB=-108.77 GT:AD:DP:GL:GQ 0/1:118,16:74:-51.32,-25.80,-191.60:99 +chr1 2607568 rs61763549 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=80.59;MQ=33.84;MQ0=16;OQ=1066.74;QD=7.90;SB=-480.14 GT:AD:DP:GL:GQ 0/1:64,70:72:-131.67,-21.72,-176.26:99 +chr1 2607579 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=1;HaplotypeScore=59.49;MQ=32.83;MQ0=15;OQ=376.87;QD=2.37;SB=-134.64 GT:AD:DP:GL:GQ 0/1:129,30:89:-67.78,-26.81,-244.98:99 +chr1 2607622 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=166;Dels=0.00;HRun=1;HaplotypeScore=74.61;MQ=28.79;MQ0=41;OQ=121.71;QD=0.73;SB=1.49 GT:AD:DP:GL:GQ 0/1:144,22:68:-35.94,-20.49,-206.61:99 +chr1 2607635 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=177;Dels=0.00;HRun=1;HaplotypeScore=30.67;MQ=24.43;MQ0=69;OQ=168.44;QD=0.95;SB=-26.38 GT:AD:DP:GL:GQ 0/1:144,24:48:-34.61,-14.49,-156.01:99 +chr1 2607650 . G A 36.08 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=194;Dels=0.00;HRun=1;HaplotypeScore=75.42;MQ=22.15;MQ0=92;QD=0.19;SB=17.06 GT:AD:DP:GL:GQ 0/1:183,11:48:-21.35,-14.46,-155.19:68.92 +chr1 2607670 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=229;Dels=0.00;HRun=0;HaplotypeScore=160.50;MQ=16.74;MQ0=141;OQ=99.29;QD=0.43;SB=62.11 GT:AD:DP:GL:GQ 0/1:219,9:33:-23.18,-9.97,-80.62:99 +chr1 2607674 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=226;Dels=0.00;HRun=0;HaplotypeScore=115.26;MQ=15.31;MQ0=147;OQ=144.37;QD=0.64;SB=59.23 GT:AD:DP:GL:GQ 0/1:144,82:32:-27.37,-9.65,-111.07:99 +chr1 2607705 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=307;Dels=0.00;HRun=0;HaplotypeScore=135.41;MQ=9.50;MQ0=238;OQ=88.23;QD=0.29;SB=44.16 GT:AD:DP:GL:GQ 0/1:293,13:26:-19.94,-7.83,-70.73:99 +chr1 2607732 . A G 46.69 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=264;Dels=0.00;HRun=0;HaplotypeScore=160.28;MQ=9.40;MQ0=205;QD=0.18;SB=38.16 GT:AD:DP:GL:GQ 0/1:246,15:21:-14.28,-6.33,-70.03:79.52 +chr1 2607768 . C G 49.76 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=95.94;MQ=10.01;MQ0=124;QD=0.30;SB=-3.98 GT:AD:DP:GL:GQ 0/1:136,25:16:-13.08,-4.82,-52.20:82.60 +chr1 2607891 rs7416366 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=122;Dels=0.00;HRun=0;HaplotypeScore=58.84;MQ=34.41;MQ0=14;OQ=1644.48;QD=13.48;SB=-506.65 GT:AD:DP:GL:GQ 0/1:59,63:73:-189.73,-22.00,-69.36:99 +chr1 2607919 . C G 24.55 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=0;HaplotypeScore=83.78;MQ=30.54;MQ0=25;QD=0.11;SB=109.84 GT:AD:DP:GL:GQ 0/1:205,16:120:-41.91,-36.17,-462.22:57.38 +chr1 2607925 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=225;Dels=0.00;HRun=1;HaplotypeScore=102.41;MQ=29.59;MQ0=28;OQ=208.07;QD=0.92;SB=12.89 GT:AD:DP:GL:GQ 0/1:171,51:116:-59.04,-34.95,-344.67:99 +chr1 2607990 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=0;HaplotypeScore=62.53;MQ=19.75;MQ0=60;OQ=143.02;QD=0.67;SB=-11.93 GT:AD:DP:GL:GQ 0/1:169,45:70:-38.68,-21.10,-211.21:99 +chr1 2608016 rs61763552 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=154;Dels=0.00;HRun=1;HaplotypeScore=33.08;MQ=18.38;MQ0=35;OQ=157.73;QD=1.02;SB=-56.91 GT:AD:DP:GL:GQ 0/1:74,80:55:-35.63,-16.57,-153.82:99 +chr1 2608035 rs60386739 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=68.10;MQ=20.23;MQ0=19;OQ=139.83;QD=0.99;SB=-34.61 GT:AD:DP:GL:GQ 0/1:123,11:68:-37.75,-20.49,-226.75:99 +chr1 2608187 . T A 19.78 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=100.91;MQ=20.82;MQ0=35;QD=0.14;SB=68.21 GT:AD:DP:GL:GQ 0/1:73,68:45:-18.82,-13.56,-139.70:52.57 +chr1 2608269 rs28464857 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.00;HRun=0;HaplotypeScore=134.04;MQ=20.25;MQ0=84;OQ=169.32;QD=0.91;SB=-92.57 GT:AD:DP:GL:GQ 0/1:170,15:57:-37.38,-17.17,-176.94:99 +chr1 2608484 rs28436796 C G 0.48 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=9.24;MQ=47.84;MQ0=1;OQ=487.04;QD=5.47;SB=-196.59 GT:AD:DP:GL:GQ 0/1:66,21:74:-74.31,-22.32,-232.63:99 +chr1 2608664 rs4074927 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=182;Dels=0.01;HRun=1;HaplotypeScore=99.89;MQ=34.06;MQ0=19;OQ=2375.90;QD=13.05;SB=-939.83 GT:AD:DP:GL:GQ 0/1:91,85:111:-274.32,-33.45,-107.97:99 +chr1 2608867 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=118;Dels=0.01;HRun=2;HaplotypeScore=20.49;MQ=45.47;MQ0=7;OQ=974.46;QD=8.26;SB=-210.08 GT:AD:DP:GL:GQ 0/1:62,55:87:-126.99,-26.26,-221.81:99 +chr1 2609068 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=3;HaplotypeScore=118.35;MQ=34.13;MQ0=24;OQ=526.94;QD=2.38;SB=137.47 GT:AD:DP:GL:GQ 0/1:93,112:118:-95.11,-39.14,-362.67:99 +chr1 2609088 rs6604995 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=244;Dels=0.00;HRun=1;HaplotypeScore=80.61;MQ=35.58;MQ0=31;OQ=2415.96;QD=9.90;SB=-1183.52 GT:AD:DP:GL:GQ 0/1:168,75:136:-285.85,-40.97,-232.15:99 +chr1 2609117 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=242;Dels=0.00;HRun=0;HaplotypeScore=86.85;MQ=40.05;MQ0=22;OQ=564.86;QD=2.33;SB=136.90 GT:AD:DP:GL:GQ 0/1:188,54:147:-104.06,-44.29,-429.75:99 +chr1 2609119 . T A 10.35 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=240;Dels=0.00;HRun=1;HaplotypeScore=66.02;MQ=40.40;MQ0=19;QD=0.04;SB=-13.71 GT:AD:DP:GL:GQ 0/1:216,24:153:-50.36,-46.09,-521.00:42.77 +chr1 2609136 rs6680012 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=252;Dels=0.00;HRun=0;HaplotypeScore=138.11;MQ=41.19;MQ0=14;OQ=1288.83;QD=5.11;SB=-20.42 GT:AD:DP:GL:GQ 0/1:111,140:159:-180.06,-47.89,-385.06:99 +chr1 2609225 rs61765683 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=279;Dels=0.00;HRun=0;HaplotypeScore=196.30;MQ=28.44;MQ0=55;OQ=715.74;QD=2.57;SB=-196.88 GT:AD:DP:GL:GQ 0/1:215,53:119:-124.19,-49.34,-290.35:99 +chr1 2609273 rs4648680 A T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=189;Dels=0.00;HRun=0;HaplotypeScore=41.61;MQ=19.84;MQ0=34;OQ=2444.19;QD=12.93;SB=-891.61 GT:AD:DP:GL:GQ 1/1:0,186:71:-248.05,-21.40,-0.04:99 +chr1 2609305 rs6672446 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=196;Dels=0.00;HRun=1;HaplotypeScore=44.27;MQ=21.28;MQ0=40;OQ=1443.42;QD=7.36;SB=-313.15 GT:AD:DP:GL:GQ 0/1:121,75:90:-174.74,-27.11,-141.16:99 +chr1 2609332 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=25.23;MQ=24.42;MQ0=31;OQ=1010.88;QD=5.29;SB=-411.33 GT:AD:DP:GL:GQ 0/1:130,60:101:-134.82,-30.45,-224.41:99 +chr1 2609354 rs61765685 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=264;Dels=0.00;HRun=0;HaplotypeScore=43.36;MQ=26.38;MQ0=47;OQ=877.95;QD=3.33;SB=-290.40 GT:AD:DP:GL:GQ 0/1:123,140:122:-127.86,-36.78,-326.56:99 +chr1 2609381 . C A 220.25 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=378;Dels=0.00;HRun=0;HaplotypeScore=205.42;MQ=26.54;MQ0=63;QD=0.58;SB=-92.16 GT:AD:DP:GL:GQ 0/1:327,50:132:-65.07,-39.76,-400.14:99 +chr1 2609387 . C A 185.57 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=439;Dels=0.00;HRun=0;HaplotypeScore=250.48;MQ=26.77;MQ0=67;QD=0.42;SB=5.95 GT:AD:DP:GL:GQ 0/1:387,52:145:-65.52,-43.68,-445.14:99 +chr1 2609389 . C T 92.18 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=450;Dels=0.00;HRun=0;HaplotypeScore=251.37;MQ=26.71;MQ0=67;QD=0.20;SB=175.01 GT:AD:DP:GL:GQ 0/1:391,58:155:-59.19,-46.69,-504.94:99 +chr1 2609452 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=378;Dels=0.00;HRun=2;HaplotypeScore=241.26;MQ=31.94;MQ0=54;OQ=971.37;QD=2.57;SB=-357.67 GT:AD:DP:GL:GQ 0/1:305,73:146:-144.40,-43.98,-395.70:99 +chr1 2609455 rs58318704 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=356;Dels=0.00;HRun=0;HaplotypeScore=220.51;MQ=31.91;MQ0=49;OQ=2158.97;QD=6.06;SB=-1017.43 GT:AD:DP:GL:GQ 0/1:79,219:141:-270.22,-51.04,-310.17:99 +chr1 2609547 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=1;HaplotypeScore=66.94;MQ=35.31;MQ0=17;OQ=674.03;QD=3.60;SB=-244.40 GT:AD:DP:GL:GQ 0/1:135,50:133:-110.75,-40.07,-356.06:99 +chr1 2609555 rs28575476 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=0;HaplotypeScore=68.51;MQ=35.35;MQ0=12;OQ=1288.35;QD=7.53;SB=-481.51 GT:AD:DP:GL:GQ 0/1:88,78:120:-168.27,-36.15,-252.36:99 +chr1 2609591 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=34.97;MQ=33.84;MQ0=11;OQ=2484.13;QD=14.44;SB=-938.03 GT:AD:DP:GL:GQ 0/1:84,88:135:-292.43,-40.73,-257.29:99 +chr1 2609644 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=353;Dels=0.00;HRun=1;HaplotypeScore=213.12;MQ=29.19;MQ0=26;OQ=1530.86;QD=4.34;SB=-311.00 GT:AD:DP:GL:GQ 0/1:205,118:177:-209.80,-53.43,-491.62:99 +chr1 2609668 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=375;Dels=0.01;HRun=0;HaplotypeScore=299.53;MQ=28.31;MQ0=38;OQ=119.51;QD=0.32;SB=-39.52 GT:AD:DP:GL:GQ 0/1:330,33:168:-65.89,-50.66,-484.68:99 +chr1 2609669 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=370;Dels=0.01;HRun=3;HaplotypeScore=295.29;MQ=28.20;MQ0=38;OQ=509.10;QD=1.38;SB=-148.65 GT:AD:DP:GL:GQ 0/1:202,146:144:-97.68,-43.48,-474.43:99 +chr1 2609682 . T C 10.13 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=358;Dels=0.00;HRun=1;HaplotypeScore=318.76;MQ=28.20;MQ0=43;QD=0.03;SB=29.61 GT:AD:DP:GL:GQ 0/1:328,21:141:-56.49,-52.23,-495.36:42.52 +chr1 2609688 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=357;Dels=0.00;HRun=0;HaplotypeScore=304.49;MQ=28.68;MQ0=43;OQ=540.31;QD=1.51;SB=-146.86 GT:AD:DP:GL:GQ 0/1:288,44:135:-97.99,-40.67,-405.76:99 +chr1 2609713 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=325;Dels=0.00;HRun=2;HaplotypeScore=235.46;MQ=29.07;MQ0=50;OQ=183.31;QD=0.56;SB=-70.06 GT:AD:DP:GL:GQ 0/1:293,30:98:-51.18,-29.56,-309.43:99 +chr1 2609764 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=67.69;MQ=41.15;MQ0=28;OQ=547.70;QD=3.06;SB=-220.32 GT:AD:DP:GL:GQ 0/1:154,22:97:-87.34,-29.29,-296.73:99 +chr1 2609770 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=51.04;MQ=41.72;MQ0=28;OQ=50.39;QD=0.29;SB=107.80 GT:AD:DP:GL:GQ 0/1:92,83:96:-37.25,-28.93,-332.67:83.23 +chr1 2609843 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=0;HaplotypeScore=18.24;MQ=41.49;MQ0=22;OQ=514.69;QD=3.78;SB=-103.96 GT:AD:DP:GL:GQ 0/1:89,47:97:-83.99,-29.23,-261.15:99 +chr1 2609879 rs60995822 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.00;HRun=0;HaplotypeScore=53.77;MQ=31.75;MQ0=20;OQ=1688.97;QD=13.62;SB=-590.07 GT:AD:DP:GL:GQ 0/1:21,102:69:-192.97,-20.79,-48.84:99 +chr1 2609938 rs61765691 T C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=210;Dels=0.00;HRun=0;HaplotypeScore=78.06;MQ=23.32;MQ0=40;OQ=3717.12;QD=17.70;SB=-1751.06 GT:AD:DP:GL:GQ 1/1:3,206:105:-370.71,-31.64,-0.05:99 +chr1 2610024 rs60041779 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.00;HRun=0;HaplotypeScore=93.88;MQ=40.95;MQ0=10;OQ=112.09;QD=0.90;SB=83.51 GT:AD:DP:GL:GQ 0/1:77,47:69:-35.30,-20.81,-248.60:99 +chr1 2610174 rs61765693 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=331;Dels=0.00;HRun=1;HaplotypeScore=45.52;MQ=28.55;MQ0=47;OQ=762.69;QD=2.30;SB=-121.02 GT:AD:DP:GL:GQ 0/1:162,168:127:-117.91,-38.35,-381.81:99 +chr1 2610186 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=354;Dels=0.00;HRun=0;HaplotypeScore=102.42;MQ=26.42;MQ0=47;OQ=1467.29;QD=4.14;SB=-129.66 GT:AD:DP:GL:GQ 0/1:303,49:127:-191.55,-41.54,-284.06:99 +chr1 2610220 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=358;Dels=0.00;HRun=0;HaplotypeScore=158.15;MQ=26.10;MQ0=33;OQ=52.73;QD=0.15;SB=-33.83 GT:AD:DP:GL:GQ 0/1:323,33:128:-47.12,-38.57,-405.99:85.57 +chr1 2610228 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=347;Dels=0.00;HRun=0;HaplotypeScore=258.31;MQ=25.86;MQ0=32;OQ=417.23;QD=1.20;SB=-217.33 GT:AD:DP:GL:GQ 0/1:235,103:129:-86.15,-41.14,-407.87:99 +chr1 2610288 rs61765694 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=240;Dels=0.00;HRun=0;HaplotypeScore=161.76;MQ=34.28;MQ0=24;OQ=460.60;QD=1.92;SB=-235.27 GT:AD:DP:GL:GQ 0/1:119,106:122:-91.58,-42.24,-307.51:99 +chr1 2610304 rs57887432 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=214;Dels=0.00;HRun=1;HaplotypeScore=126.12;MQ=34.24;MQ0=19;OQ=2078.47;QD=9.71;SB=-912.59 GT:AD:DP:GL:GQ 0/1:141,72:106:-243.09,-31.96,-204.85:99 +chr1 2610325 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=0;HaplotypeScore=58.60;MQ=38.14;MQ0=8;OQ=610.61;QD=3.94;SB=-307.83 GT:AD:DP:GL:GQ 0/1:117,38:94:-92.67,-28.33,-261.00:99 +chr1 2610342 rs58318302 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=64.33;MQ=41.99;MQ0=6;OQ=1628.60;QD=14.67;SB=-308.68 GT:AD:DP:GL:GQ 0/1:43,66:83:-191.15,-25.00,-121.94:99 +chr1 2610414 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=331;Dels=0.00;HRun=0;HaplotypeScore=235.51;MQ=30.47;MQ0=22;OQ=935.47;QD=2.83;SB=-429.72 GT:AD:DP:GL:GQ 0/1:275,53:139:-142.25,-45.42,-348.13:99 +chr1 2610415 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=337;Dels=0.00;HRun=1;HaplotypeScore=237.48;MQ=30.55;MQ0=22;OQ=1122.12;QD=3.33;SB=-419.64 GT:AD:DP:GL:GQ 0/1:156,170:150:-188.30,-72.80,-443.59:99 +chr1 2610441 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=398;Dels=0.00;HRun=0;HaplotypeScore=305.07;MQ=30.41;MQ0=29;OQ=523.24;QD=1.31;SB=-254.15 GT:AD:DP:GL:GQ 0/1:145,184:159:-118.96,-63.35,-451.63:99 +chr1 2610473 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=351;Dels=0.00;HRun=1;HaplotypeScore=331.68;MQ=29.41;MQ0=37;OQ=1376.69;QD=3.92;SB=-162.02 GT:AD:DP:GL:GQ 0/1:286,64:127:-179.22,-38.27,-253.78:99 +chr1 2610474 rs28418735 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=350;Dels=0.03;HRun=3;HaplotypeScore=309.89;MQ=29.49;MQ0=38;OQ=65.43;QD=0.19;SB=221.76 GT:AD:DP:GL:GQ 0/1:271,68:132:-49.66,-39.83,-486.19:98.27 +chr1 2610506 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=0;HaplotypeScore=143.13;MQ=32.96;MQ0=24;OQ=241.48;QD=1.21;SB=-28.90 GT:AD:DP:GL:GQ 0/1:85,107:74:-49.73,-22.29,-227.60:99 +chr1 2610517 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=3;HaplotypeScore=142.26;MQ=34.55;MQ0=20;OQ=220.80;QD=1.35;SB=75.68 GT:AD:DP:GL:GQ 0/1:65,82:63:-52.24,-26.88,-202.10:99 +chr1 2610573 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=104.72;MQ=37.56;MQ0=8;OQ=553.10;QD=3.29;SB=-39.90 GT:AD:DP:GL:GQ 0/1:88,80:80:-82.71,-24.12,-188.70:99 +chr1 2610594 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=122;Dels=0.02;HRun=0;HaplotypeScore=84.91;MQ=43.41;MQ0=3;OQ=1001.55;QD=8.21;SB=-522.00 GT:AD:DP:GL:GQ 0/1:52,66:81:-127.86,-24.42,-216.74:99 +chr1 2610598 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=2;HaplotypeScore=59.26;MQ=42.74;MQ0=3;OQ=1239.36;QD=9.61;SB=-593.34 GT:AD:DP:GL:GQ 0/1:51,77:86:-153.17,-25.95,-194.38:99 +chr1 2610632 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=184;Dels=0.00;HRun=0;HaplotypeScore=151.91;MQ=39.51;MQ0=6;OQ=369.19;QD=2.01;SB=-62.83 GT:AD:DP:GL:GQ 0/1:154,30:112:-73.95,-33.75,-316.70:99 +chr1 2610635 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=139.15;MQ=38.51;MQ0=6;OQ=274.48;QD=1.35;SB=-41.80 GT:AD:DP:GL:GQ 0/1:164,37:123:-67.82,-37.08,-455.22:99 +chr1 2610665 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=1;HaplotypeScore=315.73;MQ=36.51;MQ0=11;OQ=1591.77;QD=7.40;SB=-670.77 GT:AD:DP:GL:GQ 0/1:149,65:109:-195.35,-32.89,-252.45:99 +chr1 2610712 rs55957791 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=278;Dels=0.00;HRun=0;HaplotypeScore=331.10;MQ=30.73;MQ0=38;OQ=351.17;QD=1.26;SB=50.69 GT:AD:DP:GL:GQ 0/1:157,116:120:-81.22,-42.82,-389.65:99 +chr1 2610714 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=276;Dels=0.03;HRun=1;HaplotypeScore=276.80;MQ=30.44;MQ0=40;OQ=799.29;QD=2.90;SB=-215.74 GT:AD:DP:GL:GQ 0/1:208,58:112:-116.35,-33.14,-272.42:99 +chr1 2610938 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=0;HaplotypeScore=61.08;MQ=40.33;MQ0=9;OQ=2312.34;QD=13.21;SB=-496.11 GT:AD:DP:GL:GQ 0/1:80,95:114:-268.87,-34.35,-152.15:99 +chr1 2610982 rs61765696 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=168;Dels=0.00;HRun=1;HaplotypeScore=77.40;MQ=36.09;MQ0=4;OQ=730.22;QD=4.35;SB=-250.72 GT:AD:DP:GL:GQ 0/1:133,34:93:-104.33,-28.02,-240.35:99 +chr1 2610988 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=177;Dels=0.00;HRun=2;HaplotypeScore=104.66;MQ=37.43;MQ0=4;OQ=180.91;QD=1.02;SB=-14.66 GT:AD:DP:GL:GQ 0/1:124,53:103:-52.42,-31.04,-397.79:99 +chr1 2611005 rs28657620 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=175;Dels=0.00;HRun=0;HaplotypeScore=240.92;MQ=35.09;MQ0=11;OQ=589.04;QD=3.37;SB=-319.71 GT:AD:DP:GL:GQ 0/1:148,26:83:-87.21,-25.02,-177.35:99 +chr1 2611008 rs61765697 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=177;Dels=0.00;HRun=0;HaplotypeScore=268.58;MQ=34.75;MQ0=11;OQ=814.23;QD=4.60;SB=-203.16 GT:AD:DP:GL:GQ 0/1:94,75:81:-109.12,-24.42,-183.44:99 +chr1 2611037 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=3;HaplotypeScore=47.75;MQ=33.75;MQ0=25;OQ=310.37;QD=1.46;SB=128.35 GT:AD:DP:GL:GQ 0/1:180,32:105:-65.95,-31.63,-301.79:99 +chr1 2611075 . C A 675.15 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=198;Dels=0.00;HRun=0;HaplotypeScore=289.45;MQ=35.67;MQ0=15;QD=3.41;SB=-245.12 GT:AD:DP:GL:GQ 0/1:138,49:92:-105.75,-34.95,-225.78:99 +chr1 2611076 . C A 59.41 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=0;HaplotypeScore=288.77;MQ=35.79;MQ0=15;QD=0.30;SB=-43.36 GT:AD:DP:GL:GQ 0/1:179,20:91:-36.64,-27.42,-281.03:92.25 +chr1 2611077 . T C 1287 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=199;Dels=0.00;HRun=3;HaplotypeScore=272.49;MQ=35.97;MQ0=16;QD=6.47;SB=-518.91 GT:AD:DP:GL:GQ 0/1:56,142:93:-160.01,-28.02,-190.32:99 +chr1 2611149 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=128.93;MQ=29.89;MQ0=30;OQ=118.35;QD=0.49;SB=-20.53 GT:AD:DP:GL:GQ 0/1:190,53:92:-42.83,-27.72,-276.95:99 +chr1 2611155 rs61765698 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=245;Dels=0.00;HRun=0;HaplotypeScore=130.50;MQ=30.96;MQ0=25;OQ=203.44;QD=0.83;SB=-29.37 GT:AD:DP:GL:GQ 0/1:191,50:97:-52.56,-28.94,-359.64:99 +chr1 2611193 rs61029569 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=154;Dels=0.01;HRun=0;HaplotypeScore=78.67;MQ=38.69;MQ0=8;OQ=1417.86;QD=9.21;SB=-633.08 GT:AD:DP:GL:GQ 0/1:43,100:84:-170.37,-25.30,-121.64:99 +chr1 2611212 rs28774982 C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=125;Dels=0.00;HRun=0;HaplotypeScore=29.20;MQ=42.14;MQ0=3;OQ=3660.18;QD=29.28;SB=-1724.01 GT:AD:DP:GL:GQ 1/1:0,124:85:-365.02,-25.61,-0.03:99 +chr1 2611218 rs28581654 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=132;Dels=0.00;HRun=1;HaplotypeScore=33.13;MQ=42.84;MQ0=2;OQ=1779.64;QD=13.48;SB=-735.33 GT:AD:DP:GL:GQ 0/1:39,85:92:-211.73,-30.48,-139.53:99 +chr1 2611236 rs61765699 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=181;Dels=0.00;HRun=1;HaplotypeScore=137.95;MQ=39.80;MQ0=14;OQ=1598.49;QD=8.83;SB=-821.38 GT:AD:DP:GL:GQ 0/1:99,78:96:-192.06,-28.93,-137.58:99 +chr1 2611310 . G C 25 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=214;Dels=0.00;HRun=2;HaplotypeScore=68.15;MQ=29.71;MQ0=28;QD=0.12;SB=77.64 GT:AD:DP:GL:GQ 0/1:182,25:80:-33.47,-27.69,-302.15:57.82 +chr1 2611331 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=0;HaplotypeScore=171.01;MQ=28.57;MQ0=19;OQ=169.19;QD=1.00;SB=32.13 GT:AD:DP:GL:GQ 0/1:101,40:47:-34.37,-14.17,-141.57:99 +chr1 2611336 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=160;Dels=0.00;HRun=0;HaplotypeScore=142.89;MQ=27.04;MQ0=20;OQ=617.89;QD=3.86;SB=-201.64 GT:AD:DP:GL:GQ 0/1:32,126:45:-78.63,-13.56,-88.17:99 +chr1 2611359 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=160;Dels=0.00;HRun=2;HaplotypeScore=100.78;MQ=27.44;MQ0=19;OQ=605.72;QD=3.79;SB=-223.68 GT:AD:DP:GL:GQ 0/1:36,124:39:-75.62,-11.76,-86.35:99 +chr1 2611360 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=172;Dels=0.01;HRun=0;HaplotypeScore=100.05;MQ=27.08;MQ0=24;OQ=169.30;QD=0.98;SB=23.10 GT:AD:DP:GL:GQ 0/1:135,36:41:-32.56,-12.35,-112.95:99 +chr1 2611385 . A G 25.43 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=202;Dels=0.00;HRun=0;HaplotypeScore=141.90;MQ=28.13;MQ0=36;QD=0.13;SB=77.25 GT:AD:DP:GL:GQ 0/1:184,18:55:-22.41,-16.58,-186.56:58.25 +chr1 2611395 . C A 10.87 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=190;Dels=0.00;HRun=1;HaplotypeScore=214.46;MQ=28.47;MQ0=34;QD=0.06;SB=44.16 GT:AD:DP:GL:GQ 0/1:160,27:48:-18.79,-14.46,-145.75:43.33 +chr1 2611409 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=176;Dels=0.00;HRun=0;HaplotypeScore=170.63;MQ=30.96;MQ0=28;OQ=246.71;QD=1.40;SB=-63.23 GT:AD:DP:GL:GQ 0/1:66,90:51:-46.30,-18.34,-146.08:99 +chr1 2611417 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=201.92;MQ=31.46;MQ0=25;OQ=276.60;QD=1.55;SB=-61.04 GT:AD:DP:GL:GQ 0/1:50,88:59:-67.59,-36.64,-159.73:99 +chr1 2611440 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=180;Dels=0.00;HRun=0;HaplotypeScore=297.52;MQ=31.70;MQ0=24;OQ=229.57;QD=1.28;SB=65.18 GT:AD:DP:GL:GQ 0/1:152,22:68:-46.74,-20.49,-196.70:99 +chr1 2611441 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=175;Dels=0.00;HRun=4;HaplotypeScore=281.36;MQ=31.83;MQ0=24;OQ=677.61;QD=3.87;SB=-187.78 GT:AD:DP:GL:GQ 0/1:57,116:70:-92.13,-21.09,-155.28:99 +chr1 2611460 . G C 143.72 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=209;Dels=0.02;HRun=1;HaplotypeScore=206.53;MQ=28.72;MQ0=29;QD=0.69;SB=95.33 GT:AD:DP:GL:GQ 0/1:169,33:67:-37.89,-20.23,-223.47:99 +chr1 2611462 . G C 346.96 DPFilter;HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=0;HaplotypeScore=159.36;MQ=28.99;MQ0=26;QD=1.68;SB=95.35 GT:AD:DP:GL:GQ 0/1:176,30:73:-60.00,-22.02,-249.89:99 +chr1 2611473 . C A 226.87 DPFilter;HARD_TO_VALIDATE;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=0;HaplotypeScore=716.79;MQ=27.80;MQ0=23;QD=1.15;SB=98.33 GT:AD:DP:GL:GQ 0/1:167,28:68:-46.46,-20.49,-193.68:99 +chr1 2611481 . A C 47.15 DPFilter;HARD_TO_VALIDATE;Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=3;HaplotypeScore=376.14;MQ=26.76;MQ0=25;QD=0.22;SB=4.29 GT:AD:DP:GL:GQ 0/1:158,51:68:-32.16,-24.16,-211.95:79.99 +chr1 2611482 rs28657015 C T 493.48 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.03;HRun=0;HaplotypeScore=277.76;MQ=26.81;MQ0=24;QD=2.28;SB=-58.33 GT:AD:DP:GL:GQ 0/1:180,23:71:-73.42,-20.79,-178.37:99 +chr1 2611484 . G A 123.65 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=217;Dels=0.00;HRun=1;HaplotypeScore=257.24;MQ=26.43;MQ0=26;QD=0.57;SB=52.66 GT:AD:DP:GL:GQ 0/1:181,35:66:-35.53,-19.88,-208.25:99 +chr1 2611506 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=1;HaplotypeScore=227.39;MQ=23.92;MQ0=38;OQ=83.72;QD=0.34;SB=1.08 GT:AD:DP:GL:GQ 0/1:205,36:67:-31.84,-20.19,-209.30:99 +chr1 2611529 . G C 1369.67 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=198.19;MQ=24.21;MQ0=25;QD=7.40;SB=-595.38 GT:AD:DP:GL:GQ 0/1:36,136:57:-168.20,-27.95,-90.83:99 +chr1 2611531 . T A 49.73 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=1;HaplotypeScore=167.31;MQ=24.09;MQ0=26;QD=0.27;SB=30.12 GT:AD:DP:GL:GQ 0/1:175,9:48:-26.14,-17.88,-160.86:82.57 +chr1 2611537 . A C 10.75 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=1;HaplotypeScore=150.76;MQ=24.75;MQ0=25;QD=0.06;SB=49.53 GT:AD:DP:GL:GQ 0/1:160,17:47:-21.51,-17.19,-149.44:43.20 +chr1 2611551 . C A 34.16 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=166;Dels=0.02;HRun=1;HaplotypeScore=423.66;MQ=25.51;MQ0=20;QD=0.21;SB=47.16 GT:AD:DP:GL:GQ 0/1:139,17:37:-21.33,-14.63,-112.07:67 +chr1 2611559 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=150;Dels=0.01;HRun=3;HaplotypeScore=531.42;MQ=25.48;MQ0=17;OQ=388.67;QD=2.59;SB=-7.62 GT:AD:DP:GL:GQ 0/1:47,82:45:-90.78,-48.63,-105.70:99 +chr1 2611586 . G A 21.13 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=158;Dels=0.00;HRun=1;HaplotypeScore=127.50;MQ=28.93;MQ0=18;QD=0.13;SB=47.15 GT:AD:DP:GL:GQ 0/1:123,29:42:-18.05,-12.65,-132.34:53.94 +chr1 2611593 . C A 39.57 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=0;HaplotypeScore=189.22;MQ=30.35;MQ0=16;QD=0.29;SB=47.17 GT:AD:DP:GL:GQ 0/1:123,13:39:-18.99,-11.75,-120.10:72.41 +chr1 2611600 . T C 291.60 SnpCluster AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=2;HaplotypeScore=197.17;MQ=32.27;MQ0=10;QD=2.58;SB=-146.84 GT:AD:DP:GL:GQ 0/1:38,66:38:-47.43,-14.99,-100.79:99 +chr1 2611602 . C G 76.87 SnpCluster AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=173.17;MQ=32.76;MQ0=9;QD=0.68;SB=-63.17 GT:AD:DP:GL:GQ 0/1:81,31:39:-22.73,-11.76,-142.68:99 +chr1 2611613 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=122.16;MQ=34.85;MQ0=5;OQ=326.72;QD=4.08;SB=-171.57 GT:AD:DP:GL:GQ 0/1:20,59:33:-49.07,-13.11,-79.40:99 +chr1 2611623 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=114.07;MQ=31.99;MQ0=3;OQ=59.10;QD=0.57;SB=53.18 GT:AD:DP:GL:GQ 0/1:44,51:42:-30.56,-21.37,-135.55:91.94 +chr1 2611678 . C A 64.73 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=1;HaplotypeScore=80.70;MQ=27.19;MQ0=13;QD=0.45;SB=-53.00 GT:AD:DP:GL:GQ 0/1:121,21:50:-24.83,-15.07,-143.50:97.56 +chr1 2611679 . C T 18.94 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=0;HaplotypeScore=77.77;MQ=26.46;MQ0=13;QD=0.14;SB=-28.00 GT:AD:DP:GL:GQ 0/1:130,7:48:-19.64,-14.46,-152.87:51.72 +chr1 2611680 . C A 348.12 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=72.18;MQ=26.57;MQ0=13;QD=2.58;SB=-130.78 GT:AD:DP:GL:GQ 0/1:71,64:46:-51.95,-13.86,-109.26:99 +chr1 2611697 rs28420770 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.01;HRun=1;HaplotypeScore=63.25;MQ=30.55;MQ0=12;OQ=549.37;QD=5.97;SB=-271.47 GT:AD:DP:GL:GQ 0/1:70,21:28:-66.35,-8.13,-30.04:99 +chr1 2611699 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=39.05;MQ=32.12;MQ0=10;OQ=169.31;QD=2.23;SB=14.08 GT:AD:DP:GL:GQ 0/1:20,50:24:-27.45,-7.24,-73.47:99 +chr1 2611710 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=70.70;MQ=31.94;MQ0=10;OQ=120.36;QD=1.56;SB=14.06 GT:AD:DP:GL:GQ 0/1:29,48:25:-22.85,-7.53,-69.69:99 +chr1 2611716 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=60.36;MQ=32.04;MQ0=11;OQ=222.09;QD=2.71;SB=-31.85 GT:AD:DP:GL:GQ 0/1:24,55:26:-33.33,-7.83,-79.05:99 +chr1 2611761 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=2;HaplotypeScore=77.17;MQ=34.64;MQ0=9;OQ=73.97;QD=1.01;SB=-32.72 GT:AD:DP:GL:GQ 0/1:30,33:31:-23.41,-12.73,-88.75:99 +chr1 2611777 . A C 23.19 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=20.98;MQ=38.72;MQ0=5;QD=0.42;SB=23.10 GT:AD:DP:GL:GQ 0/1:24,30:28:-14.03,-8.43,-89.75:56.01 +chr1 2611805 . A G 44.82 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=14.04;MQ=39.70;MQ0=6;QD=0.79;SB=-36.77 GT:AD:DP:GL:GQ 0/1:29,28:32:-17.41,-9.64,-104.85:77.66 +chr1 2611822 . C T 55.46 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=121;Dels=0.00;HRun=0;HaplotypeScore=122.77;MQ=30.12;MQ0=10;QD=0.46;SB=-42.84 GT:AD:DP:GL:GQ 0/1:92,29:48:-23.31,-14.48,-136.72:88.30 +chr1 2611823 . G A 42.96 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=122.08;MQ=30.26;MQ0=10;QD=0.35;SB=5.54 GT:AD:DP:GL:GQ 0/1:91,15:51:-29.64,-22.06,-149.48:75.79 +chr1 2611827 . C G 117.16 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=127;Dels=0.00;HRun=1;HaplotypeScore=109.01;MQ=29.94;MQ0=10;QD=0.92;SB=-46.17 GT:AD:DP:GL:GQ 0/1:97,15:52:-50.99,-35.99,-189.94:99 +chr1 2611857 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=244;Dels=0.00;HRun=1;HaplotypeScore=130.70;MQ=25.34;MQ0=25;OQ=261.41;QD=1.07;SB=-55.24 GT:AD:DP:GL:GQ 0/1:221,22:85:-55.03,-25.61,-242.15:99 +chr1 2611880 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=242.50;MQ=25.49;MQ0=23;OQ=371.36;QD=1.47;SB=-110.03 GT:AD:DP:GL:GQ 0/1:223,22:91:-74.78,-34.36,-326.09:99 +chr1 2611909 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=0;HaplotypeScore=117.77;MQ=27.67;MQ0=16;OQ=1593.34;QD=8.80;SB=-695.72 GT:AD:DP:GL:GQ 0/1:25,155:74:-184.91,-22.29,-95.32:99 +chr1 2611913 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=162;Dels=0.01;HRun=0;HaplotypeScore=121.10;MQ=28.43;MQ0=16;OQ=688.73;QD=4.25;SB=-310.55 GT:AD:DP:GL:GQ 0/1:24,47:69:-160.80,-88.65,-165.59:99 +chr1 2611940 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=1;HaplotypeScore=46.12;MQ=30.62;MQ0=15;OQ=640.18;QD=4.61;SB=-181.43 GT:AD:DP:GL:GQ 0/1:50,89:56:-84.19,-16.88,-155.00:99 +chr1 2611948 . A C 23.15 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=138;Dels=0.00;HRun=1;HaplotypeScore=36.39;MQ=28.65;MQ0=12;QD=0.17;SB=47.17 GT:AD:DP:GL:GQ 0/1:116,20:55:-22.17,-16.57,-171.47:55.97 +chr1 2612014 rs28499205 G C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=56.64;MQ=32.76;MQ0=15;OQ=1145.21;QD=14.50;SB=-563.07 GT:AD:DP:GL:GQ 1/1:1,78:27:-118.11,-8.13,-0.01:81.27 +chr1 2612058 rs61765702 C T 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.00;HRun=0;HaplotypeScore=18.96;MQ=27.13;MQ0=31;OQ=323.91;QD=1.80;SB=-155.18 GT:AD:DP:GL:GQ 0/1:143,37:66:-55.56,-19.88,-179.35:99 +chr1 2612062 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=184;Dels=0.00;HRun=0;HaplotypeScore=39.83;MQ=27.44;MQ0=33;OQ=304.96;QD=1.66;SB=-159.14 GT:AD:DP:GL:GQ 0/1:147,37:67:-53.98,-20.20,-229.14:99 +chr1 2612081 rs61765703 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=136;Dels=0.01;HRun=2;HaplotypeScore=85.10;MQ=27.93;MQ0=25;OQ=1205.35;QD=8.86;SB=-216.92 GT:AD:DP:GL:GQ 0/1:19,114:53:-139.78,-15.97,-53.09:99 +chr1 2612085 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=1;HaplotypeScore=63.07;MQ=28.64;MQ0=22;OQ=1108.83;QD=8.66;SB=-225.89 GT:AD:DP:GL:GQ 0/1:16,110:51:-129.53,-15.36,-50.00:99 +chr1 2612107 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=161;Dels=0.00;HRun=1;HaplotypeScore=61.85;MQ=27.81;MQ0=21;OQ=276.90;QD=1.72;SB=-68.50 GT:AD:DP:GL:GQ 0/1:116,39:58:-48.45,-17.48,-165.18:99 +chr1 2612151 rs61765704 A C 24.50 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=129;Dels=0.02;HRun=0;HaplotypeScore=220.24;MQ=28.08;MQ0=15;QD=0.19;SB=6.59 GT:AD:DP:GL:GQ 0/1:44,80:28:-14.16,-8.43,-88.22:57.33 +chr1 2612161 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=149;Dels=0.05;HRun=2;HaplotypeScore=289.32;MQ=26.74;MQ0=14;OQ=154.71;QD=1.04;SB=-60.88 GT:AD:DP:GL:GQ 0/1:35,100:29:-27.20,-8.44,-77.78:99 +chr1 2612175 rs61765705 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=189;Dels=0.00;HRun=1;HaplotypeScore=208.27;MQ=26.09;MQ0=18;OQ=54.71;QD=0.29;SB=-8.07 GT:AD:DP:GL:GQ 0/1:131,51:39:-26.91,-18.15,-132.87:87.54 +chr1 2612187 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=211.77;MQ=24.98;MQ0=26;OQ=72.89;QD=0.35;SB=45.47 GT:AD:DP:GL:GQ 0/1:143,55:44:-28.75,-18.18,-125.97:99 +chr1 2612211 . C A 45.89 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=1;HaplotypeScore=262.96;MQ=25.29;MQ0=30;QD=0.22;SB=-5.55 GT:AD:DP:GL:GQ 0/1:190,13:50:-25.52,-17.65,-153.60:78.73 +chr1 2612261 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=1;HaplotypeScore=73.22;MQ=36.24;MQ0=2;OQ=156.42;QD=1.55;SB=-48.52 GT:AD:DP:GL:GQ 0/1:66,32:53:-34.90,-15.97,-147.29:99 +chr1 2612283 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=4;HaplotypeScore=43.06;MQ=38.47;MQ0=2;OQ=327.02;QD=4.74;SB=-23.62 GT:AD:DP:GL:GQ 0/1:32,34:36:-46.54,-10.55,-82.71:99 +chr1 2612309 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=19.73;MQ=36.93;MQ0=0;OQ=479.11;QD=9.39;SB=-112.96 GT:AD:DP:GL:GQ 0/1:16,33:31:-63.92,-12.72,-54.61:99 +chr1 2612321 rs58055515 A C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.06;HRun=2;HaplotypeScore=36.08;MQ=38.02;MQ0=0;OQ=654.82;QD=13.64;SB=-115.75 GT:AD:DP:GL:GQ 1/1:1,35:27:-89.55,-24.40,-20.49:39.17 +chr1 2612344 . C G 24.81 LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=2;HaplotypeScore=34.46;MQ=40.80;MQ0=2;QD=0.48;SB=-19.81 GT:AD:DP:GL:GQ 0/1:23,28:23:-12.71,-6.94,-79.49:57.63 +chr1 2612349 rs56814247 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=26.66;MQ=40.32;MQ0=2;OQ=741.43;QD=14.54;SB=-345.45 GT:AD:DP:GL:GQ 1/1:6,45:24:-77.75,-7.24,-0.02:72.17 +chr1 2612359 . A C 18.09 LowQual AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=26.16;MQ=43.64;MQ0=3;QD=0.33;SB=-28.97 GT:AD:DP:GL:GQ 0/1:34,20:31:-14.42,-9.34,-99.97:50.86 +chr1 2612360 . A C 30.50 LowQual AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=3;HaplotypeScore=20.17;MQ=44.05;MQ0=2;QD=0.58;SB=-0.42 GT:AD:DP:GL:GQ 0/1:26,25:28:-14.77,-8.43,-87.24:63.33 +chr1 2612401 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=42.26;MQ=44.22;MQ0=1;OQ=144.16;QD=2.72;SB=-18.17 GT:AD:DP:GL:GQ 0/1:29,20:34:-31.58,-13.88,-103.42:99 +chr1 2612402 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=41.27;MQ=43.87;MQ0=1;OQ=96.43;QD=1.85;SB=-29.80 GT:AD:DP:GL:GQ 0/1:26,21:30:-21.97,-9.04,-85.20:99 +chr1 2612447 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=39.94;MQ=46.94;MQ0=0;OQ=81.12;QD=1.66;SB=23.03 GT:AD:DP:GL:GQ 0/1:31,17:32:-23.40,-12.01,-88.55:99 +chr1 2612451 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=20.86;MQ=47.66;MQ0=0;OQ=53.68;QD=1.14;SB=26.08 GT:AD:DP:GL:GQ 0/1:30,14:32:-18.30,-9.65,-100.77:86.52 +chr1 2612461 . A C 44.60 LowQual AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=34.01;MQ=47.11;MQ0=0;QD=0.86;SB=-23.85 GT:AD:DP:GL:GQ 0/1:42,10:33:-17.68,-9.94,-101.23:77.43 +chr1 2612468 . C G 44.05 LowQual AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=46.41;MQ=45.54;MQ0=0;QD=0.76;SB=-1.30 GT:AD:DP:GL:GQ 0/1:51,7:35:-18.24,-10.55,-129.78:76.89 +chr1 2612500 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=0;HaplotypeScore=111.55;MQ=36.58;MQ0=2;OQ=75.18;QD=0.91;SB=-6.47 GT:AD:DP:GL:GQ 0/1:42,40:29:-19.55,-8.75,-75.63:99 +chr1 2612520 . C T 19.28 LowQual AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=133.17;MQ=33.82;MQ0=3;QD=0.19;SB=-16.60 GT:AD:DP:GL:GQ 0/1:87,13:36:-16.06,-10.85,-103.87:52.07 +chr1 2612521 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=3;HaplotypeScore=133.17;MQ=33.95;MQ0=3;OQ=122.65;QD=1.20;SB=-13.90 GT:AD:DP:GL:GQ 0/1:59,34:32:-39.02,-23.47,-101.66:99 +chr1 2612546 rs56822453 C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=145.71;MQ=34.54;MQ0=2;OQ=1448.77;QD=15.58;SB=-452.10 GT:AD:DP:GL:GQ 1/1:7,78:40:-172.07,-31.81,-23.61:81.95 +chr1 2612548 . A G 23.46 LowQual AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=0;HaplotypeScore=130.25;MQ=34.63;MQ0=2;QD=0.24;SB=-12.60 GT:AD:DP:GL:GQ 0/1:76,19:32:-15.27,-9.65,-107.66:56.27 +chr1 2612572 rs61765712 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=119.88;MQ=29.64;MQ0=12;OQ=136.28;QD=1.57;SB=-70.93 GT:AD:DP:GL:GQ 0/1:30,56:22:-23.54,-6.63,-51.28:99 +chr1 2612576 . C G 19.60 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=1;HaplotypeScore=117.65;MQ=28.19;MQ0=14;QD=0.19;SB=-14.55 GT:AD:DP:GL:GQ 0/1:68,14:25:-20.23,-14.99,-84.25:52.39 +chr1 2612600 . A C 31.76 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=4;HaplotypeScore=156.76;MQ=23.41;MQ0=28;QD=0.14;SB=30.15 GT:AD:DP:GL:GQ 0/1:163,45:61:-27.98,-21.52,-181.64:64.60 +chr1 2612627 . A C 39.29 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=243;Dels=0.00;HRun=0;HaplotypeScore=198.32;MQ=23.30;MQ0=41;QD=0.16;SB=-11.41 GT:AD:DP:GL:GQ 0/1:198,41:66:-27.09,-19.88,-204.81:72.12 +chr1 2612682 . A C 10.13 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=52.92;MQ=47.05;MQ0=0;QD=0.24;SB=14.06 GT:AD:DP:GL:GQ 0/1:27,14:23:-11.18,-6.93,-67.83:42.53 +chr1 2612696 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=17.87;MQ=44.37;MQ0=2;OQ=127.11;QD=2.08;SB=-25.83 GT:AD:DP:GL:GQ 0/1:32,29:31:-25.34,-9.35,-104.60:99 +chr1 2612737 rs61765713 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=31.73;MQ=37.37;MQ0=1;OQ=431.17;QD=5.01;SB=-153.88 GT:AD:DP:GL:GQ 0/1:41,45:46:-60.27,-13.87,-108.65:99 +chr1 2612767 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=55.42;MQ=39.20;MQ0=1;OQ=525.18;QD=6.48;SB=-145.82 GT:AD:DP:GL:GQ 0/1:30,49:46:-69.66,-13.86,-97.51:99 +chr1 2612773 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=50.07;MQ=38.87;MQ0=1;OQ=424.50;QD=5.31;SB=-154.37 GT:AD:DP:GL:GQ 0/1:53,27:45:-59.30,-13.57,-131.50:99 +chr1 2612799 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=27.45;MQ=41.43;MQ0=1;OQ=164.57;QD=2.70;SB=-62.57 GT:AD:DP:GL:GQ 0/1:27,34:35:-30.28,-10.54,-94.10:99 +chr1 2612844 rs55724072 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=94.30;MQ=38.07;MQ0=8;OQ=665.81;QD=9.12;SB=-251.98 GT:AD:DP:GL:GQ 0/1:45,26:28:-81.79,-11.92,-21.81:98.87 +chr1 2612950 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=215;Dels=0.00;HRun=0;HaplotypeScore=255.70;MQ=27.55;MQ0=15;OQ=78.72;QD=0.37;SB=19.51 GT:AD:DP:GL:GQ 0/1:145,61:50:-33.24,-22.08,-169.61:99 +chr1 2612958 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=205;Dels=0.05;HRun=2;HaplotypeScore=345.72;MQ=28.14;MQ0=11;OQ=268.77;QD=1.31;SB=-87.58 GT:AD:DP:GL:GQ 0/1:82,113:44:-43.44,-13.28,-132.37:99 +chr1 2612962 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=206;Dels=0.01;HRun=1;HaplotypeScore=293.73;MQ=28.22;MQ0=11;OQ=53.07;QD=0.26;SB=-7.29 GT:AD:DP:GL:GQ 0/1:160,36:46:-29.48,-20.89,-140.25:85.91 +chr1 2612982 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=165;Dels=0.00;HRun=0;HaplotypeScore=272.98;MQ=28.95;MQ0=11;OQ=81.29;QD=0.49;SB=23.09 GT:AD:DP:GL:GQ 0/1:43,117:27:-19.56,-8.14,-70.61:99 +chr1 2612988 rs28729890 C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=157;Dels=0.00;HRun=1;HaplotypeScore=282.08;MQ=29.13;MQ0=10;OQ=1088.24;QD=6.93;SB=-426.67 GT:AD:DP:GL:GQ 1/1:3,146:27:-116.69,-11.76,-4.28:74.86 +chr1 2613013 . G A 31.52 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=131;Dels=0.00;HRun=1;HaplotypeScore=164.33;MQ=32.03;MQ0=7;QD=0.24;SB=26.10 GT:AD:DP:GL:GQ 0/1:117,14:35:-16.98,-10.54,-112.15:64.35 +chr1 2613017 . T C 180.98 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=137.52;MQ=33.34;MQ0=7;QD=1.65;SB=26.11 GT:AD:DP:GL:GQ 0/1:27,81:34:-31.63,-10.24,-97.73:99 +chr1 2613018 rs28484972 G C 140.73 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=110;Dels=0.00;HRun=0;HaplotypeScore=137.35;MQ=33.34;MQ0=7;QD=1.28;SB=31.01 GT:AD:DP:GL:GQ 0/1:28,44:35:-37.27,-19.91,-118.50:99 +chr1 2613040 rs55713073 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=61.60;MQ=39.34;MQ0=3;OQ=876.14;QD=14.13;SB=-413.05 GT:AD:DP:GL:GQ 0/1:33,24:31:-100.24,-9.35,-30.73:99 +chr1 2613043 . T C 38.29 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=3;HaplotypeScore=55.65;MQ=43.83;MQ0=2;QD=0.78;SB=29.13 GT:AD:DP:GL:GQ 0/1:25,20:28:-15.55,-8.44,-93.33:71.12 +chr1 2613090 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=62.85;MQ=32.34;MQ0=20;OQ=113.77;QD=0.92;SB=20.02 GT:AD:DP:GL:GQ 0/1:89,34:35:-25.22,-10.56,-90.70:99 +chr1 2613132 . T C 17.83 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=135.62;MQ=34.15;MQ0=7;QD=0.19;SB=20.93 GT:AD:DP:GL:GQ 0/1:49,17:34:-18.39,-13.34,-109.40:50.59 +chr1 2613155 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=54.50;MQ=36.94;MQ0=5;OQ=56.13;QD=0.85;SB=-8.31 GT:AD:DP:GL:GQ 0/1:26,40:25:-16.44,-7.54,-66.14:88.97 +chr1 2613166 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=54;Dels=0.04;HRun=0;HaplotypeScore=39.25;MQ=40.07;MQ0=1;OQ=108.06;QD=2.00;SB=-13.35 GT:AD:DP:GL:GQ 0/1:25,27:25:-21.62,-7.53,-86.20:99 +chr1 2613178 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=39.82;MQ=40.42;MQ0=1;OQ=87.18;QD=1.53;SB=-9.45 GT:AD:DP:GL:GQ 0/1:38,18:28:-20.44,-8.44,-74.35:99 +chr1 2613186 rs28398452 A T 0.15 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=19.52;MQ=46.06;MQ0=0;OQ=818.22;QD=19.96;SB=-414.28 GT:AD:DP:GL:GQ 1/1:0,40:23:-85.41,-6.93,-0.01:69.21 +chr1 2613234 . C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=40.12;MQ=46.29;MQ0=1;OQ=1357.25;QD=31.56;SB=-584.52 GT:AD:DP:GL:GQ 1/1:1,41:32:-139.32,-9.64,-0.01:96.32 +chr1 2613318 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=61.23;MQ=29.57;MQ0=14;OQ=124.73;QD=1.48;SB=-14.36 GT:AD:DP:GL:GQ 0/1:67,16:36:-26.61,-10.86,-123.23:99 +chr1 2613323 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=0;HaplotypeScore=72.34;MQ=25.61;MQ0=20;OQ=95.66;QD=0.62;SB=33.80 GT:AD:DP:GL:GQ 0/1:133,12:61:-34.86,-22.01,-226.45:99 +chr1 2613370 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=400;Dels=0.00;HRun=0;HaplotypeScore=293.23;MQ=21.10;MQ0=61;OQ=714.05;QD=1.79;SB=-288.95 GT:AD:DP:GL:GQ 0/1:327,73:124:-112.05,-37.36,-344.59:99 +chr1 2613374 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=416;Dels=0.00;HRun=0;HaplotypeScore=328.46;MQ=20.95;MQ0=62;OQ=571.93;QD=1.37;SB=-114.36 GT:AD:DP:GL:GQ 0/1:288,118:123:-97.54,-37.07,-375.44:99 +chr1 2613385 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=437;Dels=0.00;HRun=0;HaplotypeScore=225.97;MQ=20.17;MQ0=68;OQ=628.49;QD=1.44;SB=-284.83 GT:AD:DP:GL:GQ 0/1:363,65:125:-113.05,-46.91,-348.87:99 +chr1 2613405 rs61765715 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=430;Dels=0.00;HRun=0;HaplotypeScore=214.90;MQ=20.78;MQ0=65;OQ=1559.54;QD=3.63;SB=-415.95 GT:AD:DP:GL:GQ 0/1:296,132:120:-195.39,-36.15,-225.88:99 +chr1 2613406 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=428;Dels=0.00;HRun=0;HaplotypeScore=190.35;MQ=20.81;MQ0=64;OQ=96.31;QD=0.23;SB=35.50 GT:AD:DP:GL:GQ 0/1:369,32:113:-77.37,-64.46,-359.74:99 +chr1 2613418 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=358;Dels=0.00;HRun=0;HaplotypeScore=49.55;MQ=21.34;MQ0=50;OQ=281.60;QD=0.79;SB=32.81 GT:AD:DP:GL:GQ 0/1:313,45:98:-60.98,-29.53,-359.08:99 +chr1 2613432 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=200;Dels=0.00;HRun=2;HaplotypeScore=59.86;MQ=23.20;MQ0=28;OQ=127.98;QD=0.64;SB=-77.60 GT:AD:DP:GL:GQ 0/1:175,24:60:-37.72,-21.64,-201.76:99 +chr1 2613443 rs61765716 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=4;HaplotypeScore=21.82;MQ=28.33;MQ0=15;OQ=129.32;QD=1.54;SB=2.14 GT:AD:DP:GL:GQ 0/1:37,47:28:-24.65,-8.44,-74.06:99 +chr1 2613523 rs61765738 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=4;HaplotypeScore=30.76;MQ=30.14;MQ0=9;OQ=85.37;QD=1.61;SB=5.05 GT:AD:DP:GL:GQ 0/1:23,13:17:-22.76,-10.94,-45.61:99 +chr1 2613566 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=71;Dels=0.04;HRun=3;HaplotypeScore=57.78;MQ=26.34;MQ0=13;OQ=54.80;QD=0.77;SB=8.05 GT:AD:DP:GL:GQ 0/1:32,29:23:-15.40,-6.63,-70.44:87.64 +chr1 2613630 . G A 0.07 PASS AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=13.24;MQ=22.14;MQ0=5;OQ=193.82;QD=10.20;SB=-82.32 GT:AD:DP:GL:GQ 1/1:2,17:6:-22.96,-1.81,-0.00:18.06 +chr1 2613635 . G A 0.05 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=13.88;MQ=20.75;MQ0=5;OQ=116.09;QD=7.26;SB=-82.32 GT:AD:DP:GL:GQ 1/1:1,15:4:-15.15,-1.21,-0.00:12.04 +chr1 2613646 . G C 10.99 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.07;HRun=2;HaplotypeScore=14.02;MQ=19.81;MQ0=4;QD=0.79;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,8:1:-4.35,-0.30,-0.00:1.76 +chr1 2613690 . T C 13.23 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=116.33;MQ=18.38;MQ0=8;QD=0.19;SB=-10.00 GT:AD:DP:GL:GQ 0/1:49,18:4:-5.79,-1.21,-8.34:45.86 +chr1 2613693 . G C 35.94 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=149.70;MQ=18.45;MQ0=8;QD=0.45;SB=-10.00 GT:AD:DP:GL:GQ 0/1:76,3:6:-8.69,-1.81,-15.69:68.78 +chr1 2613698 . T G 15.64 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=2;HaplotypeScore=190.59;MQ=18.98;MQ0=9;QD=0.16;SB=-10.00 GT:AD:DP:GL:GQ 0/1:64,7:8:-12.71,-7.87,-20.94:48.35 +chr1 2613700 . G A 196.12 SnpCluster AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=236.20;MQ=18.98;MQ0=9;QD=2.06;SB=-10.00 GT:AD:DP:GL:GQ 0/1:6,83:8:-25.29,-2.41,-3.47:10.61 +chr1 2613710 . G A 290.78 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=258.37;MQ=18.71;MQ0=19;QD=1.88;SB=-45.65 GT:AD:DP:GL:GQ 0/1:71,77:15:-43.35,-10.99,-17.24:62.53 +chr1 2613712 . A G 19.12 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=162;Dels=0.00;HRun=1;HaplotypeScore=303.47;MQ=18.88;MQ0=19;QD=0.12;SB=-3.98 GT:AD:DP:GL:GQ 0/1:153,6:17:-10.32,-5.13,-49.10:51.90 +chr1 2613717 . C G 26.91 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=408.47;MQ=18.72;MQ0=23;QD=0.14;SB=-6.99 GT:AD:DP:GL:GQ 0/1:167,10:18:-16.44,-10.47,-59.87:59.74 +chr1 2613725 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=210;Dels=0.00;HRun=0;HaplotypeScore=344.41;MQ=18.80;MQ0=26;OQ=51.69;QD=0.25;SB=-6.99 GT:AD:DP:GL:GQ 0/1:188,19:21:-17.15,-8.70,-57.87:84.53 +chr1 2613732 . A C 62.04 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=212;Dels=0.00;HRun=0;HaplotypeScore=339.87;MQ=19.08;MQ0=26;QD=0.29;SB=-6.99 GT:AD:DP:GL:GQ 0/1:184,21:14:-13.71,-4.22,-32.30:94.88 +chr1 2613741 . C T 167.14 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=432.19;MQ=19.10;MQ0=22;QD=0.81;SB=-10.00 GT:AD:DP:GL:GQ 0/1:175,24:13:-27.15,-7.15,-25.74:99 +chr1 2613742 . T A 554.18 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=437.29;MQ=19.15;MQ0=21;QD=2.73;SB=-10.00 GT:AD:DP:GL:GQ 1/1:10,159:27:-96.09,-42.87,-37.09:57.79 +chr1 2613744 . C T 234.43 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=208;Dels=0.00;HRun=0;HaplotypeScore=584.09;MQ=19.37;MQ0=21;QD=1.13;SB=-10.00 GT:AD:DP:GL:GQ 0/1:171,26:22:-36.59,-9.87,-49.51:99 +chr1 2613745 . C G 76.87 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=0;HaplotypeScore=579.63;MQ=19.38;MQ0=20;QD=0.37;SB=-10.00 GT:AD:DP:GL:GQ 0/1:148,19:15:-15.49,-4.52,-49.92:99 +chr1 2613750 . G A 306.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=658.57;MQ=19.32;MQ0=20;QD=1.48;SB=-7.01 GT:AD:DP:GL:GQ 0/1:99,104:19:-39.62,-5.73,-26.69:99 +chr1 2613754 . C A 11.17 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=223;Dels=0.00;HRun=1;HaplotypeScore=578.78;MQ=19.04;MQ0=24;QD=0.05;SB=-7.00 GT:AD:DP:GL:GQ 0/1:199,19:23:-11.29,-6.93,-65.57:43.66 +chr1 2613765 . C A 112.66 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=0;HaplotypeScore=358.32;MQ=18.80;MQ0=30;QD=0.49;SB=-6.99 GT:AD:DP:GL:GQ 0/1:192,30:26:-22.38,-7.83,-66.37:99 +chr1 2613766 . C G 145.08 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=229;Dels=0.00;HRun=0;HaplotypeScore=340.83;MQ=18.60;MQ0=30;QD=0.63;SB=-3.99 GT:AD:DP:GL:GQ 0/1:197,20:34:-28.04,-10.25,-119.31:99 +chr1 2613770 . T C 33.51 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=219;Dels=0.00;HRun=0;HaplotypeScore=286.65;MQ=18.56;MQ0=29;QD=0.15;SB=-3.99 GT:AD:DP:GL:GQ 0/1:176,33:38:-18.09,-11.45,-126.83:66.35 +chr1 2613772 . A G 57.20 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=1;HaplotypeScore=261.18;MQ=18.59;MQ0=29;QD=0.26;SB=-0.97 GT:AD:DP:GL:GQ 0/1:199,13:41:-24.12,-15.12,-140.12:90.03 +chr1 2613796 . G C 177.04 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=135;Dels=0.04;HRun=2;HaplotypeScore=330.87;MQ=18.33;MQ0=22;QD=1.31;SB=-45.45 GT:AD:DP:GL:GQ 0/1:71,48:21:-34.21,-13.22,-61.82:99 +chr1 2613800 . G A 69.22 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=111;Dels=0.04;HRun=0;HaplotypeScore=218.43;MQ=17.88;MQ0=19;QD=0.62;SB=-7.00 GT:AD:DP:GL:GQ 0/1:92,15:13:-14.13,-3.92,-31.45:99 +chr1 2613801 . C G 13.55 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=246.51;MQ=18.17;MQ0=17;QD=0.12;SB=-7.00 GT:AD:DP:GL:GQ 0/1:104,4:15:-12.67,-8.05,-55.30:46.19 +chr1 2613803 . C A 151.29 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=1;HaplotypeScore=241.51;MQ=18.66;MQ0=17;QD=1.36;SB=-3.98 GT:AD:DP:GL:GQ 0/1:89,19:17:-27.02,-8.61,-39.19:99 +chr1 2613805 . C T 87.71 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=0;HaplotypeScore=208.83;MQ=18.81;MQ0=15;QD=0.80;SB=-0.98 GT:AD:DP:GL:GQ 0/1:93,15:13:-15.97,-3.92,-32.68:99 +chr1 2613807 . C T 57.07 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=165.36;MQ=18.87;MQ0=15;QD=0.53;SB=-3.99 GT:AD:DP:GL:GQ 0/1:93,9:11:-12.30,-3.31,-28.01:89.90 +chr1 2613812 . G A 29.24 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=106.13;MQ=18.30;MQ0=14;QD=0.32;SB=-3.99 GT:AD:DP:GL:GQ 0/1:75,16:5:-7.71,-1.51,-10.06:62.07 +chr1 2613813 . T C 74.94 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=91.21;MQ=18.35;MQ0=14;QD=0.88;SB=-6.99 GT:AD:DP:GL:GQ 0/1:16,66:5:-12.29,-1.51,-3.76:22.52 +chr1 2613826 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=36.04;MQ=20.56;MQ0=13;OQ=192.78;QD=2.30;SB=-28.63 GT:AD:DP:GL:GQ 0/1:21,57:13:-29.99,-7.43,-22.77:99 +chr1 2613831 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=1;HaplotypeScore=23.92;MQ=20.73;MQ0=14;OQ=180.38;QD=2.20;SB=-29.94 GT:AD:DP:GL:GQ 0/1:21,61:13:-25.24,-3.92,-19.14:99 +chr1 2613859 . G T 41.43 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=24.92;MQ=20.48;MQ0=13;QD=0.62;SB=-43.38 GT:AD:DP:GL:GQ 0/1:19,47:11:-10.74,-3.32,-20.71:74.26 +chr1 2613869 rs28391329 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=60.53;MQ=21.20;MQ0=15;OQ=293.59;QD=2.94;SB=-0.98 GT:AD:DP:GL:GQ 0/1:82,18:19:-38.38,-5.73,-37.90:99 +chr1 2613889 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=72.75;MQ=25.64;MQ0=15;OQ=180.19;QD=1.96;SB=-114.68 GT:AD:DP:GL:GQ 0/1:18,61:28:-47.05,-25.75,-76.38:99 +chr1 2613903 rs11486068 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=48.68;MQ=24.40;MQ0=19;OQ=50.76;QD=0.51;SB=-13.14 GT:AD:DP:GL:GQ 0/1:40,15:30:-30.07,-21.71,-94.96:83.60 +chr1 2613959 rs61765741 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=0;HaplotypeScore=30.66;MQ=19.75;MQ0=50;OQ=129.32;QD=0.85;SB=-3.99 GT:AD:DP:GL:GQ 0/1:135,11:45:-36.43,-20.22,-129.55:99 +chr1 2613977 rs61765742 T A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=20.51;MQ=18.10;MQ0=36;OQ=631.54;QD=6.19;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,87:32:-76.08,-9.64,-40.58:99 +chr1 2614061 . C G 47.32 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=9.70;MQ=18.60;MQ0=18;QD=1.05;SB=-42.45 GT:AD:DP:GL:GQ 0/1:29,16:12:-11.64,-3.62,-36.27:80.16 +chr1 2614087 rs61765744 A C 20.16 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=3;HaplotypeScore=20.71;MQ=12.14;MQ0=19;QD=0.63;SB=-6.99 GT:AD:DP:GL:GQ 0/1:25,7:6:-7.10,-1.81,-13.92:52.96 +chr1 2614090 . A G 19.51 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=1;HaplotypeScore=20.91;MQ=12.88;MQ0=18;QD=0.59;SB=-6.99 GT:AD:DP:GL:GQ 0/1:21,12:7:-7.34,-2.11,-20.39:52.30 +chr1 2614091 . G C 37.94 HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=21.91;MQ=12.37;MQ0=20;QD=1.05;SB=-6.99 GT:AD:DP:GL:GQ 0/1:28,8:7:-9.19,-2.11,-21.58:70.77 +chr1 2614114 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=32.88;MQ=18.47;MQ0=36;OQ=121.42;QD=1.52;SB=-36.64 GT:AD:DP:GL:GQ 0/1:36,44:20:-21.46,-6.03,-44.98:99 +chr1 2614128 . T C 13.34 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=4;HaplotypeScore=47.41;MQ=18.72;MQ0=40;QD=0.11;SB=-2.29 GT:AD:DP:GL:GQ 0/1:78,34:26:-19.39,-14.79,-91.44:45.97 +chr1 2614209 . G A 41.24 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=1;HaplotypeScore=24.29;MQ=22.02;MQ0=31;QD=0.45;SB=-24.59 GT:AD:DP:GL:GQ 0/1:55,36:29:-16.14,-8.74,-87.91:74.08 +chr1 2614364 rs28730517 A C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=28.46;MQ=18.26;MQ0=16;OQ=311.67;QD=6.23;SB=-151.28 GT:AD:DP:GL:GQ 1/1:14,32:12:-37.44,-3.62,-2.80:8.16 +chr1 2614590 rs28497985 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=34.12;MQ=28.69;MQ0=18;OQ=755.20;QD=6.74;SB=-383.20 GT:AD:DP:GL:GQ 0/1:87,25:65:-98.40,-19.59,-181.93:99 +chr1 2614771 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=1;HaplotypeScore=33.03;MQ=8.84;MQ0=54;OQ=63.99;QD=0.94;SB=-10.00 GT:AD:DP:GL:GQ 0/1:54,14:6:-11.49,-1.81,-12.10:96.82 +chr1 2614794 . A C 36.23 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=12.63;MQ=15.22;MQ0=54;QD=0.39;SB=8.03 GT:AD:DP:GL:GQ 0/1:56,38:25:-14.44,-7.53,-71.85:69.07 +chr1 2614835 rs61765748 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=146;Dels=0.00;HRun=0;HaplotypeScore=67.43;MQ=23.43;MQ0=43;OQ=134.71;QD=0.92;SB=83.23 GT:AD:DP:GL:GQ 0/1:105,39:61:-35.15,-18.40,-166.15:99 +chr1 2615014 . A G 45.47 PASS AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=21.27;MQ0=3;OQ=106.85;QD=8.90;SB=-34.66 GT:AD:DP:GL:GQ 1/1:0,12:5:-14.25,-1.51,-0.01:15.01 +chr1 2615159 . C A 49.14 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=220;Dels=0.00;HRun=2;HaplotypeScore=142.59;MQ=8.79;MQ0=169;QD=0.22;SB=-7.86 GT:AD:DP:GL:GQ 0/1:185,31:17:-13.32,-5.12,-43.12:81.98 +chr1 2615230 . C G 11.72 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=6.15;MQ=11.52;MQ0=52;QD=0.14;SB=-26.39 GT:AD:DP:GL:GQ 0/1:72,12:14:-8.65,-4.23,-47.78:44.25 +chr1 2615372 . G A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=29.65;MQ=17.03;MQ0=60;OQ=691.36;QD=8.13;SB=-292.88 GT:AD:DP:GL:GQ 1/1:59,24:18:-72.73,-5.42,-0.01:54.18 +chr1 2615442 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=52.99;MQ=12.22;MQ0=96;OQ=368.66;QD=2.38;SB=-99.96 GT:AD:DP:GL:GQ 0/1:30,125:25:-47.68,-7.53,-41.84:99 +chr1 2615466 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=61.50;MQ=14.17;MQ0=69;OQ=112.35;QD=0.77;SB=-18.60 GT:AD:DP:GL:GQ 0/1:116,29:31:-23.86,-9.34,-81.69:99 +chr1 2615470 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=0;HaplotypeScore=63.31;MQ=14.07;MQ0=68;OQ=351.94;QD=2.53;SB=-90.74 GT:AD:DP:GL:GQ 0/1:65,72:34:-48.72,-10.24,-70.14:99 +chr1 2615502 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=32.33;MQ=16.10;MQ0=38;OQ=288.56;QD=3.65;SB=2.03 GT:AD:DP:GL:GQ 0/1:49,30:24:-39.38,-7.24,-59.32:99 +chr1 2615515 . T G 27.54 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=32.70;MQ=13.65;MQ0=43;QD=0.37;SB=-0.98 GT:AD:DP:GL:GQ 0/1:31,13:15:-18.30,-12.26,-45.52:60.37 +chr1 2615553 . G A 21.44 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=1;HaplotypeScore=33.08;MQ=9.60;MQ0=74;QD=0.23;SB=-3.99 GT:AD:DP:GL:GQ 0/1:70,24:9:-8.14,-2.71,-26.22:54.25 +chr1 2615563 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=52.83;MQ=8.09;MQ0=76;OQ=64.78;QD=0.70;SB=-10.00 GT:AD:DP:GL:GQ 0/1:82,10:5:-11.27,-1.51,-6.24:47.31 +chr1 2615689 . T C 30.94 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=62.56;MQ=10.13;MQ0=88;QD=0.28;SB=-3.98 GT:AD:DP:GL:GQ 0/1:18,89:9:-9.09,-2.71,-22.98:63.77 +chr1 2615717 rs61765669 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=37.80;MQ=10.99;MQ0=80;OQ=103.09;QD=0.95;SB=-3.99 GT:AD:DP:GL:GQ 0/1:26,83:10:-16.61,-3.01,-17.76:99 +chr1 2615757 . C A 39.74 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=1;HaplotypeScore=30.17;MQ=13.18;MQ0=60;QD=0.43;SB=0.17 GT:AD:DP:GL:GQ 0/1:71,20:17:-15.95,-8.69,-48.17:72.57 +chr1 2615837 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=39.99;MQ=26.86;MQ0=21;OQ=73.19;QD=1.33;SB=-36.22 GT:AD:DP:GL:GQ 0/1:29,26:20:-16.63,-6.03,-56.46:99 +chr1 2615892 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=3;HaplotypeScore=44.02;MQ=30.58;MQ0=2;OQ=63.96;QD=1.12;SB=26.10 GT:AD:DP:GL:GQ 0/1:25,32:26:-17.51,-7.83,-73.92:96.79 +chr1 2615945 rs28619423 T C 0.80 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=8.32;MQ=22.59;MQ0=1;OQ=99.94;QD=5.26;SB=-76.91 GT:AD:DP:GL:GQ 1/1:3,15:4:-13.53,-1.21,-0.00:12.03 +chr1 2615949 rs28373809 G A 10.26 LowQual AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=9.32;MQ=19.47;MQ0=1;QD=0.68;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,14:1:-4.27,-0.30,-0.00:1.76 +chr1 2615990 . C G 0.11 PASS AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=8.97;MQ=20.31;MQ0=1;OQ=58.76;QD=6.53;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:2:-9.28,-0.60,-0.00:6.02 +chr1 2615997 . G A 36.46 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=29.63;MQ=20.63;MQ0=6;QD=1.35;SB=-7.00 GT:AD:DP:GL:GQ 0/1:18,9:5:-8.44,-1.51,-10.16:69.30 +chr1 2616009 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=2;HaplotypeScore=37.74;MQ=29.64;MQ0=6;OQ=112.90;QD=3.53;SB=-3.99 GT:AD:DP:GL:GQ 0/1:15,17:12:-18.19,-3.62,-24.59:99 +chr1 2616012 . A C 43.77 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=39.70;MQ=31.56;MQ0=5;QD=1.41;SB=-0.98 GT:AD:DP:GL:GQ 0/1:13,18:11:-10.97,-3.31,-27.78:76.61 +chr1 2616021 . C A 30.19 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=71.42;MQ=30.54;MQ0=5;QD=0.70;SB=-0.98 GT:AD:DP:GL:GQ 0/1:37,6:16:-11.12,-4.82,-46.67:63.02 +chr1 2616048 . A C 104.33 Indel AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=256.69;MQ=33.48;MQ0=5;QD=1.53;SB=-0.98 GT:AD:DP:GL:GQ 0/1:26,38:27:-21.85,-8.13,-76.79:99 +chr1 2616053 . A C 36.21 Indel;LowQual AC=1;AF=0.50;AN=2;DP=80;Dels=0.06;HRun=3;HaplotypeScore=159.99;MQ=31.20;MQ0=8;QD=0.45;SB=-3.99 GT:AD:DP:GL:GQ 0/1:43,32:27:-15.04,-8.13,-81.51:69.04 +chr1 2616066 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=127.16;MQ=28.37;MQ0=17;OQ=116.17;QD=0.90;SB=11.03 GT:AD:DP:GL:GQ 0/1:64,41:40:-43.16,-28.26,-112.08:99 +chr1 2616091 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=152;Dels=0.02;HRun=3;HaplotypeScore=245.31;MQ=26.01;MQ0=24;OQ=74.30;QD=0.49;SB=8.05 GT:AD:DP:GL:GQ 0/1:77,30:40:-32.83,-22.11,-117.91:99 +chr1 2616098 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=238.65;MQ=25.86;MQ0=23;OQ=203.33;QD=1.36;SB=8.03 GT:AD:DP:GL:GQ 0/1:83,65:39:-35.37,-11.76,-97.26:99 +chr1 2616121 rs28707614 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=1;HaplotypeScore=348.16;MQ=25.38;MQ0=21;OQ=754.79;QD=6.92;SB=-132.69 GT:AD:DP:GL:GQ 0/1:14,95:27:-86.90,-8.14,-12.11:39.77 +chr1 2616201 rs28495110 G T 0.10 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=18.82;MQ=45.96;MQ0=6;OQ=1088.68;QD=25.92;SB=-422.58 GT:AD:DP:GL:GQ 1/1:8,34:31:-112.47,-9.34,-0.01:93.25 +chr1 2616235 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=22.81;MQ=34.27;MQ0=9;OQ=189.73;QD=2.67;SB=-88.83 GT:AD:DP:GL:GQ 0/1:28,43:31:-31.59,-9.34,-82.55:99 +chr1 2616250 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=198;Dels=0.00;HRun=1;HaplotypeScore=98.35;MQ=24.83;MQ0=26;OQ=53.95;QD=0.27;SB=-52.26 GT:AD:DP:GL:GQ 0/1:175,16:77:-39.01,-30.33,-235.94:86.79 +chr1 2616284 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=316;Dels=0.00;HRun=0;HaplotypeScore=207.75;MQ=22.41;MQ0=34;OQ=472.89;QD=1.50;SB=-261.05 GT:AD:DP:GL:GQ 0/1:280,35:108:-83.11,-32.54,-299.84:99 +chr1 2616291 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=0;HaplotypeScore=168.73;MQ=22.17;MQ0=35;OQ=503.17;QD=1.63;SB=-147.25 GT:AD:DP:GL:GQ 0/1:228,77:110:-86.74,-33.14,-306.67:99 +chr1 2616303 rs61765755 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=285;Dels=0.00;HRun=0;HaplotypeScore=48.79;MQ=22.14;MQ0=36;OQ=3893.80;QD=13.66;SB=-1294.80 GT:AD:DP:GL:GQ 0/1:13,240:102:-388.38,-54.71,-62.45:77.36 +chr1 2616333 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=234;Dels=0.00;HRun=0;HaplotypeScore=268.36;MQ=23.38;MQ0=29;OQ=127.30;QD=0.54;SB=-30.73 GT:AD:DP:GL:GQ 0/1:215,16:95:-44.63,-28.62,-299.60:99 +chr1 2616354 rs7544898 A C 1854.66 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=113;Dels=0.00;HRun=1;HaplotypeScore=61.29;MQ=28.89;MQ0=15;QD=16.41;SB=-484.04 GT:AD:DP:GL:GQ 1/1:2,105:53:-193.02,-19.43,-3.97:99 +chr1 2616358 . A G 865.25 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=1;HaplotypeScore=46.74;MQ=30.83;MQ0=11;QD=8.83;SB=-6.56 GT:AD:DP:GL:GQ 0/1:29,69:51:-105.17,-15.36,-93.21:99 +chr1 2616363 . G C 842.15 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=1;HaplotypeScore=46.38;MQ=31.26;MQ0=12;QD=8.68;SB=-14.79 GT:AD:DP:GL:GQ 0/1:55,42:53:-103.48,-15.98,-115.82:99 +chr1 2616398 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=48.31;MQ=34.63;MQ0=12;OQ=554.46;QD=5.84;SB=10.29 GT:AD:DP:GL:GQ 0/1:66,29:54:-75.00,-16.28,-154.28:99 +chr1 2616612 . G C 20.97 LowQual AC=1;AF=0.50;AN=2;DP=70;Dels=0.01;HRun=0;HaplotypeScore=165.26;MQ=30.37;MQ0=2;QD=0.30;SB=-32.74 GT:AD:DP:GL:GQ 0/1:19,45:24:-19.94,-14.57,-91.68:53.77 +chr1 2616615 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=3;HaplotypeScore=70.16;MQ=28.36;MQ0=2;OQ=89.21;QD=1.29;SB=-14.35 GT:AD:DP:GL:GQ 0/1:26,38:19:-17.94,-5.74,-58.45:99 +chr1 2616647 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=0;HaplotypeScore=217.54;MQ=24.00;MQ0=30;OQ=94.92;QD=0.69;SB=35.11 GT:AD:DP:GL:GQ 0/1:84,43:37:-23.93,-11.16,-103.88:99 +chr1 2616654 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=1;HaplotypeScore=223.04;MQ=23.83;MQ0=42;OQ=359.87;QD=1.99;SB=35.13 GT:AD:DP:GL:GQ 0/1:140,35:44:-52.54,-13.27,-92.39:99 +chr1 2616670 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=198;Dels=0.00;HRun=0;HaplotypeScore=299.99;MQ=23.86;MQ0=44;OQ=60.86;QD=0.31;SB=35.11 GT:AD:DP:GL:GQ 0/1:127,67:50:-24.46,-15.09,-137.52:93.69 +chr1 2616692 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=0;HaplotypeScore=231.37;MQ=26.06;MQ0=26;OQ=91.62;QD=0.55;SB=35.13 GT:AD:DP:GL:GQ 0/1:91,73:56:-32.64,-20.19,-183.88:99 +chr1 2616713 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=98.28;MQ=31.06;MQ0=12;OQ=565.06;QD=6.81;SB=-40.25 GT:AD:DP:GL:GQ 0/1:27,50:40:-78.76,-18.97,-82.14:99 +chr1 2616803 . G C 11.63 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=76;Dels=0.01;HRun=0;HaplotypeScore=115.33;MQ=32.59;MQ0=10;QD=0.15;SB=23.09 GT:AD:DP:GL:GQ 0/1:27,42:23:-11.36,-6.95,-79.45:44.16 +chr1 2616826 . T C 18.72 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=39.74;MQ=39.24;MQ0=2;QD=0.38;SB=20.09 GT:AD:DP:GL:GQ 0/1:24,24:22:-11.78,-6.63,-68.52:51.50 +chr1 2616954 rs28486014 C A 1246.57 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=172;Dels=0.00;HRun=0;HaplotypeScore=118.85;MQ=19.01;MQ0=19;QD=7.25;SB=-604.12 GT:AD:DP:GL:GQ 1/1:2,165:36:-131.25,-13.77,-3.01:99 +chr1 2616962 . A G 25.32 DPFilter;HARD_TO_VALIDATE;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=218;Dels=0.00;HRun=0;HaplotypeScore=150.59;MQ=18.32;MQ0=25;QD=0.12;SB=17.48 GT:AD:DP:GL:GQ 0/1:179,39:39:-17.57,-11.75,-132.90:58.14 +chr1 2616963 . C G 90.14 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=0;HaplotypeScore=167.60;MQ=18.42;MQ0=25;QD=0.41;SB=8.17 GT:AD:DP:GL:GQ 0/1:182,34:40:-27.79,-15.49,-139.11:99 +chr1 2616976 . C A 13.99 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=267;Dels=0.00;HRun=0;HaplotypeScore=283.46;MQ=18.62;MQ0=35;QD=0.05;SB=55.93 GT:AD:DP:GL:GQ 0/1:236,26:51:-20.03,-15.36,-160.20:46.65 +chr1 2616982 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=0;HaplotypeScore=251.51;MQ=19.64;MQ0=37;OQ=486.76;QD=1.74;SB=8.99 GT:AD:DP:GL:GQ 0/1:187,73:54:-71.97,-20.01,-131.66:99 +chr1 2617013 . A C 16.86 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=5;HaplotypeScore=227.22;MQ=22.36;MQ0=34;QD=0.07;SB=14.07 GT:AD:DP:GL:GQ 0/1:208,22:59:-25.00,-20.04,-187.42:49.60 +chr1 2617015 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=222;Dels=0.00;HRun=0;HaplotypeScore=200.07;MQ=22.66;MQ0=33;OQ=161.89;QD=0.73;SB=20.10 GT:AD:DP:GL:GQ 0/1:186,27:59:-43.12,-23.65,-203.21:99 +chr1 2617028 rs61765757 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=178;Dels=0.00;HRun=0;HaplotypeScore=111.43;MQ=24.75;MQ0=28;OQ=1236.03;QD=6.94;SB=-23.31 GT:AD:DP:GL:GQ 0/1:36,141:55:-143.45,-16.57,-61.22:99 +chr1 2617033 rs61765759 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=173;Dels=0.00;HRun=0;HaplotypeScore=123.68;MQ=24.76;MQ0=29;OQ=945.67;QD=5.47;SB=-60.88 GT:AD:DP:GL:GQ 0/1:19,129:49:-112.61,-14.76,-62.28:99 +chr1 2617058 rs28585375 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=236;Dels=0.00;HRun=0;HaplotypeScore=112.06;MQ=22.97;MQ0=54;OQ=357.80;QD=1.52;SB=-120.52 GT:AD:DP:GL:GQ 0/1:214,20:72:-60.76,-21.69,-192.59:99 +chr1 2617101 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=207;Dels=0.00;HRun=1;HaplotypeScore=89.01;MQ=23.73;MQ0=48;OQ=1884.44;QD=9.10;SB=-387.68 GT:AD:DP:GL:GQ 0/1:34,172:76:-214.63,-22.90,-42.31:99 +chr1 2617123 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=48.50;MQ=26.08;MQ0=56;OQ=129.18;QD=0.64;SB=-72.20 GT:AD:DP:GL:GQ 0/1:185,17:80:-40.33,-24.13,-284.57:99 +chr1 2617151 . G C 42.86 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=2;HaplotypeScore=97.11;MQ=23.22;MQ0=69;QD=0.22;SB=-10.77 GT:AD:DP:GL:GQ 0/1:167,21:55:-24.18,-16.61,-193.30:75.70 +chr1 2617160 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=181;Dels=0.00;HRun=1;HaplotypeScore=68.35;MQ=20.95;MQ0=76;OQ=103.39;QD=0.57;SB=17.08 GT:AD:DP:GL:GQ 0/1:148,32:50:-28.69,-15.07,-157.59:99 +chr1 2617178 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.01;HRun=4;HaplotypeScore=67.98;MQ=19.71;MQ0=69;OQ=224.46;QD=1.59;SB=-23.83 GT:AD:DP:GL:GQ 0/1:56,82:32:-35.39,-9.66,-90.46:99 +chr1 2617216 . T C 14.18 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=2;HaplotypeScore=54.33;MQ=16.92;MQ0=58;QD=0.13;SB=5.04 GT:AD:DP:GL:GQ 0/1:54,55:21:-11.01,-6.33,-70.16:46.85 +chr1 2617218 . C G 13.85 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=0;HaplotypeScore=69.57;MQ=15.97;MQ0=58;QD=0.13;SB=5.05 GT:AD:DP:GL:GQ 0/1:87,20:21:-10.98,-6.33,-76.68:46.51 +chr1 2617261 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=41.53;MQ=20.71;MQ0=16;OQ=109.26;QD=1.79;SB=-48.91 GT:AD:DP:GL:GQ 0/1:26,35:19:-19.93,-5.73,-46.91:99 +chr1 2617273 rs61466658 T C 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=31.65;MQ=19.33;MQ0=33;OQ=744.68;QD=8.97;SB=-307.99 GT:AD:DP:GL:GQ 1/1:6,73:24:-80.83,-7.23,-2.78:44.58 +chr1 2617320 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=383;Dels=0.00;HRun=2;HaplotypeScore=179.89;MQ=20.12;MQ0=69;OQ=511.87;QD=1.34;SB=-192.93 GT:AD:DP:GL:GQ 0/1:271,102:88:-80.98,-26.51,-240.14:99 +chr1 2617333 . A C 189.16 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=412;Dels=0.00;HRun=1;HaplotypeScore=324.51;MQ=20.25;MQ0=68;QD=0.46;SB=-46.42 GT:AD:DP:GL:GQ 0/1:362,48:102:-52.93,-30.73,-310.85:99 +chr1 2617334 . C T 347.52 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=413;Dels=0.00;HRun=0;HaplotypeScore=315.80;MQ=20.22;MQ0=68;QD=0.84;SB=-93.66 GT:AD:DP:GL:GQ 0/1:367,35:98:-67.59,-29.55,-258.47:99 +chr1 2617338 . C G 222.34 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=432;Dels=0.00;HRun=0;HaplotypeScore=396.78;MQ=20.69;MQ0=66;QD=0.51;SB=19.38 GT:AD:DP:GL:GQ 0/1:381,42:103:-66.44,-40.92,-386.05:99 +chr1 2617341 . G T 154.66 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=435;Dels=0.00;HRun=1;HaplotypeScore=393.28;MQ=20.73;MQ0=66;QD=0.36;SB=-27.31 GT:AD:DP:GL:GQ 0/1:377,44:114:-56.17,-37.42,-341.25:99 +chr1 2617354 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=456;Dels=0.00;HRun=0;HaplotypeScore=284.18;MQ=21.50;MQ0=65;OQ=410.45;QD=0.90;SB=-157.97 GT:AD:DP:GL:GQ 0/1:367,88:128:-86.24,-41.91,-394.71:99 +chr1 2617375 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=397;Dels=0.00;HRun=0;HaplotypeScore=286.33;MQ=23.04;MQ0=37;OQ=238.47;QD=0.60;SB=-127.61 GT:AD:DP:GL:GQ 0/1:316,80:131:-66.59,-39.46,-400.07:99 +chr1 2617377 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=393;Dels=0.00;HRun=0;HaplotypeScore=264.38;MQ=23.09;MQ0=38;OQ=52.53;QD=0.13;SB=34.31 GT:AD:DP:GL:GQ 0/1:349,42:132:-48.29,-39.76,-421.34:85.37 +chr1 2617406 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=150.38;MQ=24.81;MQ0=30;OQ=1026.09;QD=4.44;SB=-81.56 GT:AD:DP:GL:GQ 0/1:71,150:85:-131.52,-25.63,-230.33:99 +chr1 2617434 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=111.67;MQ=24.27;MQ0=28;OQ=290.81;QD=2.02;SB=-29.80 GT:AD:DP:GL:GQ 0/1:61,70:56:-59.33,-26.96,-156.98:99 +chr1 2617463 rs56282610 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=58.94;MQ=24.92;MQ0=20;OQ=411.11;QD=4.42;SB=-153.67 GT:AD:DP:GL:GQ 0/1:29,63:36:-55.25,-10.85,-76.21:99 +chr1 2617490 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=85.26;MQ=28.92;MQ0=14;OQ=93.54;QD=0.96;SB=32.09 GT:AD:DP:GL:GQ 0/1:84,12:39:-24.38,-11.75,-112.74:99 +chr1 2617496 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=107.91;MQ=30.31;MQ0=12;OQ=102.53;QD=1.11;SB=32.10 GT:AD:DP:GL:GQ 0/1:79,12:38:-24.98,-11.44,-111.78:99 +chr1 2617505 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=81.67;MQ=32.33;MQ0=11;OQ=247.78;QD=2.69;SB=-60.73 GT:AD:DP:GL:GQ 0/1:40,39:40:-40.11,-12.05,-107.49:99 +chr1 2617521 rs56279030 G C 42.50 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=0;HaplotypeScore=51.30;MQ=31.83;MQ0=12;QD=0.40;SB=0.26 GT:AD:DP:GL:GQ 0/1:94,13:44:-20.79,-13.26,-170.49:75.34 +chr1 2617526 rs28536771 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.00;HRun=0;HaplotypeScore=63.55;MQ=32.40;MQ0=9;OQ=160.23;QD=1.53;SB=-3.57 GT:AD:DP:GL:GQ 0/1:45,55:37:-30.46,-11.15,-113.20:99 +chr1 2617584 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=87.31;MQ=28.18;MQ0=10;OQ=524.04;QD=3.59;SB=-151.92 GT:AD:DP:GL:GQ 0/1:49,97:62:-74.37,-18.69,-162.12:99 +chr1 2617611 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=154;Dels=0.01;HRun=0;HaplotypeScore=176.05;MQ=27.08;MQ0=16;OQ=81.66;QD=0.53;SB=-0.83 GT:AD:DP:GL:GQ 0/1:126,24:59:-29.22,-17.77,-179.32:99 +chr1 2617617 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=177.05;MQ=27.20;MQ0=14;OQ=126.07;QD=0.84;SB=8.21 GT:AD:DP:GL:GQ 0/1:125,25:58:-33.36,-17.47,-170.99:99 +chr1 2617626 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=0;HaplotypeScore=162.52;MQ=28.40;MQ0=11;OQ=508.32;QD=3.63;SB=-161.48 GT:AD:DP:GL:GQ 0/1:40,77:57:-73.89,-19.78,-125.32:99 +chr1 2617630 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=1;HaplotypeScore=122.08;MQ=28.20;MQ0=11;OQ=734.14;QD=5.13;SB=-361.31 GT:AD:DP:GL:GQ 0/1:73,47:61:-98.65,-21.95,-111.48:99 +chr1 2617659 rs55801140 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.00;HRun=0;HaplotypeScore=125.08;MQ=27.55;MQ0=12;OQ=175.93;QD=1.11;SB=23.11 GT:AD:DP:GL:GQ 0/1:141,12:44:-34.15,-13.27,-148.76:99 +chr1 2617668 rs28535687 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=255.63;MQ=27.99;MQ0=8;OQ=172.40;QD=1.28;SB=-72.12 GT:AD:DP:GL:GQ 0/1:31,69:32:-40.65,-20.12,-107.26:99 +chr1 2617672 . G T 32.81 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=0;HaplotypeScore=245.46;MQ=28.29;MQ0=7;QD=0.25;SB=11.06 GT:AD:DP:GL:GQ 0/1:84,46:25:-14.10,-7.54,-64.41:65.64 +chr1 2617713 . C T 25.50 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=0;HaplotypeScore=235.92;MQ=23.71;MQ0=16;QD=0.15;SB=11.61 GT:AD:DP:GL:GQ 0/1:80,75:31:-15.18,-9.35,-88.30:58.32 +chr1 2617737 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=1;HaplotypeScore=196.10;MQ=25.34;MQ0=20;OQ=242.18;QD=1.19;SB=-124.57 GT:AD:DP:GL:GQ 0/1:154,44:50:-42.56,-15.06,-131.92:99 +chr1 2617767 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=115.66;MQ=29.10;MQ0=18;OQ=374.38;QD=2.92;SB=-46.69 GT:AD:DP:GL:GQ 0/1:37,72:41:-53.07,-12.35,-97.04:99 +chr1 2617781 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=110.28;MQ=28.42;MQ0=22;OQ=65.20;QD=0.50;SB=26.12 GT:AD:DP:GL:GQ 0/1:110,18:43:-22.77,-12.97,-156.99:98.03 +chr1 2617809 rs28698520 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.01;HRun=1;HaplotypeScore=154.47;MQ=26.46;MQ0=29;OQ=544.53;QD=4.54;SB=20.07 GT:AD:DP:GL:GQ 0/1:74,45:37:-68.88,-11.15,-59.02:99 +chr1 2617834 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=1;HaplotypeScore=142.69;MQ=25.75;MQ0=33;OQ=247.39;QD=1.66;SB=-8.79 GT:AD:DP:GL:GQ 0/1:101,20:44:-48.54,-20.52,-132.57:99 +chr1 2617846 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=163;Dels=0.00;HRun=0;HaplotypeScore=110.83;MQ=27.45;MQ0=31;OQ=574.67;QD=3.53;SB=-169.29 GT:AD:DP:GL:GQ 0/1:34,98:52:-84.16,-23.41,-106.75:99 +chr1 2617859 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=258;Dels=0.00;HRun=0;HaplotypeScore=189.65;MQ=26.24;MQ0=36;OQ=661.11;QD=2.56;SB=-188.93 GT:AD:DP:GL:GQ 0/1:183,74:74:-91.72,-22.32,-216.13:99 +chr1 2617878 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=308;Dels=0.00;HRun=0;HaplotypeScore=214.86;MQ=26.40;MQ0=36;OQ=1364.14;QD=4.43;SB=-695.16 GT:AD:DP:GL:GQ 0/1:245,61:100:-169.82,-30.12,-204.71:99 +chr1 2617913 rs61766463 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=276;Dels=0.00;HRun=0;HaplotypeScore=33.34;MQ=34.26;MQ0=23;OQ=345.85;QD=1.25;SB=54.43 GT:AD:DP:GL:GQ 0/1:130,145:134:-78.24,-40.37,-397.42:99 +chr1 2617929 rs61766464 G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=313;Dels=0.00;HRun=0;HaplotypeScore=209.86;MQ=34.59;MQ0=24;OQ=2475.95;QD=7.91;SB=-469.20 GT:AD:DP:GL:GQ 0/1:207,106:147:-295.16,-44.28,-232.82:99 +chr1 2617945 rs61766465 G A 678.02 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=327;Dels=0.00;HRun=0;HaplotypeScore=293.41;MQ=35.76;MQ0=33;QD=2.07;SB=57.72 GT:AD:DP:GL:GQ 0/1:285,42:156:-118.09,-47.00,-457.61:99 +chr1 2617948 . A T 1515.78 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=339;Dels=0.00;HRun=0;HaplotypeScore=339.78;MQ=35.84;MQ0=34;QD=4.47;SB=-315.59 GT:AD:DP:GL:GQ 0/1:267,71:155:-201.56,-46.69,-377.16:99 +chr1 2617953 rs61766466 C A 621.95 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=348;Dels=0.00;HRun=0;HaplotypeScore=257.70;MQ=36.09;MQ0=43;QD=1.79;SB=55.33 GT:AD:DP:GL:GQ 0/1:287,49:168:-116.08,-50.61,-483.68:99 +chr1 2618063 rs28379532 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.02;HRun=0;HaplotypeScore=36.25;MQ=31.70;MQ0=29;OQ=1863.52;QD=13.03;SB=-253.52 GT:AD:DP:GL:GQ 0/1:27,111:85:-215.25,-25.61,-83.05:99 +chr1 2618135 rs28499404 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=183;Dels=0.00;HRun=0;HaplotypeScore=48.32;MQ=27.35;MQ0=42;OQ=347.83;QD=1.90;SB=-174.55 GT:AD:DP:GL:GQ 0/1:162,21:105:-69.72,-31.65,-366.58:99 +chr1 2618152 rs61766467 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=192;Dels=0.00;HRun=1;HaplotypeScore=85.82;MQ=26.36;MQ0=44;OQ=458.63;QD=2.39;SB=-15.83 GT:AD:DP:GL:GQ 0/1:151,41:104:-80.48,-31.33,-290.41:99 +chr1 2618186 rs28655771 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=193;Dels=0.00;HRun=1;HaplotypeScore=114.84;MQ=21.49;MQ0=56;OQ=2645.92;QD=13.71;SB=-1050.69 GT:AD:DP:GL:GQ 1/1:5,188:77:-268.22,-23.20,-0.04:99 +chr1 2618191 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=203;Dels=0.00;HRun=0;HaplotypeScore=161.00;MQ=22.90;MQ0=57;OQ=50.10;QD=0.25;SB=39.02 GT:AD:DP:GL:GQ 0/1:173,30:86:-34.21,-25.91,-268.48:82.93 +chr1 2618226 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=268;Dels=0.00;HRun=0;HaplotypeScore=192.42;MQ=33.49;MQ0=36;OQ=337.18;QD=1.26;SB=-53.39 GT:AD:DP:GL:GQ 0/1:227,40:152:-82.80,-45.80,-457.42:99 +chr1 2618254 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=296;Dels=0.00;HRun=0;HaplotypeScore=166.54;MQ=37.41;MQ0=24;OQ=808.97;QD=2.73;SB=-397.12 GT:AD:DP:GL:GQ 0/1:225,67:181:-140.83,-56.65,-515.36:99 +chr1 2618301 . C A 998.94 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=292;Dels=0.00;HRun=0;HaplotypeScore=277.61;MQ=43.53;MQ0=9;QD=3.42;SB=-458.03 GT:AD:DP:GL:GQ 0/1:215,74:195:-161.93,-58.75,-524.06:99 +chr1 2618303 . C A 591.91 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=295;Dels=0.00;HRun=0;HaplotypeScore=301.39;MQ=43.31;MQ0=10;QD=2.01;SB=-293.38 GT:AD:DP:GL:GQ 0/1:236,56:205:-124.23,-61.75,-600.14:99 +chr1 2618307 . G A 971.72 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=283;Dels=0.00;HRun=0;HaplotypeScore=193.14;MQ=43.47;MQ0=11;QD=3.43;SB=-273.43 GT:AD:DP:GL:GQ 0/1:228,48:199:-160.42,-59.96,-556.19:99 +chr1 2618320 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=309;Dels=0.00;HRun=0;HaplotypeScore=150.76;MQ=41.04;MQ0=29;OQ=452.34;QD=1.46;SB=-151.56 GT:AD:DP:GL:GQ 0/1:223,31:184:-121.13,-72.62,-509.07:99 +chr1 2618366 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=558;Dels=0.00;HRun=0;HaplotypeScore=219.65;MQ=26.44;MQ0=134;OQ=289.23;QD=0.52;SB=167.70 GT:AD:DP:GL:GQ 0/1:454,69:221:-105.97,-73.77,-728.70:99 +chr1 2618375 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=585;Dels=0.00;HRun=0;HaplotypeScore=337.36;MQ=25.16;MQ0=141;OQ=507.21;QD=0.87;SB=196.74 GT:AD:DP:GL:GQ 0/1:487,75:227:-128.47,-74.47,-700.80:99 +chr1 2618378 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=594;Dels=0.00;HRun=0;HaplotypeScore=307.01;MQ=24.92;MQ0=142;OQ=386.51;QD=0.65;SB=-74.59 GT:AD:DP:GL:GQ 0/1:524,66:225:-115.59,-73.65,-670.89:99 +chr1 2618414 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=573;Dels=0.00;HRun=1;HaplotypeScore=206.56;MQ=24.36;MQ0=140;OQ=719.44;QD=1.26;SB=-72.20 GT:AD:DP:GL:GQ 0/1:439,119:210:-138.50,-63.27,-592.09:99 +chr1 2618418 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=531;Dels=0.00;HRun=0;HaplotypeScore=181.25;MQ=24.54;MQ0=131;OQ=939.27;QD=1.77;SB=-76.38 GT:AD:DP:GL:GQ 0/1:427,103:204:-158.68,-61.47,-574.55:99 +chr1 2618432 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=412;Dels=0.00;HRun=0;HaplotypeScore=70.50;MQ=25.62;MQ0=105;OQ=877.24;QD=2.13;SB=-428.33 GT:AD:DP:GL:GQ 0/1:368,44:152:-136.86,-45.86,-364.87:99 +chr1 2618444 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=352;Dels=0.00;HRun=1;HaplotypeScore=46.24;MQ=26.18;MQ0=89;OQ=1301.34;QD=3.70;SB=170.58 GT:AD:DP:GL:GQ 0/1:167,181:143:-176.57,-43.15,-394.32:99 +chr1 2618459 rs61766471 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=309;Dels=0.00;HRun=0;HaplotypeScore=122.77;MQ=27.15;MQ0=60;OQ=430.68;QD=1.39;SB=-167.89 GT:AD:DP:GL:GQ 0/1:283,25:135:-87.04,-40.69,-380.50:99 +chr1 2618482 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=0;HaplotypeScore=91.95;MQ=32.62;MQ0=31;OQ=752.10;QD=3.36;SB=-248.53 GT:AD:DP:GL:GQ 0/1:115,107:101:-108.92,-30.43,-254.35:99 +chr1 2618501 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=234;Dels=0.01;HRun=4;HaplotypeScore=341.35;MQ=30.82;MQ0=33;OQ=155.62;QD=0.67;SB=92.01 GT:AD:DP:GL:GQ 0/1:155,66:98:-53.97,-35.12,-329.58:99 +chr1 2618530 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=231;Dels=0.00;HRun=0;HaplotypeScore=168.93;MQ=32.32;MQ0=29;OQ=236.35;QD=1.02;SB=-122.19 GT:AD:DP:GL:GQ 0/1:211,19:107:-59.16,-32.24,-318.05:99 +chr1 2618557 rs28411025 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=156;Dels=0.00;HRun=0;HaplotypeScore=133.44;MQ=39.19;MQ0=9;OQ=2883.82;QD=18.49;SB=-1383.19 GT:AD:DP:GL:GQ 0/1:27,128:92:-319.41,-27.74,-64.72:99 +chr1 2618577 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=228;Dels=0.01;HRun=1;HaplotypeScore=243.04;MQ=34.35;MQ0=14;OQ=206.46;QD=0.91;SB=-125.59 GT:AD:DP:GL:GQ 0/1:119,105:92:-51.66,-27.73,-260.87:99 +chr1 2618590 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=341;Dels=0.00;HRun=0;HaplotypeScore=269.37;MQ=32.40;MQ0=23;OQ=694.60;QD=2.04;SB=-10.03 GT:AD:DP:GL:GQ 0/1:206,129:134:-115.74,-43.00,-326.10:99 +chr1 2618603 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=385;Dels=0.00;HRun=0;HaplotypeScore=742.67;MQ=32.24;MQ0=20;OQ=374.09;QD=0.97;SB=-84.54 GT:AD:DP:GL:GQ 0/1:213,140:157:-94.37,-53.68,-577.68:99 +chr1 2618613 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=414;Dels=0.00;HRun=1;HaplotypeScore=803.50;MQ=31.66;MQ0=23;OQ=626.38;QD=1.51;SB=181.82 GT:AD:DP:GL:GQ 0/1:349,58:175:-118.68,-52.76,-621.84:99 +chr1 2618617 . A C 34.85 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=417;Dels=0.00;HRun=1;HaplotypeScore=645.23;MQ=31.22;MQ0=23;QD=0.08;SB=-15.32 GT:AD:DP:GL:GQ 0/1:232,176:163:-62.01,-55.24,-512.02:67.68 +chr1 2618648 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=485;Dels=0.00;HRun=0;HaplotypeScore=582.18;MQ=29.51;MQ0=32;OQ=1313.91;QD=2.71;SB=163.03 GT:AD:DP:GL:GQ 0/1:367,113:208:-197.35,-62.68,-695.38:99 +chr1 2618651 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=487;Dels=0.00;HRun=0;HaplotypeScore=686.95;MQ=29.46;MQ0=33;OQ=108.10;QD=0.22;SB=256.13 GT:AD:DP:GL:GQ 0/1:431,46:211:-84.08,-69.98,-671.09:99 +chr1 2618685 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=500;Dels=0.00;HRun=1;HaplotypeScore=291.67;MQ=27.86;MQ0=33;OQ=4318.30;QD=8.64;SB=-761.47 GT:AD:DP:GL:GQ 0/1:182,284:216:-430.83,-67.58,-458.35:99 +chr1 2618707 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=462;Dels=0.01;HRun=4;HaplotypeScore=721.39;MQ=29.06;MQ0=34;OQ=2615.02;QD=5.66;SB=-699.35 GT:AD:DP:GL:GQ 0/1:165,282:202:-327.27,-62.48,-383.70:99 +chr1 2618711 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=464;Dels=0.00;HRun=0;HaplotypeScore=458.70;MQ=28.79;MQ0=35;OQ=1658.43;QD=3.57;SB=-180.55 GT:AD:DP:GL:GQ 0/1:156,178:185:-246.74,-77.62,-433.93:99 +chr1 2618743 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=565;Dels=0.00;HRun=1;HaplotypeScore=594.08;MQ=28.52;MQ0=39;OQ=195.57;QD=0.35;SB=27.58 GT:AD:DP:GL:GQ 0/1:503,58:268:-103.62,-80.78,-771.76:99 +chr1 2618776 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=541;Dels=0.00;HRun=0;HaplotypeScore=502.52;MQ=30.93;MQ0=35;OQ=5244.83;QD=9.69;SB=-856.66 GT:AD:DP:GL:GQ 0/1:182,353:279:-523.48,-84.06,-514.94:99 +chr1 2618784 . C T 23.85 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=542;Dels=0.00;HRun=0;HaplotypeScore=612.02;MQ=31.33;MQ0=33;QD=0.04;SB=67.53 GT:AD:DP:GL:GQ 0/1:386,152:218:-71.34,-65.68,-703.92:56.67 +chr1 2618799 rs61766473 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=520;Dels=0.00;HRun=1;HaplotypeScore=456.03;MQ=31.14;MQ0=35;OQ=4809.01;QD=9.25;SB=-828.34 GT:AD:DP:GL:GQ 0/1:169,328:274:-479.90,-94.56,-523.76:99 +chr1 2618813 rs28570043 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=586;Dels=0.00;HRun=0;HaplotypeScore=299.20;MQ=30.92;MQ0=47;OQ=1856.68;QD=3.17;SB=-717.31 GT:AD:DP:GL:GQ 0/1:501,75:250:-270.75,-81.80,-777.18:99 +chr1 2618823 rs61766474 A T 4860.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=562;Dels=0.00;HRun=0;HaplotypeScore=709.32;MQ=30.48;MQ0=44;QD=8.65;SB=-560.15 GT:AD:DP:GL:GQ 0/1:287,273:277:-485.00,-83.44,-550.46:99 +chr1 2618832 . C G 1479.75 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=512;Dels=0.00;HRun=2;HaplotypeScore=411.64;MQ=30.81;MQ0=42;QD=2.89;SB=-17.36 GT:AD:DP:GL:GQ 0/1:367,94:241:-231.26,-80.00,-778.36:99 +chr1 2618833 . G C 375.40 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=513;Dels=0.00;HRun=1;HaplotypeScore=505.52;MQ=30.67;MQ0=42;QD=0.73;SB=152.53 GT:AD:DP:GL:GQ 0/1:466,47:236:-112.05,-71.23,-847.97:99 +chr1 2618853 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=470;Dels=0.00;HRun=0;HaplotypeScore=742.82;MQ=31.02;MQ0=40;OQ=917.98;QD=1.95;SB=-4.91 GT:AD:DP:GL:GQ 0/1:336,89:211:-236.75,-141.67,-586.15:99 +chr1 2618854 rs61766475 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=465;Dels=0.00;HRun=1;HaplotypeScore=675.66;MQ=31.14;MQ0=39;OQ=3030.86;QD=6.52;SB=-170.15 GT:AD:DP:GL:GQ 0/1:129,210:216:-470.96,-164.59,-497.24:99 +chr1 2618865 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=505;Dels=0.00;HRun=0;HaplotypeScore=338.61;MQ=30.47;MQ0=44;OQ=342.56;QD=0.68;SB=-14.42 GT:AD:DP:GL:GQ 0/1:439,53:231:-117.83,-80.29,-726.19:99 +chr1 2618904 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=499;Dels=0.00;HRun=4;HaplotypeScore=608.12;MQ=29.15;MQ0=44;OQ=1769.15;QD=3.55;SB=89.28 GT:AD:DP:GL:GQ 0/1:280,197:227:-252.16,-71.97,-553.68:99 +chr1 2618905 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=514;Dels=0.00;HRun=0;HaplotypeScore=596.36;MQ=29.03;MQ0=46;OQ=337.81;QD=0.66;SB=-30.28 GT:AD:DP:GL:GQ 0/1:424,43:227:-138.22,-101.16,-705.27:99 +chr1 2618928 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=624;Dels=0.00;HRun=2;HaplotypeScore=323.04;MQ=29.42;MQ0=49;OQ=696.10;QD=1.12;SB=42.74 GT:AD:DP:GL:GQ 0/1:499,120:322:-169.90,-97.01,-976.27:99 +chr1 2618942 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=632;Dels=0.00;HRun=0;HaplotypeScore=427.92;MQ=29.57;MQ0=51;OQ=1430.20;QD=2.26;SB=-6.35 GT:AD:DP:GL:GQ 0/1:441,177:340:-255.05,-108.75,-1027.84:99 +chr1 2618944 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=660;Dels=0.01;HRun=1;HaplotypeScore=381.00;MQ=29.09;MQ0=58;OQ=94.18;QD=0.14;SB=-52.32 GT:AD:DP:GL:GQ 0/1:544,51:336:-209.60,-196.90,-1072.15:99 +chr1 2619010 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=979;Dels=0.00;HRun=0;HaplotypeScore=447.29;MQ=26.60;MQ0=70;OQ=796.25;QD=0.81;SB=-92.06 GT:AD:DP:GL:GQ 0/1:864,98:425:-220.34,-137.43,-1275.90:99 +chr1 2619053 rs28733941 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=909;Dels=0.00;HRun=0;HaplotypeScore=595.79;MQ=27.09;MQ0=60;OQ=13631.67;QD=15.00;SB=-2975.80 GT:AD:DP:GL:GQ 0/1:104,553:419:-1362.17,-600.80,-836.54:99 +chr1 2619065 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1083;Dels=0.00;HRun=0;HaplotypeScore=883.09;MQ=27.27;MQ0=55;OQ=741.35;QD=0.68;SB=-174.53 GT:AD:DP:GL:GQ 0/1:939,125:552:-281.40,-203.98,-1716.07:99 +chr1 2619068 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1124;Dels=0.00;HRun=1;HaplotypeScore=958.29;MQ=27.28;MQ0=55;OQ=693.79;QD=0.62;SB=-203.14 GT:AD:DP:GL:GQ 0/1:985,132:593:-257.34,-184.67,-1827.88:99 +chr1 2619088 rs28368434 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=1328;Dels=0.00;HRun=2;HaplotypeScore=334.46;MQ=28.00;MQ0=46;OQ=7035.59;QD=5.30;SB=-1628.81 GT:AD:DP:GL:GQ 0/1:1024,295:793:-702.56,-254.86,-2119.90:99 +chr1 2619105 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=1330;Dels=0.00;HRun=0;HaplotypeScore=932.09;MQ=28.23;MQ0=29;OQ=2367.59;QD=1.78;SB=-1159.72 GT:AD:DP:GL:GQ 0/1:991,151:799:-779.65,-539.60,-2921.50:99 +chr1 2619148 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=990;Dels=0.00;HRun=0;HaplotypeScore=340.48;MQ=27.70;MQ0=55;OQ=2332.09;QD=2.36;SB=-739.43 GT:AD:DP:GL:GQ 0/1:796,178:558:-439.22,-202.73,-1989.78:99 +chr1 2619186 . A C 371.93 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=419;Dels=0.00;HRun=2;HaplotypeScore=464.28;MQ=28.43;MQ0=32;QD=0.89;SB=-209.63 GT:AD:DP:GL:GQ 0/1:320,97:190:-97.71,-57.24,-585.62:99 +chr1 2619187 . A C 430.91 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=400;Dels=0.00;HRun=1;HaplotypeScore=324.16;MQ=28.26;MQ0=30;QD=1.08;SB=-112.57 GT:AD:DP:GL:GQ 0/1:310,88:169:-97.29,-50.91,-502.75:99 +chr1 2619196 rs61766477 C T 639.34 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=339;Dels=0.00;HRun=0;HaplotypeScore=406.21;MQ=29.84;MQ0=24;QD=1.89;SB=-240.09 GT:AD:DP:GL:GQ 0/1:283,37:141:-134.06,-66.84,-411.36:99 +chr1 2619205 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=257;Dels=0.00;HRun=0;HaplotypeScore=259.69;MQ=32.70;MQ0=16;OQ=1928.35;QD=7.50;SB=-426.10 GT:AD:DP:GL:GQ 0/1:80,173:106:-228.05,-31.94,-159.03:99 +chr1 2619218 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=235;Dels=0.00;HRun=1;HaplotypeScore=278.38;MQ=35.10;MQ0=10;OQ=372.83;QD=1.59;SB=-167.14 GT:AD:DP:GL:GQ 0/1:174,58:82:-65.27,-24.71,-216.22:99 +chr1 2619230 . G A 206.96 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=238;Dels=0.00;HRun=1;HaplotypeScore=422.57;MQ=34.96;MQ0=8;QD=0.87;SB=86.30 GT:AD:DP:GL:GQ 0/1:192,38:100:-59.43,-35.45,-312.61:99 +chr1 2619232 . T C 831.94 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=232;Dels=0.00;HRun=0;HaplotypeScore=355.75;MQ=35.18;MQ0=8;QD=3.59;SB=-351.57 GT:AD:DP:GL:GQ 0/1:163,64:87:-112.72,-26.24,-194.80:99 +chr1 2619238 . G T 230.19 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=214;Dels=0.00;HRun=0;HaplotypeScore=374.27;MQ=36.67;MQ0=6;QD=1.08;SB=104.29 GT:AD:DP:GL:GQ 0/1:105,106:92:-54.02,-27.71,-267.56:99 +chr1 2619244 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=201;Dels=0.00;HRun=0;HaplotypeScore=269.42;MQ=37.21;MQ0=7;OQ=1921.19;QD=9.56;SB=-479.90 GT:AD:DP:GL:GQ 0/1:57,142:93:-223.42,-28.02,-104.14:99 +chr1 2619306 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=2;HaplotypeScore=23.50;MQ=42.95;MQ0=2;OQ=983.37;QD=8.48;SB=-151.45 GT:AD:DP:GL:GQ 0/1:49,66:80:-128.94,-27.32,-178.83:99 +chr1 2619313 . T G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=14.58;MQ=45.37;MQ0=2;OQ=717.70;QD=7.40;SB=-61.81 GT:AD:DP:GL:GQ 0/1:47,50:71:-96.45,-21.40,-150.45:99 +chr1 2619324 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=29.83;MQ=44.91;MQ0=2;OQ=606.68;QD=6.74;SB=-59.89 GT:AD:DP:GL:GQ 0/1:45,45:58:-81.45,-17.50,-117.39:99 +chr1 2619346 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=198;Dels=0.01;HRun=2;HaplotypeScore=304.95;MQ=34.96;MQ0=2;OQ=1893.09;QD=9.56;SB=62.22 GT:AD:DP:GL:GQ 0/1:48,144:92:-224.02,-31.43,-163.64:99 +chr1 2619351 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=249;Dels=0.00;HRun=1;HaplotypeScore=417.56;MQ=32.10;MQ0=4;OQ=1347.04;QD=5.41;SB=71.23 GT:AD:DP:GL:GQ 0/1:80,143:111:-171.44,-33.46,-209.78:99 +chr1 2619360 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=388;Dels=0.00;HRun=1;HaplotypeScore=438.87;MQ=28.93;MQ0=6;OQ=112.12;QD=0.29;SB=98.35 GT:AD:DP:GL:GQ 0/1:301,77:156:-68.00,-53.51,-526.40:99 +chr1 2619395 rs61766478 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=748;Dels=0.00;HRun=0;HaplotypeScore=964.64;MQ=26.94;MQ0=26;OQ=5287.26;QD=7.07;SB=128.59 GT:AD:DP:GL:GQ 0/1:216,518:288:-527.73,-89.49,-471.13:99 +chr1 2619416 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=775;Dels=0.00;HRun=0;HaplotypeScore=727.49;MQ=27.55;MQ0=26;OQ=6889.43;QD=8.89;SB=178.09 GT:AD:DP:GL:GQ 0/1:249,511:342:-687.94,-103.01,-497.11:99 +chr1 2619432 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=738;Dels=0.01;HRun=0;HaplotypeScore=785.98;MQ=28.56;MQ0=15;OQ=287.49;QD=0.39;SB=162.31 GT:AD:DP:GL:GQ 0/1:586,116:299:-161.89,-129.86,-1001.87:99 +chr1 2619446 rs61766479 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=555;Dels=0.00;HRun=1;HaplotypeScore=580.47;MQ=30.08;MQ0=12;OQ=4833.38;QD=8.71;SB=183.30 GT:AD:DP:GL:GQ 0/1:214,317:283:-482.34,-118.04,-540.99:99 +chr1 2619465 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=306;Dels=0.02;HRun=1;HaplotypeScore=404.44;MQ=32.23;MQ0=6;OQ=129.50;QD=0.42;SB=102.00 GT:AD:DP:GL:GQ 0/1:203,74:120:-64.50,-48.27,-416.86:99 +chr1 2619467 rs61766480 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=303;Dels=0.02;HRun=1;HaplotypeScore=363.13;MQ=31.91;MQ0=6;OQ=4502.12;QD=14.86;SB=-1253.39 GT:AD:DP:GL:GQ 0/1:40,252:153:-449.21,-45.80,-111.82:99 +chr1 2619477 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=279;Dels=0.00;HRun=0;HaplotypeScore=335.87;MQ=32.02;MQ0=7;OQ=542.66;QD=1.95;SB=122.33 GT:AD:DP:GL:GQ 0/1:161,107:129:-96.42,-38.87,-351.57:99 +chr1 2619489 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=268;Dels=0.00;HRun=1;HaplotypeScore=215.67;MQ=32.52;MQ0=8;OQ=1128.11;QD=4.21;SB=95.32 GT:AD:DP:GL:GQ 0/1:114,145:131:-166.02,-49.92,-331.55:99 +chr1 2619505 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=271;Dels=0.00;HRun=0;HaplotypeScore=305.81;MQ=31.15;MQ0=10;OQ=135.21;QD=0.50;SB=68.22 GT:AD:DP:GL:GQ 0/1:237,31:129:-55.67,-38.86,-389.56:99 +chr1 2619511 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=262;Dels=0.00;HRun=0;HaplotypeScore=356.76;MQ=30.03;MQ0=11;OQ=250.01;QD=0.95;SB=47.18 GT:AD:DP:GL:GQ 0/1:212,49:118:-63.84,-35.55,-351.09:99 +chr1 2619524 rs34081960 A G 343.80 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.00;HRun=1;HaplotypeScore=217.57;MQ=30.42;MQ0=7;QD=1.59;SB=47.18 GT:AD:DP:GL:GQ 0/1:179,33:102:-68.39,-30.73,-325.69:99 +chr1 2619526 . C A 23.86 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=205;Dels=0.00;HRun=1;HaplotypeScore=236.96;MQ=30.18;MQ0=8;QD=0.12;SB=44.17 GT:AD:DP:GL:GQ 0/1:190,11:95:-34.28,-28.61,-300.58:56.68 +chr1 2619527 . A C 538.74 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=197;Dels=0.00;HRun=1;HaplotypeScore=224.55;MQ=30.05;MQ0=8;QD=2.73;SB=-87.11 GT:AD:DP:GL:GQ 0/1:122,73:87:-83.37,-26.21,-226.60:99 +chr1 2619530 . T G 866.27 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=215.21;MQ=31.06;MQ0=6;QD=4.84;SB=12.12 GT:AD:DP:GL:GQ 0/1:87,85:86:-126.63,-36.72,-179.70:99 +chr1 2619534 . A G 264.68 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=172;Dels=0.00;HRun=1;HaplotypeScore=280.66;MQ=30.98;MQ0=7;QD=1.54;SB=41.16 GT:AD:DP:GL:GQ 0/1:139,33:74:-52.04,-22.29,-233.98:99 +chr1 2619544 . C T 108.85 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=155;Dels=0.06;HRun=0;HaplotypeScore=267.97;MQ=31.40;MQ0=5;QD=0.70;SB=38.12 GT:AD:DP:GL:GQ 0/1:124,16:57:-34.75,-20.58,-177.62:99 +chr1 2619546 . C G 37.35 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=150;Dels=0.00;HRun=0;HaplotypeScore=251.96;MQ=31.91;MQ0=5;QD=0.25;SB=38.15 GT:AD:DP:GL:GQ 0/1:138,7:61:-25.40,-18.38,-245.36:70.19 +chr1 2619553 . A G 821.41 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=113.41;MQ=33.54;MQ0=5;QD=6.96;SB=23.10 GT:AD:DP:GL:GQ 0/1:33,83:56:-102.29,-16.87,-105.73:99 +chr1 2619570 rs12757527 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=61.91;MQ=39.68;MQ0=1;OQ=223.25;QD=2.51;SB=41.15 GT:AD:DP:GL:GQ 0/1:39,49:45:-39.17,-13.56,-132.69:99 +chr1 2619576 rs11516512 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=85.98;MQ=40.41;MQ0=1;OQ=1215.90;QD=15.59;SB=-537.94 GT:AD:DP:GL:GQ 0/1:9,69:47:-139.03,-14.16,-23.39:92.31 +chr1 2619644 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=167.24;MQ=38.77;MQ0=11;OQ=65.21;QD=0.53;SB=59.09 GT:AD:DP:GL:GQ 0/1:83,36:47:-23.99,-14.18,-125.75:98.05 +chr1 2619667 rs12757684 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=110;Dels=0.02;HRun=3;HaplotypeScore=150.20;MQ=38.48;MQ0=2;OQ=87.98;QD=0.80;SB=-4.94 GT:AD:DP:GL:GQ 0/1:62,46:39:-23.84,-11.75,-110.18:99 +chr1 2619672 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=2;HaplotypeScore=165.55;MQ=38.18;MQ0=2;OQ=67.69;QD=0.61;SB=56.21 GT:AD:DP:GL:GQ 0/1:58,23:45:-37.64,-27.58,-156.78:99 +chr1 2619717 rs35537872 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=158.55;MQ=37.91;MQ0=1;OQ=82.21;QD=0.81;SB=12.47 GT:AD:DP:GL:GQ 0/1:41,55:41:-23.87,-12.36,-127.50:99 +chr1 2619725 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=160.68;MQ=38.53;MQ0=0;OQ=110.57;QD=1.00;SB=59.22 GT:AD:DP:GL:GQ 0/1:96,15:49:-29.10,-14.76,-154.28:99 +chr1 2619755 rs35198281 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=135.67;MQ=40.63;MQ0=1;OQ=77.36;QD=0.78;SB=-26.15 GT:AD:DP:GL:GQ 0/1:44,49:41:-23.37,-12.36,-121.95:99 +chr1 2619802 . G A 11.69 LowQual AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=1;HaplotypeScore=127.16;MQ=33.63;MQ0=4;QD=0.12;SB=-22.48 GT:AD:DP:GL:GQ 0/1:79,20:38:-15.87,-11.45,-120.55:44.22 +chr1 2619811 rs11516513 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=94.34;MQ=31.96;MQ0=5;OQ=1057.97;QD=11.02;SB=-282.04 GT:AD:DP:GL:GQ 0/1:29,63:37:-120.23,-11.15,-15.87:47.21 +chr1 2619844 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=163.21;MQ=35.54;MQ0=9;OQ=150.26;QD=1.60;SB=-85.59 GT:AD:DP:GL:GQ 0/1:35,58:32:-27.96,-9.65,-83.83:99 +chr1 2619873 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=1;HaplotypeScore=84.94;MQ=33.03;MQ0=22;OQ=528.32;QD=3.80;SB=-259.93 GT:AD:DP:GL:GQ 0/1:45,94:55:-72.69,-16.57,-137.30:99 +chr1 2619885 rs4648686 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=143;Dels=0.00;HRun=0;HaplotypeScore=76.46;MQ=34.20;MQ0=29;OQ=72.77;QD=0.51;SB=-32.15 GT:AD:DP:GL:GQ 0/1:107,35:58:-28.03,-17.47,-178.69:99 +chr1 2619907 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=129;Dels=0.02;HRun=0;HaplotypeScore=75.23;MQ=35.05;MQ0=37;OQ=78.76;QD=0.61;SB=20.08 GT:AD:DP:GL:GQ 0/1:80,29:48:-28.88,-17.72,-148.42:99 +chr1 2619934 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=0;HaplotypeScore=66.32;MQ=35.85;MQ0=29;OQ=172.74;QD=1.52;SB=-28.24 GT:AD:DP:GL:GQ 0/1:48,66:48:-35.03,-14.47,-147.33:99 +chr1 2619955 rs6604996 C G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=63.40;MQ=33.93;MQ0=36;OQ=1440.37;QD=13.21;SB=-479.54 GT:AD:DP:GL:GQ 1/1:0,108:38:-147.67,-11.48,-0.04:99 +chr1 2620070 rs12740972 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=47.55;MQ=45.30;MQ0=8;OQ=554.48;QD=5.72;SB=-255.88 GT:AD:DP:GL:GQ 0/1:70,21:53:-74.72,-15.98,-142.31:99 +chr1 2620085 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=54.16;MQ=39.71;MQ0=11;OQ=120.34;QD=1.02;SB=-33.16 GT:AD:DP:GL:GQ 0/1:69,45:56:-32.19,-16.87,-164.99:99 +chr1 2620124 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=144;Dels=0.00;HRun=0;HaplotypeScore=63.81;MQ=34.92;MQ0=3;OQ=525.60;QD=3.65;SB=47.19 GT:AD:DP:GL:GQ 0/1:42,93:57:-80.08,-24.23,-172.63:99 +chr1 2620133 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=151;Dels=0.00;HRun=1;HaplotypeScore=107.36;MQ=34.37;MQ0=3;OQ=432.59;QD=2.86;SB=-11.69 GT:AD:DP:GL:GQ 0/1:52,96:55:-63.12,-16.58,-172.84:99 +chr1 2620148 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=3;HaplotypeScore=138.11;MQ=33.81;MQ0=6;OQ=406.05;QD=2.39;SB=-68.70 GT:AD:DP:GL:GQ 0/1:52,113:57:-61.06,-17.17,-159.71:99 +chr1 2620167 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=206;Dels=0.00;HRun=1;HaplotypeScore=129.33;MQ=31.98;MQ0=15;OQ=238.76;QD=1.16;SB=-5.73 GT:AD:DP:GL:GQ 0/1:136,68:69:-47.94,-20.78,-212.90:99 +chr1 2620268 rs12741311 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=74.94;MQ=48.87;MQ0=0;OQ=615.93;QD=7.90;SB=-166.53 GT:AD:DP:GL:GQ 0/1:39,39:52:-80.54,-15.66,-101.64:99 +chr1 2620338 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=10.27;MQ=42.72;MQ0=7;OQ=159.57;QD=1.60;SB=-79.74 GT:AD:DP:GL:GQ 0/1:47,53:53:-35.21,-15.97,-154.39:99 +chr1 2620373 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=37.37;MQ=38.59;MQ0=9;OQ=479.31;QD=3.40;SB=-63.47 GT:AD:DP:GL:GQ 0/1:49,92:64:-70.51,-19.30,-148.48:99 +chr1 2620382 . G A 119.16 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=95.95;MQ=37.22;MQ0=9;QD=0.82;SB=68.14 GT:AD:DP:GL:GQ 0/1:86,59:65:-34.81,-19.61,-177.00:99 +chr1 2620388 . A C 105.30 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=153;Dels=0.00;HRun=1;HaplotypeScore=83.57;MQ=35.41;MQ0=9;QD=0.69;SB=-45.48 GT:AD:DP:GL:GQ 0/1:132,21:67:-34.00,-20.19,-204.42:99 +chr1 2620390 rs28376921 A C 238.82 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.00;HRun=3;HaplotypeScore=84.30;MQ=34.68;MQ0=9;QD=1.57;SB=-137.48 GT:AD:DP:GL:GQ 0/1:57,64:66:-69.75,-42.59,-188.12:99 +chr1 2620438 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=39.76;MQ=41.64;MQ0=7;OQ=388.27;QD=3.70;SB=-212.33 GT:AD:DP:GL:GQ 0/1:46,59:60:-60.19,-18.08,-149.44:99 +chr1 2620448 . T C 36.03 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=0;HaplotypeScore=55.60;MQ=44.75;MQ0=3;QD=0.36;SB=59.63 GT:AD:DP:GL:GQ 0/1:72,27:62:-25.58,-18.69,-209.22:68.86 +chr1 2620451 rs28507126 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=42.59;MQ=44.33;MQ0=4;OQ=207.39;QD=2.07;SB=-2.70 GT:AD:DP:GL:GQ 0/1:56,44:55:-40.61,-16.58,-162.04:99 +chr1 2620498 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=143;Dels=0.00;HRun=0;HaplotypeScore=117.30;MQ=35.77;MQ0=21;OQ=96.72;QD=0.68;SB=-10.89 GT:AD:DP:GL:GQ 0/1:119,24:63:-31.93,-18.98,-196.03:99 +chr1 2620509 . C A 44.02 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=155;Dels=0.00;HRun=1;HaplotypeScore=149.75;MQ=36.71;MQ0=19;QD=0.28;SB=8.48 GT:AD:DP:GL:GQ 0/1:122,32:70:-28.77,-21.09,-215.81:76.85 +chr1 2620530 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.01;HRun=0;HaplotypeScore=86.24;MQ=39.02;MQ0=10;OQ=202.63;QD=1.69;SB=-58.78 GT:AD:DP:GL:GQ 0/1:60,45:53:-46.29,-22.74,-131.05:99 +chr1 2620553 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=4;HaplotypeScore=12.66;MQ=42.96;MQ0=4;OQ=154.29;QD=1.66;SB=6.59 GT:AD:DP:GL:GQ 0/1:47,46:55:-35.28,-16.57,-164.62:99 +chr1 2620589 rs4648687 C A 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=19.10;MQ=49.13;MQ0=2;OQ=495.80;QD=9.01;SB=-265.29 GT:AD:DP:GL:GQ 0/1:36,19:38:-64.31,-11.45,-69.99:99 +chr1 2620786 rs12742092 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=51.45;MQ=48.85;MQ0=1;OQ=289.75;QD=5.57;SB=-99.04 GT:AD:DP:GL:GQ 0/1:36,16:30:-41.30,-9.04,-64.97:99 +chr1 2620835 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=99.62;MQ=36.59;MQ0=7;OQ=441.17;QD=4.64;SB=-224.20 GT:AD:DP:GL:GQ 0/1:74,18:36:-60.73,-13.33,-87.56:99 +chr1 2620875 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=107.69;MQ=35.97;MQ0=15;OQ=95.46;QD=0.71;SB=-26.90 GT:AD:DP:GL:GQ 0/1:113,19:59:-30.61,-17.78,-174.51:99 +chr1 2620960 . T A 14.94 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=17.98;MQ=48.66;MQ0=1;QD=0.38;SB=38.15 GT:AD:DP:GL:GQ 0/1:35,4:38:-16.21,-11.45,-119.38:47.63 +chr1 2621024 . C A 47.37 LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=15.73;MQ=45.56;MQ0=1;QD=1.18;SB=-9.87 GT:AD:DP:GL:GQ 0/1:33,7:35:-18.56,-10.54,-104.34:80.21 +chr1 2621154 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=51.59;MQ=53.22;MQ0=2;OQ=488.50;QD=9.77;SB=-206.66 GT:AD:DP:GL:GQ 0/1:29,19:38:-63.61,-11.47,-88.44:99 +chr1 2621346 rs12746691 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=78.63;MQ=48.13;MQ0=0;OQ=876.62;QD=14.61;SB=-440.96 GT:AD:DP:GL:GQ 0/1:34,26:44:-104.20,-13.26,-62.31:99 +chr1 2621414 rs12746841 C G 50.04 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=5.31;MQ=55.95;MQ0=0;OQ=526.83;QD=11.97;SB=-219.19 GT:AD:DP:GL:GQ 0/1:24,20:36:-66.82,-10.85,-82.62:99 +chr1 2621575 rs61766505 T A 0.76 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=9.78;MQ=51.58;MQ0=2;OQ=514.79;QD=12.26;SB=-105.13 GT:AD:DP:GL:GQ 0/1:24,18:33:-64.70,-9.94,-57.89:99 +chr1 2621592 rs11516514 C A 2.97 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=7.05;MQ=51.18;MQ0=2;OQ=412.67;QD=8.78;SB=-93.77 GT:AD:DP:GL:GQ 0/1:31,16:35:-55.10,-10.55,-68.38:99 +chr1 2621664 rs12743419 G A 126.86 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=54.07;MQ0=3;OQ=805.45;QD=17.14;SB=-279.82 GT:AD:DP:GL:GQ 0/1:16,31:40:-95.89,-12.06,-46.66:99 +chr1 2621957 rs12751643 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.02;HRun=1;HaplotypeScore=33.34;MQ=53.32;MQ0=0;OQ=1019.18;QD=17.27;SB=-299.66 GT:AD:DP:GL:GQ 0/1:24,34:54:-121.47,-16.27,-70.01:99 +chr1 2622417 . C G 34.36 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=22.88;MQ0=7;QD=1.01;SB=-10.00 GT:AD:DP:GL:GQ 0/1:28,6:20:-12.75,-6.03,-74.77:67.20 +chr1 2622422 rs11488613 G T 0.62 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=6.76;MQ=21.77;MQ0=7;OQ=525.32;QD=15.45;SB=-10.00 GT:AD:DP:GL:GQ 1/1:3,31:16:-56.12,-4.82,-0.00:48.14 +chr1 2622433 rs12752340 C A 26.89 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=20.67;MQ0=10;QD=0.75;SB=-10.00 GT:AD:DP:GL:GQ 0/1:30,6:16:-10.79,-4.82,-42.41:59.72 +chr1 2674088 . C G 42.96 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=0;HaplotypeScore=11.98;MQ=19.55;MQ0=6;QD=3.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,3:5:-9.09,-1.51,-12.64:75.79 +chr1 2674094 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=17.86;MQ=18.47;MQ0=6;OQ=64.31;QD=4.95;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,3:4:-10.92,-1.20,-3.26:20.53 +chr1 2674111 . T A 27.07 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=32.32;MQ0=6;QD=1.80;SB=-6.99 GT:AD:DP:GL:GQ 0/1:12,3:7:-8.10,-2.11,-18.86:59.90 +chr1 2674112 . A G 16.12 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=32.32;MQ0=6;QD=1.07;SB=-6.99 GT:AD:DP:GL:GQ 0/1:12,3:7:-6.99,-2.11,-20.42:48.85 +chr1 2674407 . A G 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=13.44;MQ=45.39;MQ0=5;OQ=445.12;QD=11.41;SB=-215.68 GT:AD:DP:GL:GQ 0/1:16,22:32:-57.44,-9.65,-56.21:99 +chr1 2674852 rs61766513 G A 450.01 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=13.17;MQ0=18;OQ=519.69;QD=10.39;SB=-286.88 GT:AD:DP:GL:GQ 1/1:0,50:14:-55.56,-4.22,-0.00:42.14 +chr1 2676124 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=1;HaplotypeScore=15.64;MQ=24.04;MQ0=14;OQ=178.81;QD=2.03;SB=-90.56 GT:AD:DP:GL:GQ 0/1:59,29:40:-33.21,-12.05,-114.97:99 +chr1 2676150 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=19.23;MQ=23.09;MQ0=22;OQ=221.70;QD=2.33;SB=-83.88 GT:AD:DP:GL:GQ 0/1:54,41:38:-36.91,-11.46,-90.41:99 +chr1 2676190 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=39.71;MQ=18.24;MQ0=31;OQ=65.56;QD=0.85;SB=-25.50 GT:AD:DP:GL:GQ 0/1:64,13:22:-16.48,-6.63,-57.54:98.40 +chr1 2676191 . G A 29.02 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=39.71;MQ=17.81;MQ0=31;QD=0.39;SB=26.10 GT:AD:DP:GL:GQ 0/1:60,14:18:-11.61,-5.43,-50.51:61.85 +chr1 2676208 . G A 16.39 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.26;MQ=15.36;MQ0=32;QD=0.30;SB=-24.49 GT:AD:DP:GL:GQ 0/1:43,10:12:-8.53,-3.62,-33.94:49.13 +chr1 2676293 rs11486072 G T 42.12 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=21.44;MQ0=18;QD=0.68;SB=83.26 GT:AD:DP:GL:GQ 0/1:53,9:41:-19.85,-12.35,-121.85:74.96 +chr1 2676409 . C G 16.08 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=24.91;MQ=14.80;MQ0=58;QD=0.16;SB=-10.00 GT:AD:DP:GL:GQ 0/1:83,17:12:-8.50,-3.62,-44.92:48.81 +chr1 2677515 . G T 19.05 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=14.46;MQ=8.37;MQ0=110;QD=0.16;SB=-10.00 GT:AD:DP:GL:GQ 0/1:117,3:8:-7.59,-2.41,-19.90:51.83 +chr1 2677525 . C T 16.29 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=1;HaplotypeScore=20.34;MQ=9.26;MQ0=102;QD=0.14;SB=-10.00 GT:AD:DP:GL:GQ 0/1:110,4:10:-7.91,-3.01,-27.95:49.02 +chr1 2677552 . A T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=0;HaplotypeScore=12.35;MQ=15.52;MQ0=82;OQ=53.71;QD=0.48;SB=0.32 GT:AD:DP:GL:GQ 0/1:89,18:28:-23.83,-15.18,-91.71:86.54 +chr1 2677675 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=104;Dels=0.00;HRun=0;HaplotypeScore=15.33;MQ=33.22;MQ0=25;OQ=57.19;QD=0.55;SB=35.14 GT:AD:DP:GL:GQ 0/1:87,15:66:-28.89,-19.89,-231.82:90.03 +chr1 2677743 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=0;HaplotypeScore=4.26;MQ=19.03;MQ0=67;OQ=90.19;QD=0.78;SB=-10.00 GT:AD:DP:GL:GQ 0/1:98,17:39:-24.05,-11.75,-110.96:99 +chr1 2677829 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=23.79;MQ=23.13;MQ0=70;OQ=279.18;QD=2.18;SB=-0.99 GT:AD:DP:GL:GQ 0/1:107,21:47:-45.38,-14.18,-109.88:99 +chr1 2677890 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=0;HaplotypeScore=41.46;MQ=39.72;MQ0=24;OQ=334.00;QD=2.24;SB=-111.40 GT:AD:DP:GL:GQ 0/1:125,24:98:-66.21,-29.53,-281.36:99 +chr1 2677918 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=22.75;MQ=42.78;MQ0=7;OQ=406.29;QD=3.01;SB=-222.57 GT:AD:DP:GL:GQ 0/1:111,24:99:-73.74,-29.83,-281.76:99 +chr1 2678023 rs4601526 G T 43.97 LowQual AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=8.77;MQ=39.66;MQ0=3;QD=0.46;SB=-45.56 GT:AD:DP:GL:GQ 0/1:69,27:71:-29.07,-21.39,-211.74:76.81 +chr1 2678153 rs4287119 C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=112;Dels=0.00;HRun=0;HaplotypeScore=21.76;MQ=40.92;MQ0=5;OQ=2547.58;QD=22.75;SB=-1076.65 GT:AD:DP:GL:GQ 0/1:21,91:87:-284.26,-26.22,-47.57:99 +chr1 2679458 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=42.73;MQ=34.12;MQ0=11;OQ=188.41;QD=2.36;SB=-47.79 GT:AD:DP:GL:GQ 0/1:51,29:31:-31.49,-9.36,-91.42:99 +chr1 2679642 . C G 45.83 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=7.58;MQ=33.48;MQ0=11;QD=0.45;SB=71.27 GT:AD:DP:GL:GQ 0/1:93,9:79:-31.68,-23.81,-299.21:78.67 +chr1 2679803 rs56221638 T A 49.73 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=28.41;MQ=20.22;MQ0=17;QD=0.80;SB=-24.63 GT:AD:DP:GL:GQ 0/1:36,25:21:-14.59,-6.33,-59.48:82.57 +chr1 2679816 rs4648571 G A 0.30 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=13.76;MQ=19.63;MQ0=17;OQ=484.56;QD=8.35;SB=18.94 GT:AD:DP:GL:GQ 1/1:9,49:16:-54.94,-4.82,-2.91:19.19 +chr1 2680538 rs58288263 C A 0.59 PASS AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=19.45;MQ0=42;OQ=235.18;QD=2.28;SB=-135.60 GT:AD:DP:GL:GQ 0/1:70,33:45:-40.37,-13.56,-115.16:99 +chr1 2681143 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=43.31;MQ=7.59;MQ0=129;OQ=216.62;QD=1.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:128,12:8:-27.36,-2.41,-6.90:44.81 +chr1 2681205 . C T 16.27 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=0;HaplotypeScore=11.46;MQ=9.18;MQ0=122;QD=0.12;SB=-10.00 GT:AD:DP:GL:GQ 0/1:130,4:11:-8.21,-3.31,-32.22:49.01 +chr1 2681386 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=85;Dels=0.02;HRun=1;HaplotypeScore=17.33;MQ=40.82;MQ0=2;OQ=547.52;QD=6.44;SB=26.11 GT:AD:DP:GL:GQ 0/1:58,25:71:-78.82,-20.79,-186.55:99 +chr1 2681420 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=13.55;MQ=31.27;MQ0=32;OQ=249.95;QD=2.34;SB=17.08 GT:AD:DP:GL:GQ 0/1:90,15:70:-49.36,-21.09,-234.22:99 +chr1 2681440 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=2;HaplotypeScore=12.17;MQ=28.00;MQ0=51;OQ=57.67;QD=0.49;SB=-0.98 GT:AD:DP:GL:GQ 0/1:103,11:57:-26.23,-17.18,-176.09:90.51 +chr1 2681463 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=112;Dels=0.00;HRun=0;HaplotypeScore=17.45;MQ=24.10;MQ0=61;OQ=86.42;QD=0.77;SB=-10.00 GT:AD:DP:GL:GQ 0/1:104,8:47:-26.08,-14.16,-135.23:99 +chr1 2681473 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=11.36;MQ=22.15;MQ0=63;OQ=86.11;QD=0.79;SB=-10.00 GT:AD:DP:GL:GQ 0/1:101,7:42:-24.54,-12.65,-127.26:99 +chr1 2681679 rs61766519 A T 2.14 PASS AC=1;AF=0.50;AN=2;DB;DP=109;Dels=0.00;HRun=0;HaplotypeScore=3.86;MQ=46.07;MQ0=2;OQ=403.94;QD=3.71;SB=-208.28 GT:AD:DP:GL:GQ 0/1:86,23:102:-74.40,-30.73,-305.98:99 +chr1 2681697 . C G 10.09 PASS AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=45.11;MQ0=2;OQ=843.38;QD=7.21;SB=-230.77 GT:AD:DP:GL:GQ 0/1:84,33:113:-121.68,-34.06,-367.48:99 +chr1 2681715 rs4430271 G A 32.27 PASS AC=2;AF=1.00;AN=2;DB;DP=112;Dels=0.00;HRun=1;HaplotypeScore=3.54;MQ=44.60;MQ0=4;OQ=4104.48;QD=36.65;SB=-1313.32 GT:AD:DP:GL:GQ 1/1:1,111:104:-409.45,-31.34,-0.04:99 +chr1 2681869 . T C 23.42 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=42.88;MQ0=2;QD=0.35;SB=71.26 GT:AD:DP:GL:GQ 0/1:51,15:54:-21.90,-16.27,-186.51:56.24 +chr1 2681986 rs11586212 G A 7.71 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.27;MQ=47.82;MQ0=3;OQ=510.08;QD=6.80;SB=56.19 GT:AD:DP:GL:GQ 0/1:53,22:70:-75.38,-21.09,-180.91:99 +chr1 2682337 . G A 7.34 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=27.22;MQ0=23;OQ=345.10;QD=8.03;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,23:16:-42.61,-4.82,-16.65:99 +chr1 2682347 . G T 0.70 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=19.93;MQ0=26;OQ=183.77;QD=4.59;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,20:10:-24.67,-3.01,-11.27:82.62 +chr1 2682645 . C A 19.07 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.93;MQ=11.47;MQ0=37;QD=0.33;SB=-0.98 GT:AD:DP:GL:GQ 0/1:31,27:8:-7.60,-2.41,-19.17:51.85 +chr1 2683816 rs10909957 C T 271.77 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.42;MQ=46.26;MQ0=0;OQ=686.46;QD=13.46;SB=-268.23 GT:AD:DP:GL:GQ 0/1:24,27:45:-85.49,-13.56,-81.02:99 +chr1 2684356 rs6424062 G A 144.95 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.15;MQ0=0;OQ=655.97;QD=13.39;SB=-112.11 GT:AD:DP:GL:GQ 0/1:26,23:46:-82.76,-13.88,-73.01:99 +chr1 2687573 rs4648459 G T 323.17 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=991.84;QD=18.37;SB=-411.82 GT:AD:DP:GL:GQ 0/1:20,34:49:-117.23,-14.76,-57.58:99 +chr1 2689509 rs4648499 A C 571.48 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=812.32;QD=13.32;SB=-346.80 GT:AD:DP:GL:GQ 0/1:31,30:60:-102.59,-18.07,-113.17:99 +chr1 2689977 rs4648502 C G 37.31 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=4.68;MQ=58.83;MQ0=0;OQ=362.80;QD=11.34;SB=-98.64 GT:AD:DP:GL:GQ 0/1:15,17:26:-47.41,-7.85,-58.24:99 +chr1 2691287 rs10909982 A C 5.74 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=1.88;MQ=58.74;MQ0=0;OQ=1314.76;QD=31.30;SB=-536.04 GT:AD:DP:GL:GQ 1/1:0,42:39:-135.08,-11.75,-0.02:99 +chr1 2691405 . T C 26.51 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.83;MQ=54.55;MQ0=0;QD=0.72;SB=1.18 GT:AD:DP:GL:GQ 0/1:31,6:36:-16.78,-10.85,-121.87:59.34 +chr1 2691676 rs1456462 C G 51.18 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=56.36;MQ0=0;OQ=806.36;QD=17.53;SB=-304.60 GT:AD:DP:GL:GQ 0/1:21,25:41:-96.28,-12.36,-77.64:99 +chr1 2694331 rs12748553 C T 3.51 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=8.78;MQ=58.48;MQ0=0;OQ=835.97;QD=17.06;SB=-250.13 GT:AD:DP:GL:GQ 0/1:21,26:46:-100.74,-13.86,-71.99:99 +chr1 2694778 rs55972083 G T 162.91 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.66;MQ0=0;OQ=915.47;QD=16.64;SB=-316.68 GT:AD:DP:GL:GQ 0/1:25,30:54:-111.10,-16.27,-82.95:99 +chr1 2697298 rs7526311 A T 117.22 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.01;MQ0=0;OQ=185.29;QD=9.75;SB=-41.37 GT:AD:DP:GL:GQ 0/1:12,7:18:-27.23,-5.42,-39.59:99 +chr1 2697760 . G T 0.81 PASS AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=344.69;QD=12.77;SB=-29.36 GT:AD:DP:GL:GQ 0/1:13,14:25:-45.29,-7.54,-35.79:99 +chr1 2697817 rs57572926 T A 7.58 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.48;MQ0=0;OQ=773.03;QD=21.47;SB=-134.51 GT:AD:DP:GL:GQ 0/1:11,25:35:-91.13,-10.54,-41.10:99 +chr1 2699252 rs12044475 G A 223.02 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.73;MQ0=0;OQ=1184.05;QD=17.41;SB=-586.14 GT:AD:DP:GL:GQ 0/1:32,36:66:-141.59,-19.90,-99.06:99 +chr1 2699436 rs12024170 C T 193.04 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.75;MQ0=0;OQ=1445.81;QD=19.54;SB=-655.75 GT:AD:DP:GL:GQ 0/1:31,43:72:-169.56,-21.69,-100.95:99 +chr1 2699862 rs6687680 G A 230.47 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.28;MQ0=0;OQ=1732.28;QD=19.25;SB=-761.79 GT:AD:DP:GL:GQ 0/1:40,50:89:-203.33,-26.82,-125.78:99 +chr1 2700237 . G A 246.23 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1343.35;QD=18.92;SB=-523.75 GT:AD:DP:GL:GQ 0/1:31,40:71:-159.02,-21.40,-102.65:99 +chr1 2702030 rs12731995 A G 434.35 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=677.81;QD=11.11;SB=-347.04 GT:AD:DP:GL:GQ 0/1:33,28:60:-89.15,-18.08,-132.37:99 +chr1 2703187 rs2377041 C T 502.97 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=621.61;QD=15.54;SB=-277.29 GT:AD:DP:GL:GQ 0/1:21,19:39:-77.20,-11.76,-63.03:99 +chr1 2704632 . T C 38.02 LowQual AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=4;HaplotypeScore=7.59;MQ=52.48;MQ0=0;QD=2.38;SB=-19.89 GT:AD:DP:GL:GQ 0/1:10,6:12:-10.71,-3.62,-29.51:70.86 +chr1 2704685 . G A 22.35 LowQual AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=7.62;MQ=56.04;MQ0=0;QD=1.86;SB=-34.51 GT:AD:DP:GL:GQ 0/1:9,2:7:-7.63,-2.11,-16.67:55.16 +chr1 2704950 . A G 2.25 PASS AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=48.87;MQ0=0;OQ=588.34;QD=32.69;SB=-143.72 GT:AD:DP:GL:GQ 1/1:0,18:17:-62.42,-5.12,-0.01:51.15 +chr1 2705371 . T C 47.74 LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=3.65;MQ=60.80;MQ0=0;QD=2.51;SB=-6.99 GT:AD:DP:GL:GQ 0/1:12,6:14:-12.28,-4.22,-38.37:80.58 +chr1 2705380 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=2;HaplotypeScore=2.68;MQ=59.93;MQ0=0;OQ=62.82;QD=3.31;SB=-3.98 GT:AD:DP:GL:GQ 0/1:14,5:17:-14.69,-5.13,-40.99:95.66 +chr1 2706146 . A G 47.67 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=5;HaplotypeScore=3.46;MQ=57.94;MQ0=0;QD=1.40;SB=47.18 GT:AD:DP:GL:GQ 0/1:26,7:27:-16.19,-8.14,-86.26:80.50 +chr1 2706767 rs751358 G C 35.53 PASS AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=240.08;QD=16.01;SB=-112.68 GT:AD:DP:GL:GQ 0/1:7,8:15:-31.82,-4.53,-27.47:99 +chr1 2708350 rs897627 T C 68.67 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.23;MQ0=0;OQ=241.23;QD=8.04;SB=-88.78 GT:AD:DP:GL:GQ 0/1:18,12:26:-35.25,-7.84,-56.33:99 +chr1 2709162 rs897626 T C 124.16 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=58.50;MQ0=0;OQ=297.67;QD=9.60;SB=-169.49 GT:AD:DP:GL:GQ 0/1:13,16:23:-39.99,-6.94,-39.26:99 +chr1 2709764 rs12725202 C A 209.03 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=59.58;MQ0=0;OQ=806.35;QD=14.66;SB=-275.34 GT:AD:DP:GL:GQ 0/1:27,28:48:-98.38,-14.47,-61.56:99 +chr1 2711436 rs897623 A G 190.36 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=58.98;MQ0=0;OQ=627.29;QD=15.30;SB=-199.45 GT:AD:DP:GL:GQ 0/1:15,26:39:-77.77,-11.76,-60.17:99 +chr1 2712708 rs6692145 C T 11.73 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=7.75;MQ=59.11;MQ0=0;OQ=873.72;QD=16.80;SB=-440.44 GT:AD:DP:GL:GQ 0/1:21,31:48:-105.13,-14.48,-65.51:99 +chr1 2713074 rs4648450 C A 220.10 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.19;MQ0=0;OQ=931.32;QD=16.34;SB=-352.41 GT:AD:DP:GL:GQ 0/1:24,33:49:-111.18,-14.76,-58.95:99 +chr1 2713205 rs4648360 C T 362.23 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.64;MQ0=0;OQ=808.14;QD=12.63;SB=-348.52 GT:AD:DP:GL:GQ 0/1:38,26:64:-103.39,-19.29,-126.27:99 +chr1 2713822 rs11588256 T C 179.59 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.44;MQ0=0;OQ=1164.73;QD=28.41;SB=-522.80 GT:AD:DP:GL:GQ 1/1:0,40:39:-122.64,-14.15,-2.58:99 +chr1 2715335 rs7537581 C A 258.05 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.30;MQ0=0;OQ=476.92;QD=14.45;SB=-256.43 GT:AD:DP:GL:GQ 0/1:16,17:32:-60.62,-9.64,-51.47:99 +chr1 2715367 rs56038961 C T 199.13 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.45;MQ0=0;OQ=479.64;QD=15.99;SB=-264.20 GT:AD:DP:GL:GQ 0/1:12,18:27:-59.39,-8.14,-35.88:99 +chr1 2716724 rs17387572 C G 92.23 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=58.95;MQ0=0;OQ=183.11;QD=8.32;SB=-57.73 GT:AD:DP:GL:GQ 0/1:14,8:19:-27.33,-5.74,-48.15:99 +chr1 2717498 rs10909879 G A 568.71 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=638.90;QD=14.20;SB=-321.91 GT:AD:DP:GL:GQ 0/1:24,21:43:-80.13,-12.96,-77.89:99 +chr1 2717664 rs10909880 C T 111.56 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.85;MQ=58.20;MQ0=0;OQ=901.98;QD=16.40;SB=-412.72 GT:AD:DP:GL:GQ 0/1:27,27:53:-109.45,-15.96,-95.84:99 +chr1 2718581 rs2290583 C T 466.48 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.90;MQ0=0;OQ=858.25;QD=15.60;SB=-364.54 GT:AD:DP:GL:GQ 0/1:27,28:51:-104.48,-15.37,-82.61:99 +chr1 2720957 rs56242447 T C 191.02 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=60.00;MQ0=0;OQ=720.09;QD=11.43;SB=-266.23 GT:AD:DP:GL:GQ 0/1:29,34:60:-93.39,-18.10,-112.64:99 +chr1 2725957 rs4648454 C A 155.77 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.23;MQ0=0;OQ=2137.84;QD=35.63;SB=-968.57 GT:AD:DP:GL:GQ 1/1:0,60:60:-217.39,-18.07,-0.02:99 +chr1 2727346 rs4515734 C T 401.62 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=1193.72;QD=37.30;SB=-333.34 GT:AD:DP:GL:GQ 1/1:0,32:32:-122.97,-9.64,-0.01:96.30 +chr1 2728125 rs11584658 C T 220.84 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=58.92;MQ0=0;OQ=363.72;QD=9.33;SB=-203.89 GT:AD:DP:GL:GQ 0/1:25,14:38:-51.11,-11.46,-81.85:99 +chr1 2728509 . C G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=7.07;MQ=57.48;MQ0=0;OQ=153.44;QD=5.48;SB=38.15 GT:AD:DP:GL:GQ 0/1:17,11:22:-25.28,-6.65,-60.78:99 +chr1 2728983 rs12025517 T C 254.56 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.46;MQ0=0;OQ=692.09;QD=16.10;SB=-320.61 GT:AD:DP:GL:GQ 0/1:17,25:42:-87.78,-15.29,-69.40:99 +chr1 2731560 rs897622 T C 5.62 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.40;MQ=59.38;MQ0=0;OQ=1158.40;QD=31.31;SB=-281.53 GT:AD:DP:GL:GQ 1/1:0,37:35:-119.44,-10.55,-0.02:99 +chr1 2734276 rs56400103 G A 253.28 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=949.71;QD=17.92;SB=-409.46 GT:AD:DP:GL:GQ 0/1:24,29:51:-113.64,-15.38,-67.18:99 +chr1 2734570 rs12747919 T C 241.01 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.34;MQ0=0;OQ=778.48;QD=12.36;SB=-342.05 GT:AD:DP:GL:GQ 0/1:32,31:63:-100.12,-18.99,-128.39:99 +chr1 2734737 rs12125787 G A 71.93 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.70;MQ=57.83;MQ0=0;OQ=2028.15;QD=37.56;SB=-957.98 GT:AD:DP:GL:GQ 1/1:0,54:53:-206.42,-15.97,-0.02:99 +chr1 2735743 rs4609377 C T 266.10 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=58.76;MQ0=0;OQ=803.58;QD=14.35;SB=-286.83 GT:AD:DP:GL:GQ 0/1:31,25:54:-99.92,-16.28,-93.51:99 +chr1 2735926 rs1001620 G C 451.59 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.61;MQ0=0;OQ=977.15;QD=12.69;SB=-354.56 GT:AD:DP:GL:GQ 0/1:46,31:77:-124.21,-23.21,-202.34:99 +chr1 2739474 rs10797389 G A 308.93 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=60.00;MQ0=0;OQ=750.99;QD=15.65;SB=-309.79 GT:AD:DP:GL:GQ 0/1:23,25:47:-92.55,-14.16,-81.12:99 +chr1 2739576 rs4648481 G T 368.63 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=60.00;MQ0=0;OQ=793.99;QD=14.70;SB=-305.02 GT:AD:DP:GL:GQ 0/1:26,28:52:-98.35,-15.67,-82.42:99 +chr1 2739781 rs4648482 T C 14.80 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=4.29;MQ=58.44;MQ0=0;OQ=365.14;QD=8.69;SB=-69.92 GT:AD:DP:GL:GQ 0/1:24,18:40:-51.86,-12.06,-91.45:99 +chr1 2740297 rs1563471 C T 85.39 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=5.94;MQ=59.22;MQ0=0;OQ=682.02;QD=11.56;SB=-286.79 GT:AD:DP:GL:GQ 0/1:33,26:55:-88.08,-16.60,-99.20:99 +chr1 2740756 rs12132067 G A 288.53 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.87;MQ=59.52;MQ0=0;OQ=623.21;QD=12.98;SB=-250.12 GT:AD:DP:GL:GQ 0/1:27,21:48:-80.07,-14.46,-95.69:99 +chr1 2742125 rs7511879 A G 408.25 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.68;MQ0=0;OQ=942.16;QD=16.24;SB=-438.99 GT:AD:DP:GL:GQ 0/1:24,34:55:-114.07,-16.57,-91.14:99 +chr1 2742553 rs10797390 C T 146.24 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.59;MQ0=0;OQ=1057.36;QD=18.88;SB=-301.83 GT:AD:DP:GL:GQ 0/1:24,32:56:-125.89,-16.87,-83.67:99 +chr1 2743097 rs12031493 A G 99.82 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=5.23;MQ=59.34;MQ0=0;OQ=647.93;QD=9.26;SB=-314.90 GT:AD:DP:GL:GQ 0/1:40,29:67:-88.27,-20.19,-156.45:99 +chr1 2743232 rs11803074 T C 136.13 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.52;MQ0=0;OQ=450.58;QD=9.39;SB=-159.47 GT:AD:DP:GL:GQ 0/1:26,22:43:-61.31,-12.96,-94.61:99 +chr1 2743923 rs2377040 G A 85.94 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.57;MQ0=0;OQ=1679.85;QD=39.07;SB=-699.34 GT:AD:DP:GL:GQ 1/1:0,43:43:-171.58,-12.96,-0.02:99 +chr1 2744048 rs6691019 A G 253.73 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=599.61;QD=12.24;SB=-315.28 GT:AD:DP:GL:GQ 0/1:24,25:46:-77.11,-13.87,-86.95:99 +chr1 2744266 rs729045 A G 494.21 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=550.14;QD=10.19;SB=-251.93 GT:AD:DP:GL:GQ 0/1:30,24:53:-74.27,-15.97,-120.98:99 +chr1 2744372 rs6680471 C T 188.10 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=58.81;MQ0=0;OQ=743.73;QD=13.52;SB=-388.16 GT:AD:DP:GL:GQ 0/1:30,25:50:-92.73,-15.07,-87.39:99 +chr1 2744840 rs7541827 T G 3.84 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=3.30;MQ=53.60;MQ0=0;OQ=317.87;QD=7.95;SB=-163.88 GT:AD:DP:GL:GQ 0/1:27,13:38:-46.52,-11.45,-85.79:99 +chr1 2745157 rs10909938 C G 278.22 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.10;MQ0=0;OQ=946.24;QD=11.98;SB=-426.32 GT:AD:DP:GL:GQ 0/1:47,32:78:-121.44,-23.53,-202.08:99 +chr1 2745633 rs10909941 A G 382.13 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.59;MQ0=0;OQ=1890.77;QD=33.76;SB=-793.15 GT:AD:DP:GL:GQ 1/1:0,56:54:-192.68,-16.26,-0.02:99 +chr1 2746148 rs4648382 C T 75.36 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=4.95;MQ=58.25;MQ0=0;OQ=1103.18;QD=17.24;SB=-437.97 GT:AD:DP:GL:GQ 0/1:30,34:62:-132.29,-18.69,-91.91:99 +chr1 2746257 rs4648383 C T 112.72 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.45;MQ0=0;OQ=1198.75;QD=17.63;SB=-573.37 GT:AD:DP:GL:GQ 0/1:33,35:67:-143.34,-20.18,-115.97:99 +chr1 2746481 rs4648384 C A 147.70 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=2.23;MQ=58.55;MQ0=0;OQ=974.97;QD=15.98;SB=-482.87 GT:AD:DP:GL:GQ 0/1:29,32:59:-118.55,-17.77,-93.40:99 +chr1 2746667 rs7516014 G T 183 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=60.00;MQ0=0;OQ=529.64;QD=10.81;SB=-238.43 GT:AD:DP:GL:GQ 0/1:28,20:47:-70.41,-14.16,-95.06:99 +chr1 2746749 rs7548023 T G 93.22 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=3.08;MQ=57.92;MQ0=0;OQ=762.24;QD=14.12;SB=-346.84 GT:AD:DP:GL:GQ 0/1:27,27:54:-95.77,-16.26,-99.72:99 +chr1 2747056 rs4648495 T C 0.66 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=4;HaplotypeScore=4.04;MQ=53.57;MQ0=0;OQ=334.06;QD=9.83;SB=-158.61 GT:AD:DP:GL:GQ 0/1:15,19:25:-44.23,-7.54,-43.47:99 +chr1 2747271 rs4648496 A T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=20.04;MQ=49.89;MQ0=0;OQ=70.38;QD=0.95;SB=-47.55 GT:AD:DP:GL:GQ 0/1:64,10:68:-30.81,-20.49,-219.78:99 +chr1 2747291 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=65;Dels=0.03;HRun=0;HaplotypeScore=32.13;MQ=46.89;MQ0=0;OQ=444.72;QD=6.84;SB=-168.12 GT:AD:DP:GL:GQ 0/1:44,19:62:-65.84,-18.08,-149.47:99 +chr1 2747315 . A T 0.07 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=12.70;MQ=47.25;MQ0=0;OQ=757.92;QD=13.53;SB=-390.15 GT:AD:DP:GL:GQ 0/1:29,27:49:-93.84,-14.77,-85.21:99 +chr1 2747334 rs36040910 C G 1014.60 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.02;HRun=0;HaplotypeScore=10.13;MQ=46.42;MQ0=0;QD=19.14;SB=-531.73 GT:AD:DP:GL:GQ 0/1:24,28:52:-120.42,-15.67,-100.79:99 +chr1 2747338 . G C 826.30 SnpCluster AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=9.97;MQ=47.26;MQ0=0;QD=17.21;SB=-358.43 GT:AD:DP:GL:GQ 0/1:23,24:47:-99.78,-13.86,-101.33:99 +chr1 2747339 . A T 752.39 SnpCluster AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=3.00;MQ=47.26;MQ0=0;QD=15.67;SB=-313.68 GT:AD:DP:GL:GQ 0/1:23,24:47:-92.38,-13.86,-82.64:99 +chr1 2747369 . A T 3.22 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=49.16;MQ0=0;OQ=703.99;QD=14.37;SB=-261.27 GT:AD:DP:GL:GQ 0/1:25,24:47:-87.84,-14.16,-92.00:99 +chr1 2747375 rs61766530 T A 10.44 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=7.95;MQ=48.99;MQ0=0;OQ=615.25;QD=13.37;SB=-274.62 GT:AD:DP:GL:GQ 0/1:24,22:43:-77.76,-12.95,-81.15:99 +chr1 2747387 rs34464542 A T 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.05;HRun=0;HaplotypeScore=17.99;MQ=50.33;MQ0=0;OQ=475.32;QD=10.80;SB=-181.51 GT:AD:DP:GL:GQ 0/1:25,17:43:-63.16,-12.35,-94.24:99 +chr1 2747397 rs12739189 C T 56.98 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=5.47;MQ=51.77;MQ0=0;OQ=606.36;QD=14.44;SB=-321.86 GT:AD:DP:GL:GQ 0/1:23,19:42:-76.58,-12.66,-74.78:99 +chr1 2747562 rs35401657 A G 338.79 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=54.94;MQ0=0;OQ=916.49;QD=12.73;SB=-443.41 GT:AD:DP:GL:GQ 0/1:37,34:70:-119.52,-24.59,-154.08:99 +chr1 2747592 rs34262355 G A 349.69 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=54.28;MQ0=0;OQ=1032.22;QD=12.74;SB=-451.44 GT:AD:DP:GL:GQ 0/1:45,35:78:-130.02,-23.51,-145.95:99 +chr1 2747610 rs34202711 A G 414.76 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.97;MQ0=0;OQ=1011.04;QD=11.89;SB=-504.68 GT:AD:DP:GL:GQ 0/1:42,43:82:-129.10,-24.71,-172.46:99 +chr1 2747660 rs1456461 C T 603.75 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.82;MQ0=0;OQ=891.16;QD=15.63;SB=-457.95 GT:AD:DP:GL:GQ 0/1:30,27:57:-109.57,-17.17,-111.30:99 +chr1 2748044 rs12740180 C A 413.82 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=606.44;QD=10.83;SB=-262.28 GT:AD:DP:GL:GQ 0/1:33,23:54:-80.19,-16.26,-114.41:99 +chr1 2748753 rs2889541 G A 337.75 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.41;MQ0=0;OQ=1139.69;QD=16.05;SB=-477.50 GT:AD:DP:GL:GQ 0/1:37,34:70:-138.35,-21.10,-115.20:99 +chr1 2749666 rs12037615 A T 1.80 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=5;HaplotypeScore=1.16;MQ=59.20;MQ0=0;OQ=1128.99;QD=14.86;SB=-549.41 GT:AD:DP:GL:GQ 0/1:40,36:76:-139.07,-22.89,-148.90:99 +chr1 2749715 rs12047690 C T 131.06 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=816.13;QD=12.95;SB=-150.20 GT:AD:DP:GL:GQ 0/1:36,27:60:-102.99,-18.09,-107.52:99 +chr1 2751235 rs12049543 C A 405.31 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.56;MQ0=0;OQ=1060.86;QD=12.63;SB=-512.22 GT:AD:DP:GL:GQ 0/1:47,37:84:-134.67,-25.30,-168.73:99 +chr1 2751390 rs1840738 T C 158.28 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=56.95;MQ0=0;OQ=466.03;QD=9.14;SB=-238.28 GT:AD:DP:GL:GQ 0/1:29,21:47:-64.06,-14.17,-105.57:99 +chr1 2751392 rs1840737 T C 150.88 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=56.89;MQ0=0;OQ=432.09;QD=8.64;SB=-211.35 GT:AD:DP:GL:GQ 0/1:30,20:46:-60.36,-13.87,-105.49:99 +chr1 2751468 rs1840736 C T 225.14 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=58.99;MQ0=0;OQ=538.81;QD=11.71;SB=-284.82 GT:AD:DP:GL:GQ 0/1:28,18:46:-71.04,-13.87,-86.92:99 +chr1 2751723 rs1456460 G T 356.16 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=57.19;MQ0=0;OQ=1157.64;QD=13.31;SB=-342.38 GT:AD:DP:GL:GQ 0/1:48,39:87:-145.25,-26.21,-162.75:99 +chr1 2753129 rs6424080 T C 316.66 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.51;MQ0=0;OQ=966.99;QD=12.24;SB=-274.18 GT:AD:DP:GL:GQ 0/1:43,36:77:-123.19,-23.21,-165.41:99 +chr1 2753241 rs6424081 G C 7.87 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=4;HaplotypeScore=2.76;MQ=58.85;MQ0=0;OQ=855.86;QD=17.47;SB=-443.74 GT:AD:DP:GL:GQ 0/1:25,24:49:-103.64,-14.77,-108.86:99 +chr1 2753928 rs10909950 G C 275.97 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.98;MQ0=0;OQ=738.28;QD=13.67;SB=-369.83 GT:AD:DP:GL:GQ 0/1:27,27:50:-92.19,-15.07,-120.46:99 +chr1 2754032 rs7553697 T C 122.97 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=50.90;MQ0=0;OQ=845.37;QD=27.27;SB=-371.38 GT:AD:DP:GL:GQ 1/1:0,31:28:-88.15,-8.45,-0.03:84.18 +chr1 2754183 rs6424082 A G 8.12 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=5.05;MQ=58.51;MQ0=0;OQ=416.20;QD=9.46;SB=-192.43 GT:AD:DP:GL:GQ 0/1:23,21:40:-56.97,-12.06,-83.18:99 +chr1 2754298 rs6424083 C G 173.34 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=55.35;MQ0=0;OQ=1296.80;QD=37.05;SB=-603.86 GT:AD:DP:GL:GQ 1/1:0,35:33:-133.29,-9.95,-0.02:99 +chr1 2754773 . G A 0.64 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=3.22;MQ=60.00;MQ0=0;OQ=1109.61;QD=18.81;SB=-280.74 GT:AD:DP:GL:GQ 0/1:25,34:58:-131.72,-17.47,-86.47:99 +chr1 2754949 rs34133714 C T 67.94 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=57.50;MQ0=0;OQ=577.42;QD=16.98;SB=-168.27 GT:AD:DP:GL:GQ 0/1:16,18:34:-71.28,-10.25,-51.84:99 +chr1 2755031 rs34352177 T C 19.62 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=7.41;MQ=59.06;MQ0=0;OQ=899.29;QD=13.03;SB=-455.95 GT:AD:DP:GL:GQ 0/1:36,31:67:-116.13,-22.92,-145.73:99 +chr1 2755403 rs11806141 T G 18.81 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=6.77;MQ=51.89;MQ0=9;QD=0.27;SB=74.23 GT:AD:DP:GL:GQ 0/1:49,20:51:-20.52,-15.36,-159.70:51.59 +chr1 2755508 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=79;Dels=0.06;HRun=2;HaplotypeScore=38.09;MQ=49.34;MQ0=4;OQ=65.07;QD=0.82;SB=71.26 GT:AD:DP:GL:GQ 0/1:58,15:62:-27.57,-17.78,-196.95:97.90 +chr1 2755529 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=65.45;MQ=46.51;MQ0=7;OQ=513.73;QD=7.04;SB=-185.79 GT:AD:DP:GL:GQ 0/1:43,30:51:-70.02,-15.37,-107.03:99 +chr1 2755532 . A G 42.46 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=67.89;MQ=46.23;MQ0=7;QD=0.57;SB=41.14 GT:AD:DP:GL:GQ 0/1:61,13:50:-22.60,-15.07,-170.16:75.29 +chr1 2755579 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=21.20;MQ=45.33;MQ0=9;OQ=157.48;QD=2.02;SB=-23.25 GT:AD:DP:GL:GQ 0/1:60,12:47:-33.22,-14.19,-119.56:99 +chr1 2755596 rs11806928 A G 0.11 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=12.62;MQ=45.10;MQ0=9;OQ=205.66;QD=2.78;SB=-15.21 GT:AD:DP:GL:GQ 0/1:58,16:54:-40.13,-16.28,-162.81:99 +chr1 2755612 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=11.17;MQ=46.38;MQ0=5;OQ=126.58;QD=1.73;SB=14.62 GT:AD:DP:GL:GQ 0/1:63,10:57:-33.13,-17.19,-158.30:99 +chr1 2755632 rs10909952 C T 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=10.73;MQ=46.85;MQ0=3;OQ=64.17;QD=0.87;SB=26.06 GT:AD:DP:GL:GQ 0/1:61,13:47:-23.87,-14.17,-131.74:97 +chr1 2755643 . C T 0.06 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=7.11;MQ=46.66;MQ0=2;OQ=370.42;QD=5.22;SB=-83.91 GT:AD:DP:GL:GQ 0/1:46,20:49:-55.11,-14.78,-108.17:99 +chr1 2755657 rs61763677 G T 0.15 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=8.88;MQ=44.97;MQ0=5;OQ=282.63;QD=3.29;SB=-9.61 GT:AD:DP:GL:GQ 0/1:69,17:72:-53.24,-21.69,-193.61:99 +chr1 2755674 rs61763678 C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=0;HaplotypeScore=23.01;MQ=44.47;MQ0=7;OQ=292.56;QD=2.76;SB=-24.23 GT:AD:DP:GL:GQ 0/1:76,27:79:-56.37,-23.83,-203.58:99 +chr1 2755706 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=46.46;MQ=43.46;MQ0=6;OQ=100.65;QD=1.01;SB=48.33 GT:AD:DP:GL:GQ 0/1:73,19:68:-33.86,-20.51,-216.35:99 +chr1 2755733 rs10909953 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=134.56;MQ=44.60;MQ0=11;OQ=218.03;QD=1.83;SB=-68.77 GT:AD:DP:GL:GQ 0/1:91,18:82:-72.98,-47.89,-237.50:99 +chr1 2755738 rs10909954 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.00;HRun=0;HaplotypeScore=94.54;MQ=44.07;MQ0=12;OQ=119.63;QD=1.01;SB=15.66 GT:AD:DP:GL:GQ 0/1:86,29:80:-42.04,-26.79,-256.64:99 +chr1 2755753 . G A 11.77 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=1;HaplotypeScore=33.32;MQ=44.33;MQ0=10;QD=0.09;SB=66.29 GT:AD:DP:GL:GQ 0/1:116,10:95:-33.05,-28.62,-308.21:44.31 +chr1 2755755 rs57067996 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=130;Dels=0.00;HRun=1;HaplotypeScore=39.46;MQ=44.65;MQ0=10;OQ=1208.64;QD=9.30;SB=-349.24 GT:AD:DP:GL:GQ 0/1:72,52:91:-151.57,-27.42,-186.87:99 +chr1 2755787 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=209;Dels=0.00;HRun=0;HaplotypeScore=9.86;MQ=44.22;MQ0=18;OQ=212.29;QD=1.02;SB=84.79 GT:AD:DP:GL:GQ 0/1:175,28:147:-68.83,-44.32,-479.03:99 +chr1 2755816 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=1;HaplotypeScore=62.94;MQ=43.89;MQ0=23;OQ=172.99;QD=0.80;SB=63.05 GT:AD:DP:GL:GQ 0/1:192,24:159:-68.50,-47.92,-487.91:99 +chr1 2755844 rs4991850 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=164;Dels=0.00;HRun=0;HaplotypeScore=53.96;MQ=43.72;MQ0=16;OQ=1135.99;QD=6.93;SB=-394.17 GT:AD:DP:GL:GQ 0/1:112,52:121:-153.35,-36.47,-275.01:99 +chr1 2755847 rs57868894 T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=161;Dels=0.00;HRun=1;HaplotypeScore=64.38;MQ=43.84;MQ0=16;OQ=859.67;QD=5.34;SB=-128.73 GT:AD:DP:GL:GQ 0/1:103,58:122:-126.01,-36.76,-296.17:99 +chr1 2755864 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=139;Dels=0.00;HRun=0;HaplotypeScore=32.56;MQ=44.46;MQ0=14;OQ=96.62;QD=0.70;SB=30.17 GT:AD:DP:GL:GQ 0/1:117,20:102:-43.73,-30.78,-282.87:99 +chr1 2755889 rs4991849 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=114;Dels=0.04;HRun=2;HaplotypeScore=40.28;MQ=47.08;MQ0=9;OQ=2321.13;QD=20.36;SB=-1120.12 GT:AD:DP:GL:GQ 0/1:18,92:93:-262.51,-27.11,-65.29:99 +chr1 2755910 rs12728224 T G 16.56 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=49.38;MQ0=5;QD=0.17;SB=88.35 GT:AD:DP:GL:GQ 0/1:84,11:79:-28.73,-23.80,-253.95:49.30 +chr1 2755924 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=18.40;MQ=49.90;MQ0=6;OQ=1394.92;QD=15.16;SB=-476.13 GT:AD:DP:GL:GQ 0/1:39,53:66:-162.68,-19.90,-75.57:99 +chr1 2755992 . G A 33.66 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=19.55;MQ=45.20;MQ0=8;QD=0.40;SB=27.48 GT:AD:DP:GL:GQ 0/1:73,12:61:-25.05,-18.40,-176.14:66.50 +chr1 2756013 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=17.90;MQ=45.32;MQ0=5;OQ=157.50;QD=2.67;SB=-33.78 GT:AD:DP:GL:GQ 0/1:38,21:37:-30.19,-11.15,-106.30:99 +chr1 2756025 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=4.66;MQ=45.60;MQ0=4;OQ=63.13;QD=1.15;SB=26.12 GT:AD:DP:GL:GQ 0/1:45,10:38:-21.07,-11.48,-129.01:95.97 +chr1 2756051 rs4992290 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=36.34;MQ=44.26;MQ0=6;OQ=205.91;QD=3.38;SB=35.13 GT:AD:DP:GL:GQ 0/1:37,24:36:-34.74,-10.86,-87.18:99 +chr1 2756088 rs6676347 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=50.22;MQ=41.73;MQ0=14;OQ=1315.11;QD=15.29;SB=-568.14 GT:AD:DP:GL:GQ 0/1:37,49:48:-149.26,-14.46,-35.10:99 +chr1 2756101 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=1;HaplotypeScore=21.36;MQ=40.87;MQ0=15;OQ=73.71;QD=0.88;SB=47.17 GT:AD:DP:GL:GQ 0/1:64,20:51:-26.02,-15.36,-158.57:99 +chr1 2756151 rs4648513 T C 97.75 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=4.14;MQ=50.77;MQ0=9;OQ=1380.54;QD=20.92;SB=-651.39 GT:AD:DP:GL:GQ 1/1:9,57:48:-150.01,-14.48,-8.38:61.01 +chr1 2756174 rs59048447 G A 70.95 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=5.41;MQ=56.28;MQ0=2;OQ=675.24;QD=12.74;SB=-328.31 GT:AD:DP:GL:GQ 0/1:26,27:46:-84.67,-13.86,-86.53:99 +chr1 2756831 rs4648515 C T 238.63 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=59.11;MQ0=0;OQ=2661.31;QD=39.14;SB=-1337.11 GT:AD:DP:GL:GQ 1/1:1,67:68:-272.30,-20.49,-2.59:99 +chr1 2757061 rs4648518 A G 438.92 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1894.09;QD=32.66;SB=-719.10 GT:AD:DP:GL:GQ 1/1:0,58:55:-193.02,-16.57,-0.02:99 +chr1 2757563 rs4648519 C T 617.31 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=2063.43;QD=38.21;SB=-1058.93 GT:AD:DP:GL:GQ 1/1:0,54:53:-209.94,-15.97,-0.02:99 +chr1 2758482 . C T 0.54 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=50.17;MQ0=3;OQ=191.27;QD=4.25;SB=-120.51 GT:AD:DP:GL:GQ 0/1:31,14:38:-33.86,-11.45,-100.08:99 +chr1 2758751 . T G 48.69 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=34.31;MQ0=7;QD=1.62;SB=-11.91 GT:AD:DP:GL:GQ 0/1:21,9:22:-14.78,-6.63,-62.96:81.53 +chr1 2758819 . A G 182.25 PASS AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=42.84;MQ0=2;OQ=868.67;QD=27.15;SB=-395.30 GT:AD:DP:GL:GQ 1/1:1,31:28:-90.48,-8.45,-0.03:84.20 +chr1 2758861 . T C 30.75 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.14;MQ=44.85;MQ0=1;QD=0.90;SB=29.12 GT:AD:DP:GL:GQ 0/1:26,7:26:-14.19,-7.84,-86.43:63.58 +chr1 2758882 . G A 6.14 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=35.37;MQ0=5;OQ=748.79;QD=17.41;SB=-255.79 GT:AD:DP:GL:GQ 0/1:14,29:29:-86.90,-8.74,-21.14:99 +chr1 2758933 . T C 5.05 PASS AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=4.40;MQ=30.24;MQ0=6;OQ=270.13;QD=7.50;SB=-156.34 GT:AD:DP:GL:GQ 0/1:9,26:16:-35.12,-4.83,-17.51:99 +chr1 2758959 . T G 27.66 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=27.02;MQ0=8;QD=0.92;SB=-23.52 GT:AD:DP:GL:GQ 0/1:24,6:11:-9.36,-3.32,-25.67:60.48 +chr1 2759011 . T G 0.06 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=3.83;MQ=18.26;MQ0=23;OQ=314.04;QD=4.42;SB=-69.87 GT:AD:DP:GL:GQ 0/1:37,34:26:-42.52,-7.83,-50.68:99 +chr1 2759038 . G T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=15.13;MQ=25.49;MQ0=29;OQ=89.07;QD=0.97;SB=-9.29 GT:AD:DP:GL:GQ 0/1:85,7:35:-22.74,-10.55,-90.79:99 +chr1 2759090 . G T 15.10 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=11.61;MQ=28.51;MQ0=10;QD=0.35;SB=-6.99 GT:AD:DP:GL:GQ 0/1:32,11:16:-9.61,-4.83,-35.57:47.80 +chr1 2759130 rs61763686 T C 37.28 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=18.78;MQ0=1;QD=12.43;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:2:-7.14,-0.60,-0.00:6.02 +chr1 2759142 . G A 1.53 PASS AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=18.78;MQ0=2;OQ=80.16;QD=13.36;SB=-10.00 GT:AD:DP:GL:GQ 0/1:3,3:4:-12.50,-1.21,-3.10:18.91 +chr1 2759167 . G T 2.82 PASS AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=26.71;MQ0=4;OQ=151.71;QD=6.90;SB=-6.99 GT:AD:DP:GL:GQ 0/1:16,6:14:-22.67,-4.22,-28.76:99 +chr1 2759193 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=15.10;MQ=26.07;MQ0=10;OQ=142.00;QD=2.90;SB=-61.29 GT:AD:DP:GL:GQ 0/1:38,11:32:-27.13,-9.65,-83.88:99 +chr1 2759219 . G T 0.58 PASS AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=27.42;MQ0=13;OQ=233.66;QD=3.03;SB=-10.31 GT:AD:DP:GL:GQ 0/1:59,18:48:-41.11,-14.46,-126.09:99 +chr1 2759237 rs10909961 G A 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=9.56;MQ=30.14;MQ0=15;OQ=68.31;QD=0.77;SB=29.11 GT:AD:DP:GL:GQ 0/1:82,7:55:-26.69,-16.57,-172.16:99 +chr1 2759271 . G T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=31.60;MQ0=17;OQ=103.26;QD=1.09;SB=14.07 GT:AD:DP:GL:GQ 0/1:79,16:53:-29.57,-15.96,-157.88:99 +chr1 2759402 rs10752737 G A 706.16 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.81;MQ0=0;OQ=3330.93;QD=38.29;SB=-1475.63 GT:AD:DP:GL:GQ 1/1:0,87:84:-332.09,-25.31,-0.03:99 +chr1 2759793 rs6665646 C T 285.69 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.67;MQ0=0;OQ=1210.11;QD=17.54;SB=-511.14 GT:AD:DP:GL:GQ 0/1:33,36:69:-145.09,-20.79,-106.44:99 +chr1 2760042 rs6679343 A T 0.12 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=6;HaplotypeScore=1.76;MQ=59.01;MQ0=0;OQ=2240.29;QD=33.94;SB=-793.89 GT:AD:DP:GL:GQ 1/1:0,66:63:-227.64,-18.99,-0.03:99 +chr1 2761186 . C G 0.63 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=4;HaplotypeScore=1.71;MQ=59.37;MQ0=0;OQ=541.38;QD=12.30;SB=-216.32 GT:AD:DP:GL:GQ 0/1:26,18:41:-69.78,-12.36,-101.99:99 +chr1 2761364 rs12743952 G A 204.61 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=59.65;MQ0=0;OQ=611.70;QD=11.33;SB=-279.20 GT:AD:DP:GL:GQ 0/1:32,22:50:-79.52,-15.07,-100.94:99 +chr1 2761375 rs12743965 G A 240.15 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.65;MQ0=0;OQ=726.42;QD=13.45;SB=-307.80 GT:AD:DP:GL:GQ 0/1:31,23:53:-91.89,-15.96,-108.39:99 +chr1 2761483 rs34161193 G A 219.36 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=58.78;MQ0=0;OQ=505.10;QD=13.29;SB=-258.15 GT:AD:DP:GL:GQ 0/1:20,17:37:-64.94,-11.15,-70.90:99 +chr1 2761516 rs35134901 G C 42.78 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=58.89;MQ0=0;OQ=485.26;QD=11.55;SB=-253.13 GT:AD:DP:GL:GQ 0/1:25,17:38:-63.28,-11.47,-90.46:99 +chr1 2761538 rs35767265 C A 434.92 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=663.44;QD=13.54;SB=-277.32 GT:AD:DP:GL:GQ 0/1:26,23:47:-83.79,-14.16,-83.28:99 +chr1 2761907 rs35313744 A C 3.99 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=4;HaplotypeScore=1.29;MQ=59.00;MQ0=0;OQ=545.25;QD=12.98;SB=-173.29 GT:AD:DP:GL:GQ 0/1:20,22:40:-69.86,-12.05,-71.88:99 +chr1 2762054 rs6694484 G A 356.15 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.79;MQ0=0;OQ=715.90;QD=13.26;SB=-315.29 GT:AD:DP:GL:GQ 0/1:29,25:51:-90.24,-15.37,-99.20:99 +chr1 2762207 rs6675221 C A 216.75 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.45;MQ0=0;OQ=527.73;QD=12.57;SB=-249.28 GT:AD:DP:GL:GQ 0/1:21,20:39:-67.80,-11.75,-71.40:99 +chr1 2762658 rs12727394 T C 169.21 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=60.00;MQ0=0;OQ=383.94;QD=11.63;SB=-133.29 GT:AD:DP:GL:GQ 0/1:17,15:29:-50.42,-8.74,-57.72:99 +chr1 2763115 rs12729596 C T 224.28 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.16;MQ0=0;OQ=609.66;QD=12.19;SB=-271.12 GT:AD:DP:GL:GQ 0/1:30,20:50:-79.31,-15.06,-107.78:99 +chr1 2763349 rs6660680 C G 206.84 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.16;MQ=59.65;MQ0=0;OQ=809.85;QD=15.28;SB=-407.93 GT:AD:DP:GL:GQ 0/1:28,25:49:-99.04,-14.78,-104.68:99 +chr1 2763426 rs6660759 C T 169.45 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.89;MQ0=0;OQ=778.20;QD=18.53;SB=-350.90 GT:AD:DP:GL:GQ 0/1:15,27:38:-92.57,-11.46,-40.16:99 +chr1 2763555 rs6674204 A G 358.56 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1244.75;QD=33.64;SB=-466.51 GT:AD:DP:GL:GQ 1/1:0,37:36:-128.07,-10.85,-0.01:99 +chr1 2763913 rs7529000 A G 539.75 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=590.27;QD=13.73;SB=-268.99 GT:AD:DP:GL:GQ 0/1:19,24:38:-73.77,-11.46,-59.16:99 +chr1 2765576 . A G 299.17 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.30;MQ0=1;OQ=708.87;QD=14.18;SB=-362.49 GT:AD:DP:GL:GQ 0/1:25,25:46:-88.03,-13.85,-86.85:99 +chr1 2765703 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=40;Dels=0.03;HRun=1;HaplotypeScore=65.65;MQ=34.06;MQ0=6;OQ=224.51;QD=5.61;SB=-69.85 GT:AD:DP:GL:GQ 0/1:16,18:20:-31.76,-6.02,-57.23:99 +chr1 2765716 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=45.86;MQ=31.67;MQ0=6;OQ=473.81;QD=11.56;SB=-227.60 GT:AD:DP:GL:GQ 0/1:7,34:22:-57.29,-6.63,-24.20:99 +chr1 2765718 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=49.51;MQ=31.73;MQ0=6;OQ=139.31;QD=3.48;SB=14.07 GT:AD:DP:GL:GQ 0/1:34,6:18:-22.64,-5.42,-43.65:99 +chr1 2765729 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=2;HaplotypeScore=101.24;MQ=39.70;MQ0=5;OQ=348.53;QD=8.30;SB=-73.03 GT:AD:DP:GL:GQ 0/1:25,16:29:-48.99,-10.85,-57.39:99 +chr1 2765740 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=21.54;MQ=47.97;MQ0=0;OQ=288.34;QD=9.94;SB=-104.59 GT:AD:DP:GL:GQ 0/1:16,13:26:-39.95,-7.84,-58.99:99 +chr1 2765813 . A G 11.29 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=51.84;MQ0=0;OQ=780.70;QD=15.61;SB=-390.27 GT:AD:DP:GL:GQ 0/1:21,28:48:-95.81,-14.46,-83.37:99 +chr1 2765894 . A C 0.06 PASS AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=11.31;MQ=45.14;MQ0=0;OQ=337.42;QD=9.37;SB=-140.89 GT:AD:DP:GL:GQ 0/1:21,15:33:-46.96,-9.94,-71.34:99 +chr1 2765910 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=53;Dels=0.02;HRun=1;HaplotypeScore=33.31;MQ=38.51;MQ0=0;OQ=588.92;QD=11.11;SB=23.11 GT:AD:DP:GL:GQ 0/1:28,24:46:-75.73,-13.55,-102.75:99 +chr1 2765957 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=2;HaplotypeScore=176.91;MQ=27.98;MQ0=17;OQ=352.77;QD=3.12;SB=2.45 GT:AD:DP:GL:GQ 0/1:85,28:53:-54.54,-15.98,-142.28:99 +chr1 2765968 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=118.45;MQ=28.99;MQ0=17;OQ=151.04;QD=1.26;SB=-15.93 GT:AD:DP:GL:GQ 0/1:95,25:59:-36.17,-17.78,-173.10:99 +chr1 2765995 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=52.19;MQ=34.85;MQ0=7;OQ=128.24;QD=1.78;SB=-51.69 GT:AD:DP:GL:GQ 0/1:61,11:54:-32.38,-16.27,-203.82:99 +chr1 2765996 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=51.72;MQ=35.05;MQ0=7;OQ=180.10;QD=2.54;SB=-41.96 GT:AD:DP:GL:GQ 0/1:59,12:54:-37.57,-16.27,-158.22:99 +chr1 2766902 rs34376289 C T 393.03 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.48;MQ0=0;OQ=811.67;QD=17.64;SB=-367.51 GT:AD:DP:GL:GQ 0/1:20,26:45:-98.01,-13.56,-71.88:99 +chr1 2768626 rs10909992 C T 335.77 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.57;MQ0=0;OQ=811.02;QD=12.48;SB=-416.42 GT:AD:DP:GL:GQ 0/1:35,29:62:-103.08,-18.70,-112.11:99 +chr1 2768752 rs12409918 A C 74.45 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.55;MQ=59.57;MQ0=0;OQ=965.61;QD=17.88;SB=-402.66 GT:AD:DP:GL:GQ 0/1:20,34:50:-114.91,-15.06,-60.43:99 +chr1 2768903 rs12409348 T C 172.05 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.28;MQ=60.00;MQ0=0;OQ=398.89;QD=10.50;SB=-78.75 GT:AD:DP:GL:GQ 0/1:20,17:35:-53.71,-10.54,-80.33:99 +chr1 2769019 rs10909995 C G 17.82 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=58.48;MQ0=0;OQ=1462.05;QD=36.55;SB=-653.43 GT:AD:DP:GL:GQ 1/1:0,40:35:-149.81,-10.55,-0.02:99 +chr1 2769620 rs28600853 C T 67.23 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.53;MQ0=0;OQ=1091.29;QD=28.72;SB=-540.63 GT:AD:DP:GL:GQ 0/1:4,33:36:-123.26,-10.85,-13.62:27.66 +chr1 2769674 rs4648542 G A 90.82 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=51.80;MQ0=1;OQ=271.91;QD=9.71;SB=-148.61 GT:AD:DP:GL:GQ 0/1:13,15:21:-36.80,-6.33,-39.42:99 +chr1 2769679 rs28367217 C G 36.02 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=51.80;MQ0=1;OQ=209.26;QD=8.37;SB=2.04 GT:AD:DP:GL:GQ 0/1:15,10:18:-29.64,-5.43,-44.14:99 +chr1 2769692 rs28478242 A G 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=4;HaplotypeScore=0.82;MQ=53.88;MQ0=1;OQ=89.42;QD=4.26;SB=5.05 GT:AD:DP:GL:GQ 0/1:15,6:17:-17.35,-5.12,-46.13:99 +chr1 2769752 rs7542593 T C 75.28 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.77;MQ0=0;OQ=136.56;QD=6.21;SB=-67.76 GT:AD:DP:GL:GQ 0/1:10,12:17:-22.07,-5.13,-38.52:99 +chr1 2769805 rs4648543 T G 0.02 FDRtranche1.00to2.00 AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=4;HaplotypeScore=2.68;MQ=55.12;MQ0=0;OQ=754.89;QD=29.03;SB=-110.69 GT:AD:DP:GL:GQ 1/1:0,26:23:-79.08,-6.93,-0.01:69.18 +chr1 2770855 rs729178 T G 35.70 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=57.97;MQ0=0;OQ=332.17;QD=14.44;SB=-62.09 GT:AD:DP:GL:GQ 0/1:7,16:18:-41.92,-5.42,-18.71:99 +chr1 2770856 rs729177 T C 47.89 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=57.97;MQ0=0;OQ=319.36;QD=13.89;SB=-53.86 GT:AD:DP:GL:GQ 0/1:7,16:20:-41.25,-6.03,-26.63:99 +chr1 2772453 rs12119163 G A 585.03 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1388.32;QD=37.52;SB=-625.84 GT:AD:DP:GL:GQ 1/1:0,37:36:-142.43,-10.85,-0.01:99 +chr1 2772603 rs7551868 T C 19.40 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=3.77;MQ=58.92;MQ0=0;OQ=1140.34;QD=29.24;SB=-578.97 GT:AD:DP:GL:GQ 1/1:0,39:37:-117.66,-11.16,-0.04:99 +chr1 2772900 rs4648402 T C 156.21 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.00;MQ0=0;OQ=994.66;QD=28.42;SB=-468.49 GT:AD:DP:GL:GQ 1/1:0,35:33:-103.09,-9.96,-0.03:99 +chr1 2773675 rs12752112 G C 9.49 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.95;MQ0=0;OQ=859.11;QD=39.05;SB=-325.45 GT:AD:DP:GL:GQ 1/1:0,22:21:-89.50,-6.33,-0.01:63.21 +chr1 2776554 rs1563470 T C 23.92 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=60.00;MQ0=0;OQ=1838.24;QD=33.42;SB=-908.03 GT:AD:DP:GL:GQ 1/1:0,55:52:-187.42,-15.66,-0.02:99 +chr1 2777013 rs897616 C G 7.16 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=3;HaplotypeScore=1.07;MQ=58.26;MQ0=0;OQ=1193.61;QD=34.10;SB=-446.20 GT:AD:DP:GL:GQ 1/1:0,35:30:-122.96,-9.05,-0.02:90.29 +chr1 2777567 rs897620 C G 317.44 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1920.95;QD=42.69;SB=-716.92 GT:AD:DP:GL:GQ 1/1:0,45:44:-195.69,-13.26,-0.01:99 +chr1 2778573 rs56273341 A G 89.85 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=1164.73;QD=29.12;SB=-590.57 GT:AD:DP:GL:GQ 1/1:0,40:37:-120.09,-11.16,-0.03:99 +chr1 2779035 rs12569164 T C 119.85 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=49.75;MQ0=0;OQ=1623.80;QD=28.49;SB=-755.66 GT:AD:DP:GL:GQ 1/1:0,57:53:-166.02,-15.99,-0.06:99 +chr1 2779347 . T C 140.90 Indel AC=1;AF=0.50;AN=2;DP=70;Dels=0.03;HRun=0;HaplotypeScore=53.64;MQ=31.59;MQ0=1;QD=2.01;SB=-93.61 GT:AD:DP:GL:GQ 0/1:59,9:55:-33.34,-15.96,-177.98:99 +chr1 2779357 rs55740077 T C 137.39 Indel;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=61.84;MQ=29.83;MQ0=1;QD=1.99;SB=-25.89 GT:AD:DP:GL:GQ 0/1:28,41:15:-21.54,-4.52,-37.07:99 +chr1 2779361 rs55927204 T C 380.25 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=52.10;MQ=29.71;MQ0=1;QD=5.51;SB=-184.74 GT:AD:DP:GL:GQ 0/1:7,62:16:-46.13,-4.82,-12.60:77.76 +chr1 2779365 . T C 528.78 SnpCluster AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=50.77;MQ=30.92;MQ0=1;QD=7.24;SB=-289.59 GT:AD:DP:GL:GQ 0/1:6,67:20:-62.19,-6.02,-12.60:65.71 +chr1 2779369 . T C 809.75 SnpCluster AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=40.71;MQ=31.11;MQ0=1;QD=10.52;SB=-337.36 GT:AD:DP:GL:GQ 0/1:9,68:31:-93.60,-9.34,-19.91:99 +chr1 2779373 rs56012041 T C 260.44 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=37.08;MQ=32.24;MQ0=1;QD=3.38;SB=-116.63 GT:AD:DP:GL:GQ 0/1:28,49:21:-35.65,-6.33,-44.87:99 +chr1 2779421 rs5023660 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=3;HaplotypeScore=23.36;MQ=40.90;MQ0=1;OQ=1397.64;QD=21.18;SB=-647.72 GT:AD:DP:GL:GQ 0/1:24,41:55:-159.31,-16.27,-52.10:99 +chr1 2779423 rs56155638 T C 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=0;HaplotypeScore=20.03;MQ=40.90;MQ0=1;OQ=1243.01;QD=18.83;SB=-541.02 GT:AD:DP:GL:GQ 0/1:23,42:56:-144.15,-16.57,-59.53:99 +chr1 2779766 rs2124661 C G 42.55 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=49.71;MQ0=0;OQ=2767.03;QD=41.92;SB=-1222.51 GT:AD:DP:GL:GQ 1/1:0,66:63:-280.30,-18.98,-0.02:99 +chr1 2779832 rs2168531 C T 260.48 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.21;MQ=50.55;MQ0=0;OQ=2553.68;QD=38.69;SB=-1139.52 GT:AD:DP:GL:GQ 1/1:0,66:66:-258.98,-19.89,-0.03:99 +chr1 2780005 . G C 32.52 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=15.63;MQ=58.92;MQ0=0;QD=0.76;SB=44.18 GT:AD:DP:GL:GQ 0/1:33,10:29:-15.29,-8.76,-103.60:65.36 +chr1 2781003 rs10910023 C T 121.93 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.11;MQ0=0;OQ=1930.80;QD=37.13;SB=-708.95 GT:AD:DP:GL:GQ 1/1:0,52:49:-196.68,-14.76,-0.01:99 +chr1 2781813 rs12131393 C T 195.76 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=701.85;QD=13.76;SB=-265.19 GT:AD:DP:GL:GQ 0/1:28,23:44:-86.73,-13.26,-75.43:99 +chr1 2781975 rs12131450 C T 0.88 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=915.40;QD=20.80;SB=-418.48 GT:AD:DP:GL:GQ 0/1:17,27:44:-108.08,-13.26,-61.20:99 +chr1 2784004 rs10909791 C T 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=18.57;MQ=55.20;MQ0=0;OQ=554.87;QD=8.95;SB=-141.63 GT:AD:DP:GL:GQ 0/1:38,21:51:-74.16,-15.38,-99.65:99 +chr1 2784009 rs6673503 T C 0.75 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=15.72;MQ=55.44;MQ0=0;OQ=828.36;QD=14.04;SB=-284.66 GT:AD:DP:GL:GQ 0/1:19,40:49:-100.91,-14.79,-59.84:99 +chr1 2784113 rs6658584 G A 324.36 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.61;MQ0=0;OQ=573.55;QD=11.95;SB=-252.51 GT:AD:DP:GL:GQ 0/1:29,19:42:-73.29,-12.65,-86.05:99 +chr1 2784397 rs6668620 C T 83.28 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.97;MQ0=0;OQ=989.63;QD=21.99;SB=-434.99 GT:AD:DP:GL:GQ 0/1:12,32:41:-114.60,-12.35,-43.77:99 +chr1 2784411 rs10909793 G T 285.59 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=987.49;QD=22.44;SB=-485.97 GT:AD:DP:GL:GQ 0/1:11,33:43:-114.99,-12.95,-39.80:99 +chr1 2785397 rs6679954 T C 177.95 PASS AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=57.39;MQ0=0;OQ=162.89;QD=9.05;SB=-99.99 GT:AD:DP:GL:GQ 0/1:9,8:15:-24.09,-4.52,-32.21:99 +chr1 2785861 rs10797340 G C 110.31 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=2067.39;QD=39.01;SB=-1035.13 GT:AD:DP:GL:GQ 1/1:0,53:49:-210.35,-14.77,-0.02:99 +chr1 2786415 rs10752722 A G 154.88 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.07;MQ0=0;OQ=1517.85;QD=30.36;SB=-724.72 GT:AD:DP:GL:GQ 1/1:0,50:49:-155.42,-14.78,-0.05:99 +chr1 2786479 rs4648406 T C 92.49 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.34;MQ0=0;OQ=883.04;QD=25.23;SB=-376.38 GT:AD:DP:GL:GQ 1/1:0,35:29:-91.92,-8.75,-0.03:87.18 +chr1 2787126 rs6424057 T G 92.26 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.46;MQ0=0;OQ=1311.97;QD=30.51;SB=-464.84 GT:AD:DP:GL:GQ 1/1:0,43:41:-134.82,-12.36,-0.04:99 +chr1 2787716 rs10797342 C T 575.89 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=717.10;QD=14.63;SB=-344.49 GT:AD:DP:GL:GQ 0/1:27,22:49:-89.77,-14.77,-84.62:99 +chr1 2788065 rs2124662 G C 9.64 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=5.21;MQ=57.80;MQ0=0;OQ=437.50;QD=13.67;SB=-215.17 GT:AD:DP:GL:GQ 0/1:15,17:26:-54.88,-7.85,-48.57:99 +chr1 2788136 rs1563472 G A 261.94 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.38;MQ0=0;OQ=469.47;QD=12.69;SB=-131.12 GT:AD:DP:GL:GQ 0/1:19,18:28:-58.68,-8.45,-41.51:99 +chr1 2788195 rs1563473 T G 178.79 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=57.45;MQ0=0;OQ=577.74;QD=12.56;SB=-216.84 GT:AD:DP:GL:GQ 0/1:19,27:43:-74.02,-12.96,-66.19:99 +chr1 2788317 rs1563474 G A 94.33 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=3.84;MQ=58.45;MQ0=0;OQ=661.75;QD=14.71;SB=-298.81 GT:AD:DP:GL:GQ 0/1:21,24:41:-81.83,-12.37,-60.24:99 +chr1 2788572 rs4373707 T C 44.63 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=5.22;MQ=58.97;MQ0=0;OQ=526.05;QD=11.69;SB=-185.63 GT:AD:DP:GL:GQ 0/1:22,23:42:-68.55,-12.66,-84.21:99 +chr1 2788907 rs2377038 A G 118.41 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.81;MQ=59.09;MQ0=0;OQ=482.56;QD=10.49;SB=-194.43 GT:AD:DP:GL:GQ 0/1:24,21:41:-63.90,-12.36,-79.61:99 +chr1 2789039 rs729965 G C 149.04 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=2442.19;QD=42.11;SB=-956.71 GT:AD:DP:GL:GQ 1/1:0,58:57:-247.82,-17.18,-0.02:99 +chr1 2789321 rs897629 T C 12.44 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=3.68;MQ=58.87;MQ0=0;OQ=1220.90;QD=29.78;SB=-560.89 GT:AD:DP:GL:GQ 1/1:0,40:39:-125.71,-11.76,-0.03:99 +chr1 2789340 rs11580768 C T 285.25 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.21;MQ=58.92;MQ0=0;OQ=699.84;QD=16.28;SB=-316.84 GT:AD:DP:GL:GQ 0/1:20,23:40:-85.33,-12.06,-59.14:99 +chr1 2789623 rs729419 G T 32.76 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=4.03;MQ=56.89;MQ0=0;OQ=1157.82;QD=30.47;SB=-604.54 GT:AD:DP:GL:GQ 1/1:0,38:33:-119.38,-9.94,-0.01:99 +chr1 2789978 rs4233022 T C 8.90 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=58.32;MQ0=0;OQ=1306.00;QD=33.49;SB=-393.50 GT:AD:DP:GL:GQ 1/1:0,38:38:-137.49,-14.36,-3.31:99 +chr1 2790214 rs61763695 G T 159.83 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=59.41;MQ0=0;OQ=678.47;QD=17.40;SB=-357.12 GT:AD:DP:GL:GQ 0/1:15,24:37:-82.28,-11.15,-45.69:99 +chr1 2790614 rs2061229 A G 424.36 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=1321.60;QD=28.73;SB=-492.17 GT:AD:DP:GL:GQ 1/1:0,46:43:-135.79,-12.97,-0.04:99 +chr1 2791688 rs4648429 A G 0.41 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.02;HRun=3;HaplotypeScore=3.60;MQ=59.05;MQ0=0;OQ=1300.58;QD=29.56;SB=-615.14 GT:AD:DP:GL:GQ 1/1:0,43:39:-133.67,-11.76,-0.03:99 +chr1 2791895 rs10737188 A G 0.06 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=11.58;MQ=57.39;MQ0=0;OQ=1158.45;QD=32.18;SB=-423.17 GT:AD:DP:GL:GQ 1/1:0,36:33:-119.44,-9.94,-0.01:99 +chr1 2791912 rs12127835 C T 0.23 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=15.40;MQ=57.73;MQ0=0;OQ=440.23;QD=14.20;SB=-189.24 GT:AD:DP:GL:GQ 0/1:15,16:28:-55.74,-8.44,-48.73:99 +chr1 2791917 rs12124890 G A 0.74 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=10.20;MQ=56.96;MQ0=0;OQ=462.23;QD=14.91;SB=-204.21 GT:AD:DP:GL:GQ 0/1:14,16:28:-57.95,-8.44,-40.79:99 +chr1 2792072 rs10752725 T C 491.80 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=1748.59;QD=30.68;SB=-570.96 GT:AD:DP:GL:GQ 1/1:0,57:55:-178.49,-16.59,-0.05:99 +chr1 2792208 rs7552943 A G 158.94 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.00;MQ0=0;OQ=672.02;QD=16.00;SB=-219.52 GT:AD:DP:GL:GQ 0/1:13,29:36:-81.33,-10.85,-44.36:99 +chr1 2792422 . G A 42.68 PASS AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.28;MQ0=0;OQ=1176.82;QD=18.39;SB=-377.70 GT:AD:DP:GL:GQ 0/1:28,36:64:-140.25,-19.29,-99.03:99 +chr1 2793407 rs3001793 G A 9.14 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=57.81;MQ0=0;OQ=925.83;QD=30.86;SB=-281.35 GT:AD:DP:GL:GQ 1/1:0,30:25:-96.18,-7.54,-0.02:75.22 +chr1 2793666 rs2377039 C T 77.79 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=60.00;MQ0=0;OQ=452.51;QD=18.10;SB=-252.58 GT:AD:DP:GL:GQ 0/1:10,15:20:-54.56,-6.03,-20.77:99 +chr1 2794138 rs3001794 C G 65.67 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=352.40;QD=13.05;SB=-39.43 GT:AD:DP:GL:GQ 0/1:15,12:26:-46.37,-7.84,-60.81:99 +chr1 2800878 rs2842928 T C 235.55 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=901.11;QD=33.37;SB=-249.77 GT:AD:DP:GL:GQ 1/1:0,27:26:-93.71,-7.83,-0.01:78.23 +chr1 2802104 rs10909834 G C 0.87 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=3;HaplotypeScore=3.91;MQ=59.36;MQ0=0;OQ=721.69;QD=20.05;SB=-360.48 GT:AD:DP:GL:GQ 0/1:15,21:32:-85.11,-9.65,-46.55:99 +chr1 2803334 rs10909835 C A 282.86 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.29;MQ0=0;OQ=1113.78;QD=16.14;SB=-524.88 GT:AD:DP:GL:GQ 0/1:32,37:69:-135.44,-20.78,-115.35:99 +chr1 2809215 . C A 24.19 LowQual AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=33.87;MQ0=3;QD=0.67;SB=-3.99 GT:AD:DP:GL:GQ 0/1:32,3:16:-10.52,-4.82,-48.73:57.01 +chr1 2812608 rs12091184 T C 225.17 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.35;MQ0=0;OQ=707.81;QD=11.06;SB=-307.08 GT:AD:DP:GL:GQ 0/1:33,31:62:-92.76,-18.69,-131.04:99 +chr1 2813319 rs12035436 G T 336.68 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.54;MQ0=0;OQ=779.74;QD=15.59;SB=-317.29 GT:AD:DP:GL:GQ 0/1:23,27:47:-95.42,-14.16,-69.60:99 +chr1 2815014 rs880724 C T 302.73 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=894.47;QD=16.56;SB=-357.16 GT:AD:DP:GL:GQ 0/1:25,29:52:-108.41,-15.68,-73.43:99 +chr1 2816229 rs34114281 G A 56.60 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.49;MQ0=0;OQ=818.99;QD=18.20;SB=-240.71 GT:AD:DP:GL:GQ 0/1:20,25:44:-98.44,-13.25,-71.30:99 +chr1 2816447 rs12738063 G A 183.56 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=436.36;QD=11.79;SB=-199.90 GT:AD:DP:GL:GQ 0/1:21,16:33:-56.87,-9.95,-58.54:99 +chr1 2819411 rs1869970 A G 323.79 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=58.68;MQ0=0;OQ=562.16;QD=12.22;SB=-263.95 GT:AD:DP:GL:GQ 0/1:23,23:46:-73.37,-13.87,-93.65:99 +chr1 2819722 rs10797359 G A 80.30 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=58.97;MQ0=0;OQ=661.62;QD=14.70;SB=-329.32 GT:AD:DP:GL:GQ 0/1:24,21:45:-83.00,-13.56,-85.88:99 +chr1 2819782 rs10797360 T C 62.98 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=58.11;MQ0=0;OQ=276.31;QD=7.47;SB=-143.57 GT:AD:DP:GL:GQ 0/1:22,15:35:-41.46,-10.55,-86.74:99 +chr1 2821229 rs2606408 T C 106.74 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=3.39;MQ=59.56;MQ0=0;OQ=598.54;QD=11.51;SB=-201.20 GT:AD:DP:GL:GQ 0/1:29,23:50:-78.20,-15.07,-111.31:99 +chr1 2821448 rs1563475 G T 119.77 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=513.38;QD=12.83;SB=-112.67 GT:AD:DP:GL:GQ 0/1:19,21:38:-66.07,-11.45,-67.04:99 +chr1 2821650 rs11590100 A G 136.28 PASS AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.60;MQ0=0;OQ=943.28;QD=10.14;SB=-480.61 GT:AD:DP:GL:GQ 0/1:51,42:88:-124.13,-26.52,-198.52:99 +chr1 2822111 rs3001796 T C 212.38 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=55.14;MQ0=0;OQ=802.13;QD=11.80;SB=-349.06 GT:AD:DP:GL:GQ 0/1:33,34:64:-102.79,-19.29,-127.57:99 +chr1 2822273 rs3001797 G A 0.27 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=14.80;MQ=58.82;MQ0=1;OQ=1009.61;QD=19.42;SB=-317.35 GT:AD:DP:GL:GQ 0/1:22,30:49:-119.01,-14.77,-60.02:99 +chr1 2822628 rs6696129 C T 18.64 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=6.89;MQ=57.91;MQ0=1;OQ=832.22;QD=14.35;SB=-326.29 GT:AD:DP:GL:GQ 0/1:32,26:55:-103.07,-16.57,-105.26:99 +chr1 2823020 rs1869971 C T 374.03 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=57.94;MQ0=0;OQ=535.79;QD=14.48;SB=-291.84 GT:AD:DP:GL:GQ 0/1:19,18:35:-67.42,-10.56,-54.80:99 +chr1 2823154 rs7339944 G A 129.22 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=59.45;MQ0=0;OQ=957.99;QD=19.16;SB=-392.16 GT:AD:DP:GL:GQ 0/1:19,31:48:-113.55,-14.46,-66.11:99 +chr1 2823192 rs7340016 A G 29.60 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=3.35;MQ=59.34;MQ0=0;OQ=422.29;QD=10.05;SB=-179.53 GT:AD:DP:GL:GQ 0/1:21,21:36:-56.37,-10.85,-73.83:99 +chr1 2823287 rs2124663 C T 42.06 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.59;MQ0=0;OQ=634.70;QD=14.10;SB=-71.85 GT:AD:DP:GL:GQ 0/1:24,21:45:-80.32,-13.56,-82.96:99 +chr1 2823310 rs1563466 T C 23.75 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.63;MQ=58.92;MQ0=0;OQ=514.85;QD=13.20;SB=-114.69 GT:AD:DP:GL:GQ 0/1:19,20:38:-66.22,-11.45,-76.59:99 +chr1 2823513 rs11587665 C T 40.96 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=6.13;MQ=59.14;MQ0=0;OQ=737.31;QD=13.65;SB=-373.35 GT:AD:DP:GL:GQ 0/1:29,25:51:-92.39,-15.38,-90.11:99 +chr1 2823603 rs1563468 T C 458.79 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.00;MQ0=0;OQ=947.27;QD=14.14;SB=-372.60 GT:AD:DP:GL:GQ 0/1:28,39:64:-117.31,-19.30,-107.37:99 +chr1 2823870 rs11809099 C T 295.64 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.56;MQ0=0;OQ=690.45;QD=13.28;SB=-256.23 GT:AD:DP:GL:GQ 0/1:28,23:49:-87.09,-14.76,-98.54:99 +chr1 2823885 rs2842926 G A 181.65 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.53;MQ0=0;OQ=786.09;QD=16.04;SB=-320.86 GT:AD:DP:GL:GQ 0/1:23,26:46:-95.76,-13.86,-71.19:99 +chr1 2825347 rs897633 A C 527.30 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=683.77;QD=14.86;SB=-280.84 GT:AD:DP:GL:GQ 0/1:21,25:45:-85.22,-13.56,-75.45:99 +chr1 2825552 rs897634 T C 95.40 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1172.99;QD=30.08;SB=-560.88 GT:AD:DP:GL:GQ 1/1:0,39:37:-120.91,-11.16,-0.03:99 +chr1 2825769 rs2606409 A G 32.95 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=5.74;MQ=57.77;MQ0=0;OQ=329.46;QD=7.84;SB=-164.95 GT:AD:DP:GL:GQ 0/1:25,16:40:-48.29,-12.06,-98.69:99 +chr1 2825959 rs2606410 C T 311.17 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.19;MQ=59.57;MQ0=0;OQ=951.03;QD=17.61;SB=-434.47 GT:AD:DP:GL:GQ 0/1:25,29:51:-113.75,-15.36,-82.67:99 +chr1 2827304 rs55855166 G A 337.28 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.37;MQ0=0;OQ=391.24;QD=9.10;SB=-201.88 GT:AD:DP:GL:GQ 0/1:27,16:41:-54.76,-12.35,-93.92:99 +chr1 2828084 rs35844499 A C 0.13 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=8.95;MQ=33.58;MQ0=13;OQ=215.00;QD=4.89;SB=-66.98 GT:AD:DP:GL:GQ 0/1:23,20:16:-29.61,-4.82,-23.59:99 +chr1 2831038 . C T 212.41 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=614.63;QD=14.29;SB=-239.55 GT:AD:DP:GL:GQ 0/1:23,20:43:-77.70,-12.96,-79.28:99 +chr1 2833249 . C T 39.44 LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=2.90;MQ=56.74;MQ0=0;QD=1.36;SB=-41.03 GT:AD:DP:GL:GQ 0/1:24,4:19:-12.96,-5.74,-47.17:72.28 +chr1 2833472 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=11.49;MQ=58.05;MQ0=0;OQ=54.69;QD=1.52;SB=-45.69 GT:AD:DP:GL:GQ 0/1:28,8:19:-14.49,-5.74,-59.79:87.52 +chr1 2837348 rs2606411 T C 351.83 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=583.14;QD=14.58;SB=-128.66 GT:AD:DP:GL:GQ 0/1:14,26:36:-72.45,-10.85,-55.84:99 +chr1 2838116 rs35880479 G A 202.84 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=58.64;MQ0=0;OQ=848.27;QD=13.05;SB=-379.33 GT:AD:DP:GL:GQ 0/1:37,28:62:-106.79,-18.68,-116.44:99 +chr1 2844321 rs12120163 C T 361.45 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.44;MQ0=0;OQ=1226.99;QD=16.58;SB=-528.52 GT:AD:DP:GL:GQ 0/1:36,38:72:-147.69,-21.70,-111.75:99 +chr1 2849584 rs2842909 C T 85.45 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=5.45;MQ=57.20;MQ0=0;OQ=445.80;QD=10.87;SB=-188.84 GT:AD:DP:GL:GQ 0/1:22,19:36:-58.71,-10.85,-74.85:99 +chr1 2850791 rs2925499 C T 367.47 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.73;MQ0=0;OQ=1163.55;QD=17.11;SB=-509.17 GT:AD:DP:GL:GQ 0/1:33,35:67:-139.83,-20.19,-105.50:99 +chr1 2856184 . C T 37.47 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=14.17;MQ0=11;QD=1.63;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,10:4:-8.24,-1.21,-6.09:48.87 +chr1 2856380 rs3010827 T C 18.54 LowQual AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=21.91;MQ0=3;QD=0.66;SB=-6.99 GT:AD:DP:GL:GQ 0/1:20,8:5:-6.64,-1.51,-11.98:51.31 +chr1 2865080 rs2788089 G A 618.40 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2745.57;QD=39.79;SB=-1234.70 GT:AD:DP:GL:GQ 1/1:0,69:69:-278.16,-20.78,-0.02:99 +chr1 2866385 rs10909845 T C 68.38 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.49;MQ=58.86;MQ0=0;OQ=1786.40;QD=31.34;SB=-680.16 GT:AD:DP:GL:GQ 1/1:0,57:53:-182.25,-15.97,-0.03:99 +chr1 2866462 rs6663830 A G 10.39 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.42;MQ=57.19;MQ0=0;OQ=455.20;QD=23.96;SB=-149.73 GT:AD:DP:GL:GQ 1/1:1,18:16:-49.13,-4.83,-0.02:48.09 +chr1 2866480 rs12132266 C G 0.75 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=2;HaplotypeScore=2.31;MQ=54.22;MQ0=2;OQ=483.83;QD=32.26;SB=-138.40 GT:AD:DP:GL:GQ 1/1:2,13:12:-51.97,-3.62,-0.01:36.12 +chr1 2866511 rs12129394 G A 181.92 PASS AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.76;MQ0=0;OQ=82.01;QD=27.34;SB=-47.56 GT:AD:DP:GL:GQ 1/1:0,3:3:-11.69,-0.90,-0.00:9.03 +chr1 2866552 rs11582761 G A 15.30 PASS AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=47.10;MQ0=0;OQ=87.13;QD=17.43;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,4:3:-12.20,-0.90,-0.00:9.03 +chr1 2868226 rs11583804 G A 591.81 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.37;MQ0=0;OQ=1019.85;QD=15.45;SB=-422.44 GT:AD:DP:GL:GQ 0/1:35,31:65:-124.85,-19.58,-125.50:99 +chr1 2872997 rs10909848 G T 338.03 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=59.67;MQ0=0;OQ=904.50;QD=15.87;SB=-468.05 GT:AD:DP:GL:GQ 0/1:25,32:54:-110.00,-16.27,-78.02:99 +chr1 2873890 . G C 11.21 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=4;HaplotypeScore=5.27;MQ=55.45;MQ0=0;QD=0.59;SB=14.08 GT:AD:DP:GL:GQ 0/1:10,9:11:-7.69,-3.32,-38.19:43.71 +chr1 2874116 rs2993507 T C 16.38 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=58.76;MQ0=0;OQ=1405.38;QD=31.23;SB=-680.25 GT:AD:DP:GL:GQ 1/1:0,45:40:-144.14,-12.05,-0.01:99 +chr1 2876216 rs2842925 A G 411.29 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1144.93;QD=30.13;SB=-502.20 GT:AD:DP:GL:GQ 1/1:0,38:36:-118.11,-10.86,-0.03:99 +chr1 2876326 rs12752801 C T 372.85 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.51;MQ0=0;OQ=555.75;QD=11.82;SB=-279.71 GT:AD:DP:GL:GQ 0/1:29,18:46:-72.72,-13.86,-94.69:99 +chr1 2876664 rs1104934 C T 153.01 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.11;MQ0=0;OQ=873.37;QD=18.58;SB=-376.40 GT:AD:DP:GL:GQ 0/1:19,28:45:-104.19,-13.57,-58.40:99 +chr1 2876848 rs4072769 G A 397.29 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.29;MQ0=0;OQ=569.53;QD=13.56;SB=-264.25 GT:AD:DP:GL:GQ 0/1:22,20:41:-72.60,-12.36,-71.89:99 +chr1 2877278 rs12731895 T A 88.65 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.47;MQ0=0;OQ=1142.36;QD=32.64;SB=-433.66 GT:AD:DP:GL:GQ 1/1:0,35:33:-117.84,-9.95,-0.02:99 +chr1 2877329 rs12727338 A G 1.05 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=6.87;MQ=57.26;MQ0=0;OQ=1138.52;QD=25.30;SB=-341.40 GT:AD:DP:GL:GQ 1/1:0,45:36:-117.47,-10.86,-0.03:99 +chr1 2877535 rs4648443 G C 93.54 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=59.43;MQ0=0;OQ=1023.89;QD=31.03;SB=-246.78 GT:AD:DP:GL:GQ 1/1:0,33:28:-106.01,-8.47,-0.04:84.26 +chr1 2878321 rs10797371 T C 561.61 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=1137.37;QD=29.16;SB=-576.99 GT:AD:DP:GL:GQ 1/1:0,39:37:-117.36,-11.16,-0.04:99 +chr1 2878374 rs10797372 A G 151.87 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.80;MQ0=0;OQ=958.51;QD=27.39;SB=-485.14 GT:AD:DP:GL:GQ 1/1:0,35:31:-99.47,-9.35,-0.03:93.21 +chr1 2878478 rs57027760 G T 756.85 Indel AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=16.93;MQ=60.84;MQ0=0;QD=20.46;SB=-136.60 GT:AD:DP:GL:GQ 0/1:7,30:29:-87.69,-8.74,-9.78:10.36 +chr1 2879008 rs56619891 G A 46.74 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=58.68;MQ0=0;OQ=1774.48;QD=38.58;SB=-601.31 GT:AD:DP:GL:GQ 1/1:0,46:45:-181.04,-13.56,-0.01:99 +chr1 2879409 rs2495273 T A 230.62 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=58.81;MQ0=0;OQ=1962.54;QD=35.68;SB=-1002.53 GT:AD:DP:GL:GQ 1/1:0,55:54:-199.86,-16.27,-0.02:99 +chr1 2879437 rs12044030 C T 157.06 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.24;MQ=58.72;MQ0=0;OQ=1987.31;QD=38.97;SB=-989.84 GT:AD:DP:GL:GQ 1/1:0,51:51:-202.33,-15.37,-0.02:99 +chr1 2880205 rs4648445 G A 0.49 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=7.53;MQ=59.36;MQ0=0;OQ=1380.04;QD=38.33;SB=-528.20 GT:AD:DP:GL:GQ 1/1:1,35:35:-141.60,-10.54,-0.01:99 +chr1 2880574 rs4648446 C T 93.96 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=58.80;MQ0=0;OQ=2154.57;QD=37.15;SB=-942.74 GT:AD:DP:GL:GQ 1/1:0,58:56:-219.07,-16.88,-0.03:99 +chr1 2880814 rs35060945 G T 115.68 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.36;MQ0=0;OQ=1511.10;QD=32.85;SB=-647.26 GT:AD:DP:GL:GQ 1/1:0,46:43:-154.71,-12.95,-0.02:99 +chr1 2880975 rs9661752 C T 171.39 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=57.35;MQ0=0;OQ=1967.63;QD=36.44;SB=-881.18 GT:AD:DP:GL:GQ 1/1:0,54:51:-200.37,-15.37,-0.02:99 +chr1 2880988 rs35377179 C A 115.57 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=57.03;MQ0=0;OQ=1298.02;QD=29.50;SB=-650.95 GT:AD:DP:GL:GQ 1/1:1,43:37:-133.40,-11.15,-0.01:99 +chr1 2881030 . C A 0.40 PASS AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=3.41;MQ=54.52;MQ0=1;OQ=214.49;QD=8.25;SB=26.09 GT:AD:DP:GL:GQ 0/1:17,8:22:-34.34,-9.60,-47.09:99 +chr1 2881446 rs12046122 C A 164.77 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=56.73;MQ0=0;OQ=1555.86;QD=34.57;SB=-803.87 GT:AD:DP:GL:GQ 1/1:0,45:44:-159.18,-13.25,-0.01:99 +chr1 2881573 rs12046158 C T 78.52 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=1075.02;QD=38.39;SB=-495.01 GT:AD:DP:GL:GQ 1/1:0,28:28:-111.09,-8.43,-0.01:84.27 +chr1 2882784 rs12096719 A G 679.62 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.77;MQ0=0;OQ=1529.67;QD=33.99;SB=-756.19 GT:AD:DP:GL:GQ 1/1:0,45:44:-156.57,-13.25,-0.01:99 +chr1 2883117 rs34709641 C A 0.13 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=10.20;MQ=27.00;MQ0=0;OQ=541.23;QD=24.60;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,21:16:-57.72,-4.82,-0.01:48.13 +chr1 2883336 . T C 0.07 PASS AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=28.41;MQ0=1;OQ=55.83;QD=2.15;SB=35.13 GT:AD:DP:GL:GQ 0/1:19,7:19:-14.60,-5.73,-55.04:88.67 +chr1 2883474 . C T 16.42 PASS AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=19.09;MQ0=3;OQ=91.28;QD=9.13;SB=-10.00 GT:AD:DP:GL:GQ 1/1:6,3:4:-15.26,-3.77,-2.60:11.70 +chr1 2883529 . A G 32.82 LowQual AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=16.58;MQ0=2;QD=4.69;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:2:-6.69,-0.60,-0.00:6.01 +chr1 2883801 . G C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.62;MQ=34.13;MQ0=1;OQ=549.05;QD=22.88;SB=-205.68 GT:AD:DP:GL:GQ 0/1:3,21:17:-63.31,-5.13,-9.19:40.68 +chr1 2883821 . C G 1.10 PASS AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=5.35;MQ=22.36;MQ0=5;OQ=186.32;QD=8.47;SB=-39.88 GT:AD:DP:GL:GQ 0/1:7,15:10:-24.93,-3.02,-15.34:99 +chr1 2883940 . C G 0.08 PASS AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=7.32;MQ=24.85;MQ0=3;OQ=119.37;QD=7.02;SB=-3.99 GT:AD:DP:GL:GQ 0/1:4,13:7:-17.34,-2.12,-7.20:50.86 +chr1 2883991 . G A 9.80 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=39.91;MQ0=4;OQ=393.88;QD=7.16;SB=-196.17 GT:AD:DP:GL:GQ 0/1:36,19:38:-54.13,-11.46,-77.08:99 +chr1 2884111 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=5.45;MQ=48.57;MQ0=0;OQ=67.53;QD=1.73;SB=-58.84 GT:AD:DP:GL:GQ 0/1:29,10:26:-17.87,-7.84,-79.49:99 +chr1 2884204 . C G 13.82 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=48;Dels=0.02;HRun=0;HaplotypeScore=10.52;MQ=37.87;MQ0=5;QD=0.29;SB=17.09 GT:AD:DP:GL:GQ 0/1:44,3:31:-13.69,-9.05,-110.48:46.47 +chr1 2884224 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=33.65;MQ0=6;OQ=99.62;QD=2.69;SB=-73.89 GT:AD:DP:GL:GQ 0/1:22,14:21:-19.58,-6.34,-62.85:99 +chr1 2884275 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=8.64;MQ=43.29;MQ0=0;OQ=54.38;QD=1.36;SB=23.10 GT:AD:DP:GL:GQ 0/1:34,6:34:-18.98,-10.26,-119.97:87.22 +chr1 2884325 . G C 41.80 PASS AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=49.14;MQ0=0;OQ=1253.36;QD=33.87;SB=-646.42 GT:AD:DP:GL:GQ 1/1:0,37:34:-128.97,-10.28,-0.05:99 +chr1 2885060 rs63721360 G T 452.04 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1106.85;QD=29.13;SB=-549.16 GT:AD:DP:GL:GQ 1/1:0,38:32:-114.28,-9.64,-0.01:96.27 +chr1 2885413 rs34183832 C T 53.59 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=1297.32;QD=37.07;SB=-499.18 GT:AD:DP:GL:GQ 1/1:0,35:34:-133.33,-10.25,-0.01:99 +chr1 2885666 rs12746525 C T 345.32 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.87;MQ0=0;OQ=771.21;QD=35.05;SB=-307.40 GT:AD:DP:GL:GQ 1/1:0,22:21:-80.72,-6.33,-0.01:63.20 +chr1 2885725 rs12731464 G A 43.96 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.36;MQ0=0;OQ=1296.44;QD=36.01;SB=-473.63 GT:AD:DP:GL:GQ 1/1:0,36:34:-133.24,-10.25,-0.01:99 +chr1 2885912 rs12746985 C T 116.03 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.54;MQ0=0;OQ=1570.34;QD=38.30;SB=-739.01 GT:AD:DP:GL:GQ 1/1:0,40:40:-160.63,-12.05,-0.01:99 +chr1 2886057 rs12747179 C G 228.04 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1558.47;QD=39.96;SB=-692.89 GT:AD:DP:GL:GQ 1/1:0,39:37:-159.45,-11.15,-0.01:99 +chr1 2886368 rs7519674 G T 104.99 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=58.92;MQ0=0;OQ=1251.61;QD=32.09;SB=-486.26 GT:AD:DP:GL:GQ 1/1:0,39:37:-128.76,-11.15,-0.02:99 +chr1 2886595 rs7533362 A G 145.09 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=59.61;MQ0=0;OQ=2108.67;QD=35.74;SB=-1026.73 GT:AD:DP:GL:GQ 1/1:0,59:59:-214.47,-17.77,-0.02:99 +chr1 2886944 rs10909849 A G 437.20 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.80;MQ0=0;OQ=1258.82;QD=27.97;SB=-649.76 GT:AD:DP:GL:GQ 1/1:0,45:41:-129.52,-12.37,-0.05:99 +chr1 2886953 rs2788088 G A 571.84 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.80;MQ0=0;OQ=615.00;QD=13.67;SB=-320.48 GT:AD:DP:GL:GQ 0/1:23,22:41:-77.15,-12.37,-67.43:99 +chr1 2887315 rs3001801 T C 293.49 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.55;MQ0=0;OQ=285.37;QD=12.41;SB=-113.63 GT:AD:DP:GL:GQ 0/1:11,12:22:-38.45,-6.63,-44.08:99 +chr1 2887325 rs2495272 A G 0.48 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=3;HaplotypeScore=1.25;MQ=56.85;MQ0=0;OQ=451.51;QD=25.08;SB=-251.59 GT:AD:DP:GL:GQ 1/1:0,18:15:-48.75,-4.52,-0.01:45.11 +chr1 2887439 . A G 0.37 PASS AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=3.88;MQ=55.21;MQ0=0;OQ=257.68;QD=9.20;SB=-92.00 GT:AD:DP:GL:GQ 0/1:17,11:26:-36.89,-7.84,-61.45:99 +chr1 2887454 . A G 0.28 PASS AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=2;HaplotypeScore=5.31;MQ=55.54;MQ0=0;OQ=380.48;QD=12.68;SB=-84.99 GT:AD:DP:GL:GQ 0/1:15,15:27:-49.47,-8.14,-52.46:99 +chr1 2887461 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=56.64;MQ0=0;OQ=82.14;QD=2.65;SB=-24.50 GT:AD:DP:GL:GQ 0/1:26,5:30:-20.54,-9.04,-87.21:99 +chr1 2887469 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=10.99;MQ=56.64;MQ0=0;OQ=56.39;QD=1.82;SB=-10.59 GT:AD:DP:GL:GQ 0/1:26,5:30:-17.96,-9.04,-99.17:89.23 +chr1 2887476 rs61763639 G A 1.06 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=10.80;MQ=56.85;MQ0=0;OQ=400.87;QD=12.15;SB=-209.95 GT:AD:DP:GL:GQ 0/1:19,13:29:-55.44,-12.07,-58.42:99 +chr1 2887567 rs61763640 G C 352.27 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=547.00;QD=15.63;SB=-239.40 GT:AD:DP:GL:GQ 0/1:19,16:35:-68.53,-10.55,-82.14:99 +chr1 2887764 rs35529252 C G 80.76 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=1.06;MQ=57.39;MQ0=0;OQ=226.67;QD=8.40;SB=2.03 GT:AD:DP:GL:GQ 0/1:18,9:23:-32.89,-6.94,-62.31:99 +chr1 2887828 rs56335850 C G 110.15 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=58.45;MQ0=0;OQ=748.06;QD=17.40;SB=-393.99 GT:AD:DP:GL:GQ 0/1:21,22:42:-90.75,-12.66,-91.15:99 +chr1 2888083 rs56195961 C T 7.84 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.95;MQ=60.00;MQ0=0;OQ=1112.19;QD=20.22;SB=-391.16 GT:AD:DP:GL:GQ 0/1:22,33:55:-131.08,-16.58,-71.48:99 +chr1 2888354 rs17391563 T C 531.46 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=612.67;QD=11.56;SB=-261.21 GT:AD:DP:GL:GQ 0/1:27,26:52:-80.22,-15.67,-108.53:99 +chr1 2888416 rs6681331 C T 397.61 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.62;MQ0=0;OQ=831.46;QD=13.63;SB=-416.81 GT:AD:DP:GL:GQ 0/1:34,27:59:-104.22,-17.79,-102.21:99 +chr1 2888820 rs6681741 C T 399.97 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=909.46;QD=13.78;SB=-406.91 GT:AD:DP:GL:GQ 0/1:37,29:64:-113.53,-19.30,-110.49:99 +chr1 2889209 rs12043738 C T 43 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=2.99;MQ=59.70;MQ0=0;OQ=782.92;QD=12.63;SB=-392.82 GT:AD:DP:GL:GQ 0/1:36,26:56:-98.47,-16.89,-96.75:99 +chr1 2889348 rs12046140 T C 210.74 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=58.78;MQ0=0;OQ=758.51;QD=11.67;SB=-309.09 GT:AD:DP:GL:GQ 0/1:33,31:62:-97.83,-18.69,-124.67:99 +chr1 2891988 rs1572657 C T 224.13 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=58.69;MQ0=0;OQ=1966.14;QD=39.32;SB=-982.30 GT:AD:DP:GL:GQ 1/1:0,50:49:-200.21,-14.76,-0.01:99 +chr1 2893019 rs16823303 A G 473.80 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1016.72;QD=15.17;SB=-513.96 GT:AD:DP:GL:GQ 0/1:31,36:67:-125.14,-20.19,-125.83:99 +chr1 2893437 rs4350139 T C 494.03 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=627.58;QD=13.35;SB=-219.43 GT:AD:DP:GL:GQ 0/1:23,24:46:-79.90,-13.86,-93.15:99 +chr1 2893916 rs10797373 G A 257.26 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.18;MQ=59.61;MQ0=0;OQ=845.53;QD=14.33;SB=-302.29 GT:AD:DP:GL:GQ 0/1:31,28:56:-104.72,-16.88,-95.11:99 +chr1 2895465 rs10909852 T C 196.72 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=3.24;MQ=59.46;MQ0=0;OQ=1273.07;QD=16.32;SB=-516.27 GT:AD:DP:GL:GQ 0/1:36,42:76:-153.48,-22.89,-141.76:99 +chr1 2897295 rs7546695 C A 472.44 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.44;MQ0=0;OQ=1069.83;QD=15.97;SB=-543.65 GT:AD:DP:GL:GQ 0/1:30,37:66:-130.15,-19.88,-106.29:99 +chr1 2897527 rs12411019 T C 97.34 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.42;MQ0=0;OQ=164.92;QD=5.15;SB=-60.30 GT:AD:DP:GL:GQ 0/1:21,11:29:-28.52,-8.74,-78.99:99 +chr1 2897840 rs58882615 A T 78.36 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=58.81;MQ0=0;OQ=696.78;QD=12.67;SB=-96.85 GT:AD:DP:GL:GQ 0/1:28,27:52:-88.62,-15.66,-107.99:99 +chr1 2897930 rs10909854 A G 302.68 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=59.44;MQ0=0;OQ=922.43;QD=11.25;SB=-327.10 GT:AD:DP:GL:GQ 0/1:45,37:81:-119.94,-24.41,-179.92:99 +chr1 2898248 rs10909855 C T 438.64 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.39;MQ0=0;OQ=1131.76;QD=16.40;SB=-432.83 GT:AD:DP:GL:GQ 0/1:34,35:68:-136.95,-20.49,-112.64:99 +chr1 2898666 . G A 72.98 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=60.00;MQ0=0;OQ=1136.24;QD=18.33;SB=-578.42 GT:AD:DP:GL:GQ 0/1:27,35:58:-134.38,-17.48,-83.03:99 +chr1 2898708 rs56000855 G T 262.99 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=393.56;QD=10.09;SB=-213.51 GT:AD:DP:GL:GQ 0/1:23,16:38:-54.09,-11.45,-79.61:99 +chr1 2899110 rs16823315 A G 251.56 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.58;MQ=58.82;MQ0=0;OQ=851.48;QD=14.43;SB=-403.32 GT:AD:DP:GL:GQ 0/1:28,31:58:-105.90,-17.47,-115.59:99 +chr1 2899231 rs17391750 G A 437.47 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1161.97;QD=13.51;SB=-467.04 GT:AD:DP:GL:GQ 0/1:50,36:85:-145.10,-25.62,-160.28:99 +chr1 2899576 rs4335321 A G 105.18 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=58.00;MQ0=0;OQ=946.55;QD=13.52;SB=-144.87 GT:AD:DP:GL:GQ 0/1:37,33:68:-118.42,-20.48,-143.93:99 +chr1 2899597 . A T 1.69 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=3.60;MQ=57.30;MQ0=0;OQ=711.73;QD=11.67;SB=-108.79 GT:AD:DP:GL:GQ 0/1:34,27:58:-91.93,-17.47,-124.49:99 +chr1 2899698 . C A 3.06 PASS AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=964.27;QD=14.39;SB=-495.28 GT:AD:DP:GL:GQ 0/1:34,33:65:-119.29,-19.58,-112.82:99 +chr1 2899893 . T C 127.63 PASS AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.77;MQ=59.43;MQ0=0;OQ=700.47;QD=10.61;SB=-280.59 GT:AD:DP:GL:GQ 0/1:36,30:65:-92.92,-19.59,-144.88:99 +chr1 2900185 rs57720952 A G 235.22 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.13;MQ0=0;OQ=624.52;QD=11.78;SB=-194.60 GT:AD:DP:GL:GQ 0/1:27,26:53:-81.72,-15.98,-107.90:99 +chr1 2900204 rs58538272 A G 481.46 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=755.97;QD=13.50;SB=-350.98 GT:AD:DP:GL:GQ 0/1:26,30:55:-95.46,-16.58,-99.09:99 +chr1 2900256 rs60017523 T C 269.60 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.37;MQ0=0;OQ=740.61;QD=11.22;SB=-378.62 GT:AD:DP:GL:GQ 0/1:33,33:62:-96.04,-18.69,-126.33:99 +chr1 2901217 rs58445466 T C 331.41 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=47.93;MQ0=0;OQ=860.37;QD=15.36;SB=-212.50 GT:AD:DP:GL:GQ 0/1:26,30:54:-105.58,-16.26,-101.98:99 +chr1 2901454 rs56337009 G A 18.57 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=49.33;MQ0=1;OQ=975.13;QD=34.83;SB=-240.32 GT:AD:DP:GL:GQ 1/1:2,26:25:-101.11,-7.53,-0.01:75.24 +chr1 2902060 rs12022594 C T 230.71 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=53.29;MQ0=0;OQ=1320.21;QD=14.67;SB=-682.37 GT:AD:DP:GL:GQ 0/1:48,42:84:-160.62,-25.31,-148.07:99 +chr1 2902087 rs12059864 C T 220.44 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=55.08;MQ0=0;OQ=1120.96;QD=14.95;SB=-477.46 GT:AD:DP:GL:GQ 0/1:41,34:69:-136.16,-20.78,-131.24:99 +chr1 2902707 rs10909856 T C 237.57 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=59.08;MQ0=0;OQ=1121.38;QD=13.04;SB=-473.58 GT:AD:DP:GL:GQ 0/1:47,39:85:-141.02,-25.60,-190.53:99 +chr1 2902862 rs12401989 C A 536.26 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=929.32;QD=11.47;SB=-426.42 GT:AD:DP:GL:GQ 0/1:49,32:81:-120.61,-24.40,-176.66:99 +chr1 2903095 rs60435231 A G 179.93 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=2.39;MQ=59.67;MQ0=0;OQ=920.63;QD=13.15;SB=-378.56 GT:AD:DP:GL:GQ 0/1:39,31:70:-116.43,-21.08,-161.00:99 +chr1 2903159 rs59407673 T C 419.08 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=752.64;QD=11.07;SB=-260.51 GT:AD:DP:GL:GQ 0/1:41,27:66:-98.43,-19.88,-155.58:99 +chr1 2903756 . C T 100.01 PASS AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.38;MQ0=0;OQ=1160.57;QD=15.47;SB=-488.46 GT:AD:DP:GL:GQ 0/1:41,34:75:-141.93,-22.59,-152.72:99 +chr1 2903757 . C T 97.23 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.38;MQ0=0;OQ=1040.83;QD=14.07;SB=-405.37 GT:AD:DP:GL:GQ 0/1:41,33:72:-129.05,-21.68,-151.62:99 +chr1 2903785 . C T 13.14 PASS AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=3;HaplotypeScore=0.97;MQ=59.68;MQ0=0;OQ=1201.38;QD=16.69;SB=-623.18 GT:AD:DP:GL:GQ 0/1:36,36:71:-144.81,-21.39,-125.25:99 +chr1 2904148 rs34909435 G C 261.36 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.06;MQ0=0;OQ=923.50;QD=16.20;SB=-375.83 GT:AD:DP:GL:GQ 0/1:30,27:56:-112.51,-16.88,-128.89:99 +chr1 2904478 rs34453862 G T 153.72 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.73;MQ=59.34;MQ0=0;OQ=843.87;QD=14.80;SB=-424.19 GT:AD:DP:GL:GQ 0/1:29,28:55:-104.24,-16.57,-85.73:99 +chr1 2904922 . G A 6.65 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=986.03;QD=18.26;SB=-298.76 GT:AD:DP:GL:GQ 0/1:24,30:53:-117.86,-15.97,-81.07:99 +chr1 2904988 . G T 192.75 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.69;MQ0=0;OQ=850.19;QD=14.17;SB=-430.19 GT:AD:DP:GL:GQ 0/1:30,30:56:-105.17,-16.87,-90.14:99 +chr1 2905123 rs12049173 C A 190.89 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.62;MQ0=0;OQ=810.47;QD=14.22;SB=-367.40 GT:AD:DP:GL:GQ 0/1:30,27:57:-101.50,-17.17,-107.52:99 +chr1 2905133 rs12046411 G A 347.03 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.57;MQ0=0;OQ=1037.17;QD=16.73;SB=-437.83 GT:AD:DP:GL:GQ 0/1:30,32:59:-124.78,-17.78,-92.83:99 +chr1 2905422 rs12049274 C T 603.53 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=930.71;QD=16.05;SB=-490.47 GT:AD:DP:GL:GQ 0/1:30,28:58:-113.82,-17.47,-110.72:99 +chr1 2905744 . G A 180.07 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=873.90;QD=13.87;SB=-441.80 GT:AD:DP:GL:GQ 0/1:36,27:62:-109.35,-18.68,-126.71:99 +chr1 2905997 rs12239064 T G 232.27 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=59.60;MQ0=0;OQ=846.38;QD=14.85;SB=-338.82 GT:AD:DP:GL:GQ 0/1:27,30:56:-104.79,-16.87,-99.38:99 +chr1 2906020 rs12240128 G A 259.44 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=59.61;MQ0=0;OQ=950.01;QD=16.10;SB=-410.72 GT:AD:DP:GL:GQ 0/1:30,29:59:-116.06,-17.77,-109.83:99 +chr1 2906205 . C T 60.99 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=59.51;MQ0=0;OQ=509.22;QD=13.40;SB=-258.23 GT:AD:DP:GL:GQ 0/1:18,20:34:-64.46,-10.25,-58.74:99 +chr1 2906216 rs59653178 T C 119.56 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=59.54;MQ0=0;OQ=444.86;QD=10.85;SB=-210.25 GT:AD:DP:GL:GQ 0/1:22,19:37:-58.92,-11.15,-79.90:99 +chr1 2906318 . G C 294.79 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=687.54;QD=14.03;SB=-349.42 GT:AD:DP:GL:GQ 0/1:28,21:48:-86.50,-14.46,-122.06:99 +chr1 2906331 . T C 64.13 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=486.38;QD=9.01;SB=-239.89 GT:AD:DP:GL:GQ 0/1:34,20:53:-67.89,-15.97,-133.79:99 +chr1 2906530 rs16823325 A G 170.42 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=627.60;QD=14.26;SB=-219.26 GT:AD:DP:GL:GQ 0/1:22,22:44:-79.30,-13.26,-90.47:99 +chr1 2906541 rs57711454 A G 139.66 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.54;MQ0=0;OQ=394.78;QD=7.90;SB=-84.54 GT:AD:DP:GL:GQ 0/1:29,20:47:-56.93,-14.17,-116.48:99 +chr1 2906996 rs10909857 T C 66.55 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.62;MQ=57.79;MQ0=0;OQ=652.62;QD=12.31;SB=-287.16 GT:AD:DP:GL:GQ 0/1:27,26:51:-83.92,-15.38,-97.87:99 +chr1 2907051 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=17;HaplotypeScore=24.33;MQ=55.91;MQ0=0;OQ=72.31;QD=0.98;SB=54.68 GT:AD:DP:GL:GQ 0/1:56,17:51:-25.89,-15.37,-146.19:99 +chr1 2907237 rs12025260 T C 432.13 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.22;MQ0=0;OQ=586.66;QD=11.73;SB=-318.24 GT:AD:DP:GL:GQ 0/1:25,25:46:-75.82,-13.87,-89.45:99 +chr1 2907320 rs10797374 C G 183.78 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=56.79;MQ0=0;OQ=866.79;QD=16.35;SB=-401.99 GT:AD:DP:GL:GQ 0/1:26,27:47:-104.13,-14.17,-96.80:99 +chr1 2907323 rs10797375 C T 107.89 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=56.36;MQ0=0;OQ=897.14;QD=16.31;SB=-320.30 GT:AD:DP:GL:GQ 0/1:27,28:53:-108.97,-15.97,-91.39:99 +chr1 2907332 rs10797376 A G 569.46 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.97;MQ0=0;OQ=769.31;QD=13.26;SB=-314.20 GT:AD:DP:GL:GQ 0/1:28,30:54:-96.49,-16.28,-97.60:99 +chr1 2907425 rs17389607 C T 13.36 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=8.86;MQ=57.83;MQ0=0;OQ=822.69;QD=15.82;SB=-373.37 GT:AD:DP:GL:GQ 0/1:24,28:48:-100.02,-14.47,-70.94:99 +chr1 2907558 rs10909859 C T 467.69 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=759.55;QD=17.26;SB=-317.87 GT:AD:DP:GL:GQ 0/1:21,23:40:-91.30,-12.06,-54.32:99 +chr1 2907881 rs56008028 A G 101.20 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=60.00;MQ0=0;OQ=314.58;QD=9.83;SB=-73.78 GT:AD:DP:GL:GQ 0/1:16,16:27:-42.88,-8.14,-52.46:99 +chr1 2908045 rs12562237 C T 38.60 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=3.04;MQ=57.73;MQ0=0;OQ=402.69;QD=12.99;SB=-180.26 GT:AD:DP:GL:GQ 0/1:14,17:26:-51.39,-7.84,-42.83:99 +chr1 2908055 rs3924055 G A 76.12 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=57.57;MQ0=0;OQ=483.15;QD=16.66;SB=-242.76 GT:AD:DP:GL:GQ 0/1:13,16:26:-59.44,-7.84,-34.72:99 +chr1 2908089 rs16823330 C T 124.82 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.14;MQ0=0;OQ=508.46;QD=18.83;SB=-215.91 GT:AD:DP:GL:GQ 0/1:11,16:27:-62.27,-8.14,-34.10:99 +chr1 2908371 . G A 74.23 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.57;MQ0=0;OQ=788.94;QD=18.35;SB=-397.93 GT:AD:DP:GL:GQ 0/1:18,24:36:-93.03,-10.85,-43.26:99 +chr1 2908432 . T C 8.81 PASS AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=56.92;MQ0=0;OQ=358.32;QD=15.58;SB=-114.66 GT:AD:DP:GL:GQ 0/1:9,14:19:-44.84,-5.73,-23.69:99 +chr1 2908471 . G A 46.40 LowQual AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=4.79;MQ=51.77;MQ0=0;QD=1.93;SB=-32.97 GT:AD:DP:GL:GQ 0/1:20,4:22:-14.55,-6.63,-62.87:79.23 +chr1 2908486 . G A 26.78 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=9.20;MQ=53.95;MQ0=0;QD=1.12;SB=-23.58 GT:AD:DP:GL:GQ 0/1:21,3:20:-11.99,-6.02,-60.39:59.60 +chr1 2908487 . G A 23.81 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=9.20;MQ=53.95;MQ0=0;QD=0.99;SB=-23.59 GT:AD:DP:GL:GQ 0/1:21,3:20:-11.69,-6.03,-57.69:56.63 +chr1 2908489 rs7413322 A G 127.27 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=7.20;MQ=53.67;MQ0=0;QD=5.53;SB=-41.81 GT:AD:DP:GL:GQ 0/1:15,7:21:-22.34,-6.33,-53.28:99 +chr1 2908502 . G A 0.58 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=3.89;MQ=54.56;MQ0=0;OQ=132.59;QD=4.28;SB=-84.55 GT:AD:DP:GL:GQ 0/1:22,9:26:-24.37,-7.83,-71.82:99 +chr1 2908503 . G A 2.61 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=3.89;MQ=54.56;MQ0=0;OQ=189.68;QD=6.12;SB=-101.89 GT:AD:DP:GL:GQ 0/1:22,9:28:-30.69,-8.44,-70.32:99 +chr1 2908532 . T C 3.50 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.76;MQ=54.67;MQ0=0;OQ=250.55;QD=6.77;SB=-66.91 GT:AD:DP:GL:GQ 0/1:24,13:35:-38.89,-10.55,-92.28:99 +chr1 2908533 . G A 0.93 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=4.66;MQ=54.15;MQ0=0;OQ=217.08;QD=5.71;SB=-54.22 GT:AD:DP:GL:GQ 0/1:25,13:33:-34.93,-9.94,-84.25:99 +chr1 2908644 . G A 90.84 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.24;MQ=55.47;MQ0=0;OQ=799.27;QD=15.67;SB=-377.10 GT:AD:DP:GL:GQ 0/1:25,26:51:-98.58,-15.37,-88.82:99 +chr1 2908650 . T C 65.40 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=55.56;MQ0=0;OQ=744.55;QD=14.32;SB=-322.26 GT:AD:DP:GL:GQ 0/1:26,26:52:-93.41,-15.67,-101.68:99 +chr1 2908671 . T C 96.67 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=55.57;MQ0=0;OQ=663.38;QD=13.01;SB=-328.92 GT:AD:DP:GL:GQ 0/1:26,25:50:-84.69,-15.07,-101.18:99 +chr1 2908691 rs7524813 A G 287.06 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.53;MQ0=0;OQ=655.21;QD=13.10;SB=-352.07 GT:AD:DP:GL:GQ 0/1:22,28:47:-82.98,-14.17,-84.04:99 +chr1 2908767 . C T 11.79 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=50.29;MQ0=0;OQ=630.57;QD=18.02;SB=-203.89 GT:AD:DP:GL:GQ 0/1:14,21:32:-75.99,-9.65,-40.87:99 +chr1 2908798 rs7520336 C T 363.17 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=53.82;MQ0=0;OQ=459.08;QD=13.12;SB=-219.69 GT:AD:DP:GL:GQ 0/1:20,15:31:-58.54,-9.34,-53.07:99 +chr1 2909329 rs6424067 A G 0.51 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=3.24;MQ=54.59;MQ0=0;OQ=434.74;QD=9.88;SB=-243.29 GT:AD:DP:GL:GQ 0/1:26,18:41:-59.12,-12.36,-92.44:99 +chr1 2909490 rs12025062 C T 390.05 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.85;MQ0=0;OQ=616.92;QD=11.64;SB=-324.31 GT:AD:DP:GL:GQ 0/1:32,21:52:-80.64,-15.67,-112.78:99 +chr1 2909802 rs12022429 G A 318.87 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=605.69;QD=12.36;SB=-271.15 GT:AD:DP:GL:GQ 0/1:27,22:47:-78.02,-14.16,-93.88:99 +chr1 2909879 rs12025167 C T 200.91 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.12;MQ=58.32;MQ0=0;OQ=594.51;QD=15.24;SB=-283.81 GT:AD:DP:GL:GQ 0/1:20,19:35:-73.29,-10.56,-48.45:99 +chr1 2909902 rs12022456 G A 164.15 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.51;MQ=58.51;MQ0=0;OQ=722.60;QD=16.42;SB=-335.48 GT:AD:DP:GL:GQ 0/1:20,24:41:-87.91,-12.37,-56.64:99 +chr1 2910018 rs16823332 C T 243.36 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=942.08;QD=19.23;SB=-418.46 GT:AD:DP:GL:GQ 0/1:20,28:45:-111.06,-13.56,-54.54:99 +chr1 2910291 rs12066017 A G 366.01 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=575.67;QD=14.76;SB=-270.53 GT:AD:DP:GL:GQ 0/1:19,20:38:-72.30,-11.45,-69.20:99 +chr1 2911142 . G A 41.67 PASS AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.51;MQ=59.36;MQ0=0;OQ=1099.50;QD=16.92;SB=-501.68 GT:AD:DP:GL:GQ 0/1:32,33:61:-131.61,-18.38,-102.89:99 +chr1 2911277 . C G 44.53 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.86;MQ=58.95;MQ0=0;OQ=436.44;QD=10.91;SB=-233.06 GT:AD:DP:GL:GQ 0/1:26,14:40:-58.99,-12.06,-109.38:99 +chr1 2911306 . G C 234.71 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.10;MQ0=0;OQ=519.44;QD=14.04;SB=-251.08 GT:AD:DP:GL:GQ 0/1:21,16:36:-66.08,-10.85,-90.14:99 +chr1 2911720 rs16823335 G A 261.73 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=59.20;MQ0=0;OQ=681.92;QD=11.76;SB=-297.82 GT:AD:DP:GL:GQ 0/1:33,24:53:-87.45,-15.98,-100.90:99 +chr1 2912187 rs12028094 C T 355.65 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.31;MQ0=0;OQ=839.47;QD=15.55;SB=-427.81 GT:AD:DP:GL:GQ 0/1:28,26:51:-102.60,-15.37,-81.01:99 +chr1 2912604 rs10797377 G A 324.39 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=59.31;MQ0=0;OQ=1121.19;QD=18.38;SB=-566.38 GT:AD:DP:GL:GQ 0/1:27,34:59:-133.18,-17.78,-89.26:99 +chr1 2913061 . G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=14.44;MQ=58.67;MQ0=0;OQ=1557.84;QD=18.11;SB=-803.34 GT:AD:DP:GL:GQ 0/1:39,47:82:-183.77,-24.70,-131.16:99 +chr1 2913244 rs12063869 T A 356.59 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.21;MQ0=0;OQ=1259.24;QD=16.35;SB=-327.01 GT:AD:DP:GL:GQ 0/1:37,40:76:-152.10,-22.89,-141.13:99 +chr1 2913685 . T A 78.15 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=72;Dels=0.01;HRun=7;HaplotypeScore=10.99;MQ=58.04;MQ0=0;QD=1.09;SB=89.27 GT:AD:DP:GL:GQ 0/1:54,17:56:-27.67,-16.57,-168.58:99 +chr1 2914586 rs2889476 T C 86.82 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=59.50;MQ0=0;OQ=1018.41;QD=13.58;SB=-348.57 GT:AD:DP:GL:GQ 0/1:38,37:73:-127.11,-21.99,-156.39:99 +chr1 2915216 . C A 133.06 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=840.99;QD=15.57;SB=-328.03 GT:AD:DP:GL:GQ 0/1:26,28:54:-103.65,-16.27,-91.36:99 +chr1 2915282 rs946175 A G 382.87 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.34;MQ0=0;OQ=951.27;QD=13.59;SB=-404.30 GT:AD:DP:GL:GQ 0/1:37,33:69:-119.20,-20.78,-144.79:99 +chr1 2915357 rs946176 C T 193.41 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=60.00;MQ0=0;OQ=877.87;QD=15.14;SB=-352.31 GT:AD:DP:GL:GQ 0/1:30,28:58:-108.55,-17.48,-106.40:99 +chr1 2915382 rs946177 A G 311.86 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=60.00;MQ0=0;OQ=696.00;QD=12.21;SB=-254.19 GT:AD:DP:GL:GQ 0/1:29,28:55:-89.46,-16.58,-112.38:99 +chr1 2916239 rs2027262 T C 443.46 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=530.92;QD=9.65;SB=-168.92 GT:AD:DP:GL:GQ 0/1:28,27:51:-71.75,-15.38,-111.87:99 +chr1 2916397 rs2027263 A G 6.58 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=4.33;MQ=58.92;MQ0=0;OQ=1007.60;QD=17.99;SB=-520.31 GT:AD:DP:GL:GQ 0/1:22,34:54:-120.31,-16.27,-82.47:99 +chr1 2916415 rs2027264 G A 412.83 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=890.12;QD=17.45;SB=-464.45 GT:AD:DP:GL:GQ 0/1:23,27:49:-107.06,-14.77,-75.59:99 +chr1 2916645 . C T 34.34 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=56.98;MQ0=0;OQ=878.75;QD=16.90;SB=-242.23 GT:AD:DP:GL:GQ 0/1:24,28:50:-106.23,-15.07,-83.70:99 +chr1 2916833 rs11802804 T G 172.47 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=53.08;MQ0=1;OQ=929.71;QD=12.91;SB=-466.74 GT:AD:DP:GL:GQ 0/1:38,34:69:-117.04,-20.78,-128.73:99 +chr1 2916871 . T G 0.62 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=5.93;MQ=46.04;MQ0=1;OQ=612.93;QD=10.57;SB=-101.87 GT:AD:DP:GL:GQ 0/1:33,25:54:-80.84,-16.27,-108.92:99 +chr1 2916874 . G A 4.25 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=3.93;MQ=45.85;MQ0=1;OQ=812.26;QD=13.32;SB=-234.49 GT:AD:DP:GL:GQ 0/1:33,28:56:-101.38,-16.87,-110.18:99 +chr1 2917035 rs12028439 A G 6.74 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=4.28;MQ=54.23;MQ0=0;OQ=1040.90;QD=18.93;SB=-369.97 GT:AD:DP:GL:GQ 0/1:20,35:53:-123.34,-15.97,-76.66:99 +chr1 2917114 rs12024879 G A 187.61 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=55.08;MQ0=0;OQ=934.32;QD=17.30;SB=-362.51 GT:AD:DP:GL:GQ 0/1:25,29:52:-112.38,-15.67,-83.45:99 +chr1 2917331 rs12027818 C T 143.12 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=58.15;MQ0=1;OQ=1252.97;QD=20.21;SB=-536.07 GT:AD:DP:GL:GQ 0/1:25,37:61:-146.97,-18.38,-79.78:99 +chr1 2917538 rs12027883 C T 346.92 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=58.55;MQ0=0;OQ=1081.24;QD=14.42;SB=-345.82 GT:AD:DP:GL:GQ 0/1:42,33:74:-133.70,-22.29,-151.25:99 +chr1 2918836 rs6681651 C T 64.93 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=454.13;QD=15.66;SB=-29.51 GT:AD:DP:GL:GQ 0/1:13,16:27:-56.83,-8.14,-47.37:99 +chr1 2921187 rs6691208 C A 92.06 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=715.52;QD=11.36;SB=-355.27 GT:AD:DP:GL:GQ 0/1:37,26:61:-93.21,-18.38,-116.36:99 +chr1 2921274 rs4357486 G C 320.40 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=59.45;MQ0=0;OQ=673.44;QD=16.03;SB=-361.79 GT:AD:DP:GL:GQ 0/1:20,22:41:-83.00,-12.37,-84.03:99 +chr1 2921300 rs4486390 C T 182.10 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.96;MQ=59.45;MQ0=0;OQ=737.41;QD=17.56;SB=-360.43 GT:AD:DP:GL:GQ 0/1:18,24:38:-88.48,-11.46,-48.81:99 +chr1 2922007 rs59869348 T C 59.62 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.22;MQ=59.22;MQ0=0;OQ=864.59;QD=16.01;SB=-414.28 GT:AD:DP:GL:GQ 0/1:23,31:52:-105.41,-15.67,-90.49:99 +chr1 2922076 rs59041920 C T 58.92 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=4.59;MQ=59.36;MQ0=0;OQ=1222.53;QD=18.81;SB=-446.93 GT:AD:DP:GL:GQ 0/1:26,38:58:-143.01,-17.47,-78.18:99 +chr1 2922420 . C T 142.55 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=58.20;MQ0=0;OQ=828.62;QD=13.81;SB=-355.45 GT:AD:DP:GL:GQ 0/1:34,26:58:-103.62,-17.47,-119.28:99 +chr1 2922927 . A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=1;HaplotypeScore=3.70;MQ=45.44;MQ0=1;OQ=81.65;QD=2.92;SB=-41.94 GT:AD:DP:GL:GQ 0/1:20,8:20:-17.47,-6.02,-59.35:99 +chr1 2923073 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=21;Dels=0.05;HRun=1;HaplotypeScore=30.97;MQ=45.34;MQ0=0;OQ=111.92;QD=5.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,8:13:-18.39,-3.92,-26.21:99 +chr1 2923110 . A C 47.42 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=28.91;MQ=36.30;MQ0=0;QD=3.65;SB=5.05 GT:AD:DP:GL:GQ 0/1:6,4:10:-13.77,-5.74,-26.81:80.25 +chr1 2923762 rs6680573 C G 6.28 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=3.37;MQ=60.00;MQ0=0;OQ=313.93;QD=10.46;SB=-109.66 GT:AD:DP:GL:GQ 0/1:20,10:28:-43.13,-8.46,-67.50:99 +chr1 2924595 rs56200661 C T 138.23 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.81;MQ0=0;OQ=702.85;QD=18.02;SB=-315.84 GT:AD:DP:GL:GQ 0/1:17,22:37:-84.72,-11.16,-50.65:99 +chr1 2924706 . G A 66.14 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.09;MQ0=0;OQ=681.79;QD=16.63;SB=-295.78 GT:AD:DP:GL:GQ 0/1:19,22:39:-83.22,-11.75,-60.51:99 +chr1 2926246 rs12564456 C G 10.43 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=2.61;MQ=58.69;MQ0=0;OQ=646.12;QD=12.92;SB=-206.63 GT:AD:DP:GL:GQ 0/1:26,24:45:-81.49,-13.60,-94.41:99 +chr1 2926340 rs10752732 T C 133.80 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=58.78;MQ0=0;OQ=1282.63;QD=33.75;SB=-620.25 GT:AD:DP:GL:GQ 1/1:0,38:38:-131.87,-11.45,-0.02:99 +chr1 2926606 rs55949537 A T 46.15 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=3.14;MQ=59.67;MQ0=0;OQ=1017.41;QD=14.13;SB=-469.52 GT:AD:DP:GL:GQ 0/1:36,35:69:-125.81,-20.79,-130.04:99 +chr1 2926614 rs55784203 G T 254.87 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=59.65;MQ0=0;OQ=972.92;QD=14.31;SB=-412.15 GT:AD:DP:GL:GQ 0/1:33,35:66:-120.46,-19.89,-108.03:99 +chr1 2926663 rs56091202 A G 268.72 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=59.60;MQ0=0;OQ=738.64;QD=12.74;SB=-307.21 GT:AD:DP:GL:GQ 0/1:29,29:57:-94.32,-17.18,-112.23:99 +chr1 2926891 . A G 0.34 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=3;HaplotypeScore=3.44;MQ=59.42;MQ0=0;OQ=538.71;QD=11.22;SB=-143.63 GT:AD:DP:GL:GQ 0/1:27,21:47:-71.31,-14.16,-109.92:99 +chr1 2927088 rs61266721 G A 167.43 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=3.88;MQ=59.23;MQ0=0;OQ=1016.77;QD=16.95;SB=-453.45 GT:AD:DP:GL:GQ 0/1:30,30:57:-122.14,-17.18,-86.53:99 +chr1 2927410 rs12033927 A G 358.86 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=59.13;MQ0=0;OQ=706.05;QD=14.71;SB=-368.25 GT:AD:DP:GL:GQ 0/1:23,25:48:-88.35,-14.46,-94.54:99 +chr1 2927411 rs12034794 T G 337.44 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=59.15;MQ0=0;OQ=614.57;QD=12.54;SB=-294.80 GT:AD:DP:GL:GQ 0/1:24,25:47:-78.90,-14.16,-89.23:99 +chr1 2928125 rs4576609 C T 277.54 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=4.12;MQ=57.60;MQ0=0;OQ=875.52;QD=14.35;SB=-423.82 GT:AD:DP:GL:GQ 0/1:31,30:59:-108.62,-17.78,-98.44:99 +chr1 2928429 rs35806103 C T 10.78 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.15;MQ=59.80;MQ0=0;OQ=886.08;QD=19.69;SB=-315.84 GT:AD:DP:GL:GQ 0/1:17,27:42:-104.54,-12.65,-59.38:99 +chr1 2928557 rs3795262 T G 88 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.78;MQ0=0;OQ=296.95;QD=7.81;SB=-58.83 GT:AD:DP:GL:GQ 0/1:21,17:33:-42.92,-9.94,-74.02:99 +chr1 2928784 . T G 4.50 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.61;MQ=58.98;MQ0=0;OQ=615.11;QD=15.00;SB=-301.85 GT:AD:DP:GL:GQ 0/1:17,24:38:-76.24,-11.45,-59.09:99 +chr1 2929872 rs55873718 A G 218.87 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.73;MQ0=0;OQ=845.74;QD=10.07;SB=-404.66 GT:AD:DP:GL:GQ 0/1:48,36:83:-112.88,-25.02,-189.40:99 +chr1 2930858 rs56176404 A G 226.80 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.44;MQ0=0;OQ=1022.49;QD=13.82;SB=-491.10 GT:AD:DP:GL:GQ 0/1:38,36:73:-127.52,-21.99,-154.69:99 +chr1 2932289 rs55885250 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.04;HRun=0;HaplotypeScore=32.21;MQ=45.88;MQ0=1;OQ=148.06;QD=1.90;SB=104.37 GT:AD:DP:GL:GQ 0/1:58,16:68:-38.29,-20.20,-216.63:99 +chr1 2932299 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=92;Dels=0.02;HRun=0;HaplotypeScore=97.52;MQ=43.85;MQ0=0;OQ=59.90;QD=0.65;SB=104.31 GT:AD:DP:GL:GQ 0/1:78,12:69:-29.77,-20.49,-208.32:92.74 +chr1 2932325 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=91;Dels=0.02;HRun=1;HaplotypeScore=195.32;MQ=42.40;MQ0=0;OQ=612.63;QD=6.73;SB=-162.19 GT:AD:DP:GL:GQ 0/1:51,38:73:-86.24,-21.70,-183.14:99 +chr1 2932341 . A G 250.48 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=1;HaplotypeScore=40.55;MQ=40.81;MQ0=0;QD=2.04;SB=89.32 GT:AD:DP:GL:GQ 0/1:96,27:107:-60.57,-32.24,-364.33:99 +chr1 2932343 . G A 487.06 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=123;Dels=0.01;HRun=0;HaplotypeScore=44.00;MQ=40.81;MQ0=0;QD=3.96;SB=58.75 GT:AD:DP:GL:GQ 0/1:99,23:108:-84.22,-32.23,-314.56:99 +chr1 2932349 . G A 708.07 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=1;HaplotypeScore=35.72;MQ=40.62;MQ0=0;QD=5.80;SB=89.29 GT:AD:DP:GL:GQ 0/1:95,27:119:-109.94,-35.84,-335.64:99 +chr1 2932354 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=77.99;MQ=40.25;MQ0=0;OQ=691.65;QD=5.49;SB=86.28 GT:AD:DP:GL:GQ 0/1:97,29:123:-109.51,-37.06,-349.27:99 +chr1 2932376 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=2;HaplotypeScore=11.36;MQ=39.42;MQ0=0;OQ=679.31;QD=5.27;SB=92.31 GT:AD:DP:GL:GQ 0/1:96,32:117:-106.47,-35.26,-303.35:99 +chr1 2932379 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=125;Dels=0.01;HRun=1;HaplotypeScore=36.27;MQ=39.15;MQ0=0;OQ=716.76;QD=5.73;SB=92.27 GT:AD:DP:GL:GQ 0/1:94,28:121:-111.11,-36.16,-333.12:99 +chr1 2932387 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=36.67;MQ=38.20;MQ0=0;OQ=140.95;QD=1.25;SB=77.24 GT:AD:DP:GL:GQ 0/1:93,19:101:-47.83,-30.45,-304.67:99 +chr1 2932417 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=80.35;MQ=36.74;MQ0=0;OQ=291.45;QD=2.83;SB=86.26 GT:AD:DP:GL:GQ 0/1:76,27:77:-55.63,-23.21,-217.09:99 +chr1 2932437 . G A 14.74 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=80.96;MQ=35.05;MQ0=0;QD=0.16;SB=80.26 GT:AD:DP:GL:GQ 0/1:79,12:67:-24.93,-20.19,-214.14:47.43 +chr1 2932441 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=78.31;MQ=34.28;MQ0=0;OQ=251.61;QD=2.83;SB=77.24 GT:AD:DP:GL:GQ 0/1:70,19:66:-48.33,-19.89,-185.59:99 +chr1 2932450 rs55992205 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=52.98;MQ=32.53;MQ0=0;OQ=616.18;QD=7.16;SB=92.26 GT:AD:DP:GL:GQ 0/1:64,22:76:-87.80,-22.90,-186.06:99 +chr1 2932474 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=98;Dels=0.05;HRun=0;HaplotypeScore=121.87;MQ=31.47;MQ0=0;OQ=770.86;QD=7.87;SB=104.31 GT:AD:DP:GL:GQ 0/1:66,27:80:-104.48,-24.11,-189.46:99 +chr1 2932495 . A G 458.76 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=1;HaplotypeScore=104.10;MQ=35.05;MQ0=0;QD=4.59;SB=98.32 GT:AD:DP:GL:GQ 0/1:77,23:78:-72.67,-23.51,-220.09:99 +chr1 2932498 . G A 771.99 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=0;HaplotypeScore=85.95;MQ=35.28;MQ0=0;QD=8.04;SB=59.63 GT:AD:DP:GL:GQ 0/1:70,26:76:-103.38,-22.90,-174.72:99 +chr1 2932501 . G A 15.55 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=78.10;MQ=36.15;MQ0=0;QD=0.16;SB=-7.88 GT:AD:DP:GL:GQ 0/1:82,13:64:-24.12,-19.29,-198.59:48.26 +chr1 2932516 . A G 437.11 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=2;HaplotypeScore=90.55;MQ=38.01;MQ0=0;QD=4.37;SB=68.24 GT:AD:DP:GL:GQ 0/1:78,20:76:-69.30,-22.30,-207.20:99 +chr1 2932519 . A G 420.64 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=1;HaplotypeScore=127.72;MQ=37.64;MQ0=1;QD=3.72;SB=86.29 GT:AD:DP:GL:GQ 0/1:90,23:88:-71.87,-26.52,-261.50:99 +chr1 2932522 . A G 354.05 SnpCluster AC=1;AF=0.50;AN=2;DP=116;Dels=0.02;HRun=1;HaplotypeScore=155.74;MQ=37.22;MQ0=2;QD=3.05;SB=-178.30 GT:AD:DP:GL:GQ 0/1:89,24:100:-68.22,-29.53,-308.19:99 +chr1 2932531 . G A 40.28 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=127;Dels=0.02;HRun=0;HaplotypeScore=95.96;MQ=37.07;MQ0=3;QD=0.32;SB=-35.75 GT:AD:DP:GL:GQ 0/1:114,11:85:-32.32,-25.01,-255.84:73.11 +chr1 2932543 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=0;HaplotypeScore=90.42;MQ=36.51;MQ0=3;OQ=448.17;QD=3.59;SB=-29.75 GT:AD:DP:GL:GQ 0/1:94,23:99:-91.60,-43.50,-272.82:99 +chr1 2932549 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=1;HaplotypeScore=106.24;MQ=36.58;MQ0=3;OQ=776.41;QD=6.81;SB=20.21 GT:AD:DP:GL:GQ 0/1:80,34:91:-108.36,-27.43,-223.52:99 +chr1 2932558 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=87.01;MQ=36.91;MQ0=2;OQ=55.94;QD=0.53;SB=50.16 GT:AD:DP:GL:GQ 0/1:89,16:77:-32.08,-23.20,-238.58:88.78 +chr1 2932594 . A G 95.90 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=101;Dels=0.01;HRun=2;HaplotypeScore=79.79;MQ=37.41;MQ0=0;QD=0.95;SB=41.16 GT:AD:DP:GL:GQ 0/1:85,15:78:-36.37,-23.50,-267.93:99 +chr1 2932595 . G T 858.77 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=99;Dels=0.01;HRun=0;HaplotypeScore=92.92;MQ=37.56;MQ0=0;QD=8.67;SB=50.17 GT:AD:DP:GL:GQ 0/1:57,41:82:-113.86,-24.70,-181.24:99 +chr1 2932597 . A G 613.75 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=100;Dels=0.01;HRun=2;HaplotypeScore=83.48;MQ=37.85;MQ0=0;QD=6.14;SB=53.19 GT:AD:DP:GL:GQ 0/1:69,29:84:-89.97,-25.31,-224.02:99 +chr1 2932647 . A G 424.25 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=1;HaplotypeScore=36.34;MQ=40.26;MQ0=1;QD=3.82;SB=65.23 GT:AD:DP:GL:GQ 0/1:87,24:95:-74.33,-28.62,-285.65:99 +chr1 2932650 . G A 15.47 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=0;HaplotypeScore=35.26;MQ=39.92;MQ0=1;QD=0.13;SB=83.21 GT:AD:DP:GL:GQ 0/1:106,9:104:-36.16,-31.34,-318.46:48.18 +chr1 2932656 . G A 597.61 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=0;HaplotypeScore=41.23;MQ=39.70;MQ0=1;QD=5.24;SB=83.24 GT:AD:DP:GL:GQ 0/1:85,29:104:-94.39,-31.34,-268.84:99 +chr1 2932671 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=1;HaplotypeScore=55.64;MQ=38.11;MQ0=1;OQ=790.23;QD=6.17;SB=74.25 GT:AD:DP:GL:GQ 0/1:94,34:113:-116.34,-34.04,-292.03:99 +chr1 2932680 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=32.69;MQ=37.68;MQ0=1;OQ=1237.37;QD=9.67;SB=74.20 GT:AD:DP:GL:GQ 0/1:85,43:122:-163.79,-36.76,-270.86:99 +chr1 2932682 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=0;HaplotypeScore=26.80;MQ=37.61;MQ0=1;OQ=704.94;QD=5.42;SB=71.27 GT:AD:DP:GL:GQ 0/1:103,27:122:-110.54,-36.77,-411.49:99 +chr1 2932721 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=0;HaplotypeScore=36.50;MQ=39.93;MQ0=0;OQ=181.45;QD=1.51;SB=92.30 GT:AD:DP:GL:GQ 0/1:93,27:104:-52.76,-31.33,-321.47:99 +chr1 2932727 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=27.86;MQ=40.16;MQ0=0;OQ=588.52;QD=5.35;SB=83.30 GT:AD:DP:GL:GQ 0/1:83,27:109:-94.97,-32.83,-329.92:99 +chr1 2932738 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=1;HaplotypeScore=39.11;MQ=39.53;MQ0=0;OQ=873.00;QD=7.94;SB=74.25 GT:AD:DP:GL:GQ 0/1:74,36:108:-123.12,-32.54,-289.99:99 +chr1 2932769 . G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=7.13;MQ=40.78;MQ0=0;OQ=619.13;QD=6.59;SB=56.17 GT:AD:DP:GL:GQ 0/1:71,23:91:-92.61,-27.42,-231.77:99 +chr1 2933043 rs7412983 A C 563.74 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=861.61;QD=12.67;SB=-438.69 GT:AD:DP:GL:GQ 0/1:37,31:65:-109.02,-19.58,-126.93:99 +chr1 2933258 rs58265521 C A 261.91 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.67;MQ0=0;OQ=928.26;QD=16.29;SB=-439.21 GT:AD:DP:GL:GQ 0/1:24,33:53:-112.08,-15.97,-65.68:99 +chr1 2933528 rs60287244 A G 23.05 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.04;MQ=58.03;MQ0=0;OQ=739.69;QD=12.98;SB=-372.23 GT:AD:DP:GL:GQ 0/1:30,27:55:-93.82,-16.57,-116.71:99 +chr1 2933898 rs12034766 A G 35.30 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=1.69;MQ=58.27;MQ0=0;OQ=600.73;QD=11.12;SB=-275.56 GT:AD:DP:GL:GQ 0/1:26,28:51:-78.73,-15.38,-104.98:99 +chr1 2933946 rs12033401 C T 155.60 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.82;MQ=57.46;MQ0=0;OQ=525.20;QD=14.19;SB=-282.22 GT:AD:DP:GL:GQ 0/1:16,21:31:-65.15,-9.35,-44.32:99 +chr1 2934531 rs57893585 T A 124.36 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.24;MQ0=0;OQ=372.99;QD=15.54;SB=-168.83 GT:AD:DP:GL:GQ 0/1:10,14:21:-46.91,-6.33,-28.06:99 +chr1 2935764 rs12035292 C T 0.26 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=10.18;MQ=43.51;MQ0=2;OQ=248.84;QD=4.70;SB=-149.59 GT:AD:DP:GL:GQ 0/1:30,23:31:-37.51,-9.34,-74.68:99 +chr1 2935800 rs6693975 G A 0.65 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=6.49;MQ=45.50;MQ0=1;OQ=189.85;QD=4.75;SB=-111.56 GT:AD:DP:GL:GQ 0/1:24,16:23:-29.21,-6.94,-45.54:99 +chr1 2935836 rs6693982 G A 38.33 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.48;MQ=49.72;MQ0=2;OQ=286.18;QD=6.36;SB=-139.13 GT:AD:DP:GL:GQ 0/1:25,20:29:-40.65,-8.75,-58.79:99 +chr1 2936586 rs12038530 T A 386.33 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=538.23;QD=11.21;SB=-193.51 GT:AD:DP:GL:GQ 0/1:29,19:46:-70.96,-13.86,-104.56:99 +chr1 2937616 rs12037307 C A 453.51 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=785.06;QD=15.10;SB=-326.01 GT:AD:DP:GL:GQ 0/1:25,27:52:-97.46,-15.67,-88.48:99 +chr1 2937769 rs12039548 T C 374.78 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.69;MQ=59.62;MQ0=0;OQ=1018.45;QD=16.97;SB=-485.32 GT:AD:DP:GL:GQ 0/1:25,35:58:-122.60,-17.48,-90.45:99 +chr1 2937880 rs12034573 G A 539.50 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=601.18;QD=13.36;SB=-263.26 GT:AD:DP:GL:GQ 0/1:25,20:44:-76.67,-13.27,-77.09:99 +chr1 2938038 rs10909864 T C 31.93 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=3.17;MQ=58.15;MQ0=0;OQ=603.85;QD=12.58;SB=-301.61 GT:AD:DP:GL:GQ 0/1:20,28:44:-76.94,-13.27,-79.42:99 +chr1 2938888 rs1890338 C T 331.53 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=59.50;MQ0=0;OQ=622.92;QD=13.54;SB=-315.86 GT:AD:DP:GL:GQ 0/1:22,23:40:-77.64,-12.06,-61.98:99 +chr1 2939215 rs12039132 C T 18.71 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=58.67;MQ0=0;OQ=590.59;QD=16.87;SB=-94.60 GT:AD:DP:GL:GQ 0/1:16,19:32:-71.99,-9.65,-41.59:99 +chr1 2939467 rs7514166 G C 161.11 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=58.11;MQ0=0;OQ=380.76;QD=10.29;SB=-57.73 GT:AD:DP:GL:GQ 0/1:23,14:34:-51.61,-10.25,-87.39:99 +chr1 2939859 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=9;HaplotypeScore=3.75;MQ=51.46;MQ0=0;OQ=333.21;QD=11.49;SB=-54.83 GT:AD:DP:GL:GQ 0/1:17,12:25:-44.15,-7.55,-58.82:99 +chr1 2939927 rs34408665 T C 431.23 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.91;MQ0=0;OQ=752.79;QD=11.76;SB=-348.05 GT:AD:DP:GL:GQ 0/1:32,32:61:-96.95,-18.39,-123.70:99 +chr1 2939954 rs58052947 T C 258.56 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=58.84;MQ0=0;OQ=891.02;QD=13.92;SB=-428.88 GT:AD:DP:GL:GQ 0/1:28,36:63:-111.38,-19.00,-108.25:99 +chr1 2940097 rs56398543 G A 185.44 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=57.77;MQ0=0;OQ=622.10;QD=14.81;SB=-266.78 GT:AD:DP:GL:GQ 0/1:21,21:40:-77.55,-12.06,-68.06:99 +chr1 2940194 rs6661908 G A 424.22 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.03;MQ0=0;OQ=1140.17;QD=20.00;SB=-442.95 GT:AD:DP:GL:GQ 0/1:24,33:57:-134.47,-17.17,-86.30:99 +chr1 2940230 rs41334845 G T 113.62 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.36;MQ0=0;OQ=1373.67;QD=21.13;SB=-590.07 GT:AD:DP:GL:GQ 0/1:21,44:63:-159.63,-18.98,-64.63:99 +chr1 2940454 rs6679678 T C 216.89 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=522.35;QD=9.16;SB=-250.32 GT:AD:DP:GL:GQ 0/1:31,26:48:-69.99,-14.47,-101.54:99 +chr1 2940732 rs12042403 T C 312.83 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=888.06;QD=12.51;SB=-433.91 GT:AD:DP:GL:GQ 0/1:39,32:70:-113.18,-21.09,-157.81:99 +chr1 2940746 rs12041583 A G 452.19 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=809.95;QD=12.27;SB=-418.24 GT:AD:DP:GL:GQ 0/1:35,31:63:-103.26,-18.98,-134.35:99 +chr1 2940894 rs12041634 A T 208.26 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=886.35;QD=14.77;SB=-371.51 GT:AD:DP:GL:GQ 0/1:30,30:60:-110.00,-18.08,-114.34:99 +chr1 2940901 rs12040299 C T 487.76 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=953.57;QD=15.63;SB=-409.79 GT:AD:DP:GL:GQ 0/1:31,30:60:-116.73,-18.09,-97.56:99 +chr1 2941104 rs10489589 T C 232.05 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.67;MQ0=0;OQ=498.13;QD=8.90;SB=-202.46 GT:AD:DP:GL:GQ 0/1:33,23:54:-69.37,-16.27,-132.36:99 +chr1 2941207 . G A 104.13 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.25;MQ0=0;OQ=904.38;QD=16.15;SB=-378.12 GT:AD:DP:GL:GQ 0/1:27,29:55:-110.29,-16.57,-94.24:99 +chr1 2941209 . T C 102.69 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.25;MQ0=0;OQ=663.66;QD=11.85;SB=-280.62 GT:AD:DP:GL:GQ 0/1:26,30:53:-85.63,-15.98,-103.85:99 +chr1 2941371 rs12408197 C T 428.36 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=717.16;QD=12.36;SB=-246.23 GT:AD:DP:GL:GQ 0/1:33,25:52:-90.68,-15.68,-91.34:99 +chr1 2941666 . T C 142.44 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.70;MQ0=0;OQ=433.61;QD=8.50;SB=-223.24 GT:AD:DP:GL:GQ 0/1:30,21:49:-61.42,-14.77,-117.95:99 +chr1 2941694 rs10489588 G A 184.48 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.01;MQ=58.17;MQ0=0;OQ=458.21;QD=8.98;SB=-152.21 GT:AD:DP:GL:GQ 0/1:34,17:47:-63.28,-14.17,-98.47:99 +chr1 2941849 . C T 36.18 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.75;MQ=59.44;MQ0=0;OQ=1385.60;QD=18.72;SB=-578.48 GT:AD:DP:GL:GQ 0/1:29,44:70:-162.94,-21.10,-91.88:99 +chr1 2942163 rs2017600 A C 566.08 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2376.48;QD=32.55;SB=-930.21 GT:AD:DP:GL:GQ 1/1:0,72:69:-241.26,-20.78,-0.03:99 +chr1 2942474 rs1005471 T C 5.22 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=441.09;QD=10.02;SB=-191.58 GT:AD:DP:GL:GQ 0/1:27,17:44:-60.65,-13.26,-106.56:99 +chr1 2942683 rs9660819 C T 0.66 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=5.17;MQ=58.20;MQ0=0;OQ=155.13;QD=5.97;SB=-65.81 GT:AD:DP:GL:GQ 0/1:19,7:24:-26.03,-7.23,-63.04:99 +chr1 2942700 rs9661525 T G 36.57 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.11;MQ0=0;OQ=126.09;QD=4.85;SB=-19.97 GT:AD:DP:GL:GQ 0/1:19,7:25:-23.42,-7.53,-64.66:99 +chr1 2943003 . G A 0.16 PASS AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.14;MQ0=0;OQ=556.71;QD=20.62;SB=-180.72 GT:AD:DP:GL:GQ 0/1:10,17:27:-67.10,-8.14,-31.23:99 +chr1 2943693 rs16823392 C G 180.70 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.22;MQ=57.09;MQ0=0;OQ=626.82;QD=16.07;SB=-312.19 GT:AD:DP:GL:GQ 0/1:21,18:38:-77.42,-11.46,-83.70:99 +chr1 2943891 . A G 12.02 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=54.82;MQ0=0;OQ=422.22;QD=8.28;SB=-205.52 GT:AD:DP:GL:GQ 0/1:33,18:49:-60.27,-14.76,-127.83:99 +chr1 2943911 . C T 10.41 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.91;MQ=52.84;MQ0=0;QD=0.25;SB=11.05 GT:AD:DP:GL:GQ 0/1:24,17:24:-11.53,-7.24,-65.03:42.84 +chr1 2943915 . A G 396.79 SnpCluster AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=1.74;MQ=53.20;MQ0=0;QD=9.23;SB=-114.71 GT:AD:DP:GL:GQ 0/1:25,18:39:-54.71,-11.75,-89.79:99 +chr1 2943921 . G A 412.53 SnpCluster AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=53.30;MQ0=0;QD=10.31;SB=-110.52 GT:AD:DP:GL:GQ 0/1:23,17:37:-55.69,-11.15,-76.61:99 +chr1 2943983 . T C 18.12 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.49;MQ=57.65;MQ0=0;OQ=359.40;QD=9.46;SB=-125.65 GT:AD:DP:GL:GQ 0/1:21,17:36:-50.07,-10.85,-82.05:99 +chr1 2944025 . C T 103.45 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.94;MQ0=0;OQ=634.89;QD=13.23;SB=-327.90 GT:AD:DP:GL:GQ 0/1:27,21:45:-80.34,-13.56,-81.81:99 +chr1 2944063 . C T 0.51 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=4;HaplotypeScore=2.62;MQ=59.46;MQ0=0;OQ=776.27;QD=15.22;SB=-389.17 GT:AD:DP:GL:GQ 0/1:26,25:47:-95.07,-14.16,-76.30:99 +chr1 2944068 . G A 119.57 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=59.46;MQ0=0;OQ=782.48;QD=15.34;SB=-373.90 GT:AD:DP:GL:GQ 0/1:25,26:49:-96.29,-14.76,-89.91:99 +chr1 2944090 . T C 3.70 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.56;MQ=59.48;MQ0=0;OQ=656.17;QD=12.38;SB=-215.36 GT:AD:DP:GL:GQ 0/1:27,26:49:-83.67,-14.77,-97.10:99 +chr1 2944157 . T C 29.83 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=59.30;MQ0=0;OQ=936.38;QD=15.61;SB=-205.50 GT:AD:DP:GL:GQ 0/1:27,33:58:-114.40,-17.47,-101.34:99 +chr1 2944208 rs4996810 A C 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=3.45;MQ=56.26;MQ0=1;OQ=219.14;QD=3.48;SB=-132.81 GT:AD:DP:GL:GQ 0/1:47,15:56:-42.07,-16.87,-150.42:99 +chr1 2944226 . G A 136.97 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.40;MQ0=1;OQ=501.67;QD=8.36;SB=-261.69 GT:AD:DP:GL:GQ 0/1:41,19:55:-70.03,-16.58,-122.86:99 +chr1 2944238 . T C 5.54 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=54.51;MQ0=0;OQ=327.91;QD=6.43;SB=-156.50 GT:AD:DP:GL:GQ 0/1:37,14:48:-50.53,-14.46,-136.22:99 +chr1 2944239 . T C 1.08 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=4.23;MQ=54.83;MQ0=0;OQ=279.86;QD=5.18;SB=-104.43 GT:AD:DP:GL:GQ 0/1:40,14:49:-46.04,-14.77,-139.11:99 +chr1 2945018 rs12036378 G A 163.77 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.58;MQ0=0;OQ=895.36;QD=16.28;SB=-275.78 GT:AD:DP:GL:GQ 0/1:27,28:53:-108.80,-15.98,-79.65:99 +chr1 2945105 rs55863899 C G 134.28 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.52;MQ0=0;OQ=868.77;QD=18.10;SB=-284.96 GT:AD:DP:GL:GQ 0/1:21,27:46:-104.04,-13.88,-85.12:99 +chr1 2945790 . A G 4.08 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=57.28;MQ0=0;OQ=318.97;QD=15.19;SB=-83.80 GT:AD:DP:GL:GQ 0/1:8,13:20:-41.21,-6.03,-32.48:99 +chr1 2946023 rs10909865 A G 147.02 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.15;MQ=60.00;MQ0=0;OQ=547.73;QD=10.74;SB=-195.64 GT:AD:DP:GL:GQ 0/1:24,27:47:-72.23,-14.17,-93.16:99 +chr1 2946442 . A G 66.31 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.61;MQ0=0;OQ=798.37;QD=10.79;SB=-385.01 GT:AD:DP:GL:GQ 0/1:39,35:70:-104.22,-21.10,-152.02:99 +chr1 2946526 rs2993510 T C 256.19 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.44;MQ0=0;OQ=807.53;QD=9.73;SB=-328.89 GT:AD:DP:GL:GQ 0/1:47,36:81:-108.45,-24.41,-191.18:99 +chr1 2946859 rs12567620 T G 251.94 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.22;MQ0=0;OQ=588.28;QD=9.97;SB=-221.33 GT:AD:DP:GL:GQ 0/1:35,23:57:-79.28,-17.17,-127.60:99 +chr1 2947460 rs12409277 T C 554.91 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1261.63;QD=14.67;SB=-598.55 GT:AD:DP:GL:GQ 0/1:39,47:86:-155.36,-25.92,-158.90:99 +chr1 2948421 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=83;Dels=0.02;HRun=17;HaplotypeScore=13.52;MQ=50.26;MQ0=0;OQ=57.24;QD=0.69;SB=67.75 GT:AD:DP:GL:GQ 0/1:69,12:60:-26.49,-17.48,-170.55:90.07 +chr1 2948568 rs12044162 A G 115.23 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.63;MQ0=0;OQ=498.67;QD=9.23;SB=-105.58 GT:AD:DP:GL:GQ 0/1:33,21:52:-68.82,-15.67,-126.86:99 +chr1 2949062 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=21.05;MQ=49.42;MQ0=0;OQ=103.70;QD=2.53;SB=-31.97 GT:AD:DP:GL:GQ 0/1:35,6:34:-23.91,-10.25,-88.62:99 +chr1 2949076 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=103.01;MQ=49.60;MQ0=0;OQ=345.15;QD=7.50;SB=-146.53 GT:AD:DP:GL:GQ 0/1:33,13:40:-49.87,-12.07,-111.45:99 +chr1 2949080 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=47.15;MQ=49.74;MQ0=0;OQ=115.37;QD=2.35;SB=-79.50 GT:AD:DP:GL:GQ 0/1:37,11:45:-31.37,-16.54,-140.93:99 +chr1 2949088 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=39.37;MQ=50.39;MQ0=0;OQ=395.27;QD=7.60;SB=-176.85 GT:AD:DP:GL:GQ 0/1:38,14:46:-56.68,-13.87,-100.52:99 +chr1 2949107 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=4.13;MQ=51.92;MQ0=0;OQ=58.43;QD=0.96;SB=-33.78 GT:AD:DP:GL:GQ 0/1:53,8:55:-25.70,-16.57,-188.08:91.26 +chr1 2949470 rs6692292 T C 310.38 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=58.36;MQ0=0;OQ=1146.89;QD=15.93;SB=-322.30 GT:AD:DP:GL:GQ 0/1:33,39:71:-139.36,-21.39,-132.11:99 +chr1 2949881 rs56213325 G A 8.56 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=3.87;MQ=58.97;MQ0=0;OQ=1032.99;QD=16.40;SB=-387.12 GT:AD:DP:GL:GQ 0/1:30,33:61:-124.96,-18.37,-109.42:99 +chr1 2950052 rs12045368 A G 278.87 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=53.32;MQ0=0;OQ=936.38;QD=14.41;SB=-275.26 GT:AD:DP:GL:GQ 0/1:28,37:62:-115.61,-18.69,-106.66:99 +chr1 2950232 rs10909866 C T 182.72 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=57.68;MQ0=0;OQ=969.99;QD=15.90;SB=-309.81 GT:AD:DP:GL:GQ 0/1:32,29:61:-118.67,-18.38,-109.12:99 +chr1 2950468 rs12046233 A G 39.17 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.71;MQ=59.23;MQ0=0;OQ=754.54;QD=12.58;SB=-279.44 GT:AD:DP:GL:GQ 0/1:30,30:55:-95.31,-16.57,-110.00:99 +chr1 2950650 rs12044848 C T 194.31 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.52;MQ0=0;OQ=784.81;QD=16.35;SB=-285.29 GT:AD:DP:GL:GQ 0/1:24,24:47:-95.92,-14.16,-84.23:99 +chr1 2950883 . C A 3.38 PASS AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=60.00;MQ0=0;OQ=1395.15;QD=16.81;SB=-283.26 GT:AD:DP:GL:GQ 0/1:36,46:82:-170.17,-27.37,-127.09:99 +chr1 2951230 rs56088946 T C 7.58 PASS AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.61;MQ0=0;OQ=1944.95;QD=16.34;SB=-964.49 GT:AD:DP:GL:GQ 0/1:53,66:118:-233.32,-35.54,-213.54:99 +chr1 2951262 rs10909867 G T 333.68 PASS AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=59.76;MQ0=0;OQ=1581.91;QD=16.48;SB=-612.08 GT:AD:DP:GL:GQ 0/1:44,52:95:-190.09,-28.61,-155.75:99 +chr1 2952067 rs10909868 A C 183.71 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=60.00;MQ0=0;OQ=929.11;QD=14.75;SB=-149.21 GT:AD:DP:GL:GQ 0/1:29,34:62:-114.87,-18.67,-108.28:99 +chr1 2952085 rs12048975 T C 158.31 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=956.32;QD=14.94;SB=-180.58 GT:AD:DP:GL:GQ 0/1:30,34:62:-117.59,-18.68,-121.18:99 +chr1 2952452 rs2981859 G A 525.66 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2597.04;QD=39.95;SB=-874.18 GT:AD:DP:GL:GQ 1/1:0,65:65:-263.30,-19.58,-0.02:99 +chr1 2953353 rs7339938 G C 184.28 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1644.05;QD=21.35;SB=-832.89 GT:AD:DP:GL:GQ 0/1:34,43:75:-190.30,-22.61,-128.08:99 +chr1 2954257 rs12044831 A C 328.96 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.75;MQ0=0;OQ=969.03;QD=12.75;SB=-480.26 GT:AD:DP:GL:GQ 0/1:35,41:74:-122.48,-22.29,-132.71:99 +chr1 2956899 rs2993479 A T 39.42 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=7.90;MQ=58.88;MQ0=0;OQ=639.75;QD=11.85;SB=-334.02 GT:AD:DP:GL:GQ 0/1:32,22:53:-83.22,-15.96,-119.83:99 +chr1 2958839 . C T 167.01 PASS AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.03;MQ0=0;OQ=1118.18;QD=16.69;SB=-463.99 GT:AD:DP:GL:GQ 0/1:31,36:62:-133.80,-18.70,-86.01:99 +chr1 2958843 . G C 98.75 PASS AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=58.98;MQ0=0;OQ=1122.63;QD=17.54;SB=-409.32 GT:AD:DP:GL:GQ 0/1:29,34:58:-133.03,-17.49,-113.54:99 +chr1 2960143 rs56298939 A T 308.60 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.67;MQ0=0;OQ=788.46;QD=14.08;SB=-295.64 GT:AD:DP:GL:GQ 0/1:29,27:56:-99.00,-16.87,-109.64:99 +chr1 2960324 rs717795 T C 9.89 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=3;HaplotypeScore=2.74;MQ=59.13;MQ0=0;OQ=443.35;QD=8.37;SB=-240.88 GT:AD:DP:GL:GQ 0/1:32,21:49:-62.39,-14.77,-120.82:99 +chr1 2961312 rs56069604 T C 18.15 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=0.73;MQ=58.64;MQ0=0;OQ=450.45;QD=14.53;SB=-212.67 GT:AD:DP:GL:GQ 0/1:13,18:29:-57.07,-8.74,-51.18:99 +chr1 2961381 rs2981857 T C 166.54 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=60.00;MQ0=0;OQ=428.10;QD=15.29;SB=-207.68 GT:AD:DP:GL:GQ 0/1:10,18:28:-54.54,-8.45,-38.77:99 +chr1 2962384 rs2981856 T C 282.12 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=862.73;QD=12.32;SB=-362.96 GT:AD:DP:GL:GQ 0/1:34,36:67:-109.75,-20.19,-134.76:99 +chr1 2963182 rs2993480 C T 393.42 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=959.18;QD=15.72;SB=-400.92 GT:AD:DP:GL:GQ 0/1:31,30:60:-117.29,-18.09,-96.43:99 +chr1 2963293 rs2993481 A T 141.58 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.01;MQ=59.62;MQ0=0;OQ=743.23;QD=12.39;SB=-349.56 GT:AD:DP:GL:GQ 0/1:34,26:58:-95.08,-17.48,-119.69:99 +chr1 2963436 rs1109251 G A 197.81 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=1.34;MQ=60.00;MQ0=0;OQ=932.59;QD=15.04;SB=-469.42 GT:AD:DP:GL:GQ 0/1:34,28:62:-115.22,-18.68,-120.45:99 +chr1 2963924 . A G 132.32 PASS AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.54;MQ0=0;OQ=1229.61;QD=13.51;SB=-579.93 GT:AD:DP:GL:GQ 0/1:47,44:90:-153.35,-27.11,-189.83:99 +chr1 2964602 rs1125017 A C 413.02 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=773.70;QD=11.90;SB=-364.77 GT:AD:DP:GL:GQ 0/1:35,30:63:-99.63,-18.98,-121.64:99 +chr1 2964712 rs2376821 T C 458.38 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=2329.60;QD=30.25;SB=-1071.67 GT:AD:DP:GL:GQ 1/1:0,77:75:-236.63,-22.63,-0.08:99 +chr1 2964979 rs55775305 C G 191.90 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=59.60;MQ0=0;OQ=1095.41;QD=18.89;SB=-526.68 GT:AD:DP:GL:GQ 0/1:27,31:56:-129.70,-16.87,-112.36:99 +chr1 2966676 rs1138513 T C 342.07 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=60.00;MQ0=0;OQ=1004.23;QD=15.45;SB=-395.31 GT:AD:DP:GL:GQ 0/1:29,36:64:-122.99,-19.29,-112.84:99 +chr1 2967377 rs2981855 A G 110.32 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.78;MQ0=0;OQ=2017.68;QD=35.40;SB=-766.96 GT:AD:DP:GL:GQ 1/1:0,57:57:-205.37,-17.17,-0.02:99 +chr1 2967903 rs2075969 G C 175.65 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.42;MQ0=0;OQ=486.84;QD=12.17;SB=-253.09 GT:AD:DP:GL:GQ 0/1:21,19:36:-62.83,-10.86,-80.92:99 +chr1 2969034 rs41315262 C T 141.67 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=432.24;QD=14.90;SB=-163.20 GT:AD:DP:GL:GQ 0/1:14,15:28:-54.95,-8.44,-49.21:99 +chr1 2970137 rs2072732 T C 36.95 LowQual AC=1;AF=0.50;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.39;MQ0=0;QD=4.11;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,4:7:-9.09,-2.11,-16.67:69.79 +chr1 2970438 . C T 1.69 PASS AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=60.00;MQ0=0;OQ=106.79;QD=5.62;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,5:16:-18.78,-4.82,-35.96:99 +chr1 2973178 rs2788091 T C 354.06 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.56;MQ0=0;OQ=657.96;QD=12.65;SB=-286.58 GT:AD:DP:GL:GQ 0/1:29,23:52:-84.74,-15.66,-115.27:99 +chr1 2973823 rs2297828 G A 18.50 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=95.21;QD=3.97;SB=-16.50 GT:AD:DP:GL:GQ 0/1:18,6:22:-19.43,-6.63,-57.66:99 +chr1 2975672 . C G 0.31 PASS AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=6.00;MQ=60.00;MQ0=0;OQ=69.47;QD=7.72;SB=-10.00 GT:AD:DP:GL:GQ 1/1:3,6:3:-10.44,-0.91,-0.01:9.02 +chr1 2977743 rs909510 G C 79.39 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.50;MQ=58.73;MQ0=0;OQ=593.38;QD=17.98;SB=-309.99 GT:AD:DP:GL:GQ 0/1:15,18:31:-71.97,-9.35,-58.08:99 +chr1 2979403 rs1572656 T G 132.71 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.39;MQ0=0;OQ=227.87;QD=7.86;SB=-74.87 GT:AD:DP:GL:GQ 0/1:16,12:27:-34.21,-8.14,-59.65:99 +chr1 2982894 rs2981889 T C 0.49 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=3.40;MQ=59.07;MQ0=0;OQ=530.79;QD=10.62;SB=-197.61 GT:AD:DP:GL:GQ 0/1:25,25:44:-69.63,-13.27,-84.86:99 +chr1 2983498 rs2993486 G A 189.84 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.11;MQ0=0;OQ=2009.66;QD=38.65;SB=-804.34 GT:AD:DP:GL:GQ 1/1:0,52:51:-204.56,-15.36,-0.01:99 +chr1 2983667 rs2981888 C G 249.66 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=760.63;QD=16.54;SB=-378.87 GT:AD:DP:GL:GQ 0/1:20,26:44:-92.63,-13.28,-85.11:99 +chr1 2984196 rs4648359 G C 304.72 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=59.62;MQ0=0;OQ=739.36;QD=15.09;SB=-327.39 GT:AD:DP:GL:GQ 0/1:26,23:45:-90.79,-13.57,-98.24:99 +chr1 2984400 rs2788092 C G 25.02 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.57;MQ0=0;OQ=997.66;QD=18.48;SB=-280.54 GT:AD:DP:GL:GQ 0/1:23,31:51:-118.43,-15.38,-97.87:99 +chr1 2985122 rs2742689 T G 341.54 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.79;MQ0=0;OQ=737.00;QD=13.65;SB=-353.07 GT:AD:DP:GL:GQ 0/1:26,28:52:-92.65,-15.66,-91.92:99 +chr1 2985309 rs7515436 G A 254.33 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.36;MQ0=0;OQ=1107.59;QD=17.04;SB=-525.74 GT:AD:DP:GL:GQ 0/1:30,35:61:-132.42,-18.38,-99.41:99 +chr1 2985493 rs2788093 C T 164.52 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=52.54;MQ0=0;OQ=672.12;QD=14.61;SB=-188.18 GT:AD:DP:GL:GQ 0/1:25,21:45:-84.06,-13.57,-76.74:99 +chr1 2985947 . G A 42.58 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=59.42;MQ0=0;QD=1.06;SB=86.29 GT:AD:DP:GL:GQ 0/1:35,5:38:-18.99,-11.45,-122.25:75.41 +chr1 2986056 rs7525173 C G 198.19 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=57.11;MQ0=0;OQ=1235.82;QD=21.68;SB=-610.55 GT:AD:DP:GL:GQ 0/1:22,35:54:-143.14,-16.27,-91.10:99 +chr1 2986416 rs1569420 C G 131.69 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.22;MQ0=0;OQ=1047.24;QD=19.39;SB=-356.09 GT:AD:DP:GL:GQ 0/1:24,30:53:-123.98,-15.97,-102.98:99 +chr1 2986462 rs1569419 T C 443.07 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1686.91;QD=29.59;SB=-810.28 GT:AD:DP:GL:GQ 1/1:0,57:54:-172.33,-16.29,-0.05:99 +chr1 2988794 rs2742686 T C 110.98 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.81;MQ=59.55;MQ0=0;OQ=633.23;QD=12.42;SB=-265.98 GT:AD:DP:GL:GQ 0/1:26,25:48:-81.08,-14.47,-95.70:99 +chr1 2988858 rs10909873 C G 203.72 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.25;MQ=59.51;MQ0=0;OQ=629.03;QD=13.38;SB=-304.03 GT:AD:DP:GL:GQ 0/1:24,23:43:-79.16,-12.98,-98.92:99 +chr1 2988928 rs2981886 T G 27.89 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=1.77;MQ=60.00;MQ0=0;OQ=713.08;QD=17.39;SB=-342.06 GT:AD:DP:GL:GQ 0/1:16,25:41:-86.94,-12.35,-58.67:99 +chr1 2989062 rs2742685 T C 91.91 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=59.38;MQ0=0;OQ=332.13;QD=8.98;SB=-168.61 GT:AD:DP:GL:GQ 0/1:21,16:36:-47.35,-10.86,-77.27:99 +chr1 2989275 rs760570 T C 183.83 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=60.00;MQ0=0;OQ=452.99;QD=11.62;SB=-195.61 GT:AD:DP:GL:GQ 0/1:18,21:37:-59.74,-11.16,-71.21:99 +chr1 2989352 rs11580403 C T 17.69 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=6.35;MQ=58.51;MQ0=0;OQ=786.31;QD=16.73;SB=-390.18 GT:AD:DP:GL:GQ 0/1:22,25:44:-95.18,-13.26,-64.65:99 +chr1 2989378 rs11581212 A G 26.01 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=4.12;MQ=58.01;MQ0=0;OQ=610.70;QD=12.99;SB=-220.27 GT:AD:DP:GL:GQ 0/1:23,24:41:-76.70,-12.35,-80.42:99 +chr1 2989575 rs6674036 G T 86.25 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=60.00;MQ0=0;OQ=295.75;QD=8.45;SB=-112.67 GT:AD:DP:GL:GQ 0/1:22,13:32:-42.50,-9.64,-70.40:99 +chr1 2989750 rs6683976 C G 152.72 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=58.25;MQ0=0;OQ=588.86;QD=14.72;SB=-197.30 GT:AD:DP:GL:GQ 0/1:21,19:38:-73.63,-11.46,-80.42:99 +chr1 2989984 rs760569 A G 0.34 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=3;HaplotypeScore=3.04;MQ=55.35;MQ0=1;OQ=203.26;QD=6.78;SB=-13.61 GT:AD:DP:GL:GQ 0/1:16,14:25:-31.15,-7.54,-61.01:99 +chr1 2990301 rs760568 A G 305.79 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=56.76;MQ0=0;OQ=713.37;QD=13.99;SB=-336.34 GT:AD:DP:GL:GQ 0/1:22,29:50:-89.69,-15.07,-88.33:99 +chr1 2990325 rs760567 A G 357.24 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=57.34;MQ0=0;OQ=769.95;QD=14.53;SB=-388.67 GT:AD:DP:GL:GQ 0/1:25,28:52:-95.94,-15.67,-100.59:99 +chr1 2990784 rs6695131 T C 278.73 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.71;MQ=59.69;MQ0=0;OQ=1038.17;QD=17.02;SB=-324.30 GT:AD:DP:GL:GQ 0/1:25,36:59:-124.87,-17.77,-99.97:99 +chr1 2991113 rs760566 T C 528.98 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=1563.77;QD=31.91;SB=-755.58 GT:AD:DP:GL:GQ 1/1:0,49:46:-159.99,-13.86,-0.02:99 +chr1 2991563 rs6690540 C T 182.97 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=58.34;MQ0=0;OQ=662.57;QD=14.72;SB=-343.52 GT:AD:DP:GL:GQ 0/1:23,22:42:-82.21,-12.67,-65.85:99 +chr1 2991617 rs2742682 T C 232.59 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.38;MQ0=0;OQ=410.76;QD=11.10;SB=-215.29 GT:AD:DP:GL:GQ 0/1:16,19:33:-54.32,-9.96,-57.14:99 +chr1 2991708 rs2742681 T G 14.52 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=58.98;MQ0=0;OQ=365.17;QD=8.91;SB=-102.16 GT:AD:DP:GL:GQ 0/1:24,17:38:-51.25,-11.45,-78.22:99 +chr1 2992174 rs2742680 C G 300.14 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.13;MQ=58.66;MQ0=0;OQ=934.85;QD=17.98;SB=-447.39 GT:AD:DP:GL:GQ 0/1:22,30:49:-111.56,-14.79,-83.87:99 +chr1 2992195 rs2742679 C T 269.04 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=58.13;MQ0=0;OQ=860.87;QD=17.22;SB=-384.13 GT:AD:DP:GL:GQ 0/1:23,27:48:-103.84,-14.47,-74.36:99 +chr1 2992210 rs2742678 G A 296.42 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=57.39;MQ0=0;OQ=701.27;QD=15.58;SB=-336.35 GT:AD:DP:GL:GQ 0/1:23,22:43:-86.37,-12.96,-74.58:99 +chr1 2993392 rs11801109 G A 5.62 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=59.59;MQ0=0;OQ=759.83;QD=16.52;SB=-91.91 GT:AD:DP:GL:GQ 0/1:23,23:45:-92.82,-13.56,-77.23:99 +chr1 2993874 rs2981883 T C 12.34 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.37;MQ=58.95;MQ0=0;OQ=1316.25;QD=29.91;SB=-475.45 GT:AD:DP:GL:GQ 1/1:0,44:39:-135.23,-11.75,-0.02:99 +chr1 2994092 rs2981882 A G 168.83 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=59.63;MQ0=0;OQ=1897.54;QD=30.61;SB=-828.34 GT:AD:DP:GL:GQ 1/1:0,62:61:-193.40,-18.40,-0.06:99 +chr1 2994217 rs2981881 T C 270.84 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=58.88;MQ0=0;OQ=1946.57;QD=31.40;SB=-838.62 GT:AD:DP:GL:GQ 1/1:1,61:56:-198.26,-16.87,-0.02:99 +chr1 2994648 rs2981880 T C 6.41 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=4.30;MQ=56.36;MQ0=0;OQ=1597.03;QD=34.72;SB=-433.18 GT:AD:DP:GL:GQ 1/1:0,45:44:-163.30,-13.25,-0.01:99 +chr1 2994734 rs2981879 T C 43.37 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.75;MQ0=0;OQ=1057.22;QD=35.24;SB=-208.08 GT:AD:DP:GL:GQ 1/1:0,30:30:-109.32,-9.04,-0.01:90.26 +chr1 2994945 rs34014659 G A 271.04 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.59;MQ0=1;OQ=187.11;QD=9.85;SB=-73.30 GT:AD:DP:GL:GQ 0/1:11,8:17:-27.12,-5.12,-33.00:99 +chr1 2995445 rs2981878 A G 132.19 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=56.06;MQ0=1;OQ=382.82;QD=11.96;SB=-131.28 GT:AD:DP:GL:GQ 0/1:16,16:31:-50.91,-9.34,-62.42:99 +chr1 2995487 rs6676479 G A 196.19 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=57.97;MQ0=1;OQ=534.41;QD=14.06;SB=-244.76 GT:AD:DP:GL:GQ 0/1:21,17:34:-66.98,-10.25,-53.48:99 +chr1 2995498 rs34884268 C T 260.47 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=626.01;QD=14.90;SB=-317.32 GT:AD:DP:GL:GQ 0/1:22,20:41:-78.24,-12.36,-68.94:99 +chr1 2995610 rs34782467 G A 183.72 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.56;MQ0=0;OQ=857.05;QD=16.48;SB=-325.85 GT:AD:DP:GL:GQ 0/1:26,26:50:-104.07,-15.08,-74.92:99 +chr1 2995991 rs926246 T C 314.46 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=57.39;MQ0=0;OQ=671.24;QD=12.43;SB=-260.51 GT:AD:DP:GL:GQ 0/1:30,24:53:-86.37,-15.96,-115.93:99 +chr1 2996058 rs926245 C A 105.01 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=53.36;MQ0=0;OQ=705.06;QD=12.82;SB=-99.80 GT:AD:DP:GL:GQ 0/1:29,26:52:-89.45,-15.66,-93.51:99 +chr1 2996143 rs926244 A G 215.10 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=58.61;MQ0=0;OQ=1978.79;QD=31.92;SB=-947.90 GT:AD:DP:GL:GQ 1/1:0,60:58:-201.49,-17.47,-0.03:99 +chr1 2996175 rs926243 T G 426.34 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=690.75;QD=11.32;SB=-265.78 GT:AD:DP:GL:GQ 0/1:31,30:58:-89.83,-17.48,-108.47:99 +chr1 2996487 rs55932943 C T 3.20 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=10.54;MQ=58.03;MQ0=1;OQ=1021.25;QD=14.80;SB=-443.45 GT:AD:DP:GL:GQ 0/1:37,31:63:-124.40,-18.99,-104.76:99 +chr1 2996899 rs2817165 A G 93.99 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.80;MQ0=0;OQ=288.71;QD=8.25;SB=-166.95 GT:AD:DP:GL:GQ 0/1:21,13:29:-40.90,-8.74,-67.04:99 +chr1 2997535 rs34300623 G A 185.66 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.69;MQ0=0;OQ=968.84;QD=15.88;SB=-326.31 GT:AD:DP:GL:GQ 0/1:32,29:60:-118.25,-18.08,-106.92:99 +chr1 2997956 rs6693385 C T 247.24 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=59.55;MQ0=0;OQ=876.50;QD=17.19;SB=-364.90 GT:AD:DP:GL:GQ 0/1:22,29:45:-104.50,-13.57,-57.88:99 +chr1 2998547 rs2376820 C G 2318.28 Indel AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=17.39;MQ=51.50;MQ0=0;QD=40.67;SB=-1149.31 GT:AD:DP:GL:GQ 1/1:0,55:56:-238.28,-19.61,-2.86:99 +chr1 3000177 rs760565 A T 219.18 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=708.84;QD=15.75;SB=-333.07 GT:AD:DP:GL:GQ 0/1:21,24:41:-86.52,-12.35,-66.91:99 +chr1 3001189 rs2981873 T C 24.60 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=57.66;MQ0=0;OQ=381.92;QD=12.73;SB=-154.31 GT:AD:DP:GL:GQ 0/1:16,14:30:-50.52,-9.04,-62.50:99 +chr1 3002186 rs12135325 T C 1.38 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=4.32;MQ=58.67;MQ0=0;OQ=210.96;QD=6.03;SB=-111.21 GT:AD:DP:GL:GQ 0/1:22,13:32:-34.02,-9.64,-84.87:99 +chr1 3002840 rs6666748 A G 255.15 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.28;MQ=60.00;MQ0=0;OQ=801.41;QD=14.84;SB=-400.31 GT:AD:DP:GL:GQ 0/1:21,33:50:-98.50,-15.08,-74.39:99 +chr1 3003005 rs2788097 A C 59.19 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.07;MQ=59.05;MQ0=0;OQ=463.07;QD=10.52;SB=-200.91 GT:AD:DP:GL:GQ 0/1:25,19:39:-61.34,-11.75,-74.66:99 +chr1 3005383 rs2981870 G A 337.06 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.45;MQ0=0;OQ=532.89;QD=12.69;SB=-258.26 GT:AD:DP:GL:GQ 0/1:23,19:40:-68.63,-12.06,-71.78:99 +chr1 3005452 rs55674255 C T 63.22 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.20;MQ=60.00;MQ0=0;OQ=640.76;QD=14.56;SB=-293.19 GT:AD:DP:GL:GQ 0/1:24,20:44:-80.62,-13.26,-82.30:99 +chr1 3005702 rs55784774 G A 50.92 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.79;MQ=59.56;MQ0=0;OQ=701.05;QD=13.23;SB=-358.53 GT:AD:DP:GL:GQ 0/1:30,23:49:-88.16,-14.77,-89.46:99 +chr1 3005947 . C T 228.82 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.77;MQ0=0;OQ=514.40;QD=13.54;SB=-233.73 GT:AD:DP:GL:GQ 0/1:21,17:37:-65.88,-11.16,-63.18:99 +chr1 3005977 . G A 25.43 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=57.94;MQ0=0;OQ=561.32;QD=13.69;SB=-151.18 GT:AD:DP:GL:GQ 0/1:21,20:37:-70.56,-11.15,-69.03:99 +chr1 3006143 rs2981869 C T 155.48 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=58.84;MQ0=0;OQ=588.68;QD=14.72;SB=-230.75 GT:AD:DP:GL:GQ 0/1:19,21:38:-73.61,-11.45,-64.86:99 +chr1 3007018 . G A 13.33 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=4.77;MQ=59.05;MQ0=0;OQ=465.01;QD=10.57;SB=-225.50 GT:AD:DP:GL:GQ 0/1:25,18:41:-64.52,-14.73,-86.50:99 +chr1 3008086 rs2993492 G A 197.87 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.53;MQ0=0;OQ=913.42;QD=18.64;SB=-406.43 GT:AD:DP:GL:GQ 0/1:20,29:46:-108.49,-13.86,-62.00:99 +chr1 3009487 rs12131890 G A 77.41 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.17;MQ0=0;OQ=935.16;QD=20.78;SB=-364.90 GT:AD:DP:GL:GQ 0/1:15,30:42:-109.46,-12.66,-48.94:99 +chr1 3010048 rs56029998 T C 182.76 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=59.24;MQ0=0;OQ=609.91;QD=11.09;SB=-261.57 GT:AD:DP:GL:GQ 0/1:31,24:54:-80.54,-16.27,-125.83:99 +chr1 3010106 rs2993493 C A 285.53 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=59.63;MQ0=0;OQ=789.70;QD=15.48;SB=-315.68 GT:AD:DP:GL:GQ 0/1:25,26:51:-97.62,-15.36,-86.35:99 +chr1 3010923 rs2993494 G A 362.80 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=449.17;QD=13.21;SB=-177.14 GT:AD:DP:GL:GQ 0/1:18,16:33:-58.15,-9.95,-61.38:99 +chr1 3011156 rs55898371 A C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=5;HaplotypeScore=4.00;MQ=58.74;MQ0=0;OQ=420.03;QD=11.35;SB=-193.92 GT:AD:DP:GL:GQ 0/1:18,19:33:-55.23,-9.95,-57.05:99 +chr1 3011412 rs12133978 G A 162.16 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=59.34;MQ0=0;OQ=429.68;QD=12.28;SB=-187.26 GT:AD:DP:GL:GQ 0/1:20,15:33:-56.20,-9.95,-61.55:99 +chr1 3011547 rs11808136 C T 5.88 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=59.52;MQ0=0;OQ=731.81;QD=18.76;SB=-195.18 GT:AD:DP:GL:GQ 0/1:16,23:36:-87.31,-10.85,-49.60:99 +chr1 3012571 rs2993495 A G 13.64 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=549.01;QD=28.90;SB=-194.71 GT:AD:DP:GL:GQ 1/1:0,19:18:-58.50,-5.43,-0.01:54.13 +chr1 3012575 rs2993496 T C 83.64 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=58.78;MQ0=0;OQ=196.75;QD=10.36;SB=-98.00 GT:AD:DP:GL:GQ 0/1:9,10:18:-28.39,-5.43,-32.68:99 +chr1 3012992 rs2993497 G A 7 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.90;MQ=59.59;MQ0=0;OQ=932.60;QD=20.72;SB=-424.82 GT:AD:DP:GL:GQ 0/1:16,29:42:-109.20,-12.66,-48.01:99 +chr1 3013111 rs56363358 C A 42.53 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.28;MQ0=0;OQ=749.52;QD=19.72;SB=-289.38 GT:AD:DP:GL:GQ 0/1:12,26:36:-89.08,-10.85,-37.10:99 +chr1 3013255 rs2993498 T C 497.69 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=1211.16;QD=31.87;SB=-545.88 GT:AD:DP:GL:GQ 1/1:0,38:36:-124.72,-10.85,-0.02:99 +chr1 3013565 rs6667850 A C 171.48 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.41;MQ0=0;OQ=400.63;QD=10.27;SB=-101.88 GT:AD:DP:GL:GQ 0/1:20,19:37:-54.50,-11.15,-69.04:99 +chr1 3013819 rs1890337 A G 45.08 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=58.49;MQ0=0;OQ=1788.78;QD=31.38;SB=-712.22 GT:AD:DP:GL:GQ 1/1:0,56:52:-182.49,-15.67,-0.02:99 +chr1 3014125 rs1890336 A C 168.89 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.71;MQ0=0;OQ=1775.96;QD=32.89;SB=-886.08 GT:AD:DP:GL:GQ 1/1:0,54:51:-181.20,-15.36,-0.02:99 +chr1 3014227 rs2993499 T C 143.46 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=0.04;MQ=59.50;MQ0=0;OQ=1217.03;QD=32.89;SB=-587.31 GT:AD:DP:GL:GQ 1/1:0,37:36:-125.31,-10.85,-0.02:99 +chr1 3014565 rs2993500 C T 15.68 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=4.44;MQ=59.65;MQ0=0;OQ=1234.24;QD=18.99;SB=-544.80 GT:AD:DP:GL:GQ 0/1:29,36:64:-145.99,-19.28,-92.77:99 +chr1 3015706 rs12137954 T A 122.03 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.40;MQ0=0;OQ=345.66;QD=6.91;SB=-177.77 GT:AD:DP:GL:GQ 0/1:35,15:48:-52.31,-14.46,-129.85:99 +chr1 3015846 rs2993501 A C 217.20 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=57.44;MQ0=0;OQ=1649.50;QD=29.99;SB=-596.80 GT:AD:DP:GL:GQ 1/1:0,55:53:-168.59,-15.98,-0.05:99 +chr1 3015960 rs12135664 C T 346.44 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=60.00;MQ0=0;OQ=1146.10;QD=16.85;SB=-550.79 GT:AD:DP:GL:GQ 0/1:34,34:67:-138.08,-20.19,-108.20:99 +chr1 3016120 rs2981868 T A 119.84 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=4.10;MQ=59.44;MQ0=0;OQ=1114.65;QD=15.06;SB=-570.99 GT:AD:DP:GL:GQ 0/1:37,36:67:-134.93,-20.18,-118.55:99 +chr1 3016369 rs59909070 G A 353.97 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.69;MQ0=0;OQ=434.09;QD=10.10;SB=-171.10 GT:AD:DP:GL:GQ 0/1:27,16:42:-59.35,-12.65,-95.52:99 +chr1 3016502 . T C 0.18 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=2;HaplotypeScore=5.91;MQ=44.72;MQ0=3;OQ=351.94;QD=7.65;SB=-166.48 GT:AD:DP:GL:GQ 0/1:25,21:36:-49.33,-10.85,-81.52:99 +chr1 3016606 . A C 15.74 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.75;MQ=48.95;MQ0=1;OQ=373.22;QD=9.82;SB=-133.20 GT:AD:DP:GL:GQ 0/1:18,17:27:-48.74,-8.13,-43.17:99 +chr1 3016839 rs56010213 A T 12.71 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=38.33;MQ0=7;QD=0.33;SB=20.09 GT:AD:DP:GL:GQ 0/1:34,5:23:-11.46,-6.93,-70.69:45.31 +chr1 3017201 rs2993502 C T 589.72 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.38;MQ0=0;OQ=2029.57;QD=38.29;SB=-936.75 GT:AD:DP:GL:GQ 1/1:0,53:51:-206.56,-15.36,-0.01:99 +chr1 3017765 . T C 156.29 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=257.37;QD=12.26;SB=-133.69 GT:AD:DP:GL:GQ 0/1:7,14:18:-34.45,-5.43,-28.78:99 +chr1 3017780 . C T 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=1;HaplotypeScore=2.01;MQ=59.03;MQ0=0;OQ=567.81;QD=23.66;SB=-154.18 GT:AD:DP:GL:GQ 0/1:6,18:22:-66.70,-6.63,-18.59:99 +chr1 3018779 rs11808946 C T 272.66 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=781.20;QD=16.62;SB=-355.56 GT:AD:DP:GL:GQ 0/1:22,25:44:-94.67,-13.26,-66.92:99 +chr1 3018847 rs2993503 A G 82.10 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=59.16;MQ0=0;OQ=1494.14;QD=27.17;SB=-767.73 GT:AD:DP:GL:GQ 1/1:0,55:49:-153.05,-14.78,-0.05:99 +chr1 3018941 rs2072733 C T 12.61 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=59.46;MQ0=0;OQ=605.93;QD=14.09;SB=-165.23 GT:AD:DP:GL:GQ 0/1:22,21:41:-76.24,-12.36,-69.17:99 +chr1 3019072 rs10909875 C T 272.35 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.03;MQ0=0;OQ=534.00;QD=11.12;SB=-208.44 GT:AD:DP:GL:GQ 0/1:28,20:45:-70.25,-13.56,-92.78:99 +chr1 3019517 rs12136745 G A 248.92 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=59.62;MQ0=0;OQ=984.07;QD=16.40;SB=-470.51 GT:AD:DP:GL:GQ 0/1:28,32:55:-118.26,-16.57,-87.88:99 +chr1 3019842 rs58968988 G A 56.19 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=4.37;MQ=58.92;MQ0=0;OQ=590.92;QD=13.74;SB=-159.22 GT:AD:DP:GL:GQ 0/1:22,21:39:-74.13,-11.75,-67.01:99 +chr1 3020484 rs2981867 G C 387.41 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=547.74;QD=12.17;SB=-190.58 GT:AD:DP:GL:GQ 0/1:29,16:44:-71.32,-13.26,-119.60:99 +chr1 3020597 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=37.34;MQ=39.25;MQ0=1;OQ=144.44;QD=4.25;SB=-87.67 GT:AD:DP:GL:GQ 0/1:24,10:27:-25.87,-8.14,-74.17:99 +chr1 3020599 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=45.49;MQ=39.25;MQ0=1;OQ=360.48;QD=10.60;SB=-127.10 GT:AD:DP:GL:GQ 0/1:21,13:31:-48.68,-9.35,-60.35:99 +chr1 3020611 . A G 19.24 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=21.97;MQ=37.81;MQ0=1;QD=0.62;SB=-30.78 GT:AD:DP:GL:GQ 0/1:24,7:24:-12.43,-7.23,-80.13:52.02 +chr1 3020613 rs6691894 A G 41.97 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=22.61;MQ=37.81;MQ0=1;QD=1.35;SB=-10.86 GT:AD:DP:GL:GQ 0/1:24,7:20:-13.51,-6.02,-64.69:74.80 +chr1 3020615 rs6691895 A G 400.54 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=24.36;MQ=38.97;MQ0=1;QD=12.92;SB=-173.99 GT:AD:DP:GL:GQ 0/1:14,17:24:-50.58,-7.24,-30.30:99 +chr1 3020629 . A G 22.23 LowQual AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=19.42;MQ=38.02;MQ0=1;QD=0.85;SB=-32.78 GT:AD:DP:GL:GQ 0/1:21,5:22:-12.14,-6.63,-70.51:55.04 +chr1 3020688 rs6691996 A G 381.91 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.90;MQ0=0;OQ=370.45;QD=11.58;SB=-184.01 GT:AD:DP:GL:GQ 0/1:14,18:30:-49.38,-9.05,-56.94:99 +chr1 3020691 rs6695017 T C 343.03 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.28;MQ0=0;OQ=495.78;QD=14.58;SB=-192.66 GT:AD:DP:GL:GQ 0/1:16,18:34:-63.11,-10.25,-58.83:99 +chr1 3020744 rs6687292 C T 95.65 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.34;MQ=56.56;MQ0=0;OQ=522.71;QD=9.33;SB=-137.11 GT:AD:DP:GL:GQ 0/1:34,22:53:-71.53,-15.97,-120.29:99 +chr1 3020924 rs2981866 G A 33.28 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.17;MQ0=0;OQ=1933.34;QD=38.67;SB=-489.14 GT:AD:DP:GL:GQ 1/1:0,50:49:-196.94,-14.76,-0.02:99 +chr1 3020982 rs10909876 A G 347.22 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=54.47;MQ0=0;OQ=796.80;QD=13.06;SB=-340.94 GT:AD:DP:GL:GQ 0/1:29,32:61:-101.36,-18.40,-112.11:99 +chr1 3020998 rs10909877 T A 2173.88 Indel AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=54.79;MQ0=0;QD=36.23;SB=-1033.22 GT:AD:DP:GL:GQ 1/1:0,60:59:-220.99,-17.77,-0.02:99 +chr1 3021182 . G A 53.76 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.25;MQ0=0;OQ=405.03;QD=13.07;SB=-180.66 GT:AD:DP:GL:GQ 0/1:18,13:30:-52.83,-9.04,-54.54:99 +chr1 3022425 rs2981865 G C 1.40 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.81;MQ0=0;OQ=743.56;QD=24.79;SB=-346.46 GT:AD:DP:GL:GQ 0/1:9,21:29:-86.39,-8.75,-34.33:99 +chr1 3024466 rs10909878 A G 299.96 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=58.18;MQ0=0;OQ=619.53;QD=13.18;SB=-324.31 GT:AD:DP:GL:GQ 0/1:20,27:45:-78.81,-13.57,-80.16:99 +chr1 3024530 rs12141827 T C 99.60 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=53.26;MQ0=0;OQ=329.91;QD=8.25;SB=-169.50 GT:AD:DP:GL:GQ 0/1:24,16:37:-47.43,-11.15,-87.85:99 +chr1 3025087 rs6690373 A G 254.01 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.67;MQ0=0;OQ=819.31;QD=14.63;SB=-343.19 GT:AD:DP:GL:GQ 0/1:23,33:54:-101.49,-16.28,-89.82:99 +chr1 3025597 rs2981864 A G 2.03 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=59.23;MQ0=0;OQ=762.15;QD=25.41;SB=-232.49 GT:AD:DP:GL:GQ 1/1:0,28:25:-82.46,-10.02,-2.66:73.60 +chr1 3025622 rs12409836 A G 68.57 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.74;MQ0=0;OQ=225.89;QD=6.11;SB=-44.83 GT:AD:DP:GL:GQ 0/1:23,14:30:-34.92,-9.04,-72.62:99 +chr1 3025639 rs2472822 C G 79.91 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=1446.74;QD=36.17;SB=-602.98 GT:AD:DP:GL:GQ 1/1:0,40:36:-148.28,-10.86,-0.02:99 +chr1 3027473 rs876740 C T 271.81 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=2215.19;QD=38.19;SB=-1128.00 GT:AD:DP:GL:GQ 1/1:0,58:56:-225.12,-16.87,-0.02:99 +chr1 3028483 rs2742672 A G 23.82 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.51;MQ0=0;OQ=1087.23;QD=28.61;SB=-502.17 GT:AD:DP:GL:GQ 1/1:0,38:36:-112.35,-10.86,-0.04:99 +chr1 3029008 rs2817171 C A 191.92 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.65;MQ0=0;OQ=733.04;QD=13.57;SB=-391.11 GT:AD:DP:GL:GQ 0/1:29,25:54:-92.85,-16.26,-102.92:99 +chr1 3030045 rs2981863 G C 66.05 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.63;MQ0=0;OQ=889.03;QD=17.78;SB=-256.52 GT:AD:DP:GL:GQ 0/1:23,27:46:-106.06,-13.87,-86.32:99 +chr1 3030624 rs2012731 G A 16.06 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=4.70;MQ=59.61;MQ0=0;OQ=1536.02;QD=32.00;SB=-433.32 GT:AD:DP:GL:GQ 1/1:0,48:41:-157.21,-12.36,-0.02:99 +chr1 3031379 rs2817172 T C 144.04 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1381.66;QD=30.70;SB=-636.88 GT:AD:DP:GL:GQ 1/1:0,45:44:-141.79,-13.27,-0.04:99 +chr1 3032241 rs2472820 G A 108.60 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=58.74;MQ0=0;OQ=572.26;QD=15.47;SB=-176.66 GT:AD:DP:GL:GQ 0/1:19,18:36:-71.36,-10.85,-60.89:99 +chr1 3032694 . C T 55.78 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=60.00;MQ0=0;OQ=546.49;QD=14.77;SB=-205.90 GT:AD:DP:GL:GQ 0/1:19,18:36:-68.78,-10.85,-58.80:99 +chr1 3033426 rs12410830 A G 6.05 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=3.60;MQ=59.16;MQ0=0;OQ=614.56;QD=12.29;SB=-235.29 GT:AD:DP:GL:GQ 0/1:27,23:49:-79.50,-14.76,-107.00:99 +chr1 3034041 rs2817174 T C 277.92 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.38;MQ0=0;OQ=1499.60;QD=26.78;SB=-664.93 GT:AD:DP:GL:GQ 1/1:0,56:48:-153.59,-14.48,-0.05:99 +chr1 3034512 rs35529420 C T 72.11 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.41;MQ=59.18;MQ0=0;OQ=899.04;QD=15.77;SB=-264.19 GT:AD:DP:GL:GQ 0/1:27,29:53:-109.16,-15.97,-86.82:99 +chr1 3034731 rs35951269 T C 58.31 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=2.40;MQ=58.97;MQ0=0;OQ=780.41;QD=12.39;SB=-339.30 GT:AD:DP:GL:GQ 0/1:36,27:63:-100.30,-18.98,-146.89:99 +chr1 3035225 rs2742670 A G 75.82 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.62;MQ=60.00;MQ0=0;OQ=1811.56;QD=33.55;SB=-920.03 GT:AD:DP:GL:GQ 1/1:0,54:51:-184.76,-15.36,-0.02:99 +chr1 3035475 rs2817175 T C 135.77 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=57.17;MQ0=0;OQ=1487.18;QD=29.74;SB=-663.57 GT:AD:DP:GL:GQ 1/1:0,50:49:-152.36,-14.79,-0.06:99 +chr1 3035871 rs2817176 A G 10.06 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=58.80;MQ0=0;OQ=1642.91;QD=28.33;SB=-799.47 GT:AD:DP:GL:GQ 1/1:0,58:54:-167.94,-16.30,-0.07:99 +chr1 3036323 rs2817177 T C 492.31 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=1385.60;QD=34.64;SB=-536.41 GT:AD:DP:GL:GQ 1/1:0,40:39:-142.16,-11.75,-0.01:99 +chr1 3036571 rs35625823 T G 1.28 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.02;HRun=1;HaplotypeScore=8.04;MQ=58.17;MQ0=0;OQ=682.10;QD=13.37;SB=-105.91 GT:AD:DP:GL:GQ 0/1:25,25:50:-86.26,-14.76,-86.59:99 +chr1 3036686 rs35201154 G T 212.09 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.64;MQ0=0;OQ=542.18;QD=11.30;SB=-157.49 GT:AD:DP:GL:GQ 0/1:27,21:48:-71.97,-14.46,-93.11:99 +chr1 3037032 rs2788086 A G 87.83 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.14;MQ0=0;OQ=1440.07;QD=26.67;SB=-745.96 GT:AD:DP:GL:GQ 1/1:1,53:49:-151.81,-14.78,-4.21:99 +chr1 3037112 rs2817178 T C 138.65 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.50;MQ=59.01;MQ0=0;OQ=1783.83;QD=33.66;SB=-780.99 GT:AD:DP:GL:GQ 1/1:0,53:51:-182.00,-15.37,-0.03:99 +chr1 3037307 rs10797378 T C 263.69 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=57.77;MQ0=0;OQ=673.03;QD=12.02;SB=-270.24 GT:AD:DP:GL:GQ 0/1:24,31:50:-85.66,-15.07,-91.32:99 +chr1 3037312 rs2788087 A G 5.84 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=3;HaplotypeScore=4.61;MQ=57.43;MQ0=0;OQ=719.26;QD=12.40;SB=-323.12 GT:AD:DP:GL:GQ 0/1:28,30:54:-91.49,-16.28,-101.63:99 +chr1 3037323 rs10909881 G A 169.28 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.31;MQ=57.69;MQ0=0;OQ=859.60;QD=14.57;SB=-445.45 GT:AD:DP:GL:GQ 0/1:30,29:55:-105.83,-16.59,-85.38:99 +chr1 3038158 rs2817180 T C 101.32 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.60;MQ0=0;OQ=1662.63;QD=29.17;SB=-686.71 GT:AD:DP:GL:GQ 1/1:0,57:52:-169.90,-15.69,-0.05:99 +chr1 3038602 rs35360783 A G 220.53 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.65;MQ0=0;OQ=463.18;QD=8.74;SB=-235.89 GT:AD:DP:GL:GQ 0/1:32,21:53:-65.58,-15.98,-127.69:99 +chr1 3039222 rs12024620 C T 40.79 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=4.42;MQ=59.20;MQ0=0;OQ=839.66;QD=14.48;SB=-156.21 GT:AD:DP:GL:GQ 0/1:32,26:56:-104.13,-16.88,-98.69:99 +chr1 3039241 rs12021948 G C 56.36 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.56;MQ0=0;OQ=946.79;QD=17.86;SB=-223.20 GT:AD:DP:GL:GQ 0/1:25,28:53:-113.94,-15.98,-109.97:99 +chr1 3039433 rs12740389 C T 216.94 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.36;MQ0=0;OQ=1244.61;QD=19.15;SB=-628.67 GT:AD:DP:GL:GQ 0/1:28,37:63:-146.73,-18.98,-86.83:99 +chr1 3039715 rs35999894 C T 445.61 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1131.40;QD=18.86;SB=-581.12 GT:AD:DP:GL:GQ 0/1:26,34:58:-133.91,-17.48,-78.73:99 +chr1 3039945 rs34733164 A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=4;HaplotypeScore=2.38;MQ=59.17;MQ0=0;OQ=103.23;QD=3.69;SB=-48.95 GT:AD:DP:GL:GQ 0/1:18,10:23:-20.53,-6.93,-62.39:99 +chr1 3040081 rs12022170 G A 254.38 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.17;MQ0=0;OQ=717.02;QD=15.93;SB=-327.88 GT:AD:DP:GL:GQ 0/1:23,22:43:-87.95,-12.96,-65.92:99 +chr1 3040191 rs12028027 T C 223.73 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.03;MQ0=0;OQ=428.68;QD=8.93;SB=-212.28 GT:AD:DP:GL:GQ 0/1:28,20:45:-59.72,-13.57,-97.74:99 +chr1 3040222 rs12027117 A G 229.27 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.46;MQ0=0;OQ=557.56;QD=12.97;SB=-281.47 GT:AD:DP:GL:GQ 0/1:21,22:42:-71.69,-12.65,-82.66:99 +chr1 3040357 rs10909883 A G 344.92 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.62;MQ0=0;OQ=754.58;QD=12.37;SB=-348.58 GT:AD:DP:GL:GQ 0/1:28,33:59:-96.53,-17.79,-109.54:99 +chr1 3040454 rs12120879 C G 45.73 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.33;MQ=58.92;MQ0=0;OQ=1009.80;QD=18.03;SB=-357.43 GT:AD:DP:GL:GQ 0/1:27,29:53:-120.25,-15.98,-106.43:99 +chr1 3040798 rs35848773 T C 267.80 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.65;MQ0=0;OQ=685.07;QD=12.69;SB=-277.27 GT:AD:DP:GL:GQ 0/1:21,33:48:-86.26,-14.47,-82.32:99 +chr1 3040900 rs12731315 G C 3.75 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=3;HaplotypeScore=3.13;MQ=60.00;MQ0=0;OQ=656.27;QD=17.74;SB=-310.23 GT:AD:DP:GL:GQ 0/1:18,19:37:-80.07,-11.16,-76.94:99 +chr1 3041210 rs12724921 T A 454.48 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=611.82;QD=12.00;SB=-313.55 GT:AD:DP:GL:GQ 0/1:28,23:48:-78.92,-14.46,-101.94:99 +chr1 3041481 rs909509 A G 48.89 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.12;MQ=59.51;MQ0=0;OQ=373.32;QD=7.94;SB=-138.54 GT:AD:DP:GL:GQ 0/1:28,18:38:-52.08,-11.46,-81.04:99 +chr1 3041609 rs12725529 T C 111.43 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=58.62;MQ0=0;OQ=287.04;QD=7.76;SB=-113.62 GT:AD:DP:GL:GQ 0/1:21,16:34:-42.24,-10.25,-81.99:99 +chr1 3042125 rs7535865 A C 10.52 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=7.89;MQ=58.97;MQ0=0;OQ=623.66;QD=13.86;SB=-308.90 GT:AD:DP:GL:GQ 0/1:18,27:40:-77.70,-12.05,-63.90:99 +chr1 3042361 rs4648363 C T 227.69 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.42;MQ0=0;OQ=413.64;QD=10.34;SB=-159.64 GT:AD:DP:GL:GQ 0/1:26,14:37:-55.80,-11.16,-73.37:99 +chr1 3043023 rs35794895 G A 293.61 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=58.64;MQ0=0;OQ=693.50;QD=14.45;SB=-320.87 GT:AD:DP:GL:GQ 0/1:21,26:42:-85.30,-12.67,-60.57:99 +chr1 3043817 rs12741594 A T 497.03 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=877.02;QD=14.62;SB=-406.56 GT:AD:DP:GL:GQ 0/1:31,29:60:-109.06,-18.07,-115.07:99 +chr1 3043966 rs2235176 T C 337.32 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=677.48;QD=12.55;SB=-208.33 GT:AD:DP:GL:GQ 0/1:27,27:53:-87.00,-15.97,-104.05:99 +chr1 3044349 rs35877876 C T 270.74 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.61;MQ0=0;OQ=969.79;QD=16.44;SB=-358.48 GT:AD:DP:GL:GQ 0/1:30,29:59:-118.04,-17.77,-107.71:99 +chr1 3045481 rs10797379 T C 126.05 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.62;MQ0=0;OQ=1290.17;QD=29.32;SB=-604.23 GT:AD:DP:GL:GQ 1/1:0,44:42:-132.64,-12.67,-0.04:99 +chr1 3045736 rs10797380 A G 12.13 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=4.39;MQ=59.03;MQ0=0;OQ=1384.53;QD=28.84;SB=-697.60 GT:AD:DP:GL:GQ 1/1:0,48:44:-142.08,-13.27,-0.04:99 +chr1 3046509 rs7354964 C G 181.06 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.06;MQ0=0;OQ=756.10;QD=18.90;SB=-387.98 GT:AD:DP:GL:GQ 0/1:19,21:40:-90.95,-12.05,-80.97:99 +chr1 3047001 rs2817181 A G 378.95 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=2402.64;QD=34.32;SB=-979.90 GT:AD:DP:GL:GQ 1/1:0,70:68:-243.87,-20.48,-0.03:99 +chr1 3047521 rs7538096 T C 291.96 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.64;MQ0=0;OQ=861.01;QD=13.45;SB=-250.18 GT:AD:DP:GL:GQ 0/1:31,33:64:-108.67,-19.29,-124.47:99 +chr1 3048093 rs2742666 T C 36.97 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=6.22;MQ=57.02;MQ0=0;OQ=594.94;QD=12.93;SB=-209.63 GT:AD:DP:GL:GQ 0/1:23,23:42:-75.43,-12.65,-85.93:99 +chr1 3048098 rs2742665 A C 100.54 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=57.17;MQ0=0;OQ=617.42;QD=15.44;SB=-256.42 GT:AD:DP:GL:GQ 0/1:17,23:38:-76.47,-11.45,-58.49:99 +chr1 3048109 rs2817183 A G 380.39 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.05;MQ0=0;OQ=578.38;QD=14.46;SB=-222.56 GT:AD:DP:GL:GQ 0/1:19,21:39:-72.87,-11.75,-75.47:99 +chr1 3048230 rs2817184 G A 543.37 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=743.48;QD=15.82;SB=-334.86 GT:AD:DP:GL:GQ 0/1:23,24:46:-91.50,-13.86,-76.30:99 +chr1 3050041 rs6684093 C T 40.49 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=5.68;MQ=58.71;MQ0=0;OQ=937.27;QD=17.36;SB=-475.05 GT:AD:DP:GL:GQ 0/1:24,30:51:-112.38,-15.37,-76.51:99 +chr1 3051143 rs1875449 C A 6.39 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=5.78;MQ=59.44;MQ0=0;OQ=367.51;QD=8.96;SB=-206.89 GT:AD:DP:GL:GQ 0/1:23,18:37:-51.19,-11.15,-77.66:99 +chr1 3052735 rs2817187 G T 176.34 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.61;MQ0=0;OQ=2057.17;QD=34.87;SB=-1041.53 GT:AD:DP:GL:GQ 1/1:0,59:58:-209.32,-17.47,-0.02:99 +chr1 3066300 . C T 85.23 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.28;MQ0=0;OQ=957.84;QD=16.51;SB=-344.34 GT:AD:DP:GL:GQ 0/1:29,29:58:-116.54,-17.47,-102.34:99 +chr1 3068821 . G A 12.77 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.86;MQ=59.41;MQ0=0;OQ=492.51;QD=12.63;SB=-226.54 GT:AD:DP:GL:GQ 0/1:19,20:34:-62.79,-10.25,-59.33:99 +chr1 3069601 rs34175350 G C 4.56 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=15.60;MQ0=24;OQ=307.57;QD=4.16;SB=-10.00 GT:AD:DP:GL:GQ 0/1:61,13:26:-41.87,-7.83,-71.98:99 +chr1 3071991 . T C 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=7.33;MQ=54.00;MQ0=2;OQ=261.16;QD=5.02;SB=-67.51 GT:AD:DP:GL:GQ 0/1:33,19:40:-41.45,-12.05,-111.58:99 +chr1 3072015 . C T 17.95 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=6.27;MQ=51.72;MQ0=4;QD=0.46;SB=-17.49 GT:AD:DP:GL:GQ 0/1:29,10:20:-11.10,-6.03,-56.69:50.72 +chr1 3077233 rs10909887 A T 53.28 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=59.65;MQ0=0;OQ=1671.94;QD=31.55;SB=-810.23 GT:AD:DP:GL:GQ 1/1:0,53:48:-170.81,-14.47,-0.03:99 +chr1 3078302 rs2817127 C G 3.71 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=58.92;MQ0=0;OQ=1590.78;QD=40.79;SB=-669.44 GT:AD:DP:GL:GQ 1/1:0,39:38:-162.68,-11.46,-0.02:99 +chr1 3078602 rs2651936 C T 556.62 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1763.78;QD=38.34;SB=-617.01 GT:AD:DP:GL:GQ 1/1:0,46:45:-179.97,-13.55,-0.01:99 +chr1 3078803 rs2817128 T C 41.66 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=0.92;MQ=58.79;MQ0=0;OQ=1700.76;QD=31.50;SB=-627.85 GT:AD:DP:GL:GQ 1/1:0,54:53:-173.71,-15.98,-0.05:99 +chr1 3078920 rs2817129 G C 420.84 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2270.90;QD=42.85;SB=-927.24 GT:AD:DP:GL:GQ 1/1:0,53:53:-230.70,-15.98,-0.02:99 +chr1 3079836 rs3795268 G A 518.97 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2012.53;QD=38.70;SB=-765.66 GT:AD:DP:GL:GQ 1/1:0,52:51:-204.85,-15.36,-0.01:99 +chr1 3082486 rs61759169 A T 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=17.96;MQ=49.98;MQ0=1;OQ=467.66;QD=5.85;SB=-63.76 GT:AD:DP:GL:GQ 0/1:57,23:74:-72.34,-22.29,-212.74:99 +chr1 3082576 rs59307218 T C 89.31 Indel AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.00;HRun=1;HaplotypeScore=16.28;MQ=58.32;MQ0=0;QD=0.84;SB=-6.84 GT:AD:DP:GL:GQ 0/1:94,12:100:-42.34,-30.13,-353.31:99 +chr1 3082715 rs61759170 T C 0.15 PASS AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=1;HaplotypeScore=13.70;MQ=54.13;MQ0=0;OQ=433.59;QD=4.61;SB=-120.39 GT:AD:DP:GL:GQ 0/1:66,28:84:-71.95,-25.31,-255.13:99 +chr1 3082724 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=20.17;MQ=53.56;MQ0=0;OQ=265.77;QD=3.09;SB=-1.90 GT:AD:DP:GL:GQ 0/1:64,21:77:-55.36,-25.50,-226.03:99 +chr1 3082730 rs61759171 A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=25.02;MQ=53.60;MQ0=0;OQ=115.19;QD=1.46;SB=35.65 GT:AD:DP:GL:GQ 0/1:62,16:69:-35.59,-20.79,-209.49:99 +chr1 3083610 rs2817131 T C 1.92 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=7.31;MQ=58.76;MQ0=0;OQ=2679.05;QD=35.25;SB=-1269.49 GT:AD:DP:GL:GQ 1/1:0,76:75:-271.51,-22.59,-0.03:99 +chr1 3086215 rs868718 G A 224.01 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.60;MQ0=0;OQ=2257.57;QD=38.92;SB=-929.74 GT:AD:DP:GL:GQ 1/1:0,58:57:-229.36,-17.17,-0.02:99 +chr1 3086338 rs2817132 T C 256.47 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1749.39;QD=34.30;SB=-792.14 GT:AD:DP:GL:GQ 1/1:0,51:49:-178.54,-14.76,-0.01:99 +chr1 3086971 . G A 6.54 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=59.63;MQ0=0;OQ=869.92;QD=17.06;SB=-366.15 GT:AD:DP:GL:GQ 0/1:23,28:49:-105.05,-14.78,-70.17:99 +chr1 3087284 rs28576654 G A 0.62 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=8.45;MQ=55.21;MQ0=0;OQ=1827.21;QD=37.29;SB=-761.03 GT:AD:DP:GL:GQ 1/1:1,48:47:-186.32,-14.16,-0.02:99 +chr1 3087324 rs36042320 A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=36.16;MQ=53.71;MQ0=0;OQ=1199.13;QD=20.32;SB=-596.19 GT:AD:DP:GL:GQ 1/1:10,49:47:-136.03,-14.18,-12.56:16.27 +chr1 3087368 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=62.15;MQ=52.02;MQ0=2;OQ=84.05;QD=0.99;SB=68.22 GT:AD:DP:GL:GQ 0/1:64,20:65:-31.27,-19.58,-199.12:99 +chr1 3087405 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=113.18;MQ=45.62;MQ0=12;OQ=152.20;QD=1.23;SB=83.17 GT:AD:DP:GL:GQ 0/1:93,25:100:-54.91,-36.41,-286.94:99 +chr1 3087421 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=108;Dels=0.01;HRun=1;HaplotypeScore=157.91;MQ=45.44;MQ0=13;OQ=317.87;QD=2.94;SB=62.22 GT:AD:DP:GL:GQ 0/1:65,42:72:-56.46,-21.39,-222.98:99 +chr1 3087430 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=100;Dels=0.09;HRun=0;HaplotypeScore=131.45;MQ=45.35;MQ0=13;OQ=71.40;QD=0.71;SB=68.23 GT:AD:DP:GL:GQ 0/1:57,34:61:-28.82,-18.40,-174.57:99 +chr1 3087432 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=125.43;MQ=44.68;MQ0=16;OQ=349.00;QD=3.39;SB=68.23 GT:AD:DP:GL:GQ 0/1:85,18:67:-58.39,-20.20,-173.08:99 +chr1 3087446 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=34.86;MQ=42.41;MQ0=15;OQ=253.15;QD=2.81;SB=53.16 GT:AD:DP:GL:GQ 0/1:47,43:54:-44.89,-16.29,-135.66:99 +chr1 3087456 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=33.91;MQ=40.94;MQ0=15;OQ=574.41;QD=6.38;SB=41.15 GT:AD:DP:GL:GQ 0/1:47,43:59:-78.52,-17.79,-127.78:99 +chr1 3087469 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=37.75;MQ=38.93;MQ0=14;OQ=420.06;QD=4.94;SB=41.09 GT:AD:DP:GL:GQ 0/1:56,29:63:-64.29,-19.00,-146.93:99 +chr1 3087482 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=75.90;MQ=37.38;MQ0=13;OQ=93.48;QD=1.23;SB=56.14 GT:AD:DP:GL:GQ 0/1:55,21:54:-28.92,-16.29,-150.91:99 +chr1 3087484 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=59.86;MQ=36.69;MQ0=13;OQ=224.49;QD=2.95;SB=47.15 GT:AD:DP:GL:GQ 0/1:64,12:51:-41.12,-15.38,-130.32:99 +chr1 3087496 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.18;HRun=0;HaplotypeScore=92.35;MQ=35.16;MQ0=7;OQ=80.55;QD=1.41;SB=-35.75 GT:AD:DP:GL:GQ 0/1:30,16:29:-20.09,-8.75,-100.50:99 +chr1 3087498 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=70.78;MQ=33.76;MQ0=7;OQ=147.15;QD=2.58;SB=-95.04 GT:AD:DP:GL:GQ 0/1:41,16:33:-27.95,-9.95,-82.07:99 +chr1 3087509 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.05;HRun=0;HaplotypeScore=74.81;MQ=32.58;MQ0=5;OQ=64.70;QD=1.06;SB=56.11 GT:AD:DP:GL:GQ 0/1:52,6:35:-20.32,-10.56,-93.36:97.54 +chr1 3087512 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=54.96;MQ=31.97;MQ0=5;OQ=503.11;QD=8.11;SB=-236.10 GT:AD:DP:GL:GQ 0/1:31,31:45:-67.16,-13.57,-94.41:99 +chr1 3087536 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=33.03;MQ=32.40;MQ0=3;OQ=59.37;QD=0.74;SB=89.25 GT:AD:DP:GL:GQ 0/1:72,7:63:-28.22,-18.99,-181.57:92.21 +chr1 3087538 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=37.44;MQ=32.40;MQ0=3;OQ=247.27;QD=3.09;SB=80.25 GT:AD:DP:GL:GQ 0/1:65,15:63:-46.99,-18.98,-180.33:99 +chr1 3087608 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=168;Dels=0.01;HRun=0;HaplotypeScore=54.40;MQ=37.28;MQ0=13;OQ=1887.72;QD=11.24;SB=-729.24 GT:AD:DP:GL:GQ 0/1:104,63:145:-235.47,-43.42,-271.37:99 +chr1 3087617 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=0;HaplotypeScore=53.68;MQ=37.94;MQ0=15;OQ=1635.04;QD=8.84;SB=-493.28 GT:AD:DP:GL:GQ 0/1:114,71:160:-215.01,-48.22,-344.93:99 +chr1 3087664 . A G 18.84 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=189;Dels=0.01;HRun=0;HaplotypeScore=131.51;MQ=40.84;MQ0=15;QD=0.10;SB=241.96 GT:AD:DP:GL:GQ 0/1:170,18:163:-53.97,-48.81,-580.79:51.62 +chr1 3087667 . C T 165.92 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=188;Dels=0.01;HRun=0;HaplotypeScore=132.64;MQ=41.11;MQ0=15;QD=0.88;SB=179.60 GT:AD:DP:GL:GQ 0/1:167,20:158:-67.18,-47.30,-486.26:99 +chr1 3087668 . A G 310.08 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=187;Dels=0.01;HRun=1;HaplotypeScore=124.54;MQ=41.17;MQ0=15;QD=1.66;SB=124.04 GT:AD:DP:GL:GQ 0/1:158,28:160:-82.20,-47.90,-540.31:99 +chr1 3087734 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=114;Dels=0.00;HRun=1;HaplotypeScore=13.23;MQ=44.53;MQ0=2;OQ=55.34;QD=0.49;SB=-14.90 GT:AD:DP:GL:GQ 0/1:101,11:104:-40.16,-31.34,-369.37:88.18 +chr1 3087747 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=0;HaplotypeScore=23.95;MQ=43.49;MQ0=2;OQ=1649.29;QD=15.71;SB=-709.98 GT:AD:DP:GL:GQ 0/1:48,57:100:-198.34,-30.13,-180.84:99 +chr1 3087772 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=133;Dels=0.00;HRun=0;HaplotypeScore=99.40;MQ=37.75;MQ0=7;OQ=762.57;QD=5.73;SB=-239.63 GT:AD:DP:GL:GQ 0/1:102,30:117:-114.83,-35.29,-281.68:99 +chr1 3087833 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=1;HaplotypeScore=261.50;MQ=29.30;MQ0=7;OQ=1486.23;QD=9.78;SB=-676.51 GT:AD:DP:GL:GQ 0/1:100,52:130:-191.07,-39.17,-253.74:99 +chr1 3087850 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=106.63;MQ=29.08;MQ0=7;OQ=1055.92;QD=7.23;SB=-459.23 GT:AD:DP:GL:GQ 0/1:100,46:125:-146.56,-37.68,-289.33:99 +chr1 3087853 . C A 11.81 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=0;HaplotypeScore=84.96;MQ=29.13;MQ0=6;QD=0.08;SB=22.69 GT:AD:DP:GL:GQ 0/1:134,14:133:-44.49,-40.06,-434.86:44.36 +chr1 3087861 . A C 168.29 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=135;Dels=0.00;HRun=0;HaplotypeScore=23.28;MQ=29.00;MQ0=4;QD=1.25;SB=-17.42 GT:AD:DP:GL:GQ 0/1:115,20:120:-56.26,-36.15,-379.05:99 +chr1 3087900 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=22.94;MQ=28.28;MQ0=1;OQ=423.78;QD=5.81;SB=-214.40 GT:AD:DP:GL:GQ 0/1:51,22:68:-66.15,-20.49,-189.92:99 +chr1 3087911 . C T 880.08 SnpCluster AC=1;AF=0.50;AN=2;DP=69;Dels=0.03;HRun=0;HaplotypeScore=32.89;MQ=28.46;MQ0=0;QD=12.75;SB=-315.83 GT:AD:DP:GL:GQ 0/1:40,27:49:-105.45,-14.16,-69.50:99 +chr1 3087912 . A G 1267.81 SnpCluster AC=1;AF=0.50;AN=2;DP=68;Dels=0.03;HRun=1;HaplotypeScore=32.88;MQ=28.45;MQ0=0;QD=18.64;SB=-474.20 GT:AD:DP:GL:GQ 0/1:22,44:48:-143.92,-13.86,-20.32:64.59 +chr1 3087920 . G A 574.31 SnpCluster AC=1;AF=0.50;AN=2;DP=74;Dels=0.04;HRun=0;HaplotypeScore=182.60;MQ=28.60;MQ0=0;QD=7.76;SB=-289.69 GT:AD:DP:GL:GQ 0/1:50,21:71:-81.21,-20.50,-157.25:99 +chr1 3087952 . G A 1075.62 Indel AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=58.78;MQ=31.99;MQ0=0;QD=13.62;SB=-555.39 GT:AD:DP:GL:GQ 0/1:45,34:75:-133.45,-22.61,-136.49:99 +chr1 3087978 . A G 38.22 DPFilter;Indel;LowQual AC=1;AF=0.50;AN=2;DP=109;Dels=0.02;HRun=1;HaplotypeScore=54.40;MQ=36.04;MQ0=0;QD=0.35;SB=94.63 GT:AD:DP:GL:GQ 0/1:93,14:103:-37.54,-30.43,-360.90:71.06 +chr1 3088004 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=0;HaplotypeScore=30.72;MQ=40.10;MQ0=2;OQ=423.13;QD=3.00;SB=9.29 GT:AD:DP:GL:GQ 0/1:121,20:123:-82.68,-37.08,-335.63:99 +chr1 3088013 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=142;Dels=0.03;HRun=0;HaplotypeScore=47.98;MQ=41.19;MQ0=4;OQ=426.97;QD=3.01;SB=-54.18 GT:AD:DP:GL:GQ 0/1:112,26:133:-84.85,-38.87,-412.97:99 +chr1 3088015 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=145;Dels=0.00;HRun=0;HaplotypeScore=42.51;MQ=41.21;MQ0=4;OQ=465.21;QD=3.21;SB=-60.11 GT:AD:DP:GL:GQ 0/1:116,29:131:-89.28,-39.48,-409.01:99 +chr1 3088100 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=132;Dels=0.00;HRun=0;HaplotypeScore=4.53;MQ=40.45;MQ0=11;OQ=130.52;QD=0.99;SB=-31.41 GT:AD:DP:GL:GQ 0/1:119,13:106:-48.30,-31.97,-302.63:99 +chr1 3088101 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=0;HaplotypeScore=4.53;MQ=40.49;MQ0=10;OQ=71.07;QD=0.55;SB=-5.78 GT:AD:DP:GL:GQ 0/1:117,11:111:-47.37,-36.98,-326.83:99 +chr1 3088217 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=80;Dels=0.01;HRun=0;HaplotypeScore=17.08;MQ=42.86;MQ0=1;OQ=126.54;QD=1.58;SB=-85.23 GT:AD:DP:GL:GQ 0/1:66,13:74:-37.94,-22.00,-241.16:99 +chr1 3088220 rs34886760 A G 0.65 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.01;HRun=1;HaplotypeScore=12.97;MQ=43.96;MQ0=1;OQ=1584.16;QD=20.84;SB=-521.89 GT:AD:DP:GL:GQ 0/1:11,64:65:-181.29,-19.59,-39.63:99 +chr1 3088304 rs61759175 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=118;Dels=0.08;HRun=0;HaplotypeScore=55.59;MQ=46.00;MQ0=11;OQ=251.71;QD=2.13;SB=81.71 GT:AD:DP:GL:GQ 0/1:90,18:102:-58.89,-30.43,-301.97:99 +chr1 3088575 rs2817134 T C 3.03 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=5.64;MQ=59.45;MQ0=0;OQ=1472.39;QD=35.06;SB=-604.20 GT:AD:DP:GL:GQ 1/1:0,42:42:-150.84,-12.65,-0.02:99 +chr1 3088745 rs2651931 C T 32.64 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.49;MQ=59.44;MQ0=0;OQ=1502.67;QD=36.65;SB=-632.85 GT:AD:DP:GL:GQ 1/1:0,40:38:-153.86,-11.45,-0.01:99 +chr1 3088761 rs2817135 T C 98.95 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.39;MQ0=0;OQ=1114.54;QD=29.33;SB=-484.51 GT:AD:DP:GL:GQ 1/1:0,38:36:-115.07,-10.86,-0.04:99 +chr1 3089054 rs950200 A G 135.40 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.38;MQ0=0;OQ=1494.35;QD=33.21;SB=-586.20 GT:AD:DP:GL:GQ 1/1:0,45:43:-153.04,-12.95,-0.02:99 +chr1 3091593 rs9660914 G A 174.18 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.63;MQ0=0;OQ=2157.13;QD=34.24;SB=-1073.97 GT:AD:DP:GL:GQ 1/1:0,63:58:-219.33,-17.49,-0.04:99 +chr1 3093686 rs4233024 C T 199.19 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.75;MQ0=0;OQ=1964.65;QD=37.78;SB=-829.97 GT:AD:DP:GL:GQ 1/1:0,52:51:-200.08,-15.37,-0.03:99 +chr1 3094490 rs10752733 A G 125.27 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1561.08;QD=30.61;SB=-635.88 GT:AD:DP:GL:GQ 1/1:0,51:49:-159.74,-14.78,-0.04:99 +chr1 3094942 rs2817136 G A 89.99 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1690.06;QD=36.74;SB=-568.32 GT:AD:DP:GL:GQ 1/1:0,46:44:-172.61,-13.26,-0.02:99 +chr1 3095136 rs2817138 T G 4.52 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=58.92;MQ0=0;OQ=1072.43;QD=24.94;SB=-511.45 GT:AD:DP:GL:GQ 1/1:0,43:37:-110.87,-11.16,-0.04:99 +chr1 3095423 rs2651919 G T 722.39 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2110.88;QD=35.78;SB=-952.39 GT:AD:DP:GL:GQ 1/1:0,59:58:-214.69,-17.47,-0.02:99 +chr1 3095697 rs2651918 T C 14.21 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=3.68;MQ=59.20;MQ0=0;OQ=1955.56;QD=33.72;SB=-956.98 GT:AD:DP:GL:GQ 1/1:0,58:55:-199.16,-16.57,-0.02:99 +chr1 3095769 rs2817139 A G 514.86 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.29;MQ0=0;OQ=1684.86;QD=27.18;SB=-755.66 GT:AD:DP:GL:GQ 1/1:0,62:53:-172.12,-15.99,-0.05:99 +chr1 3095922 rs7530075 G A 526.13 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=1784.81;QD=39.66;SB=-851.64 GT:AD:DP:GL:GQ 1/1:0,45:45:-182.08,-13.55,-0.01:99 +chr1 3096128 rs2651917 C G 97.32 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.80;MQ0=0;OQ=1717.27;QD=36.54;SB=-542.46 GT:AD:DP:GL:GQ 1/1:0,47:42:-175.34,-12.67,-0.03:99 +chr1 3096165 rs7545798 A G 335.50 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=1218.45;QD=30.46;SB=-546.04 GT:AD:DP:GL:GQ 1/1:0,40:39:-125.47,-11.76,-0.04:99 +chr1 3096243 rs7545871 A G 179.87 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1274.76;QD=30.35;SB=-481.26 GT:AD:DP:GL:GQ 1/1:0,42:39:-131.09,-11.76,-0.02:99 +chr1 3096257 rs2651916 C T 670.34 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1810.18;QD=36.20;SB=-763.02 GT:AD:DP:GL:GQ 1/1:0,50:47:-184.62,-14.16,-0.02:99 +chr1 3096476 rs2817140 A G 6.35 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=1038.30;QD=28.84;SB=-515.16 GT:AD:DP:GL:GQ 1/1:0,36:34:-107.45,-10.26,-0.04:99 +chr1 3096661 rs61759179 G A 1.83 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.55;MQ=53.62;MQ0=2;OQ=1172.74;QD=30.07;SB=-520.65 GT:AD:DP:GL:GQ 1/1:8,31:31:-120.87,-9.34,-0.01:93.29 +chr1 3096814 rs2817141 T C 22.79 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=1.30;MQ=59.19;MQ0=0;OQ=1269.17;QD=27.59;SB=-620.79 GT:AD:DP:GL:GQ 1/1:0,46:42:-130.56,-12.68,-0.06:99 +chr1 3097140 rs1875451 C T 277.41 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.63;MQ0=0;OQ=1807.86;QD=35.45;SB=-805.30 GT:AD:DP:GL:GQ 1/1:0,51:46:-184.39,-13.86,-0.02:99 +chr1 3098276 rs2651914 T G 143.53 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=2148.66;QD=35.22;SB=-1029.38 GT:AD:DP:GL:GQ 1/1:0,61:61:-218.47,-18.37,-0.02:99 +chr1 3098356 rs10737190 G A 615.19 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=3298.92;QD=39.75;SB=-1410.68 GT:AD:DP:GL:GQ 1/1:0,83:81:-328.89,-24.40,-0.02:99 +chr1 3098377 rs6685614 G A 280.84 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.78;MQ0=0;OQ=3233.06;QD=38.95;SB=-1261.68 GT:AD:DP:GL:GQ 1/1:0,83:82:-327.11,-24.71,-0.03:99 +chr1 3099011 rs7539775 G A 230.88 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.47;MQ0=0;OQ=1818.76;QD=34.98;SB=-678.01 GT:AD:DP:GL:GQ 1/1:1,51:49:-188.18,-14.77,-2.72:99 +chr1 3100277 rs2651913 C G 465.83 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1755.38;QD=41.79;SB=-899.81 GT:AD:DP:GL:GQ 1/1:0,42:41:-179.13,-12.35,-0.01:99 +chr1 3100595 rs2651912 T C 68.37 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=4.22;MQ=58.95;MQ0=0;OQ=646.58;QD=10.43;SB=-279.12 GT:AD:DP:GL:GQ 0/1:33,29:56:-84.82,-16.88,-119.30:99 +chr1 3104232 . G A 37.52 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=60.00;MQ0=0;OQ=572.60;QD=16.36;SB=-260.57 GT:AD:DP:GL:GQ 0/1:16,19:33:-70.49,-9.94,-51.89:99 +chr1 3105581 rs950449 C G 114.98 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=352.20;QD=14.09;SB=-136.76 GT:AD:DP:GL:GQ 0/1:14,11:24:-45.74,-7.23,-56.39:99 +chr1 3106518 rs2651923 T C 555.63 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.18;MQ0=0;OQ=1262.70;QD=28.70;SB=-607.93 GT:AD:DP:GL:GQ 1/1:0,44:40:-129.89,-12.07,-0.04:99 +chr1 3110061 rs2817142 T C 84.27 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=58.76;MQ0=0;OQ=950.22;QD=27.95;SB=-463.20 GT:AD:DP:GL:GQ 1/1:1,33:31:-98.64,-9.35,-0.03:93.20 +chr1 3113619 rs2817143 T C 475.54 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1485.25;QD=30.31;SB=-541.01 GT:AD:DP:GL:GQ 1/1:0,49:46:-152.15,-13.87,-0.04:99 +chr1 3119305 . C T 6.85 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=482.22;QD=12.06;SB=-197.28 GT:AD:DP:GL:GQ 0/1:23,17:38:-62.96,-11.45,-76.10:99 +chr1 3119433 rs60892783 T A 341.04 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.85;MQ0=0;OQ=778.15;QD=15.26;SB=-381.44 GT:AD:DP:GL:GQ 0/1:26,25:51:-96.46,-15.36,-96.60:99 +chr1 3124191 rs12124147 C T 18.37 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=4;HaplotypeScore=1.41;MQ=60.00;MQ0=0;OQ=2106.36;QD=38.30;SB=-923.21 GT:AD:DP:GL:GQ 1/1:0,55:54:-214.24,-16.27,-0.02:99 +chr1 3125697 . G A 48.02 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.90;MQ=59.58;MQ0=0;OQ=894.40;QD=16.26;SB=-426.44 GT:AD:DP:GL:GQ 0/1:28,27:53:-108.70,-15.98,-81.48:99 +chr1 3133804 rs10737191 T C 216.08 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.05;MQ0=0;OQ=1310.90;QD=29.79;SB=-629.85 GT:AD:DP:GL:GQ 1/1:0,44:43:-134.73,-12.98,-0.05:99 +chr1 3137939 rs2651921 T C 31.09 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.62;MQ=57.88;MQ0=0;OQ=1318.12;QD=31.38;SB=-539.87 GT:AD:DP:GL:GQ 1/1:0,42:38:-135.41,-11.45,-0.01:99 +chr1 3139859 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=4;HaplotypeScore=1.59;MQ=58.84;MQ0=0;OQ=177.35;QD=4.43;SB=56.21 GT:AD:DP:GL:GQ 0/1:24,16:34:-31.27,-10.25,-94.47:99 +chr1 3140395 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=11.19;MQ=58.95;MQ0=0;OQ=93.28;QD=2.12;SB=71.27 GT:AD:DP:GL:GQ 0/1:31,13:33:-22.56,-9.95,-125.01:99 +chr1 3146326 rs2455112 A G 135.43 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=60.00;MQ0=0;OQ=1096.93;QD=16.88;SB=-503.18 GT:AD:DP:GL:GQ 0/1:28,37:65:-132.56,-19.58,-110.95:99 +chr1 3151094 . T G 27.85 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=10.51;MQ=58.72;MQ0=0;QD=0.55;SB=62.22 GT:AD:DP:GL:GQ 0/1:29,22:34:-16.31,-10.24,-101.82:60.68 +chr1 3154977 . C T 20.55 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.05;MQ0=0;OQ=960.26;QD=19.60;SB=-359.36 GT:AD:DP:GL:GQ 0/1:20,29:48:-113.77,-14.46,-73.03:99 +chr1 3155966 rs1105111 C A 740.08 Indel AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=6;HaplotypeScore=0.00;MQ=60.39;MQ0=0;QD=13.46;SB=-187.60 GT:AD:DP:GL:GQ 0/1:28,27:54:-93.56,-16.26,-102.62:99 +chr1 3156860 . C A 1.29 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=2.70;MQ=59.41;MQ0=0;OQ=714.68;QD=18.33;SB=-335.33 GT:AD:DP:GL:GQ 0/1:15,24:39:-86.50,-11.75,-50.10:99 +chr1 3157063 rs60443258 C G 197.93 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.43;MQ0=0;OQ=467.30;QD=14.16;SB=-190.23 GT:AD:DP:GL:GQ 0/1:18,15:33:-59.97,-9.95,-75.73:99 +chr1 3158034 rs11589327 C T 221.90 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=55.82;MQ0=0;OQ=602.02;QD=14.68;SB=-226.92 GT:AD:DP:GL:GQ 0/1:22,19:39:-75.24,-11.75,-65.81:99 +chr1 3158063 rs61759183 G A 105.26 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.23;MQ=54.25;MQ0=0;OQ=859.64;QD=18.29;SB=-349.39 GT:AD:DP:GL:GQ 0/1:17,30:44:-102.53,-13.28,-49.01:99 +chr1 3158107 rs55987640 G A 184.91 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=55.61;MQ0=0;OQ=836.43;QD=16.73;SB=-292.80 GT:AD:DP:GL:GQ 0/1:21,29:42:-99.58,-12.65,-57.74:99 +chr1 3158110 rs10909910 G C 37.93 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=55.78;MQ0=0;OQ=2043.92;QD=39.31;SB=-983.24 GT:AD:DP:GL:GQ 1/1:0,52:49:-208.00,-14.77,-0.02:99 +chr1 3158140 rs10797386 A G 147.32 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=58.66;MQ0=0;OQ=1752.75;QD=33.71;SB=-820.65 GT:AD:DP:GL:GQ 1/1:0,52:49:-178.87,-14.76,-0.02:99 +chr1 3158322 rs12143201 C T 107.15 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=58.81;MQ0=0;OQ=1087.80;QD=19.78;SB=-426.85 GT:AD:DP:GL:GQ 0/1:23,32:54:-128.34,-16.28,-69.54:99 +chr1 3158948 rs7539489 G A 212.35 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.64;MQ=59.50;MQ0=0;OQ=701.66;QD=15.25;SB=-203.89 GT:AD:DP:GL:GQ 0/1:22,24:42:-86.11,-12.66,-64.73:99 +chr1 3160428 rs56015432 C G 319.35 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=42.71;MQ0=18;OQ=1056.37;QD=11.61;SB=-361.10 GT:AD:DP:GL:GQ 0/1:52,38:68:-131.78,-22.86,-160.18:99 +chr1 3160647 rs2376494 T C 490.07 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.54;MQ0=5;OQ=1049.98;QD=13.46;SB=-449.81 GT:AD:DP:GL:GQ 0/1:34,44:69:-129.08,-20.80,-121.01:99 +chr1 3160969 rs61691507 T C 83.17 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=3;HaplotypeScore=0.96;MQ=48.88;MQ0=0;OQ=936.08;QD=14.18;SB=-414.90 GT:AD:DP:GL:GQ 0/1:32,34:63:-115.87,-18.98,-126.60:99 +chr1 3161244 rs28883366 T C 328.67 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=20.07;MQ0=44;OQ=827.10;QD=11.18;SB=-204.07 GT:AD:DP:GL:GQ 1/1:25,49:28:-86.33,-8.45,-0.03:84.18 +chr1 3161789 rs4648464 G A 197.91 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=53.22;MQ0=0;OQ=1078.68;QD=20.35;SB=-414.45 GT:AD:DP:GL:GQ 0/1:21,32:51:-126.53,-15.37,-60.62:99 +chr1 3161922 rs4648465 G A 93.86 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=50.73;MQ0=0;OQ=1117.60;QD=22.35;SB=-454.98 GT:AD:DP:GL:GQ 0/1:18,32:50:-130.11,-15.06,-59.43:99 +chr1 3162133 rs2455100 T C 1.91 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=58.24;MQ0=0;OQ=1353.88;QD=28.21;SB=-366.45 GT:AD:DP:GL:GQ 1/1:0,48:45:-139.02,-13.58,-0.05:99 +chr1 3162911 rs6699624 G C 272.84 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.50;MQ0=0;OQ=1093.08;QD=16.07;SB=-449.43 GT:AD:DP:GL:GQ 0/1:32,35:63:-131.59,-19.00,-134.16:99 +chr1 3163088 rs1971330 C T 114.07 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=49.78;MQ0=0;OQ=900.72;QD=19.58;SB=-445.49 GT:AD:DP:GL:GQ 0/1:19,27:44:-106.61,-13.25,-68.73:99 +chr1 3163142 rs1971331 A G 155.18 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=39.25;MQ0=0;OQ=1400.23;QD=30.44;SB=-715.29 GT:AD:DP:GL:GQ 1/1:0,46:45:-143.65,-13.57,-0.04:99 +chr1 3165231 rs10909912 T G 383.69 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.06;MQ0=0;OQ=430.36;QD=10.76;SB=-234.78 GT:AD:DP:GL:GQ 0/1:20,20:39:-58.07,-11.75,-73.52:99 +chr1 3165588 rs2455101 A G 194.31 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.36;MQ0=0;OQ=514.34;QD=12.86;SB=-185.55 GT:AD:DP:GL:GQ 0/1:18,22:37:-65.87,-11.15,-65.63:99 +chr1 3165783 . C T 13.80 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=427.64;QD=9.30;SB=-160.18 GT:AD:DP:GL:GQ 0/1:30,16:42:-58.70,-12.66,-94.89:99 +chr1 3166230 . C G 139.63 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=825.87;QD=15.88;SB=-367.51 GT:AD:DP:GL:GQ 0/1:23,29:49:-100.65,-14.78,-100.14:99 +chr1 3167106 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=181.43;MQ=36.47;MQ0=0;OQ=530.53;QD=4.31;SB=-209.32 GT:AD:DP:GL:GQ 0/1:66,39:92:-95.27,-38.93,-253.94:99 +chr1 3167116 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=174;Dels=0.01;HRun=1;HaplotypeScore=260.94;MQ=34.61;MQ0=0;OQ=942.41;QD=5.42;SB=-369.43 GT:AD:DP:GL:GQ 0/1:66,57:123:-208.12,-110.59,-323.19:99 +chr1 3167119 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=191;Dels=0.00;HRun=1;HaplotypeScore=217.51;MQ=34.08;MQ0=0;OQ=198.48;QD=1.04;SB=93.36 GT:AD:DP:GL:GQ 0/1:148,42:118:-61.70,-38.57,-398.62:99 +chr1 3167131 . G A 38.92 DPFilter;Indel;LowQual AC=1;AF=0.50;AN=2;DP=216;Dels=0.00;HRun=0;HaplotypeScore=418.78;MQ=33.67;MQ0=0;QD=0.18;SB=-15.26 GT:AD:DP:GL:GQ 0/1:171,44:118:-42.73,-35.55,-373.47:71.75 +chr1 3167160 . G A 609.50 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=190;Dels=0.00;HRun=0;HaplotypeScore=319.28;MQ=32.32;MQ0=1;QD=3.21;SB=-149.32 GT:AD:DP:GL:GQ 0/1:134,56:72:-85.93,-21.70,-173.92:99 +chr1 3167161 . T C 245.51 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=188;Dels=0.00;HRun=0;HaplotypeScore=318.96;MQ=32.30;MQ0=1;QD=1.31;SB=53.20 GT:AD:DP:GL:GQ 0/1:174,14:59:-45.63,-17.79,-171.10:99 +chr1 3167162 . G A 200.87 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=187;Dels=0.00;HRun=0;HaplotypeScore=336.60;MQ=32.32;MQ0=1;QD=1.07;SB=56.18 GT:AD:DP:GL:GQ 0/1:174,10:62:-51.08,-27.71,-180.52:99 +chr1 3167163 . G A 107.11 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=184;Dels=0.00;HRun=0;HaplotypeScore=325.93;MQ=32.20;MQ0=1;QD=0.58;SB=-62.93 GT:AD:DP:GL:GQ 0/1:163,18:64:-33.28,-19.29,-195.22:99 +chr1 3167166 . A G 243.37 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=314.12;MQ=31.98;MQ0=1;QD=1.36;SB=56.35 GT:AD:DP:GL:GQ 0/1:138,41:62:-46.30,-18.68,-187.52:99 +chr1 3167169 . A G 120.84 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=185;Dels=0.00;HRun=1;HaplotypeScore=387.92;MQ=32.13;MQ0=1;QD=0.65;SB=76.41 GT:AD:DP:GL:GQ 0/1:141,44:79:-39.18,-23.81,-262.75:99 +chr1 3167180 rs57179041 G A 114.65 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=141;Dels=0.00;HRun=1;HaplotypeScore=408.58;MQ=31.71;MQ0=1;QD=0.81;SB=86.30 GT:AD:DP:GL:GQ 0/1:118,23:43:-27.70,-12.95,-132.25:99 +chr1 3167181 . A G 38.85 DPFilter;Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=1;HaplotypeScore=419.93;MQ=31.63;MQ0=1;QD=0.28;SB=86.30 GT:AD:DP:GL:GQ 0/1:108,33:42:-19.82,-12.66,-143.77:71.68 +chr1 3167187 . T C 11.48 DPFilter;Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=120;Dels=0.41;HRun=0;HaplotypeScore=330.20;MQ=31.90;MQ0=1;QD=0.10;SB=5.04 GT:AD:DP:GL:GQ 0/1:52,5:44:-17.05,-12.65,-148.02:44 +chr1 3167189 . G A 33.08 DPFilter;Indel;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=123;Dels=0.12;HRun=1;HaplotypeScore=208.65;MQ=32.18;MQ0=1;QD=0.27;SB=8.05 GT:AD:DP:GL:GQ 0/1:103,5:46:-20.45,-13.86,-154.58:65.91 +chr1 3167200 rs57648616 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.00;HRun=0;HaplotypeScore=125.27;MQ=33.30;MQ0=1;OQ=406.22;QD=3.41;SB=39.53 GT:AD:DP:GL:GQ 0/1:44,74:56:-63.73,-19.82,-152.72:99 +chr1 3167205 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=1;HaplotypeScore=95.81;MQ=33.44;MQ0=1;OQ=560.09;QD=4.87;SB=72.41 GT:AD:DP:GL:GQ 0/1:70,45:71:-80.68,-21.39,-190.32:99 +chr1 3167222 rs57879698 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=105.67;MQ=36.94;MQ0=1;OQ=371.38;QD=4.08;SB=65.41 GT:AD:DP:GL:GQ 0/1:54,36:67:-60.61,-20.18,-198.91:99 +chr1 3167226 . A G 25.97 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=1;HaplotypeScore=94.17;MQ=37.02;MQ0=1;QD=0.29;SB=104.36 GT:AD:DP:GL:GQ 0/1:77,13:68:-26.37,-20.49,-239.07:58.80 +chr1 3167247 . A G 94.62 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=9.30;MQ=43.30;MQ0=0;QD=1.30;SB=66.40 GT:AD:DP:GL:GQ 0/1:60,13:64:-32.03,-19.29,-213.53:99 +chr1 3167248 rs61151413 C T 166.25 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=15.29;MQ=43.46;MQ0=0;QD=2.31;SB=80.73 GT:AD:DP:GL:GQ 0/1:59,13:65:-39.51,-19.60,-174.44:99 +chr1 3167253 . A G 43.60 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=1;HaplotypeScore=18.65;MQ=43.75;MQ0=0;QD=0.56;SB=110.39 GT:AD:DP:GL:GQ 0/1:68,10:69:-28.43,-20.79,-243.20:76.44 +chr1 3167258 . G A 29.42 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=1;HaplotypeScore=29.46;MQ=43.75;MQ0=0;QD=0.38;SB=107.33 GT:AD:DP:GL:GQ 0/1:71,7:70:-27.32,-21.09,-225.20:62.25 +chr1 3167340 rs3002685 A G 235.56 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=44.86;MQ0=0;OQ=812.94;QD=11.29;SB=-432.88 GT:AD:DP:GL:GQ 0/1:35,37:64:-103.87,-19.29,-131.86:99 +chr1 3167551 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=15;HaplotypeScore=12.64;MQ=52.48;MQ0=0;OQ=368.96;QD=5.95;SB=77.28 GT:AD:DP:GL:GQ 0/1:44,18:52:-55.84,-15.67,-137.44:99 +chr1 3168576 . C T 188.74 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=823.49;QD=13.72;SB=-404.84 GT:AD:DP:GL:GQ 0/1:34,26:58:-103.11,-17.48,-109.21:99 +chr1 3169081 . C T 79.34 PASS AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.66;MQ0=0;OQ=1096.77;QD=16.37;SB=-547.56 GT:AD:DP:GL:GQ 0/1:32,35:63:-131.94,-18.98,-108.41:99 +chr1 3169567 rs1501611 G A 10.13 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=8.26;MQ=58.29;MQ0=0;OQ=520.16;QD=12.69;SB=-281.22 GT:AD:DP:GL:GQ 0/1:21,20:36:-66.15,-10.85,-62.40:99 +chr1 3169746 rs2455106 G C 285.96 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1036.68;QD=23.56;SB=-535.79 GT:AD:DP:GL:GQ 0/1:15,29:43:-119.91,-12.96,-65.17:99 +chr1 3170018 rs2455107 T G 277.10 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.50;MQ0=0;OQ=669.75;QD=14.56;SB=-280.87 GT:AD:DP:GL:GQ 0/1:21,25:42:-82.91,-12.65,-66.12:99 +chr1 3170493 rs2455102 A G 356.81 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.62;MQ0=0;OQ=653.73;QD=10.21;SB=-205.32 GT:AD:DP:GL:GQ 0/1:37,27:63:-87.64,-18.99,-144.47:99 +chr1 3170958 . C T 1.10 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=5.86;MQ=59.55;MQ0=0;OQ=1035.67;QD=20.31;SB=-528.11 GT:AD:DP:GL:GQ 0/1:20,31:50:-121.92,-15.07,-64.72:99 +chr1 3171559 rs2500250 T C 389.53 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=559.12;QD=10.55;SB=-252.33 GT:AD:DP:GL:GQ 0/1:30,23:52:-74.86,-15.66,-123.43:99 +chr1 3171782 rs10909913 A G 116.69 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=2.90;MQ=59.63;MQ0=0;OQ=1003.48;QD=15.93;SB=-509.29 GT:AD:DP:GL:GQ 0/1:27,35:61:-122.01,-18.38,-106.15:99 +chr1 3172391 rs2455096 A C 43.29 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=287.98;QD=8.47;SB=-120.97 GT:AD:DP:GL:GQ 0/1:18,16:31:-41.43,-9.34,-63.22:99 +chr1 3172429 rs56042628 C T 96.48 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=280.31;QD=9.34;SB=-80.59 GT:AD:DP:GL:GQ 0/1:19,11:28:-39.76,-8.44,-58.47:99 +chr1 3173020 rs2455094 G A 166.70 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=59.53;MQ0=0;OQ=444.07;QD=11.10;SB=-203.69 GT:AD:DP:GL:GQ 0/1:22,17:34:-57.94,-10.25,-64.34:99 +chr1 3173727 rs2455093 A G 256.03 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=832.24;QD=16.98;SB=-357.94 GT:AD:DP:GL:GQ 0/1:20,29:47:-100.67,-14.16,-75.12:99 +chr1 3174715 rs2455119 G T 285.04 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.49;MQ0=0;OQ=576.42;QD=12.81;SB=-209.45 GT:AD:DP:GL:GQ 0/1:23,22:42:-73.58,-12.65,-77.54:99 +chr1 3176001 . C T 83.35 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.70;MQ0=0;OQ=696.01;QD=13.92;SB=-293.84 GT:AD:DP:GL:GQ 0/1:26,23:46:-86.76,-13.88,-73.45:99 +chr1 3176267 . T G 76.55 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=60.00;MQ0=0;OQ=841.56;QD=14.76;SB=-394.65 GT:AD:DP:GL:GQ 0/1:27,30:56:-104.31,-16.87,-93.27:99 +chr1 3177045 rs3002687 T G 225.19 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.21;MQ=59.59;MQ0=0;OQ=571.62;QD=12.43;SB=-258.88 GT:AD:DP:GL:GQ 0/1:24,22:45:-74.00,-13.56,-84.05:99 +chr1 3177468 . C T 3.04 PASS AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.42;MQ0=0;OQ=538.59;QD=16.83;SB=-100.92 GT:AD:DP:GL:GQ 0/1:14,18:31:-66.48,-9.34,-49.83:99 +chr1 3177939 rs2500308 A G 95.88 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=59.39;MQ0=0;OQ=763.00;QD=10.04;SB=-332.88 GT:AD:DP:GL:GQ 0/1:45,31:71:-100.98,-21.39,-171.46:99 +chr1 3178661 . G A 33.39 PASS AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=60.00;MQ0=0;OQ=796.34;QD=18.96;SB=-401.21 GT:AD:DP:GL:GQ 0/1:18,24:42:-95.58,-12.66,-58.00:99 +chr1 3178998 rs2455127 A G 173.30 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=58.67;MQ0=0;OQ=507.17;QD=14.49;SB=-257.35 GT:AD:DP:GL:GQ 0/1:11,24:30:-63.05,-9.05,-41.23:99 +chr1 3179379 . A G 65.56 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=58.32;MQ0=0;OQ=481.41;QD=12.34;SB=-241.93 GT:AD:DP:GL:GQ 0/1:18,21:37:-62.58,-11.16,-65.22:99 +chr1 3179574 rs2455128 A G 108.65 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.62;MQ0=0;OQ=838.70;QD=13.98;SB=-378.24 GT:AD:DP:GL:GQ 0/1:31,29:59:-104.93,-17.77,-121.27:99 +chr1 3179592 rs2500307 T A 726.45 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2101.50;QD=36.23;SB=-987.86 GT:AD:DP:GL:GQ 1/1:0,58:58:-213.75,-17.47,-0.02:99 +chr1 3182386 rs2500304 T C 246 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.51;MQ0=0;OQ=550.86;QD=11.72;SB=-174.37 GT:AD:DP:GL:GQ 0/1:23,24:45:-71.94,-13.57,-90.75:99 +chr1 3182819 rs2455131 A G 160.52 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=53.72;MQ0=0;OQ=380.67;QD=9.28;SB=-185.58 GT:AD:DP:GL:GQ 0/1:26,15:41:-53.71,-12.35,-99.70:99 +chr1 3183091 . T G 31.12 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.54;MQ=48.96;MQ0=0;QD=0.80;SB=16.16 GT:AD:DP:GL:GQ 0/1:34,5:37:-17.54,-11.14,-116.34:63.95 +chr1 3183092 . C A 30.14 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=9.54;MQ=48.87;MQ0=0;QD=0.74;SB=14.77 GT:AD:DP:GL:GQ 0/1:36,5:37:-17.45,-11.16,-100.79:62.97 +chr1 3183861 rs55923982 G C 139.29 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.45;MQ=57.45;MQ0=0;OQ=542.30;QD=11.79;SB=-148.38 GT:AD:DP:GL:GQ 0/1:27,19:44:-70.78,-13.27,-111.52:99 +chr1 3184193 rs2455115 A G 314.03 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=53.52;MQ0=0;OQ=598.87;QD=12.22;SB=-281.59 GT:AD:DP:GL:GQ 0/1:25,24:48:-77.64,-14.47,-94.87:99 +chr1 3185401 . G T 101.68 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.51;MQ0=0;OQ=440.43;QD=11.59;SB=-233.97 GT:AD:DP:GL:GQ 0/1:19,19:33:-57.27,-9.94,-56.75:99 +chr1 3187015 . G A 77.56 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=59.67;MQ0=0;OQ=971.62;QD=17.05;SB=-421.44 GT:AD:DP:GL:GQ 0/1:28,29:55:-117.01,-16.57,-95.93:99 +chr1 3188693 rs905137 A G 186.40 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.61;MQ0=0;OQ=484.36;QD=10.09;SB=-266.22 GT:AD:DP:GL:GQ 0/1:25,23:44:-64.98,-13.26,-96.26:99 +chr1 3189244 rs905136 A G 4.18 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=4;HaplotypeScore=2.03;MQ=60.00;MQ0=0;OQ=654.87;QD=15.97;SB=-328.31 GT:AD:DP:GL:GQ 0/1:18,23:38:-80.22,-11.45,-60.36:99 +chr1 3189344 rs905135 A C 1.64 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=6.41;MQ=59.54;MQ0=0;OQ=215.02;QD=4.30;SB=-100.13 GT:AD:DP:GL:GQ 0/1:35,15:44:-38.04,-13.26,-114.24:99 +chr1 3189859 rs2500302 T C 241.97 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.92;MQ0=0;OQ=339.74;QD=8.71;SB=-144.67 GT:AD:DP:GL:GQ 0/1:23,16:37:-48.41,-11.15,-86.58:99 +chr1 3190143 rs56004439 G A 2.42 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=8.41;MQ=57.37;MQ0=0;OQ=401.65;QD=8.37;SB=-155.21 GT:AD:DP:GL:GQ 0/1:33,15:46:-57.32,-13.87,-99.82:99 +chr1 3190754 . G A 32.75 PASS AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1225.08;QD=18.85;SB=-426.92 GT:AD:DP:GL:GQ 0/1:29,36:64:-145.07,-19.28,-99.09:99 +chr1 3190930 rs6685398 C A 88.85 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=4.12;MQ=60.00;MQ0=0;OQ=531.21;QD=13.28;SB=-273.35 GT:AD:DP:GL:GQ 0/1:21,19:39:-68.15,-11.75,-68.57:99 +chr1 3190993 rs6690217 A C 128.36 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1454.60;QD=28.52;SB=-648.68 GT:AD:DP:GL:GQ 1/1:0,51:48:-149.09,-14.47,-0.05:99 +chr1 3192051 . C T 11.01 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.25;MQ0=0;OQ=927.90;QD=18.56;SB=-215.90 GT:AD:DP:GL:GQ 0/1:20,30:48:-110.53,-14.46,-70.14:99 +chr1 3192870 rs10797387 A C 142.29 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.89;MQ=59.80;MQ0=0;OQ=775.82;QD=12.93;SB=-322.85 GT:AD:DP:GL:GQ 0/1:30,30:54:-97.13,-16.27,-96.18:99 +chr1 3193262 . A G 27.47 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=435.09;QD=14.04;SB=-158.61 GT:AD:DP:GL:GQ 0/1:13,18:29:-55.53,-8.74,-48.24:99 +chr1 3193691 rs12024838 G C 0.85 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=9.20;MQ=52.13;MQ0=0;OQ=313.95;QD=12.08;SB=-105.65 GT:AD:DP:GL:GQ 0/1:16,10:19:-40.41,-5.73,-35.18:99 +chr1 3193692 rs61759191 C T 0.47 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=9.20;MQ=52.13;MQ0=0;OQ=179.56;QD=6.91;SB=-26.50 GT:AD:DP:GL:GQ 0/1:18,8:19:-26.97,-5.73,-38.66:99 +chr1 3193738 rs10909916 C G 2.42 PASS AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=6.33;MQ=40.46;MQ0=4;OQ=154.87;QD=11.06;SB=-44.90 GT:AD:DP:GL:GQ 0/1:9,5:7:-20.88,-2.11,-8.99:68.77 +chr1 3194086 rs6687930 T C 3.78 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=48.01;MQ0=1;OQ=344.21;QD=18.12;SB=-6.99 GT:AD:DP:GL:GQ 0/1:2,17:14:-41.92,-4.22,-8.13:39.10 +chr1 3194355 rs2134119 C G 59.27 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=4.23;MQ=54.23;MQ0=0;OQ=781.76;QD=15.95;SB=-353.76 GT:AD:DP:GL:GQ 0/1:22,27:44:-94.74,-13.28,-81.77:99 +chr1 3194394 rs2455117 T A 339.54 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.31;MQ0=0;OQ=679.10;QD=15.43;SB=-276.72 GT:AD:DP:GL:GQ 0/1:22,22:42:-83.84,-12.65,-73.08:99 +chr1 3197040 rs2250291 C T 260.09 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.34;MQ0=0;OQ=469.67;QD=13.42;SB=-216.70 GT:AD:DP:GL:GQ 0/1:18,17:34:-60.50,-10.25,-62.96:99 +chr1 3197640 rs55866132 G A 241.93 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=60.00;MQ0=0;OQ=793.46;QD=13.45;SB=-307.77 GT:AD:DP:GL:GQ 0/1:34,25:59:-100.40,-17.77,-123.91:99 +chr1 3197902 rs2500297 C T 238.37 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=60.00;MQ0=0;OQ=756.06;QD=14.00;SB=-170.24 GT:AD:DP:GL:GQ 0/1:30,24:49:-93.65,-14.77,-87.43:99 +chr1 3198235 rs10909918 A G 238.34 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=60.00;MQ0=0;OQ=490.49;QD=8.92;SB=-208.46 GT:AD:DP:GL:GQ 0/1:32,23:51:-67.70,-15.37,-121.94:99 +chr1 3198466 . G A 262.64 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=604.73;QD=12.34;SB=-281.22 GT:AD:DP:GL:GQ 0/1:28,21:46:-77.62,-13.87,-86.11:99 +chr1 3199356 rs2500295 T C 571.16 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.75;MQ0=0;OQ=1482.44;QD=28.51;SB=-763.58 GT:AD:DP:GL:GQ 1/1:0,52:48:-151.88,-14.48,-0.05:99 +chr1 3199491 rs4648376 G A 14.27 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=4.90;MQ=58.90;MQ0=0;OQ=2231.72;QD=37.83;SB=-1015.37 GT:AD:DP:GL:GQ 1/1:0,59:58:-226.79,-17.49,-0.03:99 +chr1 3199627 rs2500294 C T 622.47 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=2326.22;QD=38.77;SB=-1091.37 GT:AD:DP:GL:GQ 1/1:0,60:58:-236.22,-17.47,-0.02:99 +chr1 3199783 rs1553291 A G 564.79 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=1581.83;QD=29.29;SB=-575.98 GT:AD:DP:GL:GQ 1/1:0,54:51:-161.82,-15.38,-0.05:99 +chr1 3200187 . C T 35.88 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.26;MQ=59.60;MQ0=0;OQ=491.30;QD=10.45;SB=-217.71 GT:AD:DP:GL:GQ 0/1:29,18:43:-65.37,-12.96,-91.60:99 +chr1 3200810 rs4648468 A G 447.48 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=1398.57;QD=30.40;SB=-596.06 GT:AD:DP:GL:GQ 1/1:0,46:43:-143.47,-12.96,-0.03:99 +chr1 3201105 rs10047257 C T 220.48 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=596.34;QD=15.29;SB=-318.86 GT:AD:DP:GL:GQ 0/1:20,19:38:-74.37,-11.45,-63.70:99 +chr1 3201318 rs4648377 A C 538.98 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1615.09;QD=33.65;SB=-661.05 GT:AD:DP:GL:GQ 1/1:0,48:47:-165.11,-14.16,-0.02:99 +chr1 3201410 rs4648469 A G 202.17 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1230.36;QD=30.76;SB=-513.23 GT:AD:DP:GL:GQ 1/1:0,39:38:-126.64,-11.45,-0.02:99 +chr1 3201613 rs4648470 C T 79.16 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=1081.89;QD=24.59;SB=-515.59 GT:AD:DP:GL:GQ 0/1:12,32:43:-124.44,-12.96,-36.35:99 +chr1 3202053 rs2500292 A G 471 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1432.25;QD=32.55;SB=-511.16 GT:AD:DP:GL:GQ 1/1:0,44:41:-146.83,-12.35,-0.02:99 +chr1 3202174 rs2500291 C T 728.69 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2429.46;QD=38.56;SB=-1207.61 GT:AD:DP:GL:GQ 1/1:1,62:61:-246.55,-18.37,-0.01:99 +chr1 3202451 rs2500290 G C 18.43 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.98;MQ=58.98;MQ0=0;OQ=1616.44;QD=39.43;SB=-797.54 GT:AD:DP:GL:GQ 1/1:0,41:39:-165.25,-11.76,-0.02:99 +chr1 3202782 rs1875452 C G 157.50 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.36;MQ=59.54;MQ0=0;OQ=2035.33;QD=40.71;SB=-884.21 GT:AD:DP:GL:GQ 1/1:0,50:48:-207.14,-14.47,-0.02:99 +chr1 3202806 rs2500289 A G 260.23 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=59.19;MQ0=0;OQ=1923.10;QD=33.74;SB=-724.29 GT:AD:DP:GL:GQ 1/1:0,57:54:-195.91,-16.27,-0.02:99 +chr1 3203962 rs2500288 T C 186.16 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.58;MQ0=0;OQ=1801.36;QD=32.75;SB=-828.32 GT:AD:DP:GL:GQ 1/1:0,55:51:-183.74,-15.36,-0.02:99 +chr1 3204030 rs7553849 T C 226.01 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=56.20;MQ0=0;OQ=1684.70;QD=29.05;SB=-851.52 GT:AD:DP:GL:GQ 1/1:0,58:53:-172.10,-15.99,-0.05:99 +chr1 3204380 rs10442593 A G 67.15 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=958.98;QD=29.97;SB=-369.57 GT:AD:DP:GL:GQ 1/1:0,32:28:-99.49,-8.43,-0.01:84.24 +chr1 3204592 rs2455144 A G 617.75 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2332.51;QD=29.90;SB=-1027.75 GT:AD:DP:GL:GQ 1/1:0,78:74:-236.91,-22.33,-0.08:99 +chr1 3204835 . G A 53.06 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.06;MQ=60.00;MQ0=0;OQ=892.55;QD=15.13;SB=-296.23 GT:AD:DP:GL:GQ 0/1:30,29:55:-109.11,-16.57,-93.52:99 +chr1 3204852 rs2500287 G T 86 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=60.00;MQ0=0;OQ=2470.97;QD=33.85;SB=-613.02 GT:AD:DP:GL:GQ 1/1:1,71:71:-250.71,-21.39,-0.03:99 +chr1 3205054 . A G 35.05 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.07;MQ=60.00;MQ0=0;OQ=563.88;QD=10.44;SB=-299.62 GT:AD:DP:GL:GQ 0/1:29,25:52:-75.34,-15.67,-118.24:99 +chr1 3205180 rs2455143 A T 124.60 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=58.71;MQ0=0;OQ=2383.23;QD=36.67;SB=-1091.65 GT:AD:DP:GL:GQ 1/1:0,65:64:-241.93,-19.28,-0.02:99 +chr1 3205492 rs2455142 T G 512.17 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.74;MQ0=0;OQ=2083.81;QD=29.77;SB=-759.91 GT:AD:DP:GL:GQ 1/1:0,70:70:-212.03,-21.10,-0.07:99 +chr1 3205734 rs2455141 A C 27.67 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=40.69;MQ0=0;OQ=504.37;QD=19.40;SB=-155.27 GT:AD:DP:GL:GQ 1/1:2,24:21:-57.94,-6.33,-3.92:24.11 +chr1 3205761 rs2455140 T G 0.29 PASS AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=2.39;MQ=22.97;MQ0=1;OQ=235.32;QD=18.10;SB=-39.00 GT:AD:DP:GL:GQ 0/1:2,10:9:-29.50,-2.71,-3.64:9.30 +chr1 3205805 rs12728296 T C 26.83 LowQual AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=13.68;MQ0=0;QD=1.79;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:2:-6.09,-0.60,-0.00:6.01 +chr1 3205846 . G A 232.99 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.36;MQ0=0;OQ=538.85;QD=13.47;SB=-237.77 GT:AD:DP:GL:GQ 0/1:19,21:21:-63.50,-6.33,-16.25:99 +chr1 3206300 rs12036713 A G 35.28 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=14.04;MQ0=4;QD=5.04;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,7:2:-6.94,-0.60,-0.00:6.02 +chr1 3206493 . T G 46.28 PASS AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=17.34;MQ0=4;OQ=70.14;QD=6.38;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,10:3:-10.50,-0.90,-0.00:9.03 +chr1 3206505 . T C 3.40 PASS AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=18.66;MQ0=4;OQ=95.85;QD=6.85;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,9:5:-14.37,-1.51,-4.06:25.51 +chr1 3206506 . A G 5.49 PASS AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=18.66;MQ0=4;OQ=74.94;QD=5.35;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,9:5:-12.29,-1.51,-3.97:24.63 +chr1 3206538 . G A 1.11 PASS AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=18.43;MQ0=3;OQ=73.15;QD=5.23;SB=-10.00 GT:AD:DP:GL:GQ 0/1:7,7:4:-11.80,-1.21,-3.10:18.92 +chr1 3206554 rs56276321 T G 10.51 LowQual AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=19.60;MQ0=3;QD=0.53;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,5:8:-6.70,-2.41,-21.47:42.94 +chr1 3206566 . T C 28.09 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=22.53;MQ0=2;OQ=145.15;QD=6.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,9:12:-21.41,-3.62,-22.84:99 +chr1 3206567 . A G 6.01 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.53;MQ0=2;OQ=85.83;QD=4.09;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,9:11:-15.19,-3.32,-21.71:99 +chr1 3206577 . C T 7.20 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=22.19;MQ0=2;OQ=218.94;QD=10.43;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,11:11:-28.49,-3.31,-13.17:98.62 +chr1 3206588 . A C 10.65 LowQual AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=2.88;MQ=22.98;MQ0=0;QD=0.59;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,6:7:-6.42,-2.11,-14.50:43.09 +chr1 3206599 . G A 2.11 PASS AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=22.00;MQ0=0;OQ=65.71;QD=4.11;SB=-10.00 GT:AD:DP:GL:GQ 0/1:7,9:7:-11.98,-2.12,-8.40:62.78 +chr1 3206700 . A G 0.69 PASS AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.64;MQ0=1;OQ=276.82;QD=18.45;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,14:12:-34.36,-3.62,-3.48:2.36 +chr1 3206761 . A G 22.65 LowQual AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=26.60;MQ0=1;QD=0.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:32,10:32:-15.20,-9.65,-103.92:55.47 +chr1 3206926 rs61759194 A G 113.52 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=2.49;MQ=46.00;MQ0=0;OQ=649.36;QD=10.82;SB=-346.23 GT:AD:DP:GL:GQ 0/1:29,31:46:-82.08,-13.86,-88.11:99 +chr1 3207011 rs2455137 C T 379.46 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=48.62;MQ0=0;OQ=1983.22;QD=35.41;SB=-860.00 GT:AD:DP:GL:GQ 1/1:0,56:50:-201.92,-15.06,-0.01:99 +chr1 3207294 rs2500284 G A 102.13 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=58.88;MQ0=0;OQ=2616.26;QD=39.05;SB=-1335.76 GT:AD:DP:GL:GQ 1/1:1,66:66:-265.23,-19.89,-0.02:99 +chr1 3208189 rs2455136 A T 142.28 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=59.12;MQ0=0;OQ=2529.01;QD=36.65;SB=-1261.52 GT:AD:DP:GL:GQ 1/1:0,69:68:-256.50,-20.48,-0.02:99 +chr1 3208783 rs2500283 G C 612.26 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2831.75;QD=42.91;SB=-1184.48 GT:AD:DP:GL:GQ 1/1:0,66:66:-286.78,-19.89,-0.02:99 +chr1 3209357 rs2500282 A G 594.44 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1981.22;QD=32.48;SB=-526.13 GT:AD:DP:GL:GQ 1/1:0,61:61:-201.75,-18.39,-0.04:99 +chr1 3209761 rs2455135 A G 63.74 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1623.95;QD=30.64;SB=-619.36 GT:AD:DP:GL:GQ 1/1:0,53:46:-165.99,-13.85,-0.01:99 +chr1 3210242 rs2500281 G A 563.38 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.01;MQ0=0;OQ=1613.10;QD=35.07;SB=-716.96 GT:AD:DP:GL:GQ 1/1:0,46:42:-164.91,-12.65,-0.01:99 +chr1 3210275 rs2455134 A G 102.15 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=34.21;MQ0=0;OQ=983.95;QD=25.89;SB=-399.50 GT:AD:DP:GL:GQ 1/1:0,38:28:-101.99,-8.43,-0.01:84.26 +chr1 3210353 rs2455133 C G 65.09 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=35.62;MQ0=2;OQ=1518.72;QD=29.78;SB=-723.73 GT:AD:DP:GL:GQ 1/1:4,47:41:-164.26,-12.36,-8.80:35.57 +chr1 3210943 rs2455132 T C 34.33 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=58.65;MQ0=0;OQ=1292.96;QD=28.73;SB=-546.03 GT:AD:DP:GL:GQ 1/1:1,44:43:-137.07,-12.97,-4.19:87.75 +chr1 3211298 rs56357655 G T 236.14 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=570.69;QD=13.59;SB=-286.33 GT:AD:DP:GL:GQ 0/1:20,22:39:-72.10,-11.75,-66.92:99 +chr1 3211481 rs4648378 A T 264.07 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1968.99;QD=35.80;SB=-994.60 GT:AD:DP:GL:GQ 1/1:0,55:54:-200.50,-16.27,-0.02:99 +chr1 3212566 rs3923081 A G 604.08 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1445.27;QD=30.75;SB=-602.58 GT:AD:DP:GL:GQ 1/1:0,47:46:-148.15,-13.87,-0.04:99 +chr1 3213090 rs4648471 A G 181.27 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=58.96;MQ0=0;OQ=1176.67;QD=14.53;SB=-570.90 GT:AD:DP:GL:GQ 0/1:40,41:78:-144.45,-23.50,-149.52:99 +chr1 3213140 rs4233025 C T 288.86 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.52;MQ0=0;OQ=3371.29;QD=38.75;SB=-1393.36 GT:AD:DP:GL:GQ 1/1:0,86:84:-336.13,-25.31,-0.03:99 +chr1 3213393 rs4648472 G A 290.65 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=58.95;MQ0=0;OQ=2168.73;QD=34.98;SB=-915.32 GT:AD:DP:GL:GQ 1/1:0,61:56:-220.48,-16.87,-0.02:99 +chr1 3213624 rs4648473 A G 299.83 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=60.00;MQ0=0;OQ=2351.35;QD=35.09;SB=-1180.73 GT:AD:DP:GL:GQ 1/1:0,67:67:-238.75,-20.18,-0.03:99 +chr1 3213815 rs4145901 A G 578.32 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=1913.13;QD=34.78;SB=-765.19 GT:AD:DP:GL:GQ 1/1:0,55:55:-194.92,-16.57,-0.02:99 +chr1 3214070 rs4145900 C T 633.07 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.20;MQ0=0;OQ=2312.37;QD=39.87;SB=-883.19 GT:AD:DP:GL:GQ 1/1:0,58:58:-234.84,-17.47,-0.01:99 +chr1 3214663 rs2483258 A G 141.81 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.74;MQ=58.20;MQ0=0;OQ=1545.60;QD=32.89;SB=-781.14 GT:AD:DP:GL:GQ 1/1:0,47:45:-158.16,-13.56,-0.02:99 +chr1 3215654 rs2500279 A G 10.26 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1630.84;QD=29.65;SB=-792.65 GT:AD:DP:GL:GQ 1/1:0,55:51:-166.71,-15.38,-0.04:99 +chr1 3215800 rs2500278 C T 196.13 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.49;MQ=60.00;MQ0=0;OQ=2097.43;QD=35.55;SB=-1034.29 GT:AD:DP:GL:GQ 1/1:1,57:55:-213.35,-16.58,-0.03:99 +chr1 3216399 rs59127130 T A 71.30 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=3.18;MQ=59.01;MQ0=0;OQ=500.47;QD=10.65;SB=-267.66 GT:AD:DP:GL:GQ 0/1:27,19:45:-66.90,-13.56,-91.26:99 +chr1 3218505 . G T 13.88 PASS AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.49;MQ=59.42;MQ0=0;OQ=562.03;QD=14.05;SB=-143.82 GT:AD:DP:GL:GQ 0/1:17,23:34:-69.73,-10.24,-51.47:99 +chr1 3223491 rs2500277 T C 605.12 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=1039.56;QD=14.85;SB=-437.57 GT:AD:DP:GL:GQ 0/1:34,36:70:-128.33,-21.09,-137.20:99 +chr1 3227069 rs2500274 G A 733.97 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2547.84;QD=38.03;SB=-1230.64 GT:AD:DP:GL:GQ 1/1:0,67:65:-258.39,-19.58,-0.02:99 +chr1 3231689 rs2500271 A G 65.84 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=6.09;MQ=58.05;MQ0=0;OQ=618.77;QD=12.89;SB=-326.13 GT:AD:DP:GL:GQ 0/1:22,25:43:-80.91,-15.74,-76.88:99 +chr1 3232314 rs2500270 C T 276.80 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=58.93;MQ0=0;OQ=890.12;QD=13.69;SB=-466.96 GT:AD:DP:GL:GQ 0/1:37,28:63:-111.27,-18.97,-132.21:99 +chr1 3232391 rs7521865 T C 80.12 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.46;MQ0=0;OQ=581.07;QD=12.11;SB=-302.66 GT:AD:DP:GL:GQ 0/1:25,23:45:-74.95,-13.56,-94.63:99 +chr1 3232424 rs11576578 C T 337.83 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=583.63;QD=16.21;SB=-245.53 GT:AD:DP:GL:GQ 0/1:18,18:35:-72.19,-10.55,-57.05:99 +chr1 3232513 rs2500268 C T 2.29 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.10;MQ0=0;OQ=81.92;QD=2.64;SB=-51.23 GT:AD:DP:GL:GQ 0/1:26,5:28:-19.91,-8.44,-80.68:99 +chr1 3232545 rs7550743 G C 135.04 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=204.00;QD=6.18;SB=-89.25 GT:AD:DP:GL:GQ 0/1:25,8:26:-31.53,-7.85,-72.48:99 +chr1 3233210 rs2483268 C T 55.97 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.45;MQ0=0;OQ=685.34;QD=20.16;SB=-292.33 GT:AD:DP:GL:GQ 0/1:13,21:31:-81.16,-9.34,-34.58:99 +chr1 3233282 rs2483269 C T 150.37 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.51;MQ0=0;OQ=931.05;QD=19.81;SB=-450.84 GT:AD:DP:GL:GQ 0/1:20,27:46:-110.24,-13.86,-67.60:99 +chr1 3234117 rs2483270 T C 92.91 PASS AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=54.48;MQ0=0;OQ=186.80;QD=8.90;SB=-89.99 GT:AD:DP:GL:GQ 0/1:13,8:21:-28.30,-6.33,-49.94:99 +chr1 3235659 rs56368529 T G 3.22 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=4.81;MQ=58.01;MQ0=0;OQ=299.04;QD=9.06;SB=-59.90 GT:AD:DP:GL:GQ 0/1:16,17:27:-41.32,-8.14,-54.29:99 +chr1 3236031 rs55929121 A G 111.89 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=59.44;MQ0=0;OQ=382.21;QD=9.32;SB=-138.40 GT:AD:DP:GL:GQ 0/1:24,17:41:-53.86,-12.36,-96.85:99 +chr1 3237249 rs2483272 T C 227.71 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.89;MQ0=0;OQ=695.19;QD=16.55;SB=-364.39 GT:AD:DP:GL:GQ 0/1:17,25:40:-84.86,-12.05,-61.97:99 +chr1 3237696 rs11577229 A C 60.92 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=59.46;MQ0=0;OQ=605.90;QD=14.09;SB=-151.87 GT:AD:DP:GL:GQ 0/1:20,23:42:-76.53,-12.66,-70.16:99 +chr1 3237725 rs2483273 C T 273.62 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=458.56;QD=11.46;SB=-253.26 GT:AD:DP:GL:GQ 0/1:23,17:37:-60.29,-11.15,-74.02:99 +chr1 3237958 rs2483274 A G 334.60 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=489.91;QD=10.42;SB=-162.48 GT:AD:DP:GL:GQ 0/1:24,23:45:-65.84,-13.57,-92.79:99 +chr1 3238582 rs56033677 T C 21.15 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.43;MQ0=0;OQ=296.91;QD=9.00;SB=-160.33 GT:AD:DP:GL:GQ 0/1:18,15:30:-42.02,-9.04,-67.71:99 +chr1 3238892 rs55807399 G T 41.07 PASS AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=58.83;MQ0=0;OQ=103.10;QD=6.44;SB=-69.87 GT:AD:DP:GL:GQ 0/1:10,6:13:-17.51,-3.92,-27.55:99 +chr1 3239158 . C T 1.04 PASS AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.48;MQ0=0;OQ=666.04;QD=18.50;SB=-35.64 GT:AD:DP:GL:GQ 0/1:16,20:35:-80.44,-10.55,-47.82:99 +chr1 3239323 . G A 79.22 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=885.68;QD=16.10;SB=-289.76 GT:AD:DP:GL:GQ 0/1:28,27:52:-107.52,-15.67,-84.40:99 +chr1 3240283 rs1889121 A G 183.83 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=58.44;MQ0=0;OQ=423.56;QD=10.86;SB=-163.96 GT:AD:DP:GL:GQ 0/1:18,20:36:-60.24,-14.60,-67.49:99 +chr1 3241019 rs1110307 T C 317.91 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.03;MQ0=0;OQ=790.39;QD=11.80;SB=-362.96 GT:AD:DP:GL:GQ 0/1:34,33:66:-102.22,-19.90,-132.82:99 +chr1 3241835 rs4648477 G A 340.85 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.63;MQ0=0;OQ=880.63;QD=17.27;SB=-457.99 GT:AD:DP:GL:GQ 0/1:24,27:48:-105.81,-14.46,-75.34:99 +chr1 3241867 rs4648478 C T 165.67 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.81;MQ=58.72;MQ0=0;OQ=927.39;QD=18.18;SB=-291.79 GT:AD:DP:GL:GQ 0/1:22,29:49:-110.80,-14.77,-66.95:99 +chr1 3241964 rs2483278 C T 199.87 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=4.49;MQ=58.47;MQ0=0;OQ=815.99;QD=11.33;SB=-270.80 GT:AD:DP:GL:GQ 0/1:44,28:65:-104.47,-19.59,-130.43:99 +chr1 3242641 rs10797388 C T 87.31 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.66;MQ0=0;OQ=1468.23;QD=21.91;SB=-716.28 GT:AD:DP:GL:GQ 0/1:24,43:63:-169.09,-18.98,-69.99:99 +chr1 3243022 rs4648479 C G 270.01 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.32;MQ0=0;OQ=1259.62;QD=18.52;SB=-604.54 GT:AD:DP:GL:GQ 0/1:33,35:68:-149.74,-20.49,-145.47:99 +chr1 3243475 rs2500264 A G 371.99 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=57.70;MQ0=0;OQ=965.24;QD=13.04;SB=-435.59 GT:AD:DP:GL:GQ 0/1:35,39:72:-121.52,-21.71,-132.46:99 +chr1 3243538 rs2500263 C T 449.25 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=59.43;MQ0=0;OQ=1163.15;QD=14.36;SB=-551.30 GT:AD:DP:GL:GQ 0/1:44,37:79:-143.40,-23.80,-157.59:99 +chr1 3243563 rs10909933 A T 21.76 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=5.38;MQ=58.82;MQ0=0;OQ=1256.33;QD=15.90;SB=-624.35 GT:AD:DP:GL:GQ 0/1:39,40:77:-152.11,-23.19,-142.90:99 +chr1 3243699 rs7516137 C G 384.73 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.95;MQ0=1;OQ=1414.58;QD=19.38;SB=-612.10 GT:AD:DP:GL:GQ 0/1:31,42:71:-166.15,-21.41,-133.01:99 +chr1 3243749 rs7516150 C T 110.03 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.27;MQ=59.28;MQ0=0;OQ=1059.88;QD=16.56;SB=-511.08 GT:AD:DP:GL:GQ 0/1:31,33:63:-128.25,-18.98,-110.55:99 +chr1 3243801 rs7552331 G A 50.88 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=3.37;MQ=59.68;MQ0=0;OQ=1395.05;QD=19.38;SB=-586.45 GT:AD:DP:GL:GQ 0/1:31,41:71:-164.18,-21.39,-100.20:99 +chr1 3244201 rs1572038 G A 223.38 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=60.00;MQ0=0;OQ=849.89;QD=14.40;SB=-320.28 GT:AD:DP:GL:GQ 0/1:33,26:58:-105.75,-17.48,-105.23:99 +chr1 3244229 rs1572037 T C 103.02 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=1.14;MQ=59.74;MQ0=0;OQ=759.65;QD=10.70;SB=-211.19 GT:AD:DP:GL:GQ 0/1:40,31:70:-100.34,-21.09,-160.53:99 +chr1 3245634 . G A 2.67 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=5.38;MQ=59.21;MQ0=0;OQ=768.53;QD=14.50;SB=-362.88 GT:AD:DP:GL:GQ 0/1:27,25:49:-94.91,-14.77,-78.82:99 +chr1 3245968 rs1999527 C A 270.72 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.55;MQ0=0;OQ=832.76;QD=16.33;SB=-309.70 GT:AD:DP:GL:GQ 0/1:20,31:46:-100.42,-13.86,-57.62:99 +chr1 3246110 rs1999526 G A 145.25 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.11;MQ=60.00;MQ0=0;OQ=722.36;QD=13.89;SB=-206.02 GT:AD:DP:GL:GQ 0/1:25,26:46:-91.77,-16.25,-79.35:99 +chr1 3247225 rs944819 T G 210.34 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=59.73;MQ0=0;OQ=1004.82;QD=11.68;SB=-427.67 GT:AD:DP:GL:GQ 0/1:50,36:86:-129.67,-25.90,-183.72:99 +chr1 3247599 rs2483281 C T 240.23 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=58.98;MQ0=0;OQ=504.82;QD=12.31;SB=-180.16 GT:AD:DP:GL:GQ 0/1:24,17:38:-65.21,-11.45,-77.36:99 +chr1 3251376 rs4648379 C T 354.38 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=59.76;MQ0=0;OQ=1302.21;QD=16.91;SB=-654.31 GT:AD:DP:GL:GQ 0/1:37,40:76:-156.40,-22.89,-133.27:99 +chr1 3251542 rs4415513 C T 583.60 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1033.27;QD=16.67;SB=-449.45 GT:AD:DP:GL:GQ 0/1:31,31:61:-125.00,-18.39,-98.88:99 +chr1 3252129 rs12564920 A G 258.43 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.38;MQ0=0;OQ=448.15;QD=9.96;SB=-222.39 GT:AD:DP:GL:GQ 0/1:23,22:39:-59.86,-11.76,-74.90:99 +chr1 3253722 . G A 5.82 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=951.14;QD=18.65;SB=-376.90 GT:AD:DP:GL:GQ 0/1:22,29:50:-113.46,-15.06,-78.22:99 +chr1 3254050 rs2483289 A C 189.02 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=800.56;QD=13.80;SB=-367.58 GT:AD:DP:GL:GQ 0/1:28,30:55:-99.91,-16.57,-92.54:99 +chr1 3254157 rs2500257 A G 11.73 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=3.42;MQ=59.13;MQ0=0;OQ=570.29;QD=13.26;SB=-176.97 GT:AD:DP:GL:GQ 0/1:21,22:40:-72.37,-12.05,-79.78:99 +chr1 3257948 . G C 98.91 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=35.14;MQ0=0;QD=7.07;SB=14.07 GT:AD:DP:GL:GQ 0/1:10,4:12:-16.79,-3.62,-31.08:99 +chr1 3257994 rs60920916 T C 0.33 PASS AC=1;AF=0.50;AN=2;DB;DP=17;Dels=0.00;HRun=2;HaplotypeScore=2.63;MQ=42.15;MQ0=0;OQ=77.87;QD=4.58;SB=20.08 GT:AD:DP:GL:GQ 0/1:13,4:15:-15.59,-4.52,-39.62:99 +chr1 3258005 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=3;HaplotypeScore=6.10;MQ=42.12;MQ0=0;OQ=65.85;QD=3.29;SB=23.09 GT:AD:DP:GL:GQ 0/1:16,4:17:-15.00,-5.13,-47.65:98.69 +chr1 3258920 . C T 2.85 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=553.46;QD=12.87;SB=-213.92 GT:AD:DP:GL:GQ 0/1:24,19:40:-70.69,-12.06,-71.24:99 +chr1 3262401 rs7550526 G A 60.02 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=58.89;MQ0=0;OQ=1567.02;QD=37.31;SB=-629.85 GT:AD:DP:GL:GQ 1/1:0,42:40:-160.30,-12.05,-0.01:99 +chr1 3262685 rs946759 C A 62.68 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=57.75;MQ0=0;OQ=630.41;QD=19.70;SB=-314.39 GT:AD:DP:GL:GQ 1/1:3,29:21:-69.14,-6.33,-2.51:38.17 +chr1 3262923 rs946758 G A 287.49 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=59.58;MQ0=0;OQ=2113.36;QD=38.42;SB=-1046.71 GT:AD:DP:GL:GQ 1/1:0,55:53:-214.93,-15.96,-0.01:99 +chr1 3263976 rs55805251 C T 94.04 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=58.59;MQ0=0;OQ=518.72;QD=15.72;SB=-142.59 GT:AD:DP:GL:GQ 0/1:15,18:30:-64.20,-9.04,-43.17:99 +chr1 3264566 rs2483265 T C 43.57 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=868.82;QD=26.33;SB=-460.17 GT:AD:DP:GL:GQ 1/1:0,33:29:-90.50,-8.75,-0.03:87.17 +chr1 3265009 rs12748963 C T 26.51 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=5.21;MQ=58.97;MQ0=0;OQ=826.30;QD=18.36;SB=-347.35 GT:AD:DP:GL:GQ 0/1:19,25:43:-98.87,-12.96,-59.86:99 +chr1 3266234 rs12073172 G A 592.78 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=1102.37;QD=35.56;SB=-562.26 GT:AD:DP:GL:GQ 1/1:0,31:30:-113.84,-9.05,-0.02:90.27 +chr1 3266600 rs2500280 G C 2.70 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=8.93;MQ=59.31;MQ0=0;OQ=2375.28;QD=38.94;SB=-992.26 GT:AD:DP:GL:GQ 1/1:0,60:56:-241.13,-16.87,-0.02:99 +chr1 3266936 . G A 52.38 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.54;MQ=59.62;MQ0=0;OQ=518.77;QD=10.59;SB=-162.22 GT:AD:DP:GL:GQ 0/1:32,17:48:-69.63,-14.47,-101.23:99 +chr1 3267606 rs884308 C T 94.95 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1579.42;QD=39.49;SB=-771.63 GT:AD:DP:GL:GQ 1/1:0,40:40:-161.54,-12.05,-0.01:99 +chr1 3268390 rs11583116 G A 130.53 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=58.33;MQ0=0;OQ=690.56;QD=13.81;SB=-242.25 GT:AD:DP:GL:GQ 0/1:26,24:43:-85.30,-12.96,-65.77:99 +chr1 3269184 rs7524171 A G 11.38 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=5.01;MQ=59.60;MQ0=0;OQ=1781.26;QD=30.71;SB=-880.26 GT:AD:DP:GL:GQ 1/1:0,58:53:-181.75,-15.98,-0.04:99 +chr1 3269881 rs2500262 T C 201.27 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.11;MQ0=0;OQ=1534.16;QD=29.50;SB=-546.01 GT:AD:DP:GL:GQ 1/1:0,52:49:-157.05,-14.78,-0.05:99 +chr1 3271322 . C T 58.72 PASS AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=59.40;MQ0=0;OQ=375.26;QD=12.11;SB=-208.89 GT:AD:DP:GL:GQ 0/1:17,14:28:-49.26,-8.45,-45.56:99 +chr1 3273388 rs4648485 G A 602.36 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2075.89;QD=37.74;SB=-912.72 GT:AD:DP:GL:GQ 1/1:0,55:53:-211.19,-15.97,-0.02:99 +chr1 3275010 rs4648486 C T 123.41 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=58.75;MQ0=0;OQ=2039.90;QD=39.23;SB=-914.69 GT:AD:DP:GL:GQ 1/1:0,52:51:-207.59,-15.36,-0.01:99 +chr1 3275164 rs4648487 T C 21.75 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=5.20;MQ=59.14;MQ0=0;OQ=1843.56;QD=34.14;SB=-799.67 GT:AD:DP:GL:GQ 1/1:0,54:53:-187.96,-15.97,-0.02:99 +chr1 3275488 rs6424073 G A 234.48 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2488.63;QD=39.50;SB=-1214.11 GT:AD:DP:GL:GQ 1/1:0,63:63:-252.47,-18.98,-0.02:99 +chr1 3277411 rs12138292 A G 1.83 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.96;MQ=56.17;MQ0=0;OQ=1416.27;QD=24.85;SB=-414.15 GT:AD:DP:GL:GQ 1/1:0,57:48:-145.28,-14.50,-0.07:99 +chr1 3279384 rs12135987 G A 273.93 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.39;MQ0=0;OQ=2572.74;QD=37.83;SB=-927.33 GT:AD:DP:GL:GQ 1/1:0,68:65:-260.88,-19.58,-0.02:99 +chr1 3279467 rs6688949 T C 3.82 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=57.66;MQ0=0;OQ=1297.10;QD=25.94;SB=-450.26 GT:AD:DP:GL:GQ 1/1:0,50:40:-133.33,-12.06,-0.03:99 +chr1 3279589 rs1333190 C T 668.27 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1807.78;QD=36.89;SB=-784.69 GT:AD:DP:GL:GQ 1/1:0,49:46:-184.37,-13.86,-0.01:99 +chr1 3279831 rs1333189 C T 229.74 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.13;MQ0=0;OQ=1483.34;QD=36.18;SB=-765.52 GT:AD:DP:GL:GQ 1/1:0,40:38:-151.93,-11.45,-0.01:99 +chr1 3280999 rs2249860 A C 81.57 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=57.93;MQ0=0;OQ=1454.60;QD=33.83;SB=-752.07 GT:AD:DP:GL:GQ 1/1:0,43:42:-149.06,-12.65,-0.01:99 +chr1 3281067 rs2368593 G T 64.28 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.86;MQ=58.09;MQ0=0;OQ=2257.03;QD=31.79;SB=-1064.90 GT:AD:DP:GL:GQ 1/1:0,70:66:-229.32,-19.89,-0.04:99 +chr1 3281249 . G A 160.30 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.53;MQ0=0;OQ=717.46;QD=13.54;SB=-318.84 GT:AD:DP:GL:GQ 0/1:27,26:46:-88.90,-13.87,-75.19:99 +chr1 3282736 rs4648488 C T 347.36 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.52;MQ0=0;OQ=841.46;QD=17.53;SB=-434.81 GT:AD:DP:GL:GQ 0/1:21,27:46:-101.29,-13.86,-70.83:99 +chr1 3283525 rs4648489 A G 474.54 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1662.64;QD=30.23;SB=-834.46 GT:AD:DP:GL:GQ 1/1:0,55:53:-169.90,-15.99,-0.06:99 +chr1 3284832 rs1538693 G A 695.45 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1980.96;QD=38.10;SB=-939.35 GT:AD:DP:GL:GQ 1/1:0,52:51:-201.70,-15.37,-0.02:99 +chr1 3285724 . G A 0.22 PASS AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=1;HaplotypeScore=6.56;MQ=21.51;MQ0=1;OQ=72.03;QD=9.00;SB=-40.54 GT:AD:DP:GL:GQ 0/1:2,5:4:-11.69,-1.21,-3.37:21.64 +chr1 3285990 . G A 25.35 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=5.35;MQ=15.41;MQ0=12;QD=0.85;SB=-32.52 GT:AD:DP:GL:GQ 0/1:21,9:5:-7.32,-1.51,-9.51:58.18 +chr1 3286144 . A G 36.06 LowQual AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=14.48;MQ0=3;QD=4.51;SB=-6.99 GT:AD:DP:GL:GQ 0/1:4,3:3:-7.79,-0.90,-4.06:31.52 +chr1 3286152 . A C 0.09 PASS AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=27.22;MQ0=3;OQ=114.38;QD=16.34;SB=-46.01 GT:AD:DP:GL:GQ 1/1:0,7:4:-14.97,-1.20,-0.00:12.04 +chr1 3286284 . G A 36.93 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=3.77;MQ=31.49;MQ0=4;QD=1.27;SB=-29.53 GT:AD:DP:GL:GQ 0/1:22,7:15:-11.50,-4.52,-41.17:69.76 +chr1 3286312 . G A 19.94 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=9.31;MQ=28.36;MQ0=5;QD=0.59;SB=-24.50 GT:AD:DP:GL:GQ 0/1:27,6:17:-10.40,-5.13,-47.64:52.73 +chr1 3286320 . C A 227.39 HARD_TO_VALIDATE;Indel AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=8.75;MQ=31.04;MQ0=4;QD=5.98;SB=-25.91 GT:AD:DP:GL:GQ 0/1:27,11:20:-32.05,-6.03,-35.21:99 +chr1 3286354 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=1;HaplotypeScore=6.21;MQ=33.14;MQ0=5;OQ=87.60;QD=2.92;SB=-62.36 GT:AD:DP:GL:GQ 0/1:22,7:14:-19.10,-7.05,-34.67:99 +chr1 3286558 rs61043152 G A 1.11 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=54.01;MQ0=1;OQ=487.76;QD=11.09;SB=-75.56 GT:AD:DP:GL:GQ 0/1:23,21:40:-64.12,-12.06,-79.70:99 +chr1 3286811 . T C 44.59 PASS AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=60.00;MQ0=0;OQ=1964.33;QD=34.46;SB=-944.38 GT:AD:DP:GL:GQ 1/1:0,57:56:-200.04,-16.87,-0.02:99 +chr1 3287141 rs11584942 G A 391.20 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.82;MQ0=0;OQ=780.63;QD=15.31;SB=-324.32 GT:AD:DP:GL:GQ 0/1:25,26:47:-95.51,-14.16,-75.83:99 +chr1 3287246 rs11584967 G A 573.67 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=877.40;QD=15.67;SB=-384.91 GT:AD:DP:GL:GQ 0/1:28,28:54:-107.29,-16.27,-98.41:99 +chr1 3287659 rs4648490 A C 117.52 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=58.26;MQ0=0;OQ=1692.37;QD=33.18;SB=-840.06 GT:AD:DP:GL:GQ 1/1:0,51:50:-172.85,-15.06,-0.02:99 +chr1 3290667 rs868688 C T 279.51 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=58.44;MQ0=0;OQ=2018.08;QD=35.40;SB=-933.25 GT:AD:DP:GL:GQ 1/1:0,57:52:-205.41,-15.67,-0.02:99 +chr1 3290990 rs868689 T G 679.66 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1815.91;QD=31.86;SB=-898.65 GT:AD:DP:GL:GQ 1/1:0,57:52:-185.19,-15.66,-0.02:99 +chr1 3292591 rs11810266 C G 73.61 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.54;MQ0=0;OQ=822.36;QD=20.06;SB=-350.43 GT:AD:DP:GL:GQ 0/1:18,23:40:-97.58,-12.06,-74.61:99 +chr1 3293306 rs2245703 T C 622.87 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2385.34;QD=35.60;SB=-962.70 GT:AD:DP:GL:GQ 1/1:0,67:67:-242.14,-20.18,-0.02:99 +chr1 3293627 rs6676024 C T 186.96 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.97;MQ0=0;OQ=1016.67;QD=17.23;SB=-303.79 GT:AD:DP:GL:GQ 0/1:29,30:58:-122.43,-17.48,-92.51:99 +chr1 3293798 rs2065525 C G 62.72 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=58.34;MQ0=0;OQ=2298.73;QD=40.33;SB=-651.91 GT:AD:DP:GL:GQ 1/1:0,56:54:-233.47,-16.27,-0.01:99 +chr1 3294876 rs17399998 C T 445.68 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1142.20;QD=15.23;SB=-563.39 GT:AD:DP:GL:GQ 0/1:40,35:73:-139.51,-22.00,-126.39:99 +chr1 3295312 rs6687463 A G 1.44 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=5.24;MQ=59.03;MQ0=0;OQ=1175.21;QD=27.33;SB=-477.09 GT:AD:DP:GL:GQ 1/1:0,42:38:-121.14,-11.46,-0.04:99 +chr1 3295326 . C A 16.33 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=58.87;MQ0=0;OQ=469.13;QD=12.68;SB=-130.80 GT:AD:DP:GL:GQ 0/1:19,18:34:-60.44,-10.25,-57.03:99 +chr1 3295820 . C T 40.94 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=844.76;QD=17.60;SB=-369.85 GT:AD:DP:GL:GQ 0/1:21,27:46:-101.62,-13.86,-70.72:99 +chr1 3296384 rs6686140 C A 6.91 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=6.50;MQ=59.17;MQ0=0;OQ=324.87;QD=11.60;SB=-121.49 GT:AD:DP:GL:GQ 0/1:8,20:20:-41.81,-6.04,-18.74:99 +chr1 3296715 rs2151350 T G 0.13 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=4;HaplotypeScore=2.18;MQ=58.99;MQ0=0;OQ=1168.63;QD=25.41;SB=-611.86 GT:AD:DP:GL:GQ 1/1:0,46:39:-120.49,-11.76,-0.04:99 +chr1 3297308 rs2493281 A G 8.42 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.21;MQ=58.18;MQ0=1;OQ=1041.73;QD=26.04;SB=-499.54 GT:AD:DP:GL:GQ 1/1:1,39:33:-107.79,-9.95,-0.03:99 +chr1 3297606 rs2493278 T C 732.40 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.88;MQ0=0;OQ=2573.66;QD=35.26;SB=-1043.85 GT:AD:DP:GL:GQ 1/1:0,73:73:-260.97,-21.99,-0.02:99 +chr1 3298358 rs2493268 T C 154.09 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.44;MQ=58.22;MQ0=0;OQ=1688.23;QD=33.76;SB=-851.05 GT:AD:DP:GL:GQ 1/1:0,50:48:-172.42,-14.46,-0.02:99 +chr1 3298817 rs12139767 G C 583.17 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=898.96;QD=13.62;SB=-383.19 GT:AD:DP:GL:GQ 0/1:39,27:65:-112.80,-19.62,-153.47:99 +chr1 3299326 rs35864014 G A 497.53 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1037.02;QD=15.25;SB=-535.48 GT:AD:DP:GL:GQ 0/1:36,32:68:-127.47,-20.48,-131.88:99 +chr1 3301121 rs6702992 C T 313.10 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.53;MQ0=0;OQ=194.21;QD=10.22;SB=-113.94 GT:AD:DP:GL:GQ 0/1:12,7:19:-28.43,-5.72,-42.63:99 +chr1 3301284 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=11;HaplotypeScore=19.15;MQ=56.72;MQ0=0;OQ=88.35;QD=1.38;SB=59.21 GT:AD:DP:GL:GQ 0/1:53,11:56:-28.99,-16.87,-158.63:99 +chr1 3301891 rs883678 C G 91.33 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.56;MQ0=0;OQ=812.38;QD=19.34;SB=-299.58 GT:AD:DP:GL:GQ 0/1:20,22:42:-97.18,-12.66,-83.21:99 +chr1 3302116 rs17822575 T G 316.41 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.54;MQ0=0;OQ=510.49;QD=12.45;SB=-250.83 GT:AD:DP:GL:GQ 0/1:20,21:40:-66.39,-12.05,-67.05:99 +chr1 3302296 rs10909937 C T 502.18 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1321.67;QD=36.71;SB=-625.01 GT:AD:DP:GL:GQ 1/1:0,36:34:-135.76,-10.24,-0.01:99 +chr1 3302524 rs56378103 C T 103.94 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=58.71;MQ0=0;OQ=1572.33;QD=29.12;SB=-689.92 GT:AD:DP:GL:GQ 1/1:0,52:42:-160.84,-12.66,-0.02:99 +chr1 3302527 . C T 6.09 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=5.35;MQ=58.33;MQ0=0;OQ=1011.78;QD=18.07;SB=-471.49 GT:AD:DP:GL:GQ 0/1:25,31:52:-120.14,-15.67,-71.42:99 +chr1 3302823 rs12726710 C T 452.04 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=952.26;QD=17.31;SB=-305.83 GT:AD:DP:GL:GQ 0/1:25,30:55:-115.09,-16.58,-80.89:99 +chr1 3303142 rs7535965 G A 141.77 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.64;MQ0=0;OQ=1848.10;QD=38.50;SB=-836.62 GT:AD:DP:GL:GQ 1/1:0,48:47:-188.41,-14.16,-0.02:99 +chr1 3304456 rs17822581 A G 359.73 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=58.93;MQ0=0;OQ=1113.18;QD=17.13;SB=-574.04 GT:AD:DP:GL:GQ 0/1:27,38:62:-133.28,-18.68,-95.39:99 +chr1 3304922 rs57432749 C T 181.83 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=2.15;MQ=59.75;MQ0=0;OQ=993.31;QD=13.07;SB=-496.07 GT:AD:DP:GL:GQ 0/1:41,34:74:-127.49,-24.88,-150.46:99 +chr1 3305219 rs12144338 C T 131.32 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.67;MQ0=0;OQ=987.68;QD=17.33;SB=-284.79 GT:AD:DP:GL:GQ 0/1:26,31:53:-118.03,-15.98,-72.20:99 +chr1 3305551 . G A 103.37 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.39;MQ0=0;OQ=1099.92;QD=15.94;SB=-511.04 GT:AD:DP:GL:GQ 0/1:36,33:68:-133.77,-20.49,-112.10:99 +chr1 3305678 rs7542793 G A 440.42 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.35;MQ0=0;OQ=1064.35;QD=16.63;SB=-455.47 GT:AD:DP:GL:GQ 0/1:30,34:62:-128.41,-18.69,-93.40:99 +chr1 3305692 rs12737284 G A 493.84 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=901.95;QD=14.79;SB=-398.19 GT:AD:DP:GL:GQ 0/1:31,30:59:-111.27,-17.79,-96.32:99 +chr1 3305845 rs12117228 T C 284.95 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=60.00;MQ0=0;OQ=892.28;QD=11.74;SB=-260.21 GT:AD:DP:GL:GQ 0/1:38,38:73:-114.51,-22.00,-150.21:99 +chr1 3305873 rs7551733 C G 174.37 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.43;MQ=60.00;MQ0=0;OQ=1089.18;QD=17.02;SB=-530.69 GT:AD:DP:GL:GQ 0/1:32,32:62:-130.89,-18.69,-134.52:99 +chr1 3306535 rs10909939 T C 528.42 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=956.73;QD=17.08;SB=-375.64 GT:AD:DP:GL:GQ 0/1:23,33:55:-115.53,-16.57,-90.24:99 +chr1 3306616 rs10909940 G A 39.73 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=1181.64;QD=23.63;SB=-497.15 GT:AD:DP:GL:GQ 0/1:15,35:49:-136.22,-14.77,-45.61:99 +chr1 3306995 rs12743248 G A 92.64 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.54;MQ0=0;OQ=921.67;QD=15.36;SB=-465.48 GT:AD:DP:GL:GQ 0/1:29,31:55:-112.03,-16.58,-86.62:99 +chr1 3307093 rs12747145 G A 172.06 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.50;MQ0=0;OQ=526.33;QD=14.23;SB=-229.52 GT:AD:DP:GL:GQ 0/1:18,17:34:-69.44,-13.52,-51.06:99 +chr1 3307640 rs6424074 A G 354.64 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.52;MQ0=0;OQ=483.77;QD=10.08;SB=-196.29 GT:AD:DP:GL:GQ 0/1:28,20:48:-66.12,-14.46,-114.20:99 +chr1 3307747 rs6424075 G T 374.77 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.24;MQ0=0;OQ=884.55;QD=14.04;SB=-359.35 GT:AD:DP:GL:GQ 0/1:31,32:59:-109.52,-17.78,-88.61:99 +chr1 3308193 rs7551796 G A 363.24 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.69;MQ0=0;OQ=1293.28;QD=17.24;SB=-465.48 GT:AD:DP:GL:GQ 0/1:35,40:71:-154.00,-21.39,-119.84:99 +chr1 3308294 rs11576794 C T 278.53 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=57.73;MQ0=0;OQ=809.01;QD=14.19;SB=-410.42 GT:AD:DP:GL:GQ 0/1:31,26:56:-101.07,-16.88,-98.51:99 +chr1 3308295 rs11577526 A G 45.03 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.09;MQ=57.69;MQ0=0;OQ=1861.63;QD=33.24;SB=-741.99 GT:AD:DP:GL:GQ 1/1:0,56:55:-189.77,-16.57,-0.03:99 +chr1 3308392 rs11578011 T C 195.41 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.80;MQ0=0;OQ=1812.46;QD=30.21;SB=-790.65 GT:AD:DP:GL:GQ 1/1:0,59:59:-188.08,-20.60,-3.25:99 +chr1 3308574 rs5024246 G A 333.57 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=876.20;QD=19.47;SB=-325.85 GT:AD:DP:GL:GQ 0/1:19,26:45:-104.46,-13.56,-63.60:99 +chr1 3308629 rs10909942 C G 63.18 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.03;HRun=0;HaplotypeScore=2.61;MQ=58.12;MQ0=0;OQ=1384.57;QD=36.44;SB=-590.68 GT:AD:DP:GL:GQ 1/1:0,37:37:-142.07,-10.86,-0.03:99 +chr1 3308702 rs56148282 G A 636.18 Indel AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.59;MQ0=0;QD=19.28;SB=-248.56 GT:AD:DP:GL:GQ 0/1:12,21:30:-75.94,-9.04,-37.32:99 +chr1 3308921 rs1889124 A G 16.57 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.23;MQ=58.83;MQ0=0;OQ=1016.70;QD=28.24;SB=-485.51 GT:AD:DP:GL:GQ 1/1:0,36:33:-105.29,-9.95,-0.03:99 +chr1 3309492 rs4353034 G A 0.09 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=16.76;MQ=57.87;MQ0=0;OQ=200.25;QD=6.07;SB=-37.01 GT:AD:DP:GL:GQ 0/1:23,8:31:-40.02,-16.71,-79.20:99 +chr1 3309534 rs12562397 C T 380.45 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.05;MQ0=0;OQ=1380.14;QD=38.34;SB=-494.65 GT:AD:DP:GL:GQ 1/1:0,36:35:-141.61,-10.54,-0.01:99 +chr1 3309541 rs12562399 C G 28.59 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.39;MQ0=0;OQ=1543.76;QD=40.63;SB=-639.90 GT:AD:DP:GL:GQ 1/1:0,38:37:-157.97,-11.15,-0.01:99 +chr1 3309637 rs4471209 G A 344.14 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.51;MQ0=0;OQ=382.91;QD=10.08;SB=-184.19 GT:AD:DP:GL:GQ 0/1:25,13:37:-52.73,-11.16,-73.72:99 +chr1 3309732 rs6664364 C T 134.87 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.91;MQ0=0;OQ=1699.09;QD=36.15;SB=-803.59 GT:AD:DP:GL:GQ 1/1:0,47:44:-173.51,-13.26,-0.01:99 +chr1 3309737 rs6664369 C T 130.20 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.53;MQ0=0;OQ=1859.42;QD=37.95;SB=-907.23 GT:AD:DP:GL:GQ 1/1:0,49:48:-189.54,-14.46,-0.02:99 +chr1 3309924 rs6669407 A G 328.05 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=995.86;QD=29.29;SB=-353.80 GT:AD:DP:GL:GQ 1/1:0,34:32:-103.20,-9.65,-0.03:96.22 +chr1 3310023 rs2493286 G C 420.47 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1672.06;QD=40.78;SB=-718.73 GT:AD:DP:GL:GQ 1/1:0,41:40:-170.80,-12.05,-0.01:99 +chr1 3310336 rs6657675 G A 148.97 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=58.38;MQ0=0;OQ=936.76;QD=20.36;SB=-332.89 GT:AD:DP:GL:GQ 0/1:17,29:43:-109.92,-12.96,-52.69:99 +chr1 3310582 rs55820208 C T 260.28 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=862.76;QD=19.61;SB=-355.48 GT:AD:DP:GL:GQ 0/1:19,25:43:-102.51,-12.95,-64.90:99 +chr1 3311027 rs41315264 C A 149.68 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.45;MQ0=0;OQ=411.02;QD=12.09;SB=-182.52 GT:AD:DP:GL:GQ 0/1:19,15:31:-53.72,-9.34,-57.20:99 +chr1 3311596 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=4;HaplotypeScore=11.58;MQ=54.22;MQ0=0;OQ=65.40;QD=1.42;SB=47.17 GT:AD:DP:GL:GQ 0/1:36,10:29:-18.61,-8.78,-88.90:98.24 +chr1 3312969 rs2483222 T C 325.01 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.04;MQ0=0;OQ=585.55;QD=11.71;SB=-306.07 GT:AD:DP:GL:GQ 0/1:25,25:48:-76.31,-14.47,-93.64:99 +chr1 3313057 rs2483223 T G 88.19 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.28;MQ0=0;OQ=1723.37;QD=26.93;SB=-826.52 GT:AD:DP:GL:GQ 1/1:0,64:57:-175.98,-17.18,-0.06:99 +chr1 3313337 rs2493304 A G 110.36 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=57.61;MQ0=0;OQ=687.56;QD=10.91;SB=-122.49 GT:AD:DP:GL:GQ 0/1:35,28:61:-90.42,-18.38,-140.37:99 +chr1 3313476 rs2483224 C T 77.82 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=3.15;MQ=58.48;MQ0=0;OQ=742.74;QD=16.15;SB=-389.41 GT:AD:DP:GL:GQ 0/1:21,25:42:-90.21,-12.66,-65.08:99 +chr1 3314069 rs2493303 G C 188.15 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=4.50;MQ=59.20;MQ0=0;OQ=943.60;QD=16.27;SB=-364.47 GT:AD:DP:GL:GQ 0/1:29,29:57:-114.83,-17.19,-120.69:99 +chr1 3314293 rs2493302 A T 133.12 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=59.50;MQ0=0;OQ=1593.32;QD=34.64;SB=-633.61 GT:AD:DP:GL:GQ 1/1:0,46:43:-162.93,-12.95,-0.01:99 +chr1 3314897 rs2483225 T C 612.21 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.62;MQ0=0;OQ=1899.06;QD=30.14;SB=-687.73 GT:AD:DP:GL:GQ 1/1:0,63:60:-193.54,-18.10,-0.05:99 +chr1 3315120 rs12063572 A G 188.23 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.59;MQ0=0;OQ=550.32;QD=9.83;SB=-278.26 GT:AD:DP:GL:GQ 0/1:32,24:53:-74.29,-15.98,-116.93:99 +chr1 3315180 rs12063579 A G 62.82 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.22;MQ=57.82;MQ0=1;OQ=599.80;QD=10.91;SB=-262.60 GT:AD:DP:GL:GQ 0/1:27,28:47:-77.44,-14.18,-83.26:99 +chr1 3315190 rs2493301 G C 0.26 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=15.61;MQ=57.11;MQ0=1;OQ=860.03;QD=14.83;SB=-355.44 GT:AD:DP:GL:GQ 0/1:31,27:50:-104.37,-15.08,-104.68:99 +chr1 3315194 rs12063613 A G 1.95 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=10.46;MQ=56.06;MQ0=1;OQ=577.86;QD=9.47;SB=-271.10 GT:AD:DP:GL:GQ 0/1:30,31:51:-76.46,-15.39,-99.42:99 +chr1 3315219 . C T 17.67 DPFilter;Indel;LowQual AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=15.64;MQ=52.76;MQ0=1;QD=0.26;SB=34.67 GT:AD:DP:GL:GQ 0/1:62,6:62:-23.74,-18.70,-180.77:50.43 +chr1 3315354 rs12065021 T C 254.87 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=59.68;MQ0=0;OQ=519.08;QD=13.66;SB=-277.27 GT:AD:DP:GL:GQ 0/1:17,21:38:-66.65,-11.46,-65.47:99 +chr1 3315386 rs2493300 A G 19.22 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=1158.12;QD=28.95;SB=-549.05 GT:AD:DP:GL:GQ 1/1:0,40:37:-119.43,-11.16,-0.04:99 +chr1 3315441 rs2493299 A G 105.98 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.81;MQ=60.00;MQ0=0;OQ=1355.37;QD=28.24;SB=-603.93 GT:AD:DP:GL:GQ 1/1:0,48:44:-139.17,-13.27,-0.04:99 +chr1 3315528 rs55929648 C T 143.11 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=56.18;MQ0=0;OQ=1041.13;QD=18.59;SB=-362.91 GT:AD:DP:GL:GQ 0/1:25,31:52:-123.07,-15.67,-66.96:99 +chr1 3315772 rs2493298 C A 135.74 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=60.00;MQ0=0;OQ=850.76;QD=17.72;SB=-447.55 GT:AD:DP:GL:GQ 0/1:19,29:48:-102.82,-14.46,-64.75:99 +chr1 3315954 rs36070715 C G 3.94 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.72;MQ=51.04;MQ0=0;OQ=1102.41;QD=21.62;SB=-424.97 GT:AD:DP:GL:GQ 0/1:21,30:46:-127.39,-13.87,-69.58:99 +chr1 3316002 rs60965010 G A 53.41 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=53.52;MQ0=0;OQ=683.65;QD=15.19;SB=-341.33 GT:AD:DP:GL:GQ 0/1:23,22:41:-84.00,-12.35,-71.37:99 +chr1 3316048 rs59831144 A G 16.76 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=6.55;MQ=58.48;MQ0=0;OQ=584.41;QD=12.70;SB=-233.93 GT:AD:DP:GL:GQ 0/1:24,22:41:-74.08,-12.36,-76.23:99 +chr1 3316091 rs2493297 G A 148.61 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.53;MQ0=0;OQ=1649.32;QD=33.66;SB=-643.25 GT:AD:DP:GL:GQ 1/1:0,49:44:-168.54,-13.26,-0.02:99 +chr1 3316251 . G A 182.76 SnpCluster AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=43.92;MQ0=0;QD=3.10;SB=-111.51 GT:AD:DP:GL:GQ 0/1:47,12:54:-37.83,-16.27,-156.64:99 +chr1 3316256 . T C 219.54 SnpCluster AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=43.18;MQ0=0;QD=3.66;SB=-32.48 GT:AD:DP:GL:GQ 0/1:44,16:55:-41.82,-16.58,-163.02:99 +chr1 3316258 rs7364679 G T 370 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=43.51;MQ0=0;QD=6.07;SB=-108.68 GT:AD:DP:GL:GQ 0/1:43,18:56:-57.15,-16.87,-140.13:99 +chr1 3316271 . G T 44.21 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=42.99;MQ0=0;OQ=836.87;QD=13.72;SB=-249.23 GT:AD:DP:GL:GQ 0/1:29,32:52:-102.65,-15.68,-71.94:99 +chr1 3316274 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=55.35;MQ=42.03;MQ0=0;OQ=122.20;QD=2.07;SB=-76.97 GT:AD:DP:GL:GQ 0/1:47,12:53:-31.48,-15.98,-148.32:99 +chr1 3316287 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=56;Dels=0.04;HRun=0;HaplotypeScore=28.34;MQ=46.39;MQ0=0;OQ=249.44;QD=4.45;SB=13.22 GT:AD:DP:GL:GQ 0/1:42,12:52:-43.29,-15.07,-133.82:99 +chr1 3316288 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=24.35;MQ=46.92;MQ0=0;OQ=241.94;QD=4.17;SB=40.21 GT:AD:DP:GL:GQ 0/1:44,14:54:-43.75,-16.27,-150.33:99 +chr1 3316304 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=2;HaplotypeScore=31.71;MQ=50.98;MQ0=0;OQ=105.86;QD=1.79;SB=47.12 GT:AD:DP:GL:GQ 0/1:51,8:50:-28.93,-15.06,-145.13:99 +chr1 3316355 . A G 40.11 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=6.42;MQ=53.40;MQ0=0;QD=0.79;SB=24.53 GT:AD:DP:GL:GQ 0/1:42,9:48:-21.76,-14.47,-159.00:72.94 +chr1 3316370 . G A 1.13 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=7.87;MQ=52.81;MQ0=0;OQ=530.25;QD=10.40;SB=-291.29 GT:AD:DP:GL:GQ 0/1:31,20:45:-69.88,-13.57,-88.85:99 +chr1 3316500 rs4648494 A G 396.15 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.41;MQ0=0;OQ=1411.68;QD=27.15;SB=-591.87 GT:AD:DP:GL:GQ 1/1:0,52:46:-144.80,-13.88,-0.05:99 +chr1 3316656 rs6670123 C G 292.55 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.36;MQ=56.33;MQ0=0;OQ=1404.84;QD=19.79;SB=-673.50 GT:AD:DP:GL:GQ 0/1:33,38:68:-164.26,-20.49,-128.05:99 +chr1 3316892 rs2493296 C T 338.29 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.07;MQ0=0;OQ=702.09;QD=14.04;SB=-332.51 GT:AD:DP:GL:GQ 0/1:27,23:46:-87.37,-13.87,-76.76:99 +chr1 3317409 rs1106270 A G 118.06 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.41;MQ0=0;OQ=1192.84;QD=30.59;SB=-537.44 GT:AD:DP:GL:GQ 1/1:0,39:35:-122.88,-10.54,-0.02:99 +chr1 3317462 rs1106271 T G 1.72 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=1.32;MQ=56.98;MQ0=0;OQ=1224.22;QD=31.39;SB=-406.92 GT:AD:DP:GL:GQ 1/1:0,39:38:-126.04,-11.45,-0.03:99 +chr1 3317665 rs57382922 C T 121.84 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.88;MQ=57.50;MQ0=0;OQ=526.20;QD=15.48;SB=-279.22 GT:AD:DP:GL:GQ 0/1:15,19:32:-65.55,-9.65,-47.15:99 +chr1 3318218 rs870124 T C 46.45 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=58.35;MQ0=0;OQ=987.47;QD=31.85;SB=-495.44 GT:AD:DP:GL:GQ 1/1:0,30:29:-102.35,-8.74,-0.01:87.24 +chr1 3318519 rs2493292 C T 35.55 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=5.38;MQ=58.81;MQ0=0;OQ=410.88;QD=10.54;SB=-213.48 GT:AD:DP:GL:GQ 0/1:22,17:36:-55.22,-10.85,-74.55:99 +chr1 3319244 rs2493291 C T 128.26 PASS AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=57.07;MQ0=0;OQ=113.91;QD=8.76;SB=-36.64 GT:AD:DP:GL:GQ 0/1:8,5:13:-18.59,-3.92,-28.88:99 +chr1 3319441 . G A 108.40 PASS AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=283.86;QD=13.52;SB=-108.97 GT:AD:DP:GL:GQ 0/1:11,10:21:-38.00,-6.33,-35.64:99 +chr1 3320120 . C T 102.17 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=709.62;QD=14.78;SB=-362.53 GT:AD:DP:GL:GQ 0/1:24,23:45:-87.81,-13.57,-69.77:99 +chr1 3320537 rs2493290 G A 97.62 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.41;MQ=59.54;MQ0=0;OQ=872.79;QD=17.46;SB=-392.92 GT:AD:DP:GL:GQ 0/1:24,26:48:-105.02,-14.46,-80.60:99 +chr1 3320607 rs11578951 G A 205.49 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=56.45;MQ0=0;OQ=183.21;QD=9.16;SB=-114.08 GT:AD:DP:GL:GQ 0/1:13,7:17:-26.73,-5.12,-34.52:99 +chr1 3320622 rs2493289 A G 29.59 PASS AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=56.62;MQ0=0;OQ=591.39;QD=28.16;SB=-179.75 GT:AD:DP:GL:GQ 1/1:0,20:19:-62.74,-5.73,-0.02:57.13 +chr1 3320744 rs2493288 G A 319.17 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.00;MQ0=0;OQ=558.26;QD=13.29;SB=-286.76 GT:AD:DP:GL:GQ 0/1:23,19:41:-71.47,-12.36,-76.00:99 +chr1 3321412 rs60973157 G C 340.30 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=59.61;MQ0=0;OQ=1008.01;QD=17.08;SB=-510.27 GT:AD:DP:GL:GQ 0/1:31,28:58:-121.57,-17.48,-125.42:99 +chr1 3321593 rs2483228 T C 57.78 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=59.17;MQ0=0;OQ=862.49;QD=30.80;SB=-342.44 GT:AD:DP:GL:GQ 1/1:0,28:27:-89.85,-8.14,-0.02:81.21 +chr1 3321759 rs1999528 A G 88.85 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1263.70;QD=30.82;SB=-424.24 GT:AD:DP:GL:GQ 1/1:0,41:41:-129.99,-12.37,-0.04:99 +chr1 3322543 rs2483229 T C 158.61 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.98;MQ0=0;OQ=401.83;QD=7.31;SB=-190.61 GT:AD:DP:GL:GQ 0/1:33,22:50:-58.54,-15.08,-123.40:99 +chr1 3322811 rs1889123 T C 57.71 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=1553.51;QD=34.52;SB=-743.30 GT:AD:DP:GL:GQ 1/1:0,45:44:-158.95,-13.25,-0.01:99 +chr1 3323101 rs55713431 A G 0.68 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=4;HaplotypeScore=1.93;MQ=59.65;MQ0=0;OQ=422.62;QD=7.97;SB=-123.50 GT:AD:DP:GL:GQ 0/1:32,21:47:-59.71,-14.17,-112.42:99 +chr1 3323323 rs2068354 A G 160.11 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=738.34;QD=11.36;SB=-391.91 GT:AD:DP:GL:GQ 0/1:34,31:64:-96.41,-19.29,-135.43:99 +chr1 3324752 rs2483230 A G 139.58 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=59.42;MQ0=0;OQ=1229.51;QD=30.74;SB=-406.34 GT:AD:DP:GL:GQ 1/1:0,40:38:-126.56,-11.45,-0.03:99 +chr1 3326060 rs1984069 C T 66.93 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=2062.28;QD=37.50;SB=-721.47 GT:AD:DP:GL:GQ 1/1:0,55:53:-209.83,-15.97,-0.02:99 +chr1 3327403 rs1572040 A G 479.17 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1561.86;QD=33.95;SB=-803.63 GT:AD:DP:GL:GQ 1/1:0,46:45:-159.79,-13.56,-0.02:99 +chr1 3327481 . A G 13.29 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.51;MQ=58.78;MQ0=0;OQ=805.84;QD=11.68;SB=-333.16 GT:AD:DP:GL:GQ 0/1:35,34:66:-103.76,-19.89,-136.42:99 +chr1 3327496 rs11579873 G A 76.54 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=5.52;MQ=59.07;MQ0=0;OQ=1231.78;QD=17.60;SB=-403.19 GT:AD:DP:GL:GQ 0/1:34,36:67:-146.65,-20.19,-102.53:99 +chr1 3328305 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=2;HaplotypeScore=9.54;MQ=57.05;MQ0=0;OQ=81.44;QD=1.66;SB=56.21 GT:AD:DP:GL:GQ 0/1:35,13:31:-20.79,-9.36,-100.83:99 +chr1 3328931 rs2483231 A G 0.45 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=57.64;MQ0=0;OQ=961.69;QD=26.71;SB=-96.83 GT:AD:DP:GL:GQ 1/1:0,35:29:-99.77,-8.74,-0.01:87.24 +chr1 3329199 rs10492937 C A 94.15 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=591.17;QD=15.16;SB=-220.88 GT:AD:DP:GL:GQ 0/1:18,21:38:-73.85,-11.45,-60.07:99 +chr1 3329740 . G T 6.44 PASS AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=1;HaplotypeScore=3.49;MQ=59.36;MQ0=0;OQ=539.79;QD=14.99;SB=-294.29 GT:AD:DP:GL:GQ 0/1:15,21:33:-67.21,-9.94,-47.46:99 +chr1 3329976 rs2483232 A G 146.59 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.54;MQ0=0;OQ=1387.79;QD=27.76;SB=-682.70 GT:AD:DP:GL:GQ 1/1:0,49:45:-142.42,-13.58,-0.05:99 +chr1 3330129 rs4648385 C T 62.27 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.51;MQ0=0;OQ=1421.02;QD=37.40;SB=-712.36 GT:AD:DP:GL:GQ 1/1:0,38:36:-145.70,-10.84,-0.01:99 +chr1 3330207 rs2483233 A G 536.88 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1265.03;QD=33.29;SB=-631.30 GT:AD:DP:GL:GQ 1/1:0,38:37:-130.10,-11.15,-0.02:99 +chr1 3330527 rs2483234 A G 229.57 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1088.75;QD=27.92;SB=-544.02 GT:AD:DP:GL:GQ 1/1:0,38:35:-112.49,-10.56,-0.04:99 +chr1 3330619 rs2483235 A G 461.47 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=1699.01;QD=28.80;SB=-626.83 GT:AD:DP:GL:GQ 1/1:0,59:55:-173.55,-16.59,-0.06:99 +chr1 3330715 rs4648500 A C 461.04 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.69;MQ0=0;OQ=953.20;QD=15.63;SB=-476.30 GT:AD:DP:GL:GQ 0/1:28,33:61:-116.98,-18.37,-104.31:99 +chr1 3331400 rs2483236 C T 56.26 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=55.81;MQ0=0;OQ=1168.69;QD=36.52;SB=-534.21 GT:AD:DP:GL:GQ 1/1:0,31:30:-120.46,-9.04,-0.01:90.29 +chr1 3331651 rs1970118 A G 69.34 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=50.87;MQ0=0;OQ=938.62;QD=27.61;SB=-452.46 GT:AD:DP:GL:GQ 1/1:0,34:32:-97.49,-9.66,-0.04:96.17 +chr1 3331969 rs41303861 G T 165.88 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=56.82;MQ0=0;OQ=610.74;QD=12.99;SB=-193.66 GT:AD:DP:GL:GQ 0/1:23,24:44:-77.62,-13.26,-67.40:99 +chr1 3332390 rs2244013 G A 343.87 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.76;MQ=59.53;MQ0=0;OQ=624.83;QD=12.75;SB=-319.81 GT:AD:DP:GL:GQ 0/1:27,22:47:-79.93,-14.16,-96.24:99 +chr1 3332664 rs870171 G T 453.17 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=726.05;QD=12.10;SB=-151.13 GT:AD:DP:GL:GQ 0/1:34,26:59:-93.67,-17.78,-105.77:99 +chr1 3333105 rs7549050 A G 414.31 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=796.44;QD=10.62;SB=-292.01 GT:AD:DP:GL:GQ 0/1:42,33:74:-105.23,-22.30,-168.30:99 +chr1 3333795 rs55833861 T C 103.98 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=2.59;MQ=58.97;MQ0=0;OQ=717.11;QD=11.38;SB=-232.86 GT:AD:DP:GL:GQ 0/1:36,27:59:-92.78,-17.78,-129.42:99 +chr1 3333920 rs56196310 G T 246.95 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=59.56;MQ0=0;OQ=564.40;QD=10.65;SB=-293.98 GT:AD:DP:GL:GQ 0/1:32,21:49:-74.48,-14.76,-99.79:99 +chr1 3334336 rs61759212 A G 99.75 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=59.13;MQ0=0;OQ=418.37;QD=9.73;SB=-116.62 GT:AD:DP:GL:GQ 0/1:23,20:40:-57.18,-12.06,-85.13:99 +chr1 3334647 rs2483240 A G 15.04 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.38;MQ0=1;OQ=79.23;QD=3.96;SB=-53.29 GT:AD:DP:GL:GQ 0/1:13,7:16:-16.03,-4.82,-44.27:99 +chr1 3335005 rs2483242 A T 508.54 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.64;MQ0=0;OQ=469.82;QD=13.82;SB=-232.91 GT:AD:DP:GL:GQ 0/1:18,16:34:-60.51,-10.24,-69.68:99 +chr1 3335714 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=9.36;MQ=57.49;MQ0=0;OQ=205.84;QD=4.57;SB=56.19 GT:AD:DP:GL:GQ 0/1:25,20:36:-34.71,-10.85,-86.86:99 +chr1 3336208 rs2493277 C G 559.81 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=642.22;QD=14.94;SB=-326.21 GT:AD:DP:GL:GQ 0/1:23,20:42:-80.17,-12.66,-97.68:99 +chr1 3336263 rs11583353 C T 94.14 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.90;MQ0=0;OQ=708.85;QD=18.65;SB=-324.84 GT:AD:DP:GL:GQ 0/1:17,21:37:-85.32,-11.15,-51.45:99 +chr1 3339994 rs10752734 T C 155.05 PASS AC=2;AF=1.00;AN=2;DB;DP=17;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=27.27;MQ0=2;OQ=107.39;QD=6.32;SB=-10.00 GT:AD:DP:GL:GQ 1/1:8,9:4:-14.27,-1.20,-0.00:12.04 +chr1 3342087 rs1537406 T C 266.84 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.23;MQ0=0;OQ=2135.99;QD=33.90;SB=-825.32 GT:AD:DP:GL:GQ 1/1:0,63:60:-217.21,-18.07,-0.02:99 +chr1 3342088 rs12735779 G C 80.32 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.25;MQ0=0;OQ=2678.31;QD=41.20;SB=-987.13 GT:AD:DP:GL:GQ 1/1:0,65:62:-271.44,-18.68,-0.02:99 +chr1 3342207 rs1537405 T C 92.45 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=60.00;MQ0=0;OQ=1223.31;QD=28.45;SB=-485.50 GT:AD:DP:GL:GQ 1/1:0,43:40:-125.96,-12.07,-0.04:99 +chr1 3342363 rs1537404 G C 0.18 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=4;HaplotypeScore=2.53;MQ=57.71;MQ0=0;OQ=1605.19;QD=37.33;SB=-574.94 GT:AD:DP:GL:GQ 1/1:0,43:39:-164.12,-11.76,-0.02:99 +chr1 3342401 rs1065247 T C 218.93 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=58.89;MQ0=0;OQ=523.80;QD=12.47;SB=-250.33 GT:AD:DP:GL:GQ 0/1:20,21:38:-67.12,-11.46,-67.07:99 +chr1 3342439 rs1537402 T C 329.15 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.61;MQ0=0;OQ=1390.94;QD=29.59;SB=-663.80 GT:AD:DP:GL:GQ 1/1:0,47:44:-142.72,-13.27,-0.04:99 +chr1 3342644 rs2493267 A G 426.47 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1871.16;QD=31.71;SB=-785.23 GT:AD:DP:GL:GQ 1/1:0,59:54:-190.73,-16.27,-0.03:99 +chr1 3342725 rs35015571 C T 160.86 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=59.43;MQ0=0;OQ=266.00;QD=8.06;SB=-157.61 GT:AD:DP:GL:GQ 0/1:23,10:28:-38.32,-8.44,-61.48:99 +chr1 3342732 rs2236518 A C 16.29 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=2.32;MQ=59.45;MQ0=0;OQ=611.30;QD=17.98;SB=-246.93 GT:AD:DP:GL:GQ 0/1:10,24:30:-73.45,-9.04,-31.78:99 +chr1 3343497 rs35837267 G A 179.26 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=1.81;MQ=58.20;MQ0=0;OQ=412.37;QD=12.13;SB=-230.72 GT:AD:DP:GL:GQ 0/1:20,14:34:-54.77,-10.25,-72.54:99 +chr1 3343750 rs2493265 A G 92.52 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.09;MQ0=0;OQ=1343.75;QD=27.42;SB=-616.98 GT:AD:DP:GL:GQ 1/1:0,49:43:-138.00,-12.97,-0.04:99 +chr1 3343809 rs2493264 A G 123.80 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.40;MQ=58.91;MQ0=0;OQ=1865.11;QD=29.14;SB=-622.24 GT:AD:DP:GL:GQ 1/1:0,64:61:-190.17,-18.41,-0.07:99 +chr1 3344455 rs2483249 T C 577.76 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2266.24;QD=31.92;SB=-1078.24 GT:AD:DP:GL:GQ 1/1:0,71:70:-230.26,-21.11,-0.05:99 +chr1 3344475 rs2493263 T C 726.67 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2858.56;QD=35.29;SB=-1249.13 GT:AD:DP:GL:GQ 1/1:0,81:80:-289.47,-24.10,-0.03:99 +chr1 3345122 rs55729137 G A 38.39 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.48;MQ0=0;OQ=807.80;QD=18.36;SB=-199.91 GT:AD:DP:GL:GQ 0/1:20,24:42:-96.73,-12.66,-57.09:99 +chr1 3346265 rs2483250 A C 12.02 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.52;MQ0=0;OQ=1256.35;QD=32.21;SB=-315.07 GT:AD:DP:GL:GQ 1/1:0,39:37:-129.23,-11.15,-0.01:99 +chr1 3346495 rs2483251 T C 2.80 PASS AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=1.13;MQ=60.00;MQ0=0;OQ=525.69;QD=27.67;SB=-225.75 GT:AD:DP:GL:GQ 1/1:0,19:16:-56.16,-4.82,-0.01:48.13 +chr1 3346655 rs2493262 C G 18.99 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=2;HaplotypeScore=2.19;MQ=59.17;MQ0=0;OQ=878.66;QD=31.38;SB=-427.67 GT:AD:DP:GL:GQ 1/1:0,27:23:-91.47,-6.94,-0.02:69.23 +chr1 3346875 rs12745100 C T 10.66 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=496.33;QD=18.38;SB=-39.63 GT:AD:DP:GL:GQ 0/1:12,15:27:-61.05,-8.13,-42.91:99 +chr1 3347097 rs55892133 A G 803.11 Indel AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.17;MQ=58.79;MQ0=0;QD=12.55;SB=-200.20 GT:AD:DP:GL:GQ 0/1:34,30:60:-101.69,-18.09,-118.87:99 +chr1 3347896 rs10797392 T G 467.03 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.49;MQ0=1;OQ=720.09;QD=12.20;SB=-372.76 GT:AD:DP:GL:GQ 0/1:27,32:54:-91.57,-16.27,-88.57:99 +chr1 3348782 rs2483252 G C 20.05 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=1.07;MQ=58.41;MQ0=0;OQ=1754.48;QD=39.87;SB=-676.45 GT:AD:DP:GL:GQ 1/1:0,43:42:-179.05,-12.66,-0.02:99 +chr1 3348792 rs35536718 C G 187.57 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=58.60;MQ0=0;OQ=722.68;QD=14.45;SB=-275.28 GT:AD:DP:GL:GQ 0/1:28,22:46:-89.42,-13.87,-106.46:99 +chr1 3349040 rs2493261 C G 241.62 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=2328.68;QD=40.85;SB=-454.11 GT:AD:DP:GL:GQ 1/1:0,57:55:-236.48,-16.59,-0.03:99 +chr1 3349142 rs56009352 G T 195.97 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=58.75;MQ0=0;OQ=381.64;QD=9.09;SB=-161.15 GT:AD:DP:GL:GQ 0/1:24,18:38:-52.90,-11.45,-81.46:99 +chr1 3349843 rs11588737 T C 126.31 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.70;MQ0=0;OQ=680.83;QD=8.96;SB=-348.93 GT:AD:DP:GL:GQ 0/1:44,32:72:-93.07,-21.70,-169.44:99 +chr1 3349896 rs9424295 C A 298.32 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.90;MQ0=0;OQ=883.58;QD=12.27;SB=-371.71 GT:AD:DP:GL:GQ 0/1:40,32:69:-112.42,-20.78,-136.87:99 +chr1 3350654 . A G 19.67 PASS AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=4.82;MQ=58.94;MQ0=0;OQ=752.06;QD=11.22;SB=-353.94 GT:AD:DP:GL:GQ 0/1:36,30:64:-97.78,-19.29,-134.25:99 +chr1 3350874 rs2493260 A T 152.74 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1881.55;QD=33.01;SB=-813.90 GT:AD:DP:GL:GQ 1/1:0,54:52:-191.76,-15.67,-0.02:99 +chr1 3351164 rs2483254 G A 165.18 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.02;MQ=57.99;MQ0=0;OQ=1923.46;QD=34.35;SB=-708.45 GT:AD:DP:GL:GQ 1/1:0,56:52:-195.97,-15.68,-0.04:99 +chr1 3351668 rs61759222 T C 292.32 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.16;MQ0=0;OQ=649.71;QD=12.99;SB=-320.27 GT:AD:DP:GL:GQ 0/1:27,23:50:-83.32,-15.07,-104.64:99 +chr1 3351675 rs61759223 T C 215.70 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.56;MQ0=0;OQ=453.74;QD=8.73;SB=-214.35 GT:AD:DP:GL:GQ 0/1:31,21:51:-64.03,-15.38,-121.39:99 +chr1 3351951 rs61759224 A G 132.94 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.69;MQ0=0;OQ=462.74;QD=9.25;SB=-204.32 GT:AD:DP:GL:GQ 0/1:29,21:49:-64.32,-14.77,-119.90:99 +chr1 3352116 rs867814 C T 338.36 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.66;MQ0=0;OQ=1015.19;QD=15.15;SB=-259.14 GT:AD:DP:GL:GQ 0/1:34,33:66:-124.69,-19.89,-112.54:99 +chr1 3352233 rs55781247 C T 0.43 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=12.27;MQ=55.55;MQ0=1;OQ=438.31;QD=8.59;SB=-227.00 GT:AD:DP:GL:GQ 0/1:27,22:35:-60.74,-13.63,-60.12:99 +chr1 3352662 . G C 94.32 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.30;MQ0=0;OQ=750.60;QD=12.94;SB=-224.33 GT:AD:DP:GL:GQ 0/1:34,23:56:-95.22,-16.87,-149.91:99 +chr1 3353096 rs11808277 C G 337.37 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.63;MQ0=0;OQ=1053.89;QD=17.00;SB=-489.21 GT:AD:DP:GL:GQ 0/1:30,32:59:-126.45,-17.78,-131.54:99 +chr1 3353132 . G A 167.12 PASS AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.73;MQ0=0;OQ=1096.75;QD=16.13;SB=-431.84 GT:AD:DP:GL:GQ 0/1:34,34:67:-133.15,-20.19,-109.37:99 +chr1 3353327 rs10158332 A T 108.69 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=58.82;MQ0=0;OQ=1002.21;QD=14.12;SB=-515.47 GT:AD:DP:GL:GQ 0/1:38,33:71:-124.89,-21.39,-148.24:99 +chr1 3353449 rs10157570 G A 490.96 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=905.02;QD=15.88;SB=-430.82 GT:AD:DP:GL:GQ 0/1:30,27:56:-110.66,-16.88,-93.98:99 +chr1 3353662 rs2483255 A T 46.49 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=59.30;MQ0=0;OQ=2470.87;QD=37.44;SB=-912.35 GT:AD:DP:GL:GQ 1/1:0,66:64:-250.68,-19.27,-0.01:99 +chr1 3353786 rs2493258 A G 307.10 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.56;MQ0=0;OQ=1182.18;QD=13.91;SB=-595.40 GT:AD:DP:GL:GQ 0/1:39,46:85:-147.12,-25.62,-159.37:99 +chr1 3354380 rs61759225 T C 235.67 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=921.81;QD=12.29;SB=-424.06 GT:AD:DP:GL:GQ 0/1:42,33:74:-117.76,-22.29,-166.03:99 +chr1 3354597 rs2263010 T C 533.81 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2222.94;QD=35.85;SB=-1114.11 GT:AD:DP:GL:GQ 1/1:0,62:62:-225.90,-18.68,-0.02:99 +chr1 3354829 rs61759226 A T 251.14 PASS AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.16;MQ0=0;OQ=1748.33;QD=17.48;SB=-874.02 GT:AD:DP:GL:GQ 0/1:46,54:99:-207.93,-29.81,-176.30:99 +chr1 3355107 rs4648386 A G 12.08 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=59.31;MQ0=0;OQ=1773.45;QD=34.77;SB=-505.48 GT:AD:DP:GL:GQ 1/1:0,51:51:-180.95,-15.36,-0.02:99 +chr1 3355113 rs61759227 G A 0.86 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=6.85;MQ=58.80;MQ0=0;OQ=911.32;QD=18.60;SB=-216.88 GT:AD:DP:GL:GQ 0/1:22,27:48:-108.87,-14.46,-75.78:99 +chr1 3355993 rs55913848 G T 115.65 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=58.15;MQ0=0;OQ=1046.84;QD=16.62;SB=-492.93 GT:AD:DP:GL:GQ 0/1:29,34:61:-126.34,-18.38,-91.26:99 +chr1 3356353 rs2096102 C A 344.49 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=61.19;MQ0=0;OQ=1204.86;QD=17.21;SB=-565.00 GT:AD:DP:GL:GQ 0/1:30,40:67:-143.95,-20.18,-94.79:99 +chr1 3356461 . G A 34.92 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=63.59;MQ=46.78;MQ0=1;QD=0.83;SB=-40.97 GT:AD:DP:GL:GQ 0/1:36,6:34:-17.03,-10.25,-100.31:67.76 +chr1 3356464 . T G 27.11 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=13.28;MQ=49.36;MQ0=1;QD=0.85;SB=-38.91 GT:AD:DP:GL:GQ 0/1:28,4:29:-14.73,-8.74,-84.74:59.94 +chr1 3356466 . G T 324.76 SnpCluster AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=10.60;MQ=48.57;MQ0=1;QD=10.83;SB=-127.64 GT:AD:DP:GL:GQ 0/1:15,15:26:-43.60,-7.84,-42.90:99 +chr1 3357640 rs2487679 A G 123.35 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=59.32;MQ0=0;OQ=2260.98;QD=33.25;SB=-697.21 GT:AD:DP:GL:GQ 1/1:0,68:67:-229.71,-20.18,-0.03:99 +chr1 3357895 rs6697669 T C 43.42 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.03;HRun=0;HaplotypeScore=3.79;MQ=57.15;MQ0=0;OQ=335.02;QD=10.15;SB=-38.93 GT:AD:DP:GL:GQ 0/1:18,13:30:-45.82,-9.04,-67.57:99 +chr1 3357991 rs4648501 G A 122.29 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.97;MQ0=0;OQ=545.72;QD=10.70;SB=-291.79 GT:AD:DP:GL:GQ 0/1:33,18:50:-72.92,-15.06,-113.74:99 +chr1 3358003 rs2487670 G A 120.25 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.77;MQ0=0;OQ=1144.78;QD=22.01;SB=-472.53 GT:AD:DP:GL:GQ 0/1:18,34:50:-132.83,-15.07,-51.40:99 +chr1 3358201 rs55902179 A G 118.16 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=60.00;MQ0=0;OQ=620.71;QD=14.78;SB=-241.29 GT:AD:DP:GL:GQ 0/1:20,22:41:-77.71,-12.35,-78.03:99 +chr1 3359613 rs2487668 G A 227.96 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=59.61;MQ0=0;OQ=985.10;QD=16.70;SB=-425.79 GT:AD:DP:GL:GQ 0/1:26,32:57:-118.97,-17.18,-94.23:99 +chr1 3359684 rs34681041 A G 13.72 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=1.71;MQ=60.00;MQ0=0;OQ=330.72;QD=8.70;SB=-110.60 GT:AD:DP:GL:GQ 0/1:21,17:34:-46.60,-10.25,-79.14:99 +chr1 3361330 . G C 0.29 PASS AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=68.48;QD=6.85;SB=-10.00 GT:AD:DP:GL:GQ 0/1:6,4:9:-12.85,-2.72,-22.16:99 +chr1 3361841 rs55858614 G C 94.38 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.70;MQ0=0;OQ=503.58;QD=17.36;SB=-238.39 GT:AD:DP:GL:GQ 0/1:14,15:29:-62.38,-8.74,-58.19:99 +chr1 3362331 rs10909946 A C 12.50 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=2.71;MQ=58.18;MQ0=0;OQ=655.84;QD=12.15;SB=-228.89 GT:AD:DP:GL:GQ 0/1:26,28:47:-83.03,-14.16,-81.70:99 +chr1 3362529 rs61759232 T C 1.77 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=3.67;MQ=58.99;MQ0=0;OQ=549.81;QD=11.95;SB=-107.61 GT:AD:DP:GL:GQ 0/1:22,24:42:-70.93,-12.66,-83.77:99 +chr1 3362717 . A G 41.71 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.52;MQ=59.65;MQ0=0;OQ=773.42;QD=14.59;SB=-374.28 GT:AD:DP:GL:GQ 0/1:23,30:49:-95.39,-14.76,-86.55:99 +chr1 3363471 rs56365322 C G 249.90 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.24;MQ0=0;OQ=638.66;QD=11.61;SB=-240.06 GT:AD:DP:GL:GQ 0/1:30,25:50:-82.23,-15.08,-125.58:99 +chr1 3363827 rs2493256 A G 265.69 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=58.48;MQ0=0;OQ=531.11;QD=12.35;SB=-221.59 GT:AD:DP:GL:GQ 0/1:23,19:42:-71.22,-14.82,-89.22:99 +chr1 3364220 rs12745860 C T 264.50 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=58.78;MQ0=0;OQ=718.26;QD=12.60;SB=-212.70 GT:AD:DP:GL:GQ 0/1:33,24:53:-91.09,-15.98,-94.23:99 +chr1 3364244 rs12758368 T A 250.46 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=59.27;MQ0=0;OQ=910.80;QD=14.46;SB=-359.58 GT:AD:DP:GL:GQ 0/1:33,30:62:-113.04,-18.68,-119.17:99 +chr1 3364803 rs56242281 A G 70.18 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.36;MQ=59.30;MQ0=0;OQ=300.82;QD=9.12;SB=-84.67 GT:AD:DP:GL:GQ 0/1:18,14:30:-42.41,-9.04,-64.59:99 +chr1 3365228 rs61759235 A G 136.44 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=58.63;MQ0=0;OQ=478.85;QD=9.39;SB=-239.48 GT:AD:DP:GL:GQ 0/1:30,21:48:-65.63,-14.46,-116.95:99 +chr1 3365583 rs61759236 C G 131.55 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=835.90;QD=18.58;SB=-383.86 GT:AD:DP:GL:GQ 0/1:22,23:43:-99.85,-12.97,-77.78:99 +chr1 3366053 rs61759237 C T 131.92 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=735.43;QD=17.10;SB=-313.83 GT:AD:DP:GL:GQ 0/1:21,22:42:-89.48,-12.65,-70.75:99 +chr1 3366393 rs12059504 T C 302.48 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=609.78;QD=12.70;SB=-240.29 GT:AD:DP:GL:GQ 0/1:24,24:48:-78.73,-14.47,-96.53:99 +chr1 3366983 rs59183260 C T 199.73 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.76;MQ=59.56;MQ0=0;OQ=586.61;QD=13.97;SB=-272.28 GT:AD:DP:GL:GQ 0/1:22,20:39:-73.71,-11.76,-62.95:99 +chr1 3367203 rs2487681 T C 222.79 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=60.00;MQ0=0;OQ=351.40;QD=8.79;SB=-154.93 GT:AD:DP:GL:GQ 0/1:22,18:38:-49.88,-11.46,-85.17:99 +chr1 3372040 rs10909947 G T 39.70 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.75;MQ0=0;OQ=1667.04;QD=35.47;SB=-355.84 GT:AD:DP:GL:GQ 1/1:0,47:46:-170.30,-13.86,-0.01:99 +chr1 3372773 . T G 28.89 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=4.07;MQ=59.49;MQ0=0;QD=0.64;SB=56.17 GT:AD:DP:GL:GQ 0/1:32,13:34:-16.42,-10.24,-99.13:61.72 +chr1 3372898 rs947351 G A 372.12 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.19;MQ0=0;OQ=649.44;QD=12.49;SB=-216.21 GT:AD:DP:GL:GQ 0/1:28,24:49:-83.00,-14.77,-93.12:99 +chr1 3373453 rs3893316 G T 349.34 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=441.10;QD=14.70;SB=-201.58 GT:AD:DP:GL:GQ 0/1:13,17:29:-56.13,-8.74,-43.76:99 +chr1 3373525 rs7550948 G A 64.51 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.53;MQ0=0;OQ=1066.26;QD=21.76;SB=-418.80 GT:AD:DP:GL:GQ 0/1:18,31:47:-124.08,-14.17,-50.84:99 +chr1 3373758 rs6424078 A G 63.51 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=58.45;MQ0=0;OQ=303.09;QD=10.10;SB=-109.62 GT:AD:DP:GL:GQ 0/1:15,15:29:-42.34,-8.75,-57.35:99 +chr1 3373912 rs45512802 C T 115.92 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.77;MQ=58.81;MQ0=0;OQ=487.90;QD=12.51;SB=-154.65 GT:AD:DP:GL:GQ 0/1:21,18:37:-63.22,-11.15,-77.33:99 +chr1 3374091 rs6667361 A G 15.86 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=1.91;MQ=58.45;MQ0=0;OQ=441.93;QD=9.82;SB=-196.52 GT:AD:DP:GL:GQ 0/1:26,19:43:-60.43,-12.96,-100.55:99 +chr1 3374466 rs7522513 A G 114.35 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.36;MQ0=0;OQ=449.01;QD=11.23;SB=-195.64 GT:AD:DP:GL:GQ 0/1:20,20:37:-59.34,-11.16,-69.75:99 +chr1 3374989 rs2493250 G A 285.91 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.52;MQ0=0;OQ=823.07;QD=17.15;SB=-412.42 GT:AD:DP:GL:GQ 0/1:23,25:48:-100.06,-14.47,-73.79:99 +chr1 3374999 rs2487673 G T 438.47 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=759.07;QD=16.87;SB=-384.82 GT:AD:DP:GL:GQ 0/1:19,26:45:-92.75,-13.56,-63.83:99 +chr1 3375110 rs1417897 C A 224.44 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=57.71;MQ0=0;OQ=613.48;QD=15.73;SB=-271.51 GT:AD:DP:GL:GQ 0/1:18,21:37:-75.78,-11.15,-51.34:99 +chr1 3375116 rs1891143 A G 122.77 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=57.71;MQ0=0;OQ=346.85;QD=8.89;SB=-128.27 GT:AD:DP:GL:GQ 0/1:22,17:35:-48.52,-10.55,-81.11:99 +chr1 3375190 rs2493249 T C 0.27 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=3;HaplotypeScore=2.59;MQ=59.45;MQ0=0;OQ=889.42;QD=26.16;SB=-381.39 GT:AD:DP:GL:GQ 1/1:0,34:28:-92.55,-8.44,-0.02:84.20 +chr1 3377520 . G A 54.48 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=60.00;MQ0=0;OQ=404.10;QD=10.92;SB=-123.57 GT:AD:DP:GL:GQ 0/1:21,16:32:-53.34,-9.65,-57.04:99 +chr1 3379133 rs2298082 T C 273.90 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.53;MQ=58.32;MQ0=0;OQ=528.06;QD=13.20;SB=-222.68 GT:AD:DP:GL:GQ 0/1:19,21:37:-67.24,-11.15,-73.98:99 +chr1 3379181 rs2487687 C T 16.32 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=60.00;MQ0=0;OQ=545.94;QD=21.00;SB=-232.27 GT:AD:DP:GL:GQ 0/1:9,17:25:-65.41,-7.53,-31.41:99 +chr1 3379587 rs2185639 C T 119.32 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=58.13;MQ0=0;OQ=232.01;QD=9.28;SB=-26.61 GT:AD:DP:GL:GQ 0/1:14,10:22:-33.12,-6.63,-45.28:99 +chr1 3380098 rs2493323 T A 210.96 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1873.41;QD=38.23;SB=-364.88 GT:AD:DP:GL:GQ 1/1:0,49:49:-190.94,-14.76,-0.01:99 +chr1 3380882 rs2493322 G A 155.52 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=666.25;QD=12.34;SB=-269.17 GT:AD:DP:GL:GQ 0/1:33,21:52:-85.58,-15.67,-103.39:99 +chr1 3381466 . A G 34.09 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.23;MQ=18.93;MQ0=48;QD=0.47;SB=2.04 GT:AD:DP:GL:GQ 0/1:58,15:13:-10.61,-3.92,-40.00:66.92 +chr1 3381536 rs2493320 G A 66.96 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=9.35;MQ0=30;OQ=163.18;QD=3.98;SB=-10.00 GT:AD:DP:GL:GQ 1/1:12,29:5:-19.88,-1.51,-0.00:15.05 +chr1 3381776 rs56863381 G A 0.39 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=12.80;MQ0=34;OQ=57.75;QD=1.03;SB=5.02 GT:AD:DP:GL:GQ 0/1:40,16:11:-12.38,-3.32,-24.49:90.59 +chr1 3382016 . A G 35.80 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=12.28;MQ0=39;QD=0.55;SB=-10.00 GT:AD:DP:GL:GQ 0/1:54,11:16:-11.69,-4.82,-49.41:68.63 +chr1 3382186 rs2493318 A G 275.57 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=47.26;MQ0=1;OQ=747.71;QD=13.35;SB=-372.26 GT:AD:DP:GL:GQ 0/1:27,29:52:-93.72,-15.67,-105.01:99 +chr1 3382897 rs12124163 G T 198.71 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.56;MQ0=0;OQ=598.86;QD=14.26;SB=-222.53 GT:AD:DP:GL:GQ 0/1:21,21:41:-75.52,-12.35,-66.44:99 +chr1 3383727 rs10797394 G A 171.07 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=49.26;MQ0=0;QD=13.16;SB=8.03 GT:AD:DP:GL:GQ 0/1:7,6:12:-24.01,-3.62,-19.11:99 +chr1 3383981 rs56341824 G T 14.44 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=1.70;MQ=59.25;MQ0=0;OQ=147.62;QD=5.90;SB=-6.99 GT:AD:DP:GL:GQ 0/1:17,8:23:-24.98,-6.93,-50.77:99 +chr1 3384110 rs10909948 C T 220.05 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=54.75;MQ0=0;OQ=493.02;QD=17.00;SB=-263.55 GT:AD:DP:GL:GQ 0/1:13,16:28:-61.02,-8.44,-45.99:99 +chr1 3384316 rs4638054 T C 12.90 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.07;MQ0=0;OQ=1239.78;QD=27.55;SB=-421.16 GT:AD:DP:GL:GQ 1/1:0,45:41:-127.61,-12.37,-0.05:99 +chr1 3384500 rs4422946 A G 10.27 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=2;HaplotypeScore=1.93;MQ=60.00;MQ0=0;OQ=259.70;QD=9.27;SB=-73.94 GT:AD:DP:GL:GQ 0/1:16,12:25:-36.79,-7.54,-56.39:99 +chr1 3384534 rs4534324 T C 47.15 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.99;MQ0=0;OQ=674.08;QD=29.31;SB=-343.44 GT:AD:DP:GL:GQ 1/1:0,23:22:-71.01,-6.63,-0.02:66.16 +chr1 3384899 rs10797395 G A 51.14 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=4.52;MQ=59.38;MQ0=0;OQ=712.83;QD=19.27;SB=-338.87 GT:AD:DP:GL:GQ 0/1:16,21:35:-85.11,-10.54,-50.14:99 +chr1 3385089 rs4553117 T C 310.38 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=892.31;QD=26.24;SB=-387.26 GT:AD:DP:GL:GQ 1/1:0,34:29:-92.85,-8.75,-0.03:87.19 +chr1 3385248 rs28568519 C G 124.68 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=59.45;MQ0=0;OQ=725.71;QD=17.28;SB=-286.30 GT:AD:DP:GL:GQ 0/1:20,22:38:-87.31,-11.46,-71.37:99 +chr1 3386469 rs881978 C T 144.12 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=2.64;MQ=59.25;MQ0=0;OQ=1109.69;QD=19.82;SB=-578.43 GT:AD:DP:GL:GQ 0/1:23,33:55:-130.82,-16.57,-79.57:99 +chr1 3386922 rs56309807 G A 10.71 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=6.20;MQ=58.23;MQ0=0;OQ=434.23;QD=11.74;SB=-179.25 GT:AD:DP:GL:GQ 0/1:20,16:31:-56.05,-9.34,-54.39:99 +chr1 3387048 rs2487677 T C 22.85 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.93;MQ=58.11;MQ0=0;OQ=1498.47;QD=31.88;SB=-723.23 GT:AD:DP:GL:GQ 1/1:0,46:43:-153.45,-12.96,-0.02:99 +chr1 3387315 rs1051515 G A 124.17 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=59.55;MQ0=0;OQ=661.19;QD=15.03;SB=-242.52 GT:AD:DP:GL:GQ 0/1:21,23:41:-81.76,-12.36,-69.63:99 +chr1 3387424 rs1051517 C T 185.79 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.57;MQ0=0;OQ=722.32;QD=16.80;SB=-358.40 GT:AD:DP:GL:GQ 0/1:21,22:42:-88.17,-12.66,-71.34:99 +chr1 3387765 rs2487676 G C 0.92 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=59.56;MQ0=0;OQ=985.55;QD=23.47;SB=-402.96 GT:AD:DP:GL:GQ 0/1:13,29:39:-113.61,-11.77,-48.31:99 +chr1 3387785 rs10797396 G A 343.20 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=869.16;QD=19.75;SB=-452.50 GT:AD:DP:GL:GQ 0/1:15,29:41:-102.56,-12.36,-46.08:99 +chr1 3388739 . G C 3.92 PASS AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=47.12;MQ0=0;OQ=99.91;QD=7.14;SB=-0.98 GT:AD:DP:GL:GQ 0/1:10,4:13:-17.20,-3.93,-33.90:99 +chr1 3388844 rs11579276 C T 89.01 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=228.92;QD=8.80;SB=-0.98 GT:AD:DP:GL:GQ 0/1:16,10:21:-32.51,-6.33,-40.91:99 +chr1 3389315 rs2493316 T C 332.07 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=364.79;QD=11.40;SB=-143.65 GT:AD:DP:GL:GQ 0/1:18,14:32:-49.41,-9.65,-68.22:99 +chr1 3390585 rs12124659 C T 210.63 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=1350.80;QD=37.52;SB=-227.30 GT:AD:DP:GL:GQ 1/1:0,36:35:-138.68,-10.55,-0.01:99 +chr1 3391131 rs2487674 A G 49.46 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=2482.25;QD=31.82;SB=-1068.16 GT:AD:DP:GL:GQ 1/1:0,78:76:-251.87,-22.92,-0.06:99 +chr1 3392093 rs4648504 C T 77.49 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=53.45;MQ0=1;OQ=1952.99;QD=36.17;SB=-850.15 GT:AD:DP:GL:GQ 1/1:1,53:50:-198.90,-15.06,-0.02:99 +chr1 3394087 rs2821041 C T 330.28 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=59.75;MQ0=0;OQ=1098.32;QD=14.64;SB=-325.80 GT:AD:DP:GL:GQ 0/1:41,34:73:-135.10,-21.99,-140.04:99 +chr1 3394997 rs61759244 C G 135 PASS AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=59.37;MQ0=0;OQ=1716.91;QD=17.88;SB=-792.82 GT:AD:DP:GL:GQ 0/1:43,53:93:-203.04,-28.07,-171.23:99 +chr1 3395156 rs4648505 T C 309 PASS AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.51;MQ0=0;OQ=921.20;QD=9.70;SB=-319.80 GT:AD:DP:GL:GQ 0/1:57,38:95:-124.03,-28.62,-233.81:99 +chr1 3401826 rs2821034 T C 25.42 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=5.69;MQ=57.22;MQ0=0;OQ=336.60;QD=15.30;SB=-157.73 GT:AD:DP:GL:GQ 1/1:0,21:12:-37.26,-3.62,-0.02:36.06 +chr1 3406983 . G A 147.34 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=493.27;QD=14.51;SB=-172.20 GT:AD:DP:GL:GQ 0/1:17,17:33:-62.55,-9.94,-60.75:99 +chr1 3408031 rs7516662 A G 45.84 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=59.41;MQ0=0;OQ=599.81;QD=15.38;SB=-119.66 GT:AD:DP:GL:GQ 0/1:18,21:37:-74.41,-11.15,-64.16:99 +chr1 3408425 rs2821030 T C 291.53 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=44.95;MQ0=0;OQ=775.65;QD=13.61;SB=-335.17 GT:AD:DP:GL:GQ 0/1:17,40:43:-93.82,-12.97,-49.21:99 +chr1 3408438 rs56284135 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=5;HaplotypeScore=43.60;MQ=44.49;MQ0=0;OQ=630.57;QD=9.70;SB=-139.40 GT:AD:DP:GL:GQ 0/1:28,36:49:-81.11,-14.77,-94.33:99 +chr1 3408476 rs57408931 G C 181.30 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=164;Dels=0.03;HRun=1;HaplotypeScore=218.91;MQ=41.51;MQ0=3;QD=1.11;SB=-63.16 GT:AD:DP:GL:GQ 0/1:117,24:115:-89.58,-68.17,-379.21:99 +chr1 3408478 rs57082253 G A 513.03 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.00;HRun=0;HaplotypeScore=193.59;MQ=41.21;MQ0=2;QD=2.85;SB=-274.73 GT:AD:DP:GL:GQ 0/1:134,38:129:-95.85,-41.26,-324.12:99 +chr1 3408517 rs7368034 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=115;Dels=0.00;HRun=0;HaplotypeScore=120.54;MQ=42.22;MQ0=3;OQ=514.65;QD=4.48;SB=-116.36 GT:AD:DP:GL:GQ 0/1:73,33:82:-88.72,-33.97,-192.96:99 +chr1 3411446 rs6669870 C T 607.77 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.14;MQ0=0;OQ=1485.27;QD=36.23;SB=-614.81 GT:AD:DP:GL:GQ 1/1:0,41:39:-152.13,-11.76,-0.02:99 +chr1 3411518 rs2821009 A T 529.19 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.77;MQ0=0;OQ=1252.41;QD=34.79;SB=-623.61 GT:AD:DP:GL:GQ 1/1:0,36:35:-128.84,-10.55,-0.01:99 +chr1 3411757 rs2821008 A G 31.18 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=59.41;MQ0=0;OQ=238.32;QD=6.11;SB=-110.60 GT:AD:DP:GL:GQ 0/1:25,14:37:-38.27,-11.15,-99.52:99 +chr1 3413327 rs947344 C T 169.75 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.94;MQ=58.66;MQ0=0;OQ=1006.19;QD=19.35;SB=-478.56 GT:AD:DP:GL:GQ 0/1:21,31:45:-117.47,-13.57,-45.94:99 +chr1 3413493 rs2821006 A G 514.34 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1416.92;QD=30.15;SB=-704.80 GT:AD:DP:GL:GQ 1/1:0,47:45:-145.32,-13.57,-0.04:99 +chr1 3413602 rs10797397 C A 230.35 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.01;MQ=59.11;MQ0=0;OQ=969.58;QD=16.43;SB=-386.82 GT:AD:DP:GL:GQ 0/1:25,34:55:-116.81,-16.57,-75.73:99 +chr1 3414248 rs947345 G A 253.45 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.28;MQ=59.23;MQ0=0;OQ=855.83;QD=14.26;SB=-381.90 GT:AD:DP:GL:GQ 0/1:31,29:53:-104.84,-15.98,-85.70:99 +chr1 3415290 rs2794358 A G 117.33 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1082.49;QD=30.93;SB=-492.45 GT:AD:DP:GL:GQ 1/1:0,35:32:-111.85,-9.64,-0.02:96.25 +chr1 3416927 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=20.42;MQ=57.31;MQ0=0;OQ=341.32;QD=7.11;SB=-84.89 GT:AD:DP:GL:GQ 0/1:26,19:38:-51.91,-14.49,-87.40:99 +chr1 3416981 rs56310990 G C 2.17 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=51.26;MQ0=0;OQ=93.69;QD=3.02;SB=-14.81 GT:AD:DP:GL:GQ 0/1:25,6:25:-20.20,-7.54,-81.40:99 +chr1 3416998 . C T 35.62 PASS AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=49.93;MQ0=0;OQ=473.15;QD=15.77;SB=-230.75 GT:AD:DP:GL:GQ 0/1:10,20:24:-57.83,-7.23,-29.03:99 +chr1 3418020 rs2820999 T G 23.07 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=1.35;MQ=59.30;MQ0=0;OQ=1099.49;QD=33.32;SB=-419.27 GT:AD:DP:GL:GQ 1/1:0,32:32:-113.54,-9.64,-0.01:96.28 +chr1 3418284 rs4648391 G T 480.48 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1326.40;QD=33.16;SB=-497.29 GT:AD:DP:GL:GQ 1/1:0,40:39:-136.24,-11.75,-0.02:99 +chr1 3418288 rs4648514 C T 298.40 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=1504.64;QD=38.58;SB=-514.18 GT:AD:DP:GL:GQ 1/1:0,39:39:-154.07,-11.75,-0.02:99 +chr1 3418468 rs11585362 G A 504.11 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1061.06;QD=36.59;SB=-446.58 GT:AD:DP:GL:GQ 1/1:0,29:29:-109.71,-8.74,-0.02:87.27 +chr1 3419555 rs11587354 C A 388.99 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=2174.38;QD=35.07;SB=-358.82 GT:AD:DP:GL:GQ 1/1:0,62:58:-221.04,-17.47,-0.02:99 +chr1 3420506 . T A 214.92 PASS AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1094.09;QD=36.47;SB=-408.28 GT:AD:DP:GL:GQ 1/1:0,30:30:-113.00,-9.04,-0.01:90.28 +chr1 3422067 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=4;HaplotypeScore=5.56;MQ=56.93;MQ0=0;OQ=142.54;QD=3.85;SB=26.11 GT:AD:DP:GL:GQ 0/1:17,20:22:-24.18,-6.64,-53.52:99 +chr1 3422138 rs12045137 C G 147.05 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1703.92;QD=40.57;SB=-765.63 GT:AD:DP:GL:GQ 1/1:0,42:41:-174.00,-12.36,-0.02:99 +chr1 3422853 rs11587498 G A 175.29 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=60.00;MQ0=0;OQ=415.52;QD=12.22;SB=-203.18 GT:AD:DP:GL:GQ 0/1:20,14:31:-54.19,-9.35,-54.52:99 +chr1 3424377 rs2820995 A G 162.79 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=58.66;MQ0=0;OQ=1805.64;QD=27.36;SB=-525.83 GT:AD:DP:GL:GQ 1/1:0,66:60:-184.23,-18.11,-0.08:99 +chr1 3424844 rs2794362 G C 500.34 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1899.04;QD=42.20;SB=-801.86 GT:AD:DP:GL:GQ 1/1:0,45:44:-193.50,-13.26,-0.01:99 +chr1 3427795 rs2794365 T C 272.59 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.56;MQ0=0;OQ=540.74;QD=12.87;SB=-223.28 GT:AD:DP:GL:GQ 0/1:22,20:39:-69.11,-11.75,-73.06:99 +chr1 3428053 rs11587384 G A 58.66 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=58.59;MQ0=0;OQ=656.10;QD=19.88;SB=-350.39 GT:AD:DP:GL:GQ 0/1:13,20:30:-77.94,-9.05,-31.18:99 +chr1 3428530 rs10909958 C T 169.55 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=60.00;MQ0=0;OQ=649.49;QD=10.31;SB=-164.81 GT:AD:DP:GL:GQ 0/1:40,23:61:-86.62,-18.39,-128.91:99 +chr1 3429888 rs10797398 G C 1.63 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=0.26;MQ=58.87;MQ0=0;OQ=1501.66;QD=40.59;SB=-598.80 GT:AD:DP:GL:GQ 1/1:0,37:37:-153.77,-11.16,-0.02:99 +chr1 3430507 rs2794322 T C 118.81 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=864.34;QD=26.19;SB=-416.15 GT:AD:DP:GL:GQ 1/1:0,33:29:-90.06,-8.75,-0.04:87.16 +chr1 3430803 rs12049449 A C 10.61 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=1.13;MQ=59.39;MQ0=0;OQ=1279.24;QD=33.66;SB=-506.06 GT:AD:DP:GL:GQ 1/1:0,38:37:-131.52,-11.15,-0.02:99 +chr1 3431124 rs12093117 G A 200.25 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.17;MQ=59.61;MQ0=0;OQ=828.18;QD=17.25;SB=-263.28 GT:AD:DP:GL:GQ 0/1:20,28:45:-99.67,-13.57,-58.69:99 +chr1 3432615 rs11589895 G A 209.87 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.89;MQ0=0;OQ=771.91;QD=18.38;SB=-386.90 GT:AD:DP:GL:GQ 0/1:19,23:42:-93.13,-12.66,-62.18:99 +chr1 3433053 . C T 70.11 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=58.26;MQ0=0;OQ=707.05;QD=13.86;SB=-362.49 GT:AD:DP:GL:GQ 0/1:26,25:48:-88.45,-14.46,-91.49:99 +chr1 3435213 rs2821068 G C 38.82 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=58.11;MQ0=0;OQ=1371.97;QD=37.08;SB=-540.03 GT:AD:DP:GL:GQ 1/1:0,36:33:-140.79,-9.95,-0.01:99 +chr1 3435771 rs883427 G A 416.41 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.00;MQ0=0;OQ=1899.02;QD=38.76;SB=-741.50 GT:AD:DP:GL:GQ 1/1:0,49:48:-193.50,-14.46,-0.01:99 +chr1 3436171 rs11589175 G A 118.39 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=494.22;QD=9.88;SB=-114.31 GT:AD:DP:GL:GQ 0/1:32,17:48:-69.83,-17.13,-113.83:99 +chr1 3436855 rs11811714 C T 197.39 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=58.93;MQ0=0;OQ=2210.05;QD=36.23;SB=-988.23 GT:AD:DP:GL:GQ 1/1:0,61:58:-224.62,-17.49,-0.03:99 +chr1 3436977 rs56103034 G C 151.47 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=60.00;MQ0=0;OQ=361.61;QD=12.91;SB=-169.18 GT:AD:DP:GL:GQ 0/1:15,13:27:-47.59,-8.14,-66.07:99 +chr1 3437069 . A C 13.05 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=2;HaplotypeScore=6.13;MQ=58.68;MQ0=0;QD=0.25;SB=74.24 GT:AD:DP:GL:GQ 0/1:37,15:37:-15.71,-11.15,-109.98:45.67 +chr1 3438669 rs61762171 G A 197.19 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.08;MQ=59.50;MQ0=0;OQ=831.35;QD=18.07;SB=-356.42 GT:AD:DP:GL:GQ 0/1:21,25:43:-99.38,-12.97,-55.25:99 +chr1 3438727 rs55762450 C A 163.97 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.39;MQ=59.54;MQ0=0;OQ=660.37;QD=13.21;SB=-236.28 GT:AD:DP:GL:GQ 0/1:20,30:45:-82.89,-13.57,-69.96:99 +chr1 3440115 rs2493313 T C 297.46 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=56.74;MQ0=0;OQ=1008.77;QD=34.79;SB=-528.20 GT:AD:DP:GL:GQ 1/1:0,29:29:-104.47,-8.74,-0.01:87.25 +chr1 3444452 rs9970944 G T 111.06 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.08;MQ=58.11;MQ0=0;OQ=1564.30;QD=32.59;SB=-784.47 GT:AD:DP:GL:GQ 1/1:1,47:45:-160.04,-13.56,-0.02:99 +chr1 3445102 rs12049456 G A 432 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.32;MQ0=0;OQ=1256.64;QD=36.96;SB=-508.18 GT:AD:DP:GL:GQ 1/1:0,34:33:-129.26,-9.95,-0.01:99 +chr1 3445120 . C G 39.08 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=55.59;MQ0=2;QD=0.85;SB=59.22 GT:AD:DP:GL:GQ 0/1:40,6:41:-19.55,-12.36,-150.78:71.92 +chr1 3448511 rs2821064 A T 100.60 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.44;MQ=58.81;MQ0=0;OQ=526.36;QD=13.50;SB=-238.77 GT:AD:DP:GL:GQ 0/1:20,19:39:-67.67,-11.75,-70.26:99 +chr1 3448541 rs2794331 G C 111.94 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=58.71;MQ0=0;OQ=556.37;QD=15.45;SB=-245.10 GT:AD:DP:GL:GQ 0/1:19,17:32:-68.58,-9.65,-62.08:99 +chr1 3448992 rs12065874 C T 177.16 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.46;MQ0=0;OQ=793.34;QD=18.45;SB=-374.15 GT:AD:DP:GL:GQ 0/1:19,24:39:-94.38,-11.76,-47.24:99 +chr1 3452764 rs10797401 T C 166.54 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=59.52;MQ0=0;OQ=647.76;QD=16.61;SB=-319.33 GT:AD:DP:GL:GQ 0/1:16,23:38:-79.51,-11.45,-58.06:99 +chr1 3453088 rs28479691 G A 97.36 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=55.43;MQ0=1;OQ=249.39;QD=11.34;SB=-131.56 GT:AD:DP:GL:GQ 0/1:11,11:18:-33.65,-5.43,-32.56:99 +chr1 3453209 rs13374309 C G 5.21 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=3.14;MQ=57.20;MQ0=0;OQ=292.98;QD=15.42;SB=-154.58 GT:AD:DP:GL:GQ 0/1:9,10:17:-37.71,-5.13,-33.06:99 +chr1 3455556 rs7539836 A G 113.09 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=359.37;QD=13.82;SB=-189.55 GT:AD:DP:GL:GQ 0/1:12,14:25:-46.76,-7.53,-43.20:99 +chr1 3458010 rs7533321 G A 155.67 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.46;MQ0=0;OQ=810.48;QD=18.85;SB=-428.48 GT:AD:DP:GL:GQ 0/1:17,25:39:-96.09,-11.75,-47.40:99 +chr1 3458818 rs6413780 A C 146.27 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.53;MQ0=0;OQ=401.98;QD=8.20;SB=-115.74 GT:AD:DP:GL:GQ 0/1:29,20:47:-57.64,-14.16,-107.92:99 +chr1 3458949 rs7355038 G A 151.46 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=59.19;MQ0=0;OQ=998.13;QD=19.19;SB=-471.50 GT:AD:DP:GL:GQ 0/1:22,30:52:-118.77,-15.67,-71.64:99 +chr1 3460223 rs10909965 T G 23.16 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=1;HaplotypeScore=2.59;MQ=58.78;MQ0=0;OQ=201.44;QD=10.60;SB=-54.94 GT:AD:DP:GL:GQ 0/1:10,9:17:-28.55,-5.12,-30.64:99 +chr1 3460241 rs12078542 T C 57.79 PASS AC=1;AF=0.50;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.39;MQ0=0;OQ=207.08;QD=7.14;SB=-117.62 GT:AD:DP:GL:GQ 0/1:17,12:22:-30.63,-6.64,-46.05:99 +chr1 3460729 rs1557089 T G 340.61 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.05;MQ0=0;OQ=311.87;QD=12.99;SB=-162.75 GT:AD:DP:GL:GQ 0/1:12,12:20:-40.49,-6.02,-30.26:99 +chr1 3462253 rs7516641 A G 481.67 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=514.29;QD=11.96;SB=-180.52 GT:AD:DP:GL:GQ 0/1:23,20:43:-67.67,-12.96,-92.19:99 +chr1 3466443 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=45;Dels=0.02;HRun=17;HaplotypeScore=21.57;MQ=53.85;MQ0=0;OQ=205.19;QD=4.56;SB=-78.83 GT:AD:DP:GL:GQ 0/1:24,20:32:-33.15,-9.34,-78.96:99 +chr1 3466697 . C G 64.69 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=58.96;MQ0=0;OQ=671.74;QD=12.44;SB=-259.12 GT:AD:DP:GL:GQ 0/1:31,23:50:-85.55,-15.09,-116.59:99 +chr1 3474782 rs56410789 G A 184.63 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=59.61;MQ0=0;OQ=703.19;QD=14.65;SB=-349.63 GT:AD:DP:GL:GQ 0/1:25,22:45:-89.80,-16.20,-75.19:99 +chr1 3480873 . T C 0.25 PASS AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=3;HaplotypeScore=1.82;MQ=59.06;MQ0=0;OQ=234.33;QD=11.72;SB=-33.65 GT:AD:DP:GL:GQ 0/1:10,10:19:-32.44,-5.72,-41.44:99 +chr1 3480967 rs4431782 T C 9.06 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=2.79;MQ=59.14;MQ0=0;OQ=141.27;QD=5.23;SB=-37.66 GT:AD:DP:GL:GQ 0/1:16,11:24:-24.65,-7.24,-64.66:99 +chr1 3482056 rs2821057 A G 50.28 Indel AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.04;HRun=0;HaplotypeScore=40.06;MQ=43.76;MQ0=3;QD=0.93;SB=-23.61 GT:AD:DP:GL:GQ 0/1:44,8:48:-22.18,-13.87,-154.71:83.12 +chr1 3483124 rs2821056 A T 583.97 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.89;MQ0=0;OQ=1839.69;QD=37.54;SB=-868.96 GT:AD:DP:GL:GQ 1/1:0,49:49:-187.56,-14.76,-0.01:99 +chr1 3483560 rs2821055 T C 111.86 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=57.13;MQ0=0;OQ=1375.27;QD=31.98;SB=-687.18 GT:AD:DP:GL:GQ 1/1:0,43:41:-141.13,-12.35,-0.02:99 +chr1 3483710 rs2821054 G T 266.86 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.07;MQ0=0;OQ=1733.58;QD=34.67;SB=-747.08 GT:AD:DP:GL:GQ 1/1:0,50:50:-176.97,-15.07,-0.02:99 +chr1 3484389 rs2794348 A G 1.13 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=6.39;MQ=58.05;MQ0=0;OQ=1127.20;QD=31.31;SB=-545.88 GT:AD:DP:GL:GQ 1/1:0,36:34:-116.33,-10.25,-0.02:99 +chr1 3484478 rs2794347 G C 132.33 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.47;MQ0=0;OQ=1529.91;QD=34.77;SB=-715.91 GT:AD:DP:GL:GQ 1/1:0,44:40:-156.62,-12.09,-0.05:99 +chr1 3484580 rs2794346 G A 64.20 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=980.89;QD=28.85;SB=-342.41 GT:AD:DP:GL:GQ 1/1:1,32:27:-101.70,-8.14,-0.02:81.23 +chr1 3485237 rs2794344 G A 227.50 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=58.20;MQ0=0;OQ=1135.92;QD=18.03;SB=-434.44 GT:AD:DP:GL:GQ 0/1:26,37:58:-134.36,-17.49,-77.46:99 +chr1 3485276 rs2794343 G T 262.44 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=58.14;MQ0=0;OQ=635.86;QD=12.00;SB=-319.27 GT:AD:DP:GL:GQ 0/1:28,25:50:-81.94,-15.07,-81.25:99 +chr1 3485297 rs2794342 T C 164.76 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.19;MQ=55.76;MQ0=0;OQ=873.19;QD=16.17;SB=-382.03 GT:AD:DP:GL:GQ 0/1:20,34:51:-105.98,-15.38,-70.34:99 +chr1 3485317 . C T 0.61 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=55.51;MQ0=0;OQ=217.69;QD=4.03;SB=-62.86 GT:AD:DP:GL:GQ 0/1:42,11:46:-38.92,-13.87,-116.02:99 +chr1 3485320 . C T 0.57 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=55.81;MQ0=0;OQ=186.10;QD=3.58;SB=-62.80 GT:AD:DP:GL:GQ 0/1:41,10:44:-35.15,-13.26,-125.21:99 +chr1 3485329 rs56044258 C G 8.19 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=4.19;MQ=55.35;MQ0=0;OQ=1813.27;QD=38.58;SB=-922.42 GT:AD:DP:GL:GQ 1/1:0,47:43:-184.93,-12.96,-0.02:99 +chr1 3485401 rs2821053 T C 608.29 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.09;MQ0=0;OQ=2115.06;QD=34.11;SB=-1060.08 GT:AD:DP:GL:GQ 1/1:0,62:60:-215.11,-18.07,-0.02:99 +chr1 3485841 rs2794341 T C 133.27 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=59.57;MQ0=0;OQ=1280.08;QD=29.77;SB=-579.98 GT:AD:DP:GL:GQ 1/1:0,43:41:-131.63,-12.37,-0.04:99 +chr1 3485914 rs2821052 G C 139.61 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=59.60;MQ0=0;OQ=1918.65;QD=40.82;SB=-901.42 GT:AD:DP:GL:GQ 1/1:0,47:46:-195.47,-13.86,-0.02:99 +chr1 3486188 rs2821051 T C 180.06 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.51;MQ0=0;OQ=1502.08;QD=31.96;SB=-651.24 GT:AD:DP:GL:GQ 1/1:0,47:44:-153.81,-13.26,-0.02:99 +chr1 3486339 rs2794340 T C 195.59 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=747.54;QD=27.69;SB=-185.41 GT:AD:DP:GL:GQ 1/1:0,27:25:-78.37,-7.54,-0.03:75.17 +chr1 3486805 rs2794339 G A 3.01 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=790.02;QD=34.35;SB=-39.54 GT:AD:DP:GL:GQ 1/1:0,23:21:-82.60,-6.33,-0.01:63.20 +chr1 3486898 . C G 23.94 LowQual AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=3.33;MQ=60.00;MQ0=0;QD=2.18;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,7:5:-7.19,-1.52,-10.35:56.76 +chr1 3486969 rs2821050 A G 170.61 PASS AC=2;AF=1.00;AN=2;DB;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.66;MQ0=0;OQ=230.85;QD=23.09;SB=-101.03 GT:AD:DP:GL:GQ 1/1:0,10:9:-26.68,-2.72,-0.01:27.04 +chr1 3487085 rs2821049 G A 44.18 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.41;MQ0=1;OQ=1103.43;QD=35.59;SB=-441.32 GT:AD:DP:GL:GQ 1/1:0,31:29:-113.94,-8.74,-0.01:87.28 +chr1 3487785 rs2821048 T C 3.27 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=59.07;MQ0=0;OQ=795.96;QD=29.48;SB=-323.61 GT:AD:DP:GL:GQ 1/1:0,26:24:-83.19,-7.23,-0.01:72.20 +chr1 3488346 rs2821047 A C 41.05 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.50;MQ0=0;OQ=1833.45;QD=33.34;SB=-923.21 GT:AD:DP:GL:GQ 1/1:0,55:53:-186.95,-15.96,-0.02:99 +chr1 3488543 rs2794338 G A 5.07 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=2.25;MQ=59.38;MQ0=0;OQ=1108.21;QD=36.94;SB=-425.07 GT:AD:DP:GL:GQ 1/1:0,30:29:-114.42,-8.74,-0.01:87.27 +chr1 3488600 rs2821046 T C 153.98 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=59.16;MQ0=0;OQ=1640.68;QD=29.83;SB=-825.95 GT:AD:DP:GL:GQ 1/1:0,55:53:-167.70,-15.99,-0.05:99 +chr1 3488885 rs2794337 T G 92.94 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.67;MQ0=0;OQ=1036.65;QD=29.62;SB=-469.86 GT:AD:DP:GL:GQ 1/1:0,35:34:-107.28,-10.25,-0.03:99 +chr1 3488911 rs2794336 C A 491.72 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1159.72;QD=31.34;SB=-543.79 GT:AD:DP:GL:GQ 1/1:0,37:35:-119.58,-10.55,-0.02:99 +chr1 3489106 rs2821045 A G 0.45 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=15.70;MQ=58.09;MQ0=0;OQ=1342.02;QD=27.39;SB=-607.24 GT:AD:DP:GL:GQ 1/1:1,48:44:-137.83,-13.27,-0.05:99 +chr1 3489389 rs2794335 C G 104.49 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.91;MQ0=0;OQ=2044.98;QD=41.73;SB=-1038.63 GT:AD:DP:GL:GQ 1/1:0,49:48:-208.10,-14.46,-0.02:99 +chr1 3489541 rs2821044 A G 154.02 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=51.93;MQ0=0;OQ=1856.46;QD=32.01;SB=-939.38 GT:AD:DP:GL:GQ 1/1:0,58:53:-189.25,-15.96,-0.02:99 +chr1 3489730 . G A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=5.70;MQ=38.46;MQ0=13;OQ=219.88;QD=2.71;SB=-20.96 GT:AD:DP:GL:GQ 0/1:65,15:58:-42.77,-17.50,-145.53:99 +chr1 3489856 rs61762194 A G 22.79 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=13.90;MQ=6.46;MQ0=57;QD=0.35;SB=-34.94 GT:AD:DP:GL:GQ 0/1:19,46:3:-6.46,-0.90,-4.17:32.64 +chr1 3490108 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=122;Dels=0.00;HRun=0;HaplotypeScore=22.57;MQ=11.21;MQ0=79;OQ=52.09;QD=0.43;SB=2.03 GT:AD:DP:GL:GQ 0/1:64,55:12:-12.11,-3.62,-27.46:84.92 +chr1 3490124 . G C 37.51 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=28.89;MQ=9.24;MQ0=69;QD=0.40;SB=-36.43 GT:AD:DP:GL:GQ 0/1:52,37:3:-7.94,-0.91,-4.59:36.89 +chr1 3490204 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=9.07;MQ=18.33;MQ0=40;OQ=221.10;QD=2.91;SB=-48.02 GT:AD:DP:GL:GQ 0/1:38,34:16:-30.22,-4.83,-23.80:99 +chr1 3490220 . G C 14.47 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=1;HaplotypeScore=18.26;MQ=21.29;MQ0=44;QD=0.14;SB=5.04 GT:AD:DP:GL:GQ 0/1:89,13:27:-12.87,-8.16,-91.89:47.15 +chr1 3490238 . G C 29.48 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=1;HaplotypeScore=19.99;MQ=24.83;MQ0=54;QD=0.24;SB=65.23 GT:AD:DP:GL:GQ 0/1:92,32:39:-18.02,-11.79,-132.68:62.32 +chr1 3490274 rs61762197 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=195;Dels=0.00;HRun=0;HaplotypeScore=31.55;MQ=26.52;MQ0=97;OQ=140.78;QD=0.72;SB=53.20 GT:AD:DP:GL:GQ 0/1:172,21:60:-35.47,-18.11,-209.36:99 +chr1 3490294 rs61762198 G A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=144;Dels=0.00;HRun=0;HaplotypeScore=18.88;MQ=30.38;MQ0=61;OQ=410.69;QD=2.85;SB=-6.44 GT:AD:DP:GL:GQ 0/1:110,32:48:-58.84,-14.49,-102.11:99 +chr1 3490309 rs61762199 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=126;Dels=0.00;HRun=0;HaplotypeScore=43.37;MQ=33.08;MQ0=48;OQ=683.06;QD=5.42;SB=-30.63 GT:AD:DP:GL:GQ 0/1:101,25:47:-85.76,-14.17,-79.46:99 +chr1 3490312 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=46.24;MQ=34.26;MQ0=40;OQ=200.77;QD=1.72;SB=-32.50 GT:AD:DP:GL:GQ 0/1:85,31:40:-35.43,-12.07,-95.25:99 +chr1 3490435 rs2995009 G A 597.77 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.35;MQ0=0;OQ=1467.09;QD=38.61;SB=-711.36 GT:AD:DP:GL:GQ 1/1:0,38:38:-150.31,-11.45,-0.01:99 +chr1 3491040 rs2995008 T C 284.33 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1828.19;QD=32.07;SB=-897.29 GT:AD:DP:GL:GQ 1/1:0,57:55:-186.44,-16.58,-0.04:99 +chr1 3492147 . G A 23.72 PASS AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=55.26;MQ0=1;OQ=1679.66;QD=32.93;SB=-585.96 GT:AD:DP:GL:GQ 1/1:1,50:45:-171.57,-13.56,-0.02:99 +chr1 3492404 rs2487682 G A 109.67 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=55.97;MQ0=0;OQ=1664.54;QD=34.68;SB=-566.34 GT:AD:DP:GL:GQ 1/1:2,46:43:-170.05,-12.95,-0.01:99 +chr1 3493214 rs10909977 C T 290.65 PASS AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.46;MQ0=0;OQ=982.44;QD=37.79;SB=-341.35 GT:AD:DP:GL:GQ 1/1:0,26:26:-101.84,-7.83,-0.01:78.25 +chr1 3493427 rs12133810 G A 0.43 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=6.10;MQ=60.00;MQ0=0;OQ=1731.58;QD=36.07;SB=-586.35 GT:AD:DP:GL:GQ 1/1:0,47:45:-176.76,-13.56,-0.02:99 +chr1 3493933 rs12139206 T C 718.86 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.76;MQ0=0;OQ=2133.52;QD=33.87;SB=-1000.69 GT:AD:DP:GL:GQ 1/1:0,63:61:-216.96,-18.38,-0.03:99 +chr1 3494278 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=29.95;MQ=39.18;MQ0=0;OQ=57.06;QD=1.00;SB=32.12 GT:AD:DP:GL:GQ 0/1:51,6:50:-24.05,-15.06,-154.00:89.90 +chr1 3494280 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=31.95;MQ=39.34;MQ0=0;OQ=98.32;QD=1.76;SB=29.10 GT:AD:DP:GL:GQ 0/1:46,10:49:-27.88,-14.76,-138.47:99 +chr1 3494307 . T G 201.76 SnpCluster AC=1;AF=0.50;AN=2;DP=58;Dels=0.10;HRun=2;HaplotypeScore=112.88;MQ=32.38;MQ0=0;QD=3.48;SB=-117.62 GT:AD:DP:GL:GQ 0/1:34,18:28:-31.59,-8.13,-64.60:99 +chr1 3494310 rs61762200 C A 192.29 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=121.85;MQ=30.79;MQ0=0;QD=3.43;SB=-60.75 GT:AD:DP:GL:GQ 0/1:36,18:28:-30.95,-8.43,-66.22:99 +chr1 3494317 . G T 32.47 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=81.33;MQ=29.05;MQ0=0;QD=0.60;SB=-10.00 GT:AD:DP:GL:GQ 0/1:41,11:25:-14.06,-7.53,-79.10:65.31 +chr1 3494320 . G A 676.99 SnpCluster AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=53.82;MQ=29.06;MQ0=0;QD=13.02;SB=-10.00 GT:AD:DP:GL:GQ 0/1:6,41:24:-78.21,-7.23,-14.28:70.50 +chr1 3494331 . C T 224.74 SnpCluster AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=74.35;MQ=28.87;MQ0=0;QD=4.68;SB=-10.00 GT:AD:DP:GL:GQ 0/1:29,19:11:-29.07,-3.31,-14.19:99 +chr1 3494338 . G A 223.95 SnpCluster AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=78.36;MQ=28.88;MQ0=0;QD=4.76;SB=-10.00 GT:AD:DP:GL:GQ 0/1:25,22:10:-28.69,-3.01,-9.91:68.95 +chr1 3494340 . G A 250.50 SnpCluster AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=74.35;MQ=28.88;MQ0=0;QD=5.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,38:10:-31.35,-3.01,-6.64:36.27 +chr1 3494344 . G A 85.25 SnpCluster AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=1;HaplotypeScore=68.88;MQ=28.67;MQ0=0;QD=1.85;SB=-10.00 GT:AD:DP:GL:GQ 0/1:41,5:14:-16.03,-4.22,-34.38:99 +chr1 3494347 . A T 143.02 SnpCluster AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=0;HaplotypeScore=69.92;MQ=28.59;MQ0=0;QD=3.87;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,19:7:-19.69,-2.11,-6.98:48.71 +chr1 3494357 . G T 24.90 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=73.10;MQ=28.56;MQ0=0;QD=0.73;SB=-10.00 GT:AD:DP:GL:GQ 0/1:18,15:5:-7.28,-1.51,-10.87:57.73 +chr1 3494360 . G A 23.23 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=81.86;MQ=28.53;MQ0=0;QD=0.73;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,11:6:-7.41,-1.81,-14.17:56.05 +chr1 3494364 . G A 65.76 SnpCluster AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=67.04;MQ=28.12;MQ0=1;QD=1.93;SB=-10.00 GT:AD:DP:GL:GQ 0/1:29,5:7:-11.97,-2.11,-13.57:98.60 +chr1 3494367 . G T 116.01 SnpCluster AC=1;AF=0.50;AN=2;DP=34;Dels=0.03;HRun=0;HaplotypeScore=76.86;MQ=28.12;MQ0=1;QD=3.41;SB=-10.00 GT:AD:DP:GL:GQ 0/1:14,19:9:-17.59,-2.71,-15.13:99 +chr1 3494370 . G C 77.61 SnpCluster AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=1;HaplotypeScore=62.98;MQ=28.25;MQ0=1;QD=2.87;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,7:9:-20.69,-9.65,-24.68:99 +chr1 3494377 . G T 26.91 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=64.80;MQ=28.23;MQ0=1;QD=1.03;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,4:4:-7.18,-1.20,-7.71:59.73 +chr1 3494378 . G A 98.30 SnpCluster AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=59.24;MQ=28.44;MQ0=1;QD=3.78;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,11:7:-15.22,-2.11,-10.61:84.98 +chr1 3494380 . G A 43.51 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=65.22;MQ=28.44;MQ0=1;QD=1.67;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,15:4:-12.40,-4.77,-6.87:20.98 +chr1 3494384 . G A 26.23 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=1;HaplotypeScore=51.99;MQ=28.44;MQ0=1;QD=1.01;SB=-10.00 GT:AD:DP:GL:GQ 0/1:20,6:7:-8.02,-2.11,-15.94:59.06 +chr1 3494390 . G A 130.87 SnpCluster AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=39.84;MQ=28.27;MQ0=1;QD=6.54;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,12:6:-18.18,-1.81,-3.67:18.63 +chr1 3494414 . G A 19.25 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=1;HaplotypeScore=22.06;MQ=28.20;MQ0=1;QD=1.13;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,2:8:-7.61,-2.41,-20.11:52.04 +chr1 3494416 . G C 113.75 SnpCluster AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=18.24;MQ=27.40;MQ0=1;QD=6.32;SB=-10.00 GT:AD:DP:GL:GQ 0/1:14,4:8:-17.07,-2.41,-16.09:99 +chr1 3494417 . A T 24.41 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=25.18;MQ=27.40;MQ0=1;QD=1.36;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,5:8:-14.34,-8.61,-21.17:57.23 +chr1 3494420 . C A 17.09 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=28.79;MQ=27.40;MQ0=1;QD=0.95;SB=-10.00 GT:AD:DP:GL:GQ 0/1:7,11:6:-6.79,-1.81,-13.20:49.84 +chr1 3494428 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=21.58;MQ=27.57;MQ0=1;OQ=101.33;QD=5.07;SB=-10.00 GT:AD:DP:GL:GQ 0/1:14,6:9:-16.13,-2.71,-15.44:99 +chr1 3494440 . A G 20.51 LowQual AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=4;HaplotypeScore=16.99;MQ=27.20;MQ0=1;QD=1.28;SB=-10.00 GT:AD:DP:GL:GQ 0/1:14,2:6:-7.14,-1.81,-14.72:53.31 +chr1 3494450 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=19.98;MQ=27.07;MQ0=1;OQ=136.86;QD=9.12;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,11:7:-19.08,-2.11,-6.94:48.30 +chr1 3494456 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=17;Dels=0.12;HRun=1;HaplotypeScore=13.10;MQ=27.31;MQ0=1;OQ=95.30;QD=5.61;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,5:11:-16.13,-3.31,-22.08:99 +chr1 3494463 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=15.99;MQ=27.75;MQ0=0;OQ=76.78;QD=6.98;SB=-10.00 GT:AD:DP:GL:GQ 0/1:8,3:5:-12.47,-1.51,-7.14:56.32 +chr1 3494470 . G A 37.25 LowQual AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=9.99;MQ=29.00;MQ0=0;QD=4.66;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,6:3:-7.91,-0.90,-3.57:26.65 +chr1 3494476 . C G 10.99 LowQual AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=6.99;MQ=29.00;MQ0=0;QD=1.83;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,3:1:-4.35,-0.30,-0.00:1.76 +chr1 3494500 . C A 20.04 LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=24.21;MQ=29.00;MQ0=0;QD=1.43;SB=-10.00 GT:AD:DP:GL:GQ 0/1:6,8:6:-7.09,-1.81,-14.10:52.83 +chr1 3494506 . G A 17.29 LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.05;HRun=1;HaplotypeScore=32.64;MQ=29.00;MQ0=0;QD=0.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:14,4:10:-8.02,-3.01,-25.65:50.04 +chr1 3494513 . G A 25.23 LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=41.45;MQ=31.40;MQ0=0;QD=1.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,4:6:-7.61,-1.81,-13.27:58.06 +chr1 3494520 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=37.55;MQ=33.42;MQ0=0;OQ=64.77;QD=3.24;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,13:7:-11.87,-2.11,-12.97:97.60 +chr1 3494524 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=27.25;MQ=33.22;MQ0=0;OQ=65.77;QD=3.13;SB=-10.00 GT:AD:DP:GL:GQ 0/1:18,3:5:-11.37,-1.51,-6.04:45.31 +chr1 3494544 . G A 102.31 SnpCluster AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=1;HaplotypeScore=60.62;MQ=32.58;MQ0=0;QD=4.09;SB=-10.00 GT:AD:DP:GL:GQ 0/1:21,4:9:-16.23,-2.71,-16.04:99 +chr1 3494547 . G T 87.64 SnpCluster AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=65.61;MQ=32.58;MQ0=0;QD=3.51;SB=-10.00 GT:AD:DP:GL:GQ 0/1:19,5:8:-14.46,-2.41,-14.43:99 +chr1 3494550 . A C 79.94 SnpCluster AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=1;HaplotypeScore=55.04;MQ=32.72;MQ0=0;QD=3.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:14,6:8:-16.58,-5.30,-13.73:84.35 +chr1 3494557 . G T 60.29 SnpCluster AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=39.81;MQ=31.18;MQ0=0;QD=2.87;SB=-10.00 GT:AD:DP:GL:GQ 0/1:11,8:4:-10.52,-1.20,-3.86:26.53 +chr1 3494560 . G A 91.28 SnpCluster AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=38.65;MQ=31.18;MQ0=0;QD=4.35;SB=-10.00 GT:AD:DP:GL:GQ 1/1:7,11:4:-16.06,-4.57,-3.40:11.70 +chr1 3494564 . G A 29.24 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=1;HaplotypeScore=32.50;MQ=31.29;MQ0=0;QD=1.46;SB=-10.00 GT:AD:DP:GL:GQ 0/1:18,2:6:-8.02,-1.81,-12.47:62.07 +chr1 3494574 . A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=26.98;MQ=29.00;MQ0=0;OQ=69.17;QD=4.94;SB=-10.00 GT:AD:DP:GL:GQ 1/1:6,8:3:-10.41,-0.90,-0.00:9.03 +chr1 3494590 . G A 142.91 SnpCluster AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=22.40;MQ=29.00;MQ0=0;QD=9.53;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,8:6:-19.38,-1.81,-3.57:17.63 +chr1 3494597 . G T 106.99 SnpCluster AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=25.38;MQ=29.00;MQ0=0;QD=7.64;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,5:11:-17.30,-3.31,-21.74:99 +chr1 3494600 . G A 30.23 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=29.00;MQ0=0;QD=3.02;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,6:5:-7.81,-1.51,-10.71:63.06 +chr1 3494624 . A G 3.02 PASS AC=1;AF=0.50;AN=2;DP=6;Dels=0.00;HRun=1;HaplotypeScore=2.14;MQ=23.68;MQ0=1;OQ=61.17;QD=10.20;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,5:4:-10.61,-1.20,-4.06:28.52 +chr1 3494941 rs3122612 T C 27.60 PASS AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.13;MQ0=0;OQ=190.96;QD=21.22;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,9:7:-22.68,-2.11,-0.00:21.05 +chr1 3496357 rs2794320 A G 629.67 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.59;MQ0=0;OQ=2197.16;QD=34.88;SB=-1063.87 GT:AD:DP:GL:GQ 1/1:0,63:62:-223.32,-18.67,-0.02:99 +chr1 3497672 rs12138013 G A 514.21 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1894.53;QD=36.43;SB=-916.70 GT:AD:DP:GL:GQ 1/1:0,52:50:-193.07,-15.07,-0.03:99 +chr1 3497721 rs4648527 G A 5.98 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=5.91;MQ=58.60;MQ0=0;OQ=1808.59;QD=36.17;SB=-904.68 GT:AD:DP:GL:GQ 1/1:0,50:47:-184.46,-14.16,-0.02:99 +chr1 3497811 rs4233026 A G 453.03 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=985.33;QD=29.86;SB=-500.18 GT:AD:DP:GL:GQ 1/1:0,33:33:-102.16,-9.96,-0.04:99 +chr1 3499530 rs10909980 C T 12.32 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.36;MQ0=0;OQ=831.01;QD=36.13;SB=-270.86 GT:AD:DP:GL:GQ 1/1:0,23:22:-86.69,-6.63,-0.01:66.21 +chr1 3501794 rs7513275 A G 98.91 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=60.00;MQ0=0;OQ=215.59;QD=10.78;SB=-81.80 GT:AD:DP:GL:GQ 0/1:7,13:17:-29.97,-5.13,-27.54:99 +chr1 3502201 rs2794327 C T 251.06 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=1770.81;QD=37.68;SB=-842.63 GT:AD:DP:GL:GQ 1/1:0,47:45:-180.68,-13.55,-0.01:99 +chr1 3502376 rs2821025 T C 189.36 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.06;MQ0=0;OQ=1399.30;QD=34.13;SB=-531.22 GT:AD:DP:GL:GQ 1/1:1,40:40:-143.53,-12.05,-0.02:99 +chr1 3502406 rs2821024 G A 10.93 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.84;MQ=59.12;MQ0=0;OQ=1381.75;QD=37.34;SB=-602.98 GT:AD:DP:GL:GQ 1/1:0,37:36:-141.77,-10.85,-0.01:99 +chr1 3502660 rs2821023 T C 164.14 PASS AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.31;MQ0=0;OQ=631.91;QD=27.47;SB=-134.71 GT:AD:DP:GL:GQ 1/1:0,23:22:-66.81,-6.64,-0.03:66.13 +chr1 3503040 rs3001104 T C 11.75 LowQual AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=53.43;MQ0=0;QD=0.90;SB=-7.00 GT:AD:DP:GL:GQ 0/1:11,2:9:-7.15,-2.72,-25.40:44.29 +chr1 3503107 rs6697282 T C 2.87 PASS AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=303.24;QD=27.57;SB=-40.95 GT:AD:DP:GL:GQ 1/1:0,11:10:-33.91,-3.01,-0.00:30.08 +chr1 3503479 rs55936822 G A 66.02 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=385.29;QD=13.76;SB=-81.58 GT:AD:DP:GL:GQ 0/1:14,14:27:-49.96,-8.15,-41.31:99 +chr1 3504130 rs3001107 A T 92.54 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=1158.27;QD=35.10;SB=-515.45 GT:AD:DP:GL:GQ 1/1:0,33:32:-119.42,-9.64,-0.01:96.30 +chr1 3504221 rs2995006 A G 438.56 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1363.50;QD=34.96;SB=-648.28 GT:AD:DP:GL:GQ 1/1:0,39:39:-139.95,-11.75,-0.02:99 +chr1 3504611 rs6701230 T C 61.10 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=1071.54;QD=26.79;SB=-482.12 GT:AD:DP:GL:GQ 1/1:0,40:34:-110.77,-10.26,-0.03:99 +chr1 3505152 . C G 6.95 PASS AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=54.64;MQ0=0;OQ=215.54;QD=15.40;SB=-56.93 GT:AD:DP:GL:GQ 1/1:2,12:6:-25.13,-1.81,-0.00:18.06 +chr1 3505256 rs2794328 C A 31.98 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.33;MQ0=0;OQ=824.44;QD=29.44;SB=-191.27 GT:AD:DP:GL:GQ 1/1:1,27:24:-86.04,-7.23,-0.01:72.19 +chr1 3505590 rs2821011 T C 3.95 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=58.95;MQ0=0;OQ=1307.30;QD=29.71;SB=-329.39 GT:AD:DP:GL:GQ 1/1:0,44:40:-134.34,-12.06,-0.03:99 +chr1 3506096 rs4648395 G A 428.92 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.73;MQ0=0;OQ=1105.43;QD=35.66;SB=-453.34 GT:AD:DP:GL:GQ 1/1:0,31:29:-114.14,-8.74,-0.01:87.28 +chr1 3506280 rs7552280 C T 597.55 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1498.57;QD=38.42;SB=-699.42 GT:AD:DP:GL:GQ 1/1:0,39:38:-153.45,-11.45,-0.01:99 +chr1 3506640 rs4018202 C T 591.66 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1796.97;QD=36.67;SB=-852.00 GT:AD:DP:GL:GQ 1/1:0,49:46:-183.30,-13.86,-0.02:99 +chr1 3507139 rs4648528 C T 150.35 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.89;MQ0=0;OQ=1470.55;QD=35.01;SB=-673.24 GT:AD:DP:GL:GQ 1/1:0,42:39:-150.66,-11.76,-0.02:99 +chr1 3507337 rs61373700 C G 106.29 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.76;MQ=57.26;MQ0=0;OQ=1716.27;QD=39.91;SB=-832.44 GT:AD:DP:GL:GQ 1/1:1,42:42:-175.24,-12.66,-0.02:99 +chr1 3507396 rs6693958 G A 63.42 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=58.29;MQ0=0;OQ=1559.78;QD=38.04;SB=-721.97 GT:AD:DP:GL:GQ 1/1:0,41:40:-159.58,-12.05,-0.01:99 +chr1 3507433 rs59013990 G C 40.65 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=59.41;MQ0=0;OQ=1114.70;QD=28.58;SB=-265.33 GT:AD:DP:GL:GQ 1/1:0,38:29:-115.08,-8.75,-0.02:87.28 +chr1 3508244 rs2821012 T C 433.71 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=981.44;QD=28.87;SB=-510.19 GT:AD:DP:GL:GQ 1/1:0,34:32:-101.76,-9.65,-0.03:96.21 +chr1 3508275 rs12410528 G A 77.57 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.32;MQ0=0;OQ=639.66;QD=18.81;SB=-281.31 GT:AD:DP:GL:GQ 0/1:14,20:31:-76.59,-9.34,-39.32:99 +chr1 3508279 rs12401505 C T 12.42 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.61;MQ=59.32;MQ0=0;OQ=621.28;QD=18.27;SB=-279.19 GT:AD:DP:GL:GQ 0/1:14,19:31:-74.75,-9.34,-43.77:99 +chr1 3508347 rs56770023 C T 305.75 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.60;MQ0=0;OQ=1098.04;QD=36.60;SB=-308.27 GT:AD:DP:GL:GQ 1/1:0,30:29:-113.40,-8.74,-0.01:87.27 +chr1 3508348 rs60957843 A G 332.32 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=996.70;QD=34.37;SB=-270.42 GT:AD:DP:GL:GQ 1/1:0,29:29:-103.27,-8.74,-0.01:87.25 +chr1 3508499 rs2821013 C A 29.08 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=59.05;MQ0=0;OQ=1719.86;QD=35.10;SB=-757.10 GT:AD:DP:GL:GQ 1/1:0,49:47:-175.58,-14.15,-0.01:99 +chr1 3508603 rs7514061 C T 105.49 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.33;MQ0=0;OQ=1426.84;QD=33.97;SB=-607.00 GT:AD:DP:GL:GQ 1/1:0,42:38:-146.28,-11.45,-0.02:99 +chr1 3508717 rs2821014 A C 0.35 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=3;HaplotypeScore=1.13;MQ=59.42;MQ0=0;OQ=907.74;QD=22.69;SB=-295.54 GT:AD:DP:GL:GQ 1/1:0,37:28:-94.37,-8.43,-0.01:84.22 +chr1 3508804 rs7521546 T C 5.12 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=2;HaplotypeScore=1.42;MQ=57.17;MQ0=0;OQ=713.23;QD=28.53;SB=-330.78 GT:AD:DP:GL:GQ 1/1:0,25:24:-74.93,-7.24,-0.02:72.16 +chr1 3509294 rs12024499 A G 18.02 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=58.37;MQ0=0;OQ=1073.16;QD=24.96;SB=-338.38 GT:AD:DP:GL:GQ 1/1:0,43:37:-110.95,-11.17,-0.05:99 +chr1 3509463 rs12025426 T C 57.07 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.00;MQ0=0;OQ=1068.56;QD=25.44;SB=-559.52 GT:AD:DP:GL:GQ 1/1:0,42:36:-110.49,-10.87,-0.05:99 +chr1 3509651 rs56328010 C G 123.58 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=1.54;MQ=58.84;MQ0=0;OQ=608.86;QD=15.22;SB=-231.35 GT:AD:DP:GL:GQ 0/1:21,19:38:-75.63,-11.46,-87.10:99 +chr1 3509894 rs10752738 A G 106.20 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=57.39;MQ0=0;OQ=1124.20;QD=31.23;SB=-480.45 GT:AD:DP:GL:GQ 1/1:0,36:33:-116.02,-9.94,-0.01:99 +chr1 3509987 rs2821015 T C 88.77 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.95;MQ0=0;OQ=1023.67;QD=31.99;SB=-513.41 GT:AD:DP:GL:GQ 1/1:0,31:32:-108.71,-12.22,-2.76:94.68 +chr1 3510191 rs2794356 C A 66.82 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=58.63;MQ0=0;OQ=1082.36;QD=31.83;SB=-352.40 GT:AD:DP:GL:GQ 1/1:0,34:33:-111.84,-9.95,-0.02:99 +chr1 3510399 rs2794355 C T 148.33 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.22;MQ0=0;OQ=1723.81;QD=37.47;SB=-800.07 GT:AD:DP:GL:GQ 1/1:0,46:45:-175.99,-13.56,-0.02:99 +chr1 3510532 rs2821016 A C 65.43 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.42;MQ0=0;OQ=868.96;QD=27.16;SB=-409.86 GT:AD:DP:GL:GQ 1/1:0,32:29:-90.51,-8.74,-0.03:87.13 +chr1 3511971 rs56140438 T C 2680.91 Indel AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.68;MQ0=0;QD=34.82;SB=-1364.21 GT:AD:DP:GL:GQ 1/1:0,77:76:-271.70,-22.89,-0.02:99 +chr1 3513689 rs2794354 T C 23.29 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=60.00;MQ0=0;OQ=1332.54;QD=30.29;SB=-459.40 GT:AD:DP:GL:GQ 1/1:0,44:41:-136.87,-12.36,-0.03:99 +chr1 3513757 rs2821018 T C 1.28 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=52.28;MQ0=0;OQ=1127.31;QD=32.21;SB=-555.88 GT:AD:DP:GL:GQ 1/1:0,35:33:-116.33,-9.94,-0.01:99 +chr1 3513776 rs2821019 A C 16.58 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=3.24;MQ=52.84;MQ0=0;OQ=1256.82;QD=30.65;SB=-634.67 GT:AD:DP:GL:GQ 1/1:0,41:37:-129.29,-11.15,-0.02:99 +chr1 3513778 rs2821020 G A 39.72 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=4.08;MQ=53.03;MQ0=0;OQ=1497.87;QD=35.66;SB=-772.68 GT:AD:DP:GL:GQ 1/1:0,42:39:-153.39,-11.75,-0.01:99 +chr1 3515181 rs2794353 G C 0.02 FDRtranche1.00to2.00 AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=5;HaplotypeScore=0.32;MQ=58.30;MQ0=0;OQ=1440.93;QD=40.03;SB=-600.98 GT:AD:DP:GL:GQ 1/1:0,36:34:-147.69,-10.24,-0.01:99 +chr1 3515467 rs36031771 G A 114.23 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1598.59;QD=36.33;SB=-811.32 GT:AD:DP:GL:GQ 1/1:0,44:42:-163.46,-12.66,-0.02:99 +chr1 3515500 rs34852522 G A 546.80 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1591.31;QD=37.01;SB=-737.47 GT:AD:DP:GL:GQ 1/1:1,42:41:-162.73,-12.35,-0.01:99 +chr1 3515696 rs10909986 G A 566.50 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=1907.24;QD=38.92;SB=-905.69 GT:AD:DP:GL:GQ 1/1:0,49:48:-194.32,-14.46,-0.01:99 +chr1 3516250 rs12121341 A G 86.74 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1093.76;QD=29.56;SB=-543.02 GT:AD:DP:GL:GQ 1/1:0,37:35:-112.99,-10.56,-0.03:99 +chr1 3518397 rs57902798 C A 88.78 PASS AC=2;AF=1.00;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.13;MQ0=0;OQ=809.40;QD=32.38;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,25:24:-84.53,-7.23,-0.01:72.21 +chr1 3518534 rs1539126 G A 66.93 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=60.00;MQ0=0;OQ=1266.77;QD=36.19;SB=-476.64 GT:AD:DP:GL:GQ 1/1:0,34:33:-130.27,-9.94,-0.01:99 +chr1 3518701 rs2794326 T C 149.57 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.07;MQ0=0;OQ=1658.37;QD=33.17;SB=-790.25 GT:AD:DP:GL:GQ 1/1:0,50:49:-169.45,-14.76,-0.03:99 +chr1 3519249 rs10909987 G C 637.70 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1866.21;QD=40.57;SB=-960.72 GT:AD:DP:GL:GQ 1/1:0,45:44:-190.22,-13.26,-0.01:99 +chr1 3521082 rs4648396 C T 0.76 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=5;HaplotypeScore=1.32;MQ=59.36;MQ0=0;OQ=2285.23;QD=39.40;SB=-1043.37 GT:AD:DP:GL:GQ 1/1:0,58:57:-232.12,-17.17,-0.02:99 +chr1 3521301 rs4648397 T C 39.86 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=59.20;MQ0=0;OQ=1821.49;QD=31.41;SB=-869.61 GT:AD:DP:GL:GQ 1/1:0,58:57:-185.78,-17.19,-0.04:99 +chr1 3521455 rs4648398 C T 121.83 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=58.90;MQ0=0;OQ=2021.45;QD=34.26;SB=-686.93 GT:AD:DP:GL:GQ 1/1:0,59:53:-205.75,-15.97,-0.02:99 +chr1 3522563 rs6693192 A G 270.85 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=513.63;QD=9.88;SB=-275.26 GT:AD:DP:GL:GQ 0/1:30,22:52:-70.32,-15.67,-121.33:99 +chr1 3522569 rs6678958 G A 350.18 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=670.10;QD=13.14;SB=-343.79 GT:AD:DP:GL:GQ 0/1:29,22:51:-85.67,-15.38,-96.37:99 +chr1 3523424 rs55728961 C A 42.05 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=240.49;QD=10.46;SB=-10.00 GT:AD:DP:GL:GQ 0/1:14,9:23:-34.26,-6.93,-47.21:99 +chr1 3523484 rs56385042 T C 1.74 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=3;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=309.24;QD=11.89;SB=-6.99 GT:AD:DP:GL:GQ 0/1:12,14:26:-42.05,-7.84,-46.91:99 +chr1 3523847 rs10797404 T C 200.70 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=602.56;QD=14.01;SB=-77.79 GT:AD:DP:GL:GQ 0/1:21,22:42:-76.19,-12.65,-81.56:99 +chr1 3524383 rs4648532 A G 19.20 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=2;HaplotypeScore=2.34;MQ=56.80;MQ0=0;OQ=354.98;QD=11.45;SB=-152.32 GT:AD:DP:GL:GQ 0/1:16,15:28:-47.22,-8.44,-59.85:99 +chr1 3524566 rs10909988 A G 146.87 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=60.00;MQ0=0;OQ=306.09;QD=9.28;SB=-127.66 GT:AD:DP:GL:GQ 0/1:17,15:30:-42.93,-9.04,-69.22:99 +chr1 3524652 rs7522500 G C 8.99 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=6.16;MQ=57.13;MQ0=0;OQ=583.92;QD=14.24;SB=-274.31 GT:AD:DP:GL:GQ 0/1:21,20:34:-71.93,-10.26,-66.25:99 +chr1 3524668 rs7522507 G A 205.38 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.19;MQ=57.92;MQ0=0;OQ=639.63;QD=14.21;SB=-315.32 GT:AD:DP:GL:GQ 0/1:22,23:42:-79.91,-12.67,-66.98:99 +chr1 3525324 rs7538707 A G 23.09 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=845.73;QD=19.67;SB=-223.67 GT:AD:DP:GL:GQ 0/1:16,27:42:-100.51,-12.65,-58.85:99 +chr1 3526188 rs4648533 G A 210.95 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.62;MQ0=0;OQ=1070.40;QD=17.55;SB=-483.49 GT:AD:DP:GL:GQ 0/1:29,32:60:-128.41,-18.08,-91.39:99 +chr1 3526260 rs4648534 T C 399.13 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.82;MQ0=0;OQ=652.36;QD=10.19;SB=-312.36 GT:AD:DP:GL:GQ 0/1:38,26:63:-87.50,-18.98,-151.40:99 +chr1 3526320 rs4648535 C A 306.52 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=54.45;MQ0=1;OQ=780.07;QD=10.99;SB=-371.06 GT:AD:DP:GL:GQ 0/1:40,31:67:-101.47,-20.18,-141.37:99 +chr1 3526422 rs4648399 A G 309.90 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.19;MQ0=0;OQ=1278.95;QD=17.52;SB=-632.97 GT:AD:DP:GL:GQ 0/1:30,43:71:-152.57,-21.39,-116.57:99 +chr1 3527222 rs4648400 A G 9.46 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=7.73;MQ=57.63;MQ0=0;OQ=603.16;QD=10.40;SB=-310.07 GT:AD:DP:GL:GQ 0/1:32,26:56:-80.48,-16.88,-126.15:99 +chr1 3527718 rs4648401 A G 74.64 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=1.41;MQ=56.19;MQ0=0;OQ=587.94;QD=13.67;SB=-299.61 GT:AD:DP:GL:GQ 0/1:18,25:41:-74.44,-12.36,-73.19:99 +chr1 3528340 rs4400556 A T 87.37 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.12;MQ0=0;OQ=994.97;QD=12.59;SB=-457.52 GT:AD:DP:GL:GQ 0/1:45,34:78:-126.28,-23.49,-166.80:99 +chr1 3528361 rs4364818 C T 460.83 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.38;MQ0=0;OQ=945.91;QD=13.14;SB=-450.44 GT:AD:DP:GL:GQ 0/1:42,30:72:-119.57,-21.70,-148.80:99 +chr1 3528695 rs6424087 G C 115.88 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=59.24;MQ0=0;OQ=909.93;QD=16.54;SB=-215.65 GT:AD:DP:GL:GQ 0/1:28,26:51:-109.65,-15.37,-108.54:99 +chr1 3528942 rs10909989 A G 309.85 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.12;MQ=59.00;MQ0=0;OQ=981.47;QD=13.82;SB=-369.60 GT:AD:DP:GL:GQ 0/1:36,35:70:-122.52,-21.09,-148.98:99 +chr1 3529341 rs10909990 A G 374.60 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=58.19;MQ0=0;OQ=916.10;QD=14.78;SB=-423.95 GT:AD:DP:GL:GQ 0/1:29,33:61:-113.27,-18.38,-114.82:99 +chr1 3529884 rs12757620 T G 87.41 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=2.04;MQ=59.45;MQ0=0;OQ=798.71;QD=11.75;SB=-349.72 GT:AD:DP:GL:GQ 0/1:29,39:61:-101.54,-18.38,-103.90:99 +chr1 3532172 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=4.52;MQ=58.17;MQ0=0;OQ=111.86;QD=2.19;SB=68.21 GT:AD:DP:GL:GQ 0/1:30,21:37:-25.62,-11.15,-96.21:99 +chr1 3535452 rs41315304 G A 150.86 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=58.25;MQ0=0;OQ=1069.05;QD=16.70;SB=-525.75 GT:AD:DP:GL:GQ 0/1:32,32:63:-129.18,-18.99,-99.29:99 +chr1 3536795 rs2821007 G A 330.18 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.23;MQ0=0;OQ=1047.23;QD=17.45;SB=-508.04 GT:AD:DP:GL:GQ 0/1:27,33:59:-125.78,-17.78,-94.59:99 +chr1 3537996 rs2760321 T C 53.51 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=58.11;MQ0=0;OQ=916.84;QD=24.78;SB=-335.79 GT:AD:DP:GL:GQ 1/1:0,37:31:-95.30,-9.36,-0.04:93.19 +chr1 3538692 rs2760320 G C 208.41 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.15;MQ0=0;OQ=946.49;QD=15.02;SB=-485.84 GT:AD:DP:GL:GQ 0/1:35,28:62:-116.63,-18.70,-140.41:99 +chr1 3540707 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=4;HaplotypeScore=6.24;MQ=58.05;MQ0=0;OQ=310.07;QD=8.61;SB=35.15 GT:AD:DP:GL:GQ 0/1:20,16:27:-42.43,-8.14,-74.49:99 +chr1 3542640 rs2821061 A G 174.99 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=519.03;QD=10.38;SB=-253.57 GT:AD:DP:GL:GQ 0/1:27,23:48:-69.65,-14.47,-105.26:99 +chr1 3543649 rs2821058 T C 578.48 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=1559.49;QD=29.42;SB=-616.98 GT:AD:DP:GL:GQ 1/1:0,53:50:-159.58,-15.08,-0.04:99 +chr1 3545730 rs2760318 T G 276.33 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=500.47;QD=13.53;SB=-245.40 GT:AD:DP:GL:GQ 0/1:16,21:34:-63.58,-10.25,-53.36:99 +chr1 3546316 rs2760317 T C 74.82 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=59.23;MQ0=0;OQ=365.54;QD=12.18;SB=-82.96 GT:AD:DP:GL:GQ 0/1:16,13:27:-47.97,-8.14,-53.97:99 +chr1 3546766 rs2821032 A G 15.17 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.71;MQ=58.45;MQ0=0;OQ=501.73;QD=10.45;SB=-117.63 GT:AD:DP:GL:GQ 0/1:27,21:44:-66.72,-13.26,-92.65:99 +chr1 3546958 . G C 33.36 PASS AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=52.99;MQ0=1;OQ=414.27;QD=15.34;SB=-224.70 GT:AD:DP:GL:GQ 0/1:11,16:20:-50.74,-6.03,-33.52:99 +chr1 3550868 rs12408890 C T 50.15 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=714.51;QD=21.65;SB=-10.00 GT:AD:DP:GL:GQ 0/1:11,22:31:-84.07,-9.34,-33.99:99 +chr1 3556431 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=2;HaplotypeScore=3.37;MQ=56.43;MQ0=0;OQ=64.63;QD=2.69;SB=26.11 GT:AD:DP:GL:GQ 0/1:20,4:17:-14.89,-5.14,-48.86:97.47 +chr1 3556566 rs2251098 G A 89.65 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=58.00;MQ0=0;OQ=575.61;QD=16.45;SB=-81.09 GT:AD:DP:GL:GQ 0/1:16,19:34:-71.09,-10.24,-59.62:99 +chr1 3560743 rs6697769 C T 108.18 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=2.77;MQ=59.11;MQ0=0;OQ=591.49;QD=14.08;SB=-304.84 GT:AD:DP:GL:GQ 0/1:21,21:39:-74.19,-11.76,-62.78:99 +chr1 3562592 rs10752739 A G 278.74 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=56.42;MQ0=0;OQ=804.83;QD=14.63;SB=-300.66 GT:AD:DP:GL:GQ 0/1:25,30:50:-98.83,-15.07,-88.55:99 +chr1 3562634 rs2181484 A G 237.08 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=59.09;MQ0=0;OQ=421.19;QD=9.16;SB=-138.88 GT:AD:DP:GL:GQ 0/1:25,21:41:-57.77,-12.36,-88.24:99 +chr1 3564279 rs9662739 T A 199.17 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=58.99;MQ0=0;OQ=516.88;QD=11.24;SB=-252.67 GT:AD:DP:GL:GQ 0/1:26,19:44:-68.23,-13.26,-93.50:99 +chr1 3564280 rs9662052 C A 196.24 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=58.99;MQ0=0;OQ=511.23;QD=11.11;SB=-234.91 GT:AD:DP:GL:GQ 0/1:27,19:44:-67.66,-13.26,-88.90:99 +chr1 3565050 rs2368543 T C 86.26 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=57.97;MQ0=0;OQ=928.11;QD=12.89;SB=-445.02 GT:AD:DP:GL:GQ 0/1:38,33:71:-117.49,-21.39,-151.96:99 +chr1 3565471 rs4648544 C T 133.93 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=3;HaplotypeScore=1.75;MQ=59.57;MQ0=0;OQ=791.33;QD=14.65;SB=-418.72 GT:AD:DP:GL:GQ 0/1:30,24:54:-98.68,-16.27,-109.24:99 +chr1 3565693 rs2208993 C G 156.42 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.21;MQ0=0;OQ=372.36;QD=11.28;SB=-74.78 GT:AD:DP:GL:GQ 0/1:21,12:29:-49.27,-8.75,-66.40:99 +chr1 3565739 rs2208992 C T 135.51 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=555.57;QD=16.34;SB=-208.21 GT:AD:DP:GL:GQ 0/1:17,17:34:-69.09,-10.25,-52.42:99 +chr1 3565920 rs2224718 T C 463.85 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.60;MQ0=0;OQ=705.17;QD=14.10;SB=-316.42 GT:AD:DP:GL:GQ 0/1:24,26:48:-88.27,-14.47,-84.73:99 +chr1 3567181 rs4648545 A G 559.92 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1256.11;QD=14.78;SB=-595.27 GT:AD:DP:GL:GQ 0/1:42,43:84:-154.20,-25.30,-171.31:99 +chr1 3568175 rs1885863 C T 33.02 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.95;MQ0=0;OQ=503.58;QD=17.98;SB=-117.62 GT:AD:DP:GL:GQ 0/1:13,15:28:-62.07,-8.43,-48.10:99 +chr1 3569688 rs1885861 A T 263.95 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=805.05;QD=14.38;SB=-228.60 GT:AD:DP:GL:GQ 0/1:30,26:55:-100.35,-16.57,-108.86:99 +chr1 3572104 rs6679556 T A 168.01 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.18;MQ0=0;OQ=534.82;QD=14.07;SB=-147.78 GT:AD:DP:GL:GQ 0/1:19,19:35:-67.31,-10.54,-60.93:99 +chr1 3572105 rs6679560 T G 310.70 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.18;MQ0=0;OQ=483.25;QD=12.72;SB=-122.88 GT:AD:DP:GL:GQ 0/1:19,19:35:-62.15,-10.55,-61.28:99 +chr1 3572847 rs1885860 T C 202.44 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=55.65;MQ0=0;OQ=1537.12;QD=28.47;SB=-796.29 GT:AD:DP:GL:GQ 1/1:0,54:50:-157.34,-15.08,-0.05:99 +chr1 3573552 rs1885859 G C 126.04 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=931.27;QD=19.81;SB=-452.38 GT:AD:DP:GL:GQ 0/1:21,26:45:-109.97,-13.56,-87.15:99 +chr1 3575442 rs3765694 G A 29.42 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=58.20;MQ0=0;OQ=1425.18;QD=36.54;SB=-559.30 GT:AD:DP:GL:GQ 1/1:0,39:37:-146.12,-11.15,-0.01:99 +chr1 3575611 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=3;HaplotypeScore=1.74;MQ=57.17;MQ0=0;OQ=76.89;QD=3.08;SB=14.07 GT:AD:DP:GL:GQ 0/1:14,11:13:-14.90,-3.93,-34.07:99 +chr1 3576288 rs1009345 G A 91.26 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.80;MQ0=0;OQ=1800.40;QD=39.14;SB=-661.66 GT:AD:DP:GL:GQ 1/1:0,46:46:-183.64,-13.86,-0.02:99 +chr1 3576560 rs6657895 G A 60.54 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=4.17;MQ=59.27;MQ0=0;OQ=1276.11;QD=33.58;SB=-586.96 GT:AD:DP:GL:GQ 1/1:1,37:35:-131.22,-10.55,-0.02:99 +chr1 3577406 rs3765697 C T 0.76 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.64;MQ=56.35;MQ0=0;OQ=1305.04;QD=33.46;SB=-441.58 GT:AD:DP:GL:GQ 1/1:0,39:35:-134.11,-10.55,-0.02:99 +chr1 3578761 rs3765700 G C 611.89 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=1985.98;QD=38.19;SB=-981.19 GT:AD:DP:GL:GQ 1/1:0,52:47:-202.21,-14.17,-0.02:99 +chr1 3578861 rs3765701 T A 287.36 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.60;MQ0=0;OQ=1646.63;QD=35.03;SB=-839.93 GT:AD:DP:GL:GQ 1/1:0,47:46:-168.27,-13.86,-0.02:99 +chr1 3579831 rs56255778 C A 326.05 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=59.60;MQ0=0;OQ=723.70;QD=12.70;SB=-343.37 GT:AD:DP:GL:GQ 0/1:30,27:51:-91.02,-15.37,-85.23:99 +chr1 3580285 rs6671482 G A 126.17 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=1575.76;QD=35.81;SB=-662.31 GT:AD:DP:GL:GQ 1/1:1,43:41:-161.17,-12.35,-0.01:99 +chr1 3587189 . C T 94.68 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.81;MQ0=0;OQ=415.33;QD=10.65;SB=-200.88 GT:AD:DP:GL:GQ 0/1:25,14:37:-55.97,-11.16,-70.24:99 +chr1 3594672 rs12562573 G A 160.10 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.53;MQ0=0;OQ=1829.37;QD=37.33;SB=-900.21 GT:AD:DP:GL:GQ 1/1:0,49:48:-186.54,-14.47,-0.02:99 +chr1 3594957 rs1885872 G A 83.22 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.18;MQ=59.07;MQ0=0;OQ=1704.97;QD=37.89;SB=-859.63 GT:AD:DP:GL:GQ 1/1:0,45:44:-174.10,-13.26,-0.02:99 +chr1 3595447 rs1885870 G C 563.54 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.58;MQ0=0;OQ=1514.49;QD=32.92;SB=-721.32 GT:AD:DP:GL:GQ 1/1:1,45:40:-155.08,-12.08,-0.04:99 +chr1 3596410 rs3765725 C T 84.63 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.54;MQ0=0;OQ=1239.60;QD=30.23;SB=-472.10 GT:AD:DP:GL:GQ 1/1:0,41:33:-127.56,-9.95,-0.02:99 +chr1 3596486 rs3765727 G A 208.84 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.62;MQ0=0;OQ=883.29;QD=18.03;SB=-364.54 GT:AD:DP:GL:GQ 0/1:22,27:47:-105.77,-14.16,-69.54:99 +chr1 3596710 rs3765728 G A 119.20 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.63;MQ0=0;OQ=1974.23;QD=38.71;SB=-814.08 GT:AD:DP:GL:GQ 1/1:0,51:50:-201.02,-15.06,-0.01:99 +chr1 3597380 rs3765730 G A 180.45 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.40;MQ0=0;OQ=530.99;QD=17.13;SB=-202.91 GT:AD:DP:GL:GQ 0/1:13,18:30:-65.42,-9.04,-41.88:99 +chr1 3597871 rs10732965 C T 75.34 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=57.81;MQ0=0;OQ=940.44;QD=33.59;SB=-454.61 GT:AD:DP:GL:GQ 1/1:0,27:25:-97.64,-7.53,-0.01:75.24 +chr1 3598087 rs34868661 A G 136.79 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.05;MQ0=0;OQ=432.49;QD=9.83;SB=-227.39 GT:AD:DP:GL:GQ 0/1:23,20:41:-58.89,-12.36,-89.12:99 +chr1 3598141 rs12126706 C T 141.99 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.13;MQ0=0;OQ=455.42;QD=13.01;SB=-109.06 GT:AD:DP:GL:GQ 0/1:19,16:32:-58.47,-9.65,-57.68:99 +chr1 3598905 rs1078687 G A 163.20 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.42;MQ0=0;OQ=1623.93;QD=33.83;SB=-687.95 GT:AD:DP:GL:GQ 1/1:0,47:43:-166.00,-12.96,-0.02:99 +chr1 3599033 rs879622 G A 151.46 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.44;MQ0=0;OQ=684.79;QD=16.70;SB=-307.82 GT:AD:DP:GL:GQ 0/1:19,22:37:-82.91,-11.15,-57.20:99 +chr1 3599257 rs879621 C A 346.01 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.17;MQ0=0;OQ=766.56;QD=13.69;SB=-343.33 GT:AD:DP:GL:GQ 0/1:29,27:55:-96.51,-16.57,-104.71:99 +chr1 3599783 rs2146660 A G 32.89 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=3.25;MQ=57.85;MQ0=0;OQ=1704.59;QD=34.79;SB=-814.09 GT:AD:DP:GL:GQ 1/1:0,49:49:-174.06,-14.76,-0.02:99 +chr1 3600146 . T C 37.22 LowQual AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=40.64;MQ0=2;QD=1.16;SB=-35.23 GT:AD:DP:GL:GQ 0/1:25,6:25:-14.54,-7.54,-78.76:70.05 +chr1 3600159 rs34095686 C A 8.52 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=38.58;MQ0=3;OQ=139.88;QD=4.37;SB=-64.01 GT:AD:DP:GL:GQ 0/1:23,9:27:-25.41,-8.14,-69.86:99 +chr1 3600191 . C G 0.30 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=5.79;MQ=36.62;MQ0=7;OQ=200.47;QD=5.90;SB=-62.84 GT:AD:DP:GL:GQ 0/1:21,13:22:-29.96,-6.63,-63.33:99 +chr1 3600194 rs34612797 A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=3;HaplotypeScore=5.12;MQ=34.72;MQ0=8;OQ=74.27;QD=2.12;SB=-16.93 GT:AD:DP:GL:GQ 0/1:24,11:20:-16.74,-6.03,-51.18:99 +chr1 3600242 . C T 27.02 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=31.01;MQ0=9;QD=0.82;SB=14.05 GT:AD:DP:GL:GQ 0/1:28,5:16:-10.81,-4.82,-45.03:59.85 +chr1 3600252 . G A 0.25 PASS AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=0;HaplotypeScore=5.21;MQ=33.15;MQ0=7;OQ=119.84;QD=4.99;SB=-7.00 GT:AD:DP:GL:GQ 0/1:19,5:10:-18.28,-3.02,-16.17:99 +chr1 3600264 rs61762234 A C 2.70 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=2;HaplotypeScore=2.09;MQ=34.74;MQ0=5;OQ=244.22;QD=13.57;SB=-10.00 GT:AD:DP:GL:GQ 1/1:4,14:8:-28.01,-2.41,-0.00:24.07 +chr1 3600309 . C A 44.81 LowQual AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=28.74;MQ0=1;QD=8.96;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:2:-7.89,-0.60,-0.00:6.02 +chr1 3600350 . C T 27.34 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=4.81;MQ=17.75;MQ0=4;QD=2.28;SB=-31.62 GT:AD:DP:GL:GQ 0/1:8,4:3:-6.92,-0.91,-3.40:24.94 +chr1 3600367 rs35012159 G C 33.49 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=10.16;MQ=14.95;MQ0=16;QD=0.93;SB=-40.88 GT:AD:DP:GL:GQ 0/1:29,7:6:-8.44,-1.81,-16.03:66.33 +chr1 3600427 . C T 85.30 DPFilter;HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=22.31;MQ=14.22;MQ0=48;QD=0.87;SB=11.05 GT:AD:DP:GL:GQ 0/1:88,10:24:-19.05,-7.24,-63.74:99 +chr1 3600428 . G A 105.38 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=94;Dels=0.00;HRun=0;HaplotypeScore=22.15;MQ=14.50;MQ0=46;QD=1.12;SB=-26.63 GT:AD:DP:GL:GQ 0/1:84,9:25:-21.36,-7.54,-60.74:99 +chr1 3600437 . G C 161.98 HARD_TO_VALIDATE;SnpCluster AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=2;HaplotypeScore=28.11;MQ=14.54;MQ0=44;QD=1.78;SB=-27.40 GT:AD:DP:GL:GQ 0/1:81,9:25:-27.02,-7.53,-80.42:99 +chr1 3600440 . A C 23.09 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=2;HaplotypeScore=12.59;MQ=14.51;MQ0=44;QD=0.25;SB=-17.83 GT:AD:DP:GL:GQ 0/1:72,19:25:-13.12,-7.53,-77.67:55.91 +chr1 3600470 . C T 26.44 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=13.21;MQ=11.80;MQ0=28;QD=0.61;SB=2.03 GT:AD:DP:GL:GQ 0/1:41,2:8:-8.34,-2.41,-20.77:59.27 +chr1 3600475 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=2;HaplotypeScore=2.58;MQ=10.93;MQ0=23;OQ=89.38;QD=2.48;SB=-3.98 GT:AD:DP:GL:GQ 0/1:21,15:6:-14.03,-1.81,-7.79:59.84 +chr1 3600532 . C T 45.13 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=11.72;MQ0=9;QD=2.65;SB=-47.67 GT:AD:DP:GL:GQ 1/1:12,5:2:-7.92,-0.60,-0.00:6.02 +chr1 3600545 . A C 20.73 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=18.85;MQ0=10;QD=0.80;SB=-32.99 GT:AD:DP:GL:GQ 0/1:14,12:4:-6.56,-1.20,-7.53:53.53 +chr1 3600575 . C T 0.06 PASS AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=7.34;MQ=23.21;MQ0=9;OQ=164.83;QD=5.49;SB=-77.08 GT:AD:DP:GL:GQ 0/1:24,6:9:-22.48,-2.71,-11.26:85.52 +chr1 3600578 . C T 0.49 PASS AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=5.98;MQ=23.98;MQ0=9;OQ=197.36;QD=6.81;SB=-112.62 GT:AD:DP:GL:GQ 0/1:22,7:11:-26.34,-3.32,-14.46:99 +chr1 3600596 . C T 0.28 PASS AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=33.58;MQ0=0;OQ=353.36;QD=25.24;SB=-175.22 GT:AD:DP:GL:GQ 1/1:0,14:10:-38.92,-3.01,-0.01:30.09 +chr1 3600667 . C T 19.38 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=18;Dels=0.00;HRun=1;HaplotypeScore=14.09;MQ=16.96;MQ0=7;QD=1.08;SB=-29.64 GT:AD:DP:GL:GQ 0/1:14,4:7:-7.33,-2.11,-16.23:52.17 +chr1 3600709 . C T 32.48 PASS AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=3.31;MQ=14.75;MQ0=16;OQ=271.94;QD=8.77;SB=-129.00 GT:AD:DP:GL:GQ 1/1:10,20:8:-30.78,-2.41,-0.00:24.07 +chr1 3600734 . C A 11.22 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=17.16;MQ0=10;QD=0.59;SB=-7.00 GT:AD:DP:GL:GQ 0/1:17,2:6:-6.18,-1.81,-13.77:43.72 +chr1 3600738 . C T 23.24 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=5.72;MQ=17.16;MQ0=10;QD=1.22;SB=-6.99 GT:AD:DP:GL:GQ 0/1:14,5:6:-7.41,-1.81,-13.10:56.06 +chr1 3600746 . G A 0.90 PASS AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=5.14;MQ=19.46;MQ0=10;OQ=147.44;QD=6.70;SB=-47.55 GT:AD:DP:GL:GQ 0/1:6,16:6:-19.82,-1.81,-3.10:12.90 +chr1 3600943 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=10.81;MQ0=18;OQ=79.37;QD=2.27;SB=-10.00 GT:AD:DP:GL:GQ 0/1:27,8:5:-12.73,-1.51,-3.55:20.36 +chr1 3600944 . G A 31.47 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=10.97;MQ0=17;QD=0.93;SB=-10.00 GT:AD:DP:GL:GQ 0/1:32,2:5:-7.94,-1.51,-9.29:64.30 +chr1 3600955 . C T 29.25 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=3.80;MQ=11.72;MQ0=17;QD=0.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:25,7:6:-8.02,-1.81,-11.97:62.08 +chr1 3600968 . A C 27.28 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=2;HaplotypeScore=4.96;MQ=11.75;MQ0=20;QD=0.80;SB=-10.00 GT:AD:DP:GL:GQ 0/1:18,16:5:-7.52,-1.51,-9.32:60.10 +chr1 3601000 . G C 23.03 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=2;HaplotypeScore=12.60;MQ=11.01;MQ0=30;QD=0.46;SB=-6.99 GT:AD:DP:GL:GQ 0/1:44,6:9:-8.30,-2.71,-30.70:55.84 +chr1 3601003 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=2;HaplotypeScore=15.11;MQ=12.05;MQ0=28;OQ=191.04;QD=3.75;SB=-6.99 GT:AD:DP:GL:GQ 0/1:28,23:11:-25.70,-3.31,-14.21:99 +chr1 3601025 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=13.71;MQ=14.27;MQ0=33;OQ=53.75;QD=0.96;SB=-3.99 GT:AD:DP:GL:GQ 0/1:46,9:10:-11.67,-3.01,-22.44:86.59 +chr1 3601070 rs36156048 C G 0.13 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=10.95;MQ=20.17;MQ0=10;OQ=79.41;QD=3.18;SB=-46.45 GT:AD:DP:GL:GQ 0/1:14,11:6:-13.03,-1.81,-11.69:98.78 +chr1 3601096 . G A 20.37 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=8.03;MQ=17.90;MQ0=5;QD=1.20;SB=-27.52 GT:AD:DP:GL:GQ 0/1:13,3:5:-6.83,-1.51,-8.44:53.16 +chr1 3601143 . A C 0.18 PASS AC=1;AF=0.50;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=20.37;MQ0=7;OQ=150.35;QD=6.54;SB=-72.98 GT:AD:DP:GL:GQ 0/1:14,9:10:-21.33,-3.01,-13.91:99 +chr1 3601165 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=30;Dels=0.00;HRun=0;HaplotypeScore=11.69;MQ=24.21;MQ0=10;OQ=173.39;QD=5.78;SB=-3.99 GT:AD:DP:GL:GQ 0/1:22,8:11:-23.94,-3.31,-15.90:99 +chr1 3601175 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=2;HaplotypeScore=35.74;MQ=29.63;MQ0=10;OQ=194.57;QD=4.75;SB=-123.70 GT:AD:DP:GL:GQ 0/1:27,14:21:-29.07,-6.33,-61.55:99 +chr1 3601178 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=2;HaplotypeScore=14.60;MQ=30.57;MQ0=8;OQ=427.34;QD=9.94;SB=-58.96 GT:AD:DP:GL:GQ 0/1:21,22:25:-53.55,-7.53,-34.82:99 +chr1 3601218 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=2;HaplotypeScore=16.31;MQ=41.71;MQ0=5;OQ=182.10;QD=2.43;SB=-33.64 GT:AD:DP:GL:GQ 0/1:61,14:63:-40.49,-19.00,-224.09:99 +chr1 3601225 rs12722819 A C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=3;HaplotypeScore=15.63;MQ=42.30;MQ0=5;OQ=524.29;QD=6.32;SB=-141.88 GT:AD:DP:GL:GQ 0/1:52,30:59:-73.50,-17.79,-124.07:99 +chr1 3601229 rs12727450 T C 0.93 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=3;HaplotypeScore=5.92;MQ=43.45;MQ0=6;OQ=762.30;QD=9.07;SB=-332.31 GT:AD:DP:GL:GQ 0/1:49,35:67:-99.71,-20.19,-147.26:99 +chr1 3601341 rs12239528 C T 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.01;HRun=0;HaplotypeScore=14.56;MQ=44.93;MQ0=17;OQ=62.54;QD=0.70;SB=44.13 GT:AD:DP:GL:GQ 0/1:79,8:62:-27.92,-18.38,-184.40:95.37 +chr1 3601342 rs11581562 G A 0.21 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.01;HRun=0;HaplotypeScore=14.40;MQ=44.68;MQ0=18;OQ=819.35;QD=9.10;SB=-177.16 GT:AD:DP:GL:GQ 0/1:53,33:59:-102.70,-17.49,-103.40:99 +chr1 3601389 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=2;HaplotypeScore=7.82;MQ=44.29;MQ0=18;OQ=186.02;QD=2.30;SB=-61.02 GT:AD:DP:GL:GQ 0/1:62,19:52:-37.55,-15.67,-142.29:99 +chr1 3601457 rs10910012 A G 122.78 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=54.59;MQ0=0;OQ=1506.74;QD=29.54;SB=-756.93 GT:AD:DP:GL:GQ 1/1:0,51:48:-154.31,-14.48,-0.05:99 +chr1 3601752 rs3765731 G A 361.77 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=59.28;MQ0=0;OQ=1001.62;QD=15.65;SB=-488.04 GT:AD:DP:GL:GQ 0/1:31,33:59:-121.23,-17.79,-88.90:99 +chr1 3601820 rs3765732 G A 2.96 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=59.03;MQ0=0;OQ=1613.11;QD=33.61;SB=-476.00 GT:AD:DP:GL:GQ 1/1:0,46:44:-167.13,-15.44,-2.23:99 +chr1 3602293 rs1885869 T C 376.91 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1214.50;QD=32.82;SB=-519.18 GT:AD:DP:GL:GQ 1/1:0,37:35:-125.05,-10.54,-0.02:99 +chr1 3603630 rs10910013 C T 111.93 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.47;MQ0=0;OQ=534.95;QD=15.28;SB=-205.85 GT:AD:DP:GL:GQ 0/1:18,17:34:-67.02,-10.25,-59.55:99 +chr1 3603781 rs35837097 A G 62.33 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.60;MQ=59.60;MQ0=0;OQ=546.71;QD=11.63;SB=-279.27 GT:AD:DP:GL:GQ 0/1:23,24:43:-70.92,-12.96,-83.70:99 +chr1 3605288 rs11580811 G A 73.23 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=59.17;MQ0=0;OQ=263.75;QD=9.42;SB=-51.00 GT:AD:DP:GL:GQ 0/1:17,11:22:-36.29,-6.63,-43.95:99 +chr1 3606461 rs3765736 C T 194.21 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=57.38;MQ0=0;OQ=406.81;QD=15.07;SB=-214.90 GT:AD:DP:GL:GQ 0/1:13,14:23:-50.90,-6.93,-35.03:99 +chr1 3606652 rs3765737 A G 468.77 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=799.22;QD=12.89;SB=-323.13 GT:AD:DP:GL:GQ 0/1:30,32:60:-101.29,-18.08,-117.49:99 +chr1 3606658 rs3765738 G A 253.54 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.79;MQ0=0;OQ=935.05;QD=15.08;SB=-404.78 GT:AD:DP:GL:GQ 0/1:33,29:61:-115.17,-18.38,-103.51:99 +chr1 3606835 rs4610947 C A 292.86 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.39;MQ0=0;OQ=957.03;QD=17.09;SB=-493.95 GT:AD:DP:GL:GQ 0/1:24,31:55:-115.55,-16.56,-86.20:99 +chr1 3606979 rs4378145 G A 258.79 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=57.58;MQ0=5;OQ=1287.24;QD=16.29;SB=-484.49 GT:AD:DP:GL:GQ 0/1:40,39:72:-153.70,-21.69,-124.59:99 +chr1 3607481 rs3765739 A G 35.10 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=56.52;MQ0=0;OQ=316.46;QD=9.31;SB=-99.71 GT:AD:DP:GL:GQ 0/1:16,18:27:-43.07,-8.14,-49.38:99 +chr1 3608425 rs3819959 T C 21.46 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.02;MQ=53.67;MQ0=0;OQ=372.33;QD=9.08;SB=-195.61 GT:AD:DP:GL:GQ 0/1:23,18:34:-50.76,-10.24,-80.92:99 +chr1 3608574 rs3765740 T G 43.97 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=2;HaplotypeScore=1.03;MQ=59.11;MQ0=0;OQ=373.92;QD=14.38;SB=-208.83 GT:AD:DP:GL:GQ 0/1:12,14:26:-48.51,-7.83,-42.30:99 +chr1 3608643 rs3765741 A G 139.94 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.25;MQ0=0;OQ=277.44;QD=11.10;SB=-3.99 GT:AD:DP:GL:GQ 0/1:13,12:23:-37.96,-6.93,-45.69:99 +chr1 3608686 rs3765742 G A 11.54 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=299.52;QD=14.98;SB=-7.00 GT:AD:DP:GL:GQ 0/1:9,11:19:-38.96,-5.72,-31.25:99 +chr1 3608969 rs3765743 C T 17.24 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=315.53;QD=15.78;SB=-3.99 GT:AD:DP:GL:GQ 0/1:10,10:19:-40.56,-5.72,-31.07:99 +chr1 3609567 rs4648550 T A 206.11 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=1535.78;QD=37.46;SB=-673.01 GT:AD:DP:GL:GQ 1/1:0,41:41:-157.17,-12.35,-0.01:99 +chr1 3609807 rs34881405 T C 7.83 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.49;MQ=57.54;MQ0=0;OQ=345.64;QD=7.86;SB=-128.25 GT:AD:DP:GL:GQ 0/1:24,20:40:-49.91,-12.06,-96.00:99 +chr1 3610040 rs17379833 A T 163.16 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.52;MQ0=0;OQ=999.11;QD=20.81;SB=-480.53 GT:AD:DP:GL:GQ 0/1:16,32:47:-117.35,-14.16,-58.41:99 +chr1 3610295 rs12742969 A G 136.51 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=514.16;QD=10.49;SB=-277.41 GT:AD:DP:GL:GQ 0/1:28,21:47:-68.86,-14.16,-115.22:99 +chr1 3610320 rs12735439 C A 230.39 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=60.00;MQ0=0;OQ=801.03;QD=16.35;SB=-378.77 GT:AD:DP:GL:GQ 0/1:22,27:48:-97.85,-14.46,-70.21:99 +chr1 3611339 rs3765749 A T 129.18 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=60.00;MQ0=0;OQ=640.71;QD=17.32;SB=-252.96 GT:AD:DP:GL:GQ 0/1:16,21:36:-78.20,-10.84,-56.57:99 +chr1 3612044 rs3765751 A G 0.64 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=6.05;MQ=58.84;MQ0=0;OQ=1141.41;QD=28.54;SB=-361.32 GT:AD:DP:GL:GQ 1/1:0,39:37:-117.76,-11.16,-0.04:99 +chr1 3612141 rs3765752 G A 98.32 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.42;MQ0=0;OQ=790.33;QD=19.76;SB=-403.21 GT:AD:DP:GL:GQ 0/1:16,24:40:-94.37,-12.05,-52.81:99 +chr1 3612166 rs3765753 T G 307.87 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=1135.84;QD=31.55;SB=-218.90 GT:AD:DP:GL:GQ 1/1:0,36:34:-117.19,-10.25,-0.02:99 +chr1 3612496 rs12086279 A T 144.33 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=53.76;MQ0=0;OQ=264.24;QD=12.01;SB=-145.87 GT:AD:DP:GL:GQ 0/1:12,10:20:-35.73,-6.03,-37.15:99 +chr1 3612742 rs56124535 A G 117.78 PASS AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=57.14;MQ0=0;OQ=143.16;QD=7.53;SB=-61.32 GT:AD:DP:GL:GQ 0/1:9,9:16:-22.43,-4.83,-33.66:99 +chr1 3612752 rs55976062 T C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=19;Dels=0.00;HRun=2;HaplotypeScore=16.88;MQ=55.46;MQ0=1;OQ=130.66;QD=6.88;SB=-60.86 GT:AD:DP:GL:GQ 0/1:11,8:16:-21.17,-4.82,-37.90:99 +chr1 3612857 rs10910014 T C 4.06 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=2.85;MQ=45.10;MQ0=1;OQ=122.28;QD=3.82;SB=-65.87 GT:AD:DP:GL:GQ 0/1:18,14:19:-21.24,-5.73,-45.71:99 +chr1 3612894 rs58140697 A G 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=4;HaplotypeScore=5.46;MQ=58.05;MQ0=0;OQ=210.19;QD=8.76;SB=-118.71 GT:AD:DP:GL:GQ 0/1:15,9:22:-30.93,-6.63,-52.73:99 +chr1 3612902 rs60071664 T C 130.61 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=57.06;MQ0=0;OQ=194.42;QD=7.48;SB=-106.60 GT:AD:DP:GL:GQ 0/1:16,10:25:-30.26,-7.53,-62.36:99 +chr1 3613185 rs12564843 G C 7.11 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=53.89;MQ0=0;OQ=1382.10;QD=38.39;SB=-571.48 GT:AD:DP:GL:GQ 1/1:0,36:33:-141.81,-9.95,-0.02:99 +chr1 3613274 rs9786966 A G 67.74 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.62;MQ=57.45;MQ0=0;OQ=414.03;QD=10.62;SB=-167.59 GT:AD:DP:GL:GQ 0/1:21,18:36:-55.53,-10.85,-77.07:99 +chr1 3613481 rs55657548 C T 77.12 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=58.92;MQ0=0;OQ=252.32;QD=6.47;SB=-105.49 GT:AD:DP:GL:GQ 0/1:27,11:38:-39.97,-11.45,-93.41:99 +chr1 3614769 rs10910016 G A 258.29 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=59.57;MQ0=0;OQ=815.07;QD=15.09;SB=-428.45 GT:AD:DP:GL:GQ 0/1:27,26:50:-99.87,-15.07,-79.93:99 +chr1 3615542 rs3765755 G C 6.35 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=3.76;MQ=57.56;MQ0=0;OQ=289.35;QD=10.72;SB=-124.51 GT:AD:DP:GL:GQ 0/1:17,10:20:-38.26,-6.05,-38.86:99 +chr1 3615628 rs2368540 G A 45.74 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=57.64;MQ0=0;OQ=1334.80;QD=39.26;SB=-676.69 GT:AD:DP:GL:GQ 1/1:0,34:34:-137.07,-10.24,-0.01:99 +chr1 3615736 rs2368539 G A 82.76 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.19;MQ=58.99;MQ0=0;OQ=1720.73;QD=37.41;SB=-824.61 GT:AD:DP:GL:GQ 1/1:0,46:45:-175.68,-13.56,-0.02:99 +chr1 3616028 rs12130809 G A 272.35 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=838.34;QD=17.11;SB=-389.14 GT:AD:DP:GL:GQ 0/1:23,26:48:-101.58,-14.46,-75.57:99 +chr1 3616588 rs3753208 C T 1.11 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=2.44;MQ=57.64;MQ0=0;OQ=539.82;QD=20.76;SB=-254.78 GT:AD:DP:GL:GQ 0/1:9,17:24:-64.50,-7.23,-25.72:99 +chr1 3616624 rs3753209 G A 11.81 PASS AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=58.89;MQ0=0;OQ=522.74;QD=24.89;SB=-281.33 GT:AD:DP:GL:GQ 0/1:4,17:19:-61.28,-5.73,-9.34:36.13 +chr1 3618071 rs3819961 T C 130.28 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=59.30;MQ0=0;OQ=302.64;QD=9.17;SB=-168.93 GT:AD:DP:GL:GQ 0/1:19,14:29:-42.29,-8.74,-60.25:99 +chr1 3618163 rs3819962 C T 161.54 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.36;MQ0=0;OQ=457.21;QD=12.70;SB=-166.18 GT:AD:DP:GL:GQ 0/1:20,16:35:-59.55,-10.55,-68.25:99 +chr1 3618201 rs3819963 C T 122.91 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=60.00;MQ0=0;OQ=469.25;QD=9.98;SB=-160.23 GT:AD:DP:GL:GQ 0/1:28,19:40:-62.27,-12.06,-77.68:99 +chr1 3618523 rs6424089 A G 234.40 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.55;MQ0=0;OQ=515.26;QD=10.10;SB=-135.54 GT:AD:DP:GL:GQ 0/1:28,23:50:-69.88,-15.07,-112.69:99 +chr1 3618537 rs6424090 A G 547.53 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.83;MQ0=0;OQ=1664.50;QD=30.82;SB=-446.16 GT:AD:DP:GL:GQ 1/1:0,54:52:-170.07,-15.68,-0.04:99 +chr1 3619132 rs61568045 A T 75.76 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=1.40;MQ=60.00;MQ0=0;OQ=702.41;QD=14.05;SB=-308.70 GT:AD:DP:GL:GQ 0/1:27,23:49:-88.29,-14.76,-94.54:99 +chr1 3619452 rs3765758 A G 47.37 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.30;MQ0=0;OQ=878.57;QD=26.62;SB=-355.42 GT:AD:DP:GL:GQ 1/1:0,33:30:-91.48,-9.06,-0.04:90.16 +chr1 3620336 rs3765761 C T 430.43 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.64;MQ0=0;OQ=893.13;QD=17.18;SB=-472.49 GT:AD:DP:GL:GQ 0/1:25,27:51:-107.96,-15.36,-81.84:99 +chr1 3620975 rs3765763 C A 252.43 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.39;MQ0=0;OQ=502.24;QD=13.22;SB=-232.36 GT:AD:DP:GL:GQ 0/1:20,18:37:-64.65,-11.14,-68.16:99 +chr1 3621759 rs61759267 C T 206.85 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=58.40;MQ0=0;OQ=667.68;QD=16.28;SB=-326.34 GT:AD:DP:GL:GQ 0/1:19,22:40:-82.11,-12.06,-61.46:99 +chr1 3622468 rs3753211 T C 35.06 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=6.67;MQ=58.45;MQ0=0;OQ=511.74;QD=11.37;SB=-197.62 GT:AD:DP:GL:GQ 0/1:23,22:42:-67.14,-12.68,-73.45:99 +chr1 3622590 rs4648551 G A 13.99 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=8.04;MQ=59.11;MQ0=0;OQ=881.37;QD=14.94;SB=-385.40 GT:AD:DP:GL:GQ 0/1:30,29:55:-108.00,-16.58,-90.70:99 +chr1 3623397 rs3765764 G A 5.20 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.59;MQ0=0;OQ=1699.76;QD=37.77;SB=-349.25 GT:AD:DP:GL:GQ 1/1:0,44:44:-176.03,-15.59,-2.47:99 +chr1 3624319 rs3765765 C A 38.07 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=752.18;QD=20.33;SB=-184.22 GT:AD:DP:GL:GQ 0/1:13,24:36:-89.34,-10.84,-42.24:99 +chr1 3624520 rs3765766 T C 10.08 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=2;HaplotypeScore=2.32;MQ=58.08;MQ0=0;OQ=679.70;QD=30.90;SB=-324.14 GT:AD:DP:GL:GQ 1/1:0,22:21:-71.57,-6.33,-0.02:63.16 +chr1 3625325 rs3765767 G C 128.03 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.30;MQ0=0;OQ=648.42;QD=19.65;SB=-303.36 GT:AD:DP:GL:GQ 0/1:15,18:33:-78.07,-9.95,-65.85:99 +chr1 3625451 rs3765768 C T 99.15 PASS AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=57.87;MQ0=0;OQ=372.64;QD=16.94;SB=-111.62 GT:AD:DP:GL:GQ 0/1:9,13:20:-46.58,-6.03,-24.55:99 +chr1 3625480 rs3819968 G T 164.17 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.32;MQ0=0;OQ=519.45;QD=15.28;SB=-228.94 GT:AD:DP:GL:GQ 0/1:15,19:32:-64.87,-9.64,-47.62:99 +chr1 3627107 rs3765771 G C 208.39 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.53;MQ0=0;OQ=1861.37;QD=37.99;SB=-769.21 GT:AD:DP:GL:GQ 1/1:0,49:48:-189.76,-14.49,-0.04:99 +chr1 3627319 rs12731705 C T 198.62 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.16;MQ0=0;OQ=1887.80;QD=37.76;SB=-826.61 GT:AD:DP:GL:GQ 1/1:0,50:48:-192.38,-14.46,-0.01:99 +chr1 3627473 rs2146658 T G 374.11 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.91;MQ0=0;OQ=603.03;QD=10.05;SB=-295.81 GT:AD:DP:GL:GQ 0/1:35,25:58:-81.06,-17.47,-122.08:99 +chr1 3627672 rs2181487 C A 40.28 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.14;MQ=58.10;MQ0=0;OQ=433.83;QD=7.35;SB=-156.52 GT:AD:DP:GL:GQ 0/1:34,22:49:-61.43,-14.77,-105.52:99 +chr1 3628534 rs1801174 C T 158.46 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.66;MQ0=0;OQ=2550.78;QD=38.07;SB=-965.29 GT:AD:DP:GL:GQ 1/1:0,67:65:-258.68,-19.58,-0.02:99 +chr1 3628694 rs12737840 C T 176.16 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.52;MQ=58.05;MQ0=0;OQ=694.01;QD=14.46;SB=-295.84 GT:AD:DP:GL:GQ 0/1:22,26:42:-85.35,-12.67,-62.54:99 +chr1 3629503 rs4648552 T C 338.68 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1294.39;QD=30.10;SB=-605.94 GT:AD:DP:GL:GQ 1/1:0,43:41:-133.06,-12.37,-0.04:99 +chr1 3629584 rs7537335 G A 0.43 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=58.30;MQ0=0;OQ=677.32;QD=21.85;SB=-284.30 GT:AD:DP:GL:GQ 0/1:10,21:29:-79.75,-8.74,-30.01:99 +chr1 3629945 rs6424091 C G 0.03 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=5;HaplotypeScore=2.31;MQ=58.54;MQ0=0;OQ=1470.54;QD=38.70;SB=-622.99 GT:AD:DP:GL:GQ 1/1:0,38:35:-150.65,-10.55,-0.01:99 +chr1 3630886 rs6687491 G A 255.56 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=58.48;MQ0=0;OQ=516.42;QD=12.91;SB=-227.77 GT:AD:DP:GL:GQ 0/1:22,18:36:-65.79,-10.86,-57.81:99 +chr1 3630983 rs6701784 A C 437.82 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.55;MQ0=0;OQ=1276.86;QD=28.37;SB=-579.85 GT:AD:DP:GL:GQ 1/1:0,45:42:-131.31,-12.66,-0.04:99 +chr1 3632013 rs34178965 G C 41.74 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;QD=13.91;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:2:-7.58,-0.60,-0.00:6.02 +chr1 3632108 . A G 92.54 PASS AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.46;MQ0=0;OQ=246.19;QD=30.77;SB=-85.92 GT:AD:DP:GL:GQ 1/1:0,8:8:-28.20,-2.41,-0.00:24.07 +chr1 3633787 rs2296031 A G 6.14 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=452.89;QD=19.69;SB=-150.34 GT:AD:DP:GL:GQ 0/1:6,16:22:-55.20,-6.63,-22.30:99 +chr1 3634209 rs2181486 A G 1.25 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=4;HaplotypeScore=1.69;MQ=58.39;MQ0=0;OQ=887.40;QD=30.60;SB=-422.16 GT:AD:DP:GL:GQ 1/1:0,29:29:-92.36,-8.75,-0.03:87.19 +chr1 3634234 rs2146657 A G 3.11 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=2.86;MQ=58.55;MQ0=0;OQ=912.28;QD=28.51;SB=-446.82 GT:AD:DP:GL:GQ 1/1:0,32:28:-94.83,-8.44,-0.02:84.21 +chr1 3634529 rs2236367 C T 14.74 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=-0.18;MQ=58.05;MQ0=0;OQ=381.45;QD=15.89;SB=-87.90 GT:AD:DP:GL:GQ 0/1:11,13:23:-48.37,-6.94,-31.96:99 +chr1 3634665 rs2236366 A G 76.17 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.83;MQ=58.92;MQ0=0;OQ=536.64;QD=13.76;SB=-250.32 GT:AD:DP:GL:GQ 0/1:16,23:35:-67.50,-10.56,-54.78:99 +chr1 3634718 rs2236365 G C 250.46 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=58.69;MQ0=0;OQ=951.80;QD=19.04;SB=-496.24 GT:AD:DP:GL:GQ 0/1:20,30:47:-112.65,-14.19,-78.43:99 +chr1 3634912 rs12095248 A G 50.60 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=529.65;QD=10.81;SB=-225.29 GT:AD:DP:GL:GQ 0/1:29,20:49:-71.01,-14.76,-117.85:99 +chr1 3635695 rs2254530 C A 234.40 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=56.85;MQ0=0;OQ=701.30;QD=15.58;SB=-270.34 GT:AD:DP:GL:GQ 0/1:17,28:43:-86.38,-12.96,-55.17:99 +chr1 3635704 rs2096224 G A 61.81 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.39;MQ0=0;OQ=843.06;QD=18.33;SB=-255.19 GT:AD:DP:GL:GQ 0/1:18,27:42:-100.25,-12.66,-49.65:99 +chr1 3635997 rs11589885 C T 153.88 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.19;MQ=58.55;MQ0=0;OQ=582.90;QD=18.22;SB=-289.86 GT:AD:DP:GL:GQ 0/1:14,18:32:-71.22,-9.65,-43.73:99 +chr1 3636052 rs1885867 G A 143.16 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.44;MQ0=0;OQ=1392.32;QD=33.96;SB=-648.62 GT:AD:DP:GL:GQ 1/1:1,40:37:-142.84,-11.16,-0.02:99 +chr1 3636074 rs1885866 T C 394.04 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1194.73;QD=27.15;SB=-580.01 GT:AD:DP:GL:GQ 1/1:0,44:39:-123.10,-11.76,-0.04:99 +chr1 3636151 rs1885865 G A 33.35 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.52;MQ=59.03;MQ0=0;OQ=1851.65;QD=38.58;SB=-906.66 GT:AD:DP:GL:GQ 1/1:0,48:47:-188.76,-14.16,-0.01:99 +chr1 3637822 rs1745813 T C 55.74 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=5.13;MQ=58.97;MQ0=0;OQ=680.74;QD=15.13;SB=-289.66 GT:AD:DP:GL:GQ 0/1:18,27:43:-84.33,-12.97,-62.63:99 +chr1 3638114 rs34661835 G A 68.90 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=3.56;MQ=59.01;MQ0=0;OQ=1063.39;QD=15.19;SB=-366.89 GT:AD:DP:GL:GQ 0/1:37,33:66:-129.52,-19.90,-102.17:99 +chr1 3638739 rs4648553 G A 223.38 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.68;MQ=58.64;MQ0=0;OQ=511.89;QD=10.66;SB=-215.18 GT:AD:DP:GL:GQ 0/1:26,22:40:-66.54,-12.07,-70.14:99 +chr1 3640958 rs1181869 C T 138.76 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=782.45;QD=20.06;SB=-285.16 GT:AD:DP:GL:GQ 0/1:16,23:38:-92.98,-11.45,-54.47:99 +chr1 3640986 rs1181868 G T 357.91 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=59.51;MQ0=0;OQ=742.19;QD=14.55;SB=-306.02 GT:AD:DP:GL:GQ 0/1:23,27:47:-91.66,-14.16,-72.26:99 +chr1 3641178 rs1181867 A G 3.60 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=11.13;MQ=59.11;MQ0=0;OQ=463.08;QD=9.85;SB=-239.29 GT:AD:DP:GL:GQ 0/1:24,23:43:-62.56,-12.97,-88.46:99 +chr1 3642477 rs1047928 G C 24.63 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.25;MQ0=0;OQ=1110.64;QD=19.83;SB=-354.44 GT:AD:DP:GL:GQ 0/1:25,31:54:-130.64,-16.30,-94.09:99 +chr1 3642678 rs61759293 G A 143.34 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=59.59;MQ0=0;OQ=746.17;QD=16.22;SB=-262.29 GT:AD:DP:GL:GQ 0/1:23,23:46:-91.76,-13.86,-82.87:99 +chr1 3642682 rs9800 C G 193.80 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=59.59;MQ0=0;OQ=608.81;QD=13.23;SB=-238.07 GT:AD:DP:GL:GQ 0/1:25,21:45:-77.74,-13.57,-107.75:99 +chr1 3643272 rs1181866 A C 242.81 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1714.13;QD=34.28;SB=-732.08 GT:AD:DP:GL:GQ 1/1:0,50:49:-175.01,-14.76,-0.02:99 +chr1 3643286 rs1181865 T C 423.19 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1563.43;QD=32.57;SB=-664.24 GT:AD:DP:GL:GQ 1/1:0,48:46:-159.95,-13.86,-0.02:99 +chr1 3644050 rs1181864 A G 156.69 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=57.94;MQ0=0;OQ=704.72;QD=10.36;SB=-357.09 GT:AD:DP:GL:GQ 0/1:38,30:68:-94.25,-20.50,-152.69:99 +chr1 3644355 rs41315308 C T 206.84 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=57.86;MQ0=0;OQ=957.61;QD=14.96;SB=-405.80 GT:AD:DP:GL:GQ 0/1:34,30:63:-118.03,-18.99,-105.73:99 +chr1 3646184 rs1181863 T C 89.60 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.04;MQ0=1;OQ=1725.96;QD=27.84;SB=-738.77 GT:AD:DP:GL:GQ 1/1:0,62:55:-176.23,-16.59,-0.05:99 +chr1 3647330 rs61339658 C T 216.66 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.48;MQ0=0;OQ=622.56;QD=14.15;SB=-204.90 GT:AD:DP:GL:GQ 0/1:24,20:43:-78.50,-12.96,-75.30:99 +chr1 3647619 rs12117836 G A 258.44 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.76;MQ0=0;OQ=3087.35;QD=39.58;SB=-1142.52 GT:AD:DP:GL:GQ 1/1:0,78:77:-312.34,-23.20,-0.02:99 +chr1 3647643 rs55704710 C T 372.37 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1117.31;QD=14.14;SB=-441.41 GT:AD:DP:GL:GQ 0/1:44,35:79:-138.82,-23.81,-145.27:99 +chr1 3648097 rs10797409 G A 267.01 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.27;MQ0=0;OQ=783.87;QD=15.37;SB=-396.73 GT:AD:DP:GL:GQ 0/1:26,25:51:-97.04,-15.37,-93.66:99 +chr1 3648630 rs12068191 T C 36.85 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=59.42;MQ0=0;OQ=210.22;QD=6.57;SB=-113.63 GT:AD:DP:GL:GQ 0/1:20,12:30:-33.36,-9.05,-73.41:99 +chr1 3649517 rs2298222 G A 272.39 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=58.64;MQ0=0;OQ=639.47;QD=13.32;SB=-210.21 GT:AD:DP:GL:GQ 0/1:28,20:45:-80.80,-13.57,-77.92:99 +chr1 3650201 rs10910020 A G 239.62 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=60.00;MQ0=0;OQ=830.62;QD=14.32;SB=-256.96 GT:AD:DP:GL:GQ 0/1:22,36:55:-102.93,-16.58,-89.31:99 +chr1 3650655 rs61759295 C T 319.94 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=56.32;MQ0=0;OQ=1049.42;QD=17.20;SB=-513.15 GT:AD:DP:GL:GQ 0/1:29,32:58:-125.70,-17.48,-89.86:99 +chr1 3650715 . C T 1.43 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=1;HaplotypeScore=2.94;MQ=58.05;MQ0=0;OQ=1053.29;QD=21.50;SB=-546.76 GT:AD:DP:GL:GQ 0/1:18,30:49:-126.44,-17.83,-68.95:99 +chr1 3650833 rs61759296 C T 365.26 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=780.11;QD=18.14;SB=-365.90 GT:AD:DP:GL:GQ 0/1:18,25:43:-94.25,-12.96,-66.61:99 +chr1 3650834 rs61759297 A G 444.30 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=732.78;QD=16.65;SB=-378.33 GT:AD:DP:GL:GQ 0/1:18,26:44:-89.82,-13.26,-70.47:99 +chr1 3651042 . A G 50.56 PASS AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.01;MQ0=0;OQ=2317.73;QD=30.50;SB=-942.03 GT:AD:DP:GL:GQ 1/1:0,76:75:-235.44,-22.63,-0.08:99 +chr1 3651109 . A G 1.79 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.08;MQ=56.71;MQ0=0;OQ=273.27;QD=7.01;SB=-125.50 GT:AD:DP:GL:GQ 0/1:24,15:37:-41.77,-11.16,-93.00:99 +chr1 3651611 rs61759298 C T 14.44 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=6.20;MQ=59.36;MQ0=0;OQ=487.25;QD=13.53;SB=-201.22 GT:AD:DP:GL:GQ 0/1:19,17:31:-61.35,-9.34,-53.39:99 +chr1 3651666 rs61759299 G A 290.38 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.58;MQ0=0;OQ=537.51;QD=11.69;SB=-229.48 GT:AD:DP:GL:GQ 0/1:28,18:45:-70.60,-13.56,-93.90:99 +chr1 3652705 rs3737589 A G 232.40 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1820.89;QD=33.11;SB=-644.31 GT:AD:DP:GL:GQ 1/1:0,55:53:-185.70,-15.97,-0.02:99 +chr1 3652806 . C A 30.45 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=2;HaplotypeScore=18.21;MQ=58.71;MQ0=0;QD=0.56;SB=77.26 GT:AD:DP:GL:GQ 0/1:38,16:41:-18.69,-12.36,-124.87:63.28 +chr1 3652917 rs3737590 A T 248.79 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.59;MQ0=0;OQ=534.27;QD=11.87;SB=-180.50 GT:AD:DP:GL:GQ 0/1:25,20:43:-69.67,-12.96,-88.74:99 +chr1 3652988 rs3737591 G A 355.22 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=743.37;QD=18.13;SB=-354.36 GT:AD:DP:GL:GQ 0/1:19,22:40:-89.67,-12.05,-59.56:99 +chr1 3653501 . C T 1.63 PASS AC=1;AF=0.50;AN=2;DP=24;Dels=0.00;HRun=1;HaplotypeScore=4.19;MQ=56.43;MQ0=0;OQ=295.19;QD=12.30;SB=-147.16 GT:AD:DP:GL:GQ 0/1:12,11:20:-38.83,-6.03,-35.51:99 +chr1 3654278 rs61759300 C T 319.11 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=59.50;MQ0=0;OQ=838.34;QD=14.71;SB=-382.16 GT:AD:DP:GL:GQ 0/1:29,28:55:-103.70,-16.58,-94.60:99 +chr1 3654412 . G A 1.87 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.14;MQ=59.58;MQ0=0;OQ=1116.86;QD=20.31;SB=-482.46 GT:AD:DP:GL:GQ 0/1:23,32:54:-131.23,-16.26,-80.42:99 +chr1 3655727 rs12120656 G T 277.67 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.16;MQ0=0;OQ=2493.88;QD=34.64;SB=-1022.51 GT:AD:DP:GL:GQ 1/1:0,71:69:-252.99,-20.78,-0.02:99 +chr1 3657359 rs61759301 C A 268.48 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=59.56;MQ0=0;OQ=858.70;QD=16.20;SB=-443.00 GT:AD:DP:GL:GQ 0/1:24,29:52:-104.82,-15.66,-81.51:99 +chr1 3657864 rs4648554 T C 343.27 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.67;MQ0=0;OQ=2306.57;QD=35.49;SB=-875.99 GT:AD:DP:GL:GQ 1/1:0,65:64:-234.26,-19.28,-0.02:99 +chr1 3658613 rs12128253 A C 493.82 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=800.32;QD=17.40;SB=-351.83 GT:AD:DP:GL:GQ 0/1:19,27:46:-97.17,-13.85,-71.32:99 +chr1 3658641 rs12123850 G T 445.21 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1182.07;QD=31.95;SB=-471.02 GT:AD:DP:GL:GQ 1/1:0,37:33:-121.80,-9.94,-0.01:99 +chr1 3659032 rs41315312 C T 393.31 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=747.09;QD=16.24;SB=-297.79 GT:AD:DP:GL:GQ 0/1:23,23:45:-91.55,-13.56,-71.39:99 +chr1 3659061 rs10797410 A G 617.38 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1286.97;QD=30.64;SB=-659.94 GT:AD:DP:GL:GQ 1/1:0,42:41:-132.32,-12.36,-0.04:99 +chr1 3659065 rs10910021 C G 483.45 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1547.05;QD=38.68;SB=-689.48 GT:AD:DP:GL:GQ 1/1:0,40:36:-158.30,-10.85,-0.01:99 +chr1 3659480 rs10797411 T C 0.77 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=7.27;MQ=57.71;MQ0=0;OQ=1720.61;QD=33.09;SB=-601.34 GT:AD:DP:GL:GQ 1/1:0,51:50:-175.67,-15.06,-0.02:99 +chr1 3659744 . C T 75.39 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=20;HaplotypeScore=21.91;MQ=50.61;MQ0=1;QD=1.13;SB=59.16 GT:AD:DP:GL:GQ 0/1:57,10:52:-26.50,-15.68,-150.70:99 +chr1 3659750 . T C 207.45 SnpCluster AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=50.10;MQ=49.95;MQ0=1;QD=3.05;SB=-120.43 GT:AD:DP:GL:GQ 0/1:53,15:58:-41.51,-17.48,-178.17:99 +chr1 3659751 . T C 331.47 SnpCluster AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=48.26;MQ=49.78;MQ0=1;QD=4.95;SB=-162.44 GT:AD:DP:GL:GQ 0/1:46,21:55:-53.00,-16.57,-149.72:99 +chr1 3660887 rs1181889 T C 275.60 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=59.11;MQ0=0;OQ=722.62;QD=13.90;SB=-328.30 GT:AD:DP:GL:GQ 0/1:24,28:49:-90.30,-14.76,-97.70:99 +chr1 3661651 rs1181888 A G 399.70 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=490.27;QD=11.14;SB=-251.93 GT:AD:DP:GL:GQ 0/1:22,22:42:-64.98,-12.67,-82.79:99 +chr1 3662016 rs4648555 C A 364.79 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=510.62;QD=9.46;SB=-259.25 GT:AD:DP:GL:GQ 0/1:34,20:53:-70.31,-15.96,-121.67:99 +chr1 3662783 rs12128087 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=13;HaplotypeScore=8.43;MQ=60.15;MQ0=0;OQ=558.18;QD=10.94;SB=-253.17 GT:AD:DP:GL:GQ 0/1:30,21:47:-73.27,-14.17,-94.61:99 +chr1 3663356 rs4648405 T G 117.92 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.45;MQ0=0;OQ=421.62;QD=10.04;SB=-89.84 GT:AD:DP:GL:GQ 0/1:24,18:40:-57.50,-12.05,-84.73:99 +chr1 3663862 rs1181887 T G 544.42 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1620.49;QD=34.48;SB=-656.23 GT:AD:DP:GL:GQ 1/1:0,47:47:-165.65,-14.16,-0.01:99 +chr1 3664012 rs7542464 C T 327.04 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.16;MQ0=0;OQ=1410.26;QD=37.11;SB=-358.47 GT:AD:DP:GL:GQ 1/1:0,38:38:-144.63,-11.46,-0.02:99 +chr1 3664166 . G A 2.11 PASS AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=3;HaplotypeScore=2.17;MQ=59.59;MQ0=0;OQ=801.46;QD=17.81;SB=-414.44 GT:AD:DP:GL:GQ 0/1:20,25:43:-96.39,-12.96,-61.16:99 +chr1 3664614 rs1181886 A T 88.61 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.65;MQ0=0;OQ=779.71;QD=14.44;SB=-332.65 GT:AD:DP:GL:GQ 0/1:28,26:52:-96.92,-15.66,-100.50:99 +chr1 3664618 rs9424312 T A 76.30 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=946.40;QD=17.53;SB=-254.96 GT:AD:DP:GL:GQ 0/1:24,30:54:-114.19,-16.27,-85.78:99 +chr1 3664638 rs59291549 A G 339.20 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.66;MQ0=0;OQ=754.74;QD=11.44;SB=-151.30 GT:AD:DP:GL:GQ 0/1:31,35:62:-97.45,-18.69,-125.83:99 +chr1 3664862 rs6682863 G A 201.85 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=59.78;MQ0=0;OQ=631.54;QD=12.63;SB=-190.86 GT:AD:DP:GL:GQ 0/1:30,20:45:-80.00,-13.57,-81.03:99 +chr1 3665697 rs12128570 C G 270.19 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=50.42;MQ0=0;OQ=767.84;QD=13.01;SB=-344.88 GT:AD:DP:GL:GQ 0/1:34,25:56:-96.94,-16.88,-141.00:99 +chr1 3665819 rs12131045 T G 461.26 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.52;MQ0=0;OQ=642.50;QD=12.12;SB=-333.74 GT:AD:DP:GL:GQ 0/1:24,29:50:-82.60,-15.07,-87.60:99 +chr1 3665937 rs12128669 C T 521.09 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.12;MQ0=0;OQ=862.45;QD=14.37;SB=-269.15 GT:AD:DP:GL:GQ 0/1:32,28:59:-107.30,-17.77,-116.90:99 +chr1 3666427 rs1181885 C T 33.74 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.66;MQ0=0;OQ=1204.99;QD=21.91;SB=-603.11 GT:AD:DP:GL:GQ 0/1:19,36:52:-139.46,-15.68,-54.65:99 +chr1 3666458 rs1181884 T C 438.67 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=1123.89;QD=17.56;SB=-533.09 GT:AD:DP:GL:GQ 0/1:26,38:63:-134.65,-18.98,-101.24:99 +chr1 3666632 rs12406474 T C 126.45 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=1.53;MQ=58.86;MQ0=0;OQ=740.89;QD=13.00;SB=-344.59 GT:AD:DP:GL:GQ 0/1:29,28:56:-94.24,-16.87,-116.11:99 +chr1 3667793 rs1181883 T C 251.38 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=59.64;MQ0=0;OQ=2030.56;QD=31.73;SB=-682.90 GT:AD:DP:GL:GQ 1/1:0,64:64:-206.69,-19.29,-0.05:99 +chr1 3668081 rs1181882 G C 162.48 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=60.00;MQ0=0;OQ=1618.57;QD=31.13;SB=-715.93 GT:AD:DP:GL:GQ 1/1:0,52:43:-165.50,-13.00,-0.06:99 +chr1 3668091 rs7516756 A G 107.99 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=613.13;QD=11.57;SB=-116.72 GT:AD:DP:GL:GQ 0/1:27,26:49:-79.36,-14.77,-98.00:99 +chr1 3668371 rs7516968 A G 62.28 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=209.36;QD=9.10;SB=-37.93 GT:AD:DP:GL:GQ 0/1:13,10:22:-30.85,-6.63,-52.05:99 +chr1 3668596 . G A 15.65 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=57.44;MQ0=0;OQ=384.28;QD=10.98;SB=-65.05 GT:AD:DP:GL:GQ 0/1:22,13:35:-52.26,-10.55,-81.04:99 +chr1 3668758 rs1181881 A G 16.49 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=57.96;MQ0=0;OQ=916.82;QD=30.56;SB=-341.43 GT:AD:DP:GL:GQ 1/1:0,30:29:-95.29,-8.74,-0.02:87.21 +chr1 3668764 rs1181880 C T 45.57 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.66;MQ0=0;OQ=531.41;QD=18.98;SB=-213.73 GT:AD:DP:GL:GQ 0/1:11,17:28:-64.87,-8.45,-34.91:99 +chr1 3668999 rs1181879 T C 13.01 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.38;MQ=59.44;MQ0=0;OQ=1208.95;QD=29.49;SB=-449.15 GT:AD:DP:GL:GQ 1/1:0,41:38:-124.52,-11.46,-0.04:99 +chr1 3669006 rs4648556 G A 196.56 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=59.44;MQ0=0;OQ=524.36;QD=12.79;SB=-228.74 GT:AD:DP:GL:GQ 0/1:24,17:40:-67.77,-12.05,-80.81:99 +chr1 3669167 rs4648557 T C 163.44 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=60.00;MQ0=0;OQ=314.58;QD=10.15;SB=-171.98 GT:AD:DP:GL:GQ 0/1:15,16:28:-43.19,-8.45,-53.69:99 +chr1 3669321 rs4648558 A T 213.98 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=59.30;MQ0=0;OQ=430.63;QD=13.05;SB=-151.85 GT:AD:DP:GL:GQ 0/1:18,15:33:-56.29,-9.94,-66.61:99 +chr1 3669635 rs10910024 C T 223.39 PASS AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=60.00;MQ0=0;OQ=261.53;QD=10.46;SB=-131.12 GT:AD:DP:GL:GQ 0/1:15,10:24:-36.67,-7.23,-47.59:99 +chr1 3669916 rs56079032 G A 49.43 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.11;MQ0=0;OQ=457.75;QD=17.61;SB=-143.18 GT:AD:DP:GL:GQ 0/1:10,16:25:-56.59,-7.54,-35.59:99 +chr1 3670503 rs1181878 G A 204.22 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=58.92;MQ0=0;OQ=593.13;QD=15.21;SB=-209.18 GT:AD:DP:GL:GQ 0/1:21,18:39:-74.34,-11.75,-76.92:99 +chr1 3670589 rs1181877 C T 442.14 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.71;MQ0=0;OQ=1051.46;QD=16.43;SB=-536.72 GT:AD:DP:GL:GQ 0/1:31,33:61:-126.81,-18.38,-107.46:99 +chr1 3670923 rs6669358 A G 271.22 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.35;MQ=59.49;MQ0=0;OQ=863.52;QD=11.83;SB=-442.10 GT:AD:DP:GL:GQ 0/1:40,33:71:-111.03,-21.40,-156.37:99 +chr1 3671541 rs1181876 A G 312.30 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.35;MQ0=0;OQ=557.92;QD=8.72;SB=-268.23 GT:AD:DP:GL:GQ 0/1:36,28:60:-77.16,-18.08,-144.69:99 +chr1 3671691 rs1181875 T C 354.44 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.69;MQ0=0;OQ=768.78;QD=12.60;SB=-310.35 GT:AD:DP:GL:GQ 0/1:32,29:59:-97.93,-17.77,-128.86:99 +chr1 3671930 rs1181874 C A 548.97 PASS AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1553.48;QD=14.00;SB=-588.81 GT:AD:DP:GL:GQ 0/1:58,53:110:-191.77,-33.14,-192.67:99 +chr1 3673550 rs1181873 A C 65.84 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.41;MQ0=0;OQ=502.42;QD=12.88;SB=-249.39 GT:AD:DP:GL:GQ 0/1:20,19:38:-64.97,-11.45,-71.58:99 +chr1 3673967 rs1181872 T A 314.39 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.13;MQ0=0;OQ=665.69;QD=15.48;SB=-321.70 GT:AD:DP:GL:GQ 0/1:19,24:41:-82.21,-12.35,-69.45:99 +chr1 3674181 rs1181871 A G 201.06 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=52.16;MQ0=0;OQ=271.85;QD=7.55;SB=-59.74 GT:AD:DP:GL:GQ 0/1:21,15:32:-40.11,-9.65,-77.03:99 +chr1 3674814 rs1181870 C A 305.27 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=57.69;MQ0=0;OQ=866.35;QD=12.93;SB=-280.62 GT:AD:DP:GL:GQ 0/1:36,31:65:-109.50,-19.58,-123.19:99 +chr1 3677599 rs1175552 C A 135.06 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=60.00;MQ0=0;OQ=585.48;QD=10.09;SB=-188.53 GT:AD:DP:GL:GQ 0/1:34,24:53:-77.81,-15.97,-102.27:99 +chr1 3678505 rs1175551 T C 166.68 PASS AC=1;AF=0.50;AN=2;DB;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=58.20;MQ0=0;OQ=103.01;QD=7.92;SB=-65.87 GT:AD:DP:GL:GQ 0/1:7,6:12:-17.20,-3.62,-26.14:99 +chr1 3679407 . C G 26.93 LowQual AC=1;AF=0.50;AN=2;DP=11;Dels=0.00;HRun=1;HaplotypeScore=2.22;MQ=48.93;MQ0=0;QD=2.45;SB=-6.99 GT:AD:DP:GL:GQ 0/1:3,8:4:-7.19,-1.21,-8.24:59.76 +chr1 3681100 rs1184341 C T 108.25 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=3.04;MQ=59.23;MQ0=0;OQ=426.67;QD=14.22;SB=-164.69 GT:AD:DP:GL:GQ 0/1:15,15:28:-54.39,-8.44,-49.07:99 +chr1 3681124 rs2797432 A G 199.77 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=396.40;QD=12.39;SB=-160.61 GT:AD:DP:GL:GQ 0/1:13,19:29:-51.67,-8.74,-51.47:99 +chr1 3681330 rs1181893 A C 235.23 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.61;MQ0=0;OQ=409.25;QD=27.28;SB=-143.01 GT:AD:DP:GL:GQ 1/1:0,15:13:-44.52,-3.92,-0.01:39.10 +chr1 3681388 rs1175550 A G 206.60 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.14;MQ0=0;OQ=268.33;QD=9.94;SB=-118.66 GT:AD:DP:GL:GQ 0/1:16,11:27:-38.26,-8.14,-61.45:99 +chr1 3681587 rs1175549 A C 56.97 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.73;MQ=59.28;MQ0=0;OQ=317.74;QD=9.93;SB=-135.67 GT:AD:DP:GL:GQ 0/1:18,14:31:-44.40,-9.34,-64.53:99 +chr1 3682892 rs1175548 A G 294.07 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.99;MQ0=0;OQ=521.21;QD=11.33;SB=-266.55 GT:AD:DP:GL:GQ 0/1:25,21:43:-68.36,-12.95,-93.71:99 +chr1 3683615 rs1175547 G T 106.09 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=58.25;MQ0=0;OQ=658.75;QD=16.47;SB=-219.58 GT:AD:DP:GL:GQ 0/1:18,22:39:-80.91,-11.75,-53.72:99 +chr1 3683769 rs1175546 C T 14.30 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=58.95;MQ0=0;OQ=845.89;QD=19.22;SB=-175.68 GT:AD:DP:GL:GQ 0/1:18,26:42:-100.52,-12.65,-61.88:99 +chr1 3684656 rs1891934 G A 75.40 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=59.58;MQ0=0;OQ=574.95;QD=13.07;SB=-268.25 GT:AD:DP:GL:GQ 0/1:26,18:41:-73.14,-12.36,-73.56:99 +chr1 3684836 . T G 29.95 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=2;HaplotypeScore=5.28;MQ=57.94;MQ0=0;QD=0.88;SB=50.17 GT:AD:DP:GL:GQ 0/1:20,14:25:-13.81,-7.53,-70.58:62.78 +chr1 3685860 rs2799182 T C 179.63 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.18;MQ=58.63;MQ0=0;OQ=681.56;QD=13.36;SB=-324.12 GT:AD:DP:GL:GQ 0/1:23,28:50:-86.51,-15.07,-94.22:99 +chr1 3686231 rs61759305 C T 280.07 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=512.50;QD=17.08;SB=-238.52 GT:AD:DP:GL:GQ 0/1:14,16:29:-63.27,-8.74,-47.74:99 +chr1 3686750 rs8379 A C 132.74 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.70;MQ0=0;OQ=512.51;QD=8.27;SB=-204.80 GT:AD:DP:GL:GQ 0/1:39,23:59:-72.31,-17.77,-139.60:99 +chr1 3687151 rs2996428 C T 323.10 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=59.68;MQ0=0;OQ=1332.10;QD=18.25;SB=-588.63 GT:AD:DP:GL:GQ 0/1:30,43:68:-156.98,-20.49,-102.01:99 +chr1 3688388 rs2799186 C G 198.40 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=60.00;MQ0=0;OQ=1120.38;QD=14.55;SB=-296.13 GT:AD:DP:GL:GQ 0/1:44,32:77:-141.06,-25.73,-190.14:99 +chr1 3688807 rs12122058 C T 132.91 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=788.10;QD=15.16;SB=-353.46 GT:AD:DP:GL:GQ 0/1:27,25:50:-97.16,-15.07,-93.28:99 +chr1 3689428 rs2799185 G C 86.89 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.23;MQ0=0;OQ=644.64;QD=17.42;SB=-205.64 GT:AD:DP:GL:GQ 0/1:18,19:35:-78.30,-10.56,-70.47:99 +chr1 3689489 rs2799184 T G 198.26 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=4.30;MQ=56.35;MQ0=0;OQ=514.42;QD=13.19;SB=-238.40 GT:AD:DP:GL:GQ 0/1:19,20:37:-65.87,-11.14,-65.31:99 +chr1 3689844 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=16;HaplotypeScore=12.40;MQ=56.82;MQ0=0;OQ=207.53;QD=3.10;SB=47.88 GT:AD:DP:GL:GQ 0/1:50,16:53:-40.01,-15.97,-140.82:99 +chr1 3691351 rs2996426 A G 107.45 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.66;MQ=59.77;MQ0=0;OQ=576.97;QD=11.10;SB=-273.25 GT:AD:DP:GL:GQ 0/1:26,26:49:-75.76,-14.78,-98.82:99 +chr1 3693197 rs2368537 G C 138.15 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.55;MQ0=0;OQ=1805.49;QD=35.40;SB=-781.23 GT:AD:DP:GL:GQ 1/1:0,51:46:-184.17,-13.88,-0.03:99 +chr1 3693570 rs2253143 G A 60.94 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=3.58;MQ=58.41;MQ0=0;OQ=495.55;QD=11.26;SB=-141.61 GT:AD:DP:GL:GQ 0/1:26,18:41:-65.20,-12.37,-77.20:99 +chr1 3694312 rs12142183 T G 312.97 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=59.65;MQ0=0;OQ=615.52;QD=11.61;SB=-311.76 GT:AD:DP:GL:GQ 0/1:22,31:47:-79.00,-14.16,-79.12:99 +chr1 3694564 . G C 39.33 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=6.24;MQ=58.81;MQ0=0;QD=0.72;SB=44.18 GT:AD:DP:GL:GQ 0/1:42,12:37:-18.38,-11.17,-134.23:72.16 +chr1 3701498 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=71;Dels=0.03;HRun=20;HaplotypeScore=51.30;MQ=52.45;MQ0=0;OQ=259.27;QD=3.65;SB=80.25 GT:AD:DP:GL:GQ 0/1:46,23:54:-44.89,-15.68,-134.64:99 +chr1 3708347 rs6681383 G A 128.24 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.34;MQ0=0;OQ=1078.39;QD=18.92;SB=-322.85 GT:AD:DP:GL:GQ 0/1:24,33:53:-127.10,-15.97,-69.66:99 +chr1 3712148 rs2996425 A T 193.61 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.11;MQ=59.02;MQ0=0;OQ=2222.50;QD=35.85;SB=-1018.88 GT:AD:DP:GL:GQ 1/1:0,62:60:-225.85,-18.07,-0.02:99 +chr1 3714307 rs61759320 G A 326.68 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=53.55;MQ0=0;OQ=770.50;QD=14.01;SB=-354.84 GT:AD:DP:GL:GQ 0/1:29,25:53:-96.31,-15.97,-95.14:99 +chr1 3714663 . A C 15.04 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=8.17;MQ=57.66;MQ0=0;QD=0.38;SB=56.19 GT:AD:DP:GL:GQ 0/1:24,16:28:-13.21,-8.44,-81.36:47.74 +chr1 3727878 . C T 38.08 PASS AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=59.48;MQ0=0;OQ=1399.61;QD=17.28;SB=-662.18 GT:AD:DP:GL:GQ 0/1:40,41:81:-167.65,-24.40,-140.98:99 +chr1 3731503 . A G 18.90 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=3;HaplotypeScore=1.79;MQ=54.69;MQ0=0;QD=0.73;SB=5.04 GT:AD:DP:GL:GQ 0/1:21,5:21:-11.50,-6.33,-70.25:51.68 +chr1 3735976 rs1836 A G 124.85 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.74;MQ0=0;OQ=2210.40;QD=31.13;SB=-963.45 GT:AD:DP:GL:GQ 1/1:0,70:69:-227.21,-23.18,-2.59:99 +chr1 3736114 rs2275830 T C 634.35 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=2088.07;QD=30.71;SB=-734.31 GT:AD:DP:GL:GQ 1/1:0,68:67:-212.46,-20.22,-0.07:99 +chr1 3736443 rs2275828 G T 17.64 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=3.28;MQ=59.05;MQ0=0;OQ=2655.56;QD=36.38;SB=-1342.28 GT:AD:DP:GL:GQ 1/1:0,73:72:-269.16,-21.68,-0.02:99 +chr1 3736449 rs2275826 C G 89.02 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.10;MQ0=0;OQ=3375.97;QD=43.84;SB=-1685.64 GT:AD:DP:GL:GQ 1/1:0,77:77:-336.60,-23.20,-0.02:99 +chr1 3737179 rs4648417 C T 55.97 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=58.05;MQ0=0;OQ=1230.92;QD=34.19;SB=-377.48 GT:AD:DP:GL:GQ 1/1:0,35:33:-126.70,-9.95,-0.02:99 +chr1 3737440 rs6424058 C T 106.25 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=3.83;MQ=56.84;MQ0=0;OQ=1463.09;QD=34.84;SB=-699.35 GT:AD:DP:GL:GQ 1/1:0,42:38:-149.91,-11.45,-0.01:99 +chr1 3737463 rs6413779 T C 36.87 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=57.40;MQ0=0;OQ=1023.14;QD=33.00;SB=-220.63 GT:AD:DP:GL:GQ 1/1:0,31:31:-105.92,-9.34,-0.02:93.25 +chr1 3737945 rs7522227 A G 230.87 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.22;MQ0=0;OQ=2674.63;QD=34.29;SB=-1340.60 GT:AD:DP:GL:GQ 1/1:0,77:76:-271.07,-22.89,-0.02:99 +chr1 3738031 rs7524765 T C 717.11 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2886.44;QD=35.20;SB=-1305.64 GT:AD:DP:GL:GQ 1/1:0,82:82:-292.25,-24.70,-0.03:99 +chr1 3738548 rs17403836 A C 593.74 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.20;MQ0=0;OQ=3340.65;QD=35.92;SB=-1448.19 GT:AD:DP:GL:GQ 1/1:0,93:93:-333.07,-28.01,-0.02:99 +chr1 3738842 rs61768911 C G 310.36 PASS AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.39;MQ0=2;OQ=606.83;QD=30.34;SB=-199.55 GT:AD:DP:GL:GQ 1/1:0,19:16:-64.28,-4.83,-0.01:48.16 +chr1 3738927 . T C 23.45 LowQual AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=5.48;MQ=47.67;MQ0=1;QD=0.60;SB=-5.57 GT:AD:DP:GL:GQ 0/1:32,7:31:-14.97,-9.34,-106.27:56.26 +chr1 3738930 . T C 7.68 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=48.29;MQ0=0;OQ=738.60;QD=19.44;SB=-353.38 GT:AD:DP:GL:GQ 0/1:6,32:31:-86.49,-9.35,-16.38:70.33 +chr1 3738954 rs61768912 T C 1249.83 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.18;MQ0=0;QD=28.41;SB=-561.89 GT:AD:DP:GL:GQ 1/1:0,43:40:-128.60,-12.06,-0.04:99 +chr1 3738962 rs61768913 A G 1521.07 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=53.09;MQ0=0;QD=28.17;SB=-501.21 GT:AD:DP:GL:GQ 1/1:0,54:48:-155.73,-14.47,-0.04:99 +chr1 3738964 rs61768914 A G 1823.57 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=53.35;MQ0=0;QD=32.56;SB=-678.27 GT:AD:DP:GL:GQ 1/1:0,56:52:-185.96,-15.66,-0.02:99 +chr1 3738975 rs61768915 T C 185.63 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=53.83;MQ0=0;OQ=2377.40;QD=34.96;SB=-853.97 GT:AD:DP:GL:GQ 1/1:0,68:67:-241.35,-20.18,-0.03:99 +chr1 3739217 rs6684560 G A 167.13 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=55.03;MQ0=0;OQ=2027.81;QD=36.87;SB=-859.02 GT:AD:DP:GL:GQ 1/1:1,54:53:-206.39,-15.97,-0.02:99 +chr1 3739448 rs6676260 T C 481.80 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1276.86;QD=30.40;SB=-555.08 GT:AD:DP:GL:GQ 1/1:0,42:41:-131.31,-12.36,-0.03:99 +chr1 3739507 rs10797344 C G 65.45 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=59.28;MQ0=0;OQ=2404.57;QD=37.57;SB=-1028.99 GT:AD:DP:GL:GQ 1/1:0,64:58:-244.08,-17.49,-0.04:99 +chr1 3739508 rs10797345 G A 56.93 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.68;MQ=59.28;MQ0=0;OQ=2416.64;QD=37.76;SB=-1154.54 GT:AD:DP:GL:GQ 1/1:0,64:63:-245.28,-18.99,-0.03:99 +chr1 3739554 rs6673716 A G 130.37 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.53;MQ0=0;OQ=1461.81;QD=29.83;SB=-615.96 GT:AD:DP:GL:GQ 1/1:0,49:46:-149.80,-13.87,-0.04:99 +chr1 3739633 rs6673807 A G 581.92 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=2050.62;QD=35.36;SB=-778.99 GT:AD:DP:GL:GQ 1/1:0,58:58:-208.67,-17.47,-0.02:99 +chr1 3740027 rs2368533 G A 618.30 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2881.32;QD=38.94;SB=-1374.05 GT:AD:DP:GL:GQ 1/1:0,74:73:-291.74,-21.99,-0.02:99 +chr1 3740589 rs6677381 A G 634.61 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=2780.11;QD=35.64;SB=-1088.76 GT:AD:DP:GL:GQ 1/1:0,78:77:-281.62,-23.19,-0.02:99 +chr1 3740591 rs6680017 T G 509.75 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=2637.83;QD=34.26;SB=-1082.49 GT:AD:DP:GL:GQ 1/1:0,77:75:-267.39,-22.59,-0.02:99 +chr1 3740758 . T A 7.56 PASS AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.28;MQ0=1;OQ=174.11;QD=4.71;SB=-20.31 GT:AD:DP:GL:GQ 0/1:28,9:34:-30.93,-10.24,-98.40:99 +chr1 3741138 rs2887273 C G 484.06 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2855.33;QD=43.26;SB=-1170.05 GT:AD:DP:GL:GQ 1/1:0,66:66:-289.13,-19.88,-0.02:99 +chr1 3741826 rs4648419 C G 552.08 PASS AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=0;OQ=3843.78;QD=42.24;SB=-1290.87 GT:AD:DP:GL:GQ 1/1:0,91:88:-383.38,-26.52,-0.03:99 +chr1 3742892 . G T 16.29 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=20;HaplotypeScore=18.89;MQ=55.03;MQ0=1;QD=0.28;SB=44.02 GT:AD:DP:GL:GQ 0/1:50,6:41:-19.70,-14.80,-98.51:49.02 +chr1 3742917 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.02;HRun=20;HaplotypeScore=34.21;MQ=57.45;MQ0=0;OQ=170.67;QD=3.28;SB=56.18 GT:AD:DP:GL:GQ 0/1:37,14:43:-33.01,-12.65,-114.45:99 +chr1 3742996 rs2275824 A T 710.47 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=2009.53;QD=35.25;SB=-882.57 GT:AD:DP:GL:GQ 1/1:0,57:56:-204.56,-16.87,-0.02:99 +chr1 3744349 rs12409082 G C 531.14 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3059.06;QD=43.09;SB=-1422.83 GT:AD:DP:GL:GQ 1/1:0,71:71:-309.52,-21.40,-0.02:99 +chr1 3744456 rs6683827 G T 2.38 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=4.28;MQ=58.86;MQ0=0;OQ=2501.40;QD=35.73;SB=-1071.46 GT:AD:DP:GL:GQ 1/1:0,70:69:-253.75,-20.78,-0.02:99 +chr1 3745535 rs1891941 T C 731.33 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2479.06;QD=35.42;SB=-1217.69 GT:AD:DP:GL:GQ 1/1:0,70:69:-251.51,-20.78,-0.02:99 +chr1 3745729 rs1891940 T C 456.28 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=1634.49;QD=34.78;SB=-697.28 GT:AD:DP:GL:GQ 1/1:0,47:46:-167.05,-13.85,-0.01:99 +chr1 3745735 rs1891939 T G 249.79 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=1553.73;QD=33.78;SB=-800.51 GT:AD:DP:GL:GQ 1/1:0,46:45:-158.97,-13.55,-0.02:99 +chr1 3745980 rs1539649 A G 625.14 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=2553.81;QD=30.77;SB=-1180.11 GT:AD:DP:GL:GQ 1/1:0,83:80:-259.03,-24.12,-0.06:99 +chr1 3746353 rs7535887 T C 654.18 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1854.47;QD=30.91;SB=-854.01 GT:AD:DP:GL:GQ 1/1:0,60:59:-189.08,-17.79,-0.05:99 +chr1 3746392 rs10797346 T C 305.08 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2579.74;QD=35.83;SB=-1200.15 GT:AD:DP:GL:GQ 1/1:0,72:72:-261.58,-21.69,-0.02:99 +chr1 3747160 rs10909800 C T 207.27 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2281.73;QD=39.34;SB=-904.67 GT:AD:DP:GL:GQ 1/1:0,58:58:-231.78,-17.47,-0.02:99 +chr1 3748578 rs4381131 T C 118.61 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=57.58;MQ0=0;OQ=1302.81;QD=35.21;SB=-612.36 GT:AD:DP:GL:GQ 1/1:0,37:37:-133.88,-11.14,-0.01:99 +chr1 3748616 rs4411084 A G 124.66 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.91;MQ=57.27;MQ0=0;OQ=1453.01;QD=29.06;SB=-634.87 GT:AD:DP:GL:GQ 1/1:0,50:46:-148.93,-13.88,-0.04:99 +chr1 3749212 rs3765774 T A 197.18 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=2826.29;QD=36.71;SB=-1358.75 GT:AD:DP:GL:GQ 1/1:0,77:76:-286.23,-22.89,-0.02:99 +chr1 3749644 rs10797347 A G 265.86 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=59.07;MQ0=0;OQ=1626.88;QD=34.61;SB=-812.67 GT:AD:DP:GL:GQ 1/1:0,47:46:-166.29,-13.86,-0.01:99 +chr1 3749797 rs10909801 A G 1.04 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=13.74;MQ=53.38;MQ0=0;OQ=1309.63;QD=23.81;SB=-631.48 GT:AD:DP:GL:GQ 1/1:0,53:41:-134.59,-12.37,-0.04:99 +chr1 3749921 rs6701360 G A 575.83 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.91;MQ0=0;OQ=2426.40;QD=38.51;SB=-904.68 GT:AD:DP:GL:GQ 1/1:0,63:63:-246.25,-18.99,-0.03:99 +chr1 3749974 rs6690371 A G 48.27 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=1.93;MQ=58.34;MQ0=0;OQ=1681.22;QD=35.03;SB=-728.27 GT:AD:DP:GL:GQ 1/1:0,48:48:-171.73,-14.47,-0.03:99 +chr1 3749989 rs6678020 C T 441.08 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.59;MQ0=0;OQ=1518.29;QD=37.96;SB=-571.34 GT:AD:DP:GL:GQ 1/1:0,40:39:-155.43,-11.75,-0.01:99 +chr1 3750090 rs6680552 C T 728 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.60;MQ0=1;OQ=1998.34;QD=35.06;SB=-998.84 GT:AD:DP:GL:GQ 1/1:0,57:51:-203.43,-15.36,-0.01:99 +chr1 3750216 rs6695657 T C 130.02 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.67;MQ0=0;OQ=1753.47;QD=29.72;SB=-613.96 GT:AD:DP:GL:GQ 1/1:0,59:56:-178.99,-16.89,-0.06:99 +chr1 3750378 rs10752723 A G 15.88 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.50;MQ=56.80;MQ0=0;OQ=1482.59;QD=32.95;SB=-488.54 GT:AD:DP:GL:GQ 1/1:1,43:41:-151.86,-12.35,-0.01:99 +chr1 3751141 rs6698930 T A 637.91 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=7;HaplotypeScore=46.26;MQ=41.75;MQ0=0;QD=7.78;SB=8.51 GT:AD:DP:GL:GQ 0/1:49,33:69:-87.87,-20.79,-167.40:99 +chr1 3751339 rs2275822 C T 226.46 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.23;MQ0=0;OQ=2373.96;QD=39.57;SB=-964.37 GT:AD:DP:GL:GQ 1/1:0,60:60:-241.00,-18.08,-0.02:99 +chr1 3751510 rs2275821 A G 573.45 PASS AC=2;AF=1.00;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.31;MQ0=0;OQ=3500.46;QD=35.36;SB=-1716.03 GT:AD:DP:GL:GQ 1/1:0,99:96:-349.05,-28.91,-0.03:99 +chr1 3751936 rs6699784 T C 22.54 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1634.61;QD=34.05;SB=-680.60 GT:AD:DP:GL:GQ 1/1:0,48:47:-167.07,-14.16,-0.02:99 +chr1 3751940 rs6699785 T C 457.63 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1716.61;QD=35.76;SB=-707.61 GT:AD:DP:GL:GQ 1/1:0,48:48:-175.26,-14.46,-0.02:99 +chr1 3752276 rs6687498 C A 0.86 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=7.86;MQ=58.29;MQ0=1;OQ=1565.75;QD=34.79;SB=-714.95 GT:AD:DP:GL:GQ 1/1:1,44:44:-160.17,-13.25,-0.01:99 +chr1 3752464 rs4494088 C T 130.82 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.01;MQ0=0;OQ=2585.87;QD=39.18;SB=-1275.71 GT:AD:DP:GL:GQ 1/1:0,66:65:-262.19,-19.58,-0.02:99 +chr1 3752510 . C A 11.64 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=20;HaplotypeScore=16.03;MQ=54.71;MQ0=1;QD=0.16;SB=98.34 GT:AD:DP:GL:GQ 0/1:63,8:53:-20.38,-15.96,-171.47:44.17 +chr1 3752581 rs4534323 A T 713.95 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2157.31;QD=36.56;SB=-930.57 GT:AD:DP:GL:GQ 1/1:0,59:59:-219.34,-17.77,-0.02:99 +chr1 3753724 rs12047360 G A 108.34 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=59.36;MQ0=0;OQ=1255.98;QD=34.89;SB=-564.33 GT:AD:DP:GL:GQ 1/1:0,36:33:-129.19,-9.94,-0.01:99 +chr1 3754321 rs34401151 C T 220.62 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.55;MQ0=0;OQ=2357.19;QD=36.83;SB=-1184.12 GT:AD:DP:GL:GQ 1/1:0,63:62:-242.18,-21.42,-2.88:99 +chr1 3754471 rs55873991 T C 460.04 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=2216.85;QD=34.64;SB=-478.52 GT:AD:DP:GL:GQ 1/1:0,64:60:-225.28,-18.07,-0.01:99 +chr1 3755409 rs4648346 G A 377.30 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=56.94;MQ0=0;OQ=2718.34;QD=38.83;SB=-1289.71 GT:AD:DP:GL:GQ 1/1:0,70:68:-275.43,-20.48,-0.02:99 +chr1 3755538 rs4648423 C T 3.24 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=5.11;MQ=59.49;MQ0=0;OQ=1662.33;QD=36.94;SB=-681.30 GT:AD:DP:GL:GQ 1/1:0,44:44:-169.84,-13.26,-0.02:99 +chr1 3755615 rs4648347 T C 415.08 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.19;MQ0=0;OQ=2002.26;QD=34.52;SB=-940.97 GT:AD:DP:GL:GQ 1/1:0,58:56:-203.83,-16.87,-0.02:99 +chr1 3755919 rs12097923 G T 175.21 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=59.51;MQ0=0;OQ=2007.64;QD=34.03;SB=-971.58 GT:AD:DP:GL:GQ 1/1:0,58:57:-204.37,-17.17,-0.02:99 +chr1 3756146 rs17404435 G T 642.91 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1775.93;QD=34.82;SB=-654.09 GT:AD:DP:GL:GQ 1/1:0,51:50:-181.19,-15.06,-0.02:99 +chr1 3756301 rs6683156 C T 153.50 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=59.62;MQ0=0;OQ=3593.95;QD=38.64;SB=-1767.70 GT:AD:DP:GL:GQ 1/1:0,92:90:-358.39,-27.12,-0.03:99 +chr1 3757458 rs3765779 A G 312.92 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1547.17;QD=29.19;SB=-677.55 GT:AD:DP:GL:GQ 1/1:0,53:50:-158.35,-15.08,-0.05:99 +chr1 3757556 rs3765780 C T 73.74 PASS AC=2;AF=1.00;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1220.87;QD=37.00;SB=-540.71 GT:AD:DP:GL:GQ 1/1:0,33:32:-125.68,-9.64,-0.01:96.30 +chr1 3758579 rs1539647 T C 5.15 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=3.94;MQ=58.65;MQ0=1;OQ=2215.43;QD=29.94;SB=-922.78 GT:AD:DP:GL:GQ 1/1:1,73:71:-228.15,-21.41,-3.03:99 +chr1 3758589 rs1539648 T C 162.50 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=59.09;MQ0=0;OQ=2319.86;QD=30.52;SB=-925.48 GT:AD:DP:GL:GQ 1/1:0,76:73:-235.63,-22.01,-0.06:99 +chr1 3759091 rs6657021 A G 451.01 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.04;MQ0=0;OQ=2173.33;QD=30.19;SB=-1093.08 GT:AD:DP:GL:GQ 1/1:0,72:68:-220.98,-20.51,-0.06:99 +chr1 3759136 rs6668213 G C 44.87 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.72;MQ0=0;OQ=2874.30;QD=41.66;SB=-1253.95 GT:AD:DP:GL:GQ 1/1:0,69:66:-291.04,-19.89,-0.02:99 +chr1 3759146 rs6693152 C T 203.33 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.07;MQ0=0;OQ=2711.10;QD=38.73;SB=-1194.58 GT:AD:DP:GL:GQ 1/1:0,70:68:-274.71,-20.49,-0.02:99 +chr1 3759189 rs6657132 A G 408.69 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=1707.03;QD=31.04;SB=-847.00 GT:AD:DP:GL:GQ 1/1:0,55:50:-174.32,-15.07,-0.03:99 +chr1 3759225 rs6668306 G C 258.29 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.53;MQ0=0;OQ=1917.17;QD=39.13;SB=-849.44 GT:AD:DP:GL:GQ 1/1:0,49:46:-195.32,-13.87,-0.02:99 +chr1 3759237 rs6693259 C T 255.19 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1813.57;QD=38.59;SB=-875.61 GT:AD:DP:GL:GQ 1/1:0,47:47:-184.96,-14.17,-0.02:99 +chr1 3759339 . T C 4.24 PASS AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=37.66;MQ0=0;OQ=1291.89;QD=29.36;SB=-665.80 GT:AD:DP:GL:GQ 1/1:0,44:41:-132.82,-12.37,-0.04:99 +chr1 3759424 rs11576718 T C 18.88 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.78;MQ0=0;OQ=1915.98;QD=34.84;SB=-646.27 GT:AD:DP:GL:GQ 1/1:0,55:53:-195.20,-15.96,-0.02:99 +chr1 3759450 rs11578021 G C 393.67 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=2482.73;QD=42.08;SB=-1009.18 GT:AD:DP:GL:GQ 1/1:0,59:57:-251.88,-17.18,-0.02:99 +chr1 3760255 rs4130539 C A 200.10 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=59.43;MQ0=0;OQ=2921.40;QD=36.07;SB=-1317.55 GT:AD:DP:GL:GQ 1/1:0,81:81:-295.75,-24.40,-0.03:99 +chr1 3760285 rs4233023 G A 128.17 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.42;MQ0=0;OQ=2979.99;QD=37.25;SB=-1007.64 GT:AD:DP:GL:GQ 1/1:0,80:76:-301.61,-22.90,-0.03:99 +chr1 3760596 rs4582731 T C 194.06 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1740.97;QD=31.65;SB=-868.36 GT:AD:DP:GL:GQ 1/1:0,55:54:-177.73,-16.29,-0.05:99 +chr1 3760968 rs12023761 T C 207.14 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=57.12;MQ0=0;OQ=2651.31;QD=33.99;SB=-1110.83 GT:AD:DP:GL:GQ 1/1:0,78:75:-268.74,-22.59,-0.02:99 +chr1 3760980 rs12023762 T C 71.74 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.08;MQ=56.93;MQ0=0;OQ=2310.56;QD=34.49;SB=-1074.87 GT:AD:DP:GL:GQ 1/1:0,66:64:-234.66,-19.27,-0.02:99 +chr1 3761023 rs12026284 G A 45.52 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.92;MQ0=0;OQ=1613.24;QD=38.41;SB=-773.05 GT:AD:DP:GL:GQ 1/1:0,42:41:-164.92,-12.35,-0.01:99 +chr1 3761229 rs12024538 T C 108.72 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=57.43;MQ0=0;OQ=2622.46;QD=34.06;SB=-1093.09 GT:AD:DP:GL:GQ 1/1:0,77:74:-265.86,-22.29,-0.03:99 +chr1 3761407 rs7552678 C T 182.01 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=55.63;MQ0=0;OQ=2322.80;QD=37.46;SB=-1101.95 GT:AD:DP:GL:GQ 1/1:0,61:58:-235.88,-17.47,-0.01:99 +chr1 3761583 rs10909805 A T 36.48 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=57.39;MQ0=0;OQ=1183.25;QD=32.87;SB=-378.79 GT:AD:DP:GL:GQ 1/1:0,36:34:-121.93,-10.24,-0.02:99 +chr1 3762135 rs4648348 G T 313.87 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.61;MQ0=0;OQ=2805.56;QD=36.44;SB=-1091.90 GT:AD:DP:GL:GQ 1/1:0,77:77:-284.17,-23.19,-0.03:99 +chr1 3762966 rs6424059 C T 50.97 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1794.59;QD=39.88;SB=-207.77 GT:AD:DP:GL:GQ 1/1:0,45:45:-183.06,-13.56,-0.01:99 +chr1 3763112 rs6424060 C A 1.11 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=57.94;MQ0=0;OQ=1225.37;QD=36.04;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,34:33:-126.13,-9.94,-0.01:99 +chr1 3763448 rs7542369 C G 0.46 PASS AC=2;AF=1.00;AN=2;DB;DP=15;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=407.00;QD=27.13;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,15:12:-44.31,-3.64,-0.03:36.11 +chr1 3763578 rs4648428 A G 5.56 PASS AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=286.53;QD=20.47;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,13:11:-32.26,-3.33,-0.02:33.05 +chr1 3764486 rs10909806 C A 23.23 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=2.13;MQ=58.37;MQ0=0;OQ=1559.40;QD=35.44;SB=-546.78 GT:AD:DP:GL:GQ 1/1:0,44:43:-159.54,-12.95,-0.01:99 +chr1 3765314 rs4376673 C G 417.23 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1404.99;QD=36.03;SB=-615.54 GT:AD:DP:GL:GQ 1/1:0,39:36:-144.12,-10.87,-0.03:99 +chr1 3765882 rs9786959 A G 29.68 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=1920.48;QD=30.48;SB=-862.57 GT:AD:DP:GL:GQ 1/1:0,63:60:-195.68,-18.09,-0.05:99 +chr1 3767471 rs11800725 A G 13.03 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=58.98;MQ0=0;OQ=1927.36;QD=30.11;SB=-765.33 GT:AD:DP:GL:GQ 1/1:0,64:61:-196.39,-18.41,-0.06:99 +chr1 3767577 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=17;HaplotypeScore=9.33;MQ=55.19;MQ0=0;OQ=73.00;QD=1.66;SB=10.79 GT:AD:DP:GL:GQ 0/1:33,10:33:-20.53,-9.94,-95.54:99 +chr1 3767595 . G A 13.29 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=17;HaplotypeScore=14.08;MQ=55.46;MQ0=0;QD=0.23;SB=74.24 GT:AD:DP:GL:GQ 0/1:47,10:46:-18.45,-13.86,-142.27:45.92 +chr1 3769011 rs4400555 C T 258.35 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.08;MQ0=0;OQ=2381.95;QD=39.05;SB=-1005.83 GT:AD:DP:GL:GQ 1/1:0,61:61:-241.80,-18.38,-0.02:99 +chr1 3769497 rs4573474 G C 208.99 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.06;MQ0=0;OQ=1909.70;QD=37.45;SB=-679.47 GT:AD:DP:GL:GQ 1/1:0,51:49:-194.60,-14.79,-0.05:99 +chr1 3769504 rs4475689 T C 437.54 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.81;MQ0=0;OQ=1544.26;QD=28.60;SB=-549.88 GT:AD:DP:GL:GQ 1/1:0,54:50:-158.07,-15.09,-0.05:99 +chr1 3769540 rs4393098 C T 134.88 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.73;MQ0=0;OQ=2714.04;QD=39.33;SB=-879.18 GT:AD:DP:GL:GQ 1/1:0,69:68:-275.01,-20.48,-0.02:99 +chr1 3770416 rs10909807 A G 70.24 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=59.66;MQ0=0;OQ=2327.40;QD=34.23;SB=-632.25 GT:AD:DP:GL:GQ 1/1:0,68:65:-236.35,-19.58,-0.03:99 +chr1 3770956 rs10797348 C A 725.50 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2194.69;QD=35.40;SB=-970.66 GT:AD:DP:GL:GQ 1/1:0,62:61:-223.07,-18.37,-0.02:99 +chr1 3770996 rs10752724 C G 36.73 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.68;MQ0=0;OQ=3059.04;QD=41.90;SB=-884.77 GT:AD:DP:GL:GQ 1/1:0,73:70:-309.51,-21.10,-0.03:99 +chr1 3772468 rs10909809 C T 66.95 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.41;MQ=58.92;MQ0=0;OQ=1387.22;QD=35.57;SB=-471.11 GT:AD:DP:GL:GQ 1/1:0,38:37:-142.33,-11.16,-0.02:99 +chr1 3773138 rs10909810 A C 280.94 PASS AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.04;MQ0=0;OQ=955.91;QD=32.96;SB=-323.98 GT:AD:DP:GL:GQ 1/1:0,29:29:-99.19,-8.74,-0.02:87.21 +chr1 3773433 rs10797349 C T 164.73 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=58.68;MQ0=0;OQ=1490.84;QD=33.88;SB=-752.63 GT:AD:DP:GL:GQ 1/1:0,44:39:-152.69,-11.75,-0.02:99 +chr1 3773480 rs10797350 T C 13.89 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=58.30;MQ0=0;OQ=1471.72;QD=30.66;SB=-684.88 GT:AD:DP:GL:GQ 1/1:0,48:45:-150.79,-13.57,-0.03:99 +chr1 3773523 rs10752726 T G 347.66 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=1497.10;QD=33.27;SB=-446.81 GT:AD:DP:GL:GQ 1/1:0,45:43:-153.31,-12.95,-0.01:99 +chr1 3773611 rs12035912 C T 197.79 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=58.30;MQ0=0;OQ=2493.51;QD=37.78;SB=-1130.03 GT:AD:DP:GL:GQ 1/1:0,66:64:-252.96,-19.28,-0.02:99 +chr1 3775032 . T C 552.80 SnpCluster AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=33.42;MQ=46.78;MQ0=0;QD=6.28;SB=-111.60 GT:AD:DP:GL:GQ 0/1:60,28:83:-83.58,-25.02,-222.80:99 +chr1 3775037 . G T 197.57 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=0;HaplotypeScore=30.55;MQ=47.65;MQ0=0;QD=2.00;SB=65.19 GT:AD:DP:GL:GQ 0/1:82,15:90:-57.60,-34.56,-265.76:99 +chr1 3775038 rs11801559 A G 304.07 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=1;HaplotypeScore=31.22;MQ=47.58;MQ0=0;QD=3.07;SB=-149.93 GT:AD:DP:GL:GQ 0/1:75,24:82:-58.40,-24.71,-264.98:99 +chr1 3775067 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=168;Dels=0.00;HRun=0;HaplotypeScore=55.99;MQ=43.63;MQ0=2;OQ=741.54;QD=4.41;SB=-115.85 GT:AD:DP:GL:GQ 0/1:87,38:131:-206.86,-129.42,-352.70:99 +chr1 3775068 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=171;Dels=0.00;HRun=2;HaplotypeScore=57.14;MQ=43.69;MQ0=2;OQ=621.12;QD=3.63;SB=-22.34 GT:AD:DP:GL:GQ 0/1:130,41:133:-105.49,-40.09,-359.21:99 +chr1 3775097 . C T 202.73 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=156;Dels=0.02;HRun=0;HaplotypeScore=180.15;MQ=42.01;MQ0=2;QD=1.30;SB=-48.46 GT:AD:DP:GL:GQ 0/1:127,21:125:-62.81,-39.25,-356.59:99 +chr1 3775132 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=0;HaplotypeScore=17.94;MQ=41.24;MQ0=3;OQ=65.49;QD=0.68;SB=-47.12 GT:AD:DP:GL:GQ 0/1:77,9:78:-49.90,-40.06,-295.84:98.32 +chr1 3779522 rs11581471 A G 100.85 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.41;MQ0=0;OQ=1287.54;QD=29.26;SB=-667.82 GT:AD:DP:GL:GQ 1/1:0,44:42:-132.38,-12.67,-0.05:99 +chr1 3779990 rs12130391 G A 164 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.47;MQ0=0;OQ=2160.23;QD=35.41;SB=-916.74 GT:AD:DP:GL:GQ 1/1:0,60:57:-219.63,-17.18,-0.03:99 +chr1 3780767 . T C 4.63 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=30.96;MQ0=11;OQ=368.82;QD=6.36;SB=-104.61 GT:AD:DP:GL:GQ 0/1:34,24:38:-51.63,-11.46,-83.55:99 +chr1 3781074 rs10752727 C T 2.58 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=7.70;MQ=37.12;MQ0=12;OQ=1286.15;QD=21.08;SB=-457.95 GT:AD:DP:GL:GQ 1/1:3,58:36:-135.18,-10.85,-2.98:78.66 +chr1 3783772 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=19;HaplotypeScore=32.14;MQ=55.75;MQ0=0;OQ=200.26;QD=4.01;SB=53.19 GT:AD:DP:GL:GQ 0/1:32,18:38:-34.76,-11.45,-99.41:99 +chr1 3784133 rs12132240 C T 668.84 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.52;MQ0=0;OQ=2396.10;QD=39.93;SB=-998.03 GT:AD:DP:GL:GQ 1/1:0,60:60:-243.21,-18.07,-0.02:99 +chr1 3785251 rs10737189 T C 42.26 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=4.18;MQ=59.45;MQ0=0;OQ=2617.88;QD=31.17;SB=-945.37 GT:AD:DP:GL:GQ 1/1:0,84:80:-265.43,-24.12,-0.06:99 +chr1 3786402 rs12071660 G A 151.32 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2743.00;QD=38.63;SB=-1108.49 GT:AD:DP:GL:GQ 1/1:0,71:69:-277.90,-20.79,-0.02:99 +chr1 3787079 rs4074710 T C 1.91 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=9.84;MQ=58.78;MQ0=0;OQ=1684.95;QD=27.18;SB=-797.66 GT:AD:DP:GL:GQ 1/1:2,60:56:-176.09,-16.89,-4.01:99 +chr1 3787169 rs61768959 C T 435.29 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1824.58;QD=38.82;SB=-789.07 GT:AD:DP:GL:GQ 1/1:0,47:46:-186.05,-13.86,-0.01:99 +chr1 3787855 rs4073324 C T 458.35 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1383.49;QD=37.39;SB=-414.06 GT:AD:DP:GL:GQ 1/1:0,37:37:-141.95,-11.15,-0.02:99 +chr1 3787909 rs4073323 A G 2.22 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=3.99;MQ=59.35;MQ0=0;OQ=1345.64;QD=32.04;SB=-424.45 GT:AD:DP:GL:GQ 1/1:0,42:40:-138.17,-12.05,-0.02:99 +chr1 3788260 rs12084944 C T 298.99 PASS AC=2;AF=1.00;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=888.25;QD=37.01;SB=-436.08 GT:AD:DP:GL:GQ 1/1:0,24:23:-92.42,-6.93,-0.01:69.22 +chr1 3788534 rs12030906 T C 0.68 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.02;HRun=0;HaplotypeScore=9.00;MQ=56.58;MQ0=0;OQ=1607.45;QD=29.23;SB=-436.47 GT:AD:DP:GL:GQ 1/1:0,54:48:-164.35,-14.16,-0.02:99 +chr1 3789424 rs4382652 G A 2153.41 Indel AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=4.66;MQ=56.10;MQ0=0;QD=35.30;SB=-1010.66 GT:AD:DP:GL:GQ 1/1:0,61:57:-218.95,-17.18,-0.03:99 +chr1 3790102 rs3205087 A G 382.60 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.28;MQ0=0;OQ=1027.83;QD=26.35;SB=-300.09 GT:AD:DP:GL:GQ 1/1:0,39:35:-106.42,-10.57,-0.05:99 +chr1 3790340 rs7555538 G T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=8;HaplotypeScore=0.92;MQ=59.43;MQ0=0;OQ=2444.86;QD=33.49;SB=-1058.90 GT:AD:DP:GL:GQ 1/1:0,73:70:-248.10,-21.09,-0.03:99 +chr1 3791107 rs10909817 T G 151.89 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=57.75;MQ0=0;OQ=1681.31;QD=32.33;SB=-830.07 GT:AD:DP:GL:GQ 1/1:0,51:49:-171.73,-14.76,-0.02:99 +chr1 3792631 rs11584721 G C 5.17 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=5.57;MQ=57.48;MQ0=0;OQ=2243.27;QD=40.06;SB=-1057.19 GT:AD:DP:GL:GQ 1/1:1,55:53:-227.93,-15.97,-0.02:99 +chr1 3793561 rs12136187 C A 227.66 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.95;MQ0=0;OQ=1328.46;QD=34.06;SB=-683.01 GT:AD:DP:GL:GQ 1/1:0,39:37:-136.44,-11.15,-0.01:99 +chr1 3793615 rs7367066 T C 611.54 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.19;MQ0=0;OQ=1618.23;QD=29.97;SB=-707.63 GT:AD:DP:GL:GQ 1/1:0,53:51:-165.45,-15.38,-0.04:99 +chr1 3795300 rs6678851 C T 1.35 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=5.47;MQ=59.65;MQ0=0;OQ=2468.27;QD=37.97;SB=-809.33 GT:AD:DP:GL:GQ 1/1:0,65:63:-250.43,-18.98,-0.02:99 +chr1 3795934 rs4075974 G A 558.47 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.49;MQ0=0;OQ=2140.67;QD=39.64;SB=-940.34 GT:AD:DP:GL:GQ 1/1:0,54:54:-217.66,-16.27,-0.01:99 +chr1 3796218 rs10909819 T C 98.14 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=58.14;MQ0=0;OQ=2198.60;QD=32.33;SB=-948.97 GT:AD:DP:GL:GQ 1/1:0,68:64:-223.47,-19.28,-0.03:99 +chr1 3796503 rs4520357 T A 245.19 PASS AC=2;AF=1.00;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.09;MQ0=0;OQ=3186.37;QD=35.40;SB=-1505.31 GT:AD:DP:GL:GQ 1/1:0,90:85:-322.25,-25.60,-0.02:99 +chr1 3797453 rs4274008 G C 114.81 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=59.65;MQ0=0;OQ=2739.80;QD=42.15;SB=-1186.93 GT:AD:DP:GL:GQ 1/1:0,65:64:-277.59,-19.29,-0.02:99 +chr1 3798031 rs6701422 T C 38.91 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=4.04;MQ=51.74;MQ0=0;OQ=1832.37;QD=30.04;SB=-733.76 GT:AD:DP:GL:GQ 1/1:0,60:57:-186.87,-17.19,-0.05:99 +chr1 3798222 rs4446914 G A 207.99 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=50.14;MQ0=0;OQ=2015.61;QD=38.03;SB=-988.99 GT:AD:DP:GL:GQ 1/1:0,53:52:-205.17,-15.67,-0.02:99 +chr1 3798375 . A G 51.46 PASS AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=16.12;MQ0=4;OQ=176.38;QD=13.57;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,13:6:-21.21,-1.81,-0.00:18.05 +chr1 3798911 rs12757258 A C 37.05 LowQual AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=30.57;MQ0=1;QD=7.41;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,3:2:-7.11,-0.60,-0.00:6.02 +chr1 3798957 rs12757292 A C 18.79 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.60;MQ0=1;OQ=75.37;QD=3.14;SB=-10.00 GT:AD:DP:GL:GQ 0/1:11,13:13:-14.74,-3.92,-26.95:99 +chr1 3799283 rs11807227 G A 605.39 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.57;MQ0=0;OQ=2371.97;QD=38.88;SB=-744.48 GT:AD:DP:GL:GQ 1/1:0,61:60:-240.80,-18.08,-0.02:99 +chr1 3800246 rs4568776 A G 199.91 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=2257.59;QD=31.80;SB=-934.52 GT:AD:DP:GL:GQ 1/1:0,71:68:-229.39,-20.50,-0.04:99 +chr1 3801063 rs7515869 A T 278.49 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=61.08;MQ0=0;OQ=1948.49;QD=33.03;SB=-981.77 GT:AD:DP:GL:GQ 1/1:0,57:54:-198.46,-16.27,-0.03:99 +chr1 3801228 rs6674160 G A 506.45 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.72;MQ0=0;OQ=1203.93;QD=37.62;SB=-496.15 GT:AD:DP:GL:GQ 1/1:0,32:32:-124.00,-9.65,-0.02:96.29 +chr1 3801965 rs10909822 A C 705.90 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=23;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=42.43;MQ0=0;QD=30.69;SB=-332.99 GT:AD:DP:GL:GQ 1/1:1,22:22:-74.19,-6.63,-0.02:66.14 +chr1 3801968 . T A 440.70 SnpCluster AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=38.89;MQ0=0;QD=11.60;SB=-170.81 GT:AD:DP:GL:GQ 0/1:21,17:32:-56.99,-9.64,-61.90:99 +chr1 3801971 . G T 508.15 SnpCluster AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=35.42;MQ0=0;QD=14.52;SB=-198.56 GT:AD:DP:GL:GQ 0/1:17,18:35:-64.64,-10.54,-61.42:99 +chr1 3801978 . G C 1059.09 Indel;SnpCluster AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=45.04;MQ0=0;QD=40.73;SB=-392.21 GT:AD:DP:GL:GQ 1/1:0,26:25:-109.50,-7.53,-0.01:75.25 +chr1 3802009 rs12133786 A C 321.15 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=52.45;MQ0=0;OQ=1401.55;QD=33.37;SB=-709.03 GT:AD:DP:GL:GQ 1/1:0,42:41:-143.76,-12.35,-0.02:99 +chr1 3802570 rs10797352 T C 148.57 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.68;MQ0=0;OQ=1740.38;QD=32.84;SB=-623.49 GT:AD:DP:GL:GQ 1/1:0,53:51:-177.65,-15.37,-0.03:99 +chr1 3802708 rs10797353 C G 720.59 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2712.05;QD=38.74;SB=-1379.38 GT:AD:DP:GL:GQ 1/1:0,69:70:-279.01,-24.65,-4.23:99 +chr1 3804150 rs10797354 T C 170.50 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.56;MQ0=0;OQ=1825.12;QD=32.59;SB=-712.23 GT:AD:DP:GL:GQ 1/1:0,56:54:-186.12,-16.27,-0.03:99 +chr1 3804602 rs6658198 T C 302.07 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.62;MQ0=0;OQ=2079.20;QD=34.65;SB=-977.94 GT:AD:DP:GL:GQ 1/1:0,60:60:-211.53,-18.07,-0.02:99 +chr1 3806368 rs35131135 T C 13.18 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=58.87;MQ0=0;OQ=1257.30;QD=30.67;SB=-415.16 GT:AD:DP:GL:GQ 1/1:0,40:36:-129.33,-10.85,-0.01:99 +chr1 3806714 rs61770363 G A 10.79 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.71;MQ0=0;OQ=641.87;QD=35.66;SB=-278.65 GT:AD:DP:GL:GQ 1/1:0,18:18:-67.78,-5.43,-0.01:54.17 +chr1 3806753 rs4072725 C T 77.05 PASS AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.52;MQ0=0;OQ=544.23;QD=34.01;SB=-280.66 GT:AD:DP:GL:GQ 1/1:0,16:15:-58.01,-4.52,-0.01:45.14 +chr1 3808604 rs10797355 T C 125.29 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=53.60;MQ0=1;OQ=2350.13;QD=34.56;SB=-914.68 GT:AD:DP:GL:GQ 1/1:0,68:66:-238.63,-19.89,-0.03:99 +chr1 3808731 rs10797356 G A 43.83 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.07;MQ=58.71;MQ0=0;OQ=2012.52;QD=37.27;SB=-776.06 GT:AD:DP:GL:GQ 1/1:0,54:52:-204.86,-15.67,-0.02:99 +chr1 3809184 rs6672335 A G 119.40 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.56;MQ0=0;OQ=1683.69;QD=31.77;SB=-530.84 GT:AD:DP:GL:GQ 1/1:0,53:48:-171.97,-14.46,-0.02:99 +chr1 3809865 rs10909828 G A 654.97 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=2184.41;QD=38.32;SB=-826.35 GT:AD:DP:GL:GQ 1/1:0,57:56:-222.04,-16.87,-0.02:99 +chr1 3809876 rs12139857 G C 137.16 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.22;MQ0=0;OQ=2518.12;QD=42.68;SB=-984.74 GT:AD:DP:GL:GQ 1/1:0,59:58:-255.41,-17.48,-0.02:99 +chr1 3811076 rs6687869 G A 107.90 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.45;MQ0=0;OQ=1628.97;QD=38.79;SB=-568.34 GT:AD:DP:GL:GQ 1/1:0,42:42:-166.50,-12.65,-0.01:99 +chr1 3811194 rs10797357 G A 521.93 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.15;MQ0=0;OQ=1858.19;QD=37.92;SB=-535.68 GT:AD:DP:GL:GQ 1/1:0,49:48:-189.42,-14.46,-0.01:99 +chr1 3812563 rs10909830 C T 206.83 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=58.81;MQ0=0;OQ=2305.91;QD=36.60;SB=-919.31 GT:AD:DP:GL:GQ 1/1:0,63:60:-234.20,-18.08,-0.02:99 +chr1 3812792 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=14.74;MQ=58.39;MQ0=0;OQ=154.04;QD=2.80;SB=80.30 GT:AD:DP:GL:GQ 0/1:43,12:42:-31.36,-12.67,-148.77:99 +chr1 3816486 rs35332894 A G 12.94 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.52;MQ=58.25;MQ0=1;OQ=1726.98;QD=27.41;SB=-682.71 GT:AD:DP:GL:GQ 1/1:0,63:54:-176.33,-16.29,-0.05:99 +chr1 3817341 rs61770379 C T 109.94 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.38;MQ0=0;OQ=1418.14;QD=38.33;SB=-728.97 GT:AD:DP:GL:GQ 1/1:0,37:36:-145.41,-10.84,-0.01:99 +chr1 3819020 rs34825671 C T 409.20 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1564.33;QD=39.11;SB=-750.02 GT:AD:DP:GL:GQ 1/1:0,40:40:-160.03,-12.05,-0.01:99 +chr1 3819278 rs35368826 T C 12.24 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=60.00;MQ0=0;OQ=1199.67;QD=27.90;SB=-424.22 GT:AD:DP:GL:GQ 1/1:0,43:38:-123.59,-11.46,-0.04:99 +chr1 3819474 rs35583447 A G 89.06 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.69;MQ0=0;OQ=1939.06;QD=31.79;SB=-974.91 GT:AD:DP:GL:GQ 1/1:0,61:57:-197.52,-17.18,-0.03:99 +chr1 3819901 rs34284135 A G 55.75 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.81;MQ0=0;OQ=1296.25;QD=30.15;SB=-641.91 GT:AD:DP:GL:GQ 1/1:0,43:38:-133.23,-11.45,-0.02:99 +chr1 3820479 rs4073647 C A 185.05 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=59.55;MQ0=0;OQ=1638.97;QD=32.14;SB=-804.86 GT:AD:DP:GL:GQ 1/1:0,51:47:-167.50,-14.16,-0.02:99 +chr1 3820963 rs35355307 G A 127.74 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.69;MQ0=0;OQ=2262.75;QD=37.09;SB=-711.99 GT:AD:DP:GL:GQ 1/1:0,61:59:-229.89,-17.78,-0.03:99 +chr1 3821092 rs35241263 A G 89.02 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.63;MQ0=0;OQ=1378.97;QD=27.04;SB=-599.21 GT:AD:DP:GL:GQ 1/1:0,51:45:-141.53,-13.58,-0.05:99 +chr1 3821416 rs34803434 G A 80.51 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=58.07;MQ0=0;OQ=1633.32;QD=35.51;SB=-688.34 GT:AD:DP:GL:GQ 1/1:1,45:44:-166.94,-13.26,-0.02:99 +chr1 3823053 rs61770387 C T 609.64 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2714.99;QD=39.35;SB=-1139.68 GT:AD:DP:GL:GQ 1/1:0,69:68:-275.10,-20.48,-0.02:99 +chr1 3823181 rs61770388 T C 199.61 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.19;MQ0=0;OQ=1728.56;QD=33.24;SB=-864.04 GT:AD:DP:GL:GQ 1/1:0,52:50:-176.46,-15.06,-0.02:99 +chr1 3824979 rs61770390 T C 82.45 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=55.31;MQ0=0;OQ=486.55;QD=7.85;SB=-261.22 GT:AD:DP:GL:GQ 0/1:37,25:59:-69.72,-17.78,-147.85:99 +chr1 3824990 . C T 3.46 PASS AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.66;MQ=55.46;MQ0=0;OQ=1251.91;QD=19.56;SB=-545.38 GT:AD:DP:GL:GQ 0/1:27,37:61:-146.86,-18.39,-82.02:99 +chr1 3825051 . C A 3.22 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=2;HaplotypeScore=3.18;MQ=58.29;MQ0=0;OQ=820.60;QD=11.56;SB=-414.89 GT:AD:DP:GL:GQ 0/1:42,29:71:-106.73,-21.38,-145.16:99 +chr1 3825054 . T C 10.09 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.18;MQ=58.08;MQ0=0;OQ=722.16;QD=10.47;SB=-351.97 GT:AD:DP:GL:GQ 0/1:40,28:65:-95.08,-19.58,-155.89:99 +chr1 3825324 rs61770392 A T 88.32 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=57.20;MQ0=0;OQ=1894.97;QD=35.09;SB=-920.36 GT:AD:DP:GL:GQ 1/1:0,54:51:-193.10,-15.37,-0.02:99 +chr1 3827005 . C T 22.22 LowQual AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=43.17;MQ0=3;QD=1.48;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,3:9:-8.21,-2.71,-24.78:55.03 +chr1 3827011 . C T 25.21 LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=2.11;MQ=38.99;MQ0=3;QD=1.80;SB=-10.00 GT:AD:DP:GL:GQ 0/1:12,2:8:-8.21,-2.41,-21.31:58.03 +chr1 3830505 rs35265992 A G 0.12 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=4;HaplotypeScore=5.22;MQ=58.50;MQ0=0;OQ=970.90;QD=17.34;SB=-315.39 GT:AD:DP:GL:GQ 0/1:20,36:52:-116.04,-15.67,-75.68:99 +chr1 3830738 rs35974482 G A 171.95 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=57.87;MQ0=0;OQ=551.40;QD=12.53;SB=-198.84 GT:AD:DP:GL:GQ 0/1:25,19:40:-70.48,-12.05,-78.52:99 +chr1 3830888 rs35314156 G C 209.73 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.07;MQ0=0;OQ=668.40;QD=13.37;SB=-257.46 GT:AD:DP:GL:GQ 0/1:30,20:50:-85.20,-15.08,-125.99:99 +chr1 3831972 rs34835780 T C 632.20 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.64;MQ0=0;OQ=2285.64;QD=35.16;SB=-1132.81 GT:AD:DP:GL:GQ 1/1:0,65:64:-232.17,-19.28,-0.02:99 +chr1 3833915 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=17.15;MQ=47.19;MQ0=1;OQ=288.77;QD=3.66;SB=-113.05 GT:AD:DP:GL:GQ 0/1:64,15:78:-55.66,-23.49,-226.25:99 +chr1 3895148 . C A 18 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=35.10;MQ0=1;OQ=333.31;QD=9.80;SB=-100.81 GT:AD:DP:GL:GQ 0/1:15,18:23:-43.54,-6.93,-34.49:99 +chr1 3895632 . G A 3.06 PASS AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=4;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=959.16;QD=14.11;SB=-372.32 GT:AD:DP:GL:GQ 0/1:38,30:68:-119.69,-20.49,-137.83:99 +chr1 3895766 rs61770398 T C 202.83 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.65;MQ=59.18;MQ0=0;OQ=960.24;QD=12.98;SB=-389.21 GT:AD:DP:GL:GQ 0/1:40,34:73:-121.30,-21.99,-162.55:99 +chr1 3899769 . C G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=8.09;MQ=59.49;MQ0=0;OQ=340.78;QD=7.57;SB=47.18 GT:AD:DP:GL:GQ 0/1:26,19:34:-47.63,-10.27,-85.91:99 +chr1 3902626 rs12073174 A G 196.76 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.14;MQ0=0;OQ=542.74;QD=11.31;SB=-148.64 GT:AD:DP:GL:GQ 0/1:27,21:46:-71.41,-13.85,-105.98:99 +chr1 3902680 rs61770400 C T 70.11 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=59.24;MQ0=0;OQ=954.92;QD=15.65;SB=-346.04 GT:AD:DP:GL:GQ 0/1:29,32:59:-116.56,-17.78,-99.06:99 +chr1 3903888 . C T 983.33 SnpCluster AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.15;MQ0=0;QD=17.88;SB=-501.10 GT:AD:DP:GL:GQ 0/1:24,31:52:-117.28,-15.67,-81.69:99 +chr1 3903897 rs12076404 C T 1044.63 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.20;MQ0=0;QD=18.01;SB=-538.06 GT:AD:DP:GL:GQ 0/1:25,33:54:-124.01,-16.27,-82.66:99 +chr1 3903898 . G A 621.65 SnpCluster AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.17;MQ0=0;QD=11.10;SB=-272.76 GT:AD:DP:GL:GQ 0/1:33,23:52:-81.12,-15.67,-110.15:99 +chr1 3904122 . C T 64.01 PASS AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=58.92;MQ0=0;OQ=1312.00;QD=16.00;SB=-449.98 GT:AD:DP:GL:GQ 0/1:43,39:81:-158.89,-24.40,-148.69:99 +chr1 3904123 rs7518198 G A 275.18 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.77;MQ=58.92;MQ0=0;OQ=1318.95;QD=16.08;SB=-404.76 GT:AD:DP:GL:GQ 0/1:38,44:78:-158.67,-23.50,-132.87:99 +chr1 3904259 rs55651676 C G 11.26 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=3;HaplotypeScore=0.67;MQ=58.80;MQ0=0;OQ=719.49;QD=18.45;SB=-354.47 GT:AD:DP:GL:GQ 0/1:17,22:35:-85.79,-10.56,-59.36:99 +chr1 3904673 rs56300127 T C 189.23 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.07;MQ0=0;OQ=384.21;QD=11.30;SB=-194.60 GT:AD:DP:GL:GQ 0/1:17,17:31:-51.05,-9.34,-58.99:99 +chr1 3905021 rs10915614 A G 3.58 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=4;HaplotypeScore=1.21;MQ=59.48;MQ0=0;OQ=428.89;QD=9.75;SB=-152.44 GT:AD:DP:GL:GQ 0/1:24,19:41:-58.53,-12.36,-93.35:99 +chr1 3905038 . G A 50.50 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.41;MQ0=0;OQ=477.39;QD=12.24;SB=-188.87 GT:AD:DP:GL:GQ 0/1:22,17:37:-62.18,-11.16,-67.50:99 +chr1 3905246 . C T 93.17 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=58.57;MQ0=0;OQ=1011.86;QD=16.32;SB=-440.98 GT:AD:DP:GL:GQ 0/1:30,32:58:-121.96,-17.49,-85.78:99 +chr1 3905920 rs7548668 T C 26.57 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=6.64;MQ=59.57;MQ0=0;OQ=666.76;QD=12.35;SB=-179.62 GT:AD:DP:GL:GQ 0/1:27,27:46:-83.82,-13.86,-87.80:99 +chr1 3906227 rs9793287 T C 337.13 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.61;MQ0=0;OQ=444.12;QD=9.25;SB=-215.36 GT:AD:DP:GL:GQ 0/1:27,21:46:-61.57,-13.87,-101.57:99 +chr1 3906248 rs12562706 C A 152.11 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=59.59;MQ0=0;OQ=415.45;QD=9.23;SB=-231.91 GT:AD:DP:GL:GQ 0/1:25,20:41:-57.18,-12.35,-86.80:99 +chr1 3906531 rs7526903 G A 280.93 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=909.30;QD=17.83;SB=-442.97 GT:AD:DP:GL:GQ 0/1:23,27:47:-108.38,-14.16,-65.40:99 +chr1 3906648 rs7551771 C T 37.89 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=60.06;MQ0=0;OQ=776.93;QD=15.54;SB=-354.36 GT:AD:DP:GL:GQ 0/1:26,24:48:-95.43,-14.46,-92.96:99 +chr1 3906868 rs7519349 A G 578.45 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=764.11;QD=13.64;SB=-362.95 GT:AD:DP:GL:GQ 0/1:26,30:56:-96.58,-16.88,-105.57:99 +chr1 3906970 rs7519458 A G 232.59 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.80;MQ=60.00;MQ0=0;OQ=762.22;QD=13.14;SB=-199.60 GT:AD:DP:GL:GQ 0/1:26,31:57:-96.69,-17.19,-106.25:99 +chr1 3907888 rs10799162 T C 190.81 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=58.79;MQ0=0;OQ=719.58;QD=13.33;SB=-230.44 GT:AD:DP:GL:GQ 0/1:27,27:53:-91.22,-15.97,-102.46:99 +chr1 3907889 rs10799163 G T 86.43 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=58.79;MQ0=0;OQ=758.50;QD=14.05;SB=-193.54 GT:AD:DP:GL:GQ 0/1:27,26:51:-94.50,-15.37,-86.70:99 +chr1 3907912 rs10915345 G A 203.29 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=59.62;MQ0=0;OQ=1037.45;QD=17.01;SB=-258.26 GT:AD:DP:GL:GQ 0/1:29,32:57:-124.21,-17.18,-83.11:99 +chr1 3909896 rs6683165 G A 201.77 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=59.62;MQ0=0;OQ=837.44;QD=12.88;SB=-252.13 GT:AD:DP:GL:GQ 0/1:38,27:62:-105.71,-18.68,-120.77:99 +chr1 3910104 rs10799194 C T 90.26 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.69;MQ=60.00;MQ0=0;OQ=794.06;QD=13.23;SB=-418.44 GT:AD:DP:GL:GQ 0/1:34,26:57:-99.88,-17.19,-98.75:99 +chr1 3919557 rs9426474 A G 111.97 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.97;MQ0=0;OQ=1753.83;QD=29.73;SB=-828.62 GT:AD:DP:GL:GQ 1/1:0,59:55:-179.01,-16.59,-0.05:99 +chr1 3922104 rs9426475 T C 209.50 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=54.82;MQ0=0;OQ=1570.14;QD=28.55;SB=-720.64 GT:AD:DP:GL:GQ 1/1:0,55:50:-160.65,-15.09,-0.06:99 +chr1 3922325 rs10915469 T C 562.16 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1863.57;QD=28.24;SB=-798.65 GT:AD:DP:GL:GQ 1/1:0,66:58:-189.99,-17.49,-0.05:99 +chr1 3922572 rs7540846 C T 41.15 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=0.57;MQ=53.34;MQ0=0;OQ=2905.34;QD=34.59;SB=-1359.03 GT:AD:DP:GL:GQ 1/1:0,81:75:-294.15,-22.60,-0.03:99 +chr1 3922839 rs7516192 G C 540.09 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.04;MQ0=0;OQ=2588.44;QD=42.43;SB=-1244.89 GT:AD:DP:GL:GQ 1/1:0,61:60:-262.44,-18.08,-0.02:99 +chr1 3922855 rs9426476 A G 185.57 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.74;MQ=58.63;MQ0=0;OQ=2064.09;QD=34.40;SB=-842.35 GT:AD:DP:GL:GQ 1/1:0,60:58:-210.01,-17.47,-0.02:99 +chr1 3922974 rs7541241 C A 552.27 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.64;MQ0=0;OQ=1520.98;QD=33.80;SB=-673.30 GT:AD:DP:GL:GQ 1/1:0,45:44:-155.71,-13.26,-0.03:99 +chr1 3923246 rs9426498 T C 9.78 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=52.33;MQ0=0;OQ=1450.84;QD=25.91;SB=-720.70 GT:AD:DP:GL:GQ 1/1:0,56:46:-148.71,-13.88,-0.05:99 +chr1 3923458 rs9426499 A C 507.51 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1349.47;QD=30.67;SB=-364.89 GT:AD:DP:GL:GQ 1/1:0,44:42:-138.57,-12.66,-0.04:99 +chr1 3923596 rs9426477 A G 619.10 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=2188.14;QD=34.73;SB=-945.36 GT:AD:DP:GL:GQ 1/1:0,63:61:-222.42,-18.37,-0.02:99 +chr1 3923941 rs6698811 T C 664.67 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=2773.83;QD=33.83;SB=-1404.50 GT:AD:DP:GL:GQ 1/1:0,82:80:-281.00,-24.10,-0.03:99 +chr1 3936055 rs10753378 T C 376.82 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.51;MQ0=0;OQ=543.43;QD=11.56;SB=-218.27 GT:AD:DP:GL:GQ 0/1:23,24:45:-71.19,-13.57,-90.09:99 +chr1 3938219 . C T 61.19 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.45;MQ=59.60;MQ0=0;OQ=740.10;QD=12.76;SB=-319.83 GT:AD:DP:GL:GQ 0/1:30,28:53:-93.28,-15.99,-88.25:99 +chr1 3940015 rs4654525 C T 311.29 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.10;MQ0=0;OQ=1004.75;QD=15.00;SB=-479.00 GT:AD:DP:GL:GQ 0/1:36,31:66:-123.64,-19.88,-133.78:99 +chr1 3942839 rs60972376 A C 11.72 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=4.30;MQ=58.67;MQ0=0;OQ=585.81;QD=11.96;SB=-197.90 GT:AD:DP:GL:GQ 0/1:20,28:43:-74.82,-12.96,-73.58:99 +chr1 3942909 rs55887893 C T 197.25 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.21;MQ=60.00;MQ0=0;OQ=588.30;QD=11.77;SB=-314.85 GT:AD:DP:GL:GQ 0/1:29,21:47:-76.28,-14.17,-92.23:99 +chr1 3944651 rs59118111 G C 246.41 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=60.00;MQ0=0;OQ=1068.67;QD=16.44;SB=-449.44 GT:AD:DP:GL:GQ 0/1:32,33:64:-129.45,-19.30,-140.55:99 +chr1 3945187 rs4654538 G A 29.36 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.53;MQ=58.81;MQ0=0;OQ=1094.72;QD=19.90;SB=-430.80 GT:AD:DP:GL:GQ 0/1:23,32:55:-129.32,-16.57,-83.23:99 +chr1 3947137 rs4654543 T C 110.66 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=382.96;QD=9.82;SB=-135.53 GT:AD:DP:GL:GQ 0/1:21,18:38:-53.04,-11.46,-84.39:99 +chr1 3947479 rs10449244 C A 197.72 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=60.00;MQ0=0;OQ=744.81;QD=13.07;SB=-230.89 GT:AD:DP:GL:GQ 0/1:29,28:53:-93.73,-15.97,-94.52:99 +chr1 3948534 rs4654544 A G 534.93 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=551.19;QD=12.53;SB=-251.96 GT:AD:DP:GL:GQ 0/1:21,23:44:-71.67,-13.27,-84.12:99 +chr1 3949636 rs4654436 T C 195.22 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=59.16;MQ0=0;OQ=834.97;QD=11.60;SB=-298.88 GT:AD:DP:GL:GQ 0/1:38,34:66:-106.67,-19.89,-140.32:99 +chr1 3949646 rs6426416 A T 32.24 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=2.47;MQ=59.20;MQ0=0;OQ=1168.58;QD=15.38;SB=-401.17 GT:AD:DP:GL:GQ 0/1:38,38:72:-141.84,-21.70,-126.75:99 +chr1 3950380 . A G 266.35 PASS AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1356.42;QD=15.96;SB=-652.62 GT:AD:DP:GL:GQ 0/1:40,45:85:-164.53,-25.60,-164.89:99 +chr1 3950813 rs10737411 A G 175.98 PASS AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=1;HaplotypeScore=2.09;MQ=59.83;MQ0=0;OQ=1386.28;QD=12.84;SB=-502.53 GT:AD:DP:GL:GQ 0/1:55,53:107:-174.15,-32.24,-226.13:99 +chr1 3951883 rs6657331 G C 1.76 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.77;MQ=59.14;MQ0=0;OQ=976.24;QD=22.70;SB=-437.36 GT:AD:DP:GL:GQ 0/1:16,27:40:-112.97,-12.06,-59.28:99 +chr1 3951915 rs12145443 C T 0.21 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=58.72;MQ0=0;OQ=829.82;QD=21.84;SB=-313.85 GT:AD:DP:GL:GQ 0/1:13,25:37:-97.41,-11.15,-45.43:99 +chr1 3952816 rs10799236 A G 574.49 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=747.27;QD=14.10;SB=-330.89 GT:AD:DP:GL:GQ 0/1:27,26:52:-93.67,-15.66,-106.05:99 +chr1 3953295 rs12038964 T C 361.41 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.86;MQ0=0;OQ=750.82;QD=12.31;SB=-348.04 GT:AD:DP:GL:GQ 0/1:30,31:60:-96.45,-18.08,-120.40:99 +chr1 3953370 rs12040628 A G 147.24 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=59.55;MQ0=0;OQ=749.75;QD=14.70;SB=-277.27 GT:AD:DP:GL:GQ 0/1:21,30:49:-93.03,-14.77,-83.59:99 +chr1 3954832 rs9426500 A C 437.18 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=970.97;QD=16.46;SB=-363.09 GT:AD:DP:GL:GQ 0/1:25,34:59:-118.15,-17.77,-92.14:99 +chr1 3955140 rs7413013 G C 5.69 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.97;MQ=59.17;MQ0=0;OQ=1282.99;QD=22.91;SB=-362.10 GT:AD:DP:GL:GQ 0/1:21,35:56:-148.46,-16.87,-92.34:99 +chr1 3955487 rs9426501 T C 61.29 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=4.29;MQ=58.95;MQ0=0;OQ=1025.38;QD=16.54;SB=-268.62 GT:AD:DP:GL:GQ 0/1:26,36:60:-123.90,-18.08,-97.56:99 +chr1 3956324 rs28609919 G C 274.82 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.69;MQ0=0;OQ=890.13;QD=14.84;SB=-464.74 GT:AD:DP:GL:GQ 0/1:33,27:59:-110.08,-17.78,-139.21:99 +chr1 3957249 rs12756251 G A 25.08 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=3.32;MQ=59.14;MQ0=0;OQ=1510.62;QD=18.65;SB=-581.41 GT:AD:DP:GL:GQ 0/1:36,45:78:-177.84,-23.50,-121.43:99 +chr1 3957262 rs12733769 T A 184.98 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=59.13;MQ0=0;OQ=1410.63;QD=17.63;SB=-590.40 GT:AD:DP:GL:GQ 0/1:34,46:77:-167.55,-23.20,-118.80:99 +chr1 3957348 rs12135298 A G 336.09 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.25;MQ0=0;OQ=781.36;QD=12.21;SB=-403.89 GT:AD:DP:GL:GQ 0/1:34,30:63:-100.41,-18.99,-132.61:99 +chr1 3959579 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=7.87;MQ=33.13;MQ0=5;OQ=83.58;QD=1.58;SB=-67.89 GT:AD:DP:GL:GQ 0/1:44,9:38:-23.11,-11.47,-97.21:99 +chr1 3959589 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=8.30;MQ=33.13;MQ0=5;OQ=210.60;QD=3.76;SB=-42.01 GT:AD:DP:GL:GQ 0/1:42,14:42:-37.00,-12.66,-114.99:99 +chr1 3959610 rs4654559 T C 0.08 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=19.50;MQ=38.33;MQ0=4;OQ=745.10;QD=13.55;SB=-325.28 GT:AD:DP:GL:GQ 0/1:20,35:43:-90.76,-12.97,-56.11:99 +chr1 3959618 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=35.45;MQ=40.78;MQ0=4;OQ=377.28;QD=6.50;SB=-163.72 GT:AD:DP:GL:GQ 0/1:35,17:42:-66.15,-25.14,-90.45:99 +chr1 3959638 rs12137425 A G 6.15 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=49.20;MQ0=1;OQ=205.57;QD=4.28;SB=-109.83 GT:AD:DP:GL:GQ 0/1:33,15:40:-35.90,-12.06,-107.08:99 +chr1 3959766 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=1;HaplotypeScore=11.71;MQ=40.06;MQ0=2;OQ=205.60;QD=3.54;SB=-53.76 GT:AD:DP:GL:GQ 0/1:44,14:49:-38.61,-14.76,-139.54:99 +chr1 3959787 rs11807610 T C 0.34 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=13.45;MQ=43.41;MQ0=2;OQ=585.11;QD=10.45;SB=-259.35 GT:AD:DP:GL:GQ 0/1:22,34:43:-74.76,-12.96,-79.59:99 +chr1 3959815 rs10915563 A G 47.44 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=13.21;MQ=50.51;MQ0=1;QD=0.72;SB=62.23 GT:AD:DP:GL:GQ 0/1:56,10:52:-23.70,-15.67,-173.58:80.28 +chr1 3959825 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=18.02;MQ=51.36;MQ0=1;OQ=581.75;QD=8.19;SB=-258.36 GT:AD:DP:GL:GQ 0/1:43,28:61:-79.84,-18.38,-149.14:99 +chr1 3959826 . A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=1;HaplotypeScore=9.14;MQ=50.86;MQ0=1;OQ=291.12;QD=3.93;SB=-139.48 GT:AD:DP:GL:GQ 0/1:51,23:56:-49.27,-16.88,-163.75:99 +chr1 3959854 rs10799245 C A 521.83 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.17;MQ0=0;OQ=879.17;QD=14.65;SB=-268.32 GT:AD:DP:GL:GQ 0/1:29,31:55:-107.78,-16.58,-78.49:99 +chr1 3961215 rs6670453 G C 331.68 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=59.13;MQ0=0;OQ=833.59;QD=15.73;SB=-292.89 GT:AD:DP:GL:GQ 0/1:29,24:53:-102.62,-15.98,-127.58:99 +chr1 3961230 rs6672877 G T 118.38 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.94;MQ=59.07;MQ0=0;OQ=633.10;QD=12.66;SB=-213.34 GT:AD:DP:GL:GQ 0/1:27,23:49:-81.35,-14.76,-89.22:99 +chr1 3961237 rs12045715 G A 510.42 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=793.63;QD=15.56;SB=-285.83 GT:AD:DP:GL:GQ 0/1:26,25:51:-98.03,-15.38,-79.59:99 +chr1 3961468 rs12045781 G A 286.99 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=60.00;MQ0=0;OQ=606.20;QD=13.78;SB=-238.18 GT:AD:DP:GL:GQ 0/1:24,20:42:-76.57,-12.66,-72.65:99 +chr1 3961548 rs10799247 A G 169.43 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.55;MQ=58.33;MQ0=0;OQ=674.03;QD=12.04;SB=-151.92 GT:AD:DP:GL:GQ 0/1:31,24:52:-86.36,-15.67,-108.75:99 +chr1 3962010 rs4654565 G A 105.50 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=336.97;QD=12.96;SB=-103.61 GT:AD:DP:GL:GQ 0/1:14,12:25:-44.52,-7.54,-43.04:99 +chr1 3962589 rs4654447 A G 258.32 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.65;MQ0=0;OQ=712.70;QD=13.45;SB=-356.22 GT:AD:DP:GL:GQ 0/1:26,27:50:-89.62,-15.07,-95.62:99 +chr1 3962703 rs4654448 A C 265.60 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=756.85;QD=13.52;SB=-251.86 GT:AD:DP:GL:GQ 0/1:29,27:55:-95.53,-16.56,-103.20:99 +chr1 3962856 rs4654567 T C 95.03 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=59.17;MQ0=0;OQ=415.90;QD=9.24;SB=-159.46 GT:AD:DP:GL:GQ 0/1:25,20:42:-57.53,-12.66,-94.60:99 +chr1 3962899 rs4654449 G A 419.09 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=60.00;MQ0=0;OQ=648.86;QD=14.75;SB=-335.88 GT:AD:DP:GL:GQ 0/1:22,22:42:-80.82,-12.65,-78.42:99 +chr1 3963307 rs7520607 T C 230.94 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=3.28;MQ=58.42;MQ0=0;OQ=845.59;QD=14.58;SB=-424.34 GT:AD:DP:GL:GQ 0/1:26,32:53:-103.81,-15.97,-95.34:99 +chr1 3963607 rs4654568 T G 463.03 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.07;MQ0=0;OQ=931.94;QD=16.64;SB=-413.80 GT:AD:DP:GL:GQ 0/1:24,32:56:-113.34,-16.87,-88.78:99 +chr1 3963626 rs12027462 C T 248.09 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=57.57;MQ0=0;OQ=963.52;QD=17.21;SB=-429.93 GT:AD:DP:GL:GQ 0/1:26,30:55:-116.20,-16.57,-93.29:99 +chr1 3963784 rs4654451 G A 171.09 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=59.79;MQ0=0;OQ=912.02;QD=16.00;SB=-225.51 GT:AD:DP:GL:GQ 0/1:28,28:53:-110.46,-15.98,-78.09:99 +chr1 3964643 rs6426429 A G 60.66 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=1.27;MQ=59.56;MQ0=0;OQ=582.81;QD=11.00;SB=-285.59 GT:AD:DP:GL:GQ 0/1:28,25:51:-76.94,-15.38,-106.26:99 +chr1 3965132 rs4074993 C G 325.61 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.87;MQ=59.28;MQ0=0;OQ=814.87;QD=14.05;SB=-345.07 GT:AD:DP:GL:GQ 0/1:34,24:55:-101.37,-16.60,-121.74:99 +chr1 3965479 rs4074994 T C 268.09 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=52.28;MQ0=0;OQ=617.78;QD=12.36;SB=-300.36 GT:AD:DP:GL:GQ 0/1:25,25:49:-79.83,-14.77,-98.86:99 +chr1 3965536 rs57323923 T C 0.88 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=4;HaplotypeScore=2.11;MQ=50.55;MQ0=0;OQ=424.15;QD=8.48;SB=-173.38 GT:AD:DP:GL:GQ 0/1:29,21:47:-59.86,-14.17,-115.12:99 +chr1 3965975 . C G 7.70 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=58.67;MQ0=0;OQ=589.92;QD=12.04;SB=-25.38 GT:AD:DP:GL:GQ 0/1:32,17:46:-76.14,-13.87,-119.93:99 +chr1 3965977 . T C 0.69 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=2;HaplotypeScore=1.11;MQ=58.22;MQ0=0;OQ=427.57;QD=8.55;SB=-16.87 GT:AD:DP:GL:GQ 0/1:33,17:49:-60.80,-14.76,-127.29:99 +chr1 3966027 rs7414863 A C 144.45 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.13;MQ0=0;OQ=452.26;QD=9.42;SB=-62.85 GT:AD:DP:GL:GQ 0/1:27,21:45:-62.07,-13.56,-92.65:99 +chr1 3966540 rs3935559 C G 391.87 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=1031.71;QD=18.42;SB=-312.99 GT:AD:DP:GL:GQ 0/1:24,32:56:-123.36,-16.90,-103.47:99 +chr1 3966816 . G A 1.68 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=5.13;MQ=57.97;MQ0=0;OQ=1415.89;QD=20.52;SB=-484.12 GT:AD:DP:GL:GQ 0/1:24,45:61:-163.26,-18.38,-64.39:99 +chr1 3967294 rs12747294 C T 4.07 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=8.87;MQ=56.15;MQ0=1;OQ=813.80;QD=16.95;SB=-391.14 GT:AD:DP:GL:GQ 0/1:22,26:45:-98.22,-13.56,-71.93:99 +chr1 3967372 rs6702213 C T 194.14 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=34.49;MQ0=0;OQ=718.26;QD=12.17;SB=-239.54 GT:AD:DP:GL:GQ 0/1:33,26:54:-91.39,-16.28,-98.59:99 +chr1 3967404 rs6661264 T C 167.37 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=40.81;MQ0=0;OQ=475.36;QD=8.80;SB=-244.91 GT:AD:DP:GL:GQ 0/1:34,20:52:-66.49,-15.67,-131.05:99 +chr1 3967405 rs6675434 G A 377.49 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.63;MQ0=0;OQ=533.67;QD=9.70;SB=-290.77 GT:AD:DP:GL:GQ 0/1:34,21:52:-72.31,-15.66,-122.28:99 +chr1 3967434 rs12747604 C T 38.96 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=46.12;MQ0=0;OQ=331.44;QD=7.71;SB=-108.07 GT:AD:DP:GL:GQ 0/1:29,14:41:-48.79,-12.36,-91.55:99 +chr1 3967444 rs56081307 C A 64.62 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=45.65;MQ0=0;OQ=391.03;QD=8.32;SB=-188.48 GT:AD:DP:GL:GQ 0/1:31,16:44:-55.64,-13.25,-103.38:99 +chr1 3967458 rs6661363 T C 158.21 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=46.22;MQ0=0;OQ=383.22;QD=7.82;SB=-172.51 GT:AD:DP:GL:GQ 0/1:29,19:44:-54.87,-13.26,-104.62:99 +chr1 3967912 rs6675979 G A 278.83 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.51;MQ=58.64;MQ0=0;OQ=1206.49;QD=19.46;SB=-623.12 GT:AD:DP:GL:GQ 0/1:25,37:60:-142.02,-18.08,-76.63:99 +chr1 3968006 rs12731145 A G 28.60 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=5.76;MQ=59.49;MQ0=0;OQ=439.53;QD=9.77;SB=-228.43 GT:AD:DP:GL:GQ 0/1:27,18:43:-60.19,-12.95,-105.51:99 +chr1 3968073 rs6426431 G A 223.15 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=59.56;MQ0=0;OQ=482.88;QD=9.29;SB=-221.45 GT:AD:DP:GL:GQ 0/1:34,18:50:-66.64,-15.07,-119.13:99 +chr1 3968105 rs12744667 G A 365.59 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.56;MQ0=0;OQ=827.90;QD=15.62;SB=-433.93 GT:AD:DP:GL:GQ 0/1:27,26:51:-101.44,-15.36,-92.63:99 +chr1 3968106 rs55866108 A G 217.98 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=59.57;MQ0=0;OQ=738.88;QD=13.68;SB=-284.42 GT:AD:DP:GL:GQ 0/1:27,27:53:-93.14,-15.96,-108.96:99 +chr1 3968537 rs12753281 C G 269.93 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.90;MQ0=0;OQ=1244.08;QD=14.99;SB=-559.96 GT:AD:DP:GL:GQ 0/1:45,38:83:-152.72,-25.03,-193.42:99 +chr1 3968581 rs12736036 A G 78.01 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=3.15;MQ=57.56;MQ0=0;OQ=949.82;QD=11.58;SB=-430.05 GT:AD:DP:GL:GQ 0/1:44,38:77:-121.46,-23.19,-177.75:99 +chr1 3968726 rs34940664 G T 190.81 PASS AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.33;MQ0=0;OQ=1575.63;QD=16.24;SB=-709.50 GT:AD:DP:GL:GQ 0/1:45,52:96:-189.76,-28.91,-164.22:99 +chr1 3968753 rs35749996 A G 455.09 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1487.59;QD=17.92;SB=-656.99 GT:AD:DP:GL:GQ 0/1:35,48:83:-177.04,-25.00,-145.40:99 +chr1 3968768 rs12753644 C G 340.70 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=1876.77;QD=20.85;SB=-779.42 GT:AD:DP:GL:GQ 0/1:40,50:90:-218.08,-27.12,-169.27:99 +chr1 3968858 rs12045134 A C 23.52 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=5.51;MQ=58.42;MQ0=0;OQ=708.96;QD=8.54;SB=-321.59 GT:AD:DP:GL:GQ 0/1:52,31:81:-98.58,-24.40,-189.89:99 +chr1 3968949 rs12047590 G T 243.75 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=59.74;MQ0=0;OQ=980.09;QD=13.61;SB=-395.21 GT:AD:DP:GL:GQ 0/1:39,33:71:-122.68,-21.39,-124.97:99 +chr1 3969008 rs12027284 C T 226.70 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.68;MQ0=0;OQ=1351.13;QD=18.77;SB=-463.00 GT:AD:DP:GL:GQ 0/1:32,40:69:-159.19,-20.80,-95.94:99 +chr1 3969221 rs12045225 A G 0.63 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=9.56;MQ=58.22;MQ0=0;OQ=654.37;QD=13.09;SB=-95.63 GT:AD:DP:GL:GQ 0/1:21,29:44:-81.99,-13.27,-67.60:99 +chr1 3969391 rs12046014 A G 106.22 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.88;MQ=58.95;MQ0=0;OQ=580.96;QD=9.37;SB=-244.16 GT:AD:DP:GL:GQ 0/1:36,26:57:-78.56,-17.18,-134.21:99 +chr1 3969440 rs12044268 T C 521.33 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=58.87;MQ0=0;QD=12.72;SB=-263.94 GT:AD:DP:GL:GQ 0/1:19,21:40:-67.48,-12.06,-76.36:99 +chr1 3969444 rs12048464 G T 535.50 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.71;MQ0=0;QD=14.88;SB=-256.96 GT:AD:DP:GL:GQ 0/1:18,18:36:-67.68,-10.85,-54.15:99 +chr1 3969450 rs34283588 G A 563.46 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.55;MQ0=0;QD=17.61;SB=-257.77 GT:AD:DP:GL:GQ 0/1:15,17:30:-68.67,-9.04,-41.92:99 +chr1 3969504 rs12028147 C A 128.14 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.50;MQ0=0;OQ=1173.33;QD=18.92;SB=-401.82 GT:AD:DP:GL:GQ 0/1:25,37:62:-139.29,-18.67,-88.93:99 +chr1 3969731 rs35514116 C A 193.09 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=2.36;MQ=59.11;MQ0=0;OQ=1169.40;QD=14.99;SB=-425.64 GT:AD:DP:GL:GQ 0/1:38,39:78:-146.50,-26.28,-138.29:99 +chr1 3969738 rs35902612 G T 87.34 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.60;MQ=59.14;MQ0=0;OQ=1314.22;QD=16.22;SB=-492.89 GT:AD:DP:GL:GQ 0/1:38,43:80:-158.80,-24.09,-135.14:99 +chr1 3969835 rs34306433 G C 322.67 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=60.00;MQ0=0;OQ=1225.99;QD=18.03;SB=-578.33 GT:AD:DP:GL:GQ 0/1:31,36:68:-148.71,-22.83,-138.52:99 +chr1 3970192 rs34458454 T C 115.71 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=60.00;MQ0=0;OQ=393.81;QD=8.04;SB=-222.38 GT:AD:DP:GL:GQ 0/1:28,21:43:-55.63,-12.97,-98.60:99 +chr1 3970255 rs34994381 G A 356.92 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1045.77;QD=16.09;SB=-475.47 GT:AD:DP:GL:GQ 0/1:34,31:61:-126.25,-18.39,-98.09:99 +chr1 3970431 rs35579324 A T 318.12 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.56;MQ0=0;OQ=768.67;QD=14.78;SB=-345.07 GT:AD:DP:GL:GQ 0/1:26,26:52:-95.82,-15.67,-98.48:99 +chr1 3970448 rs35474759 C T 457.86 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=955.78;QD=18.03;SB=-501.52 GT:AD:DP:GL:GQ 0/1:25,28:52:-114.52,-15.66,-86.38:99 +chr1 3970842 rs12049555 G A 157.06 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=59.39;MQ0=0;OQ=384.99;QD=10.13;SB=-163.62 GT:AD:DP:GL:GQ 0/1:23,15:35:-52.33,-10.55,-71.59:99 +chr1 3970912 rs6664533 C T 146.77 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=3.51;MQ=58.67;MQ0=0;OQ=505.76;QD=14.45;SB=-247.75 GT:AD:DP:GL:GQ 0/1:19,16:34:-64.11,-10.25,-57.21:99 +chr1 3971010 rs6664655 C G 360.39 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=59.06;MQ0=0;OQ=1105.77;QD=14.94;SB=-455.72 GT:AD:DP:GL:GQ 0/1:42,32:74:-136.16,-22.30,-181.19:99 +chr1 3971024 rs6686502 G A 241.40 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=59.09;MQ0=0;OQ=1058.60;QD=13.93;SB=-346.09 GT:AD:DP:GL:GQ 0/1:42,34:75:-131.76,-22.62,-128.76:99 +chr1 3971052 rs6672264 T C 278.60 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.20;MQ0=0;OQ=887.02;QD=10.95;SB=-268.12 GT:AD:DP:GL:GQ 0/1:49,32:80:-116.09,-24.10,-192.61:99 +chr1 3971195 rs6686709 G C 441.55 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=533.40;QD=11.85;SB=-281.29 GT:AD:DP:GL:GQ 0/1:29,16:42:-69.28,-12.66,-112.85:99 +chr1 3971259 rs6680847 A G 343.35 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=805.68;QD=13.21;SB=-291.63 GT:AD:DP:GL:GQ 0/1:33,28:60:-101.92,-18.07,-129.04:99 +chr1 3971430 rs6675053 T C 59.44 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=57.14;MQ0=0;OQ=478.62;QD=6.74;SB=-133.24 GT:AD:DP:GL:GQ 0/1:48,23:70:-72.24,-21.10,-194.61:99 +chr1 3971753 . C A 69.39 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=12;HaplotypeScore=26.59;MQ=52.60;MQ0=0;QD=1.16;SB=62.22 GT:AD:DP:GL:GQ 0/1:50,10:49:-24.98,-14.76,-146.09:99 +chr1 3971766 rs12030209 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=12;HaplotypeScore=17.56;MQ=52.68;MQ0=0;OQ=817.96;QD=12.39;SB=-315.05 GT:AD:DP:GL:GQ 0/1:32,34:60:-103.15,-18.07,-109.51:99 +chr1 3972069 rs55798869 G T 4.80 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=3;HaplotypeScore=5.71;MQ=56.04;MQ0=0;OQ=802.09;QD=13.37;SB=-418.83 GT:AD:DP:GL:GQ 0/1:32,28:52:-99.17,-15.67,-74.15:99 +chr1 3972136 rs55745368 T C 189.98 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=59.03;MQ0=0;OQ=1099.26;QD=12.08;SB=-445.57 GT:AD:DP:GL:GQ 0/1:52,39:91:-140.63,-27.42,-210.68:99 +chr1 3972189 rs7414301 T C 60.16 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=5.42;MQ=59.51;MQ0=0;OQ=1011.76;QD=11.76;SB=-466.68 GT:AD:DP:GL:GQ 0/1:46,40:86:-130.38,-25.92,-186.30:99 +chr1 3972623 . A C 192.74 PASS AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.77;MQ0=0;OQ=1230.69;QD=15.38;SB=-527.79 GT:AD:DP:GL:GQ 0/1:36,44:79:-150.15,-23.80,-134.39:99 +chr1 3972753 rs10915589 G A 130.98 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.30;MQ0=0;OQ=1165.16;QD=17.65;SB=-331.36 GT:AD:DP:GL:GQ 0/1:30,36:63:-138.78,-18.98,-103.29:99 +chr1 3972924 rs12023372 G C 321.94 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1325.91;QD=18.94;SB=-613.61 GT:AD:DP:GL:GQ 0/1:33,37:69:-156.66,-20.79,-145.10:99 +chr1 3973210 rs12023479 G A 281.53 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.70;MQ0=0;OQ=1046.55;QD=13.59;SB=-512.32 GT:AD:DP:GL:GQ 0/1:44,33:77:-131.15,-23.21,-144.02:99 +chr1 3973292 . A G 33.55 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=55.10;MQ0=0;OQ=633.05;QD=11.94;SB=-175.56 GT:AD:DP:GL:GQ 0/1:28,25:47:-80.75,-14.16,-95.41:99 +chr1 3973506 . G A 176.17 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.46;MQ0=0;OQ=876.83;QD=12.71;SB=-380.14 GT:AD:DP:GL:GQ 0/1:42,27:67:-111.16,-20.19,-131.21:99 +chr1 3973875 rs4654459 T A 52.35 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=2.73;MQ=58.55;MQ0=0;OQ=1176.09;QD=14.70;SB=-563.67 GT:AD:DP:GL:GQ 0/1:41,39:78:-144.39,-23.49,-149.95:99 +chr1 3973955 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=17;HaplotypeScore=22.03;MQ=54.06;MQ0=0;OQ=55.47;QD=1.03;SB=65.23 GT:AD:DP:GL:GQ 0/1:43,10:44:-22.08,-13.25,-133.74:88.31 +chr1 3974003 . A G 105.47 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.51;MQ0=0;OQ=461.72;QD=11.26;SB=-234.29 GT:AD:DP:GL:GQ 0/1:22,19:40:-61.51,-12.06,-83.11:99 +chr1 3974203 . T G 66.57 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.62;MQ0=0;OQ=954.85;QD=13.84;SB=-428.75 GT:AD:DP:GL:GQ 0/1:35,34:68:-119.25,-20.48,-128.89:99 +chr1 3974239 rs35998568 G A 463.07 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.48;MQ0=0;OQ=1184.56;QD=17.95;SB=-510.14 GT:AD:DP:GL:GQ 0/1:31,35:66:-141.63,-19.89,-102.39:99 +chr1 3974376 rs57696600 C T 6.14 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=4;HaplotypeScore=1.87;MQ=59.16;MQ0=0;OQ=1418.07;QD=19.70;SB=-722.06 GT:AD:DP:GL:GQ 0/1:30,42:71:-166.49,-21.40,-92.47:99 +chr1 3974614 rs4457544 A T 403.15 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=1649.20;QD=19.18;SB=-732.91 GT:AD:DP:GL:GQ 0/1:34,52:86:-194.11,-25.90,-133.63:99 +chr1 3974846 rs12025374 G A 466.59 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.31;MQ0=0;OQ=1051.59;QD=16.43;SB=-403.40 GT:AD:DP:GL:GQ 0/1:31,33:63:-127.44,-18.99,-100.16:99 +chr1 3975091 rs12049502 T C 199.42 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=58.55;MQ0=0;OQ=805.28;QD=16.78;SB=-288.47 GT:AD:DP:GL:GQ 0/1:19,29:47:-97.97,-14.16,-75.75:99 +chr1 3975721 rs34928897 A G 109.87 PASS AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=2.98;MQ=59.19;MQ0=1;OQ=1038.58;QD=10.93;SB=-532.63 GT:AD:DP:GL:GQ 0/1:53,42:94:-135.47,-28.33,-210.33:99 +chr1 3975829 rs12060834 A C 406.62 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1062.88;QD=14.56;SB=-251.81 GT:AD:DP:GL:GQ 0/1:37,36:73:-131.56,-21.98,-139.84:99 +chr1 3975904 rs12026411 G T 347.07 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=57.00;MQ0=0;OQ=1228.86;QD=14.99;SB=-454.51 GT:AD:DP:GL:GQ 0/1:42,40:82:-150.86,-24.69,-151.44:99 +chr1 3976117 rs12034312 C T 244.48 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=60.00;MQ0=0;OQ=1562.01;QD=18.38;SB=-442.95 GT:AD:DP:GL:GQ 0/1:40,45:84:-184.80,-25.32,-123.96:99 +chr1 3976389 rs35297022 T C 334.71 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=962.55;QD=13.95;SB=-357.60 GT:AD:DP:GL:GQ 0/1:35,34:68:-120.03,-20.49,-141.31:99 +chr1 3976394 rs35043594 A T 325.11 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=916.45;QD=13.68;SB=-308.03 GT:AD:DP:GL:GQ 0/1:36,31:67:-115.11,-20.18,-137.00:99 +chr1 3976477 rs4641284 A G 171.33 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=58.95;MQ0=0;OQ=487.70;QD=11.08;SB=-180.60 GT:AD:DP:GL:GQ 0/1:26,18:42:-64.71,-12.65,-94.45:99 +chr1 3976506 rs34448752 C T 57.24 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=56.85;MQ0=0;OQ=445.94;QD=14.86;SB=-105.62 GT:AD:DP:GL:GQ 0/1:16,14:29:-56.62,-8.74,-46.04:99 +chr1 3976567 . C T 0.32 PASS AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=0;HaplotypeScore=1.54;MQ=51.77;MQ0=0;OQ=226.37;QD=18.86;SB=-10.00 GT:AD:DP:GL:GQ 0/1:3,9:11:-29.24,-3.32,-8.40:50.74 +chr1 3976658 rs35326871 G T 11.99 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.52;MQ0=0;OQ=1096.88;QD=17.41;SB=-10.00 GT:AD:DP:GL:GQ 0/1:25,38:62:-131.64,-18.67,-93.14:99 +chr1 3977151 rs10915596 T G 1.14 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=3.48;MQ=59.09;MQ0=0;OQ=756.41;QD=14.83;SB=-45.56 GT:AD:DP:GL:GQ 0/1:22,29:48:-93.38,-14.46,-82.79:99 +chr1 3977453 rs4654599 G T 361.03 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.46;MQ0=0;OQ=1289.21;QD=16.74;SB=-567.82 GT:AD:DP:GL:GQ 0/1:35,42:77:-155.40,-23.19,-125.68:99 +chr1 3977541 rs4654600 T C 61.36 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=3.43;MQ=59.43;MQ0=0;OQ=838.26;QD=17.11;SB=-388.65 GT:AD:DP:GL:GQ 0/1:18,30:47:-103.58,-16.47,-75.42:99 +chr1 3977567 rs4654601 G A 272.32 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.55;MQ0=0;OQ=1148.82;QD=18.83;SB=-426.81 GT:AD:DP:GL:GQ 0/1:26,35:60:-136.24,-18.08,-87.47:99 +chr1 3977950 rs4654604 T C 322.32 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=59.65;MQ0=0;OQ=975.26;QD=14.78;SB=-339.18 GT:AD:DP:GL:GQ 0/1:28,38:65:-120.40,-19.59,-110.65:99 +chr1 3978231 rs4129099 T C 330.29 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=60.00;MQ0=0;OQ=733.04;QD=11.64;SB=-345.90 GT:AD:DP:GL:GQ 0/1:32,31:62:-95.28,-18.69,-130.06:99 +chr1 3978308 rs4129100 G A 317.73 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=1482.59;QD=16.85;SB=-689.02 GT:AD:DP:GL:GQ 0/1:42,46:86:-177.46,-25.92,-132.95:99 +chr1 3980624 rs4323679 C T 566.66 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=703.77;QD=12.13;SB=-349.85 GT:AD:DP:GL:GQ 0/1:35,23:57:-90.85,-17.19,-108.01:99 +chr1 3980746 rs35182639 G A 123.92 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=4.13;MQ=59.70;MQ0=0;OQ=1453.16;QD=18.63;SB=-621.68 GT:AD:DP:GL:GQ 0/1:35,43:76:-171.51,-22.91,-105.10:99 +chr1 3980982 rs12747944 G A 386.78 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=60.00;MQ0=0;OQ=715.67;QD=12.56;SB=-369.37 GT:AD:DP:GL:GQ 0/1:32,24:53:-90.82,-15.97,-105.07:99 +chr1 3981385 rs17404600 C T 307.96 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.06;MQ=59.56;MQ0=0;OQ=909.30;QD=17.16;SB=-459.01 GT:AD:DP:GL:GQ 0/1:26,27:49:-108.98,-14.77,-70.07:99 +chr1 3981945 . G C 7.35 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.62;MQ=59.25;MQ0=0;OQ=783.42;QD=13.99;SB=-334.02 GT:AD:DP:GL:GQ 0/1:33,23:54:-97.92,-16.29,-122.30:99 +chr1 3981947 rs10799260 C T 127.54 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=2.62;MQ=59.25;MQ0=0;OQ=721.41;QD=12.88;SB=-288.75 GT:AD:DP:GL:GQ 0/1:33,23:55:-91.99,-16.57,-116.30:99 +chr1 3982051 rs10753384 A G 287.89 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.81;MQ=59.62;MQ0=0;OQ=891.61;QD=14.62;SB=-286.59 GT:AD:DP:GL:GQ 0/1:30,31:60:-110.52,-18.08,-117.65:99 +chr1 3982227 rs10799261 T C 592.68 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=920.95;QD=13.35;SB=-433.27 GT:AD:DP:GL:GQ 0/1:35,34:67:-115.56,-20.18,-140.96:99 +chr1 3982891 rs12023925 T C 257.35 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.13;MQ0=0;OQ=486.42;QD=9.18;SB=-229.40 GT:AD:DP:GL:GQ 0/1:30,23:50:-67.00,-15.07,-113.54:99 +chr1 3984164 rs7418256 T G 46.90 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=4;HaplotypeScore=1.00;MQ=59.72;MQ0=0;OQ=1495.13;QD=18.23;SB=-531.78 GT:AD:DP:GL:GQ 0/1:33,49:80:-176.89,-24.10,-113.02:99 +chr1 3984958 rs6426436 A G 575.34 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=842.05;QD=12.95;SB=-332.89 GT:AD:DP:GL:GQ 0/1:35,30:64:-106.77,-19.28,-141.35:99 +chr1 3985143 rs5015188 T C 159.92 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=12.99;MQ=58.62;MQ0=0;QD=2.25;SB=-60.43 GT:AD:DP:GL:GQ 0/1:60,11:70:-40.36,-21.09,-240.05:99 +chr1 3985147 rs5015187 T C 314.93 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=67.96;MQ=58.31;MQ0=0;QD=4.37;SB=-165.46 GT:AD:DP:GL:GQ 0/1:57,15:70:-55.86,-21.08,-223.89:99 +chr1 3985151 rs5015186 T C 601.51 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.01;HRun=1;HaplotypeScore=11.99;MQ=58.34;MQ0=0;QD=8.24;SB=-304.19 GT:AD:DP:GL:GQ 0/1:49,23:71:-84.52,-21.09,-190.22:99 +chr1 3985364 rs4233266 A G 350.55 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=58.47;MQ0=0;OQ=817.82;QD=10.76;SB=-299.84 GT:AD:DP:GL:GQ 0/1:41,35:71:-106.46,-21.39,-162.85:99 +chr1 3985761 rs4654611 G C 378.30 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.78;MQ0=0;OQ=1274.73;QD=15.36;SB=-534.37 GT:AD:DP:GL:GQ 0/1:45,38:78:-154.27,-23.51,-187.35:99 +chr1 3985811 rs4654612 C T 99.80 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=4.68;MQ=59.17;MQ0=0;OQ=618.20;QD=11.04;SB=-273.28 GT:AD:DP:GL:GQ 0/1:30,25:47:-79.28,-14.18,-83.87:99 +chr1 3988267 rs3829818 C G 50.86 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.32;MQ0=0;OQ=1075.32;QD=19.55;SB=-391.87 GT:AD:DP:GL:GQ 0/1:26,29:54:-127.10,-16.29,-99.01:99 +chr1 3988626 rs34649702 A C 437.42 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=920.32;QD=18.41;SB=-485.28 GT:AD:DP:GL:GQ 0/1:20,30:49:-110.07,-14.76,-69.08:99 +chr1 3988704 rs55889146 T A 313.04 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=59.71;MQ0=0;OQ=1088.43;QD=16.75;SB=-492.44 GT:AD:DP:GL:GQ 0/1:29,36:65:-131.71,-19.58,-109.61:99 +chr1 3989745 rs35412083 G A 332.59 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.92;MQ0=0;OQ=1097.15;QD=11.93;SB=-405.76 GT:AD:DP:GL:GQ 0/1:55,36:89:-139.82,-26.82,-176.39:99 +chr1 3990405 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=94;Dels=0.03;HRun=18;HaplotypeScore=33.42;MQ=54.32;MQ0=1;OQ=80.49;QD=0.86;SB=90.81 GT:AD:DP:GL:GQ 0/1:76,15:73:-32.44,-21.10,-200.50:99 +chr1 3990446 rs34385055 G A 276.71 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.80;MQ=58.88;MQ0=0;OQ=865.10;QD=15.73;SB=-440.45 GT:AD:DP:GL:GQ 0/1:26,29:49:-104.56,-14.77,-74.37:99 +chr1 3990572 rs10915650 T C 322.59 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=53.91;MQ0=0;OQ=802.60;QD=15.43;SB=-363.11 GT:AD:DP:GL:GQ 0/1:19,33:50:-98.61,-15.07,-76.41:99 +chr1 3990932 rs4654614 C T 267.85 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1697.75;QD=19.97;SB=-727.98 GT:AD:DP:GL:GQ 0/1:36,49:85:-198.66,-25.60,-134.20:99 +chr1 3991939 . G T 133.26 Indel AC=1;AF=0.50;AN=2;DP=31;Dels=0.03;HRun=0;HaplotypeScore=37.12;MQ=55.25;MQ0=0;QD=4.30;SB=-33.93 GT:AD:DP:GL:GQ 0/1:22,8:23:-23.24,-6.63,-47.74:99 +chr1 3992866 rs34160796 A G 334.90 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.66;MQ0=0;OQ=483.28;QD=9.29;SB=-177.56 GT:AD:DP:GL:GQ 0/1:33,19:51:-66.97,-15.36,-129.46:99 +chr1 3993123 rs10915661 A G 223.41 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.93;MQ=58.90;MQ0=0;OQ=752.89;QD=12.76;SB=-356.58 GT:AD:DP:GL:GQ 0/1:32,27:57:-95.74,-17.17,-122.04:99 +chr1 3993398 rs10799273 A G 39.64 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.69;MQ0=0;OQ=432.60;QD=13.52;SB=-183.96 GT:AD:DP:GL:GQ 0/1:16,16:30:-55.58,-9.04,-60.72:99 +chr1 3993415 rs55877711 T C 152.20 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=59.43;MQ0=0;OQ=474.94;QD=14.39;SB=-232.31 GT:AD:DP:GL:GQ 0/1:16,17:31:-60.12,-9.34,-57.39:99 +chr1 3993656 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=16;HaplotypeScore=11.17;MQ=56.96;MQ0=0;OQ=77.46;QD=1.25;SB=65.19 GT:AD:DP:GL:GQ 0/1:50,11:45:-24.60,-13.57,-123.37:99 +chr1 3994923 rs4654469 G A 168.23 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=59.68;MQ0=0;OQ=1491.96;QD=20.44;SB=-717.78 GT:AD:DP:GL:GQ 0/1:30,43:72:-174.18,-21.70,-94.37:99 +chr1 3995705 rs34085171 T G 1347.57 Indel AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.38;MQ0=0;QD=15.85;SB=-684.75 GT:AD:DP:GL:GQ 0/1:40,45:84:-163.34,-25.30,-143.02:99 +chr1 3997814 . A G 166.71 PASS AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.77;MQ0=0;OQ=1047.22;QD=13.09;SB=-493.22 GT:AD:DP:GL:GQ 0/1:44,36:80:-132.11,-24.10,-175.80:99 +chr1 3999521 rs7533488 A C 424.91 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.32;MQ0=0;OQ=1161.71;QD=14.17;SB=-423.73 GT:AD:DP:GL:GQ 0/1:41,40:80:-143.55,-24.09,-150.24:99 +chr1 4000164 rs10753345 T C 207.13 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=54.60;MQ0=3;OQ=972.02;QD=12.62;SB=-388.88 GT:AD:DP:GL:GQ 0/1:39,38:72:-122.18,-21.70,-141.20:99 +chr1 4000350 rs10915304 A G 90.68 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=49.42;MQ0=0;OQ=302.07;QD=8.39;SB=-112.62 GT:AD:DP:GL:GQ 0/1:20,15:32:-43.14,-9.65,-72.05:99 +chr1 4001557 rs35079847 T C 179.63 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=42.74;MQ0=4;OQ=737.26;QD=10.24;SB=-356.16 GT:AD:DP:GL:GQ 0/1:43,29:67:-97.19,-20.18,-162.42:99 +chr1 4002410 rs9792845 T A 39.80 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=2;HaplotypeScore=2.16;MQ=49.63;MQ0=6;OQ=1137.13;QD=12.92;SB=-561.60 GT:AD:DP:GL:GQ 0/1:48,40:80:-141.09,-24.09,-168.17:99 +chr1 4002600 . C T 9.93 PASS AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=34.65;MQ0=18;OQ=1297.58;QD=10.30;SB=-536.53 GT:AD:DP:GL:GQ 0/1:72,54:87:-159.25,-26.21,-171.14:99 +chr1 4003027 rs7539155 C T 270.27 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=49.52;MQ0=2;OQ=1241.45;QD=15.71;SB=-511.02 GT:AD:DP:GL:GQ 0/1:40,39:77:-150.62,-23.19,-144.23:99 +chr1 4003660 rs34911143 C G 406.63 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1137.88;QD=19.96;SB=-593.22 GT:AD:DP:GL:GQ 0/1:26,31:56:-133.94,-16.87,-107.70:99 +chr1 4003790 . T C 0.57 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=1;HaplotypeScore=5.22;MQ=56.08;MQ0=0;OQ=469.98;QD=8.55;SB=-182.54 GT:AD:DP:GL:GQ 0/1:35,20:52:-65.94,-15.66,-138.69:99 +chr1 4003932 rs60522686 C T 104.95 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=60.00;MQ0=0;OQ=1130.00;QD=21.32;SB=-533.08 GT:AD:DP:GL:GQ 0/1:20,33:53:-132.25,-15.97,-67.95:99 +chr1 4004106 rs12036981 T A 126.81 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.38;MQ=56.22;MQ0=2;OQ=519.83;QD=10.19;SB=-138.13 GT:AD:DP:GL:GQ 0/1:29,21:47:-69.43,-14.17,-100.44:99 +chr1 4004617 rs12036953 A G 190.96 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.43;MQ0=0;OQ=561.78;QD=8.64;SB=-245.46 GT:AD:DP:GL:GQ 0/1:41,24:63:-78.44,-18.98,-164.76:99 +chr1 4005149 rs5018354 G T 769.64 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=5;HaplotypeScore=8.12;MQ=53.93;MQ0=0;QD=10.84;SB=-410.03 GT:AD:DP:GL:GQ 0/1:41,30:69:-101.03,-20.78,-142.34:99 +chr1 4005155 . A T 709.63 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=5;HaplotypeScore=11.69;MQ=54.09;MQ0=0;QD=10.28;SB=-304.00 GT:AD:DP:GL:GQ 0/1:43,26:65:-93.83,-19.58,-142.00:99 +chr1 4005156 . A T 576.66 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=13.11;MQ=54.00;MQ0=0;QD=8.48;SB=-291.97 GT:AD:DP:GL:GQ 0/1:44,24:63:-79.93,-18.98,-151.00:99 +chr1 4005449 rs34905442 A G 30.08 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=5.92;MQ=57.79;MQ0=0;OQ=842.19;QD=15.89;SB=-428.92 GT:AD:DP:GL:GQ 0/1:23,30:52:-103.18,-15.68,-83.89:99 +chr1 4010416 rs55645535 A G 3.25 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=3;HaplotypeScore=0.83;MQ=58.64;MQ0=0;OQ=504.55;QD=16.28;SB=-163.34 GT:AD:DP:GL:GQ 0/1:10,21:29:-62.49,-8.75,-36.79:99 +chr1 4012539 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=20;HaplotypeScore=3.78;MQ=46.27;MQ0=3;OQ=496.42;QD=5.23;SB=131.33 GT:AD:DP:GL:GQ 0/1:70,25:77:-76.14,-23.22,-185.60:99 +chr1 4012545 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=7;HaplotypeScore=6.81;MQ=48.30;MQ0=1;OQ=296.48;QD=3.12;SB=125.35 GT:AD:DP:GL:GQ 0/1:68,26:74:-55.23,-22.30,-199.64:99 +chr1 4015436 rs10799171 T C 582.11 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.51;MQ0=0;OQ=1395.24;QD=29.69;SB=-603.59 GT:AD:DP:GL:GQ 1/1:0,47:45:-143.16,-13.58,-0.05:99 +chr1 4015788 rs6426377 G C 79.87 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=58.24;MQ0=0;OQ=2118.03;QD=39.96;SB=-1018.28 GT:AD:DP:GL:GQ 1/1:0,53:49:-215.40,-14.76,-0.01:99 +chr1 4016464 rs3856168 T C 206.69 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=58.60;MQ0=0;OQ=1420.67;QD=28.41;SB=-682.89 GT:AD:DP:GL:GQ 1/1:0,50:45:-145.69,-13.57,-0.04:99 +chr1 4017003 rs4654403 T C 46.24 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.69;MQ=59.61;MQ0=0;OQ=1716.77;QD=29.10;SB=-823.60 GT:AD:DP:GL:GQ 1/1:0,59:55:-175.31,-16.59,-0.05:99 +chr1 4017098 rs4654404 C T 8.35 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=4.56;MQ=58.64;MQ0=0;OQ=1853.34;QD=38.61;SB=-777.68 GT:AD:DP:GL:GQ 1/1:0,48:47:-188.93,-14.16,-0.01:99 +chr1 4018431 rs4654475 T C 39.68 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.54;MQ0=0;OQ=1443.50;QD=28.87;SB=-682.71 GT:AD:DP:GL:GQ 1/1:0,50:46:-147.99,-13.88,-0.05:99 +chr1 4018760 rs7419106 C G 402.81 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1082.64;QD=34.92;SB=-389.10 GT:AD:DP:GL:GQ 1/1:0,31:28:-111.87,-8.45,-0.02:84.27 +chr1 4018847 rs10799175 T C 20.86 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=4.16;MQ=58.50;MQ0=0;OQ=814.89;QD=26.29;SB=-376.57 GT:AD:DP:GL:GQ 1/1:1,29:28:-88.39,-10.61,-3.32:72.94 +chr1 4019483 rs10799177 G A 473.58 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.36;MQ0=0;OQ=1615.08;QD=33.65;SB=-313.91 GT:AD:DP:GL:GQ 1/1:0,48:42:-165.11,-12.66,-0.02:99 +chr1 4019522 rs9792946 G A 281.35 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=54.50;MQ0=0;OQ=2603.69;QD=38.29;SB=-1110.00 GT:AD:DP:GL:GQ 1/1:0,68:66:-263.98,-19.89,-0.02:99 +chr1 4019590 rs7418034 G A 135.96 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=43.49;MQ0=0;OQ=1841.94;QD=30.70;SB=-845.46 GT:AD:DP:GL:GQ 1/1:0,59:50:-190.21,-17.45,-2.43:99 +chr1 4019593 rs7412152 A C 123.30 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=42.41;MQ0=0;OQ=1763.32;QD=29.89;SB=-853.08 GT:AD:DP:GL:GQ 1/1:0,59:51:-179.93,-15.36,-0.02:99 +chr1 4019614 rs7411249 C G 15.77 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=3.88;MQ=36.55;MQ0=1;OQ=1713.38;QD=32.33;SB=-801.51 GT:AD:DP:GL:GQ 1/1:0,53:41:-174.94,-12.36,-0.02:99 +chr1 4019841 rs7412217 A G 301.34 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=36.34;MQ0=0;OQ=1308.64;QD=29.08;SB=-633.25 GT:AD:DP:GL:GQ 1/1:0,45:37:-134.46,-11.14,-0.01:99 +chr1 4019863 rs4310408 A G 15.48 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=44.42;MQ0=0;OQ=1396.45;QD=30.36;SB=-620.23 GT:AD:DP:GL:GQ 1/1:0,46:40:-143.25,-12.05,-0.02:99 +chr1 4019987 rs10737398 C T 456.73 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.86;MQ0=6;OQ=1422.85;QD=30.93;SB=-467.35 GT:AD:DP:GL:GQ 1/1:0,46:37:-145.88,-11.15,-0.01:99 +chr1 4020055 rs7411353 C A 1052.58 Indel;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=9;HaplotypeScore=6.69;MQ=42.23;MQ0=1;QD=22.40;SB=-302.56 GT:AD:DP:GL:GQ 1/1:0,47:31:-108.85,-9.34,-0.01:93.27 +chr1 4020059 . T A 16.07 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=4;HaplotypeScore=6.64;MQ=40.62;MQ0=1;QD=0.41;SB=14.07 GT:AD:DP:GL:GQ 0/1:27,12:17:-10.01,-5.13,-48.93:48.79 +chr1 4020065 rs6426379 G C 834.47 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=40.47;MQ0=0;QD=30.91;SB=-369.17 GT:AD:DP:GL:GQ 1/1:1,26:20:-87.04,-6.03,-0.01:60.20 +chr1 4020216 rs6426380 C T 178.01 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=56.52;MQ0=0;OQ=2286.70;QD=38.76;SB=-938.24 GT:AD:DP:GL:GQ 1/1:0,59:59:-232.28,-17.78,-0.03:99 +chr1 4020359 rs4233255 T A 506.79 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.30;MQ0=1;OQ=1405.72;QD=30.56;SB=-629.64 GT:AD:DP:GL:GQ 1/1:0,46:40:-144.18,-12.05,-0.02:99 +chr1 4020451 rs4654476 A G 27.72 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.11;MQ0=0;OQ=1489.65;QD=28.65;SB=-689.96 GT:AD:DP:GL:GQ 1/1:0,52:47:-152.59,-14.18,-0.04:99 +chr1 4020454 rs4654477 T C 48.40 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.13;MQ=59.54;MQ0=0;OQ=1536.11;QD=30.72;SB=-613.94 GT:AD:DP:GL:GQ 1/1:0,50:48:-157.24,-14.48,-0.04:99 +chr1 4020656 rs4233256 A C 90.34 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=59.09;MQ0=0;OQ=1344.37;QD=29.23;SB=-633.78 GT:AD:DP:GL:GQ 1/1:0,46:45:-138.07,-13.57,-0.05:99 +chr1 4020738 rs4233257 G A 285.07 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=56.81;MQ0=0;OQ=1954.21;QD=35.53;SB=-857.02 GT:AD:DP:GL:GQ 1/1:0,55:50:-199.02,-15.06,-0.01:99 +chr1 4020758 rs4233258 T C 590.90 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=1509.42;QD=29.03;SB=-773.63 GT:AD:DP:GL:GQ 1/1:0,52:49:-154.57,-14.78,-0.05:99 +chr1 4020965 rs10915373 A G 41.68 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=3.05;MQ=59.15;MQ0=0;OQ=2124.75;QD=32.19;SB=-981.05 GT:AD:DP:GL:GQ 1/1:0,66:61:-216.09,-18.38,-0.03:99 +chr1 4021209 rs12087801 A G 66.82 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=59.44;MQ0=0;OQ=1399.12;QD=34.12;SB=-653.32 GT:AD:DP:GL:GQ 1/1:0,41:40:-143.51,-12.05,-0.01:99 +chr1 4021244 rs7524590 A G 21.98 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.56;MQ0=0;OQ=1518.93;QD=29.21;SB=-554.05 GT:AD:DP:GL:GQ 1/1:0,52:47:-155.52,-14.17,-0.04:99 +chr1 4021467 rs6426381 T C 70.46 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.82;MQ0=0;OQ=1271.75;QD=29.58;SB=-623.00 GT:AD:DP:GL:GQ 1/1:0,43:40:-130.79,-12.06,-0.03:99 +chr1 4021470 rs6665286 C T 565.39 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.82;MQ0=0;OQ=1632.61;QD=37.97;SB=-837.35 GT:AD:DP:GL:GQ 1/1:0,43:42:-166.86,-12.66,-0.02:99 +chr1 4021576 rs10799179 C T 140.80 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.60;MQ0=0;OQ=2105.87;QD=36.95;SB=-1023.68 GT:AD:DP:GL:GQ 1/1:0,57:54:-214.19,-16.27,-0.02:99 +chr1 4022324 rs10799180 T C 96.83 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1478.38;QD=30.80;SB=-697.61 GT:AD:DP:GL:GQ 1/1:0,48:47:-151.47,-14.18,-0.04:99 +chr1 4023064 rs12044274 A T 27.33 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.00;MQ0=0;OQ=1175.00;QD=33.57;SB=-370.25 GT:AD:DP:GL:GQ 1/1:0,34:33:-121.10,-9.94,-0.02:99 +chr1 4023346 rs12728781 C T 64.59 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.67;MQ0=0;OQ=1081.51;QD=30.90;SB=-492.01 GT:AD:DP:GL:GQ 1/1:1,34:29:-111.75,-8.74,-0.01:87.27 +chr1 4023709 rs10915381 G C 0.23 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=3.44;MQ=58.92;MQ0=0;OQ=2348.10;QD=41.93;SB=-727.93 GT:AD:DP:GL:GQ 1/1:0,56:54:-238.42,-16.28,-0.02:99 +chr1 4024015 rs6672626 C T 663.95 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=46.30;MQ0=0;OQ=1764.84;QD=37.55;SB=-805.32 GT:AD:DP:GL:GQ 1/1:0,47:46:-180.09,-13.86,-0.02:99 +chr1 4024120 rs6672716 C T 182.48 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=36.16;MQ0=0;OQ=1966.97;QD=37.83;SB=-833.61 GT:AD:DP:GL:GQ 1/1:0,51:51:-203.16,-18.10,-2.88:99 +chr1 4024270 . T A 112.05 Indel AC=1;AF=0.50;AN=2;DP=33;Dels=0.03;HRun=0;HaplotypeScore=2.93;MQ=35.48;MQ0=0;QD=3.40;SB=-51.99 GT:AD:DP:GL:GQ 0/1:21,11:28:-22.63,-8.14,-76.45:99 +chr1 4024272 . A T 86.10 Indel AC=1;AF=0.50;AN=2;DP=34;Dels=0.03;HRun=0;HaplotypeScore=5.09;MQ=34.14;MQ0=0;QD=2.53;SB=-27.82 GT:AD:DP:GL:GQ 0/1:23,10:27:-19.73,-7.83,-71.54:99 +chr1 4024295 rs6683289 T C 432.26 Indel;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=27.02;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,16:16:-46.84,-4.84,-0.03:48.07 +chr1 4024297 rs6665849 G C 696.90 Indel;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=43.56;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,16:16:-73.28,-4.82,-0.00:48.16 +chr1 4024305 . T C 154.38 Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=7.02;SB=-40.68 GT:AD:DP:GL:GQ 0/1:15,7:22:-25.35,-6.63,-60.61:99 +chr1 4024357 . T G 116.82 Indel AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=28.57;MQ0=0;QD=4.67;SB=-30.96 GT:AD:DP:GL:GQ 0/1:17,8:23:-21.89,-6.93,-59.79:99 +chr1 4024403 . G T 1246.60 Indel AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=28.45;MQ0=0;QD=33.69;SB=-622.14 GT:AD:DP:GL:GQ 1/1:0,37:35:-128.26,-10.54,-0.01:99 +chr1 4024413 . C T 38.79 Indel;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=32.72;MQ0=0;QD=0.90;SB=-26.14 GT:AD:DP:GL:GQ 0/1:37,6:40:-19.21,-12.05,-127.12:71.63 +chr1 4024463 . G C 836.03 Indel AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=5.63;MQ=36.44;MQ0=0;QD=16.39;SB=-259.21 GT:AD:DP:GL:GQ 0/1:27,24:51:-102.25,-15.37,-114.08:99 +chr1 4024467 . C T 697.56 Indel AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=4.47;MQ=36.57;MQ0=0;QD=13.95;SB=-194.79 GT:AD:DP:GL:GQ 0/1:28,22:49:-87.80,-14.76,-98.23:99 +chr1 4024517 rs28542205 C G 1129.16 Indel AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=18.36;MQ=32.35;MQ0=0;QD=26.26;SB=-522.33 GT:AD:DP:GL:GQ 0/1:8,31:35:-126.75,-10.55,-27.16:99 +chr1 4024521 . G C 975.12 Indel AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=18.89;MQ=30.36;MQ0=0;QD=23.78;SB=-491.19 GT:AD:DP:GL:GQ 0/1:9,27:35:-115.01,-14.21,-36.24:99 +chr1 4024603 . G C 2.26 PASS AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=24.41;MQ0=0;OQ=50.98;QD=5.66;SB=-6.99 GT:AD:DP:GL:GQ 0/1:1,8:3:-9.29,-0.90,-4.69:37.89 +chr1 4024673 . T C 8.19 PASS AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=30.71;MQ0=0;OQ=656.07;QD=31.24;SB=-288.45 GT:AD:DP:GL:GQ 1/1:0,21:20:-69.20,-6.03,-0.01:60.17 +chr1 4024788 . T C 850.29 Indel AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.58;MQ0=0;QD=34.01;SB=-338.76 GT:AD:DP:GL:GQ 1/1:0,25:25:-88.63,-7.53,-0.01:75.20 +chr1 4024845 . T G 1.74 PASS AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=68.85;QD=17.21;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,3:4:-11.37,-1.20,-3.44:22.35 +chr1 4024894 . T C 62.45 Indel AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=29.00;MQ0=0;QD=12.49;SB=-41.94 GT:AD:DP:GL:GQ 0/1:2,3:4:-10.73,-1.20,-4.27:30.63 +chr1 4024923 . G A 22.24 Indel;LowQual AC=1;AF=0.50;AN=2;DP=8;Dels=0.25;HRun=0;HaplotypeScore=23.92;MQ=29.00;MQ0=0;QD=2.78;SB=-0.97 GT:AD:DP:GL:GQ 0/1:4,2:6:-7.31,-1.81,-14.76:55.05 +chr1 4024936 . T G 14.90 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=16;Dels=0.06;HRun=0;HaplotypeScore=31.98;MQ=29.00;MQ0=0;QD=0.93;SB=4.38 GT:AD:DP:GL:GQ 0/1:12,2:8:-11.00,-6.24,-20.74:47.59 +chr1 4024944 . C T 21.22 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=58.95;MQ=29.00;MQ0=0;QD=1.25;SB=8.05 GT:AD:DP:GL:GQ 0/1:15,2:9:-8.11,-2.71,-25.25:54.02 +chr1 4024945 . A T 15.01 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=58.95;MQ=29.00;MQ0=0;QD=0.88;SB=8.04 GT:AD:DP:GL:GQ 0/1:13,4:9:-7.48,-2.71,-24.43:47.70 +chr1 4024946 . C T 97.28 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=17;Dels=0.00;HRun=0;HaplotypeScore=64.95;MQ=29.00;MQ0=0;QD=5.72;SB=8.05 GT:AD:DP:GL:GQ 0/1:13,4:11:-16.32,-3.31,-25.25:99 +chr1 4024979 . C T 611.81 Indel;SnpCluster AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;HRun=0;HaplotypeScore=6.71;MQ=29.00;MQ0=0;QD=33.99;SB=-293.67 GT:AD:DP:GL:GQ 1/1:0,16:16:-64.77,-4.82,-0.00:48.16 +chr1 4024982 . T G 173 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=11.86;MQ=29.00;MQ0=0;QD=9.11;SB=14.07 GT:AD:DP:GL:GQ 0/1:10,7:16:-25.40,-4.82,-33.30:99 +chr1 4024983 . C T 250.37 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=1;HaplotypeScore=11.86;MQ=29.00;MQ0=0;QD=13.18;SB=14.06 GT:AD:DP:GL:GQ 0/1:11,8:16:-33.14,-4.82,-27.15:99 +chr1 4025014 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=2;HaplotypeScore=18.19;MQ=29.00;MQ0=0;OQ=197.67;QD=9.88;SB=17.08 GT:AD:DP:GL:GQ 0/1:13,7:18:-28.47,-5.42,-39.21:99 +chr1 4025033 . G A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=9.30;MQ=27.51;MQ0=1;OQ=89.74;QD=8.97;SB=2.03 GT:AD:DP:GL:GQ 0/1:5,5:9:-14.97,-2.71,-16.97:99 +chr1 4025048 . C T 21.22 DPFilter;Indel;LowQual AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=1;HaplotypeScore=32.62;MQ=27.51;MQ0=1;QD=2.12;SB=2.04 GT:AD:DP:GL:GQ 0/1:8,2:9:-8.11,-2.71,-25.19:54.03 +chr1 4025070 . G A 35.48 LowQual AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=1;HaplotypeScore=6.00;MQ=29.00;MQ0=0;QD=8.87;SB=-6.99 GT:AD:DP:GL:GQ 0/1:2,2:3:-7.73,-0.90,-3.47:25.65 +chr1 4025144 . C T 71.12 Indel AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=8.89;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,6:5:-11.90,-1.51,-7.69:61.87 +chr1 4025168 . G C 48.97 LowQual AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=29.00;MQ0=0;QD=7.00;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,5:4:-9.39,-1.21,-8.09:68.89 +chr1 4025186 . C T 0.12 PASS AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=78.13;QD=19.53;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,3:4:-12.30,-1.20,-3.90:26.92 +chr1 4025245 . C T 49.25 LowQual;SnpCluster AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=16.42;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,2:2:-8.33,-0.60,-0.00:6.02 +chr1 4025247 . G C 137.89 SnpCluster AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.94;MQ0=1;QD=27.58;SB=-52.47 GT:AD:DP:GL:GQ 1/1:1,4:4:-17.32,-1.21,-0.00:12.04 +chr1 4025253 . T C 341.02 SnpCluster AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.68;MQ0=2;QD=26.23;SB=-182.78 GT:AD:DP:GL:GQ 1/1:1,12:11:-37.69,-3.31,-0.01:33.09 +chr1 4025355 . C T 528.21 SnpCluster AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=33.01;SB=-144.72 GT:AD:DP:GL:GQ 1/1:1,15:16:-59.68,-4.82,-3.30:15.20 +chr1 4025359 . T C 305.09 SnpCluster AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=0;HaplotypeScore=0.49;MQ=29.00;MQ0=0;QD=23.47;SB=-70.88 GT:AD:DP:GL:GQ 0/1:2,11:13:-37.71,-3.92,-7.64:37.23 +chr1 4025364 . T A 90.08 SnpCluster AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=29.00;MQ0=0;QD=18.02;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,3:3:-12.50,-0.90,-0.00:9.03 +chr1 4025431 . G C 10.49 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=10.49;SB=-10.00 GT:AD:DP:GL:GQ 0/1:0,1:1:-4.29,-0.30,-0.00:1.76 +chr1 4025466 . T C 25.23 LowQual AC=1;AF=0.50;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=29.00;MQ0=0;QD=8.41;SB=-10.00 GT:AD:DP:GL:GQ 0/1:0,2:3:-9.75,-4.24,-3.95:1.79 +chr1 4025523 . A C 21.19 LowQual AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=1;HaplotypeScore=4.30;MQ=29.00;MQ0=0;QD=4.24;SB=-10.00 GT:AD:DP:GL:GQ 0/1:3,2:3:-6.30,-0.90,-3.10:21.92 +chr1 4025542 . T C 37.83 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=12.61;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,2:2:-7.19,-0.60,-0.00:6.02 +chr1 4025586 . G C 7.40 PASS AC=1;AF=0.50;AN=2;DP=5;Dels=0.20;HRun=0;HaplotypeScore=2.25;MQ=29.00;MQ0=0;OQ=51.98;QD=10.40;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,3:3:-9.39,-0.90,-3.95:30.43 +chr1 4025618 . C T 7.86 PASS AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=29.00;MQ0=0;OQ=87.13;QD=12.45;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,5:3:-12.20,-0.90,-0.00:9.03 +chr1 4025642 . T C 158.22 Indel AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=31.64;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,5:5:-19.38,-1.51,-0.00:15.05 +chr1 4025697 . A T 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=29.00;MQ0=0;OQ=113.07;QD=22.61;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,4:5:-16.09,-1.51,-3.64:21.34 +chr1 4025746 . T G 32.28 LowQual AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=3.93;MQ=23.71;MQ0=1;QD=6.46;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,2:3:-7.41,-0.90,-3.74:28.36 +chr1 4025760 . T C 33.23 LowQual AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=3.00;MQ=26.51;MQ0=0;QD=8.31;SB=-10.00 GT:AD:DP:GL:GQ 0/1:1,2:3:-10.45,-4.14,-3.85:1.79 +chr1 4026171 . A T 209.87 Indel AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=25.28;MQ0=0;QD=14.99;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,9:8:-26.67,-2.41,-4.00:15.91 +chr1 4026180 . C G 33.92 Indel;LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=25.28;MQ0=0;QD=2.42;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,5:9:-9.39,-2.71,-29.13:66.75 +chr1 4026184 . C T 21.22 LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=25.28;MQ0=0;QD=1.52;SB=-10.00 GT:AD:DP:GL:GQ 0/1:9,5:9:-8.11,-2.71,-25.08:54.02 +chr1 4026206 . C G 51.98 Indel AC=1;AF=0.50;AN=2;DP=7;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.01;MQ0=1;QD=7.43;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,5:3:-9.39,-0.90,-4.15:32.44 +chr1 4026210 . G C 48.85 LowQual AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=20.61;MQ0=1;QD=8.14;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,5:2:-8.29,-0.60,-0.00:6.02 +chr1 4026326 . G C 28.47 Indel;LowQual AC=1;AF=0.50;AN=2;DP=15;Dels=0.00;HRun=0;HaplotypeScore=22.92;MQ=30.24;MQ0=0;QD=1.90;SB=-27.39 GT:AD:DP:GL:GQ 0/1:8,6:9:-8.84,-2.71,-32.55:61.30 +chr1 4026330 . C T 15.30 Indel;LowQual AC=1;AF=0.50;AN=2;DP=16;Dels=0.00;HRun=1;HaplotypeScore=20.94;MQ=33.42;MQ0=0;QD=0.96;SB=-6.99 GT:AD:DP:GL:GQ 0/1:14,2:11:-8.11,-3.31,-31.44:48.01 +chr1 4026341 . A T 151.96 Indel AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=32.82;MQ=37.84;MQ0=1;QD=7.24;SB=-45.98 GT:AD:DP:GL:GQ 0/1:14,7:14:-22.70,-4.22,-31.99:99 +chr1 4026383 . A G 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=27.11;MQ=37.86;MQ0=1;OQ=685.36;QD=14.58;SB=-116.05 GT:AD:DP:GL:GQ 1/1:7,40:26:-76.32,-7.85,-4.20:36.49 +chr1 4026434 . C G 29.02 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.33;MQ0=0;QD=0.81;SB=5.05 GT:AD:DP:GL:GQ 0/1:34,2:8:-8.60,-2.41,-25.63:61.85 +chr1 4026435 . A T 728.54 SnpCluster AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.33;MQ0=0;QD=20.24;SB=-50.99 GT:AD:DP:GL:GQ 1/1:2,34:20:-76.44,-6.02,-0.00:60.19 +chr1 4026437 . T A 762.24 SnpCluster AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=38.33;MQ0=0;QD=21.17;SB=-46.39 GT:AD:DP:GL:GQ 1/1:2,34:20:-79.81,-6.02,-0.00:60.20 +chr1 4026440 . T G 564.23 SnpCluster AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.87;MQ0=0;QD=17.10;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,31:17:-60.01,-5.12,-0.00:51.15 +chr1 4026444 . C G 41.07 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=34.30;MQ0=1;QD=1.28;SB=-6.99 GT:AD:DP:GL:GQ 0/1:30,2:3:-8.29,-0.90,-4.25:33.44 +chr1 4026449 . A T 483.60 SnpCluster AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=34.81;MQ0=1;QD=16.68;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,29:14:-51.95,-4.22,-0.00:42.13 +chr1 4026483 . G A 173.76 Indel AC=2;AF=1.00;AN=2;DP=7;Dels=0.14;HRun=0;HaplotypeScore=0.00;MQ=25.96;MQ0=0;QD=24.82;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,6:5:-20.94,-1.51,-0.00:15.05 +chr1 4026581 . T C 45.31 PASS AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=26.51;MQ0=0;OQ=56.13;QD=14.03;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,4:3:-9.11,-0.91,-0.01:9 +chr1 4026636 . T A 64.25 PASS AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=32.75;MQ0=0;OQ=1092.89;QD=35.25;SB=-113.17 GT:AD:DP:GL:GQ 1/1:0,31:29:-112.88,-8.73,-0.01:87.28 +chr1 4026761 . T A 283.60 PASS AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.63;MQ0=0;OQ=910.42;QD=32.51;SB=-440.82 GT:AD:DP:GL:GQ 1/1:0,28:25:-94.63,-7.53,-0.01:75.24 +chr1 4026798 . G C 10.99 LowQual AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=12.99;MQ=22.58;MQ0=0;QD=2.20;SB=-10.00 GT:AD:DP:GL:GQ 0/1:2,3:1:-4.35,-0.30,-0.00:1.76 +chr1 4026914 . T C 49.44 PASS AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.57;MQ0=0;OQ=246.59;QD=24.66;SB=-150.73 GT:AD:DP:GL:GQ 1/1:0,10:9:-28.25,-2.72,-0.01:27.05 +chr1 4026927 . A T 206.91 PASS AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.61;MQ0=0;OQ=634.07;QD=30.19;SB=-308.12 GT:AD:DP:GL:GQ 1/1:0,21:18:-67.00,-5.42,-0.01:54.16 +chr1 4027026 . C T 64.95 Indel AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=32.20;MQ0=1;QD=1.71;SB=-49.74 GT:AD:DP:GL:GQ 0/1:32,6:37:-20.92,-11.15,-115.91:97.79 +chr1 4027042 . T C 614.97 Indel AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=29.00;MQ0=0;QD=27.95;SB=-154.73 GT:AD:DP:GL:GQ 1/1:0,22:21:-65.11,-6.34,-0.03:63.13 +chr1 4027052 . T C 696.49 Indel AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=29.00;MQ0=0;QD=34.82;SB=-114.05 GT:AD:DP:GL:GQ 1/1:0,20:20:-73.24,-6.03,-0.01:60.18 +chr1 4027210 . G C 19.50 Indel;LowQual AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=26.88;MQ0=0;QD=1.39;SB=-27.39 GT:AD:DP:GL:GQ 0/1:12,2:10:-8.24,-3.01,-36.19:52.28 +chr1 4027332 . C G 36.70 PASS AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.49;MQ0=0;OQ=1976.71;QD=43.93;SB=-544.06 GT:AD:DP:GL:GQ 1/1:0,45:45:-201.27,-13.56,-0.01:99 +chr1 4027338 . T C 290.59 PASS AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=36.34;MQ0=0;OQ=1625.12;QD=35.33;SB=-497.48 GT:AD:DP:GL:GQ 1/1:0,46:46:-166.11,-13.85,-0.01:99 +chr1 4027382 rs4654478 T C 529.46 Indel AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=33.88;MQ0=0;QD=11.77;SB=-150.80 GT:AD:DP:GL:GQ 0/1:25,20:45:-69.78,-13.55,-102.60:99 +chr1 4027391 . A T 124.12 Indel AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=29.00;MQ0=0;QD=3.18;SB=-45.98 GT:AD:DP:GL:GQ 0/1:32,7:37:-26.84,-11.14,-119.06:99 +chr1 4027395 . T A 21.79 Indel;LowQual AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=29.00;MQ0=0;QD=0.61;SB=-10.00 GT:AD:DP:GL:GQ 0/1:32,4:36:-16.30,-10.84,-120.25:54.60 +chr1 4027428 rs4654405 C A 54.82 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=29.00;MQ0=0;OQ=1067.75;QD=35.59;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,30:30:-110.36,-9.03,-0.00:90.28 +chr1 4027512 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=38;Dels=0.03;HRun=0;HaplotypeScore=41.12;MQ=30.70;MQ0=0;OQ=583.71;QD=15.36;SB=-96.83 GT:AD:DP:GL:GQ 0/1:11,26:29:-70.09,-8.44,-49.32:99 +chr1 4027516 . C G 4.55 PASS AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=30.66;MQ0=0;OQ=294.17;QD=7.54;SB=2.04 GT:AD:DP:GL:GQ 0/1:30,9:29:-41.44,-8.74,-84.22:99 +chr1 4027660 rs4654407 G A 193.14 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=42.76;MQ0=0;OQ=2435.59;QD=39.28;SB=-760.64 GT:AD:DP:GL:GQ 1/1:0,62:62:-247.16,-18.68,-0.02:99 +chr1 4027721 rs4654408 C T 529.60 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.67;MQ0=0;OQ=1726.14;QD=39.23;SB=-623.32 GT:AD:DP:GL:GQ 1/1:0,44:43:-176.21,-12.95,-0.01:99 +chr1 4027907 rs4654409 G A 268.91 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.85;MQ0=0;OQ=2188.75;QD=36.48;SB=-1120.98 GT:AD:DP:GL:GQ 1/1:0,60:57:-222.49,-17.18,-0.03:99 +chr1 4028014 rs10915398 T C 85.36 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.65;MQ0=0;OQ=1826.56;QD=33.83;SB=-678.24 GT:AD:DP:GL:GQ 1/1:0,54:52:-186.26,-15.66,-0.02:99 +chr1 4028230 rs10753357 A C 280.70 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.61;MQ0=0;OQ=1933.90;QD=32.78;SB=-901.67 GT:AD:DP:GL:GQ 1/1:0,59:56:-196.99,-16.87,-0.02:99 +chr1 4028383 rs10753358 C A 101.29 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=2;HaplotypeScore=0.96;MQ=59.50;MQ0=0;OQ=3292.23;QD=35.40;SB=-1450.96 GT:AD:DP:GL:GQ 1/1:0,93:90:-328.22,-27.11,-0.03:99 +chr1 4028555 rs10915400 C T 609.81 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2231.72;QD=39.15;SB=-1113.00 GT:AD:DP:GL:GQ 1/1:0,57:57:-226.78,-17.18,-0.02:99 +chr1 4028627 rs11586513 G A 570.71 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2205.25;QD=39.38;SB=-957.37 GT:AD:DP:GL:GQ 1/1:0,56:55:-224.12,-16.57,-0.01:99 +chr1 4029107 rs17404781 C A 590.07 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2642.82;QD=36.71;SB=-848.25 GT:AD:DP:GL:GQ 1/1:0,72:72:-267.88,-21.68,-0.02:99 +chr1 4029794 rs4603097 A G 153.18 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=2799.69;QD=36.36;SB=-819.68 GT:AD:DP:GL:GQ 1/1:1,76:76:-283.57,-22.89,-0.02:99 +chr1 4030208 rs4130940 A G 693.73 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3003.68;QD=34.53;SB=-1360.53 GT:AD:DP:GL:GQ 1/1:0,87:86:-303.98,-25.91,-0.03:99 +chr1 4030429 rs4130941 T C 169.61 PASS AC=2;AF=1.00;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=60.00;MQ0=0;OQ=3432.78;QD=35.76;SB=-1689.36 GT:AD:DP:GL:GQ 1/1:0,96:95:-342.28,-28.61,-0.03:99 +chr1 4030544 rs4391636 T C 184.14 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2626.35;QD=31.27;SB=-1250.03 GT:AD:DP:GL:GQ 1/1:0,84:83:-266.29,-25.03,-0.07:99 +chr1 4030874 rs4262509 T C 686.40 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=2253.22;QD=36.34;SB=-816.67 GT:AD:DP:GL:GQ 1/1:0,62:62:-228.93,-18.68,-0.02:99 +chr1 4031041 rs4400586 C T 220 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=2740.70;QD=40.30;SB=-1397.85 GT:AD:DP:GL:GQ 1/1:0,68:68:-277.67,-20.48,-0.01:99 +chr1 4031109 rs7537141 A G 223.55 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.17;MQ=58.69;MQ0=0;OQ=2389.72;QD=33.66;SB=-1060.09 GT:AD:DP:GL:GQ 1/1:0,70:68:-242.58,-20.48,-0.02:99 +chr1 4031170 rs7537236 A G 284.86 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.42;MQ0=0;OQ=1865.29;QD=33.31;SB=-585.57 GT:AD:DP:GL:GQ 1/1:0,56:52:-190.13,-15.66,-0.02:99 +chr1 4031176 rs7537237 A G 151.85 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=58.47;MQ0=0;OQ=1912.22;QD=32.97;SB=-672.55 GT:AD:DP:GL:GQ 1/1:0,58:55:-194.84,-16.57,-0.03:99 +chr1 4031220 rs7532788 C T 294.77 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.01;MQ0=0;OQ=2323.83;QD=38.10;SB=-1060.94 GT:AD:DP:GL:GQ 1/1:0,60:59:-235.99,-17.78,-0.02:99 +chr1 4031586 rs3936238 A G 138.31 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=58.69;MQ0=0;OQ=2519.09;QD=35.48;SB=-1162.71 GT:AD:DP:GL:GQ 1/1:0,71:71:-255.52,-21.39,-0.03:99 +chr1 4031878 rs9628649 C T 644.41 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.66;MQ0=0;OQ=2284.52;QD=38.72;SB=-825.09 GT:AD:DP:GL:GQ 1/1:0,59:58:-232.06,-17.48,-0.02:99 +chr1 4031986 rs9628650 G T 130.41 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=59.09;MQ0=0;OQ=2689.72;QD=35.39;SB=-1301.17 GT:AD:DP:GL:GQ 1/1:0,75:74:-272.58,-22.29,-0.02:99 +chr1 4032433 rs7529548 G C 483.28 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=2621.92;QD=40.34;SB=-1086.06 GT:AD:DP:GL:GQ 1/1:0,65:62:-265.80,-18.69,-0.02:99 +chr1 4032637 rs7538658 C T 720.56 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2747.15;QD=39.25;SB=-1233.63 GT:AD:DP:GL:GQ 1/1:0,70:70:-278.33,-21.09,-0.03:99 +chr1 4032742 rs7529853 G C 195.26 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.01;HRun=0;HaplotypeScore=1.43;MQ=59.67;MQ0=0;OQ=2970.07;QD=42.43;SB=-1256.98 GT:AD:DP:GL:GQ 1/1:0,69:70:-300.61,-20.79,-0.02:99 +chr1 4032815 rs10157040 T G 55.91 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.79;MQ=60.00;MQ0=0;OQ=2073.63;QD=33.99;SB=-743.38 GT:AD:DP:GL:GQ 1/1:0,61:60:-210.97,-18.07,-0.02:99 +chr1 4032895 rs60405213 A G 332.98 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=1606.75;QD=29.75;SB=-645.91 GT:AD:DP:GL:GQ 1/1:0,54:50:-164.30,-15.08,-0.04:99 +chr1 4032956 rs10157057 T C 590.98 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=1852.28;QD=34.95;SB=-804.30 GT:AD:DP:GL:GQ 1/1:0,53:53:-188.83,-15.97,-0.02:99 +chr1 4033505 . A T 38.74 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=20;HaplotypeScore=16.08;MQ=50.01;MQ0=1;QD=0.73;SB=62.20 GT:AD:DP:GL:GQ 0/1:43,10:38:-18.61,-11.45,-119.32:71.58 +chr1 4035925 rs6686087 G A 676.98 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=1910.92;QD=36.06;SB=-777.68 GT:AD:DP:GL:GQ 1/1:0,53:52:-194.71,-15.68,-0.03:99 +chr1 4036210 rs7553013 A G 89.18 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=1455.02;QD=35.49;SB=-567.89 GT:AD:DP:GL:GQ 1/1:0,41:41:-149.10,-12.35,-0.01:99 +chr1 4037078 rs6671404 G A 595.18 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=49.26;MQ0=0;OQ=2338.43;QD=39.63;SB=-1084.95 GT:AD:DP:GL:GQ 1/1:0,59:59:-237.45,-17.77,-0.02:99 +chr1 4037233 . C T 0.09 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=10.47;MQ=23.53;MQ0=14;OQ=386.45;QD=7.43;SB=-174.70 GT:AD:DP:GL:GQ 0/1:24,28:16:-46.75,-4.82,-13.21:83.85 +chr1 4037300 rs12731949 G A 33.47 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=10.93;MQ=13.10;MQ0=15;QD=0.96;SB=-6.99 GT:AD:DP:GL:GQ 0/1:26,6:3:-7.53,-0.90,-3.57:26.65 +chr1 4037316 . A G 19.58 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=10.60;MQ0=15;QD=0.68;SB=-10.00 GT:AD:DP:GL:GQ 0/1:25,4:3:-6.14,-0.91,-2.76:18.51 +chr1 4037317 rs12747176 C T 33.48 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=4.32;MQ=10.78;MQ0=15;QD=1.20;SB=-10.00 GT:AD:DP:GL:GQ 0/1:25,3:3:-7.53,-0.90,-3.30:23.93 +chr1 4037349 rs55974954 C T 4.01 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=15.25;MQ0=10;OQ=78.13;QD=3.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:11,9:5:-12.60,-1.51,-5.79:42.85 +chr1 4037373 . C T 49.25 HARD_TO_VALIDATE;LowQual;SnpCluster AC=2;AF=1.00;AN=2;DP=23;Dels=0.09;HRun=0;HaplotypeScore=5.10;MQ=12.43;MQ0=14;QD=2.14;SB=-10.00 GT:AD:DP:GL:GQ 1/1:17,4:2:-8.33,-0.60,-0.00:6.02 +chr1 4037374 rs58910132 A G 67.17 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.10;HRun=0;HaplotypeScore=2.46;MQ=12.64;MQ0=13;QD=3.20;SB=-10.00 GT:AD:DP:GL:GQ 1/1:14,5:3:-10.21,-0.90,-0.00:9.03 +chr1 4037375 . C T 89.13 HARD_TO_VALIDATE;SnpCluster AC=2;AF=1.00;AN=2;DP=21;Dels=0.10;HRun=0;HaplotypeScore=2.62;MQ=12.64;MQ0=13;QD=4.24;SB=-10.00 GT:AD:DP:GL:GQ 1/1:14,5:3:-12.40,-0.90,-0.00:9.03 +chr1 4037523 . C T 36.25 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=8.14;MQ=8.07;MQ0=27;QD=0.91;SB=-10.00 GT:AD:DP:GL:GQ 0/1:35,5:3:-7.81,-0.90,-3.47:25.65 +chr1 4037532 . G A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=7.98;MQ=8.93;MQ0=30;OQ=75.12;QD=1.67;SB=-10.00 GT:AD:DP:GL:GQ 0/1:32,13:5:-12.30,-1.51,-6.19:46.86 +chr1 4037589 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=30.55;MQ=12.67;MQ0=42;OQ=141.32;QD=1.74;SB=-10.00 GT:AD:DP:GL:GQ 0/1:62,18:18:-22.84,-5.42,-40.02:99 +chr1 4037590 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=31.66;MQ=13.12;MQ0=42;OQ=99.34;QD=1.18;SB=-10.00 GT:AD:DP:GL:GQ 0/1:65,14:18:-18.65,-5.43,-43.06:99 +chr1 4037755 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=10.80;MQ=28.57;MQ0=9;OQ=123.11;QD=4.25;SB=-10.00 GT:AD:DP:GL:GQ 0/1:16,13:15:-20.11,-4.52,-34.90:99 +chr1 4037764 . G A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=27.02;MQ0=10;OQ=406.03;QD=10.68;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,21:18:-49.31,-5.43,-18.48:99 +chr1 4037797 . G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=82;Dels=0.00;HRun=1;HaplotypeScore=2.36;MQ=25.37;MQ0=16;OQ=242.41;QD=2.96;SB=-0.99 GT:AD:DP:GL:GQ 0/1:69,13:49:-42.29,-14.76,-143.27:99 +chr1 4037813 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=30.43;MQ=23.50;MQ0=19;OQ=796.43;QD=8.38;SB=2.04 GT:AD:DP:GL:GQ 0/1:48,46:55:-99.50,-16.57,-97.10:99 +chr1 4037822 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=126;Dels=0.00;HRun=0;HaplotypeScore=35.10;MQ=23.24;MQ0=31;OQ=606.69;QD=4.81;SB=-57.33 GT:AD:DP:GL:GQ 0/1:70,54:63:-82.95,-19.00,-147.74:99 +chr1 4037843 rs61768802 C A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.00;HRun=1;HaplotypeScore=17.92;MQ=21.78;MQ0=58;OQ=417.65;QD=2.32;SB=-34.91 GT:AD:DP:GL:GQ 0/1:148,32:87:-71.25,-26.21,-246.67:99 +chr1 4037880 rs61768803 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=196;Dels=0.00;HRun=0;HaplotypeScore=29.31;MQ=22.28;MQ0=61;OQ=120.84;QD=0.62;SB=11.02 GT:AD:DP:GL:GQ 0/1:165,26:69:-36.22,-20.85,-175.88:99 +chr1 4037929 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=2.77;MQ=21.90;MQ0=34;OQ=107.87;QD=1.14;SB=35.15 GT:AD:DP:GL:GQ 0/1:76,17:46:-27.95,-13.88,-137.64:99 +chr1 4037943 . C T 85.40 PASS AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=21.61;MQ0=16;OQ=809.30;QD=13.95;SB=-392.58 GT:AD:DP:GL:GQ 0/1:14,44:31:-93.56,-9.34,-20.82:99 +chr1 4037953 . T C 0.02 FDRtranche1.00to2.00 AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;HRun=3;HaplotypeScore=11.12;MQ=21.57;MQ0=12;OQ=534.72;QD=14.07;SB=-137.10 GT:AD:DP:GL:GQ 1/1:2,36:20:-60.44,-6.03,-3.38:26.46 +chr1 4037971 . G A 35.49 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=12;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=11.71;MQ0=7;QD=2.96;SB=-7.00 GT:AD:DP:GL:GQ 0/1:2,10:3:-7.73,-0.90,-2.97:20.65 +chr1 4038007 . C T 11.96 PASS AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=24.37;MQ0=17;OQ=478.18;QD=12.58;SB=-0.67 GT:AD:DP:GL:GQ 1/1:9,29:15:-54.99,-4.52,-3.70:8.18 +chr1 4038085 . G A 6.73 PASS AC=2;AF=1.00;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=25.54;MQ0=21;OQ=1434.12;QD=19.65;SB=-222.29 GT:AD:DP:GL:GQ 1/1:0,70:37:-147.01,-11.15,-0.01:99 +chr1 4038095 . A C 37.18 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=2;HaplotypeScore=5.05;MQ=31.28;MQ0=12;QD=0.48;SB=35.10 GT:AD:DP:GL:GQ 0/1:67,11:51:-22.37,-15.37,-153.89:70.01 +chr1 4038119 rs61768805 A G 52.49 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=34.39;MQ0=8;OQ=2201.59;QD=25.60;SB=-880.89 GT:AD:DP:GL:GQ 1/1:0,86:64:-223.78,-19.28,-0.04:99 +chr1 4038137 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=141;Dels=0.00;HRun=1;HaplotypeScore=16.06;MQ=35.46;MQ0=14;OQ=344.80;QD=2.45;SB=-97.28 GT:AD:DP:GL:GQ 0/1:105,36:95:-66.41,-28.65,-282.14:99 +chr1 4038181 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=266;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=35.03;MQ0=15;OQ=1093.66;QD=4.11;SB=-524.11 GT:AD:DP:GL:GQ 0/1:186,80:195:-171.41,-58.76,-524.00:99 +chr1 4038248 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=280;Dels=0.00;HRun=0;HaplotypeScore=30.85;MQ=29.46;MQ0=44;OQ=1065.01;QD=3.80;SB=-230.16 GT:AD:DP:GL:GQ 0/1:155,104:139:-156.85,-47.07,-312.49:99 +chr1 4038269 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=221;Dels=0.00;HRun=2;HaplotypeScore=13.90;MQ=27.15;MQ0=44;OQ=427.47;QD=1.93;SB=-154.75 GT:AD:DP:GL:GQ 0/1:158,62:110:-79.18,-33.15,-296.78:99 +chr1 4038306 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=30.95;MQ=24.15;MQ0=24;OQ=80.75;QD=0.71;SB=17.44 GT:AD:DP:GL:GQ 0/1:88,21:54:-27.64,-16.28,-152.20:99 +chr1 4038311 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=0;HaplotypeScore=30.17;MQ=23.18;MQ0=20;OQ=320.40;QD=3.56;SB=-113.10 GT:AD:DP:GL:GQ 0/1:60,30:46:-49.20,-13.87,-108.56:99 +chr1 4038321 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=3;HaplotypeScore=15.26;MQ=23.68;MQ0=14;OQ=766.53;QD=12.99;SB=-327.28 GT:AD:DP:GL:GQ 0/1:10,49:31:-89.28,-9.34,-16.69:73.43 +chr1 4038334 . G A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.69;MQ=25.40;MQ0=9;OQ=78.94;QD=1.49;SB=-27.72 GT:AD:DP:GL:GQ 0/1:40,11:25:-21.55,-10.37,-63.16:99 +chr1 4038397 . A G 17.54 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=29.53;MQ0=4;OQ=326.31;QD=7.42;SB=-58.84 GT:AD:DP:GL:GQ 0/1:24,20:28:-44.35,-8.44,-57.72:99 +chr1 4038422 rs61768806 G A 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=18.20;MQ=33.84;MQ0=4;OQ=183.71;QD=3.40;SB=-62.31 GT:AD:DP:GL:GQ 0/1:35,13:24:-31.46,-9.80,-50.09:99 +chr1 4038450 rs9426493 G A 0.12 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=7.50;MQ=40.53;MQ0=7;OQ=257.95;QD=3.31;SB=38.10 GT:AD:DP:GL:GQ 0/1:50,27:46:-42.95,-13.87,-108.04:99 +chr1 4038485 . T C 49.84 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=1;HaplotypeScore=36.99;MQ=38.79;MQ0=13;QD=0.38;SB=-42.38 GT:AD:DP:GL:GQ 0/1:107,23:79:-32.08,-23.81,-273.26:82.67 +chr1 4038495 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=136;Dels=0.00;HRun=3;HaplotypeScore=26.37;MQ=38.36;MQ0=11;OQ=110.49;QD=0.81;SB=81.70 GT:AD:DP:GL:GQ 0/1:101,35:77:-37.55,-23.22,-250.69:99 +chr1 4038559 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=2;HaplotypeScore=4.40;MQ=37.40;MQ0=14;OQ=181.94;QD=1.28;SB=76.72 GT:AD:DP:GL:GQ 0/1:114,27:102:-52.21,-30.74,-302.69:99 +chr1 4038595 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=10.57;MQ=44.92;MQ0=10;OQ=118.91;QD=1.67;SB=44.58 GT:AD:DP:GL:GQ 0/1:49,22:52:-30.86,-15.68,-162.15:99 +chr1 4038920 rs12240075 G A 506.65 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.13;MQ0=0;OQ=3029.69;QD=39.35;SB=-1486.40 GT:AD:DP:GL:GQ 1/1:0,77:75:-306.57,-22.59,-0.02:99 +chr1 4039098 rs4073835 G A 496.74 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2305.48;QD=39.08;SB=-997.03 GT:AD:DP:GL:GQ 1/1:0,59:59:-234.15,-17.78,-0.02:99 +chr1 4039791 rs4639725 C T 236.18 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.86;MQ=59.67;MQ0=0;OQ=2672.94;QD=38.18;SB=-1315.36 GT:AD:DP:GL:GQ 1/1:0,70:69:-270.90,-20.79,-0.02:99 +chr1 4039890 rs4436359 C A 272.88 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=60.00;MQ0=0;OQ=1804.54;QD=34.70;SB=-797.85 GT:AD:DP:GL:GQ 1/1:1,51:51:-184.06,-15.36,-0.02:99 +chr1 4040736 rs6684922 G A 149.31 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=2464.15;QD=39.74;SB=-984.31 GT:AD:DP:GL:GQ 1/1:0,62:61:-250.01,-18.37,-0.01:99 +chr1 4041212 rs7418376 A G 9.41 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=4.36;MQ=59.69;MQ0=0;OQ=2587.00;QD=34.49;SB=-1318.64 GT:AD:DP:GL:GQ 1/1:0,75:71:-262.30,-21.38,-0.02:99 +chr1 4041774 rs6657076 T C 524.19 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.94;MQ0=0;OQ=2268.81;QD=30.25;SB=-1070.20 GT:AD:DP:GL:GQ 1/1:0,75:71:-230.53,-21.41,-0.06:99 +chr1 4045735 rs10915422 A C 14.87 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=4.42;MQ=59.68;MQ0=0;OQ=2455.12;QD=33.63;SB=-728.83 GT:AD:DP:GL:GQ 1/1:0,73:71:-249.12,-21.38,-0.02:99 +chr1 4045888 rs10915423 A C 727.77 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2031.28;QD=35.02;SB=-998.12 GT:AD:DP:GL:GQ 1/1:0,58:58:-206.73,-17.47,-0.02:99 +chr1 4046948 rs10915425 T G 80.45 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=53.47;MQ0=0;OQ=1869.59;QD=31.69;SB=-736.37 GT:AD:DP:GL:GQ 1/1:0,59:55:-190.57,-16.57,-0.02:99 +chr1 4046996 rs55774050 C G 2240.61 Indel AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=9.46;MQ=51.11;MQ0=0;QD=43.09;SB=-978.74 GT:AD:DP:GL:GQ 1/1:0,52:52:-227.66,-15.67,-0.01:99 +chr1 4047821 rs11578552 T C 402.68 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2100.45;QD=30.89;SB=-846.51 GT:AD:DP:GL:GQ 1/1:0,68:66:-213.69,-19.91,-0.06:99 +chr1 4047883 rs11577344 C T 490.32 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1935.40;QD=37.95;SB=-660.87 GT:AD:DP:GL:GQ 1/1:0,51:48:-197.13,-14.46,-0.01:99 +chr1 4049164 rs7411603 A G 3.63 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=6.69;MQ=58.71;MQ0=0;OQ=1270.28;QD=27.03;SB=-493.17 GT:AD:DP:GL:GQ 1/1:0,47:41:-130.65,-12.36,-0.04:99 +chr1 4050387 rs10753365 G A 99.83 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=58.61;MQ0=0;OQ=1534.51;QD=32.65;SB=-464.08 GT:AD:DP:GL:GQ 1/1:0,46:42:-157.07,-12.67,-0.03:99 +chr1 4051611 rs4548406 T C 78.22 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1346.57;QD=28.65;SB=-544.85 GT:AD:DP:GL:GQ 1/1:0,47:44:-138.29,-13.28,-0.05:99 +chr1 4051999 rs12123119 C T 624.91 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2169.89;QD=37.41;SB=-1044.39 GT:AD:DP:GL:GQ 1/1:0,58:55:-220.59,-16.57,-0.02:99 +chr1 4052066 rs4654410 C T 678.96 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=2087.99;QD=37.96;SB=-873.17 GT:AD:DP:GL:GQ 1/1:0,55:53:-212.40,-15.97,-0.02:99 +chr1 4052788 rs4481820 C A 313.17 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.81;MQ0=0;OQ=1188.08;QD=18.86;SB=-612.83 GT:AD:DP:GL:GQ 0/1:26,37:61:-140.47,-18.38,-73.47:99 +chr1 4052947 rs6676961 T G 272.74 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=60.00;MQ0=0;OQ=1401.56;QD=15.75;SB=-713.67 GT:AD:DP:GL:GQ 0/1:39,50:87:-169.64,-26.20,-144.08:99 +chr1 4053067 rs12125719 A G 101.01 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.17;MQ0=0;OQ=1483.09;QD=29.08;SB=-606.95 GT:AD:DP:GL:GQ 1/1:0,51:48:-151.94,-14.48,-0.05:99 +chr1 4053090 rs12125725 A G 83.74 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.17;MQ0=0;OQ=1585.81;QD=31.09;SB=-493.18 GT:AD:DP:GL:GQ 1/1:0,51:49:-162.20,-14.77,-0.03:99 +chr1 4053122 rs12126649 T C 176.61 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.71;MQ=59.24;MQ0=0;OQ=907.97;QD=14.88;SB=-331.31 GT:AD:DP:GL:GQ 0/1:25,36:59:-111.87,-17.79,-96.53:99 +chr1 4055170 rs12033210 T C 0.60 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=1.74;MQ=28.53;MQ0=2;OQ=209.19;QD=4.65;SB=-102.57 GT:AD:DP:GL:GQ 0/1:32,13:39:-35.96,-11.75,-110.64:99 +chr1 4056038 rs10799198 G A 260.47 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.90;MQ=58.67;MQ0=0;OQ=782.28;QD=15.96;SB=-386.17 GT:AD:DP:GL:GQ 0/1:25,24:47:-95.68,-14.17,-75.73:99 +chr1 4057058 rs4600014 A G 442.87 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=917.69;QD=13.70;SB=-389.30 GT:AD:DP:GL:GQ 0/1:34,33:66:-114.93,-19.88,-136.81:99 +chr1 4057633 rs4361964 G C 120.54 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.73;MQ=59.22;MQ0=0;OQ=837.80;QD=15.51;SB=-437.88 GT:AD:DP:GL:GQ 0/1:29,25:53:-103.04,-15.97,-126.00:99 +chr1 4057702 rs4351611 C T 297.44 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.56;MQ0=0;OQ=594.05;QD=11.21;SB=-284.78 GT:AD:DP:GL:GQ 0/1:33,20:53:-78.67,-15.98,-105.42:99 +chr1 4057917 . A T 65.58 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.62;MQ0=0;OQ=752.30;QD=12.54;SB=-170.72 GT:AD:DP:GL:GQ 0/1:33,27:58:-95.98,-17.47,-122.23:99 +chr1 4058815 rs10915428 G T 369.02 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.39;MQ0=0;OQ=1224.65;QD=16.11;SB=-630.74 GT:AD:DP:GL:GQ 0/1:35,41:75:-148.34,-22.59,-115.71:99 +chr1 4059239 rs10799199 C T 251.96 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.66;MQ0=0;OQ=1243.57;QD=18.84;SB=-304.82 GT:AD:DP:GL:GQ 0/1:29,37:64:-146.92,-19.28,-100.42:99 +chr1 4059378 . C T 11.57 PASS AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=3;HaplotypeScore=0.47;MQ=59.47;MQ0=0;OQ=1236.26;QD=14.72;SB=-551.55 GT:AD:DP:GL:GQ 0/1:45,38:82:-151.61,-24.70,-168.36:99 +chr1 4060338 rs10799200 T C 170.59 PASS AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=152.75;QD=7.64;SB=-10.00 GT:AD:DP:GL:GQ 0/1:13,7:19:-24.28,-5.72,-48.27:99 +chr1 4064782 rs61768818 G A 481.48 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.07;MQ0=0;OQ=848.15;QD=13.90;SB=-350.47 GT:AD:DP:GL:GQ 0/1:34,27:59:-105.87,-17.77,-118.54:99 +chr1 4066674 rs12032257 C T 294.19 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=59.36;MQ0=0;OQ=916.01;QD=14.09;SB=-410.80 GT:AD:DP:GL:GQ 0/1:35,30:64:-114.18,-19.29,-113.47:99 +chr1 4067283 . T C 0.61 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=2;HaplotypeScore=4.39;MQ=59.62;MQ0=0;OQ=557.04;QD=9.13;SB=-241.90 GT:AD:DP:GL:GQ 0/1:35,25:58:-76.48,-17.49,-133.72:99 +chr1 4067926 rs7542313 A G 387.57 PASS AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=220.94;QD=10.52;SB=-100.82 GT:AD:DP:GL:GQ 0/1:11,10:19:-31.10,-5.72,-40.90:99 +chr1 4075727 . C T 158.87 PASS AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.34;MQ=59.67;MQ0=0;OQ=1143.65;QD=16.34;SB=-503.75 GT:AD:DP:GL:GQ 0/1:35,35:66:-137.54,-19.89,-102.02:99 +chr1 4075966 rs6670920 T C 606.24 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=1104.32;QD=15.13;SB=-452.80 GT:AD:DP:GL:GQ 0/1:30,43:71:-135.11,-21.40,-121.92:99 +chr1 4077630 rs4654486 G A 691.51 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2711.47;QD=39.87;SB=-1087.95 GT:AD:DP:GL:GQ 1/1:0,68:68:-274.75,-20.48,-0.02:99 +chr1 4078163 rs10737402 T C 504.16 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=530.04;QD=10.82;SB=-231.26 GT:AD:DP:GL:GQ 0/1:26,23:49:-71.06,-14.78,-100.24:99 +chr1 4080498 rs12042946 T C 249.02 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=60.30;MQ0=0;OQ=891.53;QD=12.56;SB=-237.45 GT:AD:DP:GL:GQ 0/1:37,34:69:-113.22,-20.78,-148.64:99 +chr1 4080702 rs12040805 C T 139.94 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.60;MQ0=0;OQ=776.81;QD=15.54;SB=-108.61 GT:AD:DP:GL:GQ 0/1:26,24:46:-94.83,-13.87,-71.68:99 +chr1 4081256 rs10753367 T C 35.67 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=3;HaplotypeScore=2.04;MQ=59.74;MQ0=0;OQ=1167.96;QD=12.98;SB=-513.88 GT:AD:DP:GL:GQ 0/1:48,42:88:-146.59,-26.51,-188.24:99 +chr1 4081433 rs10799203 T G 17.84 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=59.59;MQ0=0;OQ=328.89;QD=7.15;SB=-123.86 GT:AD:DP:GL:GQ 0/1:29,17:43:-49.13,-12.95,-102.00:99 +chr1 4082645 rs4400585 G T 491.60 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=492.73;QD=10.71;SB=-210.53 GT:AD:DP:GL:GQ 0/1:27,19:44:-65.81,-13.26,-82.00:99 +chr1 4082866 rs10915437 A G 75.21 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=4.59;MQ=58.36;MQ0=0;OQ=891.90;QD=12.56;SB=-289.16 GT:AD:DP:GL:GQ 0/1:37,34:68:-112.97,-20.49,-138.67:99 +chr1 4083359 rs56090673 C T 320.01 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1009.69;QD=17.11;SB=-451.46 GT:AD:DP:GL:GQ 0/1:27,32:58:-121.73,-17.48,-93.77:99 +chr1 4083978 rs7531421 A G 116.24 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=57.42;MQ0=0;OQ=435.48;QD=7.02;SB=-215.25 GT:AD:DP:GL:GQ 0/1:41,21:60:-64.91,-18.08,-162.54:99 +chr1 4084862 rs6675734 C T 47.52 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=5.09;MQ=59.20;MQ0=0;OQ=1105.86;QD=19.07;SB=-554.64 GT:AD:DP:GL:GQ 0/1:25,33:57:-131.05,-17.18,-82.44:99 +chr1 4084986 rs10753368 A G 566.85 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1198.41;QD=14.10;SB=-565.61 GT:AD:DP:GL:GQ 0/1:44,41:83:-148.13,-25.00,-168.94:99 +chr1 4085630 rs6679136 C T 24.06 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=4.32;MQ=58.42;MQ0=0;OQ=804.43;QD=14.36;SB=-252.24 GT:AD:DP:GL:GQ 0/1:29,27:53:-99.70,-15.97,-99.87:99 +chr1 4085663 rs6669476 G A 136.10 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.26;MQ=57.81;MQ0=0;OQ=833.61;QD=13.89;SB=-171.20 GT:AD:DP:GL:GQ 0/1:32,27:56:-103.51,-16.87,-106.04:99 +chr1 4086169 rs6426389 C T 138.99 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.83;MQ=59.69;MQ0=0;OQ=1183.25;QD=19.72;SB=-609.44 GT:AD:DP:GL:GQ 0/1:26,34:60:-139.68,-18.07,-94.16:99 +chr1 4086333 rs6663976 C G 599.30 PASS AC=2;AF=1.00;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=3962.79;QD=44.03;SB=-1451.88 GT:AD:DP:GL:GQ 1/1:0,90:89:-395.28,-26.81,-0.02:99 +chr1 4087812 rs4654487 T C 259.04 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=59.52;MQ0=0;OQ=1480.85;QD=30.85;SB=-766.73 GT:AD:DP:GL:GQ 1/1:0,48:47:-151.71,-14.17,-0.04:99 +chr1 4089403 . G C 16.75 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.80;MQ=58.74;MQ0=0;QD=0.45;SB=53.21 GT:AD:DP:GL:GQ 0/1:27,10:26:-12.79,-7.84,-102.04:49.49 +chr1 4089489 rs7536041 T C 90.49 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=59.19;MQ0=0;OQ=812.10;QD=15.62;SB=-146.31 GT:AD:DP:GL:GQ 0/1:23,29:51:-99.86,-15.37,-93.49:99 +chr1 4090545 rs4282783 T G 725.47 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2332.11;QD=35.34;SB=-970.80 GT:AD:DP:GL:GQ 1/1:0,66:66:-236.81,-19.88,-0.02:99 +chr1 4091584 rs4654488 A T 219.84 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=2.30;MQ=60.00;MQ0=0;OQ=743.21;QD=16.52;SB=-370.44 GT:AD:DP:GL:GQ 0/1:20,25:44:-90.86,-13.25,-75.80:99 +chr1 4092168 rs10915441 C G 2.97 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=4;HaplotypeScore=3.62;MQ=59.69;MQ0=0;OQ=1389.48;QD=18.78;SB=-645.48 GT:AD:DP:GL:GQ 0/1:35,39:69:-163.06,-20.83,-116.77:99 +chr1 4092567 rs10915442 A G 394.78 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.42;MQ0=0;OQ=572.04;QD=14.30;SB=-311.22 GT:AD:DP:GL:GQ 0/1:18,22:39:-72.24,-11.76,-67.58:99 +chr1 4093270 rs10799206 C G 674.75 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.42;MQ0=0;OQ=2045.47;QD=38.59;SB=-902.40 GT:AD:DP:GL:GQ 1/1:0,52:50:-208.16,-15.07,-0.02:99 +chr1 4093286 rs12409803 G A 414.64 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=57.03;MQ0=0;OQ=773.71;QD=14.33;SB=-322.45 GT:AD:DP:GL:GQ 0/1:28,26:51:-96.03,-15.38,-79.04:99 +chr1 4093324 rs10915443 G C 254.64 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=58.02;MQ0=0;OQ=1430.72;QD=20.15;SB=-674.45 GT:AD:DP:GL:GQ 0/1:30,40:69:-167.15,-20.79,-134.28:99 +chr1 4093733 rs6693173 A G 464.34 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1381.36;QD=28.78;SB=-644.93 GT:AD:DP:GL:GQ 1/1:0,48:45:-141.76,-13.57,-0.04:99 +chr1 4094457 rs4131506 A C 340.66 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.60;MQ0=0;OQ=704.94;QD=12.15;SB=-316.99 GT:AD:DP:GL:GQ 0/1:32,26:58:-91.25,-17.47,-120.43:99 +chr1 4094660 rs4131508 A G 571.17 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=1332.71;QD=17.31;SB=-634.89 GT:AD:DP:GL:GQ 0/1:33,44:77:-159.75,-23.19,-134.55:99 +chr1 4094683 rs4630099 A G 443.98 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1288.63;QD=16.31;SB=-670.63 GT:AD:DP:GL:GQ 0/1:36,43:77:-155.34,-23.19,-143.15:99 +chr1 4095397 rs10915444 T C 1.76 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=8.82;MQ=58.53;MQ0=0;OQ=789.45;QD=10.25;SB=-380.13 GT:AD:DP:GL:GQ 0/1:49,28:72:-103.91,-21.68,-179.32:99 +chr1 4095558 rs35986531 G A 271.33 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.49;MQ=56.64;MQ0=0;OQ=1336.75;QD=16.71;SB=-522.69 GT:AD:DP:GL:GQ 0/1:36,44:75:-159.55,-22.59,-133.47:99 +chr1 4095815 rs12118815 A T 0.50 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=1;HaplotypeScore=13.10;MQ=57.70;MQ0=3;OQ=1249.48;QD=13.88;SB=-570.06 GT:AD:DP:GL:GQ 0/1:44,46:80:-152.33,-24.10,-146.70:99 +chr1 4095919 . A T 39.64 LowQual AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=51.56;MQ0=5;QD=0.50;SB=-37.91 GT:AD:DP:GL:GQ 0/1:71,9:66:-27.13,-19.88,-223.94:72.48 +chr1 4096225 . A G 48.26 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.44;MQ=52.24;MQ0=7;QD=0.68;SB=74.28 GT:AD:DP:GL:GQ 0/1:64,7:63:-27.09,-18.98,-229.53:81.10 +chr1 4096236 . T G 0.06 PASS AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=54.07;MQ0=3;OQ=91.64;QD=1.31;SB=86.24 GT:AD:DP:GL:GQ 0/1:61,9:66:-32.33,-19.88,-208.22:99 +chr1 4096240 . A T 0.08 PASS AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=53.91;MQ0=2;OQ=161.77;QD=2.16;SB=86.29 GT:AD:DP:GL:GQ 0/1:64,11:72:-41.14,-21.68,-231.71:99 +chr1 4096257 . A T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.00;MQ=53.32;MQ0=2;OQ=207.48;QD=2.56;SB=92.31 GT:AD:DP:GL:GQ 0/1:68,13:79:-47.82,-23.79,-251.49:99 +chr1 4096278 . A G 232.76 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=27.32;MQ=52.46;MQ0=1;QD=2.68;SB=98.35 GT:AD:DP:GL:GQ 0/1:72,15:85:-52.16,-25.60,-288.15:99 +chr1 4096286 . G A 106.04 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=90;Dels=0.00;HRun=1;HaplotypeScore=48.93;MQ=51.56;MQ0=1;QD=1.18;SB=98.32 GT:AD:DP:GL:GQ 0/1:78,12:85:-39.49,-25.60,-276.62:99 +chr1 4096288 rs34088827 G A 955.67 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=1;HaplotypeScore=48.46;MQ=51.26;MQ0=1;QD=10.62;SB=-379.33 GT:AD:DP:GL:GQ 0/1:57,33:88:-125.36,-26.51,-207.05:99 +chr1 4096294 . A T 86.31 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=1;HaplotypeScore=32.32;MQ=50.46;MQ0=1;QD=0.97;SB=89.30 GT:AD:DP:GL:GQ 0/1:73,16:80:-36.01,-24.10,-264.64:99 +chr1 4096606 rs28726337 A G 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=2;HaplotypeScore=13.44;MQ=43.57;MQ0=1;OQ=262.51;QD=2.76;SB=-123.92 GT:AD:DP:GL:GQ 0/1:75,20:86:-55.44,-25.91,-287.10:99 +chr1 4096617 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=1;HaplotypeScore=34.91;MQ=42.33;MQ0=1;OQ=1160.59;QD=10.01;SB=-606.06 GT:AD:DP:GL:GQ 0/1:70,46:109:-152.17,-32.83,-258.54:99 +chr1 4096620 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=123;Dels=0.01;HRun=0;HaplotypeScore=30.11;MQ=42.25;MQ0=1;OQ=989.14;QD=8.04;SB=-388.23 GT:AD:DP:GL:GQ 0/1:72,50:106:-134.12,-31.93,-263.47:99 +chr1 4096638 rs28412783 C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=181;Dels=0.02;HRun=0;HaplotypeScore=64.64;MQ=40.70;MQ0=1;OQ=1178.07;QD=6.51;SB=-446.63 GT:AD:DP:GL:GQ 0/1:123,47:169:-194.38,-73.29,-545.37:99 +chr1 4096655 rs61768832 A G 321.42 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=228;Dels=0.00;HRun=1;HaplotypeScore=261.82;MQ=41.93;MQ0=0;QD=1.41;SB=-157.54 GT:AD:DP:GL:GQ 0/1:199,29:224:-102.90,-67.48,-791.83:99 +chr1 4096678 . T G 1342.80 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=236;Dels=0.00;HRun=0;HaplotypeScore=216.99;MQ=43.01;MQ0=0;QD=5.69;SB=-512.77 GT:AD:DP:GL:GQ 0/1:166,63:218:-227.86,-90.30,-587.53:99 +chr1 4096685 . A G 1626.24 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=239;Dels=0.00;HRun=1;HaplotypeScore=162.66;MQ=41.97;MQ0=0;QD=6.80;SB=-808.35 GT:AD:DP:GL:GQ 0/1:167,72:225:-233.68,-67.78,-652.24:99 +chr1 4096698 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=228;Dels=0.00;HRun=0;HaplotypeScore=76.98;MQ=42.62;MQ0=0;OQ=2269.48;QD=9.95;SB=-1066.45 GT:AD:DP:GL:GQ 0/1:129,90:219:-325.16,-94.93,-493.11:99 +chr1 4096706 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=1;HaplotypeScore=79.95;MQ=43.15;MQ0=0;OQ=1034.27;QD=4.50;SB=-170.01 GT:AD:DP:GL:GQ 0/1:185,45:223:-173.88,-67.17,-658.24:99 +chr1 4096718 rs61768834 G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=216;Dels=0.00;HRun=0;HaplotypeScore=38.48;MQ=44.61;MQ0=0;OQ=645.34;QD=2.99;SB=-265.93 GT:AD:DP:GL:GQ 0/1:168,32:157:-165.70,-97.89,-554.00:99 +chr1 4096731 . G A 559.62 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=179;Dels=0.00;HRun=1;HaplotypeScore=83.54;MQ=45.39;MQ0=0;QD=3.13;SB=44.95 GT:AD:DP:GL:GQ 0/1:150,29:155:-105.94,-46.69,-468.61:99 +chr1 4096732 rs61768835 A G 2251.43 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.00;HRun=2;HaplotypeScore=115.12;MQ=45.31;MQ0=0;QD=13.17;SB=-1083.79 GT:AD:DP:GL:GQ 0/1:80,91:158:-276.04,-47.61,-312.72:99 +chr1 4096736 rs61768836 A G 2066.81 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.02;HRun=0;HaplotypeScore=91.40;MQ=45.63;MQ0=0;QD=12.23;SB=-1029.89 GT:AD:DP:GL:GQ 0/1:85,81:160:-257.27,-47.30,-336.21:99 +chr1 4096755 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=129;Dels=0.00;HRun=1;HaplotypeScore=46.33;MQ=46.26;MQ0=0;OQ=201.55;QD=1.56;SB=65.52 GT:AD:DP:GL:GQ 0/1:112,17:113:-57.49,-34.05,-383.82:99 +chr1 4096759 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=124;Dels=0.00;HRun=0;HaplotypeScore=42.17;MQ=46.84;MQ0=0;OQ=310.94;QD=2.51;SB=-151.81 GT:AD:DP:GL:GQ 0/1:106,18:122:-71.13,-36.75,-367.88:99 +chr1 4096775 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=113;Dels=0.00;HRun=0;HaplotypeScore=30.95;MQ=47.51;MQ0=0;OQ=647.24;QD=5.73;SB=52.09 GT:AD:DP:GL:GQ 0/1:87,26:107:-100.24,-32.23,-298.38:99 +chr1 4096805 . A G 20.07 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=109;Dels=0.00;HRun=1;HaplotypeScore=14.94;MQ=48.07;MQ0=0;QD=0.18;SB=107.37 GT:AD:DP:GL:GQ 0/1:94,15:99:-35.11,-29.83,-355.50:52.86 +chr1 4096811 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=105;Dels=0.00;HRun=1;HaplotypeScore=14.56;MQ=47.07;MQ0=0;OQ=301.49;QD=2.87;SB=92.31 GT:AD:DP:GL:GQ 0/1:85,20:99:-63.26,-29.83,-325.00:99 +chr1 4096845 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=1;HaplotypeScore=27.21;MQ=46.78;MQ0=0;OQ=135.08;QD=1.34;SB=107.37 GT:AD:DP:GL:GQ 0/1:86,15:98:-46.31,-29.52,-344.47:99 +chr1 4096895 rs6702633 G A 282.98 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=48.03;MQ0=0;OQ=1209.14;QD=19.50;SB=-562.59 GT:AD:DP:GL:GQ 0/1:26,36:60:-142.27,-18.07,-91.55:99 +chr1 4097116 rs6663939 C T 575.23 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1353.52;QD=17.35;SB=-623.00 GT:AD:DP:GL:GQ 0/1:38,40:78:-162.13,-23.49,-140.27:99 +chr1 4097278 rs4408122 C T 90.17 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=3.55;MQ=60.00;MQ0=0;OQ=1285.61;QD=19.78;SB=-663.71 GT:AD:DP:GL:GQ 0/1:26,39:64:-151.13,-19.28,-94.25:99 +chr1 4097502 rs10915445 G A 15.47 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=4.76;MQ=58.14;MQ0=0;OQ=1551.73;QD=21.26;SB=-659.25 GT:AD:DP:GL:GQ 0/1:29,44:69:-179.24,-20.78,-91.34:99 +chr1 4097702 rs4233259 G A 393.71 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.88;MQ0=0;OQ=488.96;QD=11.64;SB=-238.49 GT:AD:DP:GL:GQ 0/1:23,19:39:-63.93,-11.75,-79.38:99 +chr1 4097847 rs4233260 A G 265.81 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=58.25;MQ0=0;OQ=841.80;QD=15.31;SB=-425.02 GT:AD:DP:GL:GQ 0/1:21,34:53:-103.45,-15.98,-81.47:99 +chr1 4098460 rs4654489 C T 575.94 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1233.62;QD=17.37;SB=-483.09 GT:AD:DP:GL:GQ 0/1:34,37:71:-148.05,-21.40,-108.91:99 +chr1 4098462 rs4654412 C G 408.58 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=1295.21;QD=18.24;SB=-423.31 GT:AD:DP:GL:GQ 0/1:36,35:70:-153.90,-21.10,-151.48:99 +chr1 4098561 rs4654490 T C 109.69 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=5.61;MQ=59.35;MQ0=0;OQ=707.20;QD=11.05;SB=-320.12 GT:AD:DP:GL:GQ 0/1:35,29:62:-92.69,-18.69,-135.70:99 +chr1 4098636 rs4654491 A T 298.65 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.55;MQ=58.32;MQ0=0;OQ=679.16;QD=12.81;SB=-348.54 GT:AD:DP:GL:GQ 0/1:28,25:51:-86.56,-15.36,-108.00:99 +chr1 4101675 rs4654492 C T 166.06 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=985.64;QD=17.92;SB=-310.22 GT:AD:DP:GL:GQ 0/1:24,31:53:-117.81,-15.96,-85.09:99 +chr1 4102203 rs10799207 G A 234.26 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=645.03;QD=15.36;SB=-340.37 GT:AD:DP:GL:GQ 0/1:22,20:41:-80.15,-12.36,-66.12:99 +chr1 4102678 rs7542208 A G 473.41 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.58;MQ0=0;OQ=945.73;QD=14.78;SB=-439.91 GT:AD:DP:GL:GQ 0/1:26,38:62:-116.54,-18.69,-104.23:99 +chr1 4102853 rs12143662 C T 77.17 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=2;HaplotypeScore=3.06;MQ=59.31;MQ0=0;OQ=653.08;QD=14.51;SB=-306.78 GT:AD:DP:GL:GQ 0/1:23,22:43:-81.54,-12.95,-84.16:99 +chr1 4103423 rs12096127 C T 146.81 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=3;HaplotypeScore=0.93;MQ=59.48;MQ0=0;OQ=1299.31;QD=16.24;SB=-452.94 GT:AD:DP:GL:GQ 0/1:42,38:79:-157.01,-23.79,-152.41:99 +chr1 4104350 . G A 39.75 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=0;HaplotypeScore=50.14;MQ=43.88;MQ0=0;QD=0.41;SB=41.13 GT:AD:DP:GL:GQ 0/1:55,43:59:-25.05,-17.79,-166.63:72.58 +chr1 4104372 . C A 158.64 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=134;Dels=0.00;HRun=1;HaplotypeScore=261.20;MQ=40.26;MQ0=0;QD=1.18;SB=50.16 GT:AD:DP:GL:GQ 0/1:118,16:102:-49.87,-30.72,-316.01:99 +chr1 4104378 . T C 1045.41 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=132;Dels=0.09;HRun=0;HaplotypeScore=252.28;MQ=39.40;MQ0=0;QD=7.92;SB=47.18 GT:AD:DP:GL:GQ 0/1:70,50:112:-140.05,-32.23,-268.85:99 +chr1 4104379 . G A 1387.27 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=131;Dels=0.09;HRun=0;HaplotypeScore=164.33;MQ=39.20;MQ0=0;QD=10.59;SB=44.10 GT:AD:DP:GL:GQ 0/1:65,54:109:-173.34,-31.33,-223.67:99 +chr1 4104399 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=192;Dels=0.00;HRun=0;HaplotypeScore=398.28;MQ=38.87;MQ0=2;OQ=296.43;QD=1.54;SB=-98.03 GT:AD:DP:GL:GQ 0/1:164,28:154:-79.31,-46.39,-472.12:99 +chr1 4104401 rs61768839 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=194;Dels=0.00;HRun=0;HaplotypeScore=419.03;MQ=39.00;MQ0=2;OQ=166.93;QD=0.86;SB=-91.09 GT:AD:DP:GL:GQ 0/1:156,37:153:-66.06,-46.09,-471.26:99 +chr1 4104420 rs56397723 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=252;Dels=0.01;HRun=1;HaplotypeScore=92.55;MQ=41.09;MQ0=3;OQ=4650.56;QD=18.45;SB=-702.42 GT:AD:DP:GL:GQ 0/1:91,159:212:-464.06,-63.56,-317.29:99 +chr1 4104448 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=303;Dels=0.00;HRun=1;HaplotypeScore=67.42;MQ=41.21;MQ0=8;OQ=4147.70;QD=13.69;SB=-263.14 GT:AD:DP:GL:GQ 0/1:172,131:260:-413.77,-78.32,-559.37:99 +chr1 4104453 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=303;Dels=0.00;HRun=0;HaplotypeScore=122.24;MQ=41.63;MQ0=7;OQ=1110.55;QD=3.67;SB=-37.03 GT:AD:DP:GL:GQ 0/1:232,70:246:-188.46,-74.12,-759.14:99 +chr1 4104461 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=296;Dels=0.01;HRun=1;HaplotypeScore=119.61;MQ=41.59;MQ0=7;OQ=214.27;QD=0.72;SB=-23.14 GT:AD:DP:GL:GQ 0/1:251,42:244:-97.34,-72.63,-828.00:99 +chr1 4104464 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=293;Dels=0.00;HRun=0;HaplotypeScore=47.37;MQ=41.56;MQ0=7;OQ=330.17;QD=1.13;SB=-9.81 GT:AD:DP:GL:GQ 0/1:251,41:246:-110.42,-74.12,-748.00:99 +chr1 4104493 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=213;Dels=0.00;HRun=1;HaplotypeScore=30.82;MQ=42.50;MQ0=6;OQ=2710.70;QD=12.73;SB=-739.33 GT:AD:DP:GL:GQ 0/1:93,120:174:-326.79,-52.44,-298.85:99 +chr1 4104517 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=157;Dels=0.00;HRun=0;HaplotypeScore=91.08;MQ=42.89;MQ0=5;OQ=579.51;QD=3.69;SB=-277.61 GT:AD:DP:GL:GQ 0/1:123,34:134:-101.62,-40.38,-368.83:99 +chr1 4104540 rs62641248 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=101.41;MQ=39.74;MQ0=1;OQ=311.08;QD=3.34;SB=-25.45 GT:AD:DP:GL:GQ 0/1:75,18:80:-58.50,-24.10,-250.10:99 +chr1 4104551 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=87.22;MQ=37.20;MQ0=4;OQ=331.14;QD=4.87;SB=-44.20 GT:AD:DP:GL:GQ 0/1:51,17:54:-52.67,-16.27,-140.50:99 +chr1 4104561 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=32.90;MQ=39.14;MQ0=4;OQ=99.56;QD=1.56;SB=92.30 GT:AD:DP:GL:GQ 0/1:53,11:58:-30.72,-17.48,-172.38:99 +chr1 4104601 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=204;Dels=0.00;HRun=0;HaplotypeScore=38.41;MQ=39.91;MQ0=6;OQ=155.34;QD=0.76;SB=68.34 GT:AD:DP:GL:GQ 0/1:183,21:180:-73.04,-54.23,-586.07:99 +chr1 4104605 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=211;Dels=0.00;HRun=1;HaplotypeScore=39.02;MQ=40.58;MQ0=6;OQ=226.77;QD=1.07;SB=164.51 GT:AD:DP:GL:GQ 0/1:188,23:190:-83.19,-57.23,-627.45:99 +chr1 4104633 rs56023565 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=168;Dels=0.00;HRun=0;HaplotypeScore=43.28;MQ=41.56;MQ0=5;OQ=1077.06;QD=6.41;SB=128.56 GT:AD:DP:GL:GQ 0/1:117,50:150:-156.17,-45.18,-408.43:99 +chr1 4104638 rs62641251 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=155;Dels=0.00;HRun=1;HaplotypeScore=82.61;MQ=42.16;MQ0=4;OQ=1017.44;QD=6.56;SB=-202.97 GT:AD:DP:GL:GQ 0/1:99,56:128:-143.60,-38.57,-325.85:99 +chr1 4104646 rs56328141 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=133;Dels=0.05;HRun=0;HaplotypeScore=83.44;MQ=42.94;MQ0=3;OQ=598.93;QD=4.50;SB=-113.26 GT:AD:DP:GL:GQ 0/1:76,33:104:-104.27,-41.10,-292.97:99 +chr1 4104661 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=114;Dels=0.03;HRun=0;HaplotypeScore=168.88;MQ=43.79;MQ0=2;OQ=339.54;QD=2.98;SB=-7.31 GT:AD:DP:GL:GQ 0/1:92,17:99:-69.57,-32.33,-280.39:99 +chr1 4104695 rs58865682 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.00;HRun=0;HaplotypeScore=26.95;MQ=46.39;MQ0=1;OQ=148.27;QD=1.39;SB=113.35 GT:AD:DP:GL:GQ 0/1:90,17:100:-48.23,-30.12,-318.63:99 +chr1 4104698 rs59763636 A C 13.51 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=104;Dels=0.00;HRun=0;HaplotypeScore=26.94;MQ=46.80;MQ0=1;QD=0.13;SB=110.36 GT:AD:DP:GL:GQ 0/1:87,17:97:-33.83,-29.22,-321.32:46.15 +chr1 4104799 rs56113813 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=1;HaplotypeScore=110.54;MQ=45.23;MQ0=4;OQ=195.94;QD=2.13;SB=86.31 GT:AD:DP:GL:GQ 0/1:78,14:77:-46.07,-23.20,-257.99:99 +chr1 4106070 rs9426471 T C 595.81 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=1098.91;QD=16.16;SB=-453.97 GT:AD:DP:GL:GQ 0/1:32,36:68:-133.66,-20.48,-129.09:99 +chr1 4106148 rs9426494 C T 344.56 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=60.00;MQ0=0;OQ=1566.25;QD=17.40;SB=-768.74 GT:AD:DP:GL:GQ 0/1:44,46:88:-186.42,-26.51,-142.07:99 +chr1 4107203 rs6680278 C T 328.94 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.92;MQ0=0;OQ=777.87;QD=13.89;SB=-285.17 GT:AD:DP:GL:GQ 0/1:32,24:55:-97.64,-16.57,-110.93:99 +chr1 4107258 rs6672998 G A 334.86 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=520.45;QD=13.01;SB=-193.18 GT:AD:DP:GL:GQ 0/1:23,17:40:-67.38,-12.05,-82.67:99 +chr1 4107272 rs17406305 C T 361.32 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=435.04;QD=9.89;SB=-220.70 GT:AD:DP:GL:GQ 0/1:26,18:41:-59.15,-12.36,-84.72:99 +chr1 4108156 rs7528351 G A 171.64 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=978.84;QD=16.88;SB=-340.32 GT:AD:DP:GL:GQ 0/1:29,29:58:-118.64,-17.47,-104.14:99 +chr1 4108402 rs7539733 C T 327.50 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=58.92;MQ0=0;OQ=799.67;QD=15.38;SB=-336.43 GT:AD:DP:GL:GQ 0/1:24,28:47:-97.41,-14.16,-80.03:99 +chr1 4108778 rs9426495 G A 284.61 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=3.59;MQ=59.34;MQ0=0;OQ=895.14;QD=14.21;SB=-321.33 GT:AD:DP:GL:GQ 0/1:34,29:62:-111.48,-18.68,-120.65:99 +chr1 4108797 rs9426472 G C 415.96 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.27;MQ0=0;OQ=1011.60;QD=17.75;SB=-519.74 GT:AD:DP:GL:GQ 0/1:27,30:53:-120.42,-15.97,-106.06:99 +chr1 4109900 . A G 31.51 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=2;HaplotypeScore=6.53;MQ=57.95;MQ0=0;QD=0.55;SB=59.23 GT:AD:DP:GL:GQ 0/1:35,22:36:-17.29,-10.85,-119.86:64.34 +chr1 4110024 rs6690263 C T 117.28 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=60.00;MQ0=0;OQ=1118.91;QD=21.11;SB=-400.94 GT:AD:DP:GL:GQ 0/1:20,32:53:-134.68,-19.51,-68.02:99 +chr1 4110064 rs6695126 A G 708.48 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1770.58;QD=35.41;SB=-875.05 GT:AD:DP:GL:GQ 1/1:0,50:50:-180.66,-15.06,-0.02:99 +chr1 4110262 rs6683453 G A 435.74 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.65;MQ0=0;OQ=1205.59;QD=18.27;SB=-574.05 GT:AD:DP:GL:GQ 0/1:29,37:64:-143.13,-19.28,-100.61:99 +chr1 4110315 rs9426473 G A 464.67 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=896.46;QD=18.68;SB=-396.93 GT:AD:DP:GL:GQ 0/1:19,29:46:-106.79,-13.86,-67.55:99 +chr1 4110338 rs9426496 A G 430.77 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=545.25;QD=11.36;SB=-275.98 GT:AD:DP:GL:GQ 0/1:25,23:47:-71.97,-14.16,-100.50:99 +chr1 4111600 rs12752733 G A 194.11 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.12;MQ0=0;OQ=1088.74;QD=20.54;SB=-407.75 GT:AD:DP:GL:GQ 0/1:20,33:51:-127.52,-15.37,-66.14:99 +chr1 4111741 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=11;HaplotypeScore=4.85;MQ=55.91;MQ0=0;OQ=88.59;QD=2.16;SB=32.11 GT:AD:DP:GL:GQ 0/1:33,8:32:-21.79,-9.64,-86.81:99 +chr1 4112024 . C T 265.51 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.50;MQ0=0;OQ=941.42;QD=16.81;SB=-396.13 GT:AD:DP:GL:GQ 0/1:27,29:55:-113.99,-16.57,-97.04:99 +chr1 4112929 rs4654494 C G 169.07 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=60.00;MQ0=0;OQ=822.69;QD=13.27;SB=-341.77 GT:AD:DP:GL:GQ 0/1:34,28:54:-101.84,-16.28,-127.78:99 +chr1 4113201 rs55759139 G A 249.56 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.37;MQ=59.68;MQ0=0;OQ=761.01;QD=13.12;SB=-311.83 GT:AD:DP:GL:GQ 0/1:32,26:53:-95.35,-15.97,-100.34:99 +chr1 4113760 rs4498774 A C 130.48 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.50;MQ=58.71;MQ0=0;OQ=628.38;QD=9.67;SB=-313.59 GT:AD:DP:GL:GQ 0/1:36,29:64:-85.41,-19.28,-138.00:99 +chr1 4114825 rs7339911 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=10;HaplotypeScore=3.32;MQ=58.55;MQ0=0;OQ=757.63;QD=12.42;SB=-183.20 GT:AD:DP:GL:GQ 0/1:36,25:59:-96.82,-17.77,-126.07:99 +chr1 4116025 rs9988443 G A 336.18 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.45;MQ0=0;OQ=1567.78;QD=20.63;SB=-720.28 GT:AD:DP:GL:GQ 0/1:30,46:75:-182.67,-22.61,-94.32:99 +chr1 4116630 rs4336820 T C 72.02 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.26;MQ=59.52;MQ0=0;OQ=1667.19;QD=34.73;SB=-687.27 GT:AD:DP:GL:GQ 1/1:0,48:47:-170.32,-14.16,-0.01:99 +chr1 4116791 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=2;HaplotypeScore=12.66;MQ=58.95;MQ0=0;OQ=57.38;QD=1.43;SB=71.25 GT:AD:DP:GL:GQ 0/1:31,9:34:-19.31,-10.29,-109.30:90.22 +chr1 4117150 rs12062237 T C 0.56 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=3;HaplotypeScore=3.14;MQ=57.94;MQ0=0;OQ=1345.47;QD=32.82;SB=-624.25 GT:AD:DP:GL:GQ 1/1:0,41:39:-138.15,-11.75,-0.02:99 +chr1 4118916 rs3890798 A G 534.42 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2055.84;QD=30.23;SB=-868.59 GT:AD:DP:GL:GQ 1/1:0,68:65:-209.23,-19.60,-0.06:99 +chr1 4119595 rs6426391 A T 243.50 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=1.16;MQ=59.73;MQ0=0;OQ=1272.79;QD=18.45;SB=-602.37 GT:AD:DP:GL:GQ 0/1:28,41:68:-151.04,-20.48,-104.90:99 +chr1 4119856 . G A 80.75 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=54.88;MQ0=1;OQ=952.98;QD=16.15;SB=-461.48 GT:AD:DP:GL:GQ 0/1:28,31:56:-115.46,-16.88,-95.51:99 +chr1 4120161 rs7549636 G A 106.14 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=3.96;MQ=59.21;MQ0=1;OQ=708.05;QD=15.39;SB=-359.50 GT:AD:DP:GL:GQ 0/1:23,23:43:-87.04,-12.95,-74.47:99 +chr1 4120271 rs6426392 T C 252.19 PASS AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.44;MQ0=0;OQ=208.98;QD=7.74;SB=-130.51 GT:AD:DP:GL:GQ 0/1:16,11:25:-31.72,-7.54,-55.62:99 +chr1 4121295 rs4414012 C T 109.52 PASS AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=243.26;QD=16.22;SB=-32.52 GT:AD:DP:GL:GQ 0/1:7,8:15:-32.13,-4.52,-23.19:99 +chr1 4121459 rs4614226 C T 3.52 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.33;MQ0=0;OQ=708.73;QD=25.31;SB=-192.72 GT:AD:DP:GL:GQ 0/1:8,20:25:-81.69,-7.53,-15.26:77.23 +chr1 4122266 rs4654495 C T 267.28 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.05;MQ0=0;OQ=844.66;QD=17.24;SB=-383.42 GT:AD:DP:GL:GQ 0/1:22,27:48:-102.21,-14.46,-81.80:99 +chr1 4122640 . C T 27.21 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=8;Dels=0.00;HRun=1;HaplotypeScore=9.85;MQ=48.82;MQ0=0;QD=3.40;SB=2.03 GT:AD:DP:GL:GQ 0/1:6,2:7:-8.11,-2.11,-18.35:60.04 +chr1 4122866 rs4654413 A G 16.01 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.58;MQ0=0;OQ=1224.52;QD=28.48;SB=-81.37 GT:AD:DP:GL:GQ 1/1:0,43:41:-126.09,-12.38,-0.05:99 +chr1 4122935 rs4654414 G A 17.67 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=53.29;MQ0=0;OQ=1666.36;QD=36.23;SB=-267.85 GT:AD:DP:GL:GQ 1/1:1,45:42:-170.23,-12.65,-0.01:99 +chr1 4123288 rs4233261 T C 17.26 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=4.16;MQ=58.63;MQ0=0;OQ=2395.13;QD=34.71;SB=-1054.42 GT:AD:DP:GL:GQ 1/1:0,69:66:-243.12,-19.88,-0.02:99 +chr1 4123748 rs6679293 T C 176.14 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.14;MQ0=0;OQ=1906.56;QD=31.26;SB=-831.63 GT:AD:DP:GL:GQ 1/1:0,61:59:-194.29,-17.79,-0.05:99 +chr1 4123963 rs4654496 C T 83.64 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=2067.60;QD=39.01;SB=-750.62 GT:AD:DP:GL:GQ 1/1:0,53:53:-210.36,-15.97,-0.02:99 +chr1 4124418 rs4654497 T C 597.93 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=1506.19;QD=30.74;SB=-582.98 GT:AD:DP:GL:GQ 1/1:0,49:47:-154.24,-14.17,-0.04:99 +chr1 4126306 rs4367764 C T 454.46 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2115.14;QD=39.17;SB=-864.64 GT:AD:DP:GL:GQ 1/1:0,54:53:-215.11,-15.97,-0.01:99 +chr1 4127324 rs12123330 C T 249.14 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1048.68;QD=17.77;SB=-496.03 GT:AD:DP:GL:GQ 0/1:27,32:56:-125.03,-16.88,-80.71:99 +chr1 4127494 rs4468133 G A 195.33 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=60.00;MQ0=0;OQ=1260.59;QD=18.01;SB=-425.95 GT:AD:DP:GL:GQ 0/1:31,38:68:-152.64,-23.30,-109.48:99 +chr1 4128172 rs4654498 A G 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.33;MQ=59.19;MQ0=0;OQ=2014.82;QD=35.35;SB=-1032.76 GT:AD:DP:GL:GQ 1/1:0,57:56:-205.08,-16.87,-0.01:99 +chr1 4128310 rs4654499 G T 305.85 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=983.44;QD=17.88;SB=-296.34 GT:AD:DP:GL:GQ 0/1:22,33:55:-118.19,-16.56,-78.95:99 +chr1 4130572 rs3890729 A T 141.84 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.07;MQ=59.18;MQ0=0;OQ=905.47;QD=17.75;SB=-227.90 GT:AD:DP:GL:GQ 0/1:23,28:51:-109.19,-15.36,-88.04:99 +chr1 4131311 rs10915460 G A 189.99 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=57.39;MQ0=0;OQ=480.50;QD=13.35;SB=-233.54 GT:AD:DP:GL:GQ 0/1:19,17:33:-61.28,-9.95,-54.49:99 +chr1 4131491 rs10915461 A G 151.47 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.56;MQ=51.87;MQ0=0;OQ=492.21;QD=9.65;SB=-268.94 GT:AD:DP:GL:GQ 0/1:28,23:49:-67.28,-14.77,-113.16:99 +chr1 4131545 rs10915462 T C 155.98 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=54.56;MQ0=0;OQ=299.94;QD=7.69;SB=-143.28 GT:AD:DP:GL:GQ 0/1:25,14:37:-44.43,-11.15,-99.76:99 +chr1 4131617 rs6688343 T C 208.72 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=58.31;MQ0=0;OQ=662.26;QD=13.25;SB=-230.45 GT:AD:DP:GL:GQ 0/1:25,25:48:-83.97,-14.46,-97.39:99 +chr1 4131656 rs6688428 T C 133.26 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=58.40;MQ0=0;OQ=444.13;QD=10.83;SB=-97.71 GT:AD:DP:GL:GQ 0/1:22,19:40:-59.75,-12.06,-84.80:99 +chr1 4131666 rs6688431 T C 70.94 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.40;MQ0=0;OQ=339.10;QD=8.27;SB=-98.71 GT:AD:DP:GL:GQ 0/1:23,18:37:-48.34,-11.15,-87.20:99 +chr1 4131704 . G A 41.43 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.69;MQ=58.60;MQ0=0;OQ=706.66;QD=14.13;SB=-238.75 GT:AD:DP:GL:GQ 0/1:28,22:49:-88.72,-14.77,-84.55:99 +chr1 4131824 rs12032295 C T 752.83 Indel AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=33.96;MQ0=0;QD=14.20;SB=-367.84 GT:AD:DP:GL:GQ 0/1:30,23:51:-93.93,-15.37,-94.00:99 +chr1 4132377 rs12405392 C T 226.32 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=4.69;MQ=59.66;MQ0=0;OQ=1021.86;QD=15.03;SB=-451.99 GT:AD:DP:GL:GQ 0/1:34,34:62:-124.15,-18.68,-109.47:99 +chr1 4132399 rs56827341 A G 272.74 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=59.66;MQ0=0;OQ=903.58;QD=13.29;SB=-319.89 GT:AD:DP:GL:GQ 0/1:32,36:65:-113.24,-19.60,-113.27:99 +chr1 4132555 rs11580927 G A 598.05 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=853.00;QD=13.76;SB=-450.44 GT:AD:DP:GL:GQ 0/1:34,28:61:-106.96,-18.38,-120.31:99 +chr1 4132654 rs11583685 T C 237.59 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.58;MQ=60.00;MQ0=0;OQ=809.75;QD=12.46;SB=-338.53 GT:AD:DP:GL:GQ 0/1:35,30:64:-103.54,-19.28,-136.81:99 +chr1 4134373 rs6690519 C T 596.27 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2577.92;QD=39.66;SB=-1051.40 GT:AD:DP:GL:GQ 1/1:0,65:64:-261.39,-19.28,-0.02:99 +chr1 4134652 rs12743431 G A 916.73 Indel AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=58.05;MQ0=0;QD=16.08;SB=-472.04 GT:AD:DP:GL:GQ 0/1:25,32:53:-110.92,-15.97,-91.04:99 +chr1 4134672 rs61037363 C T 207.69 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=58.34;MQ0=0;OQ=1244.96;QD=19.15;SB=-619.07 GT:AD:DP:GL:GQ 0/1:27,38:61:-146.16,-18.38,-83.21:99 +chr1 4135628 rs4654501 G A 449.34 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.45;MQ0=0;OQ=800.03;QD=17.78;SB=-327.85 GT:AD:DP:GL:GQ 0/1:21,24:44:-96.54,-13.26,-71.19:99 +chr1 4136297 rs4531262 C T 292.38 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.55;MQ0=0;OQ=900.23;QD=17.65;SB=-443.97 GT:AD:DP:GL:GQ 0/1:23,28:50:-108.37,-15.06,-81.34:99 +chr1 4136842 rs4233262 C T 514.56 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1175.57;QD=19.27;SB=-513.00 GT:AD:DP:GL:GQ 0/1:27,34:61:-139.22,-18.38,-97.14:99 +chr1 4137022 rs12726068 G A 202.41 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1078.50;QD=19.97;SB=-346.48 GT:AD:DP:GL:GQ 0/1:22,32:54:-127.40,-16.27,-78.49:99 +chr1 4137146 rs12741551 C T 188.79 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.60;MQ=60.00;MQ0=0;OQ=744.97;QD=14.06;SB=-275.26 GT:AD:DP:GL:GQ 0/1:28,23:51:-95.75,-17.97,-99.94:99 +chr1 4137455 rs34927664 C T 374.06 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=672.79;QD=16.41;SB=-286.16 GT:AD:DP:GL:GQ 0/1:20,21:40:-82.61,-12.05,-71.71:99 +chr1 4137533 rs6687719 A G 359.14 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.55;MQ0=0;OQ=693.89;QD=13.61;SB=-371.11 GT:AD:DP:GL:GQ 0/1:24,27:51:-88.05,-15.37,-93.98:99 +chr1 4137942 rs4654415 A G 54.66 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=3;HaplotypeScore=0.52;MQ=59.28;MQ0=0;OQ=812.82;QD=15.63;SB=-375.38 GT:AD:DP:GL:GQ 0/1:23,29:51:-99.93,-15.36,-91.58:99 +chr1 4137964 rs4654416 T C 201.40 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=58.39;MQ0=0;OQ=863.33;QD=15.70;SB=-318.29 GT:AD:DP:GL:GQ 0/1:25,30:54:-105.89,-16.27,-96.91:99 +chr1 4138124 rs4654417 A G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.04;HRun=0;HaplotypeScore=22.45;MQ=53.05;MQ0=0;OQ=979.60;QD=14.62;SB=-425.14 GT:AD:DP:GL:GQ 0/1:30,34:67:-120.52,-19.28,-120.75:99 +chr1 4138539 rs10915465 C T 116.34 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=932.04;QD=16.95;SB=-231.54 GT:AD:DP:GL:GQ 0/1:26,28:51:-111.86,-15.37,-73.76:99 +chr1 4138848 rs4233263 T C 563.43 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.57;MQ0=0;OQ=1932.95;QD=31.18;SB=-950.38 GT:AD:DP:GL:GQ 1/1:0,61:61:-196.93,-18.40,-0.06:99 +chr1 4140038 rs4233264 T C 391.03 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.43;MQ0=0;OQ=1125.34;QD=13.89;SB=-437.57 GT:AD:DP:GL:GQ 0/1:41,40:80:-139.92,-24.10,-167.96:99 +chr1 4140287 rs4654502 A G 258.40 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=716.89;QD=12.36;SB=-328.15 GT:AD:DP:GL:GQ 0/1:28,30:57:-92.15,-17.18,-113.12:99 +chr1 4140357 rs4654503 A G 175.10 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.08;MQ=60.00;MQ0=0;OQ=528.96;QD=9.98;SB=-287.63 GT:AD:DP:GL:GQ 0/1:26,24:47:-70.35,-14.17,-96.77:99 +chr1 4140721 rs12074230 G C 441.98 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=1211.59;QD=19.54;SB=-432.34 GT:AD:DP:GL:GQ 0/1:29,33:61:-142.82,-18.38,-122.06:99 +chr1 4141214 rs61770887 T A 176.81 Indel AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=41.85;MQ0=5;QD=2.39;SB=-58.97 GT:AD:DP:GL:GQ 0/1:35,39:44:-34.22,-13.25,-135.84:99 +chr1 4141739 . C G 151.90 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.44;MQ0=0;OQ=861.28;QD=11.64;SB=-403.50 GT:AD:DP:GL:GQ 0/1:45,29:72:-111.12,-21.71,-193.89:99 +chr1 4143108 rs7544125 G A 98.23 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=44.58;MQ0=4;OQ=463.56;QD=6.62;SB=-223.67 GT:AD:DP:GL:GQ 0/1:38,32:54:-65.91,-16.27,-136.81:99 +chr1 4143110 rs7515133 T G 11.80 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=44.83;MQ0=4;OQ=280.65;QD=3.95;SB=-136.72 GT:AD:DP:GL:GQ 0/1:40,31:55:-47.92,-16.57,-148.31:99 +chr1 4143183 rs4408123 T C 60.26 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.41;MQ=54.71;MQ0=0;OQ=2012.85;QD=31.45;SB=-855.54 GT:AD:DP:GL:GQ 1/1:0,63:62:-204.92,-18.70,-0.05:99 +chr1 4143665 rs4654505 C T 14.05 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=7.02;MQ=58.52;MQ0=0;OQ=1278.62;QD=17.05;SB=-644.75 GT:AD:DP:GL:GQ 0/1:36,39:72:-152.84,-21.70,-110.95:99 +chr1 4143971 rs56322069 G A 219.93 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=58.68;MQ0=0;OQ=1179.12;QD=14.38;SB=-509.98 GT:AD:DP:GL:GQ 0/1:47,35:78:-144.69,-23.49,-153.28:99 +chr1 4144717 rs4654419 G T 409.69 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=53.48;MQ0=0;OQ=576.97;QD=11.10;SB=-278.60 GT:AD:DP:GL:GQ 0/1:31,21:52:-76.65,-15.66,-108.30:99 +chr1 4144899 rs4654506 A G 59.06 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=1.57;MQ=57.19;MQ0=0;OQ=798.47;QD=12.67;SB=-355.09 GT:AD:DP:GL:GQ 0/1:32,31:63:-102.12,-18.99,-128.03:99 +chr1 4145034 rs4654420 T C 208.27 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=57.63;MQ0=0;OQ=567.20;QD=9.30;SB=-299.19 GT:AD:DP:GL:GQ 0/1:35,26:59:-77.79,-17.78,-138.00:99 +chr1 4145265 rs10799210 A G 75.28 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=52.55;MQ0=0;OQ=2612.65;QD=35.79;SB=-1182.09 GT:AD:DP:GL:GQ 1/1:0,72:73:-267.51,-24.47,-2.66:99 +chr1 4146179 rs4354511 G A 19.37 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=3;HaplotypeScore=1.79;MQ=39.00;MQ0=1;OQ=2945.76;QD=39.28;SB=-1473.93 GT:AD:DP:GL:GQ 1/1:0,75:73:-298.18,-21.99,-0.02:99 +chr1 4146185 rs61770891 T G 349.70 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=40.44;MQ0=1;OQ=1123.38;QD=15.18;SB=-586.47 GT:AD:DP:GL:GQ 0/1:35,39:73:-137.61,-21.99,-124.99:99 +chr1 4146278 rs35969529 A C 46.41 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=2.80;MQ=52.18;MQ0=0;OQ=652.54;QD=12.55;SB=-341.77 GT:AD:DP:GL:GQ 0/1:27,25:52:-84.21,-15.67,-95.88:99 +chr1 4146315 rs34096100 G A 254.13 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.76;MQ0=0;OQ=657.20;QD=13.41;SB=-218.51 GT:AD:DP:GL:GQ 0/1:28,21:47:-83.18,-14.17,-82.42:99 +chr1 4146537 . C T 111.88 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.77;MQ=53.66;MQ0=1;OQ=1107.86;QD=16.06;SB=-448.39 GT:AD:DP:GL:GQ 0/1:34,35:67:-134.26,-20.19,-114.24:99 +chr1 4146953 rs4654421 T C 433.26 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.82;MQ0=0;OQ=2189.94;QD=31.74;SB=-1040.77 GT:AD:DP:GL:GQ 1/1:0,69:68:-222.64,-20.51,-0.06:99 +chr1 4147013 rs4654422 T A 163.99 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.20;MQ0=1;OQ=3024.40;QD=36.88;SB=-1331.44 GT:AD:DP:GL:GQ 1/1:1,80:81:-309.61,-27.75,-3.59:99 +chr1 4148323 rs35837871 C T 12.81 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=2.85;MQ=58.88;MQ0=0;OQ=689.43;QD=12.77;SB=-158.63 GT:AD:DP:GL:GQ 0/1:29,24:49:-86.99,-14.77,-93.34:99 +chr1 4148556 rs10753370 A G 191.60 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.30;MQ=57.40;MQ0=0;OQ=2083.85;QD=34.73;SB=-1040.92 GT:AD:DP:GL:GQ 1/1:0,60:59:-211.99,-17.77,-0.02:99 +chr1 4149011 rs12084286 A G 120.11 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=57.86;MQ0=0;OQ=472.12;QD=10.26;SB=-116.70 GT:AD:DP:GL:GQ 0/1:26,20:42:-63.15,-12.65,-98.66:99 +chr1 4149320 rs10733015 T C 59.23 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.72;MQ=56.65;MQ0=0;OQ=2004.37;QD=30.37;SB=-729.73 GT:AD:DP:GL:GQ 1/1:0,65:63:-204.08,-19.00,-0.06:99 +chr1 4149923 rs4654507 T C 369.93 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.77;MQ0=0;OQ=1162.12;QD=14.53;SB=-509.31 GT:AD:DP:GL:GQ 0/1:40,40:79:-143.29,-23.80,-162.73:99 +chr1 4150793 rs11808641 A G 288.49 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=1163.51;QD=16.62;SB=-493.62 GT:AD:DP:GL:GQ 0/1:32,38:70:-140.72,-21.09,-129.98:99 +chr1 4151258 rs35392680 C A 277.92 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=1.25;MQ=59.48;MQ0=0;OQ=1358.51;QD=16.77;SB=-581.67 GT:AD:DP:GL:GQ 0/1:37,44:80:-163.23,-24.09,-127.72:99 +chr1 4151486 rs35452955 A T 64.63 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=1469.46;QD=19.34;SB=-729.32 GT:AD:DP:GL:GQ 0/1:30,45:74:-172.52,-22.29,-110.18:99 +chr1 4151668 rs6703301 G T 631.77 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3028.09;QD=37.38;SB=-1101.60 GT:AD:DP:GL:GQ 1/1:0,81:80:-306.41,-24.09,-0.01:99 +chr1 4151981 rs34414875 C T 365.71 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1305.64;QD=16.32;SB=-537.52 GT:AD:DP:GL:GQ 0/1:41,39:80:-157.95,-24.10,-144.69:99 +chr1 4152854 rs10915467 A T 474.45 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1268.93;QD=17.38;SB=-610.43 GT:AD:DP:GL:GQ 0/1:33,40:72:-151.86,-21.68,-124.21:99 +chr1 4153158 rs12722935 C T 465.33 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1317.34;QD=16.26;SB=-636.13 GT:AD:DP:GL:GQ 0/1:41,40:80:-159.12,-24.10,-137.48:99 +chr1 4153203 rs55974255 T G 492.94 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1277.21;QD=15.39;SB=-533.71 GT:AD:DP:GL:GQ 0/1:38,45:83:-156.01,-25.00,-142.96:99 +chr1 4153672 rs6679104 T C 519.73 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=1796.89;QD=30.98;SB=-648.94 GT:AD:DP:GL:GQ 1/1:0,58:56:-183.31,-16.88,-0.04:99 +chr1 4153751 rs12750830 G A 339.94 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=841.06;QD=12.19;SB=-424.91 GT:AD:DP:GL:GQ 0/1:41,27:67:-107.58,-20.19,-146.61:99 +chr1 4153835 rs12740143 T G 222.74 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=59.66;MQ0=0;OQ=767.69;QD=11.29;SB=-346.80 GT:AD:DP:GL:GQ 0/1:40,28:68:-100.53,-20.48,-145.06:99 +chr1 4154543 rs12143082 T C 171.80 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=1.73;MQ=59.61;MQ0=1;OQ=1104.97;QD=14.17;SB=-407.20 GT:AD:DP:GL:GQ 0/1:39,39:74:-136.07,-22.29,-143.19:99 +chr1 4154828 rs4578184 A T 236.18 PASS AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.74;MQ0=0;OQ=3286.63;QD=37.35;SB=-1618.09 GT:AD:DP:GL:GQ 1/1:0,87:86:-327.66,-25.90,-0.02:99 +chr1 4156046 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=80;Dels=0.01;HRun=20;HaplotypeScore=22.75;MQ=49.75;MQ0=0;OQ=501.86;QD=6.27;SB=92.27 GT:AD:DP:GL:GQ 0/1:48,31:64:-72.46,-18.99,-149.51:99 +chr1 4157196 rs4276878 C G 356.37 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1452.13;QD=15.78;SB=-539.06 GT:AD:DP:GL:GQ 0/1:47,45:92:-176.24,-27.75,-207.05:99 +chr1 4159822 rs34626829 T C 256.76 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=966.32;QD=13.24;SB=-369.17 GT:AD:DP:GL:GQ 0/1:40,33:72:-121.60,-21.69,-157.15:99 +chr1 4159905 rs4654509 T C 45.94 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=1.31;MQ=59.48;MQ0=0;OQ=2796.88;QD=34.96;SB=-1388.49 GT:AD:DP:GL:GQ 1/1:0,80:80:-283.30,-24.10,-0.03:99 +chr1 4160278 rs6667065 G A 347.06 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=1508.83;QD=20.12;SB=-751.28 GT:AD:DP:GL:GQ 0/1:32,43:74:-176.46,-22.30,-103.02:99 +chr1 4160487 rs6426401 C G 585.75 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=2415.89;QD=43.14;SB=-1118.15 GT:AD:DP:GL:GQ 1/1:0,56:56:-245.19,-16.88,-0.02:99 +chr1 4163843 rs4654511 A G 129.93 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=2;HaplotypeScore=0.90;MQ=59.46;MQ0=0;OQ=1014.81;QD=11.80;SB=-473.86 GT:AD:DP:GL:GQ 0/1:46,40:85:-130.38,-25.61,-186.22:99 +chr1 4163857 rs4654512 A G 307.08 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=2.37;MQ=59.44;MQ0=0;OQ=1070.59;QD=12.90;SB=-521.48 GT:AD:DP:GL:GQ 0/1:46,37:83:-135.34,-25.00,-185.85:99 +chr1 4164344 rs4529679 G C 272.38 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=59.36;MQ0=0;OQ=772.49;QD=10.73;SB=-392.69 GT:AD:DP:GL:GQ 0/1:46,26:70:-101.64,-21.10,-199.05:99 +chr1 4166949 rs16840901 T C 388.35 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.68;MQ0=0;OQ=1039.54;QD=14.24;SB=-434.53 GT:AD:DP:GL:GQ 0/1:37,36:73:-129.23,-21.99,-150.63:99 +chr1 4167749 rs10915471 T G 58.03 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=3.59;MQ=59.58;MQ0=0;OQ=744.43;QD=13.54;SB=-264.89 GT:AD:DP:GL:GQ 0/1:27,27:49:-92.49,-14.76,-80.31:99 +chr1 4168111 rs35122589 C T 228.78 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.26;MQ0=0;OQ=1364.57;QD=16.64;SB=-443.34 GT:AD:DP:GL:GQ 0/1:40,41:80:-163.84,-24.10,-142.82:99 +chr1 4168454 rs12095632 C G 92.77 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=2.95;MQ=59.32;MQ0=0;OQ=1054.00;QD=19.16;SB=-475.80 GT:AD:DP:GL:GQ 0/1:24,31:54:-124.96,-16.28,-104.73:99 +chr1 4168730 rs4130091 T C 180.54 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.33;MQ0=0;OQ=1367.19;QD=28.48;SB=-696.78 GT:AD:DP:GL:GQ 1/1:0,48:44:-140.35,-13.27,-0.05:99 +chr1 4169351 rs6426402 G T 131.41 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=3.41;MQ=58.55;MQ0=0;OQ=809.13;QD=11.40;SB=-425.17 GT:AD:DP:GL:GQ 0/1:41,30:69:-104.98,-20.78,-138.71:99 +chr1 4169394 rs6426403 C G 338.24 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.89;MQ0=0;OQ=727.35;QD=12.99;SB=-274.92 GT:AD:DP:GL:GQ 0/1:33,23:54:-92.30,-16.28,-134.02:99 +chr1 4169498 rs6426404 G A 414.13 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.75;MQ0=0;OQ=1380.19;QD=18.40;SB=-605.61 GT:AD:DP:GL:GQ 0/1:34,41:72:-163.00,-21.69,-105.58:99 +chr1 4169658 rs60017975 A G 318.13 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.77;MQ0=0;OQ=1450.14;QD=18.13;SB=-530.63 GT:AD:DP:GL:GQ 0/1:31,49:79:-172.10,-23.80,-127.67:99 +chr1 4170881 rs7550659 A G 248.87 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.70;MQ0=0;OQ=2075.07;QD=30.97;SB=-804.69 GT:AD:DP:GL:GQ 1/1:0,66:63:-211.13,-18.99,-0.04:99 +chr1 4171135 rs10799212 A G 40.61 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.91;MQ=40.70;MQ0=1;OQ=2175.11;QD=31.07;SB=-612.96 GT:AD:DP:GL:GQ 1/1:1,69:67:-221.14,-20.20,-0.04:99 +chr1 4171182 rs12410442 G A 385.57 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=27.19;MQ0=4;OQ=361.27;QD=10.95;SB=-197.20 GT:AD:DP:GL:GQ 0/1:20,13:27:-47.55,-8.14,-48.20:99 +chr1 4171315 . C A 41.63 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=20;HaplotypeScore=7.30;MQ=33.40;MQ0=5;QD=0.97;SB=41.16 GT:AD:DP:GL:GQ 0/1:37,6:31:-16.79,-9.34,-90.98:74.46 +chr1 4171344 rs10799213 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.01;HRun=20;HaplotypeScore=28.32;MQ=47.02;MQ0=1;OQ=768.09;QD=11.30;SB=-343.49 GT:AD:DP:GL:GQ 0/1:35,32:53:-95.75,-15.66,-101.72:99 +chr1 4171386 rs12022636 C A 71.32 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=6.39;MQ=55.43;MQ0=0;OQ=1032.82;QD=16.66;SB=-507.94 GT:AD:DP:GL:GQ 0/1:28,34:59:-124.34,-17.77,-88.85:99 +chr1 4171443 rs10799214 T A 380.15 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.02;MQ=52.31;MQ0=0;OQ=893.79;QD=14.65;SB=-401.19 GT:AD:DP:GL:GQ 0/1:30,31:58:-110.14,-17.48,-102.42:99 +chr1 4171775 rs7553814 A G 404.78 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.01;MQ0=0;OQ=970.08;QD=12.93;SB=-503.90 GT:AD:DP:GL:GQ 0/1:40,35:74:-122.58,-22.29,-161.95:99 +chr1 4171833 rs7553919 A G 37.31 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=59.60;MQ0=0;OQ=2384.19;QD=34.55;SB=-1112.82 GT:AD:DP:GL:GQ 1/1:0,69:66:-242.02,-19.88,-0.02:99 +chr1 4171990 rs7554028 A G 628.72 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=1;OQ=2341.28;QD=30.02;SB=-854.63 GT:AD:DP:GL:GQ 1/1:0,78:76:-237.79,-22.93,-0.08:99 +chr1 4173512 rs7517572 T A 699.45 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=2653.94;QD=34.47;SB=-1331.37 GT:AD:DP:GL:GQ 1/1:0,77:72:-269.00,-21.69,-0.02:99 +chr1 4173702 rs10753372 T C 483.13 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.88;MQ0=0;OQ=510.62;QD=9.82;SB=-265.21 GT:AD:DP:GL:GQ 0/1:30,22:52:-70.02,-15.68,-118.09:99 +chr1 4173822 rs10737404 T C 229.86 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1647.35;QD=29.95;SB=-655.93 GT:AD:DP:GL:GQ 1/1:0,55:53:-168.37,-15.99,-0.05:99 +chr1 4174045 rs10915473 C T 65.29 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=45.21;MQ0=0;OQ=1332.73;QD=36.02;SB=-585.26 GT:AD:DP:GL:GQ 1/1:0,37:35:-136.87,-10.55,-0.02:99 +chr1 4174057 . C T 1039.01 SnpCluster AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=42.84;MQ0=0;QD=33.52;SB=-399.52 GT:AD:DP:GL:GQ 1/1:2,29:27:-107.50,-8.14,-0.01:81.26 +chr1 4174060 . A C 853.72 SnpCluster AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;HRun=2;HaplotypeScore=1.07;MQ=43.67;MQ0=0;QD=27.54;SB=-294.55 GT:AD:DP:GL:GQ 1/1:0,31:26:-88.97,-7.83,-0.01:78.20 +chr1 4174064 . A C 949.90 SnpCluster AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=44.60;MQ0=0;QD=28.78;SB=-378.69 GT:AD:DP:GL:GQ 1/1:0,33:28:-98.58,-8.43,-0.01:84.24 +chr1 4174382 rs1908491 C T 0.38 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=6.22;MQ=54.65;MQ0=0;OQ=1883.08;QD=36.21;SB=-503.01 GT:AD:DP:GL:GQ 1/1:0,52:48:-191.91,-14.46,-0.01:99 +chr1 4174484 rs10915474 T A 225.63 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=55.68;MQ0=0;OQ=801.30;QD=15.41;SB=-299.67 GT:AD:DP:GL:GQ 0/1:26,26:51:-98.78,-15.36,-93.02:99 +chr1 4174489 rs1908492 C T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=7;HaplotypeScore=1.12;MQ=55.99;MQ0=0;OQ=1860.19;QD=37.20;SB=-932.70 GT:AD:DP:GL:GQ 1/1:0,50:48:-189.62,-14.46,-0.02:99 +chr1 4174597 rs1908493 C T 268.28 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.14;MQ=59.04;MQ0=0;OQ=2611.89;QD=38.41;SB=-1140.03 GT:AD:DP:GL:GQ 1/1:0,68:66:-264.79,-19.88,-0.02:99 +chr1 4174874 rs1495245 T A 732.53 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=2554.22;QD=37.56;SB=-1304.61 GT:AD:DP:GL:GQ 1/1:0,68:68:-259.02,-20.48,-0.02:99 +chr1 4174974 rs11578399 C A 12.83 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=3.61;MQ=59.22;MQ0=0;OQ=421.58;QD=7.81;SB=-139.06 GT:AD:DP:GL:GQ 0/1:37,17:52:-61.11,-15.67,-117.17:99 +chr1 4175032 rs1495246 C G 204.50 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=56.85;MQ0=0;OQ=2607.23;QD=39.50;SB=-1308.71 GT:AD:DP:GL:GQ 1/1:0,66:62:-264.33,-18.68,-0.02:99 +chr1 4175046 . T G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=2;HaplotypeScore=9.95;MQ=56.80;MQ0=0;OQ=180.72;QD=2.78;SB=92.29 GT:AD:DP:GL:GQ 0/1:40,25:50:-36.42,-15.06,-130.62:99 +chr1 4175151 rs10915476 G A 237.61 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.01;MQ0=0;OQ=567.09;QD=12.07;SB=-92.91 GT:AD:DP:GL:GQ 0/1:29,18:45:-73.55,-13.56,-90.83:99 +chr1 4175279 rs1495247 C T 209.45 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.34;MQ0=0;OQ=2597.96;QD=37.11;SB=-1279.76 GT:AD:DP:GL:GQ 1/1:0,70:67:-263.40,-20.19,-0.02:99 +chr1 4175302 rs7411802 C A 438.30 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=58.93;MQ0=0;OQ=2181.45;QD=35.76;SB=-1110.34 GT:AD:DP:GL:GQ 1/1:0,61:61:-221.75,-18.37,-0.02:99 +chr1 4175576 rs4326593 G A 325.64 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=55.58;MQ0=0;OQ=888.28;QD=16.76;SB=-433.95 GT:AD:DP:GL:GQ 0/1:25,28:48:-106.58,-14.47,-68.77:99 +chr1 4175736 rs4615813 G C 667.23 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.55;MQ0=0;OQ=2403.10;QD=41.43;SB=-1195.96 GT:AD:DP:GL:GQ 1/1:0,58:56:-243.91,-16.87,-0.02:99 +chr1 4175807 rs28600106 C T 6.13 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=7.59;MQ=48.39;MQ0=0;OQ=365.75;QD=9.89;SB=-206.69 GT:AD:DP:GL:GQ 0/1:22,15:31:-49.20,-9.35,-60.01:99 +chr1 4175944 rs2898790 T C 0.54 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=5.41;MQ=54.62;MQ0=0;OQ=1686.61;QD=30.67;SB=-329.61 GT:AD:DP:GL:GQ 1/1:0,55:50:-172.27,-15.06,-0.02:99 +chr1 4176053 rs2411737 G C 0.30 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=4.08;MQ=49.96;MQ0=0;OQ=907.29;QD=30.24;SB=-45.91 GT:AD:DP:GL:GQ 1/1:0,30:23:-94.32,-6.93,-0.01:69.23 +chr1 4176083 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=2;HaplotypeScore=5.12;MQ=50.79;MQ0=0;OQ=53.84;QD=1.17;SB=68.23 GT:AD:DP:GL:GQ 0/1:30,16:35:-19.21,-10.54,-99.51:86.68 +chr1 4176698 rs10915477 G A 75.54 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=1.92;MQ=55.80;MQ0=0;OQ=3415.18;QD=40.18;SB=-1433.92 GT:AD:DP:GL:GQ 1/1:0,85:84:-340.52,-25.30,-0.02:99 +chr1 4176748 rs12060660 A C 70.84 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=3.65;MQ=58.23;MQ0=0;OQ=2781.95;QD=35.21;SB=-941.32 GT:AD:DP:GL:GQ 1/1:0,78:78:-285.04,-25.98,-3.27:99 +chr1 4176763 rs10915478 T C 721.59 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.18;MQ0=0;OQ=2617.35;QD=33.99;SB=-1088.89 GT:AD:DP:GL:GQ 1/1:0,77:74:-265.34,-22.29,-0.02:99 +chr1 4176794 rs12060664 A G 585.06 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=2362.72;QD=33.28;SB=-1094.09 GT:AD:DP:GL:GQ 1/1:0,71:67:-239.88,-20.19,-0.03:99 +chr1 4177795 rs4654423 T C 596.30 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=1639.97;QD=29.29;SB=-739.78 GT:AD:DP:GL:GQ 1/1:0,56:52:-167.62,-15.68,-0.04:99 +chr1 4177808 rs10915479 T C 281.74 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.62;MQ0=0;OQ=507.44;QD=10.36;SB=-255.93 GT:AD:DP:GL:GQ 0/1:30,19:46:-67.89,-13.86,-108.27:99 +chr1 4179046 rs12116719 G A 182.10 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=2853.60;QD=39.09;SB=-1453.00 GT:AD:DP:GL:GQ 1/1:0,73:73:-288.97,-22.00,-0.02:99 +chr1 4179422 rs59176411 C T 132.99 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=3.16;MQ=56.41;MQ0=0;OQ=2598.61;QD=37.12;SB=-1098.00 GT:AD:DP:GL:GQ 1/1:1,69:68:-267.13,-20.49,-3.69:99 +chr1 4179485 rs10737405 A G 230.94 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=55.59;MQ0=0;OQ=1795.14;QD=34.52;SB=-680.95 GT:AD:DP:GL:GQ 1/1:1,51:52:-187.08,-15.66,-3.98:99 +chr1 4180030 rs6657617 C T 6.27 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=2.45;MQ=59.28;MQ0=0;OQ=2474.15;QD=38.66;SB=-836.62 GT:AD:DP:GL:GQ 1/1:0,64:62:-251.01,-18.68,-0.02:99 +chr1 4180081 rs6426405 G A 604.48 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2617.17;QD=39.06;SB=-1069.36 GT:AD:DP:GL:GQ 1/1:0,67:67:-265.32,-20.19,-0.02:99 +chr1 4180490 rs4592237 G A 306.85 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.29;MQ0=0;OQ=1850.80;QD=34.92;SB=-947.36 GT:AD:DP:GL:GQ 1/1:0,53:49:-188.69,-14.77,-0.02:99 +chr1 4181020 rs10799216 G A 235.59 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.51;MQ=59.57;MQ0=0;OQ=3471.51;QD=40.37;SB=-1574.60 GT:AD:DP:GL:GQ 1/1:0,86:85:-346.15,-25.60,-0.02:99 +chr1 4181670 rs4233265 T C 517.98 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.29;MQ0=0;OQ=2065.74;QD=31.30;SB=-824.68 GT:AD:DP:GL:GQ 1/1:0,66:65:-210.21,-19.60,-0.06:99 +chr1 4182159 rs4654425 A G 260.71 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1828.94;QD=35.17;SB=-776.99 GT:AD:DP:GL:GQ 1/1:0,52:51:-186.50,-15.36,-0.02:99 +chr1 4182646 rs11579829 C T 305.04 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.69;MQ0=0;OQ=2773.62;QD=37.48;SB=-1347.81 GT:AD:DP:GL:GQ 1/1:0,74:71:-280.97,-21.39,-0.02:99 +chr1 4183175 rs2132177 C A 639.97 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2919.91;QD=36.50;SB=-1144.30 GT:AD:DP:GL:GQ 1/1:0,80:79:-295.60,-23.79,-0.02:99 +chr1 4184348 rs55978003 G A 105.51 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.52;MQ=59.27;MQ0=0;OQ=776.05;QD=15.22;SB=-305.78 GT:AD:DP:GL:GQ 0/1:27,23:48:-95.35,-14.46,-90.95:99 +chr1 4184779 rs7528938 C T 220.92 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.11;MQ0=0;OQ=1623.71;QD=34.55;SB=-657.89 GT:AD:DP:GL:GQ 1/1:1,44:43:-165.98,-12.96,-0.02:99 +chr1 4185286 rs17415519 A G 242.16 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=1.28;MQ=60.00;MQ0=0;OQ=1345.26;QD=33.63;SB=-658.93 GT:AD:DP:GL:GQ 1/1:0,40:39:-138.12,-11.75,-0.01:99 +chr1 4185339 . G T 41.06 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=12;HaplotypeScore=2.80;MQ=54.83;MQ0=0;QD=0.98;SB=22.81 GT:AD:DP:GL:GQ 0/1:35,7:35:-17.93,-10.54,-103.81:73.90 +chr1 4185557 rs4654516 G C 54.16 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=1.67;MQ=58.74;MQ0=0;OQ=2607.62;QD=37.25;SB=-842.00 GT:AD:DP:GL:GQ 1/1:1,69:66:-264.40,-19.92,-0.05:99 +chr1 4187570 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=2;HaplotypeScore=8.14;MQ=58.89;MQ0=0;OQ=68.10;QD=0.81;SB=131.41 GT:AD:DP:GL:GQ 0/1:59,24:60:-28.18,-18.09,-178.30:99 +chr1 4188372 rs1874267 T G 455.60 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=59.37;MQ0=0;OQ=1048.28;QD=15.88;SB=-524.40 GT:AD:DP:GL:GQ 0/1:29,37:66:-127.99,-19.88,-107.31:99 +chr1 4188412 rs1874266 A G 468.39 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.24;MQ0=0;OQ=798.75;QD=14.52;SB=-409.67 GT:AD:DP:GL:GQ 0/1:23,32:52:-98.84,-15.68,-83.89:99 +chr1 4188663 rs10915480 A G 337.33 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.23;MQ0=0;OQ=1153.25;QD=13.73;SB=-560.60 GT:AD:DP:GL:GQ 0/1:38,45:83:-146.27,-27.66,-153.88:99 +chr1 4188905 rs10753374 A G 386.21 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1195.33;QD=15.73;SB=-552.85 GT:AD:DP:GL:GQ 0/1:35,41:76:-145.71,-22.90,-141.29:99 +chr1 4189544 rs10753375 T G 601.10 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1995.47;QD=35.01;SB=-845.10 GT:AD:DP:GL:GQ 1/1:0,57:56:-203.15,-16.86,-0.01:99 +chr1 4189582 rs10799217 A G 68.61 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=59.39;MQ0=0;OQ=909.16;QD=14.90;SB=-461.96 GT:AD:DP:GL:GQ 0/1:30,31:61:-112.58,-18.38,-119.06:99 +chr1 4189759 rs10799218 T C 84.36 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=3;HaplotypeScore=1.76;MQ=58.80;MQ0=0;OQ=827.52;QD=11.18;SB=-285.14 GT:AD:DP:GL:GQ 0/1:41,32:73:-108.03,-22.00,-167.09:99 +chr1 4191122 rs6426406 T C 3.61 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=7.31;MQ=59.57;MQ0=0;OQ=717.35;QD=10.71;SB=-224.24 GT:AD:DP:GL:GQ 0/1:37,30:64:-94.30,-19.28,-145.85:99 +chr1 4191702 rs7541544 T C 425.11 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=59.70;MQ0=0;OQ=729.14;QD=11.76;SB=-343.04 GT:AD:DP:GL:GQ 0/1:32,30:60:-94.28,-18.09,-122.33:99 +chr1 4191813 rs7534461 C G 457.73 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=1324.41;QD=15.96;SB=-593.50 GT:AD:DP:GL:GQ 0/1:46,37:83:-160.73,-25.00,-206.24:99 +chr1 4191898 rs7534558 C T 290.90 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=2.06;MQ=60.00;MQ0=0;OQ=1246.57;QD=14.17;SB=-621.73 GT:AD:DP:GL:GQ 0/1:50,38:86:-153.86,-25.92,-153.30:99 +chr1 4191985 rs10799219 G C 69.97 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=2.07;MQ=59.38;MQ0=0;OQ=1617.32;QD=21.86;SB=-548.71 GT:AD:DP:GL:GQ 0/1:32,42:72:-186.71,-21.70,-128.86:99 +chr1 4192218 rs10159168 A T 343.86 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1388.76;QD=16.94;SB=-472.56 GT:AD:DP:GL:GQ 0/1:39,43:82:-166.86,-24.70,-146.13:99 +chr1 4195817 rs1390135 T G 143.92 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=58.67;MQ0=0;OQ=705.86;QD=11.20;SB=-334.03 GT:AD:DP:GL:GQ 0/1:33,30:61:-92.25,-18.38,-113.54:99 +chr1 4197896 . G A 10.32 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.52;MQ0=0;OQ=1035.41;QD=21.57;SB=-410.45 GT:AD:DP:GL:GQ 0/1:18,30:48:-121.29,-14.46,-58.46:99 +chr1 4198535 rs1495242 A G 438.02 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1076.27;QD=12.97;SB=-544.21 GT:AD:DP:GL:GQ 0/1:44,39:81:-135.31,-24.40,-175.25:99 +chr1 4199191 rs12124378 C T 379.71 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=1302.45;QD=20.35;SB=-581.61 GT:AD:DP:GL:GQ 0/1:26,38:63:-152.50,-18.97,-95.47:99 +chr1 4199881 . G T 32.56 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=2;HaplotypeScore=5.28;MQ=57.83;MQ0=0;QD=0.74;SB=74.26 GT:AD:DP:GL:GQ 0/1:31,13:34:-16.78,-10.24,-105.31:65.40 +chr1 4200007 . G A 96.98 PASS AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.35;MQ0=0;OQ=1236.21;QD=18.45;SB=-537.73 GT:AD:DP:GL:GQ 0/1:28,39:63:-145.88,-18.98,-96.95:99 +chr1 4200165 rs6426407 A G 72.52 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=58.49;MQ0=0;OQ=1344.67;QD=18.17;SB=-519.96 GT:AD:DP:GL:GQ 0/1:29,44:72:-159.44,-21.69,-113.24:99 +chr1 4200817 rs4654518 G A 711.75 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2818.25;QD=39.69;SB=-1209.38 GT:AD:DP:GL:GQ 1/1:0,71:70:-285.42,-21.08,-0.01:99 +chr1 4202021 rs12124548 G A 209.11 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.70;MQ0=0;OQ=1241.05;QD=20.02;SB=-465.47 GT:AD:DP:GL:GQ 0/1:26,36:61:-145.77,-18.38,-85.04:99 +chr1 4202445 rs12405770 A G 576.59 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1249.87;QD=15.62;SB=-595.92 GT:AD:DP:GL:GQ 0/1:37,43:79:-152.07,-23.80,-148.48:99 +chr1 4202474 rs6426409 T G 405.59 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.78;MQ0=0;OQ=1102.86;QD=13.13;SB=-556.72 GT:AD:DP:GL:GQ 0/1:44,40:82:-138.27,-24.70,-157.66:99 +chr1 4204888 rs12132080 A T 242.23 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=1.72;MQ=45.12;MQ0=6;OQ=964.76;QD=12.69;SB=-408.56 GT:AD:DP:GL:GQ 0/1:34,42:65:-119.34,-19.58,-129.51:99 +chr1 4208143 rs6690300 T G 448.20 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.45;MQ0=0;OQ=967.38;QD=12.73;SB=-340.51 GT:AD:DP:GL:GQ 0/1:41,35:76:-122.91,-22.89,-152.81:99 +chr1 4208388 rs12239600 T C 466.70 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.66;MQ0=0;OQ=937.21;QD=13.78;SB=-484.77 GT:AD:DP:GL:GQ 0/1:32,36:68:-117.50,-20.50,-127.59:99 +chr1 4208894 rs12078298 T A 402.94 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.48;MQ0=0;OQ=1434.64;QD=16.12;SB=-624.40 GT:AD:DP:GL:GQ 0/1:43,46:88:-173.25,-26.51,-162.85:99 +chr1 4209813 rs6679489 G A 164.07 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=60.00;MQ0=0;OQ=1435.86;QD=16.89;SB=-638.14 GT:AD:DP:GL:GQ 0/1:41,44:83:-171.87,-25.00,-148.88:99 +chr1 4211295 rs4654519 C T 437.58 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.97;MQ0=0;OQ=1264.42;QD=19.76;SB=-439.80 GT:AD:DP:GL:GQ 0/1:26,38:62:-148.40,-18.68,-90.27:99 +chr1 4211773 rs10915487 T G 175.84 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=59.23;MQ0=0;OQ=638.07;QD=10.29;SB=-306.76 GT:AD:DP:GL:GQ 0/1:37,25:61:-85.47,-18.38,-128.27:99 +chr1 4212065 rs1908490 C T 369.52 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=57.82;MQ0=0;OQ=1109.73;QD=15.20;SB=-541.53 GT:AD:DP:GL:GQ 0/1:40,33:71:-135.64,-21.39,-134.48:99 +chr1 4213163 rs12741715 A T 578.55 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1267.51;QD=16.90;SB=-452.19 GT:AD:DP:GL:GQ 0/1:35,40:74:-152.32,-22.29,-133.91:99 +chr1 4215064 rs966321 G T 6.64 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=4;HaplotypeScore=2.95;MQ=59.70;MQ0=0;OQ=1037.52;QD=13.65;SB=-540.72 GT:AD:DP:GL:GQ 0/1:40,36:75:-129.62,-22.59,-142.94:99 +chr1 4215408 rs12691488 C T 601.59 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1073.26;QD=16.02;SB=-541.06 GT:AD:DP:GL:GQ 0/1:35,32:66:-130.50,-19.89,-109.64:99 +chr1 4216644 rs964715 T C 389.60 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=939.74;QD=14.46;SB=-445.57 GT:AD:DP:GL:GQ 0/1:32,33:65:-116.84,-19.58,-130.15:99 +chr1 4217111 rs1495250 T C 316.94 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=60.00;MQ0=0;OQ=777.71;QD=11.44;SB=-393.04 GT:AD:DP:GL:GQ 0/1:36,32:67:-101.25,-20.19,-143.99:99 +chr1 4218910 rs11583756 G A 393.34 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=562.25;QD=10.41;SB=-300.82 GT:AD:DP:GL:GQ 0/1:33,21:51:-74.88,-15.38,-106.07:99 +chr1 4219107 rs7545415 G A 274.25 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.24;MQ0=0;OQ=794.53;QD=14.45;SB=-389.90 GT:AD:DP:GL:GQ 0/1:30,25:51:-98.11,-15.38,-85.30:99 +chr1 4221548 rs1826719 G A 1.65 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=1;HaplotypeScore=9.57;MQ=59.01;MQ0=0;OQ=1104.32;QD=16.73;SB=-370.86 GT:AD:DP:GL:GQ 0/1:31,34:63:-132.39,-18.68,-107.97:99 +chr1 4221834 rs1390137 T A 402.30 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.24;MQ0=0;OQ=1338.31;QD=14.71;SB=-600.22 GT:AD:DP:GL:GQ 0/1:48,43:91:-164.52,-27.41,-184.18:99 +chr1 4222993 rs7526339 A G 180.71 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=860.50;QD=13.04;SB=-424.26 GT:AD:DP:GL:GQ 0/1:36,30:65:-108.91,-19.58,-143.92:99 +chr1 4225449 rs9286982 A C 384.55 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.50;MQ0=0;OQ=1099.77;QD=14.66;SB=-338.80 GT:AD:DP:GL:GQ 0/1:38,37:74:-135.55,-22.29,-134.84:99 +chr1 4226228 rs2411738 G A 332.71 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=1328.38;QD=18.98;SB=-511.52 GT:AD:DP:GL:GQ 0/1:30,40:68:-156.63,-20.50,-89.85:99 +chr1 4227495 rs2101576 C T 457.85 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.43;MQ0=0;OQ=1111.42;QD=15.22;SB=-551.59 GT:AD:DP:GL:GQ 0/1:39,34:73:-136.43,-22.01,-124.07:99 +chr1 4227724 rs10915493 G A 108.64 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=60.00;MQ0=0;OQ=1106.23;QD=18.75;SB=-402.40 GT:AD:DP:GL:GQ 0/1:26,33:59:-131.68,-17.78,-92.93:99 +chr1 4228365 . G A 59.74 PASS AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=2.28;MQ=58.73;MQ0=0;OQ=1218.17;QD=16.69;SB=-516.71 GT:AD:DP:GL:GQ 0/1:36,37:71:-146.49,-21.39,-124.67:99 +chr1 4228440 rs11586171 G A 378.40 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=59.25;MQ0=0;OQ=793.38;QD=14.17;SB=-261.74 GT:AD:DP:GL:GQ 0/1:30,26:52:-98.30,-15.68,-86.01:99 +chr1 4228626 rs10799221 A G 244.66 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=59.55;MQ0=0;OQ=773.13;QD=15.16;SB=-359.35 GT:AD:DP:GL:GQ 0/1:24,27:50:-95.66,-15.07,-89.39:99 +chr1 4230147 rs6677984 A G 313.94 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.80;MQ0=0;OQ=752.97;QD=10.61;SB=-294.25 GT:AD:DP:GL:GQ 0/1:36,35:64:-97.88,-19.30,-127.54:99 +chr1 4231035 . G A 41.87 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=59.27;MQ0=0;OQ=1023.37;QD=17.95;SB=-471.06 GT:AD:DP:GL:GQ 0/1:23,34:54:-121.89,-16.27,-83.08:99 +chr1 4231643 rs4654426 A G 357.68 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=59.13;MQ0=0;OQ=804.91;QD=14.63;SB=-368.10 GT:AD:DP:GL:GQ 0/1:22,33:51:-99.15,-15.37,-84.11:99 +chr1 4232195 . G A 71.35 PASS AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=60.00;MQ0=0;OQ=896.42;QD=13.18;SB=-396.87 GT:AD:DP:GL:GQ 0/1:39,29:68:-113.42,-20.50,-128.87:99 +chr1 4232590 rs7527612 G A 196.65 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.22;MQ=59.61;MQ0=0;OQ=598.22;QD=12.46;SB=-285.21 GT:AD:DP:GL:GQ 0/1:26,20:44:-76.37,-13.26,-81.07:99 +chr1 4233150 rs10737406 C T 190.39 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1662.89;QD=19.34;SB=-750.79 GT:AD:DP:GL:GQ 0/1:38,48:86:-195.48,-25.90,-136.98:99 +chr1 4233365 rs10737407 T C 106.83 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.79;MQ0=0;OQ=829.78;QD=9.43;SB=-420.85 GT:AD:DP:GL:GQ 0/1:52,36:87:-112.48,-26.22,-211.16:99 +chr1 4233528 rs10737408 T C 490.54 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1057.73;QD=14.90;SB=-414.29 GT:AD:DP:GL:GQ 0/1:30,41:71:-130.46,-21.40,-122.91:99 +chr1 4233635 rs10799223 G C 53.92 PASS AC=1;AF=0.50;AN=2;DB;DP=99;Dels=0.00;HRun=0;HaplotypeScore=4.97;MQ=59.34;MQ0=0;OQ=1650.26;QD=16.67;SB=-729.99 GT:AD:DP:GL:GQ 0/1:53,46:99:-198.14,-29.83,-227.12:99 +chr1 4234047 rs12095914 C T 0.73 PASS AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=9.26;MQ=42.37;MQ0=0;OQ=137.29;QD=9.81;SB=-42.54 GT:AD:DP:GL:GQ 0/1:9,5:10:-20.03,-3.01,-17.15:99 +chr1 4234051 rs56077919 C T 1.78 PASS AC=1;AF=0.50;AN=2;DB;DP=12;Dels=0.00;HRun=0;HaplotypeScore=7.11;MQ=38.66;MQ0=0;OQ=106.65;QD=8.89;SB=-40.54 GT:AD:DP:GL:GQ 0/1:8,4:8:-16.36,-2.41,-14.46:99 +chr1 4234076 . T C 1.57 PASS AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=36.23;MQ0=1;OQ=55.15;QD=6.13;SB=-6.99 GT:AD:DP:GL:GQ 0/1:6,3:7:-10.91,-2.11,-15.53:87.98 +chr1 4234095 rs12752111 C T 29.22 LowQual AC=1;AF=0.50;AN=2;DB;DP=8;Dels=0.00;HRun=1;HaplotypeScore=2.44;MQ=42.08;MQ0=1;QD=3.65;SB=-10.00 GT:AD:DP:GL:GQ 0/1:5,3:6:-8.01,-1.81,-14.07:62.05 +chr1 4234115 . T C 41.10 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=0;HaplotypeScore=27.16;MQ=46.57;MQ0=0;QD=2.94;SB=-6.99 GT:AD:DP:GL:GQ 0/1:10,4:11:-10.71,-3.31,-31.76:73.94 +chr1 4234119 . T C 26.07 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=19;Dels=0.00;HRun=0;HaplotypeScore=23.15;MQ=48.70;MQ0=0;QD=1.37;SB=-6.99 GT:AD:DP:GL:GQ 0/1:13,6:15:-10.41,-4.52,-48.38:58.90 +chr1 4234123 . T C 99.42 SnpCluster AC=1;AF=0.50;AN=2;DP=22;Dels=0.00;HRun=0;HaplotypeScore=15.26;MQ=47.83;MQ0=0;QD=4.52;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,7:16:-18.04,-4.82,-44.01:99 +chr1 4234141 . C T 11.93 LowQual AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=3;HaplotypeScore=2.90;MQ=45.82;MQ0=0;QD=0.38;SB=-10.00 GT:AD:DP:GL:GQ 0/1:27,4:24:-11.68,-7.23,-69.44:44.48 +chr1 4234162 rs55680202 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.02;HRun=14;HaplotypeScore=7.57;MQ=46.57;MQ0=0;OQ=162.83;QD=3.54;SB=-20.39 GT:AD:DP:GL:GQ 0/1:36,9:39:-31.01,-11.45,-100.16:99 +chr1 4234461 rs2898791 C A 324.76 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=54.58;MQ0=0;OQ=1440.90;QD=17.57;SB=-669.70 GT:AD:DP:GL:GQ 0/1:33,49:78:-170.87,-23.50,-98.97:99 +chr1 4235747 rs1495243 G A 21.65 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=2;HaplotypeScore=0.87;MQ=59.34;MQ0=0;OQ=727.40;QD=20.78;SB=-304.24 GT:AD:DP:GL:GQ 0/1:14,21:34:-86.27,-10.24,-44.00:99 +chr1 4235753 rs903541 A G 320.84 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=658.30;QD=17.79;SB=-304.49 GT:AD:DP:GL:GQ 0/1:15,22:36:-79.96,-10.84,-57.03:99 +chr1 4236215 rs2411739 T C 3.39 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=4;HaplotypeScore=1.73;MQ=54.14;MQ0=0;OQ=570.50;QD=9.84;SB=-308.25 GT:AD:DP:GL:GQ 0/1:27,31:50:-75.41,-15.07,-105.40:99 +chr1 4243198 rs6658727 T C 21.46 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=56.21;MQ0=0;OQ=1400.87;QD=30.45;SB=-402.32 GT:AD:DP:GL:GQ 1/1:0,46:43:-143.70,-12.96,-0.03:99 +chr1 4254604 rs1495248 G A 254.74 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.88;MQ0=0;OQ=575.96;QD=13.39;SB=-220.90 GT:AD:DP:GL:GQ 0/1:24,19:42:-73.53,-12.65,-79.75:99 +chr1 4255328 rs2130621 G A 47.37 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=4.28;MQ=59.31;MQ0=0;OQ=1064.10;QD=15.88;SB=-426.97 GT:AD:DP:GL:GQ 0/1:33,34:65:-129.28,-19.59,-111.47:99 +chr1 4255353 rs12123539 G C 316.52 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=1198.39;QD=17.89;SB=-531.27 GT:AD:DP:GL:GQ 0/1:31,36:67:-143.33,-20.20,-136.21:99 +chr1 4255453 rs2029490 A G 353.66 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.70;MQ0=0;OQ=1028.79;QD=13.19;SB=-497.67 GT:AD:DP:GL:GQ 0/1:34,44:74:-128.48,-22.32,-128.69:99 +chr1 4256070 rs61769407 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.03;HRun=0;HaplotypeScore=33.48;MQ=52.67;MQ0=1;OQ=340.13;QD=5.08;SB=-156.75 GT:AD:DP:GL:GQ 0/1:47,18:58:-54.18,-16.88,-142.71:99 +chr1 4256256 rs12563155 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=93.47;MQ=55.97;MQ0=0;OQ=536.64;QD=7.56;SB=-213.44 GT:AD:DP:GL:GQ 0/1:49,22:63:-75.92,-18.98,-150.16:99 +chr1 4256294 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=8.05;MQ=57.07;MQ0=1;OQ=87.19;QD=1.23;SB=41.60 GT:AD:DP:GL:GQ 0/1:61,10:65:-31.59,-19.59,-196.34:99 +chr1 4256295 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=7.58;MQ=57.07;MQ0=1;OQ=86.67;QD=1.22;SB=35.22 GT:AD:DP:GL:GQ 0/1:61,10:60:-30.03,-18.08,-181.58:99 +chr1 4256665 rs11487456 A C 56.20 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=2.90;MQ=57.92;MQ0=0;OQ=976.57;QD=11.10;SB=-464.71 GT:AD:DP:GL:GQ 0/1:50,38:85:-126.54,-25.60,-185.54:99 +chr1 4258667 rs10753377 G C 1.06 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=5;HaplotypeScore=1.15;MQ=59.53;MQ0=0;OQ=783.06;QD=15.98;SB=-363.09 GT:AD:DP:GL:GQ 0/1:26,23:47:-95.76,-14.17,-99.93:99 +chr1 4259991 rs592323 G T 282.55 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=1759.13;QD=36.65;SB=-870.26 GT:AD:DP:GL:GQ 1/1:0,48:48:-179.51,-14.45,-0.01:99 +chr1 4261395 rs513096 G A 177.19 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.21;MQ=58.45;MQ0=0;OQ=707.77;QD=15.73;SB=-231.55 GT:AD:DP:GL:GQ 0/1:23,22:44:-87.33,-13.26,-70.99:99 +chr1 4262899 . A G 18.25 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=43.81;MQ=48.38;MQ0=0;QD=0.33;SB=-10.00 GT:AD:DP:GL:GQ 0/1:50,5:40:-17.15,-12.05,-140.45:51.02 +chr1 4262904 rs28675202 G A 73.10 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=14.98;MQ=50.70;MQ0=0;QD=1.43;SB=-10.00 GT:AD:DP:GL:GQ 0/1:40,11:45:-24.15,-13.55,-132.97:99 +chr1 4262909 . G A 79.12 SnpCluster AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=5.00;MQ=50.76;MQ0=0;QD=1.65;SB=-10.00 GT:AD:DP:GL:GQ 0/1:37,11:43:-24.15,-12.95,-125.43:99 +chr1 4262914 rs629808 G A 33.56 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=52.89;MQ=50.96;MQ0=0;QD=0.68;SB=-10.00 GT:AD:DP:GL:GQ 0/1:39,10:44:-19.89,-13.25,-132.97:66.40 +chr1 4262923 . C T 231.89 SnpCluster AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=36.64;MQ=51.44;MQ0=0;QD=5.27;SB=-10.00 GT:AD:DP:GL:GQ 0/1:30,14:37:-37.63,-11.16,-89.50:99 +chr1 4262924 rs3124336 G A 119.70 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=42.63;MQ=51.44;MQ0=0;QD=2.72;SB=-10.00 GT:AD:DP:GL:GQ 0/1:30,14:37:-26.40,-11.15,-102.56:99 +chr1 4262928 . C T 227.91 SnpCluster AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=40.91;MQ=51.65;MQ0=0;QD=5.06;SB=-10.00 GT:AD:DP:GL:GQ 0/1:31,14:38:-37.54,-11.47,-89.09:99 +chr1 4262934 . G A 212.81 SnpCluster AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=38.78;MQ=51.84;MQ0=0;QD=4.63;SB=-10.00 GT:AD:DP:GL:GQ 0/1:35,11:39:-36.31,-11.75,-102.65:99 +chr1 4262955 . C T 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=37;Dels=0.00;HRun=1;HaplotypeScore=10.30;MQ=55.28;MQ0=0;OQ=119.85;QD=3.24;SB=-10.00 GT:AD:DP:GL:GQ 0/1:30,7:34:-25.51,-10.24,-106.69:99 +chr1 4262965 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=4.99;MQ=55.83;MQ0=0;OQ=58.64;QD=1.63;SB=-10.00 GT:AD:DP:GL:GQ 0/1:31,5:33:-19.09,-9.94,-116.28:91.47 +chr1 4263200 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=16.50;MQ=29.51;MQ0=20;OQ=97.44;QD=2.38;SB=-10.00 GT:AD:DP:GL:GQ 0/1:35,5:14:-17.24,-4.22,-36.40:99 +chr1 4263205 rs12035244 T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=20.28;MQ=30.89;MQ0=18;OQ=95.43;QD=2.27;SB=-10.00 GT:AD:DP:GL:GQ 0/1:37,5:15:-17.34,-4.52,-40.16:99 +chr1 4263595 rs34429154 C A 184.54 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=59.01;MQ0=0;OQ=488.72;QD=10.40;SB=-267.26 GT:AD:DP:GL:GQ 0/1:29,18:46:-66.01,-13.86,-101.87:99 +chr1 4263832 rs584035 G A 216.29 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.61;MQ0=0;OQ=1091.44;QD=18.50;SB=-496.53 GT:AD:DP:GL:GQ 0/1:27,32:59:-130.21,-17.78,-86.40:99 +chr1 4263930 rs503536 G A 202.82 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=59.57;MQ0=0;OQ=661.52;QD=12.25;SB=-344.44 GT:AD:DP:GL:GQ 0/1:32,22:49:-84.20,-14.76,-96.54:99 +chr1 4264086 rs693734 C T 101.31 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=2.89;MQ=58.91;MQ0=0;OQ=1021.37;QD=17.02;SB=-501.11 GT:AD:DP:GL:GQ 0/1:29,31:59:-123.20,-17.78,-92.76:99 +chr1 4264332 rs1106307 A G 290.23 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.63;MQ=59.33;MQ0=0;OQ=913.45;QD=14.73;SB=-354.33 GT:AD:DP:GL:GQ 0/1:28,34:58:-112.10,-17.47,-104.59:99 +chr1 4264424 rs2132176 A G 368.22 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=613.38;QD=11.15;SB=-237.28 GT:AD:DP:GL:GQ 0/1:30,25:53:-80.60,-15.97,-111.46:99 +chr1 4264542 rs2132174 T A 221.74 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=52.27;MQ0=0;OQ=1008.56;QD=17.69;SB=-458.63 GT:AD:DP:GL:GQ 0/1:21,35:54:-122.63,-18.49,-81.00:99 +chr1 4264801 rs3007778 G C 66.30 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.47;MQ=58.11;MQ0=0;OQ=580.26;QD=12.35;SB=-271.29 GT:AD:DP:GL:GQ 0/1:28,19:44:-74.59,-13.28,-102.55:99 +chr1 4265009 rs3007777 C A 272.57 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.09;MQ0=0;OQ=812.00;QD=17.65;SB=-415.86 GT:AD:DP:GL:GQ 0/1:19,27:45:-98.04,-13.55,-64.20:99 +chr1 4265174 . G A 199.75 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=560.44;QD=13.67;SB=-202.85 GT:AD:DP:GL:GQ 0/1:23,18:41:-71.68,-12.35,-78.36:99 +chr1 4265866 rs56198562 A G 125.40 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=2.61;MQ=59.78;MQ0=0;OQ=979.47;QD=11.66;SB=-298.20 GT:AD:DP:GL:GQ 0/1:43,41:82:-125.95,-24.72,-170.33:99 +chr1 4266398 rs1495240 C T 180.37 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.09;MQ0=0;OQ=962.96;QD=18.88;SB=-480.01 GT:AD:DP:GL:GQ 0/1:23,28:47:-113.74,-14.16,-62.01:99 +chr1 4266494 rs1845634 G A 227.70 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1124.56;QD=17.85;SB=-553.73 GT:AD:DP:GL:GQ 0/1:30,33:63:-134.72,-18.98,-108.50:99 +chr1 4267183 rs1490413 G A 163.02 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=1.58;MQ=59.39;MQ0=0;OQ=1192.58;QD=17.54;SB=-578.10 GT:AD:DP:GL:GQ 0/1:31,37:66:-142.43,-19.88,-110.71:99 +chr1 4267249 rs16838591 G A 109.35 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.45;MQ0=0;OQ=560.73;QD=16.49;SB=-154.59 GT:AD:DP:GL:GQ 0/1:17,17:34:-69.60,-10.24,-59.00:99 +chr1 4267670 rs17448695 C T 256.61 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=2.17;MQ=59.11;MQ0=0;OQ=785.86;QD=16.72;SB=-406.95 GT:AD:DP:GL:GQ 0/1:22,24:45:-95.42,-13.55,-80.15:99 +chr1 4267782 rs1817914 T C 324.51 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.97;MQ0=0;OQ=827.52;QD=14.03;SB=-394.24 GT:AD:DP:GL:GQ 0/1:29,30:58:-103.51,-17.47,-117.96:99 +chr1 4267840 rs2934983 G A 322.55 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.36;MQ0=0;OQ=1060.38;QD=18.28;SB=-513.09 GT:AD:DP:GL:GQ 0/1:26,32:57:-126.49,-17.17,-95.38:99 +chr1 4267886 rs1817913 A G 440.55 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=738.48;QD=13.43;SB=-393.26 GT:AD:DP:GL:GQ 0/1:24,31:50:-92.21,-15.08,-81.77:99 +chr1 4268301 rs351622 A T 719.15 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.09;MQ0=0;OQ=1814.47;QD=35.58;SB=-930.73 GT:AD:DP:GL:GQ 1/1:0,51:49:-185.04,-14.76,-0.01:99 +chr1 4268579 rs351621 T C 72.96 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.25;MQ0=0;OQ=1364.91;QD=27.30;SB=-524.09 GT:AD:DP:GL:GQ 1/1:0,50:43:-140.11,-12.97,-0.04:99 +chr1 4268604 rs351620 C T 134.99 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.70;MQ=59.46;MQ0=0;OQ=1433.75;QD=33.34;SB=-736.64 GT:AD:DP:GL:GQ 1/1:0,43:39:-146.99,-11.76,-0.03:99 +chr1 4268679 rs351619 G A 84.28 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=1739.98;QD=37.83;SB=-519.64 GT:AD:DP:GL:GQ 1/1:0,46:44:-177.59,-13.26,-0.01:99 +chr1 4268802 rs351618 T C 98.42 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=1092.21;QD=26.64;SB=-356.42 GT:AD:DP:GL:GQ 1/1:0,41:37:-112.85,-11.17,-0.05:99 +chr1 4268811 rs351617 C T 143.28 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1491.48;QD=36.38;SB=-509.63 GT:AD:DP:GL:GQ 1/1:1,40:39:-152.75,-11.76,-0.02:99 +chr1 4268960 rs2087571 C T 152.24 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=53.63;MQ0=0;OQ=643.83;QD=17.40;SB=-299.23 GT:AD:DP:GL:GQ 0/1:15,22:34:-77.91,-10.25,-47.03:99 +chr1 4269767 rs351616 A G 168.33 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.39;MQ=58.87;MQ0=0;OQ=1214.77;QD=29.63;SB=-431.27 GT:AD:DP:GL:GQ 1/1:0,41:38:-125.09,-11.46,-0.03:99 +chr1 4270245 rs351615 G A 292.81 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=58.55;MQ0=0;OQ=1966.57;QD=35.76;SB=-975.01 GT:AD:DP:GL:GQ 1/1:0,54:52:-200.27,-15.67,-0.02:99 +chr1 4271723 rs351614 C T 601.68 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2473.56;QD=39.90;SB=-1111.03 GT:AD:DP:GL:GQ 1/1:0,62:62:-250.96,-18.68,-0.01:99 +chr1 4271809 rs12132314 C T 430.38 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.65;MQ0=0;OQ=1181.91;QD=18.18;SB=-613.64 GT:AD:DP:GL:GQ 0/1:30,35:65:-141.06,-19.59,-97.20:99 +chr1 4273032 rs171260 A C 300.19 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=870.08;QD=12.08;SB=-225.83 GT:AD:DP:GL:GQ 0/1:41,31:71:-111.68,-21.38,-150.14:99 +chr1 4274131 rs351613 A C 265.29 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.14;MQ0=0;OQ=2299.32;QD=35.37;SB=-1119.04 GT:AD:DP:GL:GQ 1/1:0,65:65:-233.54,-19.58,-0.02:99 +chr1 4277771 rs351596 C T 568.91 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=2579.09;QD=39.68;SB=-949.23 GT:AD:DP:GL:GQ 1/1:0,65:64:-261.51,-19.28,-0.02:99 +chr1 4279737 rs876273 C G 132.40 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=4.17;MQ=59.56;MQ0=0;OQ=768.76;QD=14.78;SB=-189.63 GT:AD:DP:GL:GQ 0/1:23,29:48:-94.65,-14.49,-97.38:99 +chr1 4279818 rs351598 A T 381.51 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.53;MQ=59.66;MQ0=0;OQ=991.33;QD=14.58;SB=-452.46 GT:AD:DP:GL:GQ 0/1:35,33:67:-122.60,-20.18,-130.61:99 +chr1 4280055 rs1874269 C T 619.47 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.78;MQ0=0;OQ=2766.74;QD=39.52;SB=-1179.55 GT:AD:DP:GL:GQ 1/1:0,70:69:-280.28,-20.79,-0.02:99 +chr1 4280204 rs2411741 C A 180.72 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=1.15;MQ=60.13;MQ0=0;OQ=1218.75;QD=14.51;SB=-564.82 GT:AD:DP:GL:GQ 0/1:42,42:82:-149.85,-24.70,-149.73:99 +chr1 4280489 rs351599 C T 413.51 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.72;MQ0=0;OQ=1071.03;QD=16.23;SB=-457.49 GT:AD:DP:GL:GQ 0/1:33,33:66:-130.29,-19.90,-102.77:99 +chr1 4285644 . A G 0.07 PASS AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=4;HaplotypeScore=2.54;MQ=57.79;MQ0=0;OQ=595.83;QD=12.16;SB=-120.71 GT:AD:DP:GL:GQ 0/1:26,23:47:-77.03,-14.16,-95.21:99 +chr1 4288221 . G A 0.84 PASS AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=1;HaplotypeScore=8.13;MQ=58.71;MQ0=0;OQ=1360.73;QD=16.39;SB=-394.38 GT:AD:DP:GL:GQ 0/1:43,40:81:-163.76,-24.40,-149.01:99 +chr1 4289709 . T G 46.86 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=16.54;MQ=56.55;MQ0=0;QD=0.98;SB=53.18 GT:AD:DP:GL:GQ 0/1:27,21:32:-17.62,-9.65,-87.21:79.70 +chr1 4292594 rs34245285 G C 0.05 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=3.96;MQ=50.65;MQ0=4;OQ=195.36;QD=3.15;SB=-102.43 GT:AD:DP:GL:GQ 0/1:47,15:34:-33.09,-10.27,-97.74:99 +chr1 4293081 rs34762254 C G 17.74 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=35.42;MQ0=7;QD=0.43;SB=11.07 GT:AD:DP:GL:GQ 0/1:35,5:26:-12.90,-7.85,-90.70:50.51 +chr1 4293374 . G A 3.97 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=44.45;MQ0=2;OQ=329.37;QD=6.59;SB=0.51 GT:AD:DP:GL:GQ 0/1:31,19:40:-48.28,-12.06,-89.72:99 +chr1 4296431 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.01;HRun=0;HaplotypeScore=166.11;MQ=33.71;MQ0=1;OQ=76.77;QD=0.64;SB=116.41 GT:AD:DP:GL:GQ 0/1:95,22:100:-40.80,-29.83,-343.52:99 +chr1 4296441 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=126;Dels=0.07;HRun=0;HaplotypeScore=204.38;MQ=34.16;MQ0=1;OQ=63.06;QD=0.50;SB=111.78 GT:AD:DP:GL:GQ 0/1:104,10:96:-43.83,-34.24,-290.54:95.89 +chr1 4296449 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=0;HaplotypeScore=184.01;MQ=35.76;MQ0=1;OQ=76.57;QD=0.81;SB=108.85 GT:AD:DP:GL:GQ 0/1:78,6:65:-53.79,-42.85,-256.56:99 +chr1 4296459 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=1;HaplotypeScore=225.82;MQ=37.43;MQ0=0;OQ=345.89;QD=3.98;SB=26.09 GT:AD:DP:GL:GQ 0/1:63,24:68:-58.36,-20.48,-198.46:99 +chr1 4296469 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=95;Dels=0.00;HRun=1;HaplotypeScore=189.98;MQ=37.41;MQ0=0;OQ=75.74;QD=0.80;SB=12.63 GT:AD:DP:GL:GQ 0/1:84,11:69:-31.64,-20.79,-221.92:99 +chr1 4296493 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=88.30;MQ=41.30;MQ0=0;OQ=474.04;QD=4.65;SB=-167.48 GT:AD:DP:GL:GQ 0/1:59,36:81:-93.85,-43.16,-272.31:99 +chr1 4296506 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=103;Dels=0.03;HRun=1;HaplotypeScore=78.61;MQ=43.01;MQ0=0;OQ=51.88;QD=0.50;SB=101.36 GT:AD:DP:GL:GQ 0/1:87,13:87:-34.09,-25.62,-299.11:84.72 +chr1 4296513 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=0;HaplotypeScore=60.45;MQ=43.56;MQ0=0;OQ=185.47;QD=1.85;SB=-3.86 GT:AD:DP:GL:GQ 0/1:80,18:74:-44.13,-22.29,-236.48:99 +chr1 4296520 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=111;Dels=0.00;HRun=1;HaplotypeScore=86.57;MQ=43.66;MQ0=0;OQ=90.49;QD=0.82;SB=69.81 GT:AD:DP:GL:GQ 0/1:99,12:95:-40.96,-28.62,-301.41:99 +chr1 4296571 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=100;Dels=0.02;HRun=0;HaplotypeScore=148.81;MQ=42.35;MQ0=0;OQ=149.13;QD=1.49;SB=56.28 GT:AD:DP:GL:GQ 0/1:64,20:79:-66.77,-48.58,-247.91:99 +chr1 4296587 . G A 55.07 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=113;Dels=0.02;HRun=0;HaplotypeScore=138.42;MQ=36.11;MQ0=2;QD=0.49;SB=3.46 GT:AD:DP:GL:GQ 0/1:83,28:77:-31.99,-23.20,-236.17:87.91 +chr1 4296590 . A G 63.20 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=113;Dels=0.01;HRun=1;HaplotypeScore=134.39;MQ=36.11;MQ0=2;QD=0.56;SB=44.15 GT:AD:DP:GL:GQ 0/1:101,11:84:-34.62,-25.01,-283.57:96.04 +chr1 4296596 . G A 133.96 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=190.44;MQ=35.58;MQ0=2;QD=1.09;SB=41.12 GT:AD:DP:GL:GQ 0/1:107,16:99:-46.51,-29.83,-296.83:99 +chr1 4296607 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=125;Dels=0.00;HRun=1;HaplotypeScore=185.73;MQ=34.74;MQ0=2;OQ=309.12;QD=2.47;SB=41.15 GT:AD:DP:GL:GQ 0/1:106,19:100:-64.31,-30.12,-298.02:99 +chr1 4296636 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=128;Dels=0.00;HRun=0;HaplotypeScore=188.32;MQ=35.30;MQ0=3;OQ=116.48;QD=0.91;SB=56.18 GT:AD:DP:GL:GQ 0/1:110,17:102:-45.68,-30.75,-346.20:99 +chr1 4296642 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=130;Dels=0.00;HRun=1;HaplotypeScore=236.73;MQ=34.36;MQ0=5;OQ=253.36;QD=1.95;SB=47.15 GT:AD:DP:GL:GQ 0/1:113,17:102:-59.34,-30.72,-306.11:99 +chr1 4296665 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=107.40;MQ=33.96;MQ0=6;OQ=319.22;QD=2.73;SB=50.15 GT:AD:DP:GL:GQ 0/1:91,24:96:-64.13,-28.92,-272.83:99 +chr1 4296668 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=119;Dels=0.01;HRun=0;HaplotypeScore=114.24;MQ=34.12;MQ0=7;OQ=295.42;QD=2.48;SB=-19.17 GT:AD:DP:GL:GQ 0/1:99,19:98:-62.05,-29.23,-276.38:99 +chr1 4296677 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=110;Dels=0.03;HRun=0;HaplotypeScore=117.38;MQ=34.73;MQ0=5;OQ=320.24;QD=2.91;SB=47.14 GT:AD:DP:GL:GQ 0/1:86,21:91:-62.13,-26.82,-250.93:99 +chr1 4296686 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=54.93;MQ=36.96;MQ0=5;OQ=147.08;QD=1.67;SB=50.15 GT:AD:DP:GL:GQ 0/1:78,10:74:-40.29,-22.30,-219.44:99 +chr1 4308180 . C T 161.22 PASS AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.53;MQ0=0;OQ=1282.15;QD=17.56;SB=-488.11 GT:AD:DP:GL:GQ 0/1:35,38:73:-153.50,-22.00,-116.62:99 +chr1 4309112 . A C 86.02 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.15;MQ=59.03;MQ0=0;OQ=562.66;QD=13.09;SB=-287.67 GT:AD:DP:GL:GQ 0/1:22,20:43:-74.67,-15.12,-82.44:99 +chr1 4310347 . C T 101.72 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.41;MQ0=0;OQ=1172.68;QD=16.52;SB=-579.36 GT:AD:DP:GL:GQ 0/1:36,35:70:-141.64,-21.08,-130.80:99 +chr1 4314528 . T C 249.50 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1047.71;QD=18.38;SB=-476.64 GT:AD:DP:GL:GQ 0/1:22,35:57:-125.23,-17.17,-90.17:99 +chr1 4316332 . T G 43.87 PASS AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.09;MQ=59.28;MQ0=0;OQ=471.43;QD=14.73;SB=-242.41 GT:AD:DP:GL:GQ 0/1:14,18:31:-59.77,-9.34,-47.32:99 +chr1 4316334 . C G 15.52 PASS AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.32;MQ0=0;OQ=676.22;QD=19.89;SB=-323.04 GT:AD:DP:GL:GQ 0/1:15,19:34:-81.16,-10.25,-60.88:99 +chr1 4318103 rs349395 A G 659.54 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=1716.14;QD=31.20;SB=-834.63 GT:AD:DP:GL:GQ 1/1:0,55:54:-175.24,-16.28,-0.05:99 +chr1 4319680 rs349393 A C 563.28 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=813.26;QD=15.95;SB=-376.77 GT:AD:DP:GL:GQ 0/1:23,28:51:-99.97,-15.36,-86.41:99 +chr1 4319765 rs102083 A T 361.40 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=55.80;MQ0=0;OQ=747.97;QD=14.96;SB=-385.65 GT:AD:DP:GL:GQ 0/1:24,26:48:-92.54,-14.46,-85.84:99 +chr1 4319782 rs28431405 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=20;HaplotypeScore=17.05;MQ=53.28;MQ0=0;OQ=875.22;QD=14.59;SB=-406.12 GT:AD:DP:GL:GQ 0/1:25,35:49:-105.57,-14.76,-69.63:99 +chr1 4319814 rs102085 G A 15.88 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=5.54;MQ=52.08;MQ0=0;OQ=929.67;QD=17.22;SB=-462.49 GT:AD:DP:GL:GQ 0/1:25,29:49:-111.01,-14.76,-74.46:99 +chr1 4319857 rs17410050 C T 91.63 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.83;MQ0=0;OQ=1009.89;QD=18.36;SB=-347.35 GT:AD:DP:GL:GQ 0/1:26,29:55:-120.84,-16.57,-94.75:99 +chr1 4320268 rs349392 G T 359.85 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.27;MQ=58.71;MQ0=0;OQ=818.84;QD=15.16;SB=-433.16 GT:AD:DP:GL:GQ 0/1:23,30:49:-99.94,-14.77,-68.96:99 +chr1 4320352 rs101287 A C 9.82 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=2.94;MQ=58.91;MQ0=0;OQ=686.61;QD=10.73;SB=-323.81 GT:AD:DP:GL:GQ 0/1:36,28:61:-90.33,-18.38,-119.68:99 +chr1 4321671 rs56216403 A T 13.76 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=7.66;MQ=57.98;MQ0=0;OQ=569.50;QD=12.94;SB=-290.67 GT:AD:DP:GL:GQ 0/1:24,20:41:-72.59,-12.36,-76.85:99 +chr1 4321865 rs349391 T C 61.74 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=58.51;MQ0=0;OQ=775.30;QD=16.50;SB=-140.34 GT:AD:DP:GL:GQ 0/1:20,26:42:-93.47,-12.66,-62.46:99 +chr1 4321866 rs56376431 G A 8.49 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.58;MQ=58.51;MQ0=0;OQ=873.71;QD=18.59;SB=-178.26 GT:AD:DP:GL:GQ 0/1:21,26:42:-103.31,-12.65,-56.39:99 +chr1 4322006 rs56162804 C T 116.80 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.53;MQ0=0;OQ=1021.04;QD=20.84;SB=-534.77 GT:AD:DP:GL:GQ 0/1:19,30:49:-120.16,-14.77,-59.62:99 +chr1 4322030 rs55838104 C T 52.16 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=1120.64;QD=21.14;SB=-534.76 GT:AD:DP:GL:GQ 0/1:20,33:52:-131.01,-15.67,-66.54:99 +chr1 4322090 rs16838800 A G 416.20 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=910.62;QD=19.80;SB=-423.34 GT:AD:DP:GL:GQ 0/1:16,30:46:-108.20,-13.86,-64.49:99 +chr1 4322538 rs12403556 C G 69.76 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.92;MQ=60.00;MQ0=0;OQ=1513.57;QD=24.81;SB=-525.74 GT:AD:DP:GL:GQ 0/1:20,41:61:-173.03,-18.39,-83.32:99 +chr1 4322543 rs12404034 A G 25.15 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=3.64;MQ=60.00;MQ0=0;OQ=1221.46;QD=20.02;SB=-417.22 GT:AD:DP:GL:GQ 0/1:20,41:60:-143.50,-18.07,-80.25:99 +chr1 4322609 rs12404038 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=5;HaplotypeScore=9.16;MQ=59.56;MQ0=0;OQ=664.61;QD=12.54;SB=-143.41 GT:AD:DP:GL:GQ 0/1:24,29:49:-84.51,-14.77,-94.35:99 +chr1 4322739 rs12404366 T C 226.21 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=432.95;QD=9.41;SB=-158.54 GT:AD:DP:GL:GQ 0/1:29,17:46:-60.44,-13.86,-115.98:99 +chr1 4322916 rs12402553 G A 357.39 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.62;MQ0=0;OQ=842.62;QD=13.81;SB=-393.36 GT:AD:DP:GL:GQ 0/1:35,26:59:-105.32,-17.77,-117.60:99 +chr1 4323438 rs16838810 A G 123.66 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=0.32;MQ=59.40;MQ0=0;OQ=808.90;QD=13.05;SB=-366.96 GT:AD:DP:GL:GQ 0/1:30,32:61:-102.56,-18.39,-119.19:99 +chr1 4323490 rs55944275 G A 62.78 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.36;MQ0=0;OQ=1153.53;QD=19.89;SB=-343.36 GT:AD:DP:GL:GQ 0/1:24,34:57:-135.81,-17.17,-85.54:99 +chr1 4323756 rs349390 T C 313.61 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.62;MQ0=0;OQ=671.97;QD=11.20;SB=-140.85 GT:AD:DP:GL:GQ 0/1:34,26:58:-87.95,-17.47,-136.36:99 +chr1 4323757 rs58351078 G A 132.53 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.61;MQ0=0;OQ=802.14;QD=13.60;SB=-181.76 GT:AD:DP:GL:GQ 0/1:34,25:59:-101.27,-17.77,-124.39:99 +chr1 4323928 rs61676533 C T 374.12 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.48;MQ0=0;OQ=1036.80;QD=14.40;SB=-477.00 GT:AD:DP:GL:GQ 0/1:40,32:72:-128.65,-21.69,-142.77:99 +chr1 4323975 rs16838812 A G 340.79 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.98;MQ=59.17;MQ0=0;OQ=822.30;QD=12.09;SB=-364.22 GT:AD:DP:GL:GQ 0/1:38,30:68:-106.00,-20.49,-150.74:99 +chr1 4324005 rs16838813 G A 586.02 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.08;MQ0=0;OQ=833.74;QD=14.13;SB=-356.82 GT:AD:DP:GL:GQ 0/1:33,26:58:-104.14,-17.48,-106.56:99 +chr1 4324062 rs56775247 A G 352.77 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.86;MQ0=0;OQ=755.78;QD=11.81;SB=-150.88 GT:AD:DP:GL:GQ 0/1:37,27:64:-98.14,-19.28,-148.79:99 +chr1 4324102 rs57599092 A T 199.13 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.94;MQ=53.27;MQ0=0;OQ=1008.31;QD=14.83;SB=-333.61 GT:AD:DP:GL:GQ 0/1:34,34:66:-123.99,-19.88,-127.49:99 +chr1 4324399 rs11804096 T C 269.49 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=45.70;MQ0=1;OQ=598.48;QD=11.29;SB=-306.38 GT:AD:DP:GL:GQ 0/1:28,25:48:-77.59,-14.46,-100.69:99 +chr1 4324626 rs11803736 A G 203.50 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=51.26;MQ0=1;OQ=569.48;QD=10.55;SB=-273.41 GT:AD:DP:GL:GQ 0/1:32,22:52:-75.89,-15.66,-126.39:99 +chr1 4324693 rs11801800 G A 371.17 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=50.70;MQ0=1;OQ=920.80;QD=14.85;SB=-460.99 GT:AD:DP:GL:GQ 0/1:32,30:59:-113.14,-17.77,-113.29:99 +chr1 4324939 rs12729994 C A 219.08 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=56.71;MQ0=0;OQ=746.98;QD=16.98;SB=-320.72 GT:AD:DP:GL:GQ 0/1:18,26:42:-90.63,-12.65,-55.46:99 +chr1 4325115 rs12742617 T G 433.06 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.56;MQ0=0;OQ=1013.88;QD=12.07;SB=-397.13 GT:AD:DP:GL:GQ 0/1:47,37:83:-129.67,-25.00,-173.24:99 +chr1 4325508 rs34012704 A G 166.42 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=59.63;MQ0=0;OQ=986.31;QD=19.34;SB=-504.18 GT:AD:DP:GL:GQ 0/1:17,34:49:-116.68,-14.77,-62.75:99 +chr1 4325583 . G A 54.73 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=60.00;MQ0=0;OQ=709.46;QD=16.50;SB=-303.82 GT:AD:DP:GL:GQ 0/1:18,25:41:-86.59,-12.36,-64.70:99 +chr1 4325707 rs12405082 A G 0.52 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=6.04;MQ=58.57;MQ0=0;OQ=521.78;QD=8.42;SB=-177.38 GT:AD:DP:GL:GQ 0/1:38,24:56:-72.34,-16.88,-134.28:99 +chr1 4325759 . C T 1.66 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=2;HaplotypeScore=2.89;MQ=58.50;MQ0=0;OQ=768.28;QD=12.39;SB=-160.15 GT:AD:DP:GL:GQ 0/1:32,29:57:-97.29,-17.18,-106.60:99 +chr1 4325887 rs12403671 G C 245.59 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.67;MQ0=0;OQ=1119.45;QD=19.64;SB=-552.71 GT:AD:DP:GL:GQ 0/1:24,33:54:-131.50,-16.27,-104.02:99 +chr1 4325945 rs12404619 C T 347.85 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.65;MQ0=0;OQ=874.85;QD=15.91;SB=-387.13 GT:AD:DP:GL:GQ 0/1:26,29:53:-106.74,-15.97,-91.70:99 +chr1 4326338 rs16838819 A C 229.78 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=4.02;MQ=58.63;MQ0=0;OQ=550.44;QD=10.79;SB=-296.79 GT:AD:DP:GL:GQ 0/1:29,22:49:-73.09,-14.76,-103.75:99 +chr1 4327728 rs34472761 G C 257.96 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.05;MQ0=0;OQ=1072.08;QD=16.75;SB=-550.71 GT:AD:DP:GL:GQ 0/1:32,32:62:-129.19,-18.70,-130.17:99 +chr1 4328031 rs56108323 G A 198.39 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=626.21;QD=12.28;SB=-249.12 GT:AD:DP:GL:GQ 0/1:27,24:48:-80.37,-14.46,-97.54:99 +chr1 4329322 rs483344 A G 283.35 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=59.34;MQ0=0;OQ=672.82;QD=9.61;SB=-273.11 GT:AD:DP:GL:GQ 0/1:41,29:68:-91.06,-20.50,-159.89:99 +chr1 4331124 rs572439 A C 450.24 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.73;MQ0=0;OQ=1069.67;QD=15.73;SB=-417.82 GT:AD:DP:GL:GQ 0/1:30,38:67:-130.43,-20.18,-110.75:99 +chr1 4331158 rs572343 G A 289.61 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.72;MQ0=0;OQ=1247.65;QD=18.62;SB=-597.10 GT:AD:DP:GL:GQ 0/1:31,36:64:-147.32,-19.27,-103.83:99 +chr1 4331483 rs12750862 T C 292.32 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.22;MQ=59.55;MQ0=0;OQ=752.94;QD=14.76;SB=-378.63 GT:AD:DP:GL:GQ 0/1:24,27:49:-93.35,-14.77,-86.37:99 +chr1 4331508 . C T 49.49 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=60.00;MQ0=0;OQ=892.12;QD=17.84;SB=-369.91 GT:AD:DP:GL:GQ 0/1:18,31:43:-105.46,-12.97,-47.94:99 +chr1 4333712 rs2926485 T C 268.41 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.56;MQ=59.83;MQ0=0;OQ=1004.92;QD=15.70;SB=-484.15 GT:AD:DP:GL:GQ 0/1:28,35:61:-122.15,-18.38,-108.51:99 +chr1 4334184 rs57575485 C T 360.52 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.70;MQ0=0;OQ=1292.51;QD=16.79;SB=-566.07 GT:AD:DP:GL:GQ 0/1:37,40:76:-155.43,-22.90,-133.07:99 +chr1 4334834 rs661536 A G 714.01 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=1993.62;QD=34.98;SB=-900.02 GT:AD:DP:GL:GQ 1/1:0,57:57:-202.97,-17.17,-0.02:99 +chr1 4339520 rs902403 T C 449.51 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=846.06;QD=12.44;SB=-357.94 GT:AD:DP:GL:GQ 0/1:35,33:68:-108.38,-20.49,-140.89:99 +chr1 4339677 rs2926482 C G 218.76 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=2219.96;QD=42.69;SB=-974.35 GT:AD:DP:GL:GQ 1/1:0,52:52:-225.60,-15.67,-0.01:99 +chr1 4340373 rs590798 A C 514.93 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=2632.91;QD=34.64;SB=-1142.61 GT:AD:DP:GL:GQ 1/1:0,76:76:-266.90,-22.89,-0.03:99 +chr1 4344158 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=3;HaplotypeScore=3.49;MQ=60.00;MQ0=0;OQ=63.29;QD=1.07;SB=56.21 GT:AD:DP:GL:GQ 0/1:42,17:47:-23.79,-14.18,-151.98:96.13 +chr1 4344566 rs349413 C A 606.43 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1116.07;QD=14.69;SB=-454.53 GT:AD:DP:GL:GQ 0/1:39,37:76:-137.78,-22.89,-141.17:99 +chr1 4345038 rs164598 G A 482.03 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.02;MQ0=0;OQ=1164.61;QD=17.38;SB=-524.70 GT:AD:DP:GL:GQ 0/1:32,35:67:-139.93,-20.18,-113.85:99 +chr1 4347591 rs4654526 C T 500.86 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1310.21;QD=20.16;SB=-660.78 GT:AD:DP:GL:GQ 0/1:25,40:61:-152.69,-18.39,-71.94:99 +chr1 4351708 rs11585123 G T 52.90 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=3;HaplotypeScore=1.96;MQ=59.43;MQ0=0;OQ=956.92;QD=13.11;SB=-391.99 GT:AD:DP:GL:GQ 0/1:39,34:73:-120.97,-21.99,-133.39:99 +chr1 4352257 rs627555 G A 556.89 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=1274.67;QD=14.01;SB=-577.49 GT:AD:DP:GL:GQ 0/1:53,38:91:-158.16,-27.41,-187.48:99 +chr1 4352698 . A C 145.09 PASS AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1251.00;QD=14.55;SB=-612.69 GT:AD:DP:GL:GQ 0/1:43,43:84:-153.68,-25.30,-154.64:99 +chr1 4353326 rs7523383 C T 223.33 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1125.20;QD=18.75;SB=-322.36 GT:AD:DP:GL:GQ 0/1:24,35:55:-132.39,-16.58,-65.47:99 +chr1 4354986 rs55703746 G T 228.36 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1494.65;QD=18.68;SB=-625.43 GT:AD:DP:GL:GQ 0/1:32,48:80:-176.84,-24.10,-112.47:99 +chr1 4358435 . C T 24.59 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=1;HaplotypeScore=3.25;MQ=55.69;MQ0=0;QD=0.61;SB=41.14 GT:AD:DP:GL:GQ 0/1:35,4:36:-16.60,-10.86,-102.91:57.41 +chr1 4358482 . C G 35.61 LowQual AC=1;AF=0.50;AN=2;DP=34;Dels=0.00;HRun=0;HaplotypeScore=3.12;MQ=54.32;MQ0=0;QD=1.05;SB=-23.70 GT:AD:DP:GL:GQ 0/1:30,4:32:-16.49,-9.64,-124.37:68.45 +chr1 4359549 rs6679220 T C 288.35 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=543.81;QD=10.66;SB=-272.37 GT:AD:DP:GL:GQ 0/1:30,21:50:-72.72,-15.06,-124.68:99 +chr1 4360825 rs56081339 G A 327.33 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.43;MQ0=0;OQ=993.85;QD=13.61;SB=-456.06 GT:AD:DP:GL:GQ 0/1:40,33:70:-123.78,-21.11,-120.70:99 +chr1 4363525 rs349402 G A 561.81 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.26;MQ0=0;OQ=1290.95;QD=16.99;SB=-425.80 GT:AD:DP:GL:GQ 0/1:36,40:74:-154.68,-22.30,-119.31:99 +chr1 4367389 rs4654429 G A 56.05 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=5.58;MQ=57.65;MQ0=0;OQ=1142.68;QD=16.80;SB=-522.78 GT:AD:DP:GL:GQ 0/1:32,36:64:-136.84,-19.29,-93.56:99 +chr1 4367566 rs4654430 T C 472.63 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=611.79;QD=10.92;SB=-199.58 GT:AD:DP:GL:GQ 0/1:34,22:55:-81.03,-16.57,-131.86:99 +chr1 4368744 rs547923 C A 335.14 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=58.91;MQ0=0;OQ=794.59;QD=12.42;SB=-343.21 GT:AD:DP:GL:GQ 0/1:34,30:61:-101.12,-18.38,-116.77:99 +chr1 4369295 rs6687224 C G 567.99 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1064.80;QD=17.75;SB=-495.28 GT:AD:DP:GL:GQ 0/1:29,31:59:-127.55,-17.78,-120.89:99 +chr1 4369728 rs733308 T G 295.33 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.39;MQ=59.19;MQ0=1;OQ=894.22;QD=10.65;SB=-355.63 GT:AD:DP:GL:GQ 0/1:48,36:83:-117.71,-25.00,-176.40:99 +chr1 4370735 rs2926477 A G 468.63 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=995.20;QD=15.31;SB=-357.26 GT:AD:DP:GL:GQ 0/1:29,36:64:-122.09,-19.28,-116.14:99 +chr1 4371593 rs505933 A G 376.41 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.99;MQ0=0;OQ=894.44;QD=10.78;SB=-423.73 GT:AD:DP:GL:GQ 0/1:45,38:82:-117.44,-24.72,-179.72:99 +chr1 4371867 rs693045 T C 492.95 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.26;MQ0=0;OQ=669.20;QD=9.99;SB=-303.21 GT:AD:DP:GL:GQ 0/1:37,30:64:-89.50,-19.29,-143.01:99 +chr1 4371873 rs10915529 G C 482.75 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.33;MQ0=0;OQ=903.58;QD=12.91;SB=-393.25 GT:AD:DP:GL:GQ 0/1:40,30:69:-114.44,-20.80,-177.40:99 +chr1 4371886 rs659514 T C 97.64 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=1.39;MQ=58.28;MQ0=0;OQ=683.73;QD=10.05;SB=-268.51 GT:AD:DP:GL:GQ 0/1:42,26:67:-91.84,-20.18,-171.36:99 +chr1 4372308 rs4654533 C G 209.19 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1490.53;QD=19.61;SB=-620.61 GT:AD:DP:GL:GQ 0/1:35,41:72:-174.05,-21.72,-126.16:99 +chr1 4375044 rs349405 A C 311.25 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=541.86;QD=10.62;SB=-270.89 GT:AD:DP:GL:GQ 0/1:31,20:51:-72.83,-15.36,-116.45:99 +chr1 4375626 rs349406 T C 212.51 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=2.99;MQ=59.38;MQ0=0;OQ=1112.63;QD=14.84;SB=-554.63 GT:AD:DP:GL:GQ 0/1:36,39:72:-136.23,-21.69,-140.85:99 +chr1 4375771 rs12562242 G T 432.17 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=59.23;MQ0=0;OQ=915.50;QD=12.54;SB=-381.76 GT:AD:DP:GL:GQ 0/1:39,34:71:-116.22,-21.39,-137.78:99 +chr1 4376133 rs349407 G A 305.49 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.03;MQ0=1;OQ=1382.00;QD=18.43;SB=-530.55 GT:AD:DP:GL:GQ 0/1:31,44:71:-162.87,-21.39,-107.28:99 +chr1 4376945 rs10915530 C T 589.94 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1129.31;QD=16.13;SB=-586.64 GT:AD:DP:GL:GQ 0/1:35,35:68:-136.71,-20.50,-105.26:99 +chr1 4377252 rs1490416 T A 34.72 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.01;HRun=1;HaplotypeScore=4.80;MQ=59.18;MQ0=0;OQ=1402.77;QD=16.50;SB=-436.53 GT:AD:DP:GL:GQ 0/1:39,45:80:-167.66,-24.10,-131.13:99 +chr1 4377771 rs349409 C T 337.62 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.02;MQ=59.15;MQ0=0;OQ=1097.95;QD=15.46;SB=-477.48 GT:AD:DP:GL:GQ 0/1:37,34:69:-133.86,-20.78,-131.05:99 +chr1 4377899 rs349410 C A 42.06 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=4.55;MQ=59.19;MQ0=0;OQ=1054.50;QD=18.50;SB=-399.14 GT:AD:DP:GL:GQ 0/1:22,35:56:-125.60,-16.87,-75.99:99 +chr1 4377949 rs349411 C T 2.69 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=11.72;MQ=58.87;MQ0=0;OQ=1481.01;QD=18.06;SB=-689.93 GT:AD:DP:GL:GQ 0/1:37,45:80:-175.49,-24.10,-130.86:99 +chr1 4377999 rs10915531 A G 391.37 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.24;MQ0=0;OQ=1298.04;QD=16.23;SB=-576.28 GT:AD:DP:GL:GQ 0/1:36,44:80:-157.19,-24.10,-146.95:99 +chr1 4380137 rs493178 G C 0.36 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.09;MQ=57.06;MQ0=0;OQ=874.81;QD=23.64;SB=-165.59 GT:AD:DP:GL:GQ 0/1:11,26:34:-101.01,-10.25,-40.96:99 +chr1 4380197 . G A 21.03 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=23.38;MQ=29.95;MQ0=2;QD=0.68;SB=41.12 GT:AD:DP:GL:GQ 0/1:26,5:22:-12.01,-6.63,-63.36:53.84 +chr1 4380201 rs59237016 A T 117.83 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=21.39;MQ=30.09;MQ0=2;QD=4.36;SB=-11.73 GT:AD:DP:GL:GQ 0/1:19,6:13:-24.36,-9.29,-27.60:99 +chr1 4380203 . A G 41.11 LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=24.37;MQ=28.28;MQ0=2;QD=1.64;SB=-10.00 GT:AD:DP:GL:GQ 0/1:17,7:10:-10.41,-3.01,-27.49:73.95 +chr1 4380215 . G A 523.36 SnpCluster AC=2;AF=1.00;AN=2;DP=19;Dels=0.05;HRun=0;HaplotypeScore=13.20;MQ=29.01;MQ0=2;QD=27.55;SB=-164.67 GT:AD:DP:GL:GQ 1/1:1,17:14:-55.92,-4.22,-0.00:42.14 +chr1 4380217 rs60888156 G A 452.59 SnpCluster AC=2;AF=1.00;AN=2;DB;DP=19;Dels=0.05;HRun=0;HaplotypeScore=13.68;MQ=29.01;MQ0=2;QD=23.82;SB=-163.66 GT:AD:DP:GL:GQ 1/1:4,14:14:-51.77,-4.22,-2.97:12.46 +chr1 4380219 . G A 274.46 SnpCluster AC=1;AF=0.50;AN=2;DP=17;Dels=0.06;HRun=0;HaplotypeScore=11.89;MQ=29.85;MQ0=1;QD=16.14;SB=-148.61 GT:AD:DP:GL:GQ 0/1:5,11:13:-34.65,-3.92,-13.88:99 +chr1 4380249 . G A 49.25 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.68;MQ0=1;QD=16.42;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,3:2:-8.33,-0.60,-0.00:6.02 +chr1 4380271 rs6697112 G A 9.28 PASS AC=2;AF=1.00;AN=2;DB;DP=5;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=37.32;MQ0=0;OQ=124.22;QD=24.84;SB=-44.55 GT:AD:DP:GL:GQ 1/1:1,4:4:-15.96,-1.21,-0.00:12.04 +chr1 4380311 rs1309838 C A 157.04 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=54.85;MQ0=0;OQ=623.10;QD=14.84;SB=-208.87 GT:AD:DP:GL:GQ 0/1:19,23:41:-77.95,-12.35,-68.48:99 +chr1 4380330 rs1309839 C T 0.61 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=7.73;MQ=55.45;MQ0=0;OQ=843.65;QD=20.09;SB=-255.33 GT:AD:DP:GL:GQ 0/1:15,27:37:-98.80,-11.15,-35.58:99 +chr1 4380929 . T C 25.32 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=2;HaplotypeScore=5.44;MQ=59.32;MQ0=0;QD=0.37;SB=122.43 GT:AD:DP:GL:GQ 0/1:48,20:54:-22.08,-16.27,-188.06:58.14 +chr1 4380941 rs349386 C T 474.31 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.84;MQ0=0;OQ=1352.78;QD=17.80;SB=-554.75 GT:AD:DP:GL:GQ 0/1:36,40:74:-160.85,-22.29,-128.59:99 +chr1 4381075 rs4654432 C T 88.73 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=1.63;MQ=60.32;MQ0=0;OQ=870.11;QD=12.80;SB=-258.77 GT:AD:DP:GL:GQ 0/1:40,28:66:-110.19,-19.90,-123.57:99 +chr1 4381353 rs35799150 A G 389.01 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=820.10;QD=12.06;SB=-192.18 GT:AD:DP:GL:GQ 0/1:39,29:68:-105.78,-20.48,-159.19:99 +chr1 4381492 rs4654433 G A 604.36 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1070.93;QD=15.98;SB=-493.09 GT:AD:DP:GL:GQ 0/1:35,32:67:-130.57,-20.19,-112.83:99 +chr1 4382470 rs737324 G C 535.52 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=1310.24;QD=17.47;SB=-409.80 GT:AD:DP:GL:GQ 0/1:38,37:74:-156.61,-22.31,-151.67:99 +chr1 4382624 rs349385 A G 200.13 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=56.49;MQ0=0;OQ=1553.01;QD=28.76;SB=-619.97 GT:AD:DP:GL:GQ 1/1:0,53:51:-158.94,-15.39,-0.06:99 +chr1 4383263 rs41266223 T C 212.32 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=57.69;MQ0=0;OQ=666.08;QD=11.29;SB=-355.38 GT:AD:DP:GL:GQ 0/1:32,27:53:-85.86,-15.97,-114.12:99 +chr1 4385955 rs4654537 A G 109.83 PASS AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=60.00;MQ0=0;OQ=187.72;QD=8.16;SB=-92.99 GT:AD:DP:GL:GQ 0/1:12,10:21:-28.39,-6.33,-46.97:99 +chr1 4386470 rs1762818 A G 620.72 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=2262.65;QD=34.81;SB=-1121.77 GT:AD:DP:GL:GQ 1/1:0,65:63:-229.87,-18.98,-0.02:99 +chr1 4386565 rs2035009 T C 346.94 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=58.05;MQ0=0;OQ=655.98;QD=10.93;SB=-329.97 GT:AD:DP:GL:GQ 0/1:30,30:56:-85.78,-16.89,-109.09:99 +chr1 4386918 rs2035008 T A 56.82 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=1.25;MQ=55.07;MQ0=0;OQ=728.43;QD=12.14;SB=-228.91 GT:AD:DP:GL:GQ 0/1:33,27:58:-93.60,-17.47,-122.91:99 +chr1 4387800 . G A 279.77 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1023.92;QD=16.25;SB=-391.36 GT:AD:DP:GL:GQ 0/1:32,31:61:-124.06,-18.39,-99.73:99 +chr1 4388151 rs4654542 C T 244.41 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.62;MQ=60.00;MQ0=0;OQ=1264.25;QD=16.63;SB=-528.76 GT:AD:DP:GL:GQ 0/1:37,39:75:-152.31,-22.60,-121.60:99 +chr1 4388316 rs4654434 G A 492.22 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1047.13;QD=14.54;SB=-490.97 GT:AD:DP:GL:GQ 0/1:40,32:72:-129.68,-21.69,-147.17:99 +chr1 4388691 rs6667927 C T 322.46 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.79;MQ0=0;OQ=1604.10;QD=18.23;SB=-806.38 GT:AD:DP:GL:GQ 0/1:41,47:88:-190.20,-26.51,-149.18:99 +chr1 4388839 rs6658372 G A 449.72 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.10;MQ0=0;OQ=954.40;QD=14.24;SB=-360.06 GT:AD:DP:GL:GQ 0/1:36,31:66:-118.61,-19.88,-128.27:99 +chr1 4389258 rs6678792 T C 469.97 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.45;MQ0=0;OQ=1167.87;QD=15.37;SB=-534.97 GT:AD:DP:GL:GQ 0/1:37,39:76:-142.96,-22.89,-149.63:99 +chr1 4389389 rs10915533 G A 316.56 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=59.63;MQ0=0;OQ=829.91;QD=13.39;SB=-417.75 GT:AD:DP:GL:GQ 0/1:33,29:58:-103.75,-17.48,-109.80:99 +chr1 4389459 rs995749 T C 99.11 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.02;MQ=59.19;MQ0=0;OQ=673.64;QD=11.82;SB=-297.62 GT:AD:DP:GL:GQ 0/1:29,28:55:-87.23,-16.58,-114.38:99 +chr1 4390198 rs6676603 A T 439.97 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.38;MQ0=0;OQ=1300.48;QD=17.57;SB=-634.13 GT:AD:DP:GL:GQ 0/1:32,42:73:-155.32,-21.99,-116.56:99 +chr1 4390481 rs12128251 T C 259.49 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=57.96;MQ0=0;OQ=632.69;QD=11.94;SB=-295.21 GT:AD:DP:GL:GQ 0/1:28,25:50:-81.62,-15.07,-105.90:99 +chr1 4391861 rs2007533 T A 193.95 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=57.74;MQ0=0;OQ=586.86;QD=11.51;SB=-140.76 GT:AD:DP:GL:GQ 0/1:30,21:48:-76.43,-14.46,-99.70:99 +chr1 4391958 rs1809702 T C 301.51 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1033.40;QD=12.45;SB=-514.71 GT:AD:DP:GL:GQ 0/1:39,44:81:-131.04,-24.42,-155.02:99 +chr1 4392226 rs736265 G A 87.76 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=4.07;MQ=59.56;MQ0=0;OQ=793.67;QD=14.97;SB=-313.81 GT:AD:DP:GL:GQ 0/1:27,26:51:-98.01,-15.36,-98.57:99 +chr1 4393075 rs1556691 A G 599.93 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.74;MQ0=0;OQ=937.52;QD=14.88;SB=-473.07 GT:AD:DP:GL:GQ 0/1:29,34:61:-115.41,-18.38,-116.29:99 +chr1 4393225 rs4654435 T C 403.94 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=60.00;MQ0=0;OQ=690.21;QD=11.50;SB=-328.14 GT:AD:DP:GL:GQ 0/1:28,31:55:-88.89,-16.58,-104.73:99 +chr1 4394358 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=18;HaplotypeScore=18.20;MQ=57.05;MQ0=0;OQ=138.13;QD=2.76;SB=68.21 GT:AD:DP:GL:GQ 0/1:39,11:43:-30.06,-12.96,-119.55:99 +chr1 4394377 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=18;HaplotypeScore=17.15;MQ=55.75;MQ0=0;OQ=145.86;QD=2.75;SB=25.24 GT:AD:DP:GL:GQ 0/1:40,13:43:-30.82,-12.95,-126.23:99 +chr1 4394834 rs12072315 G A 483.58 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=835.16;QD=15.47;SB=-392.90 GT:AD:DP:GL:GQ 0/1:29,25:53:-102.78,-15.98,-90.62:99 +chr1 4394951 rs7546444 A G 181.93 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.12;MQ0=0;OQ=846.04;QD=12.26;SB=-340.27 GT:AD:DP:GL:GQ 0/1:38,31:68:-108.38,-20.49,-147.54:99 +chr1 4395538 rs1591426 T C 726.29 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=2474.70;QD=34.37;SB=-1102.69 GT:AD:DP:GL:GQ 1/1:0,72:71:-251.09,-21.39,-0.04:99 +chr1 4395562 rs1591425 A G 113.89 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.25;MQ0=0;OQ=1914.52;QD=29.01;SB=-807.30 GT:AD:DP:GL:GQ 1/1:0,66:62:-195.10,-18.70,-0.06:99 +chr1 4396040 rs10915536 C T 108.05 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=3075.21;QD=39.94;SB=-1236.02 GT:AD:DP:GL:GQ 1/1:0,77:77:-311.12,-23.19,-0.02:99 +chr1 4396189 rs1762813 C T 709.23 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.85;MQ0=0;OQ=1988.33;QD=37.52;SB=-957.81 GT:AD:DP:GL:GQ 1/1:0,52:51:-202.43,-15.36,-0.01:99 +chr1 4396377 rs1674876 G A 690.55 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=3414.62;QD=39.70;SB=-1526.04 GT:AD:DP:GL:GQ 1/1:0,86:85:-340.46,-25.61,-0.02:99 +chr1 4396770 rs1335365 G A 180.08 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=3218.44;QD=38.31;SB=-1546.06 GT:AD:DP:GL:GQ 1/1:0,84:82:-325.46,-24.71,-0.03:99 +chr1 4396978 rs6660514 C T 529.47 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2569.74;QD=40.15;SB=-881.18 GT:AD:DP:GL:GQ 1/1:0,64:63:-260.57,-18.97,-0.01:99 +chr1 4396990 rs1335363 G A 705.95 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=2655.20;QD=39.05;SB=-1068.35 GT:AD:DP:GL:GQ 1/1:0,68:67:-269.12,-20.18,-0.02:99 +chr1 4397408 rs35211041 C G 282.09 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.56;MQ0=0;OQ=845.74;QD=15.96;SB=-404.93 GT:AD:DP:GL:GQ 0/1:28,25:51:-103.22,-15.37,-116.49:99 +chr1 4397651 rs1234932 T C 32.13 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.62;MQ=59.08;MQ0=0;OQ=2038.22;QD=30.88;SB=-895.04 GT:AD:DP:GL:GQ 1/1:0,66:64:-207.46,-19.30,-0.06:99 +chr1 4399691 rs780572 T C 25.86 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=3.98;MQ=59.66;MQ0=0;OQ=2164.78;QD=32.31;SB=-610.95 GT:AD:DP:GL:GQ 1/1:0,67:65:-220.10,-19.59,-0.04:99 +chr1 4400105 rs12727067 C T 348.64 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=3168.12;QD=39.11;SB=-1535.71 GT:AD:DP:GL:GQ 1/1:0,81:79:-320.41,-23.80,-0.02:99 +chr1 4400296 rs12731060 C T 672.05 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2631.07;QD=38.69;SB=-901.20 GT:AD:DP:GL:GQ 1/1:0,68:67:-266.72,-20.19,-0.02:99 +chr1 4401014 rs6674190 C T 89.86 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.77;MQ0=0;OQ=3223.06;QD=39.79;SB=-1621.16 GT:AD:DP:GL:GQ 1/1:0,81:80:-325.90,-24.10,-0.02:99 +chr1 4401844 rs780573 A G 655.69 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=2538.38;QD=30.96;SB=-1020.34 GT:AD:DP:GL:GQ 1/1:0,82:80:-257.49,-24.12,-0.07:99 +chr1 4403585 rs780581 T C 628.63 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=2729.37;QD=35.91;SB=-1251.85 GT:AD:DP:GL:GQ 1/1:0,76:75:-276.54,-22.59,-0.02:99 +chr1 4405826 rs780587 T C 579.37 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1799.99;QD=35.29;SB=-764.96 GT:AD:DP:GL:GQ 1/1:0,51:50:-183.60,-15.06,-0.02:99 +chr1 4406185 rs780588 T G 731.95 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=2276.92;QD=35.03;SB=-1150.64 GT:AD:DP:GL:GQ 1/1:0,65:65:-231.29,-19.58,-0.02:99 +chr1 4407102 rs780589 G T 206.11 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.17;MQ0=0;OQ=2615.53;QD=35.83;SB=-1329.09 GT:AD:DP:GL:GQ 1/1:0,73:72:-265.16,-21.68,-0.02:99 +chr1 4407119 rs12032561 A G 117.17 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.23;MQ0=0;OQ=2421.51;QD=30.65;SB=-1099.12 GT:AD:DP:GL:GQ 1/1:0,79:76:-245.80,-22.92,-0.06:99 +chr1 4407230 rs780590 C A 140.01 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=60.00;MQ0=0;OQ=2388.18;QD=35.64;SB=-981.59 GT:AD:DP:GL:GQ 1/1:0,67:66:-242.42,-19.88,-0.02:99 +chr1 4407326 rs780591 G C 50.40 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.66;MQ0=0;OQ=2352.09;QD=42.77;SB=-1101.12 GT:AD:DP:GL:GQ 1/1:0,54:54:-238.81,-16.27,-0.01:99 +chr1 4407520 rs780592 G A 361.64 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3300.47;QD=41.26;SB=-1496.40 GT:AD:DP:GL:GQ 1/1:0,80:80:-329.05,-24.10,-0.02:99 +chr1 4407623 rs780594 T C 139.31 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=2.07;MQ=59.52;MQ0=0;OQ=2627.95;QD=34.13;SB=-1058.85 GT:AD:DP:GL:GQ 1/1:0,77:75:-266.41,-22.59,-0.03:99 +chr1 4408032 rs705684 C T 627.36 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2940.63;QD=39.21;SB=-1334.78 GT:AD:DP:GL:GQ 1/1:0,75:74:-297.67,-22.29,-0.02:99 +chr1 4408272 rs780595 C G 8.91 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=58.81;MQ0=0;OQ=2333.53;QD=42.43;SB=-1051.66 GT:AD:DP:GL:GQ 1/1:0,55:54:-236.95,-16.27,-0.02:99 +chr1 4408429 rs2054268 A G 302.92 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=59.14;MQ0=0;OQ=2648.73;QD=34.85;SB=-1019.36 GT:AD:DP:GL:GQ 1/1:0,76:74:-268.49,-22.29,-0.03:99 +chr1 4408966 rs780596 C G 540.01 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=3023.42;QD=42.58;SB=-1306.69 GT:AD:DP:GL:GQ 1/1:0,71:71:-305.95,-21.40,-0.02:99 +chr1 4409197 rs2054269 G A 716.76 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=2812.55;QD=39.06;SB=-1393.37 GT:AD:DP:GL:GQ 1/1:0,72:71:-284.86,-21.39,-0.02:99 +chr1 4409239 rs2054270 C A 370.19 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2523.69;QD=36.05;SB=-1226.28 GT:AD:DP:GL:GQ 1/1:0,70:69:-255.97,-20.78,-0.02:99 +chr1 4411281 rs922114 C T 206.92 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=60.00;MQ0=0;OQ=2458.23;QD=37.82;SB=-1122.24 GT:AD:DP:GL:GQ 1/1:0,65:63:-249.43,-18.99,-0.03:99 +chr1 4411941 rs56397589 A G 10.74 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=1.47;MQ=60.00;MQ0=0;OQ=772.90;QD=13.56;SB=-158.90 GT:AD:DP:GL:GQ 0/1:30,27:56:-97.44,-16.87,-122.46:99 +chr1 4412859 . G T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=17.52;MQ=58.30;MQ0=0;OQ=443.68;QD=5.55;SB=107.30 GT:AD:DP:GL:GQ 0/1:54,26:67:-67.84,-20.19,-156.44:99 +chr1 4413809 rs780599 T C 203.02 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=933.92;QD=15.06;SB=-130.24 GT:AD:DP:GL:GQ 0/1:31,31:62:-115.35,-18.67,-127.44:99 +chr1 4413942 rs1235308 A G 208.55 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.56;MQ0=0;OQ=574.66;QD=10.84;SB=-295.15 GT:AD:DP:GL:GQ 0/1:24,29:45:-74.32,-13.57,-86.44:99 +chr1 4413949 rs12135334 A G 227.02 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.57;MQ0=0;OQ=600.78;QD=11.13;SB=-278.65 GT:AD:DP:GL:GQ 0/1:25,29:50:-78.44,-15.07,-99.43:99 +chr1 4414313 rs11584026 G A 462.20 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.70;MQ0=0;OQ=1258.44;QD=16.56;SB=-579.09 GT:AD:DP:GL:GQ 0/1:37,39:74:-151.43,-22.31,-123.49:99 +chr1 4415137 rs1213919 T C 340.20 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.64;MQ0=0;OQ=1036.94;QD=16.20;SB=-428.11 GT:AD:DP:GL:GQ 0/1:27,37:63:-125.96,-18.98,-110.60:99 +chr1 4415275 rs6426411 G A 271.15 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.51;MQ=58.90;MQ0=0;OQ=891.44;QD=15.11;SB=-416.76 GT:AD:DP:GL:GQ 0/1:31,28:59:-110.20,-17.77,-112.97:99 +chr1 4415367 rs6663198 A C 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=21.51;MQ=59.22;MQ0=0;OQ=1036.43;QD=12.49;SB=-473.70 GT:AD:DP:GL:GQ 0/1:44,39:81:-131.33,-24.40,-153.13:99 +chr1 4416433 rs12131294 C T 93.74 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.89;MQ=59.15;MQ0=0;OQ=414.02;QD=9.20;SB=-113.50 GT:AD:DP:GL:GQ 0/1:24,20:37:-55.83,-11.15,-84.17:99 +chr1 4416884 . G A 3.05 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.94;MQ=57.87;MQ0=0;OQ=823.53;QD=14.97;SB=-276.27 GT:AD:DP:GL:GQ 0/1:30,25:53:-101.62,-15.98,-87.09:99 +chr1 4417194 rs7550318 A T 249.83 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.46;MQ=57.79;MQ0=0;OQ=1140.48;QD=17.28;SB=-502.48 GT:AD:DP:GL:GQ 0/1:29,37:65:-136.91,-19.58,-108.54:99 +chr1 4417494 . G A 25.73 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=20;HaplotypeScore=6.20;MQ=50.61;MQ0=1;QD=0.42;SB=98.27 GT:AD:DP:GL:GQ 0/1:53,9:50:-20.92,-15.07,-146.64:58.56 +chr1 4417741 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=20;HaplotypeScore=20.09;MQ=49.19;MQ0=1;OQ=84.58;QD=2.17;SB=26.11 GT:AD:DP:GL:GQ 0/1:26,12:27:-19.88,-8.14,-73.60:99 +chr1 4417905 rs642409 A G 618.44 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.41;MQ0=0;OQ=2544.54;QD=34.39;SB=-1201.82 GT:AD:DP:GL:GQ 1/1:0,74:71:-258.06,-21.38,-0.02:99 +chr1 4418004 rs10127576 A G 16.51 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.95;MQ=57.57;MQ0=1;OQ=493.53;QD=8.97;SB=-221.25 GT:AD:DP:GL:GQ 0/1:34,21:50:-67.70,-15.07,-117.20:99 +chr1 4420145 rs6426412 G T 345.35 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.50;MQ0=0;OQ=1296.90;QD=17.29;SB=-663.60 GT:AD:DP:GL:GQ 0/1:33,42:75:-155.57,-22.59,-114.39:99 +chr1 4420362 . C T 102.52 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=60.52;MQ0=0;OQ=920.19;QD=15.34;SB=-456.47 GT:AD:DP:GL:GQ 0/1:27,31:53:-111.28,-15.98,-79.42:99 +chr1 4421024 rs12137057 A C 291.19 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=701.05;QD=10.62;SB=-364.06 GT:AD:DP:GL:GQ 0/1:39,27:63:-92.36,-18.97,-137.12:99 +chr1 4421180 rs61771168 T G 222.08 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=1;HaplotypeScore=1.81;MQ=59.49;MQ0=0;OQ=588.51;QD=13.08;SB=-310.47 GT:AD:DP:GL:GQ 0/1:23,22:43:-75.09,-12.95,-79.35:99 +chr1 4421771 . C T 52.82 PASS AC=1;AF=0.50;AN=2;DP=35;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=58.00;MQ0=0;OQ=457.94;QD=13.08;SB=-230.51 GT:AD:DP:GL:GQ 0/1:18,17:32:-58.72,-9.64,-61.49:99 +chr1 4422658 . C T 17.02 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=3.11;MQ=59.25;MQ0=0;OQ=990.31;QD=15.97;SB=-404.43 GT:AD:DP:GL:GQ 0/1:32,30:60:-120.40,-18.09,-95.94:99 +chr1 4423184 . G A 28.31 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=59.25;MQ0=0;OQ=1264.58;QD=20.40;SB=-650.72 GT:AD:DP:GL:GQ 0/1:26,36:62:-148.42,-18.68,-94.18:99 +chr1 4423217 rs664520 C T 648.65 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1886.50;QD=38.50;SB=-821.33 GT:AD:DP:GL:GQ 1/1:0,49:49:-192.25,-14.76,-0.02:99 +chr1 4423270 rs17453664 G A 225.88 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=58.29;MQ0=0;OQ=839.10;QD=16.14;SB=-245.23 GT:AD:DP:GL:GQ 0/1:25,27:50:-102.26,-15.06,-88.51:99 +chr1 4424136 . C G 13.14 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=4.07;MQ=59.20;MQ0=0;OQ=717.79;QD=15.27;SB=-220.02 GT:AD:DP:GL:GQ 0/1:26,21:46:-88.93,-13.87,-108.02:99 +chr1 4424195 rs16839046 G A 266.41 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=59.35;MQ0=0;OQ=1078.45;QD=16.85;SB=-521.17 GT:AD:DP:GL:GQ 0/1:30,33:62:-129.81,-18.69,-96.72:99 +chr1 4424280 rs17419859 G A 351.26 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.18;MQ0=0;OQ=665.56;QD=13.05;SB=-350.50 GT:AD:DP:GL:GQ 0/1:25,26:46:-83.71,-13.87,-77.13:99 +chr1 4424589 rs681175 T C 281.02 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=1804.45;QD=35.38;SB=-864.37 GT:AD:DP:GL:GQ 1/1:0,51:50:-184.04,-15.06,-0.01:99 +chr1 4426611 rs16839061 C T 6.85 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=8.78;MQ=59.11;MQ0=0;OQ=724.58;QD=13.42;SB=-330.47 GT:AD:DP:GL:GQ 0/1:31,23:51:-91.11,-15.37,-92.01:99 +chr1 4427201 rs350167 T C 190.81 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=59.66;MQ0=0;OQ=925.11;QD=16.82;SB=-378.98 GT:AD:DP:GL:GQ 0/1:23,32:53:-111.76,-15.96,-93.83:99 +chr1 4427323 . G A 294.49 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=680.55;QD=13.09;SB=-356.53 GT:AD:DP:GL:GQ 0/1:28,24:44:-84.60,-13.26,-76.63:99 +chr1 4433698 . G A 123.19 PASS AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.52;MQ0=0;OQ=1403.52;QD=17.99;SB=-721.04 GT:AD:DP:GL:GQ 0/1:36,42:75:-166.24,-22.60,-109.14:99 +chr1 4433807 . T G 23.74 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=3;HaplotypeScore=5.51;MQ=60.00;MQ0=0;QD=0.37;SB=80.27 GT:AD:DP:GL:GQ 0/1:45,20:51:-21.03,-15.37,-149.91:56.55 +chr1 4434327 rs645724 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=38.18;MQ=55.12;MQ0=0;OQ=2008.88;QD=24.50;SB=-765.25 GT:AD:DP:GL:GQ 0/1:13,69:74:-226.47,-22.30,-33.80:99 +chr1 4434328 rs55641638 T A 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=5;HaplotypeScore=34.59;MQ=55.12;MQ0=0;OQ=2483.75;QD=30.29;SB=-1104.11 GT:AD:DP:GL:GQ 1/1:7,75:79:-274.28,-23.80,-22.35:14.43 +chr1 4434380 rs350168 C T 706.48 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.94;MQ0=0;OQ=2402.65;QD=38.14;SB=-988.02 GT:AD:DP:GL:GQ 1/1:0,63:61:-243.87,-18.38,-0.02:99 +chr1 4434761 . C A 101.78 PASS AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.39;MQ0=0;OQ=1132.04;QD=16.65;SB=-530.30 GT:AD:DP:GL:GQ 0/1:30,38:67:-136.67,-20.18,-105.81:99 +chr1 4435588 rs350169 T A 602.50 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1092.18;QD=14.76;SB=-420.48 GT:AD:DP:GL:GQ 0/1:38,36:74:-134.79,-22.29,-147.43:99 +chr1 4439106 rs610189 T C 76.59 PASS AC=2;AF=1.00;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.49;MQ0=0;OQ=3044.46;QD=31.07;SB=-1448.66 GT:AD:DP:GL:GQ 1/1:0,98:95:-308.11,-28.64,-0.07:99 +chr1 4440903 rs13376654 C A 79.52 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=3.21;MQ=58.73;MQ0=0;OQ=748.18;QD=13.60;SB=-293.00 GT:AD:DP:GL:GQ 0/1:29,26:54:-94.37,-16.27,-89.76:99 +chr1 4440904 rs638289 A G 184.76 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.21;MQ=59.14;MQ0=0;OQ=1717.40;QD=31.80;SB=-743.85 GT:AD:DP:GL:GQ 1/1:0,54:53:-175.37,-15.98,-0.04:99 +chr1 4441250 rs11799990 A C 16.32 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.98;MQ=58.47;MQ0=0;OQ=285.71;QD=5.19;SB=-147.75 GT:AD:DP:GL:GQ 0/1:37,17:50:-46.92,-15.06,-127.84:99 +chr1 4441285 rs6426418 T C 92.05 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=4.50;MQ=58.52;MQ0=0;OQ=434.66;QD=7.63;SB=-199.21 GT:AD:DP:GL:GQ 0/1:38,19:55:-63.32,-16.57,-152.10:99 +chr1 4441304 rs16839089 G A 505.50 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=685.41;QD=10.71;SB=-336.42 GT:AD:DP:GL:GQ 0/1:40,24:63:-90.81,-18.98,-145.42:99 +chr1 4441520 . C T 159.13 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.36;MQ=59.58;MQ0=0;OQ=767.39;QD=13.95;SB=-405.80 GT:AD:DP:GL:GQ 0/1:29,25:52:-95.70,-15.68,-88.39:99 +chr1 4441584 rs28597953 G C 102.96 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.54;MQ0=0;OQ=377.89;QD=7.56;SB=-189.56 GT:AD:DP:GL:GQ 0/1:35,14:50:-59.58,-18.50,-155.34:99 +chr1 4441595 rs12057544 C T 296.32 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=442.52;QD=10.06;SB=-117.50 GT:AD:DP:GL:GQ 0/1:29,15:44:-60.79,-13.25,-105.58:99 +chr1 4441615 rs12094629 G A 446.77 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.36;MQ0=0;OQ=438.29;QD=12.17;SB=-145.60 GT:AD:DP:GL:GQ 0/1:21,15:35:-57.67,-10.56,-64.23:99 +chr1 4442760 rs705686 T G 190.01 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=58.65;MQ0=0;OQ=1305.06;QD=29.00;SB=-525.86 GT:AD:DP:GL:GQ 1/1:0,45:42:-134.13,-12.66,-0.04:99 +chr1 4443102 rs16839093 T A 368.23 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=60.00;MQ0=0;OQ=943.42;QD=16.85;SB=-414.85 GT:AD:DP:GL:GQ 0/1:25,31:55:-114.19,-16.57,-93.32:99 +chr1 4443523 rs6656245 A G 229.68 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=4.49;MQ=59.68;MQ0=0;OQ=985.54;QD=13.50;SB=-516.93 GT:AD:DP:GL:GQ 0/1:35,37:70:-125.21,-23.37,-142.93:99 +chr1 4444038 rs350170 T C 370.74 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=854.91;QD=14.49;SB=-264.93 GT:AD:DP:GL:GQ 0/1:30,29:59:-106.55,-17.78,-120.47:99 +chr1 4444166 . C T 124.24 PASS AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.74;MQ0=0;OQ=1098.39;QD=15.05;SB=-487.09 GT:AD:DP:GL:GQ 0/1:39,34:70:-134.21,-21.09,-126.03:99 +chr1 4446069 rs16839101 C T 439.86 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.34;MQ0=0;OQ=969.43;QD=15.39;SB=-381.11 GT:AD:DP:GL:GQ 0/1:31,32:61:-118.60,-18.38,-109.31:99 +chr1 4448313 rs705687 A G 587.11 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.53;MQ0=0;OQ=1218.14;QD=32.06;SB=-513.41 GT:AD:DP:GL:GQ 1/1:0,38:37:-125.42,-11.15,-0.02:99 +chr1 4448490 rs10799234 G A 167.56 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=924.80;QD=18.50;SB=-481.51 GT:AD:DP:GL:GQ 0/1:22,28:50:-110.83,-15.07,-72.35:99 +chr1 4449095 . G T 15.09 PASS AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=59.46;MQ0=0;OQ=820.94;QD=19.09;SB=-383.80 GT:AD:DP:GL:GQ 0/1:15,28:42:-98.03,-12.65,-50.79:99 +chr1 4449190 . G A 102.60 PASS AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=1775.95;QD=21.93;SB=-864.43 GT:AD:DP:GL:GQ 0/1:30,51:79:-204.67,-23.80,-104.40:99 +chr1 4449240 rs705690 G A 133.54 PASS AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.24;MQ0=0;OQ=3632.63;QD=39.92;SB=-1598.65 GT:AD:DP:GL:GQ 1/1:0,91:90:-362.26,-27.11,-0.03:99 +chr1 4449262 rs780606 A G 76.06 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=59.06;MQ0=0;OQ=718.78;QD=9.71;SB=-329.85 GT:AD:DP:GL:GQ 0/1:44,30:73:-97.16,-22.00,-175.35:99 +chr1 4449723 . G A 148.11 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.81;MQ=59.52;MQ0=0;OQ=713.60;QD=14.87;SB=-335.48 GT:AD:DP:GL:GQ 0/1:25,23:48:-89.11,-14.47,-81.14:99 +chr1 4449964 rs706145 G A 636.09 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2653.69;QD=37.38;SB=-1188.98 GT:AD:DP:GL:GQ 1/1:0,71:69:-268.98,-20.79,-0.03:99 +chr1 4452662 rs1878052 G A 714.61 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2298.20;QD=38.95;SB=-1111.02 GT:AD:DP:GL:GQ 1/1:0,59:59:-233.42,-17.78,-0.02:99 +chr1 4454614 . A C 20.74 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=601.74;QD=13.68;SB=-220.89 GT:AD:DP:GL:GQ 0/1:20,24:43:-76.41,-12.95,-71.27:99 +chr1 4455561 rs10737412 T A 735.37 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2244.31;QD=37.41;SB=-1132.68 GT:AD:DP:GL:GQ 1/1:0,60:60:-228.03,-18.07,-0.02:99 +chr1 4455707 rs4654547 C T 580.91 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=1;OQ=2435.91;QD=38.67;SB=-681.41 GT:AD:DP:GL:GQ 1/1:0,63:61:-247.19,-18.38,-0.02:99 +chr1 4456823 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=121.08;MQ=43.96;MQ0=0;OQ=445.21;QD=5.86;SB=-205.75 GT:AD:DP:GL:GQ 0/1:54,22:71:-69.19,-21.39,-207.74:99 +chr1 4456825 rs61765158 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=3;HaplotypeScore=133.78;MQ=43.18;MQ0=0;OQ=324.30;QD=4.44;SB=-88.42 GT:AD:DP:GL:GQ 0/1:59,14:70:-56.80,-21.09,-201.65:99 +chr1 4456850 rs780601 T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=50.11;MQ=42.32;MQ0=0;OQ=775.14;QD=10.77;SB=-395.42 GT:AD:DP:GL:GQ 0/1:41,31:67:-100.98,-20.18,-144.33:99 +chr1 4457263 rs780603 T C 535.20 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=1544.09;QD=29.13;SB=-491.17 GT:AD:DP:GL:GQ 1/1:0,53:48:-158.03,-14.47,-0.03:99 +chr1 4457873 rs9659744 G A 216.40 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=4.18;MQ=58.81;MQ0=0;OQ=722.66;QD=13.14;SB=-250.79 GT:AD:DP:GL:GQ 0/1:29,25:52:-94.30,-18.75,-103.70:99 +chr1 4457887 rs12029583 T C 182.25 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.02;MQ=58.88;MQ0=0;OQ=815.22;QD=14.06;SB=-229.41 GT:AD:DP:GL:GQ 0/1:25,33:54:-101.08,-16.28,-89.40:99 +chr1 4458652 rs10915548 G A 313.44 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=58.63;MQ0=0;OQ=1202.04;QD=18.21;SB=-612.14 GT:AD:DP:GL:GQ 0/1:31,35:64:-142.78,-19.29,-94.64:99 +chr1 4458793 rs609506 T C 135.30 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=2002.23;QD=32.82;SB=-965.38 GT:AD:DP:GL:GQ 1/1:0,61:57:-203.83,-17.17,-0.03:99 +chr1 4458832 rs13374152 G A 510.02 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.65;MQ0=0;OQ=1323.30;QD=19.75;SB=-559.77 GT:AD:DP:GL:GQ 0/1:28,39:65:-155.19,-19.58,-97.96:99 +chr1 4459077 rs10799235 G C 517.01 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2392.46;QD=41.97;SB=-1062.67 GT:AD:DP:GL:GQ 1/1:0,57:55:-242.85,-16.57,-0.02:99 +chr1 4459761 rs4654438 T C 731.30 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.40;MQ0=0;OQ=2338.83;QD=34.91;SB=-1062.10 GT:AD:DP:GL:GQ 1/1:0,67:66:-237.49,-19.88,-0.02:99 +chr1 4460253 . G A 71.25 PASS AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=54.34;MQ0=0;OQ=761.29;QD=16.20;SB=-383.16 GT:AD:DP:GL:GQ 0/1:23,24:45:-92.98,-13.56,-67.37:99 +chr1 4460265 rs9660574 G A 698.27 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.97;MQ0=0;OQ=1971.68;QD=38.66;SB=-993.84 GT:AD:DP:GL:GQ 1/1:0,51:50:-200.77,-15.06,-0.01:99 +chr1 4460731 rs675509 A G 75.44 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.19;MQ0=0;OQ=1733.09;QD=33.33;SB=-850.97 GT:AD:DP:GL:GQ 1/1:0,52:50:-176.92,-15.06,-0.02:99 +chr1 4460821 rs675641 C T 619.56 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2267.76;QD=39.10;SB=-1112.00 GT:AD:DP:GL:GQ 1/1:0,58:57:-230.38,-17.17,-0.02:99 +chr1 4462336 rs4654548 G A 293.32 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.55;MQ0=0;OQ=1820.62;QD=35.70;SB=-883.64 GT:AD:DP:GL:GQ 1/1:0,51:47:-185.66,-14.16,-0.02:99 +chr1 4462612 rs661886 C G 122.47 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1803.84;QD=41.95;SB=-867.51 GT:AD:DP:GL:GQ 1/1:0,43:43:-183.98,-12.96,-0.01:99 +chr1 4462757 rs597453 T C 1.51 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=2.36;MQ=60.00;MQ0=0;OQ=1873.91;QD=29.28;SB=-570.21 GT:AD:DP:GL:GQ 1/1:0,64:56:-191.00,-16.87,-0.03:99 +chr1 4463867 rs10799237 G A 181.35 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.13;MQ0=0;OQ=2001.42;QD=37.76;SB=-711.98 GT:AD:DP:GL:GQ 1/1:0,53:51:-203.74,-15.36,-0.01:99 +chr1 4464187 . T C 30.12 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.10;MQ=59.33;MQ0=0;OQ=552.68;QD=8.91;SB=-289.28 GT:AD:DP:GL:GQ 0/1:39,23:60:-76.63,-18.08,-155.34:99 +chr1 4465057 rs4654549 G A 100.14 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=3.11;MQ=59.46;MQ0=0;OQ=1572.23;QD=20.42;SB=-717.81 GT:AD:DP:GL:GQ 0/1:31,46:75:-183.10,-22.59,-108.27:99 +chr1 4465240 rs4654439 A G 186.31 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.65;MQ0=0;OQ=1824.70;QD=28.07;SB=-920.11 GT:AD:DP:GL:GQ 1/1:1,64:61:-189.47,-18.40,-3.41:99 +chr1 4465350 rs4654550 C T 464.58 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.14;MQ0=0;OQ=1183.55;QD=15.57;SB=-491.13 GT:AD:DP:GL:GQ 0/1:39,37:73:-143.65,-22.01,-117.80:99 +chr1 4465703 rs16839157 C G 292.75 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.46;MQ0=0;OQ=1332.22;QD=15.49;SB=-637.02 GT:AD:DP:GL:GQ 0/1:48,38:85:-162.12,-25.61,-205.23:99 +chr1 4465766 rs10753381 C T 668.70 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2452.18;QD=39.55;SB=-960.97 GT:AD:DP:GL:GQ 1/1:0,62:62:-248.82,-18.68,-0.02:99 +chr1 4465913 rs10753382 A C 344.57 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=42.45;MQ0=0;OQ=1152.30;QD=15.16;SB=-375.76 GT:AD:DP:GL:GQ 0/1:35,41:75:-141.10,-22.59,-129.43:99 +chr1 4465925 rs4654440 A G 314.62 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=45.24;MQ0=0;OQ=2545.78;QD=35.36;SB=-1008.34 GT:AD:DP:GL:GQ 1/1:0,72:72:-258.19,-21.69,-0.03:99 +chr1 4466035 rs4654551 T C 137.52 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.71;MQ0=0;OQ=2345.07;QD=29.31;SB=-919.32 GT:AD:DP:GL:GQ 1/1:0,80:75:-238.17,-22.62,-0.07:99 +chr1 4466375 rs4654441 A G 153.58 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=1.97;MQ=59.14;MQ0=0;OQ=1252.72;QD=16.48;SB=-599.98 GT:AD:DP:GL:GQ 0/1:32,44:75:-151.15,-22.60,-128.71:99 +chr1 4466539 . G C 13.68 PASS AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=60.00;MQ0=0;OQ=1133.87;QD=19.22;SB=-442.73 GT:AD:DP:GL:GQ 0/1:26,33:58:-134.16,-17.49,-113.78:99 +chr1 4466591 rs7537577 T C 558.12 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1692.69;QD=36.01;SB=-710.63 GT:AD:DP:GL:GQ 1/1:0,47:47:-172.87,-14.16,-0.01:99 +chr1 4466655 rs1870509 A G 172.47 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=58.79;MQ0=0;OQ=1784.46;QD=27.04;SB=-725.30 GT:AD:DP:GL:GQ 1/1:0,66:58:-182.10,-17.50,-0.07:99 +chr1 4467025 rs1018306 G A 522.41 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=2397.83;QD=37.47;SB=-678.32 GT:AD:DP:GL:GQ 1/1:0,64:61:-243.39,-18.38,-0.02:99 +chr1 4467405 . G A 173.51 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=1037.40;QD=16.73;SB=-505.13 GT:AD:DP:GL:GQ 0/1:31,31:60:-125.11,-18.08,-96.58:99 +chr1 4467882 rs10799238 G A 201.42 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=57.23;MQ0=0;OQ=2039.74;QD=37.09;SB=-730.98 GT:AD:DP:GL:GQ 1/1:0,54:52:-207.58,-15.67,-0.02:99 +chr1 4468054 rs10799239 G T 526.93 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.10;MQ0=0;OQ=2381.50;QD=35.54;SB=-1199.06 GT:AD:DP:GL:GQ 1/1:0,67:66:-241.76,-19.88,-0.02:99 +chr1 4468702 rs780570 T C 301.27 PASS AC=2;AF=1.00;AN=2;DB;DP=22;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.66;MQ0=0;OQ=692.07;QD=31.46;SB=-209.70 GT:AD:DP:GL:GQ 1/1:0,22:21:-72.80,-6.33,-0.01:63.17 +chr1 4468728 . G A 3.90 PASS AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=52.20;MQ0=0;OQ=192.92;QD=6.65;SB=-94.59 GT:AD:DP:GL:GQ 0/1:18,10:25:-30.11,-7.53,-60.00:99 +chr1 4468760 rs60725706 C T 2.79 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=2.68;MQ=47.80;MQ0=0;OQ=892.66;QD=25.50;SB=-420.32 GT:AD:DP:GL:GQ 1/1:1,34:26:-92.87,-7.84,-0.02:78.22 +chr1 4468793 . C T 155.10 SnpCluster AC=1;AF=0.50;AN=2;DP=45;Dels=0.00;HRun=2;HaplotypeScore=28.66;MQ=43.47;MQ0=0;QD=3.45;SB=-75.82 GT:AD:DP:GL:GQ 0/1:34,11:31:-28.13,-9.34,-89.19:99 +chr1 4468798 rs57105176 C T 210.28 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=33.72;MQ=43.23;MQ0=0;QD=4.38;SB=-105.47 GT:AD:DP:GL:GQ 0/1:33,15:33:-34.25,-9.94,-88.69:99 +chr1 4468800 . C T 23.55 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=49;Dels=0.00;HRun=2;HaplotypeScore=34.30;MQ=43.63;MQ0=0;QD=0.48;SB=32.09 GT:AD:DP:GL:GQ 0/1:44,5:35:-16.18,-10.54,-113.19:56.36 +chr1 4468801 . T C 10.10 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=1;HaplotypeScore=35.27;MQ=44.04;MQ0=0;QD=0.21;SB=32.13 GT:AD:DP:GL:GQ 0/1:43,5:35:-14.79,-10.54,-128.12:42.49 +chr1 4469243 rs12031045 G A 324.76 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=623.89;QD=15.22;SB=-230.72 GT:AD:DP:GL:GQ 0/1:20,21:41:-78.04,-12.36,-70.49:99 +chr1 4469296 rs780569 T A 228.26 PASS AC=2;AF=1.00;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.28;MQ0=0;OQ=1316.01;QD=34.63;SB=-627.73 GT:AD:DP:GL:GQ 1/1:0,38:37:-135.20,-11.15,-0.01:99 +chr1 4469318 rs12035160 A T 129.07 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=57.81;MQ0=0;OQ=613.76;QD=19.18;SB=-234.94 GT:AD:DP:GL:GQ 0/1:11,21:31:-74.00,-9.34,-42.52:99 +chr1 4469407 rs10799241 A G 224.26 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=57.87;MQ0=0;OQ=407.85;QD=8.87;SB=-207.21 GT:AD:DP:GL:GQ 0/1:29,17:45:-57.62,-13.55,-119.36:99 +chr1 4469520 rs16839168 G A 432.40 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=846.65;QD=16.28;SB=-413.43 GT:AD:DP:GL:GQ 0/1:26,26:51:-103.31,-15.37,-89.05:99 +chr1 4469555 rs16839171 G T 425.50 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=647.76;QD=12.70;SB=-289.64 GT:AD:DP:GL:GQ 0/1:27,24:51:-83.43,-15.37,-93.72:99 +chr1 4469694 rs780568 A G 87.34 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=2;HaplotypeScore=1.60;MQ=59.63;MQ0=0;OQ=1699.95;QD=33.33;SB=-755.94 GT:AD:DP:GL:GQ 1/1:0,51:49:-173.60,-14.76,-0.02:99 +chr1 4470136 rs16839175 T C 275.26 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.63;MQ0=0;OQ=746.25;QD=11.85;SB=-286.15 GT:AD:DP:GL:GQ 0/1:31,32:61:-96.29,-18.39,-125.52:99 +chr1 4470246 rs1612698 A G 417.84 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.34;MQ=60.15;MQ0=0;OQ=917.82;QD=12.40;SB=-358.93 GT:AD:DP:GL:GQ 0/1:42,32:74:-117.36,-22.29,-169.05:99 +chr1 4470842 rs4654552 C T 182.29 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.85;MQ=59.68;MQ0=0;OQ=1084.53;QD=15.28;SB=-349.06 GT:AD:DP:GL:GQ 0/1:37,34:71:-133.13,-21.39,-131.43:99 +chr1 4471600 rs1710415 A G 89.74 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=59.45;MQ0=0;OQ=1235.30;QD=29.41;SB=-309.47 GT:AD:DP:GL:GQ 1/1:0,42:39:-127.15,-11.76,-0.03:99 +chr1 4471806 rs1762825 T A 126.40 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.16;MQ0=0;OQ=1997.53;QD=36.32;SB=-643.98 GT:AD:DP:GL:GQ 1/1:0,55:54:-203.35,-16.27,-0.02:99 +chr1 4471883 rs10915549 G A 333.26 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.45;MQ0=0;OQ=443.28;QD=10.55;SB=-159.64 GT:AD:DP:GL:GQ 0/1:26,16:40:-59.67,-12.06,-79.56:99 +chr1 4472000 rs4654442 G A 195.09 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.37;MQ0=0;OQ=2467.21;QD=37.38;SB=-970.01 GT:AD:DP:GL:GQ 1/1:0,66:62:-250.32,-18.68,-0.02:99 +chr1 4472928 rs4568797 G T 198.75 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.61;MQ=59.01;MQ0=0;OQ=1306.78;QD=17.19;SB=-394.04 GT:AD:DP:GL:GQ 0/1:30,46:73:-155.95,-21.99,-98.20:99 +chr1 4472959 rs4480324 A G 92.82 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.63;MQ0=0;OQ=1914.93;QD=30.40;SB=-560.92 GT:AD:DP:GL:GQ 1/1:0,63:60:-195.13,-18.10,-0.06:99 +chr1 4472994 rs4323680 T C 685.55 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1931.20;QD=32.73;SB=-824.33 GT:AD:DP:GL:GQ 1/1:0,59:55:-196.72,-16.57,-0.02:99 +chr1 4473017 rs4437847 T C 44.80 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=1770.27;QD=28.55;SB=-781.74 GT:AD:DP:GL:GQ 1/1:0,62:55:-180.66,-16.58,-0.05:99 +chr1 4473102 rs4442344 T C 686.66 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1772.96;QD=35.46;SB=-792.00 GT:AD:DP:GL:GQ 1/1:0,50:50:-180.90,-15.06,-0.02:99 +chr1 4473320 rs1710418 A G 44.26 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1771.10;QD=32.20;SB=-713.21 GT:AD:DP:GL:GQ 1/1:0,54:51:-180.72,-15.36,-0.02:99 +chr1 4473327 rs1762828 G A 169.38 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.60;MQ0=0;OQ=2054.72;QD=36.05;SB=-823.34 GT:AD:DP:GL:GQ 1/1:0,57:53:-209.08,-15.97,-0.02:99 +chr1 4473546 rs1710419 C A 168.66 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=2.06;MQ=57.84;MQ0=0;OQ=1495.45;QD=32.51;SB=-770.46 GT:AD:DP:GL:GQ 1/1:0,46:43:-153.15,-12.95,-0.02:99 +chr1 4473664 rs1710420 C T 149.96 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=59.20;MQ0=0;OQ=902.97;QD=15.57;SB=-230.52 GT:AD:DP:GL:GQ 0/1:30,28:57:-110.76,-17.18,-94.35:99 +chr1 4473849 rs1710421 C T 247.57 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.67;MQ0=0;OQ=2607.62;QD=37.79;SB=-1041.32 GT:AD:DP:GL:GQ 1/1:0,69:66:-264.37,-19.88,-0.02:99 +chr1 4473977 rs1710422 C T 77.88 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=58.90;MQ0=0;OQ=2084.84;QD=37.91;SB=-795.07 GT:AD:DP:GL:GQ 1/1:0,55:54:-212.09,-16.27,-0.02:99 +chr1 4473997 rs1710423 T C 135.26 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.07;MQ0=0;OQ=1147.64;QD=25.50;SB=-601.59 GT:AD:DP:GL:GQ 1/1:0,45:37:-118.39,-11.16,-0.04:99 +chr1 4474861 rs1710424 A G 675.73 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=2263.90;QD=31.89;SB=-1103.74 GT:AD:DP:GL:GQ 1/1:0,71:67:-230.02,-20.19,-0.04:99 +chr1 4475148 rs12036337 G A 158.77 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=3.64;MQ=56.87;MQ0=1;OQ=1002.66;QD=14.75;SB=-286.76 GT:AD:DP:GL:GQ 0/1:34,34:59:-121.33,-17.78,-94.02:99 +chr1 4475283 . G A 82.68 PASS AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.84;MQ=59.35;MQ0=0;OQ=845.94;QD=13.22;SB=-362.87 GT:AD:DP:GL:GQ 0/1:34,30:60:-105.97,-18.09,-111.99:99 +chr1 4475382 rs10915550 C T 345.50 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=58.10;MQ0=0;OQ=927.67;QD=14.96;SB=-380.90 GT:AD:DP:GL:GQ 0/1:33,29:62:-114.73,-18.68,-118.48:99 +chr1 4476131 rs10737413 C T 15.63 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.60;MQ0=0;OQ=1742.86;QD=37.08;SB=-655.67 GT:AD:DP:GL:GQ 1/1:0,47:45:-177.88,-13.56,-0.01:99 +chr1 4476657 rs1710430 C G 535.69 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2311.95;QD=41.28;SB=-1026.21 GT:AD:DP:GL:GQ 1/1:0,56:54:-234.80,-16.27,-0.02:99 +chr1 4476980 rs4654443 C T 562.55 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1325.65;QD=15.60;SB=-630.22 GT:AD:DP:GL:GQ 0/1:45,40:85:-161.45,-25.60,-165.34:99 +chr1 4477487 rs12033789 G T 214.07 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=905.30;QD=15.34;SB=-363.43 GT:AD:DP:GL:GQ 0/1:29,30:59:-111.58,-17.77,-100.35:99 +chr1 4477488 rs12036603 C T 258.44 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=969.57;QD=16.16;SB=-419.81 GT:AD:DP:GL:GQ 0/1:30,30:59:-118.02,-17.78,-101.27:99 +chr1 4478406 rs596607 G A 55.59 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=59.40;MQ0=0;OQ=1761.44;QD=22.88;SB=-768.34 GT:AD:DP:GL:GQ 0/1:27,50:75:-202.03,-22.60,-83.51:99 +chr1 4478558 rs12039806 T A 70.60 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=6.67;MQ=59.12;MQ0=0;OQ=1156.91;QD=14.64;SB=-441.48 GT:AD:DP:GL:GQ 0/1:42,37:77:-142.17,-23.19,-150.58:99 +chr1 4478614 rs12039814 T C 10.71 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=7.09;MQ=59.66;MQ0=0;OQ=671.25;QD=10.02;SB=-294.21 GT:AD:DP:GL:GQ 0/1:37,30:64:-89.71,-19.30,-136.10:99 +chr1 4478650 rs12038994 A T 269.76 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=1147.45;QD=17.39;SB=-509.94 GT:AD:DP:GL:GQ 0/1:28,38:64:-137.31,-19.28,-105.10:99 +chr1 4478709 . A C 2.11 PASS AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=1;HaplotypeScore=7.65;MQ=58.73;MQ0=0;OQ=1101.58;QD=15.09;SB=-425.69 GT:AD:DP:GL:GQ 0/1:30,42:69:-134.23,-20.79,-106.44:99 +chr1 4478753 rs16839198 G T 52.90 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=7.25;MQ=58.23;MQ0=0;OQ=906.23;QD=13.73;SB=-344.31 GT:AD:DP:GL:GQ 0/1:32,33:64:-113.20,-19.29,-98.09:99 +chr1 4478891 . A G 89.93 PASS AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.48;MQ=59.39;MQ0=0;OQ=917.93;QD=13.50;SB=-396.16 GT:AD:DP:GL:GQ 0/1:36,32:68:-115.57,-20.49,-141.62:99 +chr1 4478991 rs12039070 A G 301.10 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=3.59;MQ=59.71;MQ0=0;OQ=1280.19;QD=16.00;SB=-441.58 GT:AD:DP:GL:GQ 0/1:37,43:80:-155.40,-24.10,-149.81:99 +chr1 4479035 rs12034930 G A 326.95 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.45;MQ=59.68;MQ0=0;OQ=1133.14;QD=15.74;SB=-491.00 GT:AD:DP:GL:GQ 0/1:34,37:69:-137.39,-20.79,-119.61:99 +chr1 4479073 rs12039100 A G 27.26 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=3.20;MQ=58.95;MQ0=0;OQ=915.49;QD=13.87;SB=-279.55 GT:AD:DP:GL:GQ 0/1:35,31:66:-114.72,-19.89,-140.84:99 +chr1 4479099 rs12039101 A G 318.42 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.13;MQ=59.02;MQ0=0;OQ=1020.75;QD=14.38;SB=-348.94 GT:AD:DP:GL:GQ 0/1:36,35:70:-126.45,-21.09,-134.68:99 +chr1 4479118 rs1229148 A G 277.76 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.11;MQ0=0;OQ=784.46;QD=10.75;SB=-374.59 GT:AD:DP:GL:GQ 0/1:37,36:67:-101.94,-20.21,-133.99:99 +chr1 4479593 rs12035830 G A 298.83 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=3.09;MQ=59.59;MQ0=0;OQ=906.38;QD=16.19;SB=-375.12 GT:AD:DP:GL:GQ 0/1:28,28:56:-110.79,-16.87,-99.66:99 +chr1 4479841 rs13375249 G C 20.65 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=1.63;MQ=59.73;MQ0=0;OQ=1230.24;QD=17.57;SB=-290.56 GT:AD:DP:GL:GQ 0/1:33,37:66:-146.20,-19.90,-135.57:99 +chr1 4479995 rs13375764 T C 66.03 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=4.40;MQ=59.54;MQ0=0;OQ=574.33;QD=11.49;SB=-245.91 GT:AD:DP:GL:GQ 0/1:28,22:47:-74.88,-14.16,-104.49:99 +chr1 4480068 rs56226943 T C 40.29 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=4.82;MQ=59.62;MQ0=0;OQ=881.12;QD=14.44;SB=-433.94 GT:AD:DP:GL:GQ 0/1:29,32:60:-109.48,-18.08,-115.28:99 +chr1 4480417 . C T 49.35 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=55.69;MQ0=0;OQ=1159.90;QD=16.81;SB=-282.22 GT:AD:DP:GL:GQ 0/1:33,36:66:-139.16,-19.89,-99.45:99 +chr1 4480560 rs61765366 A G 285.70 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=56.94;MQ0=0;OQ=701.52;QD=11.89;SB=-268.60 GT:AD:DP:GL:GQ 0/1:29,30:57:-90.62,-17.18,-111.39:99 +chr1 4480691 rs61765367 A G 0.21 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=4.75;MQ=57.81;MQ0=0;OQ=122.26;QD=1.63;SB=-4.55 GT:AD:DP:GL:GQ 0/1:63,11:59:-33.30,-17.79,-184.25:99 +chr1 4480787 rs61765379 A G 0.06 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=7.68;MQ=56.41;MQ0=0;OQ=64.97;QD=0.82;SB=-50.25 GT:AD:DP:GL:GQ 0/1:64,12:67:-29.98,-20.20,-222.76:97.81 +chr1 4480849 rs549627 C T 251.36 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=56.04;MQ0=0;OQ=1162.07;QD=16.37;SB=-467.11 GT:AD:DP:GL:GQ 0/1:33,37:67:-139.69,-20.20,-99.87:99 +chr1 4480920 rs548786 G A 173 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.10;MQ=56.79;MQ0=1;OQ=670.11;QD=12.41;SB=-198.20 GT:AD:DP:GL:GQ 0/1:30,24:48:-84.77,-14.47,-84.01:99 +chr1 4481090 rs12039682 C T 474.84 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.78;MQ0=0;OQ=980.72;QD=14.21;SB=-480.03 GT:AD:DP:GL:GQ 0/1:39,30:68:-121.84,-20.48,-138.54:99 +chr1 4481198 rs12039710 C A 19.16 PASS AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.00;HRun=3;HaplotypeScore=2.99;MQ=59.79;MQ0=0;OQ=1468.40;QD=16.69;SB=-755.87 GT:AD:DP:GL:GQ 0/1:41,47:88:-176.63,-26.50,-144.72:99 +chr1 4481445 rs608203 T C 400.08 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=60.00;MQ0=0;OQ=763.64;QD=11.93;SB=-242.90 GT:AD:DP:GL:GQ 0/1:33,31:64:-98.94,-19.29,-134.86:99 +chr1 4481949 rs518456 T G 602.74 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1221.17;QD=15.26;SB=-525.73 GT:AD:DP:GL:GQ 0/1:37,43:77:-148.59,-23.19,-127.99:99 +chr1 4481956 rs57010025 C T 238.50 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.40;MQ0=0;OQ=1419.96;QD=18.44;SB=-598.08 GT:AD:DP:GL:GQ 0/1:35,42:76:-168.18,-22.90,-116.42:99 +chr1 4482059 rs10489135 T C 436.47 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.51;MQ0=0;OQ=1051.73;QD=13.84;SB=-549.55 GT:AD:DP:GL:GQ 0/1:39,37:73:-130.44,-21.99,-146.62:99 +chr1 4482139 rs57559146 A C 431.51 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=970.54;QD=17.33;SB=-397.86 GT:AD:DP:GL:GQ 0/1:23,33:54:-116.60,-16.26,-81.57:99 +chr1 4482422 rs60071491 T C 92.13 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=56.24;MQ0=0;OQ=1374.62;QD=16.76;SB=-668.88 GT:AD:DP:GL:GQ 0/1:37,45:82:-165.44,-24.69,-153.42:99 +chr1 4482693 rs4112336 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=102.81;MQ=56.77;MQ0=0;OQ=769.43;QD=9.27;SB=-197.80 GT:AD:DP:GL:GQ 0/1:55,28:82:-104.92,-24.70,-193.00:99 +chr1 4482708 . C A 39.18 Indel;LowQual AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=48.79;MQ=55.68;MQ0=0;QD=0.43;SB=-10.83 GT:AD:DP:GL:GQ 0/1:82,10:90:-34.30,-27.10,-291.82:72.01 +chr1 4482756 rs1229150 T G 280.23 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=57.57;MQ0=0;OQ=1600.43;QD=18.83;SB=-735.72 GT:AD:DP:GL:GQ 0/1:32,53:82:-188.02,-24.70,-112.53:99 +chr1 4482784 rs1229151 A G 1304.96 Indel AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=53.27;MQ0=0;QD=17.88;SB=-660.04 GT:AD:DP:GL:GQ 0/1:30,43:72:-155.47,-21.69,-120.71:99 +chr1 4482854 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=68;Dels=0.00;HRun=0;HaplotypeScore=78.29;MQ=48.56;MQ0=0;OQ=195.41;QD=2.87;SB=-84.58 GT:AD:DP:GL:GQ 0/1:55,13:66:-42.70,-19.88,-199.63:99 +chr1 4482959 rs2097536 C T 73.43 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.49;MQ0=0;OQ=999.17;QD=22.20;SB=-274.28 GT:AD:DP:GL:GQ 0/1:16,29:44:-116.46,-13.25,-55.39:99 +chr1 4486372 rs12040164 C T 326.57 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.99;MQ=59.42;MQ0=0;OQ=1051.54;QD=14.60;SB=-388.33 GT:AD:DP:GL:GQ 0/1:40,32:72:-130.14,-21.70,-132.54:99 +chr1 4487829 rs241237 C T 194.54 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.46;MQ0=0;OQ=801.99;QD=18.65;SB=-287.22 GT:AD:DP:GL:GQ 0/1:18,25:42:-96.14,-12.66,-58.53:99 +chr1 4488590 . G A 17.21 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1047.83;QD=22.78;SB=-295.25 GT:AD:DP:GL:GQ 0/1:15,31:44:-121.33,-13.26,-41.74:99 +chr1 4489266 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=19.48;MQ=53.94;MQ0=1;OQ=546.80;QD=8.68;SB=-157.24 GT:AD:DP:GL:GQ 0/1:31,26:42:-73.40,-15.44,-84.22:99 +chr1 4489270 rs241234 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=25.61;MQ=53.85;MQ0=1;OQ=785.85;QD=12.28;SB=-389.60 GT:AD:DP:GL:GQ 0/1:33,31:57:-99.04,-17.17,-115.38:99 +chr1 4490410 rs241233 T C 169.60 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.70;MQ=59.74;MQ0=0;OQ=1074.01;QD=14.92;SB=-553.96 GT:AD:DP:GL:GQ 0/1:36,36:72:-132.37,-21.68,-149.45:99 +chr1 4490829 rs241232 G A 84.32 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=59.60;MQ0=0;OQ=913.96;QD=19.45;SB=-389.16 GT:AD:DP:GL:GQ 0/1:20,27:47:-108.84,-14.16,-68.00:99 +chr1 4492019 . C T 107.27 PASS AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.07;MQ0=0;OQ=862.99;QD=13.28;SB=-457.42 GT:AD:DP:GL:GQ 0/1:38,27:64:-108.86,-19.28,-134.13:99 +chr1 4492104 rs241229 G A 148.93 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=59.63;MQ0=0;OQ=584.46;QD=9.28;SB=-212.39 GT:AD:DP:GL:GQ 0/1:43,20:63:-80.71,-18.98,-155.69:99 +chr1 4494463 rs537398 T C 597.93 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=930.45;QD=15.51;SB=-426.29 GT:AD:DP:GL:GQ 0/1:29,31:60:-114.40,-18.07,-118.90:99 +chr1 4494858 rs34231005 T G 11.27 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=4;HaplotypeScore=0.14;MQ=59.76;MQ0=0;OQ=881.39;QD=11.30;SB=-322.46 GT:AD:DP:GL:GQ 0/1:45,33:76:-114.31,-22.89,-158.76:99 +chr1 4495171 rs509960 T C 253.48 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=2.40;MQ=60.00;MQ0=0;OQ=1172.46;QD=18.04;SB=-611.00 GT:AD:DP:GL:GQ 0/1:27,38:65:-140.10,-19.58,-110.54:99 +chr1 4495869 . C T 861.60 Indel AC=1;AF=0.50;AN=2;DP=74;Dels=0.04;HRun=1;HaplotypeScore=22.99;MQ=51.44;MQ0=0;QD=11.64;SB=-342.41 GT:AD:DP:GL:GQ 0/1:44,27:74:-110.83,-21.38,-161.62:99 +chr1 4495871 . C A 736.52 Indel AC=1;AF=0.50;AN=2;DP=74;Dels=0.04;HRun=0;HaplotypeScore=22.99;MQ=51.44;MQ0=0;QD=9.95;SB=-304.20 GT:AD:DP:GL:GQ 0/1:44,27:74:-98.32,-21.38,-161.31:99 +chr1 4496138 rs10915553 T C 458.40 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.54;MQ0=0;OQ=880.60;QD=11.90;SB=-349.17 GT:AD:DP:GL:GQ 0/1:42,32:72:-113.03,-21.69,-158.51:99 +chr1 4496148 rs10915554 G A 271.40 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=55.61;MQ0=0;OQ=1132.53;QD=15.10;SB=-504.97 GT:AD:DP:GL:GQ 0/1:40,35:73:-138.53,-22.00,-129.42:99 +chr1 4496394 rs12084169 C T 196.40 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=59.54;MQ0=0;OQ=1321.84;QD=16.12;SB=-685.73 GT:AD:DP:GL:GQ 0/1:41,41:80:-159.57,-24.10,-141.56:99 +chr1 4496424 rs12086217 A G 463.85 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.43;MQ0=0;OQ=859.99;QD=13.23;SB=-378.26 GT:AD:DP:GL:GQ 0/1:34,31:65:-108.86,-19.58,-137.17:99 +chr1 4496942 rs623217 G C 175.34 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=59.66;MQ0=0;OQ=1355.72;QD=19.94;SB=-471.80 GT:AD:DP:GL:GQ 0/1:31,37:66:-158.75,-19.89,-127.17:99 +chr1 4496949 rs472113 G A 230.42 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.66;MQ0=0;OQ=1272.49;QD=18.99;SB=-462.43 GT:AD:DP:GL:GQ 0/1:30,37:67:-150.71,-20.18,-109.30:99 +chr1 4497460 rs556890 A G 2.32 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=9.81;MQ=58.48;MQ0=0;OQ=661.76;QD=14.39;SB=-333.32 GT:AD:DP:GL:GQ 0/1:21,24:43:-82.42,-12.96,-78.26:99 +chr1 4497578 . G A 145.29 PASS AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.42;MQ=55.81;MQ0=2;OQ=939.73;QD=13.42;SB=-372.83 GT:AD:DP:GL:GQ 0/1:38,32:59:-115.04,-17.78,-100.90:99 +chr1 4497715 rs609304 T C 122.41 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.55;MQ0=0;OQ=597.13;QD=11.71;SB=-145.28 GT:AD:DP:GL:GQ 0/1:26,25:50:-78.07,-15.08,-99.80:99 +chr1 4497726 rs554335 A T 316.28 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=640.98;QD=12.57;SB=-272.29 GT:AD:DP:GL:GQ 0/1:29,22:51:-82.74,-15.36,-107.67:99 +chr1 4497802 rs16838465 A G 196.23 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.68;MQ0=0;OQ=953.26;QD=13.06;SB=-260.95 GT:AD:DP:GL:GQ 0/1:33,40:71:-120.01,-21.40,-135.23:99 +chr1 4497821 rs553435 A G 265.49 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=3.67;MQ=59.70;MQ0=0;OQ=1049.73;QD=13.63;SB=-281.63 GT:AD:DP:GL:GQ 0/1:34,43:75:-130.87,-22.61,-136.05:99 +chr1 4497861 rs608492 G C 466.90 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.05;MQ0=0;OQ=1478.41;QD=20.82;SB=-714.38 GT:AD:DP:GL:GQ 0/1:30,41:69:-171.91,-20.79,-131.74:99 +chr1 4497881 rs12726510 T C 431.64 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=56.08;MQ0=0;OQ=981.66;QD=11.69;SB=-387.89 GT:AD:DP:GL:GQ 0/1:41,43:78:-124.95,-23.50,-161.69:99 +chr1 4497887 rs12752601 C A 191.53 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=56.08;MQ0=0;OQ=1107.25;QD=13.18;SB=-552.73 GT:AD:DP:GL:GQ 0/1:44,40:81:-138.40,-24.39,-157.12:99 +chr1 4497950 rs12737521 G A 266.94 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.10;MQ0=0;OQ=874.33;QD=12.67;SB=-378.16 GT:AD:DP:GL:GQ 0/1:41,28:69:-111.51,-20.80,-136.23:99 +chr1 4498077 rs551359 A G 240.90 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=59.32;MQ0=0;OQ=1496.06;QD=16.81;SB=-547.59 GT:AD:DP:GL:GQ 0/1:39,50:88:-179.39,-26.50,-159.21:99 +chr1 4498168 rs495682 T C 312.82 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.73;MQ0=0;OQ=1219.53;QD=14.52;SB=-615.78 GT:AD:DP:GL:GQ 0/1:41,43:83:-150.24,-25.00,-166.52:99 +chr1 4498170 rs596848 G A 305.85 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=1391.50;QD=16.77;SB=-693.72 GT:AD:DP:GL:GQ 0/1:40,43:81:-166.83,-24.40,-145.63:99 +chr1 4498284 rs596360 G A 603.53 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=984.96;QD=14.92;SB=-509.05 GT:AD:DP:GL:GQ 0/1:36,30:66:-121.68,-19.90,-113.72:99 +chr1 4498314 rs494638 T C 459.72 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.34;MQ0=0;OQ=1145.34;QD=15.69;SB=-585.28 GT:AD:DP:GL:GQ 0/1:33,40:71:-139.20,-21.39,-128.86:99 +chr1 4498825 rs489371 A G 35.40 PASS AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=4.84;MQ=56.29;MQ0=0;OQ=1173.41;QD=12.62;SB=-564.58 GT:AD:DP:GL:GQ 0/1:51,42:90:-147.73,-27.11,-207.42:99 +chr1 4498854 rs489316 A G 383.07 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=53.44;MQ0=0;OQ=1022.72;QD=11.24;SB=-456.67 GT:AD:DP:GL:GQ 0/1:50,41:90:-132.68,-27.12,-202.80:99 +chr1 4499103 rs592726 C T 522.92 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=1251.74;QD=14.06;SB=-614.59 GT:AD:DP:GL:GQ 0/1:50,39:87:-154.68,-26.22,-160.76:99 +chr1 4499256 rs6673713 A T 601.23 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.46;MQ0=0;OQ=969.14;QD=15.38;SB=-478.55 GT:AD:DP:GL:GQ 0/1:32,31:63:-119.17,-18.97,-123.21:99 +chr1 4499545 rs6677142 T C 474.20 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=56.97;MQ0=0;OQ=1056.33;QD=15.77;SB=-489.28 GT:AD:DP:GL:GQ 0/1:31,36:67:-129.10,-20.18,-124.32:99 +chr1 4499557 rs10158638 A G 600.71 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.01;MQ0=0;OQ=954.47;QD=14.46;SB=-498.28 GT:AD:DP:GL:GQ 0/1:33,33:66:-118.61,-19.88,-133.94:99 +chr1 4499695 rs28694108 C T 122.88 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=60.16;MQ0=0;OQ=1387.28;QD=20.11;SB=-460.49 GT:AD:DP:GL:GQ 0/1:27,42:67:-162.21,-20.20,-83.84:99 +chr1 4499852 rs569392 T C 181.23 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.97;MQ=59.40;MQ0=0;OQ=1301.88;QD=15.50;SB=-652.84 GT:AD:DP:GL:GQ 0/1:40,44:84:-158.78,-25.30,-162.80:99 +chr1 4499866 rs638811 G A 371.51 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.47;MQ0=0;OQ=1161.22;QD=14.70;SB=-516.05 GT:AD:DP:GL:GQ 0/1:40,38:72:-141.11,-21.71,-113.94:99 +chr1 4500093 rs627374 C A 201.56 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=3.04;MQ=56.24;MQ0=0;OQ=1409.06;QD=17.18;SB=-575.67 GT:AD:DP:GL:GQ 0/1:36,45:77:-170.76,-26.57,-102.66:99 +chr1 4500144 rs1612095 G C 191.96 PASS AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=58.14;MQ0=0;OQ=1652.98;QD=16.87;SB=-714.30 GT:AD:DP:GL:GQ 0/1:51,47:96:-197.51,-28.93,-219.71:99 +chr1 4500181 rs1612008 C T 343.92 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.55;MQ0=0;OQ=1543.90;QD=16.78;SB=-630.74 GT:AD:DP:GL:GQ 0/1:42,49:86:-183.59,-25.91,-132.31:99 +chr1 4500274 rs544513 A G 399.63 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=703.77;QD=11.00;SB=-261.96 GT:AD:DP:GL:GQ 0/1:33,31:62:-92.35,-18.69,-134.62:99 +chr1 4500351 rs543653 T G 570.98 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=699.52;QD=12.27;SB=-362.58 GT:AD:DP:GL:GQ 0/1:31,26:56:-90.10,-16.87,-111.77:99 +chr1 4500481 rs542688 C G 360.13 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.76;MQ0=0;OQ=1267.59;QD=16.05;SB=-449.73 GT:AD:DP:GL:GQ 0/1:41,38:77:-153.25,-23.20,-181.78:99 +chr1 4500512 rs625627 C T 286.16 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.37;MQ=59.08;MQ0=0;OQ=914.91;QD=12.89;SB=-281.75 GT:AD:DP:GL:GQ 0/1:39,32:67:-114.97,-20.19,-123.19:99 +chr1 4500529 rs541929 A G 325.19 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.04;MQ=59.16;MQ0=0;OQ=945.37;QD=12.28;SB=-290.30 GT:AD:DP:GL:GQ 0/1:42,34:76:-120.71,-22.89,-170.67:99 +chr1 4500606 rs10915556 C T 355.71 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1316.31;QD=19.65;SB=-489.56 GT:AD:DP:GL:GQ 0/1:29,38:66:-154.80,-19.88,-102.91:99 +chr1 4500644 rs2051642 G T 498.30 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=1142.97;QD=16.33;SB=-501.30 GT:AD:DP:GL:GQ 0/1:32,38:70:-138.67,-21.09,-110.82:99 +chr1 4500677 rs2051641 C T 126.58 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=2.61;MQ=60.00;MQ0=0;OQ=1424.93;QD=18.04;SB=-396.12 GT:AD:DP:GL:GQ 0/1:37,42:79:-169.57,-23.79,-134.20:99 +chr1 4500995 rs694361 G A 987.12 Indel AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=10;HaplotypeScore=19.73;MQ=59.67;MQ0=0;QD=14.31;SB=-451.85 GT:AD:DP:GL:GQ 0/1:36,33:64:-121.28,-19.29,-109.34:99 +chr1 4501161 rs10915557 A C 322.35 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.59;MQ0=0;OQ=772.74;QD=13.80;SB=-198.82 GT:AD:DP:GL:GQ 0/1:27,28:54:-96.83,-16.27,-94.26:99 +chr1 4501182 rs10915558 G T 398.28 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=829.24;QD=13.16;SB=-280.30 GT:AD:DP:GL:GQ 0/1:32,31:61:-104.58,-18.38,-107.72:99 +chr1 4501418 rs988089 G T 231.64 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.83;MQ0=0;OQ=785.83;QD=14.29;SB=-379.13 GT:AD:DP:GL:GQ 0/1:28,27:55:-98.43,-16.57,-95.26:99 +chr1 4501445 rs988088 G A 287.91 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.35;MQ0=0;OQ=635.25;QD=14.77;SB=-270.30 GT:AD:DP:GL:GQ 0/1:21,22:39:-78.57,-11.76,-58.80:99 +chr1 4501584 rs1988134 A T 372.09 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.72;MQ0=0;OQ=1235.61;QD=14.89;SB=-511.29 GT:AD:DP:GL:GQ 0/1:43,40:83:-151.84,-25.00,-162.60:99 +chr1 4501936 rs508056 T C 0.28 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.01;HRun=1;HaplotypeScore=15.97;MQ=59.84;MQ0=0;OQ=1145.11;QD=15.07;SB=-479.27 GT:AD:DP:GL:GQ 0/1:36,39:76:-140.39,-22.59,-147.97:99 +chr1 4501948 rs594535 A T 38.55 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.01;HRun=0;HaplotypeScore=7.00;MQ=59.51;MQ0=0;OQ=1283.54;QD=17.83;SB=-623.13 GT:AD:DP:GL:GQ 0/1:31,40:72:-153.02,-21.38,-116.42:99 +chr1 4502177 rs640624 T C 14.98 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=7.76;MQ=59.57;MQ0=0;OQ=1108.01;QD=16.29;SB=-573.02 GT:AD:DP:GL:GQ 0/1:30,38:66:-133.97,-19.88,-116.04:99 +chr1 4502677 . A G 145.65 PASS AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.30;MQ0=0;OQ=805.91;QD=12.21;SB=-395.14 GT:AD:DP:GL:GQ 0/1:37,29:66:-103.76,-19.88,-150.61:99 +chr1 4502871 rs2411775 C T 188.48 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.39;MQ0=0;OQ=1230.48;QD=17.83;SB=-330.32 GT:AD:DP:GL:GQ 0/1:32,36:67:-146.52,-20.19,-100.70:99 +chr1 4503184 rs694935 T A 28.68 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=2.73;MQ=59.33;MQ0=0;OQ=840.35;QD=13.55;SB=-222.90 GT:AD:DP:GL:GQ 0/1:31,31:58:-104.80,-17.48,-105.42:99 +chr1 4503230 rs694967 T G 352.39 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=57.78;MQ0=0;OQ=1098.27;QD=15.25;SB=-535.44 GT:AD:DP:GL:GQ 0/1:33,39:72:-134.80,-21.69,-119.88:99 +chr1 4503601 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=120;Dels=0.00;HRun=1;HaplotypeScore=106.52;MQ=39.06;MQ0=0;OQ=897.90;QD=7.48;SB=-269.21 GT:AD:DP:GL:GQ 0/1:86,34:118:-128.61,-35.54,-314.22:99 +chr1 4503616 . T C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=1;HaplotypeScore=12.83;MQ=37.47;MQ0=0;OQ=467.51;QD=3.41;SB=-122.22 GT:AD:DP:GL:GQ 0/1:111,26:134:-90.40,-40.36,-439.82:99 +chr1 4503623 rs241214 C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=148;Dels=0.00;HRun=0;HaplotypeScore=94.05;MQ=37.91;MQ0=0;OQ=4273.01;QD=28.87;SB=-1538.72 GT:AD:DP:GL:GQ 0/1:32,114:147:-426.30,-51.49,-123.04:99 +chr1 4503639 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=159;Dels=0.00;HRun=0;HaplotypeScore=260.99;MQ=37.36;MQ0=0;OQ=1166.38;QD=7.34;SB=-484.60 GT:AD:DP:GL:GQ 0/1:114,44:124:-157.27,-37.35,-295.16:99 +chr1 4503657 rs12754029 A C 1394.26 DPFilter;Indel AC=1;AF=0.50;AN=2;DB;DP=153;Dels=0.00;HRun=1;HaplotypeScore=166.14;MQ=39.29;MQ0=0;QD=9.11;SB=-599.12 GT:AD:DP:GL:GQ 0/1:73,77:122:-190.87,-48.16,-269.49:99 +chr1 4503674 rs61111938 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=147;Dels=0.00;HRun=0;HaplotypeScore=137.11;MQ=42.18;MQ0=0;OQ=392.40;QD=2.67;SB=-58.59 GT:AD:DP:GL:GQ 0/1:124,23:123:-79.58,-37.06,-405.54:99 +chr1 4503686 rs61202630 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.03;HRun=0;HaplotypeScore=163.66;MQ=45.68;MQ0=0;OQ=981.22;QD=7.91;SB=-498.66 GT:AD:DP:GL:GQ 0/1:79,40:116:-138.71,-37.31,-281.28:99 +chr1 4503715 . T C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=16.61;MQ=53.48;MQ0=0;OQ=158.20;QD=1.86;SB=-90.66 GT:AD:DP:GL:GQ 0/1:72,13:84:-44.41,-25.30,-293.89:99 +chr1 4503964 rs241215 T A 444.25 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=54.88;MQ0=0;OQ=1312.48;QD=17.50;SB=-618.08 GT:AD:DP:GL:GQ 0/1:34,41:75:-157.12,-22.59,-129.67:99 +chr1 4504029 rs241216 G A 155.80 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=4.03;MQ=59.43;MQ0=0;OQ=1251.65;QD=17.15;SB=-469.46 GT:AD:DP:GL:GQ 0/1:35,38:70:-149.55,-21.10,-107.16:99 +chr1 4504349 rs241217 C G 275.14 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1603.60;QD=22.59;SB=-778.42 GT:AD:DP:GL:GQ 0/1:29,42:71:-185.04,-21.39,-125.25:99 +chr1 4505282 rs241218 T C 43.78 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=7.22;MQ=59.15;MQ0=0;OQ=812.13;QD=11.44;SB=-395.26 GT:AD:DP:GL:GQ 0/1:37,34:67:-104.70,-20.20,-130.72:99 +chr1 4506052 rs241219 T C 334.21 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.94;MQ=59.17;MQ0=0;OQ=741.75;QD=13.25;SB=-389.65 GT:AD:DP:GL:GQ 0/1:27,29:55:-94.04,-16.58,-103.55:99 +chr1 4508064 rs241220 G A 334 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=60.00;MQ0=0;OQ=1163.49;QD=17.37;SB=-431.97 GT:AD:DP:GL:GQ 0/1:32,35:66:-139.53,-19.90,-98.33:99 +chr1 4508910 rs241221 T C 373.72 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.20;MQ0=0;OQ=874.89;QD=15.08;SB=-418.55 GT:AD:DP:GL:GQ 0/1:25,33:55:-107.34,-16.57,-97.13:99 +chr1 4509116 rs241222 G C 267.87 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=59.18;MQ0=0;OQ=1337.43;QD=18.07;SB=-676.08 GT:AD:DP:GL:GQ 0/1:37,37:72:-158.72,-21.69,-154.68:99 +chr1 4510110 rs241244 A T 180.09 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.78;MQ=60.38;MQ0=0;OQ=930.99;QD=16.33;SB=-387.46 GT:AD:DP:GL:GQ 0/1:27,30:57:-113.55,-17.17,-101.72:99 +chr1 4510493 rs241245 T C 361.78 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=851.20;QD=14.43;SB=-421.93 GT:AD:DP:GL:GQ 0/1:29,30:57:-105.58,-17.17,-107.45:99 +chr1 4510920 rs241246 T C 463.10 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.63;MQ0=0;OQ=864.46;QD=13.94;SB=-382.19 GT:AD:DP:GL:GQ 0/1:32,30:62:-108.40,-18.67,-129.80:99 +chr1 4510938 rs241247 G T 223.55 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=4.47;MQ=59.71;MQ0=0;OQ=1111.82;QD=14.07;SB=-561.61 GT:AD:DP:GL:GQ 0/1:42,37:78:-137.96,-23.49,-147.67:99 +chr1 4511101 rs241248 G A 90.66 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=4.65;MQ=58.90;MQ0=0;OQ=1137.70;QD=15.80;SB=-412.89 GT:AD:DP:GL:GQ 0/1:38,34:72:-138.74,-21.69,-139.14:99 +chr1 4512226 rs241249 C A 118.09 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=2704.76;QD=36.06;SB=-1203.75 GT:AD:DP:GL:GQ 1/1:0,75:73:-274.08,-21.98,-0.01:99 +chr1 4512612 rs12117466 C T 434.32 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1595.86;QD=21.57;SB=-705.78 GT:AD:DP:GL:GQ 0/1:28,46:74:-185.16,-22.29,-104.90:99 +chr1 4512789 rs2222050 C G 399.97 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=51.66;MQ0=0;OQ=560.26;QD=12.18;SB=-284.90 GT:AD:DP:GL:GQ 0/1:29,17:46:-73.17,-13.86,-129.73:99 +chr1 4512997 . G C 109.15 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.26;MQ0=0;OQ=1039.37;QD=14.64;SB=-540.64 GT:AD:DP:GL:GQ 0/1:41,30:70:-128.31,-21.09,-176.73:99 +chr1 4513093 rs241250 C T 592.78 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.64;MQ0=0;OQ=2215.68;QD=40.29;SB=-1120.49 GT:AD:DP:GL:GQ 1/1:0,55:55:-225.17,-16.57,-0.01:99 +chr1 4513279 rs241251 T C 191.39 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=3.46;MQ=56.17;MQ0=0;OQ=859.05;QD=12.10;SB=-428.93 GT:AD:DP:GL:GQ 0/1:40,31:71:-110.57,-21.39,-162.21:99 +chr1 4513371 rs241252 G A 678.22 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2454.05;QD=39.58;SB=-997.85 GT:AD:DP:GL:GQ 1/1:0,61:61:-249.00,-18.37,-0.01:99 +chr1 4513556 rs56948682 G C 523.60 Indel AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=3.31;MQ=55.31;MQ0=0;QD=11.90;SB=-218.66 GT:AD:DP:GL:GQ 0/1:25,19:40:-67.72,-12.07,-92.30:99 +chr1 4513868 rs241254 G A 271.50 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=58.71;MQ0=0;OQ=649.43;QD=12.03;SB=-239.26 GT:AD:DP:GL:GQ 0/1:28,25:50:-83.30,-15.07,-98.60:99 +chr1 4513881 rs241255 G C 176.18 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=58.80;MQ0=0;OQ=2370.20;QD=40.87;SB=-1167.06 GT:AD:DP:GL:GQ 1/1:0,58:55:-240.62,-16.57,-0.01:99 +chr1 4514372 rs241256 C T 582.40 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=913.61;QD=13.44;SB=-345.84 GT:AD:DP:GL:GQ 0/1:39,29:68:-115.13,-20.48,-142.92:99 +chr1 4514476 rs6426419 T A 347.17 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.60;MQ0=0;OQ=541.18;QD=9.33;SB=-252.68 GT:AD:DP:GL:GQ 0/1:37,21:57:-74.57,-17.17,-137.52:99 +chr1 4514682 rs241257 C T 286.90 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=2358.24;QD=39.97;SB=-1174.07 GT:AD:DP:GL:GQ 1/1:0,59:59:-239.42,-17.77,-0.01:99 +chr1 4514873 rs171319 C T 380.27 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.42;MQ0=0;OQ=1086.37;QD=13.58;SB=-534.53 GT:AD:DP:GL:GQ 0/1:46,34:78:-135.44,-23.52,-140.72:99 +chr1 4515369 rs241258 G A 48.68 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=2.13;MQ=47.21;MQ0=0;OQ=749.09;QD=17.42;SB=-181.27 GT:AD:DP:GL:GQ 0/1:20,23:42:-90.85,-12.66,-63.49:99 +chr1 4515444 rs241259 C G 22.32 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=50.43;MQ0=0;OQ=2118.85;QD=40.75;SB=-972.73 GT:AD:DP:GL:GQ 1/1:0,52:49:-215.48,-14.76,-0.01:99 +chr1 4515588 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=15;HaplotypeScore=4.97;MQ=51.27;MQ0=0;OQ=250.35;QD=4.47;SB=56.21 GT:AD:DP:GL:GQ 0/1:42,14:49:-43.09,-14.77,-129.95:99 +chr1 4515926 rs241260 C G 33.59 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=2.19;MQ=55.21;MQ0=0;OQ=3292.12;QD=42.21;SB=-1616.25 GT:AD:DP:GL:GQ 1/1:0,78:75:-328.21,-22.60,-0.02:99 +chr1 4515962 rs241261 T C 602.08 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.64;MQ0=0;OQ=2469.23;QD=29.75;SB=-1091.36 GT:AD:DP:GL:GQ 1/1:0,83:79:-250.58,-23.83,-0.08:99 +chr1 4516659 rs241262 T G 634.51 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2557.93;QD=35.53;SB=-1149.62 GT:AD:DP:GL:GQ 1/1:0,72:72:-259.40,-21.69,-0.02:99 +chr1 4517716 rs10799244 T C 405.95 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.15;MQ0=0;OQ=1346.22;QD=18.96;SB=-628.34 GT:AD:DP:GL:GQ 0/1:27,44:70:-158.99,-21.09,-107.87:99 +chr1 4518111 rs6685798 G A 309.27 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=59.32;MQ0=0;OQ=1238.56;QD=18.21;SB=-627.62 GT:AD:DP:GL:GQ 0/1:30,37:65:-146.72,-19.58,-98.24:99 +chr1 4518139 rs916408 T C 232.25 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.86;MQ=59.63;MQ0=0;OQ=609.90;QD=9.84;SB=-241.88 GT:AD:DP:GL:GQ 0/1:34,28:60:-82.36,-18.09,-138.61:99 +chr1 4518389 rs916407 C A 294.22 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.44;MQ0=0;OQ=593.42;QD=10.99;SB=-258.24 GT:AD:DP:GL:GQ 0/1:32,22:53:-78.59,-15.97,-110.59:99 +chr1 4518393 rs916406 T C 102.38 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.50;MQ0=0;OQ=426.60;QD=7.62;SB=-216.22 GT:AD:DP:GL:GQ 0/1:34,22:50:-61.02,-15.07,-122.30:99 +chr1 4518582 rs241263 T C 395.70 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2663.66;QD=36.49;SB=-1355.60 GT:AD:DP:GL:GQ 1/1:0,73:73:-269.97,-21.98,-0.02:99 +chr1 4518898 rs241264 C T 593.29 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3315.63;QD=40.93;SB=-1267.69 GT:AD:DP:GL:GQ 1/1:0,81:81:-330.56,-24.40,-0.02:99 +chr1 4519253 rs241265 G T 396.78 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=442.53;QD=9.42;SB=-108.63 GT:AD:DP:GL:GQ 0/1:30,17:47:-61.69,-14.15,-109.08:99 +chr1 4520150 rs241266 G A 572.22 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1309.70;QD=16.79;SB=-634.24 GT:AD:DP:GL:GQ 0/1:38,40:77:-157.45,-23.20,-135.23:99 +chr1 4520783 rs10915560 T C 479.08 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=617.89;QD=10.13;SB=-279.12 GT:AD:DP:GL:GQ 0/1:36,25:60:-83.15,-18.08,-142.30:99 +chr1 4520856 rs12120353 C A 156.50 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=694.57;QD=12.19;SB=-303.22 GT:AD:DP:GL:GQ 0/1:32,25:54:-89.01,-16.27,-103.65:99 +chr1 4521323 rs241267 C T 378.46 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=59.60;MQ0=0;OQ=620.84;QD=13.21;SB=-243.25 GT:AD:DP:GL:GQ 0/1:25,22:45:-78.94,-13.58,-74.16:99 +chr1 4521646 rs12748186 C T 419.48 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=983.89;QD=18.92;SB=-364.52 GT:AD:DP:GL:GQ 0/1:23,29:52:-117.34,-15.67,-75.86:99 +chr1 4522500 rs241268 A G 490.54 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1548.29;QD=30.97;SB=-704.61 GT:AD:DP:GL:GQ 1/1:0,50:49:-158.46,-14.78,-0.04:99 +chr1 4523101 . G T 20.08 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=16;HaplotypeScore=10.17;MQ=50.32;MQ0=0;QD=0.35;SB=50.87 GT:AD:DP:GL:GQ 0/1:48,10:42:-17.95,-12.66,-121.78:52.87 +chr1 4523283 rs241269 C T 335.48 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=806.86;QD=12.81;SB=-308.31 GT:AD:DP:GL:GQ 0/1:36,27:61:-102.37,-18.40,-111.88:99 +chr1 4523749 rs55956326 C T 46.96 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=776.69;QD=17.65;SB=-140.14 GT:AD:DP:GL:GQ 0/1:21,23:44:-94.21,-13.26,-66.49:99 +chr1 4524365 rs497517 C A 203.92 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.25;MQ=57.23;MQ0=0;OQ=2311.84;QD=35.57;SB=-943.65 GT:AD:DP:GL:GQ 1/1:0,65:64:-234.79,-19.27,-0.02:99 +chr1 4524639 rs190250 T C 96.54 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=54.62;MQ0=1;OQ=1410.76;QD=28.22;SB=-520.24 GT:AD:DP:GL:GQ 1/1:1,49:43:-144.69,-12.96,-0.03:99 +chr1 4525049 rs241270 T A 128.22 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=57.31;MQ0=0;OQ=2756.56;QD=35.80;SB=-964.62 GT:AD:DP:GL:GQ 1/1:0,76:75:-279.26,-22.59,-0.02:99 +chr1 4525775 . C T 82.15 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=60.00;MQ0=0;OQ=631.76;QD=12.39;SB=-287.21 GT:AD:DP:GL:GQ 0/1:28,23:47:-80.62,-14.16,-88.43:99 +chr1 4526115 rs241271 T C 508.56 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1796.29;QD=29.45;SB=-877.68 GT:AD:DP:GL:GQ 1/1:0,61:57:-183.26,-17.19,-0.05:99 +chr1 4526127 rs241272 T G 620.21 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=2425.30;QD=34.16;SB=-1142.12 GT:AD:DP:GL:GQ 1/1:0,71:70:-246.14,-21.08,-0.02:99 +chr1 4526146 rs1515670 A G 180.27 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=3.98;MQ=58.96;MQ0=0;OQ=860.15;QD=12.84;SB=-436.91 GT:AD:DP:GL:GQ 0/1:37,30:66:-109.18,-19.88,-145.10:99 +chr1 4526937 rs241273 A C 421.62 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=1105.42;QD=16.02;SB=-515.69 GT:AD:DP:GL:GQ 0/1:31,38:69:-134.61,-20.78,-114.90:99 +chr1 4527342 rs241274 A C 51.54 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1996.50;QD=32.20;SB=-821.03 GT:AD:DP:GL:GQ 1/1:0,62:58:-203.26,-17.47,-0.02:99 +chr1 4527839 rs241275 A G 555.63 PASS AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=2594.28;QD=29.48;SB=-1228.48 GT:AD:DP:GL:GQ 1/1:0,88:82:-263.09,-24.73,-0.08:99 +chr1 4528191 rs28665533 G A 434.73 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1407.19;QD=19.02;SB=-661.67 GT:AD:DP:GL:GQ 0/1:32,42:74:-166.29,-22.29,-115.61:99 +chr1 4528559 rs241276 C T 153.75 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=4.22;MQ=59.30;MQ0=0;OQ=909.72;QD=13.78;SB=-324.82 GT:AD:DP:GL:GQ 0/1:37,29:65:-113.86,-19.61,-110.36:99 +chr1 4529046 rs241277 A C 117.60 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=2.18;MQ=60.00;MQ0=0;OQ=2433.72;QD=33.34;SB=-1159.13 GT:AD:DP:GL:GQ 1/1:0,73:69:-246.98,-20.78,-0.02:99 +chr1 4529268 rs241278 T C 273.02 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.43;MQ=59.61;MQ0=0;OQ=2074.79;QD=35.17;SB=-848.12 GT:AD:DP:GL:GQ 1/1:0,59:58:-211.08,-17.47,-0.02:99 +chr1 4530244 rs7531281 A C 607.97 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2071.97;QD=33.42;SB=-943.11 GT:AD:DP:GL:GQ 1/1:0,62:60:-210.80,-18.07,-0.02:99 +chr1 4530343 rs7526879 C T 127.03 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.29;MQ0=0;OQ=2841.32;QD=39.46;SB=-1410.68 GT:AD:DP:GL:GQ 1/1:0,72:71:-287.74,-21.39,-0.02:99 +chr1 4531126 rs241212 G T 328.23 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=59.37;MQ0=0;OQ=847.33;QD=14.36;SB=-341.38 GT:AD:DP:GL:GQ 0/1:30,29:58:-105.49,-17.47,-104.18:99 +chr1 4531264 rs55850443 C A 105.26 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=3.29;MQ=59.66;MQ0=0;OQ=907.20;QD=13.54;SB=-364.99 GT:AD:DP:GL:GQ 0/1:34,33:65:-113.58,-19.58,-115.11:99 +chr1 4532420 rs980092 A G 568.56 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.63;MQ0=0;OQ=2136.98;QD=31.43;SB=-1016.73 GT:AD:DP:GL:GQ 1/1:0,68:67:-217.34,-20.21,-0.06:99 +chr1 4532678 rs34339970 T C 238.67 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=59.68;MQ0=0;OQ=686.96;QD=9.41;SB=-234.24 GT:AD:DP:GL:GQ 0/1:42,31:70:-93.08,-21.10,-159.73:99 +chr1 4532688 rs171317 C A 295.77 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=2546.98;QD=34.42;SB=-1274.23 GT:AD:DP:GL:GQ 1/1:0,74:71:-258.31,-21.38,-0.02:99 +chr1 4532830 rs35748829 C T 224.19 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.37;MQ0=0;OQ=1280.71;QD=19.40;SB=-516.15 GT:AD:DP:GL:GQ 0/1:29,37:64:-150.64,-19.29,-86.56:99 +chr1 4532839 rs35106071 C T 30.34 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=3;HaplotypeScore=0.47;MQ=59.31;MQ0=0;OQ=1092.68;QD=17.91;SB=-426.77 GT:AD:DP:GL:GQ 0/1:29,32:61:-130.92,-18.37,-105.58:99 +chr1 4533414 rs6673089 G A 59.57 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=5.78;MQ=59.66;MQ0=0;OQ=1175.25;QD=17.54;SB=-391.70 GT:AD:DP:GL:GQ 0/1:31,35:66:-140.69,-19.88,-114.80:99 +chr1 4533499 rs6426421 C T 279.59 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=56.21;MQ0=0;OQ=3052.51;QD=38.64;SB=-1294.73 GT:AD:DP:GL:GQ 1/1:0,79:78:-308.86,-23.50,-0.03:99 +chr1 4533545 rs7527742 G A 582.48 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.29;MQ0=0;OQ=1245.18;QD=15.19;SB=-388.08 GT:AD:DP:GL:GQ 0/1:45,37:81:-152.20,-24.40,-157.64:99 +chr1 4533745 rs241208 T C 151.85 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.23;MQ0=0;OQ=641.89;QD=11.07;SB=-289.57 GT:AD:DP:GL:GQ 0/1:35,23:57:-84.64,-17.17,-139.99:99 +chr1 4533782 rs17344823 A T 343.49 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=50.31;MQ0=0;OQ=1106.34;QD=17.56;SB=-567.72 GT:AD:DP:GL:GQ 0/1:26,37:60:-131.99,-18.07,-92.40:99 +chr1 4533944 rs241207 T G 366.15 PASS AC=2;AF=1.00;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.27;MQ0=0;OQ=1080.62;QD=29.21;SB=-322.00 GT:AD:DP:GL:GQ 1/1:0,37:32:-111.66,-9.64,-0.02:96.25 +chr1 4534250 rs11584033 T C 380.79 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=58.88;MQ0=0;OQ=947.57;QD=16.34;SB=-494.15 GT:AD:DP:GL:GQ 0/1:26,32:58:-115.51,-17.47,-106.56:99 +chr1 4534838 rs1541318 A G 459.08 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1096.76;QD=16.87;SB=-540.58 GT:AD:DP:GL:GQ 0/1:28,37:65:-132.54,-19.58,-112.37:99 +chr1 4535109 rs2411777 C T 151.18 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.69;MQ0=0;OQ=1491.80;QD=20.16;SB=-710.25 GT:AD:DP:GL:GQ 0/1:30,44:73:-174.45,-21.99,-106.04:99 +chr1 4536054 rs10799246 T A 279.36 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=56.28;MQ0=1;OQ=1123.37;QD=19.37;SB=-579.73 GT:AD:DP:GL:GQ 0/1:23,35:56:-132.49,-16.87,-78.58:99 +chr1 4536627 rs1157688 T C 729.05 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2286.18;QD=34.64;SB=-1059.42 GT:AD:DP:GL:GQ 1/1:1,65:64:-232.22,-19.28,-0.02:99 +chr1 4537253 rs12746043 A G 196.32 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.75;MQ=59.75;MQ0=0;OQ=742.34;QD=10.03;SB=-306.91 GT:AD:DP:GL:GQ 0/1:43,31:74:-99.82,-22.30,-175.74:99 +chr1 4537334 rs12073968 A T 357.38 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=1269.08;QD=15.67;SB=-567.67 GT:AD:DP:GL:GQ 0/1:40,41:80:-154.29,-24.09,-150.38:99 +chr1 4537921 rs12724503 G A 310.14 PASS AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.26;MQ=60.00;MQ0=0;OQ=1523.81;QD=15.09;SB=-617.07 GT:AD:DP:GL:GQ 0/1:55,46:100:-185.79,-30.12,-188.53:99 +chr1 4538097 rs4654561 G A 508.13 PASS AC=2;AF=1.00;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=3756.30;QD=39.96;SB=-1777.79 GT:AD:DP:GL:GQ 1/1:0,92:93:-374.63,-34.91,-7.66:99 +chr1 4538181 rs4654562 G A 215.56 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=59.13;MQ0=0;OQ=1260.80;QD=15.19;SB=-602.60 GT:AD:DP:GL:GQ 0/1:45,38:82:-154.08,-24.71,-143.05:99 +chr1 4538603 rs4654563 G A 371.27 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1202.15;QD=16.03;SB=-528.76 GT:AD:DP:GL:GQ 0/1:39,36:74:-145.80,-22.30,-125.85:99 +chr1 4538973 rs7543382 T C 333.40 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=59.17;MQ0=0;OQ=1070.40;QD=14.66;SB=-356.54 GT:AD:DP:GL:GQ 0/1:37,36:73:-132.31,-21.99,-147.75:99 +chr1 4539030 rs7540656 A G 325.75 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.39;MQ0=0;OQ=796.84;QD=11.72;SB=-299.04 GT:AD:DP:GL:GQ 0/1:36,32:68:-103.46,-20.49,-144.09:99 +chr1 4540675 rs1963269 C G 227.56 PASS AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.54;MQ0=0;OQ=1695.02;QD=16.62;SB=-763.36 GT:AD:DP:GL:GQ 0/1:55,47:97:-202.01,-29.22,-223.35:99 +chr1 4540762 rs1024139 T C 542 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.15;MQ0=0;OQ=842.09;QD=11.70;SB=-437.91 GT:AD:DP:GL:GQ 0/1:42,30:72:-109.18,-21.69,-170.21:99 +chr1 4541602 rs241225 G A 260.13 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.63;MQ0=0;OQ=2333.57;QD=37.04;SB=-1016.38 GT:AD:DP:GL:GQ 1/1:0,63:59:-236.96,-17.77,-0.01:99 +chr1 4541659 rs241224 G T 284.32 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.28;MQ0=0;OQ=2085.58;QD=35.96;SB=-859.24 GT:AD:DP:GL:GQ 1/1:0,58:57:-212.16,-17.17,-0.02:99 +chr1 4541986 rs61765446 G A 358.57 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=942.30;QD=14.28;SB=-483.10 GT:AD:DP:GL:GQ 0/1:37,29:65:-117.11,-19.59,-114.27:99 +chr1 4542017 rs241223 C T 513.72 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=2827.32;QD=39.82;SB=-1402.70 GT:AD:DP:GL:GQ 1/1:0,71:71:-286.34,-21.39,-0.02:99 +chr1 4542337 rs184781 C T 269.78 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=2680.27;QD=40.00;SB=-1072.41 GT:AD:DP:GL:GQ 1/1:0,67:66:-271.63,-19.88,-0.01:99 +chr1 4542995 . A T 0.76 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=53.06;MQ0=0;OQ=196.97;QD=3.28;SB=-90.71 GT:AD:DP:GL:GQ 0/1:48,11:53:-38.95,-15.97,-156.27:99 +chr1 4543292 rs2078573 A C 86.48 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=6.05;MQ=56.75;MQ0=0;OQ=1341.41;QD=16.77;SB=-537.82 GT:AD:DP:GL:GQ 0/1:31,48:77:-160.62,-23.19,-115.03:99 +chr1 4543548 rs515279 T C 17.62 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.93;MQ=59.29;MQ0=0;OQ=1923.64;QD=29.59;SB=-45.69 GT:AD:DP:GL:GQ 1/1:0,65:64:-196.03,-19.32,-0.08:99 +chr1 4543717 rs587108 T G 137.04 PASS AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.89;MQ0=0;OQ=716.08;QD=34.10;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,21:21:-75.20,-6.33,-0.01:63.19 +chr1 4543945 rs588347 C T 45.56 PASS AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=256.94;QD=10.71;SB=-10.00 GT:AD:DP:GL:GQ 0/1:15,9:24:-36.21,-7.23,-52.03:99 +chr1 4544067 rs588861 G A 43.71 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=54.12;MQ0=0;OQ=1783.57;QD=37.95;SB=-560.73 GT:AD:DP:GL:GQ 1/1:0,47:45:-181.96,-13.56,-0.01:99 +chr1 4544173 rs488684 T A 310.68 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.99;MQ0=0;OQ=2644.21;QD=36.73;SB=-1277.61 GT:AD:DP:GL:GQ 1/1:0,72:70:-268.02,-21.08,-0.01:99 +chr1 4545564 rs616180 T G 115.98 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.33;MQ=58.74;MQ0=0;OQ=2469.47;QD=35.28;SB=-1055.12 GT:AD:DP:GL:GQ 1/1:0,70:69:-250.55,-20.78,-0.02:99 +chr1 4545738 rs617046 T C 49.62 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=60.00;MQ0=0;OQ=1303.79;QD=31.80;SB=-288.55 GT:AD:DP:GL:GQ 1/1:0,41:40:-133.99,-12.05,-0.02:99 +chr1 4545788 rs57374319 C T 229.72 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=594.52;QD=13.51;SB=-275.28 GT:AD:DP:GL:GQ 0/1:24,20:43:-75.69,-12.95,-87.49:99 +chr1 4545807 rs563158 G C 408.48 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2250.93;QD=42.47;SB=-845.32 GT:AD:DP:GL:GQ 1/1:0,53:52:-228.70,-15.67,-0.02:99 +chr1 4545915 rs617610 A G 103.88 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=58.73;MQ0=0;OQ=1514.17;QD=27.53;SB=-766.72 GT:AD:DP:GL:GQ 1/1:0,55:49:-155.05,-14.78,-0.05:99 +chr1 4545933 rs561468 C A 155.56 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.22;MQ0=0;OQ=1902.16;QD=32.24;SB=-898.65 GT:AD:DP:GL:GQ 1/1:0,59:54:-193.82,-16.27,-0.02:99 +chr1 4546125 rs538655 G A 601.67 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.21;MQ0=0;OQ=2022.14;QD=38.15;SB=-935.74 GT:AD:DP:GL:GQ 1/1:0,53:52:-205.82,-15.67,-0.02:99 +chr1 4546239 rs619364 G A 445.90 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=837.24;QD=13.95;SB=-392.12 GT:AD:DP:GL:GQ 0/1:34,26:60:-105.08,-18.07,-121.77:99 +chr1 4546345 rs536749 A G 482 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=1853.11;QD=30.38;SB=-858.57 GT:AD:DP:GL:GQ 1/1:0,61:58:-188.95,-17.49,-0.05:99 +chr1 4546432 rs4654446 C T 238.01 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=59.28;MQ0=0;OQ=947.38;QD=16.33;SB=-474.49 GT:AD:DP:GL:GQ 0/1:28,30:56:-114.89,-16.87,-97.02:99 +chr1 4546657 rs562787 A G 229.14 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=1701.20;QD=30.38;SB=-810.66 GT:AD:DP:GL:GQ 1/1:0,56:54:-173.76,-16.29,-0.05:99 +chr1 4546823 rs532259 C T 169.24 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.40;MQ0=0;OQ=2521.38;QD=40.67;SB=-1140.51 GT:AD:DP:GL:GQ 1/1:0,62:62:-255.74,-18.67,-0.01:99 +chr1 4547018 rs559200 G C 1813.47 Indel AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.18;MQ0=0;QD=40.30;SB=-734.75 GT:AD:DP:GL:GQ 1/1:0,44:43:-184.95,-12.96,-0.01:99 +chr1 4547035 rs6691728 C T 1783.47 Indel AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=57.64;MQ0=0;QD=39.63;SB=-856.02 GT:AD:DP:GL:GQ 1/1:0,45:45:-181.94,-13.55,-0.01:99 +chr1 4547069 rs558411 G C 0.77 PASS AC=2;AF=1.00;AN=2;DB;DP=39;Dels=0.00;HRun=4;HaplotypeScore=0.63;MQ=58.20;MQ0=0;OQ=1617.71;QD=41.48;SB=-687.82 GT:AD:DP:GL:GQ 1/1:0,39:38:-165.37,-11.45,-0.01:99 +chr1 4547307 rs634075 C T 118.64 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=59.44;MQ0=0;OQ=1786.25;QD=34.35;SB=-705.43 GT:AD:DP:GL:GQ 1/1:0,51:47:-182.23,-14.17,-0.02:99 +chr1 4547329 rs644647 C A 608.94 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.55;MQ0=0;OQ=1779.42;QD=34.89;SB=-902.65 GT:AD:DP:GL:GQ 1/1:0,51:50:-181.54,-15.06,-0.02:99 +chr1 4547506 rs2674014 C T 604.69 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=3048.33;QD=39.08;SB=-1465.48 GT:AD:DP:GL:GQ 1/1:0,78:77:-308.44,-23.20,-0.02:99 +chr1 4548034 rs669252 A G 36.37 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=59.78;MQ0=0;OQ=2568.64;QD=30.58;SB=-1254.84 GT:AD:DP:GL:GQ 1/1:0,84:80:-260.52,-24.13,-0.08:99 +chr1 4548229 rs527146 C T 195.56 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.54;MQ0=0;OQ=2361.57;QD=37.49;SB=-975.04 GT:AD:DP:GL:GQ 1/1:2,61:63:-246.39,-18.98,-6.65:99 +chr1 4548230 rs553803 A G 202.91 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.54;MQ0=0;OQ=2093.62;QD=33.23;SB=-906.61 GT:AD:DP:GL:GQ 1/1:2,61:63:-221.00,-18.97,-8.05:99 +chr1 4548433 rs504274 C T 6.37 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=4;HaplotypeScore=2.30;MQ=59.56;MQ0=0;OQ=3385.81;QD=39.83;SB=-1431.01 GT:AD:DP:GL:GQ 1/1:0,85:84:-337.58,-25.30,-0.02:99 +chr1 4548537 rs916404 A G 176.85 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.01;MQ=59.60;MQ0=0;OQ=1563.60;QD=27.43;SB=-730.94 GT:AD:DP:GL:GQ 1/1:0,57:51:-160.00,-15.38,-0.05:99 +chr1 4548552 rs1811133 G A 623.08 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=2054.70;QD=38.77;SB=-776.53 GT:AD:DP:GL:GQ 1/1:0,53:52:-209.07,-15.66,-0.01:99 +chr1 4548640 rs10915566 C T 338.58 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=59.67;MQ0=0;OQ=1058.12;QD=15.12;SB=-552.39 GT:AD:DP:GL:GQ 0/1:37,33:67:-129.29,-20.20,-113.66:99 +chr1 4548685 rs2176113 C T 467.66 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1206.49;QD=16.76;SB=-424.43 GT:AD:DP:GL:GQ 0/1:37,35:72:-145.62,-21.68,-138.53:99 +chr1 4548689 rs549918 C T 547.08 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2745.70;QD=39.22;SB=-872.18 GT:AD:DP:GL:GQ 1/1:0,70:69:-278.17,-20.79,-0.02:99 +chr1 4548722 rs549150 C T 597.32 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=3119.07;QD=40.51;SB=-1266.19 GT:AD:DP:GL:GQ 1/1:0,77:77:-315.51,-23.19,-0.01:99 +chr1 4548785 rs548958 A C 587.96 PASS AC=2;AF=1.00;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.52;MQ0=0;OQ=3225.28;QD=33.25;SB=-1553.11 GT:AD:DP:GL:GQ 1/1:0,97:93:-326.16,-28.01,-0.03:99 +chr1 4548901 rs683704 G A 493.67 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2363.22;QD=39.39;SB=-1015.37 GT:AD:DP:GL:GQ 1/1:0,60:60:-239.92,-18.08,-0.02:99 +chr1 4549335 rs572875 G A 610.19 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.57;MQ0=0;OQ=2583.49;QD=39.75;SB=-1223.62 GT:AD:DP:GL:GQ 1/1:0,65:64:-261.95,-19.28,-0.01:99 +chr1 4549598 rs520532 C T 634.82 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=1;OQ=2560.49;QD=37.65;SB=-1198.62 GT:AD:DP:GL:GQ 1/1:0,68:66:-259.66,-19.89,-0.02:99 +chr1 4550061 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=20;HaplotypeScore=23.52;MQ=43.78;MQ0=0;OQ=658.49;QD=6.86;SB=83.26 GT:AD:DP:GL:GQ 0/1:53,43:71:-90.53,-21.40,-163.68:99 +chr1 4550163 rs189538 T C 1.23 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=2;HaplotypeScore=4.99;MQ=53.64;MQ0=0;OQ=1059.98;QD=26.50;SB=-540.85 GT:AD:DP:GL:GQ 1/1:0,40:35:-109.62,-10.56,-0.04:99 +chr1 4550501 rs10915567 A T 204.42 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=58.86;MQ0=0;OQ=971.67;QD=17.35;SB=-337.66 GT:AD:DP:GL:GQ 0/1:25,31:54:-116.71,-16.26,-86.04:99 +chr1 4550640 rs241213 G A 356.42 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2857.67;QD=40.25;SB=-1367.83 GT:AD:DP:GL:GQ 1/1:0,71:71:-289.37,-21.39,-0.02:99 +chr1 4550851 rs164775 A G 34.10 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=5.34;MQ=59.24;MQ0=0;OQ=775.11;QD=14.09;SB=-373.36 GT:AD:DP:GL:GQ 0/1:28,27:55:-97.36,-16.57,-110.68:99 +chr1 4551064 rs12079284 G A 324.95 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=59.55;MQ0=0;OQ=1490.67;QD=17.96;SB=-575.98 GT:AD:DP:GL:GQ 0/1:39,44:83:-177.35,-25.00,-139.24:99 +chr1 4551090 rs164774 A C 75.23 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=59.47;MQ0=0;OQ=2365.79;QD=33.80;SB=-1092.51 GT:AD:DP:GL:GQ 1/1:0,70:67:-240.18,-20.18,-0.02:99 +chr1 4551865 rs10489134 G C 328.76 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=59.44;MQ0=0;OQ=1198.12;QD=16.19;SB=-348.77 GT:AD:DP:GL:GQ 0/1:36,38:72:-144.81,-21.71,-156.52:99 +chr1 4552887 rs7554766 G A 776.54 Indel AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.13;MQ0=0;QD=12.13;SB=-327.33 GT:AD:DP:GL:GQ 0/1:39,25:57:-98.11,-17.17,-116.23:99 +chr1 4552953 rs7518655 C T 177.07 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=2.86;MQ=58.99;MQ0=0;OQ=677.30;QD=14.72;SB=-320.35 GT:AD:DP:GL:GQ 0/1:23,23:43:-83.97,-12.96,-72.15:99 +chr1 4553124 rs7518781 C A 341.53 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.10;MQ=59.31;MQ0=0;OQ=849.36;QD=13.92;SB=-331.16 GT:AD:DP:GL:GQ 0/1:30,31:56:-105.09,-16.87,-90.31:99 +chr1 4553830 rs164770 A G 0.31 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=3;HaplotypeScore=7.02;MQ=59.30;MQ0=0;OQ=1972.78;QD=32.88;SB=-746.94 GT:AD:DP:GL:GQ 1/1:2,57:55:-200.88,-16.57,-0.02:99 +chr1 4554084 rs61767667 T A 362.66 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=502.84;QD=10.48;SB=-173.16 GT:AD:DP:GL:GQ 0/1:30,18:48:-68.02,-14.46,-113.49:99 +chr1 4554189 rs61767668 G A 492.83 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=958.92;QD=14.31;SB=-387.15 GT:AD:DP:GL:GQ 0/1:38,29:66:-119.06,-19.89,-123.05:99 +chr1 4555833 rs540572 C A 391.14 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=602.48;QD=12.30;SB=-99.63 GT:AD:DP:GL:GQ 0/1:24,25:46:-77.39,-13.85,-83.99:99 +chr1 4556007 rs6426423 C A 388.51 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=59.29;MQ0=0;OQ=809.24;QD=15.27;SB=-378.16 GT:AD:DP:GL:GQ 0/1:24,29:51:-99.57,-15.36,-78.05:99 +chr1 4556396 rs531363 C T 270.22 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=785.64;QD=14.03;SB=-358.40 GT:AD:DP:GL:GQ 0/1:30,26:54:-98.13,-16.29,-91.52:99 +chr1 4556558 rs129794 G A 506.73 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=510.17;QD=11.09;SB=-262.22 GT:AD:DP:GL:GQ 0/1:29,17:46:-68.16,-13.86,-103.52:99 +chr1 4556721 rs10799248 G A 151.65 PASS AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=483.34;QD=15.10;SB=-178.66 GT:AD:DP:GL:GQ 0/1:17,15:30:-60.66,-9.04,-48.95:99 +chr1 4556909 rs526695 T C 306.82 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=58.98;MQ0=0;OQ=2857.53;QD=34.85;SB=-1208.70 GT:AD:DP:GL:GQ 1/1:0,82:80:-289.36,-24.10,-0.02:99 +chr1 4556982 rs516947 G A 448.32 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=2681.00;QD=38.86;SB=-634.83 GT:AD:DP:GL:GQ 1/1:0,69:67:-271.71,-20.19,-0.02:99 +chr1 4556992 rs516977 A G 448.48 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.27;MQ0=0;OQ=1828.72;QD=29.03;SB=-545.85 GT:AD:DP:GL:GQ 1/1:0,63:60:-186.53,-18.11,-0.07:99 +chr1 4557030 rs517092 A C 349.51 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=1428.85;QD=26.46;SB=-498.86 GT:AD:DP:GL:GQ 1/1:0,54:46:-146.51,-13.87,-0.04:99 +chr1 4557056 rs524982 C T 158.92 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.64;MQ0=0;OQ=2000.95;QD=38.48;SB=-916.28 GT:AD:DP:GL:GQ 1/1:0,52:51:-203.70,-15.37,-0.02:99 +chr1 4557155 rs651695 A T 85.58 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=3;HaplotypeScore=2.39;MQ=59.42;MQ0=0;OQ=1262.50;QD=15.98;SB=-615.05 GT:AD:DP:GL:GQ 0/1:40,39:78:-153.02,-23.49,-149.00:99 +chr1 4557694 rs653988 C T 110.63 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.82;MQ0=0;OQ=2793.65;QD=39.91;SB=-1109.49 GT:AD:DP:GL:GQ 1/1:0,70:70:-282.97,-21.09,-0.02:99 +chr1 4558171 rs549239 T C 727.04 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.17;MQ0=0;OQ=2944.97;QD=35.06;SB=-1221.82 GT:AD:DP:GL:GQ 1/1:0,84:83:-298.11,-25.00,-0.03:99 +chr1 4558199 rs12726702 T A 2233 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=6;HaplotypeScore=61.64;MQ=53.38;MQ0=0;QD=26.58;SB=-718.98 GT:AD:DP:GL:GQ 0/1:14,70:81:-250.99,-24.40,-50.82:99 +chr1 4558206 rs549087 T A 2870.37 Indel;SnpCluster AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.01;HRun=6;HaplotypeScore=46.58;MQ=52.93;MQ0=0;QD=35.88;SB=-1138.04 GT:AD:DP:GL:GQ 1/1:0,79:79:-290.65,-23.50,-0.03:99 +chr1 4558209 rs28687799 A T 819.27 Indel;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=4;HaplotypeScore=29.81;MQ=52.84;MQ0=0;QD=10.37;SB=-175.59 GT:AD:DP:GL:GQ 0/1:49,30:77:-108.41,-23.20,-171.08:99 +chr1 4558214 rs59930628 A T 84.16 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.03;HRun=4;HaplotypeScore=38.67;MQ=53.63;MQ0=0;QD=1.09;SB=56.66 GT:AD:DP:GL:GQ 0/1:66,9:73:-33.09,-21.39,-235.05:99 +chr1 4558250 rs666799 A C 496.03 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.14;MQ0=0;OQ=2047.56;QD=34.70;SB=-847.08 GT:AD:DP:GL:GQ 1/1:0,59:58:-208.36,-17.47,-0.02:99 +chr1 4558398 rs12567277 C T 337.11 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.53;MQ0=0;OQ=912.06;QD=18.61;SB=-436.84 GT:AD:DP:GL:GQ 0/1:22,27:48:-108.95,-14.46,-68.62:99 +chr1 4558676 rs553691 C T 200.13 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.21;MQ0=0;OQ=1974.68;QD=37.26;SB=-1009.66 GT:AD:DP:GL:GQ 1/1:0,53:52:-201.08,-15.67,-0.02:99 +chr1 4560412 rs589176 A G 118.19 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=1;HaplotypeScore=2.29;MQ=58.87;MQ0=0;OQ=545.72;QD=13.31;SB=-145.53 GT:AD:DP:GL:GQ 0/1:20,21:40:-69.91,-12.06,-74.33:99 +chr1 4561004 rs602244 T C 195.92 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=2.83;MQ=59.64;MQ0=0;OQ=1077.64;QD=16.84;SB=-452.16 GT:AD:DP:GL:GQ 0/1:26,38:63:-130.03,-18.98,-104.11:99 +chr1 4561499 rs604465 G A 250.02 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=59.13;MQ0=0;OQ=735.55;QD=15.32;SB=-280.30 GT:AD:DP:GL:GQ 0/1:25,23:45:-90.40,-13.56,-80.37:99 +chr1 4561737 rs563481 C T 22.90 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=3;HaplotypeScore=0.93;MQ=60.00;MQ0=0;OQ=747.56;QD=17.80;SB=-287.30 GT:AD:DP:GL:GQ 0/1:20,22:42:-90.69,-12.65,-73.13:99 +chr1 4562268 rs537761 C A 317.78 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=820.87;QD=16.75;SB=-394.13 GT:AD:DP:GL:GQ 0/1:21,28:48:-99.83,-14.46,-74.67:99 +chr1 4562392 rs618751 G A 349.01 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=60.00;MQ0=0;OQ=1032.44;QD=14.14;SB=-366.34 GT:AD:DP:GL:GQ 0/1:41,32:73:-128.52,-21.99,-148.49:99 +chr1 4562641 rs534159 C T 355.83 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=808.69;QD=13.71;SB=-376.39 GT:AD:DP:GL:GQ 0/1:33,26:58:-101.65,-17.50,-100.37:99 +chr1 4565129 rs241243 A G 370.62 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=694.01;QD=8.07;SB=-138.39 GT:AD:DP:GL:GQ 0/1:53,33:82:-97.39,-24.71,-212.58:99 +chr1 4565904 rs10915569 C A 242.27 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.39;MQ0=0;OQ=1490.43;QD=19.61;SB=-754.94 GT:AD:DP:GL:GQ 0/1:27,49:74:-174.61,-22.29,-94.95:99 +chr1 4566354 rs164780 C G 240.11 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=59.64;MQ0=0;OQ=2456.30;QD=38.38;SB=-1204.26 GT:AD:DP:GL:GQ 1/1:0,64:63:-249.27,-19.01,-0.05:99 +chr1 4566679 rs151716 A G 365.52 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=59.43;MQ0=0;OQ=771.72;QD=11.87;SB=-373.98 GT:AD:DP:GL:GQ 0/1:33,32:64:-99.75,-19.29,-131.65:99 +chr1 4567238 rs4654450 G A 244.97 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=59.42;MQ0=0;OQ=1219.09;QD=16.93;SB=-598.62 GT:AD:DP:GL:GQ 0/1:35,37:71:-146.59,-21.39,-121.89:99 +chr1 4567954 rs151715 A G 136 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.44;MQ0=0;OQ=821.52;QD=10.95;SB=-417.84 GT:AD:DP:GL:GQ 0/1:41,34:74:-107.74,-22.30,-168.10:99 +chr1 4568017 rs241242 G T 115.78 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.56;MQ=60.00;MQ0=0;OQ=1682.11;QD=33.64;SB=-638.02 GT:AD:DP:GL:GQ 1/1:0,49:48:-171.82,-14.46,-0.02:99 +chr1 4568283 rs11590266 A G 358.35 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=59.56;MQ0=0;OQ=565.36;QD=10.87;SB=-241.59 GT:AD:DP:GL:GQ 0/1:27,24:51:-77.60,-17.78,-112.88:99 +chr1 4571271 rs164779 C G 314.41 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.44;MQ0=0;OQ=1283.51;QD=17.11;SB=-664.28 GT:AD:DP:GL:GQ 0/1:38,37:72:-153.33,-21.69,-161.13:99 +chr1 4571572 . C T 90.66 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.56;MQ0=0;OQ=626.01;QD=12.04;SB=-331.33 GT:AD:DP:GL:GQ 0/1:32,20:47:-80.06,-14.17,-86.19:99 +chr1 4572354 rs164778 T C 225.65 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1559.84;QD=35.45;SB=-660.32 GT:AD:DP:GL:GQ 1/1:0,44:44:-159.58,-13.25,-0.01:99 +chr1 4572615 rs6703429 T C 577.31 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=862.43;QD=13.07;SB=-402.26 GT:AD:DP:GL:GQ 0/1:35,31:65:-109.11,-19.58,-142.67:99 +chr1 4574299 . C A 554.66 Indel AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.59;MQ0=0;QD=10.47;SB=-260.28 GT:AD:DP:GL:GQ 0/1:31,22:48:-73.21,-14.46,-96.27:99 +chr1 4576029 rs164776 C T 259.84 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.56;MQ0=0;OQ=893.05;QD=17.17;SB=-421.82 GT:AD:DP:GL:GQ 0/1:24,28:50:-107.66,-15.07,-72.44:99 +chr1 4576797 rs2411886 G C 186.46 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=59.03;MQ0=0;OQ=1978.62;QD=41.22;SB=-1006.27 GT:AD:DP:GL:GQ 1/1:0,47:46:-201.46,-13.86,-0.01:99 +chr1 4576947 rs2411887 C T 275.87 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=58.35;MQ0=0;OQ=1931.75;QD=37.88;SB=-945.28 GT:AD:DP:GL:GQ 1/1:0,51:50:-196.78,-15.07,-0.02:99 +chr1 4577395 rs4403602 C G 245.41 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=59.46;MQ0=0;OQ=1536.03;QD=35.72;SB=-775.22 GT:AD:DP:GL:GQ 1/1:0,43:41:-157.23,-12.38,-0.05:99 +chr1 4577589 rs7554628 T C 1.90 PASS AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=1;HaplotypeScore=1.47;MQ=57.95;MQ0=0;OQ=730.12;QD=22.82;SB=-185.76 GT:AD:DP:GL:GQ 1/1:0,31:25:-79.87,-10.17,-3.27:69.05 +chr1 4577983 rs7555011 T C 161.26 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.31;MQ=59.09;MQ0=0;OQ=1457.56;QD=28.58;SB=-435.18 GT:AD:DP:GL:GQ 1/1:0,51:47:-149.39,-14.18,-0.05:99 +chr1 4578231 rs35259920 T A 832.15 Indel AC=2;AF=1.00;AN=2;DB;DP=29;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.20;MQ0=0;QD=28.69;SB=-10.00 GT:AD:DP:GL:GQ 1/1:1,28:26:-86.82,-7.84,-0.02:78.19 +chr1 4578361 rs7554792 A C 303.82 PASS AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.92;MQ0=0;OQ=236.46;QD=26.27;SB=-138.00 GT:AD:DP:GL:GQ 1/1:0,9:8:-27.23,-2.41,-0.00:24.06 +chr1 4578400 . A T 84.19 Indel AC=1;AF=0.50;AN=2;DP=14;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=46.65;MQ0=0;QD=6.01;SB=-42.96 GT:AD:DP:GL:GQ 0/1:10,4:13:-15.62,-3.92,-34.97:99 +chr1 4579811 rs1905304 C A 19.42 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=58.10;MQ0=0;OQ=2321.72;QD=36.28;SB=-1110.43 GT:AD:DP:GL:GQ 1/1:0,64:63:-235.77,-18.97,-0.01:99 +chr1 4580559 rs56945522 G A 92.56 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=61.48;MQ0=0;OQ=2293.20;QD=38.87;SB=-907.71 GT:AD:DP:GL:GQ 1/1:0,59:58:-232.92,-17.48,-0.02:99 +chr1 4581964 rs6668002 T C 241.68 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=2274.26;QD=30.73;SB=-1092.12 GT:AD:DP:GL:GQ 1/1:0,73:71:-231.07,-21.41,-0.06:99 +chr1 4583570 rs1573748 A G 1957.91 Indel AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.66;MQ=60.10;MQ0=0;QD=31.08;SB=-816.28 GT:AD:DP:GL:GQ 1/1:0,63:58:-199.41,-17.48,-0.04:99 +chr1 4584109 rs6657421 G A 130.49 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.13;MQ0=0;OQ=1834.09;QD=38.21;SB=-703.35 GT:AD:DP:GL:GQ 1/1:0,48:47:-187.01,-14.16,-0.01:99 +chr1 4584165 rs6674936 T C 66.31 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.13;MQ=59.25;MQ0=0;OQ=1819.57;QD=32.49;SB=-925.04 GT:AD:DP:GL:GQ 1/1:0,56:51:-185.56,-15.36,-0.01:99 +chr1 4585082 rs1107467 G A 137.40 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=60.00;MQ0=0;OQ=1423.05;QD=35.58;SB=-452.60 GT:AD:DP:GL:GQ 1/1:0,39:38:-145.91,-11.45,-0.02:99 +chr1 4585332 rs1483199 A G 386.56 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2234.69;QD=31.04;SB=-675.88 GT:AD:DP:GL:GQ 1/1:0,72:67:-227.10,-20.19,-0.04:99 +chr1 4585508 rs875808 G A 162.26 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.39;MQ=60.00;MQ0=0;OQ=2216.84;QD=38.89;SB=-1106.64 GT:AD:DP:GL:GQ 1/1:0,57:57:-225.29,-17.17,-0.02:99 +chr1 4585532 rs875807 A G 300.51 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.66;MQ0=0;OQ=1870.43;QD=34.01;SB=-960.39 GT:AD:DP:GL:GQ 1/1:0,55:53:-190.65,-15.97,-0.02:99 +chr1 4585731 rs875806 G C 165.71 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2133.21;QD=42.66;SB=-847.32 GT:AD:DP:GL:GQ 1/1:0,50:49:-216.92,-14.76,-0.01:99 +chr1 4586501 rs56028718 G A 84.95 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=3.12;MQ=59.59;MQ0=0;OQ=1260.05;QD=18.53;SB=-634.67 GT:AD:DP:GL:GQ 0/1:31,37:66:-149.17,-19.88,-106.57:99 +chr1 4587142 rs2269620 C T 114.33 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.59;MQ0=0;OQ=2196.52;QD=39.22;SB=-630.34 GT:AD:DP:GL:GQ 1/1:0,56:56:-223.26,-16.87,-0.02:99 +chr1 4587674 rs4654576 A C 214.87 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=886.13;QD=32.82;SB=-420.04 GT:AD:DP:GL:GQ 1/1:0,27:26:-92.21,-7.83,-0.01:78.22 +chr1 4587807 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=2;HaplotypeScore=15.00;MQ=58.93;MQ0=0;OQ=113.78;QD=1.87;SB=74.25 GT:AD:DP:GL:GQ 0/1:34,27:42:-27.32,-12.66,-112.79:99 +chr1 4587893 rs6662425 C G 115.34 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.27;MQ=59.36;MQ0=0;OQ=2651.42;QD=40.79;SB=-1007.19 GT:AD:DP:GL:GQ 1/1:0,65:61:-268.75,-18.38,-0.02:99 +chr1 4588021 rs6426430 G T 639.03 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1436.10;QD=35.90;SB=-672.10 GT:AD:DP:GL:GQ 1/1:0,40:40:-147.21,-12.05,-0.01:99 +chr1 4590753 rs7527078 C T 465.85 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.20;MQ0=0;OQ=2043.97;QD=40.08;SB=-576.76 GT:AD:DP:GL:GQ 1/1:0,51:50:-207.99,-15.06,-0.01:99 +chr1 4591042 rs4654577 A G 251.52 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.37;MQ0=0;OQ=1466.76;QD=34.11;SB=-679.59 GT:AD:DP:GL:GQ 1/1:0,43:43:-150.28,-12.96,-0.02:99 +chr1 4592515 . G C 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.74;MQ=48.08;MQ0=6;OQ=54.55;QD=1.03;SB=38.38 GT:AD:DP:GL:GQ 0/1:45,8:39:-20.50,-11.76,-139.98:87.39 +chr1 4592571 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=14.42;MQ=41.26;MQ0=11;OQ=65.05;QD=1.07;SB=-23.62 GT:AD:DP:GL:GQ 0/1:49,12:36:-20.65,-10.86,-123.87:97.89 +chr1 4592585 . G C 20.06 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.14;MQ=40.25;MQ0=10;QD=0.33;SB=-5.33 GT:AD:DP:GL:GQ 0/1:54,7:37:-16.45,-11.17,-134.84:52.86 +chr1 4592620 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=1;HaplotypeScore=15.36;MQ=35.46;MQ0=10;OQ=92.00;QD=1.46;SB=0.26 GT:AD:DP:GL:GQ 0/1:54,9:42:-25.15,-12.66,-150.31:99 +chr1 4592627 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=16.06;MQ=35.72;MQ0=7;OQ=153.87;QD=2.75;SB=-54.16 GT:AD:DP:GL:GQ 0/1:46,10:37:-29.82,-11.15,-128.78:99 +chr1 4592634 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=17.36;MQ=35.58;MQ0=7;OQ=255.85;QD=4.57;SB=-124.48 GT:AD:DP:GL:GQ 0/1:41,15:33:-38.82,-9.95,-100.95:99 +chr1 4592642 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=1;HaplotypeScore=28.60;MQ=35.10;MQ0=5;OQ=106.45;QD=2.01;SB=3.57 GT:AD:DP:GL:GQ 0/1:41,12:38:-25.38,-11.45,-106.45:99 +chr1 4592649 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=27.47;MQ=35.61;MQ0=5;OQ=241.86;QD=4.65;SB=-127.53 GT:AD:DP:GL:GQ 0/1:36,16:37:-38.62,-11.15,-91.45:99 +chr1 4592656 . C A 10.05 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=32.68;MQ=34.61;MQ0=6;QD=0.18;SB=-22.79 GT:AD:DP:GL:GQ 0/1:46,10:31:-13.58,-9.34,-92.74:42.43 +chr1 4592670 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=26.44;MQ=31.55;MQ0=8;OQ=92.67;QD=1.54;SB=-36.78 GT:AD:DP:GL:GQ 0/1:47,13:38:-24.00,-11.45,-105.70:99 +chr1 4592691 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=0;HaplotypeScore=17.99;MQ=28.93;MQ0=15;OQ=182.04;QD=2.64;SB=-62.36 GT:AD:DP:GL:GQ 0/1:58,11:38:-32.95,-11.46,-95.16:99 +chr1 4592711 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=1;HaplotypeScore=17.40;MQ=30.26;MQ0=13;OQ=418.56;QD=8.21;SB=-184.24 GT:AD:DP:GL:GQ 0/1:21,29:22:-51.78,-6.64,-35.47:99 +chr1 4592725 rs7533445 C G 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=21.58;MQ=31.66;MQ0=7;OQ=325.36;QD=9.30;SB=-162.82 GT:AD:DP:GL:GQ 0/1:18,17:13:-39.75,-3.93,-11.50:75.69 +chr1 4592733 . C A 17.31 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=31;Dels=0.00;HRun=0;HaplotypeScore=13.87;MQ=30.28;MQ0=8;QD=0.56;SB=5.02 GT:AD:DP:GL:GQ 0/1:27,3:12:-8.63,-3.62,-27.94:50.06 +chr1 4592740 rs7537972 A C 0.16 PASS AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=10.05;MQ=27.67;MQ0=11;OQ=104.80;QD=3.38;SB=-67.99 GT:AD:DP:GL:GQ 0/1:22,9:8:-16.18,-2.41,-9.32:69.09 +chr1 4592747 rs7537975 A C 18.33 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DB;DP=24;Dels=0.00;HRun=1;HaplotypeScore=8.21;MQ=28.35;MQ0=11;QD=0.76;SB=-7.00 GT:AD:DP:GL:GQ 0/1:17,7:4:-6.32,-1.21,-6.24:50.29 +chr1 4592767 rs7533530 C G 42.27 HARD_TO_VALIDATE;LowQual AC=2;AF=1.00;AN=2;DB;DP=14;Dels=0.00;HRun=1;HaplotypeScore=11.04;MQ=30.06;MQ0=7;QD=3.02;SB=-43.89 GT:AD:DP:GL:GQ 1/1:8,5:2:-7.64,-0.61,-0.00:6.02 +chr1 4592837 . C G 13.29 LowQual AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=1;HaplotypeScore=4.96;MQ=12.04;MQ0=3;QD=2.66;SB=-10.00 GT:AD:DP:GL:GQ 0/1:4,1:1:-4.59,-0.30,-0.00:1.76 +chr1 4592901 . T C 5.07 PASS AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=42.32;MQ0=2;OQ=126.93;QD=6.35;SB=-77.93 GT:AD:DP:GL:GQ 0/1:9,11:15:-20.50,-4.52,-36.40:99 +chr1 4592906 . T C 0.11 PASS AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=41.84;MQ0=3;OQ=578.85;QD=25.17;SB=-157.83 GT:AD:DP:GL:GQ 1/1:0,23:17:-61.47,-5.12,-0.00:51.15 +chr1 4592960 . G C 0.12 PASS AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=4.10;MQ=41.92;MQ0=6;OQ=217.66;QD=2.79;SB=-81.57 GT:AD:DP:GL:GQ 0/1:56,22:47:-39.23,-14.18,-153.65:99 +chr1 4592971 . T C 18.17 PASS AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=3.38;MQ=41.63;MQ0=7;OQ=666.60;QD=8.55;SB=-228.49 GT:AD:DP:GL:GQ 0/1:28,48:45:-83.52,-13.57,-69.37:99 +chr1 4592996 . A C 48.48 HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=4.82;MQ=40.87;MQ0=9;QD=0.70;SB=-26.49 GT:AD:DP:GL:GQ 0/1:54,15:47:-22.29,-14.16,-139.10:81.32 +chr1 4593024 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=14.22;MQ=41.13;MQ0=10;OQ=73.34;QD=1.41;SB=-39.79 GT:AD:DP:GL:GQ 0/1:35,17:30:-19.66,-9.04,-83.95:99 +chr1 4593037 . G C 11.64 DPFilter;HARD_TO_VALIDATE;LowQual AC=1;AF=0.50;AN=2;DP=41;Dels=0.02;HRun=0;HaplotypeScore=21.01;MQ=42.10;MQ0=8;QD=0.28;SB=26.12 GT:AD:DP:GL:GQ 0/1:33,7:20:-10.45,-6.03,-72.33:44.16 +chr1 4593066 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=0;HaplotypeScore=16.64;MQ=38.83;MQ0=9;OQ=95.97;QD=2.23;SB=-64.04 GT:AD:DP:GL:GQ 0/1:31,12:22:-19.51,-6.63,-53.44:99 +chr1 4593072 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=12.35;MQ=36.60;MQ0=11;OQ=58.68;QD=1.25;SB=-50.80 GT:AD:DP:GL:GQ 0/1:40,7:24:-16.40,-7.25,-78.79:91.52 +chr1 4593128 . G C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=7.00;MQ=42.60;MQ0=10;OQ=87.22;QD=1.86;SB=11.06 GT:AD:DP:GL:GQ 0/1:39,8:24:-19.25,-7.24,-80.14:99 +chr1 4593184 . G C 48.23 LowQual AC=1;AF=0.50;AN=2;DP=32;Dels=0.00;HRun=0;HaplotypeScore=5.25;MQ=50.03;MQ0=1;QD=1.51;SB=-24.84 GT:AD:DP:GL:GQ 0/1:27,5:22:-14.75,-6.64,-72.91:81.07 +chr1 4593205 . G C 35.18 LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.11;MQ=47.39;MQ0=4;QD=0.88;SB=-15.82 GT:AD:DP:GL:GQ 0/1:35,5:30:-15.86,-9.06,-106.35:68.02 +chr1 4593241 rs12752874 A C 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.83;MQ=43.47;MQ0=5;OQ=55.07;QD=1.28;SB=-27.98 GT:AD:DP:GL:GQ 0/1:30,13:26:-16.62,-7.83,-74.90:87.90 +chr1 4594330 rs34642555 G A 223.53 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.30;MQ=59.56;MQ0=0;OQ=741.34;QD=13.99;SB=-378.39 GT:AD:DP:GL:GQ 0/1:29,24:52:-93.10,-15.68,-88.17:99 +chr1 4599106 rs10753383 T G 347.62 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.01;MQ0=0;OQ=412.58;QD=12.50;SB=-151.92 GT:AD:DP:GL:GQ 0/1:17,16:32:-54.18,-9.64,-62.40:99 +chr1 4599463 rs7513957 G C 46.62 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=2;HaplotypeScore=1.18;MQ=57.56;MQ0=0;OQ=399.60;QD=12.11;SB=-196.33 GT:AD:DP:GL:GQ 0/1:20,13:31:-52.60,-9.35,-73.06:99 +chr1 4600658 rs12122002 G A 36.86 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=2.74;MQ=58.47;MQ0=0;OQ=1298.26;QD=21.28;SB=-656.75 GT:AD:DP:GL:GQ 0/1:24,37:59:-150.88,-17.77,-80.26:99 +chr1 4601609 rs55711858 A G 373.59 PASS AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=1068.23;QD=10.68;SB=-465.77 GT:AD:DP:GL:GQ 0/1:56,44:100:-140.25,-30.14,-225.51:99 +chr1 4601750 rs2411891 G A 156.02 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1085.67;QD=16.96;SB=-561.13 GT:AD:DP:GL:GQ 0/1:31,33:63:-130.83,-18.98,-106.71:99 +chr1 4602156 rs61764994 A G 74.11 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=60.00;MQ0=0;OQ=509.21;QD=7.60;SB=-244.13 GT:AD:DP:GL:GQ 0/1:40,27:63:-73.19,-18.99,-161.05:99 +chr1 4602810 rs61764995 C T 382.37 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=850.22;QD=17.35;SB=-339.44 GT:AD:DP:GL:GQ 0/1:22,27:48:-102.77,-14.46,-79.78:99 +chr1 4602966 rs34993795 C T 235.21 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.72;MQ=59.03;MQ0=0;OQ=1118.32;QD=16.69;SB=-465.43 GT:AD:DP:GL:GQ 0/1:34,33:66:-135.00,-19.88,-119.08:99 +chr1 4604462 rs2035452 C G 271.67 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=397.56;QD=15.29;SB=-96.30 GT:AD:DP:GL:GQ 0/1:14,12:25:-50.58,-7.54,-52.60:99 +chr1 4606381 rs10915576 T C 220.72 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=882.56;QD=16.97;SB=-410.32 GT:AD:DP:GL:GQ 0/1:21,31:51:-106.90,-15.36,-86.72:99 +chr1 4606615 rs12125737 C T 418.26 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.71;MQ0=0;OQ=1209.07;QD=18.60;SB=-598.14 GT:AD:DP:GL:GQ 0/1:29,36:62:-142.87,-18.68,-88.99:99 +chr1 4607135 rs12122921 G A 2.76 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=10.90;MQ=57.40;MQ0=0;OQ=881.42;QD=13.16;SB=-408.91 GT:AD:DP:GL:GQ 0/1:36,31:56:-108.31,-16.88,-93.30:99 +chr1 4607451 rs28759408 G T 57.59 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=5.28;MQ=57.88;MQ0=1;OQ=710.71;QD=10.45;SB=-279.36 GT:AD:DP:GL:GQ 0/1:39,29:61:-92.73,-18.38,-123.60:99 +chr1 4608914 rs7535194 C A 224.06 PASS AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=57.78;MQ0=0;OQ=1544.72;QD=16.26;SB=-662.45 GT:AD:DP:GL:GQ 0/1:44,51:95:-186.37,-28.61,-160.23:99 +chr1 4609123 . C T 10.31 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=56.96;MQ0=2;QD=0.17;SB=19.65 GT:AD:DP:GL:GQ 0/1:53,6:55:-20.84,-16.57,-182.90:42.72 +chr1 4609208 rs7539862 A C 150.58 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=258.18;QD=5.87;SB=-149.80 GT:AD:DP:GL:GQ 0/1:32,12:43:-42.05,-12.95,-117.22:99 +chr1 4609234 . G A 18.35 LowQual AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=3.99;MQ=56.87;MQ0=1;QD=0.46;SB=-22.94 GT:AD:DP:GL:GQ 0/1:35,5:36:-15.96,-10.84,-114.15:51.13 +chr1 4609248 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=1;HaplotypeScore=35.67;MQ=56.49;MQ0=1;OQ=135.28;QD=2.42;SB=50.20 GT:AD:DP:GL:GQ 0/1:46,10:51:-32.18,-15.36,-170.39:99 +chr1 4609249 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=97.70;MQ=56.55;MQ0=1;OQ=82.36;QD=1.44;SB=50.16 GT:AD:DP:GL:GQ 0/1:47,10:52:-27.18,-15.66,-163.18:99 +chr1 4609260 rs61764999 C T 6.41 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=5.81;MQ=56.56;MQ0=1;OQ=641.66;QD=10.03;SB=-130.56 GT:AD:DP:GL:GQ 0/1:42,22:63:-86.43,-18.98,-148.93:99 +chr1 4609527 rs4654581 C G 33.46 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=59.43;MQ0=0;QD=0.67;SB=28.36 GT:AD:DP:GL:GQ 0/1:45,5:49:-21.39,-14.76,-192.44:66.29 +chr1 4610341 rs10799250 T C 191.96 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.62;MQ0=0;OQ=886.46;QD=10.43;SB=-400.18 GT:AD:DP:GL:GQ 0/1:51,34:83:-116.93,-25.00,-199.77:99 +chr1 4610346 rs10915577 A G 286.28 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.62;MQ0=0;OQ=927.42;QD=11.04;SB=-372.61 GT:AD:DP:GL:GQ 0/1:50,34:82:-120.73,-24.70,-201.64:99 +chr1 4611161 rs12405862 C T 55.82 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.70;MQ=59.65;MQ0=0;OQ=705.61;QD=13.31;SB=-372.08 GT:AD:DP:GL:GQ 0/1:30,23:53:-89.81,-15.97,-107.55:99 +chr1 4612905 rs1466520 A G 508.10 PASS AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.49;MQ0=0;OQ=1092.36;QD=32.13;SB=-567.90 GT:AD:DP:GL:GQ 1/1:0,34:32:-112.83,-9.64,-0.01:96.28 +chr1 4613357 rs4144451 T C 2.82 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=4;HaplotypeScore=1.16;MQ=60.00;MQ0=0;OQ=378.96;QD=8.81;SB=-197.21 GT:AD:DP:GL:GQ 0/1:27,16:40:-53.24,-12.06,-95.58:99 +chr1 4616788 rs12127797 G C 214.89 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=4.57;MQ=59.39;MQ0=0;OQ=1251.84;QD=16.47;SB=-458.74 GT:AD:DP:GL:GQ 0/1:41,34:72:-150.17,-21.70,-159.82:99 +chr1 4619890 rs7544371 G A 283.12 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.45;MQ0=0;OQ=1234.26;QD=22.04;SB=-596.70 GT:AD:DP:GL:GQ 0/1:21,35:56:-143.59,-16.88,-63.94:99 +chr1 4621067 rs6426432 G C 375.69 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.65;MQ=60.00;MQ0=0;OQ=975.42;QD=15.73;SB=-398.88 GT:AD:DP:GL:GQ 0/1:35,27:62:-119.51,-18.68,-150.23:99 +chr1 4621285 rs6658403 C T 186.42 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.63;MQ0=0;OQ=651.01;QD=10.50;SB=-348.83 GT:AD:DP:GL:GQ 0/1:39,23:60:-86.46,-18.07,-139.05:99 +chr1 4622291 rs2035454 A G 361.79 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=59.15;MQ0=0;OQ=932.32;QD=13.13;SB=-403.21 GT:AD:DP:GL:GQ 0/1:39,32:70:-117.60,-21.09,-152.00:99 +chr1 4622303 rs1531830 T C 306.21 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=59.12;MQ0=0;OQ=753.21;QD=10.92;SB=-275.11 GT:AD:DP:GL:GQ 0/1:39,30:68:-99.09,-20.49,-155.18:99 +chr1 4623109 rs10799251 G A 463.40 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=863.86;QD=15.43;SB=-362.38 GT:AD:DP:GL:GQ 0/1:30,26:56:-106.54,-16.87,-110.57:99 +chr1 4623282 rs10799252 G C 114.19 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=53.79;MQ0=0;OQ=899.36;QD=20.92;SB=-445.94 GT:AD:DP:GL:GQ 0/1:17,26:42:-105.88,-12.66,-71.37:99 +chr1 4623298 rs10799253 T C 313.76 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=52.77;MQ0=0;OQ=616.14;QD=14.00;SB=-298.33 GT:AD:DP:GL:GQ 0/1:18,26:39:-76.66,-11.76,-55.81:99 +chr1 4623777 rs10915578 A G 84.84 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=0.82;MQ=58.86;MQ0=0;OQ=552.36;QD=9.69;SB=-296.32 GT:AD:DP:GL:GQ 0/1:35,22:57:-75.70,-17.18,-138.68:99 +chr1 4623873 rs10915579 T C 271.16 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=57.84;MQ0=0;OQ=661.07;QD=10.17;SB=-259.38 GT:AD:DP:GL:GQ 0/1:40,25:64:-88.68,-19.29,-154.96:99 +chr1 4624091 rs12135245 G C 41.47 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=1.89;MQ=59.70;MQ0=0;OQ=1186.96;QD=19.14;SB=-476.78 GT:AD:DP:GL:GQ 0/1:28,34:59:-139.77,-17.79,-108.63:99 +chr1 4624130 rs12140542 T C 140.19 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=2.13;MQ=59.74;MQ0=0;OQ=656.89;QD=9.12;SB=-348.92 GT:AD:DP:GL:GQ 0/1:43,29:71:-90.37,-21.40,-172.64:99 +chr1 4624492 rs2035455 C T 468.68 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=702.27;QD=12.54;SB=-335.31 GT:AD:DP:GL:GQ 0/1:34,22:55:-90.09,-16.58,-106.86:99 +chr1 4624817 rs17421247 C T 331.36 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.99;MQ=59.65;MQ0=0;OQ=1014.16;QD=15.37;SB=-402.77 GT:AD:DP:GL:GQ 0/1:35,31:64:-123.99,-19.29,-104.67:99 +chr1 4626224 rs10915580 G C 281.25 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.07;MQ0=0;OQ=1106.61;QD=18.14;SB=-348.42 GT:AD:DP:GL:GQ 0/1:31,30:61:-132.34,-18.40,-124.48:99 +chr1 4626314 rs12567266 T C 443.89 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.48;MQ0=0;OQ=855.53;QD=18.20;SB=-345.35 GT:AD:DP:GL:GQ 0/1:19,28:47:-102.99,-14.16,-75.71:99 +chr1 4626341 rs12752003 A G 152.30 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=47.43;MQ0=0;OQ=459.90;QD=12.10;SB=-75.78 GT:AD:DP:GL:GQ 0/1:17,21:35:-59.82,-10.55,-67.90:99 +chr1 4626392 rs12565906 G A 175.56 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=1.36;MQ=51.30;MQ0=0;OQ=647.78;QD=15.42;SB=-283.17 GT:AD:DP:GL:GQ 0/1:21,21:41:-80.41,-12.35,-73.25:99 +chr1 4626545 rs12137938 T C 1.78 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=2;HaplotypeScore=6.74;MQ=54.18;MQ0=1;OQ=220.73;QD=6.49;SB=-111.61 GT:AD:DP:GL:GQ 0/1:20,14:29:-34.11,-8.75,-66.24:99 +chr1 4626759 rs10799254 A G 12.84 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=7.18;MQ=56.44;MQ0=0;OQ=516.47;QD=13.59;SB=-271.00 GT:AD:DP:GL:GQ 0/1:15,23:33:-64.88,-9.95,-53.03:99 +chr1 4626886 rs12137092 A G 70.84 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=50.68;MQ0=3;OQ=425.89;QD=8.19;SB=-166.49 GT:AD:DP:GL:GQ 0/1:30,22:47:-60.04,-14.17,-111.36:99 +chr1 4627103 rs6663166 A G 61.80 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.88;MQ0=0;OQ=507.83;QD=9.40;SB=-149.43 GT:AD:DP:GL:GQ 0/1:33,21:53:-70.04,-15.97,-130.76:99 +chr1 4627150 rs12138132 T C 261.25 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.66;MQ0=0;OQ=429.65;QD=7.81;SB=-213.21 GT:AD:DP:GL:GQ 0/1:37,18:55:-62.82,-16.57,-149.18:99 +chr1 4627390 rs12133670 G A 454.29 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.64;MQ0=0;OQ=810.38;QD=15.58;SB=-415.38 GT:AD:DP:GL:GQ 0/1:28,24:51:-99.69,-15.36,-91.80:99 +chr1 4628089 rs12133909 G T 196.70 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=59.88;MQ0=0;OQ=673.35;QD=10.52;SB=-318.02 GT:AD:DP:GL:GQ 0/1:40,24:62:-89.30,-18.68,-116.17:99 +chr1 4628258 rs6703379 G A 0.30 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=13.50;MQ=55.99;MQ0=1;OQ=611.30;QD=11.32;SB=-213.68 GT:AD:DP:GL:GQ 0/1:33,21:47:-78.59,-14.17,-86.02:99 +chr1 4628265 rs6672122 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.04;HRun=0;HaplotypeScore=25.47;MQ=56.13;MQ0=1;OQ=602.93;QD=10.77;SB=-162.48 GT:AD:DP:GL:GQ 0/1:29,25:52:-78.65,-15.07,-102.50:99 +chr1 4628677 rs6703802 G A 334.66 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=937.15;QD=18.02;SB=-393.92 GT:AD:DP:GL:GQ 0/1:24,28:51:-112.37,-15.37,-73.40:99 +chr1 4630143 rs4654582 T A 2.35 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=10.18;MQ=58.22;MQ0=0;OQ=526.78;QD=10.54;SB=-97.11 GT:AD:DP:GL:GQ 0/1:25,22:38:-67.41,-11.45,-72.86:99 +chr1 4630312 rs4654583 T C 361.82 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1108.52;QD=16.07;SB=-319.34 GT:AD:DP:GL:GQ 0/1:31,38:68:-134.62,-20.48,-127.03:99 +chr1 4630977 rs12141394 A G 593.81 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.47;MQ0=0;OQ=900.99;QD=13.45;SB=-440.92 GT:AD:DP:GL:GQ 0/1:31,36:65:-112.97,-19.59,-120.61:99 +chr1 4631016 rs12139858 C T 367.23 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=891.25;QD=15.37;SB=-441.97 GT:AD:DP:GL:GQ 0/1:31,27:57:-109.59,-17.18,-94.97:99 +chr1 4631110 rs12141432 A G 226.87 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=58.67;MQ0=0;OQ=787.70;QD=12.50;SB=-349.34 GT:AD:DP:GL:GQ 0/1:35,28:62:-100.73,-18.67,-138.62:99 +chr1 4631448 rs4144452 A G 502.74 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=648.74;QD=10.64;SB=-332.00 GT:AD:DP:GL:GQ 0/1:33,28:59:-85.94,-17.78,-131.20:99 +chr1 4631992 rs12138000 G A 396.61 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=1014.12;QD=15.85;SB=-413.79 GT:AD:DP:GL:GQ 0/1:32,32:63:-123.69,-18.99,-104.09:99 +chr1 4632333 rs1564667 A G 289.52 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=656.79;QD=8.64;SB=-323.90 GT:AD:DP:GL:GQ 0/1:44,32:72:-90.67,-21.71,-171.92:99 +chr1 4633099 rs4654585 T C 336.77 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.88;MQ=59.60;MQ0=0;OQ=968.60;QD=16.70;SB=-498.14 GT:AD:DP:GL:GQ 0/1:26,32:58:-117.61,-17.47,-104.79:99 +chr1 4633208 rs4654586 T A 613.80 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2145.98;QD=37.00;SB=-956.61 GT:AD:DP:GL:GQ 1/1:0,58:58:-218.20,-17.47,-0.01:99 +chr1 4633215 rs4654455 T C 484.54 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1991.47;QD=34.94;SB=-790.66 GT:AD:DP:GL:GQ 1/1:0,57:56:-202.75,-16.87,-0.02:99 +chr1 4636316 rs10915584 G T 377.31 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.90;MQ=59.34;MQ0=0;OQ=844.77;QD=13.41;SB=-404.78 GT:AD:DP:GL:GQ 0/1:32,31:58:-105.23,-17.47,-102.72:99 +chr1 4637265 . T C 225.79 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=776.05;QD=14.64;SB=-255.94 GT:AD:DP:GL:GQ 0/1:26,27:53:-96.86,-15.97,-103.32:99 +chr1 4638345 . G A 67.79 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.29;MQ0=0;OQ=991.16;QD=18.70;SB=-412.80 GT:AD:DP:GL:GQ 0/1:24,29:51:-117.77,-15.37,-70.20:99 +chr1 4642883 rs2859392 C G 348.55 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.26;MQ=59.71;MQ0=0;OQ=833.93;QD=12.83;SB=-304.28 GT:AD:DP:GL:GQ 0/1:37,28:61:-105.07,-18.39,-160.99:99 +chr1 4643564 rs763238 C T 66.20 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.77;MQ0=0;OQ=1042.05;QD=19.66;SB=-208.90 GT:AD:DP:GL:GQ 0/1:21,32:50:-122.56,-15.07,-63.38:99 +chr1 4644154 rs4993529 C T 334.67 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=60.00;MQ0=0;OQ=1314.27;QD=19.62;SB=-670.69 GT:AD:DP:GL:GQ 0/1:27,40:65:-154.30,-19.59,-85.13:99 +chr1 4646074 rs242043 T C 1.61 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=13.28;MQ=59.47;MQ0=0;OQ=1026.27;QD=14.45;SB=-395.20 GT:AD:DP:GL:GQ 0/1:34,37:70:-127.00,-21.09,-134.39:99 +chr1 4646297 rs61765026 G A 183.35 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=1519.28;QD=17.87;SB=-749.72 GT:AD:DP:GL:GQ 0/1:39,46:84:-180.53,-25.32,-123.19:99 +chr1 4646496 rs10915587 C T 288.71 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=3.87;MQ=60.00;MQ0=0;OQ=1042.81;QD=16.04;SB=-490.54 GT:AD:DP:GL:GQ 0/1:32,33:64:-126.86,-19.30,-98.43:99 +chr1 4646880 rs17344953 G A 102.24 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=5.33;MQ=59.62;MQ0=0;OQ=1025.96;QD=17.10;SB=-396.44 GT:AD:DP:GL:GQ 0/1:26,33:55:-122.45,-16.57,-85.52:99 +chr1 4647597 rs12747700 G A 323.59 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=59.29;MQ0=0;OQ=999.88;QD=16.95;SB=-503.14 GT:AD:DP:GL:GQ 0/1:28,31:57:-120.45,-17.18,-86.54:99 +chr1 4648034 rs6684528 G T 259.70 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.52;MQ0=0;OQ=808.60;QD=16.85;SB=-296.69 GT:AD:DP:GL:GQ 0/1:20,28:48:-98.60,-14.46,-70.03:99 +chr1 4648165 rs1076944 G T 243.38 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=58.38;MQ0=0;OQ=602.15;QD=11.58;SB=-146.14 GT:AD:DP:GL:GQ 0/1:27,25:49:-78.26,-14.76,-94.92:99 +chr1 4648936 rs4092257 G A 283.88 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=57.56;MQ0=0;OQ=450.85;QD=13.66;SB=-204.90 GT:AD:DP:GL:GQ 0/1:17,16:32:-58.02,-9.65,-54.32:99 +chr1 4649873 rs187148 C G 93.57 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=0;HaplotypeScore=3.10;MQ=59.76;MQ0=0;OQ=296.24;QD=8.98;SB=-132.74 GT:AD:DP:GL:GQ 0/1:22,11:31:-42.26,-9.35,-85.65:99 +chr1 4651624 . C A 146.63 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=797.72;QD=17.34;SB=-280.69 GT:AD:DP:GL:GQ 0/1:17,29:42:-95.71,-12.66,-50.88:99 +chr1 4652138 rs171380 A G 10.05 PASS AC=1;AF=0.50;AN=2;DB;DP=30;Dels=0.00;HRun=2;HaplotypeScore=3.45;MQ=58.45;MQ0=0;OQ=324.85;QD=10.83;SB=-162.34 GT:AD:DP:GL:GQ 0/1:14,16:28:-44.21,-8.45,-55.22:99 +chr1 4653917 rs7525374 A G 301.57 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=624.45;QD=13.58;SB=-244.30 GT:AD:DP:GL:GQ 0/1:21,25:46:-79.59,-13.86,-85.75:99 +chr1 4653963 rs7528195 T C 276.57 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.00;MQ0=0;OQ=479.46;QD=11.42;SB=-265.36 GT:AD:DP:GL:GQ 0/1:21,21:39:-62.99,-11.76,-78.32:99 +chr1 4654404 rs1076945 C T 142.94 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=4.82;MQ=58.13;MQ0=0;OQ=818.85;QD=13.65;SB=-233.53 GT:AD:DP:GL:GQ 0/1:33,27:59:-102.95,-17.78,-107.70:99 +chr1 4655581 . C T 85.40 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=59.44;MQ0=0;OQ=1224.61;QD=16.55;SB=-495.16 GT:AD:DP:GL:GQ 0/1:36,38:73:-147.75,-22.00,-119.12:99 +chr1 4656328 rs10915588 T C 75.83 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=629.83;QD=11.88;SB=-281.45 GT:AD:DP:GL:GQ 0/1:30,23:52:-81.93,-15.66,-115.22:99 +chr1 4656461 rs3886389 A G 234.27 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.53;MQ0=0;OQ=467.67;QD=9.54;SB=-232.27 GT:AD:DP:GL:GQ 0/1:28,21:49:-64.82,-14.77,-113.76:99 +chr1 4657736 rs6669203 T C 161.22 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=58.29;MQ0=0;OQ=397.97;QD=9.71;SB=-145.57 GT:AD:DP:GL:GQ 0/1:23,18:37:-54.24,-11.16,-78.29:99 +chr1 4658187 rs12121882 C T 363.11 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=849.30;QD=18.07;SB=-359.52 GT:AD:DP:GL:GQ 0/1:21,26:46:-102.08,-13.87,-62.23:99 +chr1 4659178 rs242054 A G 123.55 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=57.49;MQ0=0;OQ=1370.79;QD=30.46;SB=-653.90 GT:AD:DP:GL:GQ 1/1:0,45:44:-140.71,-13.27,-0.04:99 +chr1 4660176 rs61765031 A G 230.02 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.54;MQ=59.01;MQ0=0;OQ=811.95;QD=12.30;SB=-390.16 GT:AD:DP:GL:GQ 0/1:34,31:61:-102.85,-18.37,-129.51:99 +chr1 4663049 rs6686733 T C 216.77 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=4.72;MQ=59.04;MQ0=0;OQ=1082.32;QD=15.92;SB=-503.34 GT:AD:DP:GL:GQ 0/1:29,39:64:-130.80,-19.28,-107.21:99 +chr1 4663261 rs6681520 C T 227.08 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1006.77;QD=22.88;SB=-416.49 GT:AD:DP:GL:GQ 0/1:15,29:43:-116.92,-12.96,-47.72:99 +chr1 4665250 rs12131565 A G 49.08 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=2.95;MQ=47.43;MQ0=2;OQ=1030.19;QD=13.38;SB=-443.10 GT:AD:DP:GL:GQ 0/1:41,36:75:-128.89,-22.59,-163.25:99 +chr1 4665448 rs10915590 T C 343.30 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.85;MQ0=0;OQ=469.57;QD=9.58;SB=-224.22 GT:AD:DP:GL:GQ 0/1:29,20:48:-64.71,-14.47,-110.90:99 +chr1 4665815 rs10915592 T C 6.94 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=2.44;MQ=60.00;MQ0=0;OQ=940.71;QD=17.75;SB=-259.53 GT:AD:DP:GL:GQ 0/1:21,32:50:-112.42,-15.06,-71.48:99 +chr1 4667613 rs2101196 A G 254.46 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.34;MQ=56.97;MQ0=0;OQ=1013.81;QD=15.13;SB=-354.95 GT:AD:DP:GL:GQ 0/1:32,35:65:-124.25,-19.58,-123.74:99 +chr1 4667836 . T C 82.17 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=758.61;QD=12.24;SB=-402.64 GT:AD:DP:GL:GQ 0/1:31,31:61:-97.53,-18.39,-127.98:99 +chr1 4667882 rs2086718 C T 43.81 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.02;HRun=0;HaplotypeScore=5.21;MQ=57.79;MQ0=0;OQ=518.41;QD=9.43;SB=-229.72 GT:AD:DP:GL:GQ 0/1:31,22:40:-66.89,-11.76,-68.62:99 +chr1 4667894 . G T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=12;HaplotypeScore=6.56;MQ=55.45;MQ0=0;OQ=63.00;QD=0.98;SB=-8.73 GT:AD:DP:GL:GQ 0/1:54,10:56:-26.47,-16.89,-148.75:95.84 +chr1 4668291 rs6670802 G A 143.50 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=56.73;MQ0=0;OQ=372.96;QD=8.29;SB=-147.60 GT:AD:DP:GL:GQ 0/1:28,16:38:-52.04,-11.46,-80.12:99 +chr1 4668400 rs6688423 T C 371.01 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=710.41;QD=13.16;SB=-359.33 GT:AD:DP:GL:GQ 0/1:26,28:52:-89.99,-15.67,-104.81:99 +chr1 4668882 . T C 49.86 LowQual AC=1;AF=0.50;AN=2;DP=20;Dels=0.00;HRun=3;HaplotypeScore=9.17;MQ=57.66;MQ0=0;QD=2.49;SB=-0.98 GT:AD:DP:GL:GQ 0/1:11,9:11:-11.59,-3.32,-24.54:82.70 +chr1 4669925 rs12760917 T C 439.23 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.29;MQ0=0;OQ=917.38;QD=14.11;SB=-279.27 GT:AD:DP:GL:GQ 0/1:29,36:64:-114.31,-19.29,-115.57:99 +chr1 4670306 rs4654594 T C 240.89 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=58.06;MQ0=0;OQ=1070.08;QD=17.54;SB=-482.88 GT:AD:DP:GL:GQ 0/1:21,40:58:-127.77,-17.48,-76.71:99 +chr1 4670764 rs1483197 T C 225.25 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=4.25;MQ=58.29;MQ0=0;OQ=709.74;QD=13.65;SB=-285.29 GT:AD:DP:GL:GQ 0/1:22,29:49:-89.03,-14.77,-80.10:99 +chr1 4670879 . G T 21.82 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=60.00;MQ0=0;OQ=722.25;QD=15.70;SB=-186.19 GT:AD:DP:GL:GQ 0/1:22,24:42:-88.16,-12.65,-60.03:99 +chr1 4671525 rs989309 G C 65.26 PASS AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.00;HRun=1;HaplotypeScore=2.50;MQ=60.00;MQ0=0;OQ=327.78;QD=9.93;SB=-148.55 GT:AD:DP:GL:GQ 0/1:21,12:30:-45.12,-9.05,-74.66:99 +chr1 4671555 rs989310 G C 120.18 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=60.00;MQ0=0;OQ=521.90;QD=14.11;SB=-193.59 GT:AD:DP:GL:GQ 0/1:21,16:35:-66.02,-10.55,-86.58:99 +chr1 4671913 rs1061968 T C 32.96 PASS AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=58.55;MQ0=0;OQ=101.72;QD=6.36;SB=-10.00 GT:AD:DP:GL:GQ 0/1:10,6:16:-18.28,-4.82,-40.28:99 +chr1 4672577 rs242056 G A 47.38 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.45;MQ0=0;OQ=1114.83;QD=37.16;SB=-369.99 GT:AD:DP:GL:GQ 1/1:0,30:28:-115.07,-8.43,-0.01:84.28 +chr1 4673126 rs2071999 A C 360.34 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=60.00;MQ0=0;OQ=766.03;QD=12.77;SB=-408.20 GT:AD:DP:GL:GQ 0/1:27,33:59:-97.67,-17.78,-97.47:99 +chr1 4673232 rs56401224 C G 273.95 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.62;MQ=59.63;MQ0=0;OQ=825.52;QD=16.51;SB=-362.08 GT:AD:DP:GL:GQ 0/1:25,25:46:-99.70,-13.86,-96.30:99 +chr1 4673712 rs242057 G A 40.47 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=3;HaplotypeScore=2.46;MQ=59.65;MQ0=0;OQ=947.24;QD=14.35;SB=-485.02 GT:AD:DP:GL:GQ 0/1:36,30:63:-116.99,-18.98,-120.15:99 +chr1 4674298 rs242058 T C 345.93 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=778.59;QD=15.27;SB=-272.44 GT:AD:DP:GL:GQ 0/1:23,28:50:-96.21,-15.07,-89.60:99 +chr1 4676145 rs4654595 A C 407.01 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=2257.07;QD=35.83;SB=-1055.12 GT:AD:DP:GL:GQ 1/1:0,63:63:-229.31,-18.97,-0.02:99 +chr1 4676402 rs4654596 G A 207.21 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.44;MQ0=0;OQ=2768.52;QD=37.41;SB=-1042.40 GT:AD:DP:GL:GQ 1/1:0,74:71:-280.46,-21.39,-0.02:99 +chr1 4678092 rs3766959 C T 358.01 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.73;MQ0=0;OQ=1524.54;QD=23.10;SB=-743.34 GT:AD:DP:GL:GQ 0/1:22,44:65:-175.33,-19.59,-68.56:99 +chr1 4679148 rs242040 A G 228.84 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.49;MQ=60.00;MQ0=0;OQ=836.32;QD=13.07;SB=-312.23 GT:AD:DP:GL:GQ 0/1:34,30:63:-105.89,-18.98,-137.28:99 +chr1 4679557 rs242041 G C 23.06 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=1.52;MQ=58.81;MQ0=0;OQ=500.09;QD=9.81;SB=-250.11 GT:AD:DP:GL:GQ 0/1:32,19:47:-67.48,-14.18,-123.03:99 +chr1 4681011 rs3820251 C T 321.37 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.05;MQ0=0;OQ=1264.98;QD=15.06;SB=-599.08 GT:AD:DP:GL:GQ 0/1:45,39:83:-154.80,-25.02,-140.75:99 +chr1 4683002 rs12566272 G A 75.66 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=6.06;MQ=59.60;MQ0=0;OQ=811.79;QD=14.00;SB=-379.10 GT:AD:DP:GL:GQ 0/1:30,28:55:-101.04,-16.58,-98.62:99 +chr1 4683215 rs12085854 C T 250.87 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=58.71;MQ0=0;OQ=595.12;QD=16.53;SB=-237.77 GT:AD:DP:GL:GQ 0/1:12,24:28:-71.24,-8.44,-31.48:99 +chr1 4684416 rs3820252 C T 67.11 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.40;MQ=59.16;MQ0=0;OQ=1099.71;QD=21.99;SB=-407.20 GT:AD:DP:GL:GQ 0/1:18,32:50:-128.32,-15.07,-57.31:99 +chr1 4684710 rs4554693 C T 27.64 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.03;MQ=59.86;MQ0=0;OQ=1309.90;QD=22.98;SB=-464.01 GT:AD:DP:GL:GQ 0/1:20,37:57:-151.45,-17.18,-62.35:99 +chr1 4685955 rs11586740 G T 36.42 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=7.65;MQ=60.00;MQ0=0;OQ=1269.15;QD=17.39;SB=-560.71 GT:AD:DP:GL:GQ 0/1:30,43:69:-150.98,-20.79,-94.07:99 +chr1 4686129 . A G 0.31 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=58.20;MQ0=0;OQ=188.73;QD=3.63;SB=-3.68 GT:AD:DP:GL:GQ 0/1:41,11:52:-37.84,-15.68,-155.85:99 +chr1 4686130 . G C 4.40 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.20;MQ0=0;OQ=258.95;QD=4.98;SB=-16.68 GT:AD:DP:GL:GQ 0/1:42,10:52:-44.85,-15.67,-182.52:99 +chr1 4686979 rs242044 A G 24.21 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=2;HaplotypeScore=0.79;MQ=59.56;MQ0=0;OQ=1479.37;QD=27.91;SB=-538.14 GT:AD:DP:GL:GQ 1/1:0,52:45:-151.55,-13.56,-0.03:99 +chr1 4687176 rs242045 T C 255.59 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1371.92;QD=34.30;SB=-697.63 GT:AD:DP:GL:GQ 1/1:0,40:40:-140.79,-12.05,-0.02:99 +chr1 4687868 rs242047 A C 103.52 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=2.65;MQ=59.62;MQ0=0;OQ=770.92;QD=12.85;SB=-248.85 GT:AD:DP:GL:GQ 0/1:32,28:59:-98.15,-17.77,-114.07:99 +chr1 4688746 rs242048 A G 112.68 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=1.71;MQ=59.36;MQ0=0;OQ=768.10;QD=21.34;SB=-331.78 GT:AD:DP:GL:GQ 1/1:0,36:26:-80.42,-7.84,-0.03:78.16 +chr1 4688889 rs242049 T G 239.30 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=60.00;MQ0=0;OQ=1481.34;QD=32.92;SB=-635.03 GT:AD:DP:GL:GQ 1/1:0,45:44:-151.74,-13.26,-0.02:99 +chr1 4695274 rs446529 T C 363.34 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=55.31;MQ0=0;OQ=516.35;QD=9.93;SB=-227.25 GT:AD:DP:GL:GQ 0/1:29,23:50:-69.99,-15.07,-114.97:99 +chr1 4695606 rs648712 C T 1.54 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=10.04;MQ=47.15;MQ0=0;OQ=816.40;QD=17.01;SB=-434.45 GT:AD:DP:GL:GQ 0/1:23,25:46:-98.78,-13.86,-79.74:99 +chr1 4695607 . T G 0.18 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=11.01;MQ=47.15;MQ0=0;OQ=688.64;QD=14.35;SB=-357.86 GT:AD:DP:GL:GQ 0/1:23,25:47:-86.31,-14.16,-83.32:99 +chr1 4695638 rs432330 T A 460.16 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.80;MQ0=0;OQ=772.11;QD=15.14;SB=-337.40 GT:AD:DP:GL:GQ 0/1:24,27:50:-95.56,-15.06,-90.18:99 +chr1 4695654 rs449261 T C 245.99 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.57;MQ=53.57;MQ0=0;OQ=702.97;QD=13.52;SB=-345.62 GT:AD:DP:GL:GQ 0/1:26,26:49:-88.35,-14.77,-92.65:99 +chr1 4695676 rs435239 G C 185.06 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=2.08;MQ=57.17;MQ0=0;OQ=826.31;QD=16.53;SB=-414.36 GT:AD:DP:GL:GQ 0/1:24,26:47:-100.09,-14.18,-90.75:99 +chr1 4695734 rs416953 T C 152.01 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=59.13;MQ0=0;OQ=882.63;QD=16.65;SB=-283.45 GT:AD:DP:GL:GQ 0/1:22,31:50:-106.61,-15.06,-78.94:99 +chr1 4696083 rs383650 C G 345.55 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.53;MQ=59.10;MQ0=0;OQ=1382.15;QD=17.95;SB=-715.96 GT:AD:DP:GL:GQ 0/1:38,39:75:-164.11,-22.61,-152.21:99 +chr1 4696156 rs436132 G C 8.37 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=1112.40;QD=19.86;SB=-564.68 GT:AD:DP:GL:GQ 0/1:25,31:56:-131.40,-16.88,-111.00:99 +chr1 4696361 . A C 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=2;HaplotypeScore=10.18;MQ=60.26;MQ0=0;OQ=143.73;QD=2.08;SB=104.31 GT:AD:DP:GL:GQ 0/1:45,24:52:-33.32,-15.67,-137.68:99 +chr1 4696418 rs392630 A G 270.27 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.71;MQ0=0;OQ=1265.58;QD=13.76;SB=-582.79 GT:AD:DP:GL:GQ 0/1:45,47:87:-156.05,-26.21,-176.07:99 +chr1 4697358 rs544738 C A 298.87 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.61;MQ=59.01;MQ0=0;OQ=538.34;QD=14.17;SB=-233.94 GT:AD:DP:GL:GQ 0/1:19,19:37:-68.26,-11.15,-60.83:99 +chr1 4697618 rs445060 G A 155.17 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=59.60;MQ0=0;OQ=740.87;QD=12.77;SB=-313.26 GT:AD:DP:GL:GQ 0/1:32,26:54:-93.63,-16.26,-111.70:99 +chr1 4698713 rs578528 A G 87.54 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.36;MQ0=0;OQ=385.70;QD=10.71;SB=-193.63 GT:AD:DP:GL:GQ 0/1:21,15:36:-52.70,-10.85,-81.97:99 +chr1 4699130 rs449181 G A 397.02 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.84;MQ=59.67;MQ0=0;OQ=927.44;QD=16.56;SB=-380.14 GT:AD:DP:GL:GQ 0/1:27,29:54:-112.30,-16.28,-85.10:99 +chr1 4700289 rs13376290 T G 0.41 PASS AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=4;HaplotypeScore=0.10;MQ=48.01;MQ0=0;OQ=193.53;QD=7.44;SB=-0.43 GT:AD:DP:GL:GQ 0/1:15,11:24:-29.87,-7.23,-54.19:99 +chr1 4700426 . C G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=2;HaplotypeScore=11.52;MQ=48.42;MQ0=0;OQ=136.63;QD=5.25;SB=-6.99 GT:AD:DP:GL:GQ 0/1:7,19:10:-19.97,-3.02,-19.59:99 +chr1 4700705 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=20;HaplotypeScore=32.92;MQ=48.95;MQ0=0;OQ=199.23;QD=3.83;SB=71.25 GT:AD:DP:GL:GQ 0/1:35,17:41:-35.56,-12.35,-113.25:99 +chr1 4700881 rs529853 G C 174.83 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=3.66;MQ=53.91;MQ0=0;OQ=810.63;QD=16.54;SB=-402.70 GT:AD:DP:GL:GQ 0/1:22,27:47:-98.53,-14.18,-93.65:99 +chr1 4701141 rs381339 T C 9.53 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=2.72;MQ=59.22;MQ0=0;OQ=750.05;QD=11.54;SB=-112.61 GT:AD:DP:GL:GQ 0/1:29,33:53:-94.27,-15.98,-96.69:99 +chr1 4701497 rs382623 T C 282.35 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.48;MQ0=0;OQ=1093.69;QD=13.50;SB=-513.56 GT:AD:DP:GL:GQ 0/1:38,43:80:-136.77,-24.11,-153.00:99 +chr1 4701516 rs382646 T C 490.40 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1091.01;QD=14.36;SB=-413.27 GT:AD:DP:GL:GQ 0/1:38,38:75:-134.98,-22.59,-157.29:99 +chr1 4701783 rs392620 C T 260.56 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.19;MQ=59.38;MQ0=0;OQ=1111.05;QD=15.01;SB=-420.88 GT:AD:DP:GL:GQ 0/1:41,33:73:-136.38,-21.99,-143.11:99 +chr1 4702373 rs448741 C T 315.12 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.33;MQ0=0;OQ=1161.48;QD=16.83;SB=-516.10 GT:AD:DP:GL:GQ 0/1:33,36:68:-139.92,-20.49,-116.50:99 +chr1 4702588 rs431966 C G 301.89 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.74;MQ0=0;OQ=1167.37;QD=16.21;SB=-392.89 GT:AD:DP:GL:GQ 0/1:35,37:71:-141.44,-21.42,-151.57:99 +chr1 4703125 rs367673 G C 285.90 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.24;MQ0=0;OQ=1282.03;QD=21.02;SB=-602.59 GT:AD:DP:GL:GQ 0/1:26,35:61:-149.87,-18.38,-114.22:99 +chr1 4703446 rs540299 A G 321.95 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.50;MQ=59.10;MQ0=0;OQ=1141.42;QD=14.82;SB=-449.59 GT:AD:DP:GL:GQ 0/1:36,41:75:-140.02,-22.60,-142.02:99 +chr1 4703496 rs648346 G A 131.26 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=58.29;MQ0=0;OQ=1435.37;QD=17.50;SB=-321.28 GT:AD:DP:GL:GQ 0/1:40,42:79:-170.63,-23.81,-120.02:99 +chr1 4703694 rs393976 G A 298.73 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=59.30;MQ0=0;OQ=1022.50;QD=17.04;SB=-396.14 GT:AD:DP:GL:GQ 0/1:30,30:58:-123.01,-17.47,-100.86:99 +chr1 4704145 rs375781 T C 253.06 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=57.53;MQ0=0;OQ=380.91;QD=10.02;SB=-211.48 GT:AD:DP:GL:GQ 0/1:19,19:35:-51.92,-10.55,-74.06:99 +chr1 4704212 rs406065 A T 598.24 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.74;MQ0=0;OQ=1026.86;QD=14.88;SB=-405.55 GT:AD:DP:GL:GQ 0/1:35,34:69:-126.75,-20.78,-135.77:99 +chr1 4704412 rs396199 G A 86.73 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=1.14;MQ=59.62;MQ0=0;OQ=915.71;QD=18.69;SB=-324.82 GT:AD:DP:GL:GQ 0/1:21,28:47:-109.02,-14.16,-69.65:99 +chr1 4704606 rs413178 A G 154.93 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=56.43;MQ0=0;OQ=958.14;QD=15.45;SB=-233.27 GT:AD:DP:GL:GQ 0/1:25,37:59:-116.89,-17.79,-90.61:99 +chr1 4704966 rs414176 A C 426.79 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=751.31;QD=11.93;SB=-297.47 GT:AD:DP:GL:GQ 0/1:31,32:62:-97.10,-18.68,-109.53:99 +chr1 4705294 rs371605 A G 188.84 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=59.55;MQ0=0;OQ=418.07;QD=8.20;SB=-210.35 GT:AD:DP:GL:GQ 0/1:28,23:46:-58.96,-13.87,-104.25:99 +chr1 4705534 rs409048 T C 345.87 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.05;MQ=59.35;MQ0=0;OQ=802.66;QD=12.54;SB=-363.20 GT:AD:DP:GL:GQ 0/1:35,29:64:-102.83,-19.28,-139.39:99 +chr1 4706241 rs368808 A G 17.45 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=2;HaplotypeScore=4.09;MQ=59.49;MQ0=0;OQ=756.36;QD=9.22;SB=-230.86 GT:AD:DP:GL:GQ 0/1:48,34:80:-103.04,-24.12,-189.26:99 +chr1 4707706 rs368940 A G 105.39 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=599.08;QD=17.12;SB=-212.56 GT:AD:DP:GL:GQ 0/1:14,21:35:-73.73,-10.54,-57.28:99 +chr1 4707911 . C A 31.90 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=13;HaplotypeScore=26.77;MQ=58.47;MQ0=0;QD=0.52;SB=52.91 GT:AD:DP:GL:GQ 0/1:52,9:48:-20.93,-14.46,-146.08:64.73 +chr1 4708314 rs2802721 G A 450.84 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=56.44;MQ0=0;OQ=981.54;QD=15.34;SB=-489.03 GT:AD:DP:GL:GQ 0/1:28,36:59:-119.22,-17.78,-99.55:99 +chr1 4708405 rs394808 C A 233.49 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=56.69;MQ0=0;OQ=782.76;QD=14.77;SB=-324.34 GT:AD:DP:GL:GQ 0/1:26,27:51:-96.92,-15.37,-78.87:99 +chr1 4708536 rs395145 C T 383.51 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1269.10;QD=19.83;SB=-521.54 GT:AD:DP:GL:GQ 0/1:25,39:63:-149.18,-18.98,-84.36:99 +chr1 4708674 rs4654602 A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=69.80;MQ=46.48;MQ0=0;OQ=293.59;QD=4.19;SB=-93.14 GT:AD:DP:GL:GQ 0/1:56,14:66:-52.53,-19.89,-198.60:99 +chr1 4708678 rs406913 A G 32.76 DPFilter;LowQual AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=20.07;MQ=45.13;MQ0=0;QD=0.48;SB=9.87 GT:AD:DP:GL:GQ 0/1:59,9:58:-24.04,-17.48,-194.48:65.59 +chr1 4708830 rs433427 A G 13.73 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=6.55;MQ=59.08;MQ0=0;OQ=748.71;QD=10.55;SB=-350.04 GT:AD:DP:GL:GQ 0/1:40,31:70:-99.25,-21.09,-163.31:99 +chr1 4708980 rs2802720 C T 373.55 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=55.41;MQ0=0;OQ=1008.97;QD=15.29;SB=-359.05 GT:AD:DP:GL:GQ 0/1:35,31:66:-124.06,-19.88,-124.56:99 +chr1 4710412 rs364642 C T 180.53 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=3.52;MQ=58.91;MQ0=0;OQ=814.43;QD=13.57;SB=-402.86 GT:AD:DP:GL:GQ 0/1:32,28:58:-102.20,-17.48,-113.74:99 +chr1 4712675 rs381240 A G 265.51 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=57.93;MQ0=0;OQ=805.26;QD=10.19;SB=-382.86 GT:AD:DP:GL:GQ 0/1:44,35:76:-106.72,-22.91,-172.59:99 +chr1 4712931 rs448221 T C 105.17 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=56.15;MQ0=0;OQ=384.09;QD=10.38;SB=-115.63 GT:AD:DP:GL:GQ 0/1:18,19:34:-51.95,-10.25,-67.62:99 +chr1 4712934 rs431884 C T 132.31 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=56.04;MQ0=0;OQ=441.73;QD=12.27;SB=-157.22 GT:AD:DP:GL:GQ 0/1:18,18:33:-57.41,-9.95,-59.19:99 +chr1 4712975 rs380239 A G 454.99 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=55.78;MQ0=0;OQ=728.95;QD=12.57;SB=-369.58 GT:AD:DP:GL:GQ 0/1:31,26:56:-93.05,-16.87,-121.44:99 +chr1 4713977 rs434474 A T 435.77 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.38;MQ0=0;OQ=788.95;QD=11.78;SB=-384.44 GT:AD:DP:GL:GQ 0/1:40,27:64:-101.46,-19.28,-136.23:99 +chr1 4714260 rs428001 G A 188.72 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=394.17;QD=7.58;SB=-208.83 GT:AD:DP:GL:GQ 0/1:37,15:47:-56.86,-14.16,-117.42:99 +chr1 4714368 rs413383 G C 359.15 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=902.57;QD=15.56;SB=-389.66 GT:AD:DP:GL:GQ 0/1:30,28:56:-110.43,-16.89,-123.48:99 +chr1 4714807 rs401110 C T 341.51 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=642.13;QD=13.96;SB=-230.50 GT:AD:DP:GL:GQ 0/1:24,21:44:-80.76,-13.26,-78.68:99 +chr1 4715337 rs434504 G A 250 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.39;MQ0=0;OQ=582.19;QD=15.32;SB=-195.19 GT:AD:DP:GL:GQ 0/1:19,19:36:-72.35,-10.85,-57.76:99 +chr1 4718265 rs423796 G A 245.56 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.32;MQ=58.44;MQ0=0;OQ=1032.37;QD=16.92;SB=-496.08 GT:AD:DP:GL:GQ 0/1:28,33:59:-124.29,-17.77,-98.91:99 +chr1 4718977 rs41511844 A C 15.67 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=3;HaplotypeScore=0.79;MQ=59.53;MQ0=0;OQ=807.51;QD=16.48;SB=-276.90 GT:AD:DP:GL:GQ 0/1:21,28:49:-98.80,-14.76,-77.17:99 +chr1 4719527 rs523141 G A 331.15 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.63;MQ0=1;OQ=362.25;QD=9.29;SB=-60.24 GT:AD:DP:GL:GQ 0/1:25,14:36:-50.35,-10.84,-83.10:99 +chr1 4719663 rs368420 T C 450.85 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=60.00;MQ0=0;OQ=1132.30;QD=16.90;SB=-528.33 GT:AD:DP:GL:GQ 0/1:29,38:66:-136.39,-19.88,-119.33:99 +chr1 4720200 rs34125417 T A 155.86 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=3.33;MQ=59.59;MQ0=0;OQ=796.97;QD=13.51;SB=-224.76 GT:AD:DP:GL:GQ 0/1:29,29:54:-99.25,-16.27,-103.01:99 +chr1 4720659 rs397559 C T 380.37 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.71;MQ0=0;OQ=1207.74;QD=18.87;SB=-534.79 GT:AD:DP:GL:GQ 0/1:27,37:63:-143.05,-18.99,-86.17:99 +chr1 4721157 rs443850 C T 216.92 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=4.76;MQ=59.51;MQ0=0;OQ=1138.02;QD=14.97;SB=-525.69 GT:AD:DP:GL:GQ 0/1:42,34:73:-139.07,-21.99,-142.33:99 +chr1 4721448 rs9426481 G T 366.43 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=988.26;QD=14.53;SB=-519.87 GT:AD:DP:GL:GQ 0/1:35,33:67:-122.29,-20.18,-120.50:99 +chr1 4722600 rs742245 A C 591.38 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1064.86;QD=15.00;SB=-554.90 GT:AD:DP:GL:GQ 0/1:34,37:68:-130.25,-20.48,-117.18:99 +chr1 4722971 rs760815 C A 224.06 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=59.29;MQ0=0;OQ=950.16;QD=16.10;SB=-349.23 GT:AD:DP:GL:GQ 0/1:26,33:58:-115.77,-17.47,-92.37:99 +chr1 4723061 rs2743978 G A 259.98 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=60.00;MQ0=0;OQ=829.12;QD=15.07;SB=-390.87 GT:AD:DP:GL:GQ 0/1:28,27:53:-102.17,-15.97,-92.75:99 +chr1 4723683 rs411832 G C 0.53 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.02;HRun=0;HaplotypeScore=12.73;MQ=59.54;MQ0=0;OQ=809.82;QD=16.20;SB=-394.90 GT:AD:DP:GL:GQ 0/1:25,24:48:-98.44,-14.17,-99.99:99 +chr1 4723923 rs425005 C A 167.26 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=59.70;MQ0=0;OQ=997.52;QD=16.09;SB=-361.25 GT:AD:DP:GL:GQ 0/1:28,34:61:-121.41,-18.38,-98.67:99 +chr1 4724602 rs424723 C T 274.96 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.39;MQ0=0;OQ=1215.08;QD=19.92;SB=-584.11 GT:AD:DP:GL:GQ 0/1:24,36:58:-142.27,-17.47,-75.15:99 +chr1 4725012 rs2743979 G A 336.31 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.68;MQ0=0;OQ=1008.07;QD=17.38;SB=-481.48 GT:AD:DP:GL:GQ 0/1:28,30:57:-121.27,-17.17,-91.06:99 +chr1 4725752 rs57646199 C T 319.32 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1002.06;QD=17.89;SB=-467.46 GT:AD:DP:GL:GQ 0/1:26,30:56:-120.36,-16.87,-93.54:99 +chr1 4725910 rs2802717 C T 220.45 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=59.68;MQ0=0;OQ=1230.52;QD=17.09;SB=-300.80 GT:AD:DP:GL:GQ 0/1:35,36:70:-147.42,-21.09,-124.52:99 +chr1 4725964 rs2802716 C A 41.54 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=4;HaplotypeScore=0.93;MQ=59.48;MQ0=0;OQ=1484.28;QD=18.55;SB=-734.49 GT:AD:DP:GL:GQ 0/1:32,48:80:-175.81,-24.10,-113.80:99 +chr1 4726365 rs9426502 G A 127.06 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.67;MQ0=0;OQ=1140.71;QD=16.53;SB=-410.70 GT:AD:DP:GL:GQ 0/1:35,34:69:-138.14,-20.78,-128.81:99 +chr1 4726520 rs2743980 G A 355.47 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=1.45;MQ=59.68;MQ0=0;OQ=913.23;QD=12.68;SB=-432.39 GT:AD:DP:GL:GQ 0/1:43,29:72:-116.30,-21.69,-156.11:99 +chr1 4726900 rs7548728 G A 477.89 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=780.16;QD=13.69;SB=-340.47 GT:AD:DP:GL:GQ 0/1:32,25:55:-97.88,-16.58,-97.83:99 +chr1 4727923 rs426095 G A 378.93 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.64;MQ0=0;OQ=878.95;QD=13.73;SB=-378.83 GT:AD:DP:GL:GQ 0/1:36,28:61:-109.56,-18.38,-120.39:99 +chr1 4728243 rs396629 C T 353.19 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.62;MQ0=0;OQ=1145.27;QD=18.77;SB=-564.43 GT:AD:DP:GL:GQ 0/1:27,34:61:-136.20,-18.39,-85.13:99 +chr1 4728440 . G A 47.68 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.39;MQ=58.84;MQ0=0;OQ=1100.89;QD=19.66;SB=-554.66 GT:AD:DP:GL:GQ 0/1:23,33:56:-130.25,-16.88,-72.13:99 +chr1 4730266 rs410413 T C 266.24 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.84;MQ0=0;OQ=500.27;QD=10.01;SB=-265.95 GT:AD:DP:GL:GQ 0/1:25,25:45:-66.88,-13.57,-94.91:99 +chr1 4730269 rs410414 T C 250.89 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=57.08;MQ0=0;OQ=462.87;QD=9.85;SB=-198.61 GT:AD:DP:GL:GQ 0/1:25,22:45:-63.14,-13.57,-96.77:99 +chr1 4730645 rs395467 A G 11.96 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=4.91;MQ=52.28;MQ0=0;OQ=653.20;QD=9.90;SB=-279.13 GT:AD:DP:GL:GQ 0/1:38,27:64:-87.89,-19.29,-148.52:99 +chr1 4730689 rs9426503 G C 129.77 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.89;MQ=56.81;MQ0=0;OQ=1027.62;QD=14.27;SB=-322.37 GT:AD:DP:GL:GQ 0/1:41,31:67:-126.24,-20.20,-160.02:99 +chr1 4730760 rs9426483 C T 334.33 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.53;MQ=58.90;MQ0=0;OQ=750.53;QD=13.65;SB=-332.36 GT:AD:DP:GL:GQ 0/1:31,24:54:-94.60,-16.27,-107.97:99 +chr1 4730936 rs423285 C T 421.63 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=56.95;MQ0=0;OQ=670.76;QD=11.37;SB=-300.79 GT:AD:DP:GL:GQ 0/1:33,25:55:-86.95,-16.59,-101.75:99 +chr1 4730990 rs395508 G A 57.05 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.76;MQ=59.27;MQ0=0;OQ=529.54;QD=9.29;SB=-260.10 GT:AD:DP:GL:GQ 0/1:38,19:53:-72.20,-15.97,-127.10:99 +chr1 4731053 rs418045 T C 525.89 PASS AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=529.19;QD=11.50;SB=-290.44 GT:AD:DP:GL:GQ 0/1:26,20:45:-69.76,-13.55,-105.89:99 +chr1 4731180 rs396112 G A 318.68 PASS AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=740.76;QD=17.64;SB=-379.17 GT:AD:DP:GL:GQ 0/1:19,23:39:-89.12,-11.76,-51.25:99 +chr1 4731341 rs406847 A G 411.20 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.80;MQ0=0;OQ=513.60;QD=14.67;SB=-259.91 GT:AD:DP:GL:GQ 0/1:17,18:35:-65.19,-10.54,-67.57:99 +chr1 4731471 rs428580 C T 186.08 PASS AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=867.64;QD=20.18;SB=-459.01 GT:AD:DP:GL:GQ 0/1:17,26:42:-102.70,-12.65,-55.85:99 +chr1 4731684 rs407301 C T 107.33 PASS AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=57.23;MQ0=0;OQ=697.47;QD=20.51;SB=-327.88 GT:AD:DP:GL:GQ 0/1:12,22:33:-82.98,-9.95,-39.91:99 +chr1 4732014 . T A 875.95 Indel AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=12.12;MQ=51.16;MQ0=0;QD=14.13;SB=-350.44 GT:AD:DP:GL:GQ 0/1:31,31:60:-108.95,-18.08,-110.80:99 +chr1 4732015 . T A 970.99 Indel AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=9;HaplotypeScore=12.28;MQ=51.00;MQ0=0;QD=15.92;SB=-364.45 GT:AD:DP:GL:GQ 0/1:29,32:58:-117.85,-17.47,-98.32:99 +chr1 4733241 rs414434 G C 239.58 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1334.69;QD=20.22;SB=-556.62 GT:AD:DP:GL:GQ 0/1:28,38:63:-155.75,-19.00,-107.17:99 +chr1 4734056 rs9426504 G A 5.32 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=4;HaplotypeScore=2.44;MQ=58.18;MQ0=0;OQ=895.74;QD=16.59;SB=-312.82 GT:AD:DP:GL:GQ 0/1:25,29:51:-108.23,-15.38,-75.31:99 +chr1 4734062 rs451162 G C 249.29 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.31;MQ=58.57;MQ0=0;OQ=977.80;QD=18.80;SB=-417.05 GT:AD:DP:GL:GQ 0/1:24,28:49:-115.83,-14.77,-93.28:99 +chr1 4734089 rs388631 T C 200.06 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.48;MQ=59.01;MQ0=0;OQ=598.20;QD=12.73;SB=-188.41 GT:AD:DP:GL:GQ 0/1:21,25:44:-76.37,-13.27,-78.74:99 +chr1 4734466 rs389959 T C 132.65 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.40;MQ=60.00;MQ0=0;OQ=323.31;QD=6.22;SB=-138.87 GT:AD:DP:GL:GQ 0/1:33,18:48:-50.08,-14.47,-128.38:99 +chr1 4734711 rs397852 T C 337.97 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.07;MQ=60.00;MQ0=0;OQ=458.03;QD=9.35;SB=-228.25 GT:AD:DP:GL:GQ 0/1:29,20:49:-63.86,-14.77,-115.16:99 +chr1 4735235 rs399377 T C 222.18 PASS AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=339.75;QD=9.71;SB=-124.62 GT:AD:DP:GL:GQ 0/1:21,14:33:-47.20,-9.94,-76.89:99 +chr1 4735981 rs394594 A G 305.79 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=773.72;QD=10.46;SB=-332.92 GT:AD:DP:GL:GQ 0/1:41,33:73:-102.66,-22.01,-163.48:99 +chr1 4738101 rs414909 C T 441.62 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1084.42;QD=16.19;SB=-452.94 GT:AD:DP:GL:GQ 0/1:35,32:67:-131.91,-20.18,-129.56:99 +chr1 4738908 rs381304 A G 65.84 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=2.37;MQ=58.77;MQ0=0;OQ=1458.03;QD=16.76;SB=-529.55 GT:AD:DP:GL:GQ 0/1:36,51:84:-174.40,-25.31,-140.93:99 +chr1 4739028 rs392984 T C 105.21 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=5.08;MQ=58.80;MQ0=0;OQ=588.16;QD=10.14;SB=-181.39 GT:AD:DP:GL:GQ 0/1:30,28:53:-78.07,-15.97,-115.29:99 +chr1 4739512 rs2802719 A G 384.48 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.81;MQ0=0;OQ=757.23;QD=14.85;SB=-244.45 GT:AD:DP:GL:GQ 0/1:23,28:48:-93.47,-14.47,-78.98:99 +chr1 4739710 rs2802718 G C 11.18 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=3;HaplotypeScore=0.83;MQ=56.67;MQ0=0;OQ=1199.49;QD=18.74;SB=-370.48 GT:AD:DP:GL:GQ 0/1:31,33:60:-141.32,-18.09,-113.09:99 +chr1 4740018 rs7544523 T C 161.93 PASS AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=58.16;MQ0=0;OQ=429.98;QD=11.94;SB=-175.51 GT:AD:DP:GL:GQ 0/1:18,18:35:-56.83,-10.55,-68.38:99 +chr1 4744236 rs9426506 C T 327.10 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.29;MQ=58.57;MQ0=0;OQ=856.13;QD=13.81;SB=-428.92 GT:AD:DP:GL:GQ 0/1:35,27:62:-107.57,-18.68,-125.85:99 +chr1 4744972 rs9426484 G A 347.64 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.65;MQ0=0;OQ=799.48;QD=12.30;SB=-407.88 GT:AD:DP:GL:GQ 0/1:38,27:60:-101.32,-18.09,-111.41:99 +chr1 4745752 rs6426434 G A 271.15 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=60.00;MQ0=0;OQ=1169.68;QD=19.49;SB=-538.80 GT:AD:DP:GL:GQ 0/1:24,36:57:-137.43,-17.18,-72.34:99 +chr1 4747705 rs4654460 G A 332.93 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=755.91;QD=18.90;SB=-379.91 GT:AD:DP:GL:GQ 0/1:17,23:38:-90.34,-11.46,-46.09:99 +chr1 4748668 rs12133924 A G 455.19 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1019.13;QD=13.07;SB=-468.04 GT:AD:DP:GL:GQ 0/1:42,36:77:-128.39,-23.20,-162.75:99 +chr1 4748969 rs6701069 A G 376.11 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.72;MQ0=0;OQ=1003.27;QD=12.39;SB=-469.20 GT:AD:DP:GL:GQ 0/1:46,35:80:-127.71,-24.10,-182.44:99 +chr1 4749244 rs2235438 T C 581.54 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=891.88;QD=13.12;SB=-467.00 GT:AD:DP:GL:GQ 0/1:32,36:65:-112.06,-19.59,-124.79:99 +chr1 4750683 rs909757 T C 410.80 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.22;MQ0=0;OQ=683.00;QD=11.78;SB=-347.56 GT:AD:DP:GL:GQ 0/1:31,27:55:-88.15,-16.57,-119.32:99 +chr1 4751405 rs17345239 T G 179.05 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=774.24;QD=13.12;SB=-344.85 GT:AD:DP:GL:GQ 0/1:30,29:56:-97.57,-16.87,-106.85:99 +chr1 4753272 rs742246 A C 355.98 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=617.26;QD=14.03;SB=-196.34 GT:AD:DP:GL:GQ 0/1:21,23:43:-77.96,-12.95,-77.17:99 +chr1 4753548 rs932350 T C 408.09 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.22;MQ0=0;OQ=924.37;QD=14.22;SB=-295.30 GT:AD:DP:GL:GQ 0/1:29,36:64:-115.01,-19.29,-116.32:99 +chr1 4753607 rs12082538 G C 138.47 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=3.84;MQ=60.48;MQ0=0;OQ=606.35;QD=13.47;SB=-132.52 GT:AD:DP:GL:GQ 0/1:25,20:43:-76.88,-12.96,-107.57:99 +chr1 4753770 rs7519688 C T 2.09 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=3;HaplotypeScore=5.33;MQ=59.09;MQ0=0;OQ=802.41;QD=15.73;SB=-282.79 GT:AD:DP:GL:GQ 0/1:25,26:48:-97.99,-14.47,-73.03:99 +chr1 4755384 rs727906 C T 371.77 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.67;MQ=60.00;MQ0=0;OQ=954.50;QD=12.40;SB=-422.82 GT:AD:DP:GL:GQ 0/1:47,30:76:-121.64,-22.91,-153.23:99 +chr1 4756029 rs2411946 T A 426.26 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.59;MQ0=0;OQ=610.43;QD=13.57;SB=-308.69 GT:AD:DP:GL:GQ 0/1:23,22:44:-77.58,-13.26,-87.22:99 +chr1 4756791 rs760816 A G 307.58 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=2.08;MQ=60.00;MQ0=0;OQ=644.43;QD=11.51;SB=-270.35 GT:AD:DP:GL:GQ 0/1:29,27:54:-84.00,-16.27,-113.95:99 +chr1 4758251 . A G 4.99 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=3;HaplotypeScore=0.95;MQ=59.34;MQ0=1;OQ=796.90;QD=10.77;SB=-383.18 GT:AD:DP:GL:GQ 0/1:42,32:64:-102.26,-19.28,-139.02:99 +chr1 4758268 rs4654606 T G 84.96 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.06;MQ=59.35;MQ0=0;OQ=681.65;QD=10.65;SB=-311.85 GT:AD:DP:GL:GQ 0/1:38,26:61:-89.83,-18.38,-124.54:99 +chr1 4759471 rs2142949 C T 488.93 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=986.38;QD=17.01;SB=-326.41 GT:AD:DP:GL:GQ 0/1:27,31:57:-119.09,-17.17,-96.06:99 +chr1 4761020 rs4654607 C T 187.79 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=1317.32;QD=16.67;SB=-650.17 GT:AD:DP:GL:GQ 0/1:40,39:77:-158.21,-23.19,-137.71:99 +chr1 4763236 rs2064168 C T 278.30 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1185.65;QD=19.12;SB=-513.73 GT:AD:DP:GL:GQ 0/1:25,37:60:-139.92,-18.08,-90.33:99 +chr1 4763773 rs760817 T C 455.12 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.94;MQ=59.11;MQ0=0;OQ=932.67;QD=12.78;SB=-440.55 GT:AD:DP:GL:GQ 0/1:40,33:73:-118.54,-21.99,-163.26:99 +chr1 4764845 rs10915606 A G 585.97 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1075.05;QD=14.15;SB=-528.93 GT:AD:DP:GL:GQ 0/1:37,39:74:-133.08,-22.29,-148.56:99 +chr1 4765718 rs10429868 G A 452.05 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1155.78;QD=15.62;SB=-602.60 GT:AD:DP:GL:GQ 0/1:39,35:74:-141.15,-22.29,-141.78:99 +chr1 4766001 rs12022466 T A 597.92 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1259.06;QD=15.94;SB=-558.66 GT:AD:DP:GL:GQ 0/1:39,40:79:-152.98,-23.79,-151.51:99 +chr1 4766045 . G A 13.96 PASS AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1207.52;QD=14.55;SB=-582.08 GT:AD:DP:GL:GQ 0/1:47,36:81:-148.43,-24.40,-164.42:99 +chr1 4766280 rs12752806 G T 477.99 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.50;MQ0=0;OQ=1250.24;QD=15.06;SB=-480.84 GT:AD:DP:GL:GQ 0/1:42,41:81:-152.70,-24.39,-146.62:99 +chr1 4767409 rs7534770 A T 437.84 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1042.20;QD=14.28;SB=-531.39 GT:AD:DP:GL:GQ 0/1:39,34:72:-129.19,-21.69,-145.29:99 +chr1 4767544 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=6;HaplotypeScore=47.32;MQ=56.17;MQ0=2;OQ=190.67;QD=2.98;SB=86.31 GT:AD:DP:GL:GQ 0/1:48,16:57:-39.52,-17.17,-173.24:99 +chr1 4769118 rs10915610 A C 208.85 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=4.78;MQ=58.87;MQ0=0;OQ=1164.63;QD=14.93;SB=-551.67 GT:AD:DP:GL:GQ 0/1:37,39:77:-145.10,-25.36,-142.76:99 +chr1 4770972 . C A 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=2;HaplotypeScore=8.28;MQ=56.35;MQ0=0;OQ=111.37;QD=1.89;SB=65.23 GT:AD:DP:GL:GQ 0/1:35,24:40:-26.47,-12.05,-113.84:99 +chr1 4771531 rs1118009 A G 323.35 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=56.74;MQ0=0;OQ=1333.25;QD=15.32;SB=-605.42 GT:AD:DP:GL:GQ 0/1:38,49:86:-162.53,-25.92,-151.96:99 +chr1 4771617 rs1118010 C T 407.70 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=60.00;MQ0=0;OQ=1431.00;QD=18.58;SB=-550.33 GT:AD:DP:GL:GQ 0/1:34,43:77:-169.58,-23.20,-123.43:99 +chr1 4772431 rs10799262 G A 68.65 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=0.32;MQ=59.76;MQ0=0;OQ=1610.76;QD=20.65;SB=-755.30 GT:AD:DP:GL:GQ 0/1:32,46:78:-187.86,-23.50,-115.14:99 +chr1 4772511 rs10915611 C T 585.75 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1219.72;QD=17.42;SB=-547.54 GT:AD:DP:GL:GQ 0/1:34,36:70:-146.34,-21.08,-121.82:99 +chr1 4772916 rs10915612 A G 195.17 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=58.68;MQ0=0;OQ=1058.43;QD=15.80;SB=-539.98 GT:AD:DP:GL:GQ 0/1:30,37:67:-129.31,-20.19,-122.36:99 +chr1 4773270 rs7540367 G A 242.80 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.44;MQ0=0;OQ=792.22;QD=13.66;SB=-213.92 GT:AD:DP:GL:GQ 0/1:33,25:57:-99.68,-17.18,-105.56:99 +chr1 4773658 . G A 112.25 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.50;MQ0=0;OQ=985.30;QD=17.59;SB=-495.06 GT:AD:DP:GL:GQ 0/1:26,30:55:-118.38,-16.57,-94.83:99 +chr1 4773754 rs12120205 T A 372.54 PASS AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1585.82;QD=16.18;SB=-556.42 GT:AD:DP:GL:GQ 0/1:49,49:98:-191.38,-29.51,-188.67:99 +chr1 4774287 rs10799263 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=7;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1045.47;QD=15.84;SB=-449.52 GT:AD:DP:GL:GQ 0/1:30,36:65:-127.41,-19.58,-109.32:99 +chr1 4774365 rs10915613 G A 361.24 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1223.17;QD=16.31;SB=-630.64 GT:AD:DP:GL:GQ 0/1:38,37:73:-147.61,-22.01,-118.37:99 +chr1 4776755 rs12145180 C G 356.13 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=59.64;MQ0=0;OQ=975.57;QD=15.24;SB=-415.28 GT:AD:DP:GL:GQ 0/1:32,32:62:-119.54,-18.70,-139.99:99 +chr1 4776903 rs10915615 C A 330.11 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=59.69;MQ0=0;OQ=909.18;QD=12.12;SB=-404.10 GT:AD:DP:GL:GQ 0/1:43,32:72:-115.90,-21.70,-128.82:99 +chr1 4777460 rs12118812 T G 167.49 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=842.15;QD=11.86;SB=-431.75 GT:AD:DP:GL:GQ 0/1:41,30:70:-108.58,-21.08,-144.58:99 +chr1 4777525 rs12118818 T G 101.66 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=59.72;MQ0=0;OQ=940.16;QD=13.63;SB=-473.22 GT:AD:DP:GL:GQ 0/1:36,33:67:-117.48,-20.18,-125.31:99 +chr1 4777535 rs12143219 G T 70.17 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=4;HaplotypeScore=0.27;MQ=60.00;MQ0=0;OQ=1005.40;QD=15.47;SB=-447.46 GT:AD:DP:GL:GQ 0/1:32,33:65:-123.40,-19.58,-114.32:99 +chr1 4778731 rs1120120 C T 347.86 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=1.94;MQ=59.78;MQ0=0;OQ=1277.01;QD=15.02;SB=-471.94 GT:AD:DP:GL:GQ 0/1:47,38:84:-156.28,-25.30,-171.76:99 +chr1 4780340 rs10915616 C T 196.28 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=881.43;QD=16.95;SB=-113.96 GT:AD:DP:GL:GQ 0/1:26,26:52:-107.09,-15.66,-92.07:99 +chr1 4780435 rs12121890 T C 347.71 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.73;MQ0=0;OQ=1105.50;QD=16.26;SB=-426.60 GT:AD:DP:GL:GQ 0/1:30,38:67:-134.02,-20.18,-117.11:99 +chr1 4781127 rs12122126 T C 314.12 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.69;MQ0=0;OQ=674.99;QD=13.50;SB=-298.62 GT:AD:DP:GL:GQ 0/1:26,24:49:-85.54,-14.76,-106.72:99 +chr1 4781899 rs12117810 G A 242.85 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=58.88;MQ0=0;OQ=1031.36;QD=17.78;SB=-437.45 GT:AD:DP:GL:GQ 0/1:28,30:56:-123.30,-16.88,-83.86:99 +chr1 4782182 rs10915619 A T 438.63 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=58.65;MQ0=0;OQ=1009.97;QD=12.47;SB=-431.43 GT:AD:DP:GL:GQ 0/1:47,34:80:-128.38,-24.10,-172.98:99 +chr1 4782516 rs1883345 G A 146.28 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.45;MQ0=0;OQ=906.47;QD=11.93;SB=-338.27 GT:AD:DP:GL:GQ 0/1:44,32:71:-115.32,-21.39,-152.63:99 +chr1 4782885 rs1883346 T A 397.96 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.70;MQ=58.75;MQ0=0;OQ=1064.02;QD=14.99;SB=-456.50 GT:AD:DP:GL:GQ 0/1:37,34:70:-130.77,-21.08,-141.61:99 +chr1 4782955 rs1883347 T C 221.56 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=4.24;MQ=59.50;MQ0=0;OQ=856.09;QD=11.57;SB=-450.96 GT:AD:DP:GL:GQ 0/1:43,30:73:-110.88,-21.99,-176.74:99 +chr1 4783491 rs4654610 T C 960.35 Indel AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=11.46;MQ=47.61;MQ0=0;QD=14.12;SB=-407.25 GT:AD:DP:GL:GQ 0/1:31,37:63:-118.30,-18.98,-112.03:99 +chr1 4793106 rs61766789 G A 240.39 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.34;MQ=58.98;MQ0=1;OQ=1230.74;QD=17.33;SB=-554.58 GT:AD:DP:GL:GQ 0/1:35,36:69:-147.14,-20.78,-120.71:99 +chr1 4794663 . C T 274.23 PASS AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=833.44;QD=12.63;SB=-440.37 GT:AD:DP:GL:GQ 0/1:40,26:66:-106.51,-19.88,-144.25:99 +chr1 4794952 rs12074481 C A 271.91 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=57.82;MQ0=0;OQ=1066.30;QD=15.02;SB=-452.97 GT:AD:DP:GL:GQ 0/1:33,38:69:-130.70,-20.79,-110.83:99 +chr1 4798693 rs7522386 A G 341.25 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.98;MQ=58.39;MQ0=0;OQ=1056.56;QD=15.77;SB=-495.12 GT:AD:DP:GL:GQ 0/1:31,36:65:-128.52,-19.58,-122.92:99 +chr1 4801597 rs7527319 C A 582.07 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=923.07;QD=13.78;SB=-344.17 GT:AD:DP:GL:GQ 0/1:34,33:66:-115.47,-19.88,-121.89:99 +chr1 4806096 rs7547779 T C 457.63 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.53;MQ0=0;OQ=897.02;QD=13.39;SB=-364.21 GT:AD:DP:GL:GQ 0/1:34,33:65:-112.57,-19.58,-135.93:99 +chr1 4807563 rs11582327 T C 467.91 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.73;MQ0=0;OQ=911.00;QD=13.40;SB=-422.86 GT:AD:DP:GL:GQ 0/1:32,36:67:-114.58,-20.19,-127.73:99 +chr1 4807672 rs7536960 T C 326.99 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=60.00;MQ0=0;OQ=720.71;QD=12.64;SB=-286.29 GT:AD:DP:GL:GQ 0/1:27,30:55:-91.93,-16.58,-105.91:99 +chr1 4808516 rs6669130 G A 323.43 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=59.98;MQ0=0;OQ=1529.46;QD=17.58;SB=-724.76 GT:AD:DP:GL:GQ 0/1:42,45:83:-181.23,-25.00,-146.35:99 +chr1 4808719 . T G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=2;HaplotypeScore=4.69;MQ=58.91;MQ0=0;OQ=57.76;QD=0.90;SB=95.29 GT:AD:DP:GL:GQ 0/1:40,24:48:-23.52,-14.46,-139.84:90.60 +chr1 4808761 rs6683849 A G 156.55 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=737.58;QD=13.17;SB=-272.54 GT:AD:DP:GL:GQ 0/1:30,26:56:-93.91,-16.87,-119.65:99 +chr1 4808953 rs12725011 G A 96.81 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=3;HaplotypeScore=1.25;MQ=59.67;MQ0=0;OQ=1362.18;QD=19.46;SB=-645.68 GT:AD:DP:GL:GQ 0/1:29,41:69:-160.29,-20.79,-101.64:99 +chr1 4808976 rs11582462 A G 74 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=3.61;MQ=59.32;MQ0=0;OQ=923.86;QD=13.59;SB=-481.59 GT:AD:DP:GL:GQ 0/1:33,35:64:-114.94,-19.28,-135.51:99 +chr1 4809567 rs11582936 A C 302.66 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.32;MQ=59.67;MQ0=0;OQ=605.80;QD=10.63;SB=-281.94 GT:AD:DP:GL:GQ 0/1:26,30:52:-79.53,-15.67,-97.13:99 +chr1 4809668 rs7543326 T C 173.23 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=2;HaplotypeScore=1.68;MQ=59.71;MQ0=0;OQ=1092.10;QD=13.82;SB=-474.60 GT:AD:DP:GL:GQ 0/1:37,42:79:-136.31,-23.81,-148.02:99 +chr1 4811032 rs6693945 T C 292.95 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=59.41;MQ0=0;OQ=916.53;QD=14.55;SB=-321.25 GT:AD:DP:GL:GQ 0/1:30,31:62:-117.13,-22.19,-125.33:99 +chr1 4811983 rs2209167 G A 414.43 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=59.70;MQ0=0;OQ=1021.76;QD=13.10;SB=-414.40 GT:AD:DP:GL:GQ 0/1:45,33:75:-128.08,-22.62,-135.03:99 +chr1 4813003 rs6426439 C T 133.12 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=3.37;MQ=59.50;MQ0=0;OQ=1367.37;QD=18.48;SB=-705.27 GT:AD:DP:GL:GQ 0/1:34,40:72:-161.71,-21.69,-122.06:99 +chr1 4813419 rs1886113 T G 294.59 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=612.34;QD=12.76;SB=-248.40 GT:AD:DP:GL:GQ 0/1:25,23:47:-78.67,-14.15,-95.57:99 +chr1 4813733 rs10915628 T C 146.41 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=870.49;QD=12.26;SB=-270.52 GT:AD:DP:GL:GQ 0/1:41,30:71:-111.72,-21.39,-167.00:99 +chr1 4813800 rs10915631 C T 467.08 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=60.00;MQ0=0;OQ=1109.44;QD=15.20;SB=-509.01 GT:AD:DP:GL:GQ 0/1:39,34:73:-136.22,-21.99,-139.36:99 +chr1 4813826 rs10799266 A G 440.81 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=1025.69;QD=13.50;SB=-528.56 GT:AD:DP:GL:GQ 0/1:40,36:76:-128.75,-22.90,-159.57:99 +chr1 4814770 rs6426440 C A 361.03 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=60.00;MQ0=0;OQ=964.05;QD=12.68;SB=-378.13 GT:AD:DP:GL:GQ 0/1:42,34:76:-122.59,-22.91,-131.06:99 +chr1 4814802 rs6426441 A T 191.96 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=5.04;MQ=59.57;MQ0=0;OQ=882.35;QD=13.17;SB=-416.80 GT:AD:DP:GL:GQ 0/1:37,30:65:-111.10,-19.58,-134.21:99 +chr1 4815146 rs2411949 G T 0.34 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=15.15;MQ=59.31;MQ0=0;OQ=1233.12;QD=16.23;SB=-582.79 GT:AD:DP:GL:GQ 0/1:35,40:72:-148.29,-21.69,-101.37:99 +chr1 4815330 rs6658680 A G 154.72 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=57.17;MQ0=0;OQ=454.29;QD=9.09;SB=-126.50 GT:AD:DP:GL:GQ 0/1:29,21:47:-62.88,-14.17,-108.85:99 +chr1 4815340 rs6692964 G T 169.92 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=56.50;MQ0=0;OQ=607.11;QD=11.90;SB=-203.41 GT:AD:DP:GL:GQ 0/1:29,22:51:-79.35,-15.36,-103.70:99 +chr1 4815344 rs6692966 G A 446.58 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.57;MQ0=0;OQ=669.90;QD=12.88;SB=-297.81 GT:AD:DP:GL:GQ 0/1:28,24:50:-85.35,-15.08,-90.67:99 +chr1 4815634 rs2147028 C A 82.12 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=1.79;MQ=59.43;MQ0=0;OQ=1001.39;QD=15.41;SB=-277.32 GT:AD:DP:GL:GQ 0/1:32,33:62:-122.10,-18.67,-102.09:99 +chr1 4815904 rs2209166 G A 117.08 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=60.00;MQ0=0;OQ=1754.50;QD=22.21;SB=-892.01 GT:AD:DP:GL:GQ 0/1:28,51:79:-202.53,-23.80,-99.82:99 +chr1 4816064 rs6693706 G T 446.40 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.64;MQ0=0;OQ=733.52;QD=14.11;SB=-350.37 GT:AD:DP:GL:GQ 0/1:26,26:52:-92.30,-15.67,-93.55:99 +chr1 4816465 rs1535736 C T 112.29 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=1112.33;QD=17.38;SB=-338.80 GT:AD:DP:GL:GQ 0/1:31,33:64:-133.80,-19.28,-110.54:99 +chr1 4816766 rs1535734 A G 420.29 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=908.64;QD=12.62;SB=-359.52 GT:AD:DP:GL:GQ 0/1:39,33:70:-115.23,-21.09,-156.36:99 +chr1 4817101 rs6693352 A G 227.39 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=3.08;MQ=59.68;MQ0=0;OQ=949.71;QD=13.19;SB=-443.55 GT:AD:DP:GL:GQ 0/1:38,34:70:-119.35,-21.09,-147.05:99 +chr1 4817128 rs2898848 G A 216.99 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=1195.65;QD=16.61;SB=-558.57 GT:AD:DP:GL:GQ 0/1:36,36:72:-144.54,-21.69,-131.83:99 +chr1 4817320 rs2209165 C T 145.82 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.39;MQ0=0;OQ=1415.52;QD=20.82;SB=-731.10 GT:AD:DP:GL:GQ 0/1:27,41:68:-165.32,-20.49,-90.68:99 +chr1 4817405 rs2209164 A G 118.02 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.63;MQ0=0;OQ=527.84;QD=8.51;SB=-187.44 GT:AD:DP:GL:GQ 0/1:40,22:60:-74.14,-18.07,-157.62:99 +chr1 4817514 rs2209163 G A 238.41 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=933.49;QD=13.93;SB=-217.50 GT:AD:DP:GL:GQ 0/1:38,29:66:-116.53,-19.90,-117.09:99 +chr1 4817749 rs3938469 A G 107.60 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=486.41;QD=8.11;SB=-117.18 GT:AD:DP:GL:GQ 0/1:41,19:60:-70.00,-18.07,-168.54:99 +chr1 4817969 rs2093769 G A 229.16 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.14;MQ=59.44;MQ0=0;OQ=1190.09;QD=14.51;SB=-381.33 GT:AD:DP:GL:GQ 0/1:44,38:79:-146.09,-23.80,-153.77:99 +chr1 4818044 rs2093768 A G 314.22 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.33;MQ0=0;OQ=811.36;QD=13.09;SB=-280.55 GT:AD:DP:GL:GQ 0/1:29,33:61:-102.81,-18.39,-114.06:99 +chr1 4818509 rs10159142 G A 308.93 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.55;MQ=58.95;MQ0=0;OQ=899.59;QD=15.51;SB=-448.42 GT:AD:DP:GL:GQ 0/1:30,28:58:-110.72,-17.47,-107.08:99 +chr1 4818666 rs10799268 T C 278.30 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=59.42;MQ0=0;OQ=887.47;QD=13.87;SB=-404.24 GT:AD:DP:GL:GQ 0/1:33,31:62:-110.70,-18.67,-130.15:99 +chr1 4818872 rs10753387 T C 88.47 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.63;MQ=55.54;MQ0=0;OQ=718.25;QD=13.30;SB=-324.13 GT:AD:DP:GL:GQ 0/1:25,29:53:-91.08,-15.98,-99.45:99 +chr1 4819100 rs10753388 G A 0.17 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=17.64;MQ=55.33;MQ0=0;OQ=1324.27;QD=17.66;SB=-679.33 GT:AD:DP:GL:GQ 0/1:36,39:70:-156.80,-21.09,-111.06:99 +chr1 4819163 rs10753389 A G 70.61 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=49.63;MQ0=1;OQ=764.05;QD=12.53;SB=-256.89 GT:AD:DP:GL:GQ 0/1:33,28:59:-97.46,-17.77,-133.52:99 +chr1 4819348 rs10915632 G A 8.54 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=2;HaplotypeScore=6.46;MQ=58.48;MQ0=0;OQ=1415.77;QD=15.91;SB=-658.28 GT:AD:DP:GL:GQ 0/1:47,42:87:-171.06,-26.20,-164.95:99 +chr1 4819622 rs10799269 C G 347.45 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=59.05;MQ0=0;OQ=934.79;QD=12.98;SB=-429.59 GT:AD:DP:GL:GQ 0/1:41,31:69:-117.56,-20.80,-181.53:99 +chr1 4819655 rs10799270 G A 353.44 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.56;MQ0=0;OQ=1064.88;QD=14.39;SB=-436.38 GT:AD:DP:GL:GQ 0/1:41,33:74:-132.06,-22.29,-148.73:99 +chr1 4819737 rs2147027 T C 200.63 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.22;MQ=55.94;MQ0=0;OQ=778.52;QD=14.69;SB=-321.29 GT:AD:DP:GL:GQ 0/1:25,28:51:-96.50,-15.36,-95.69:99 +chr1 4820060 rs2181701 T C 0.91 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=11.39;MQ=52.25;MQ0=0;OQ=485.51;QD=9.52;SB=-244.48 GT:AD:DP:GL:GQ 0/1:29,22:49:-66.61,-14.77,-110.48:99 +chr1 4820091 rs4265399 G A 243.46 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=50.14;MQ0=0;OQ=512.92;QD=10.06;SB=-45.99 GT:AD:DP:GL:GQ 0/1:32,19:48:-69.05,-14.48,-96.83:99 +chr1 4820096 rs2181700 T G 75.96 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=50.99;MQ0=0;OQ=433.90;QD=8.34;SB=-40.01 GT:AD:DP:GL:GQ 0/1:33,19:51:-62.03,-15.36,-122.01:99 +chr1 4820154 rs9725470 C T 281.54 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.90;MQ0=2;OQ=495.62;QD=9.01;SB=-102.52 GT:AD:DP:GL:GQ 0/1:37,18:51:-68.22,-15.38,-108.69:99 +chr1 4820216 rs9726479 T G 79.72 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.15;MQ=45.62;MQ0=0;OQ=697.41;QD=12.24;SB=-299.44 GT:AD:DP:GL:GQ 0/1:30,27:55:-89.59,-16.56,-110.14:99 +chr1 4820227 rs9725796 C A 40.52 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=3;HaplotypeScore=0.33;MQ=47.59;MQ0=0;OQ=717.90;QD=11.58;SB=-300.16 GT:AD:DP:GL:GQ 0/1:34,28:59:-92.84,-17.77,-118.69:99 +chr1 4820388 rs9726805 T C 201.46 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=2.98;MQ=51.02;MQ0=0;OQ=985.45;QD=12.17;SB=-457.03 GT:AD:DP:GL:GQ 0/1:42,39:76:-124.72,-22.89,-168.04:99 +chr1 4820748 . A G 1.13 PASS AC=1;AF=0.50;AN=2;DP=50;Dels=0.00;HRun=0;HaplotypeScore=3.54;MQ=35.53;MQ0=6;OQ=268.28;QD=5.37;SB=-1.83 GT:AD:DP:GL:GQ 0/1:28,21:34:-40.35,-10.24,-88.65:99 +chr1 4820850 . T C 0.21 PASS AC=1;AF=0.50;AN=2;DP=27;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=43.66;MQ0=1;OQ=84.14;QD=3.12;SB=-53.32 GT:AD:DP:GL:GQ 0/1:14,12:16:-16.52,-4.83,-39.77:99 +chr1 4820858 . G A 0.93 PASS AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=4.23;MQ=41.11;MQ0=1;OQ=153.45;QD=5.29;SB=-40.65 GT:AD:DP:GL:GQ 0/1:13,15:17:-23.75,-5.12,-38.01:99 +chr1 4820952 rs61766808 C T 152.82 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=38.70;MQ0=1;OQ=409.25;QD=9.09;SB=-225.93 GT:AD:DP:GL:GQ 0/1:30,15:42:-56.86,-12.66,-95.36:99 +chr1 4821240 rs9726227 C T 470.14 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=37.63;MQ0=1;OQ=887.90;QD=12.87;SB=-408.68 GT:AD:DP:GL:GQ 0/1:36,33:62:-110.75,-18.67,-130.57:99 +chr1 4821376 rs9726241 C A 8.68 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=39.07;MQ0=5;OQ=305.92;QD=4.86;SB=-1.55 GT:AD:DP:GL:GQ 0/1:37,26:47:-48.04,-14.16,-121.88:99 +chr1 4821609 rs9726885 A C 47.17 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=36.89;MQ0=14;OQ=448.17;QD=5.67;SB=-207.28 GT:AD:DP:GL:GQ 0/1:47,32:61:-66.47,-18.37,-159.23:99 +chr1 4821773 rs9726925 A G 101.03 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=38.22;MQ0=2;OQ=859.75;QD=9.35;SB=-417.48 GT:AD:DP:GL:GQ 0/1:47,45:74:-111.55,-22.29,-173.37:99 +chr1 4821818 rs12135318 C A 320.75 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=44.85;MQ0=0;OQ=1111.50;QD=12.21;SB=-470.83 GT:AD:DP:GL:GQ 0/1:41,50:79:-138.22,-23.79,-149.34:99 +chr1 4821875 rs10915634 A G 55.48 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=46.72;MQ0=5;OQ=657.16;QD=7.64;SB=-166.48 GT:AD:DP:GL:GQ 0/1:46,40:75:-91.61,-22.61,-188.45:99 +chr1 4822060 rs7411909 A G 472.44 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.58;MQ0=0;OQ=844.08;QD=14.07;SB=-331.93 GT:AD:DP:GL:GQ 0/1:31,29:60:-105.77,-18.08,-125.13:99 +chr1 4822115 rs4617370 G A 221.57 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=59.00;MQ0=0;OQ=1387.37;QD=17.13;SB=-675.38 GT:AD:DP:GL:GQ 0/1:40,41:81:-166.44,-24.42,-127.76:99 +chr1 4822681 rs6660173 C T 0.10 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.01;HRun=3;HaplotypeScore=10.96;MQ=52.45;MQ0=0;OQ=1014.70;QD=13.71;SB=-426.92 GT:AD:DP:GL:GQ 0/1:42,31:73:-126.44,-21.69,-150.88:99 +chr1 4822687 rs6660177 C A 163.11 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=4.00;MQ=52.56;MQ0=0;OQ=900.97;QD=12.01;SB=-430.11 GT:AD:DP:GL:GQ 0/1:44,31:74:-115.67,-22.28,-156.45:99 +chr1 4822710 rs6668068 T C 72.65 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=2.96;MQ=50.82;MQ0=0;OQ=906.69;QD=11.78;SB=-477.93 GT:AD:DP:GL:GQ 0/1:44,33:75:-116.54,-22.59,-176.01:99 +chr1 4822958 rs6665282 A G 464.18 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.16;MQ0=0;OQ=785.44;QD=13.78;SB=-331.28 GT:AD:DP:GL:GQ 0/1:30,27:57:-99.00,-17.17,-122.67:99 +chr1 4823049 rs6665388 A G 56.61 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=2.47;MQ=55.61;MQ0=0;OQ=907.22;QD=12.60;SB=-445.14 GT:AD:DP:GL:GQ 0/1:36,36:67:-114.19,-20.18,-139.94:99 +chr1 4823137 rs12087020 A G 358.36 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=54.38;MQ0=0;OQ=1125.73;QD=15.86;SB=-588.93 GT:AD:DP:GL:GQ 0/1:32,39:69:-136.64,-20.78,-130.19:99 +chr1 4823207 rs10915638 C T 285.22 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=57.74;MQ0=0;OQ=1338.14;QD=15.93;SB=-487.03 GT:AD:DP:GL:GQ 0/1:44,40:82:-161.79,-24.70,-152.84:99 +chr1 4823247 rs10915639 C T 70.93 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=3;HaplotypeScore=1.40;MQ=59.24;MQ0=0;OQ=1272.31;QD=17.19;SB=-602.12 GT:AD:DP:GL:GQ 0/1:37,37:73:-152.51,-22.00,-119.03:99 +chr1 4823334 rs10915640 G T 485.36 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.40;MQ0=0;OQ=978.54;QD=13.05;SB=-397.99 GT:AD:DP:GL:GQ 0/1:40,35:71:-122.52,-21.38,-136.84:99 +chr1 4823422 rs10915641 G A 453.84 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=45.14;MQ0=3;OQ=955.26;QD=11.79;SB=-332.42 GT:AD:DP:GL:GQ 0/1:46,35:73:-120.80,-21.99,-150.35:99 +chr1 4824006 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=60;Dels=0.03;HRun=20;HaplotypeScore=17.44;MQ=44.47;MQ0=0;OQ=216.45;QD=3.61;SB=56.16 GT:AD:DP:GL:GQ 0/1:34,24:43:-37.29,-12.36,-108.08:99 +chr1 4824255 rs6656943 G A 241.34 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=48.13;MQ0=0;OQ=486.99;QD=9.37;SB=-207.48 GT:AD:DP:GL:GQ 0/1:29,22:45:-65.55,-13.57,-87.60:99 +chr1 4824523 rs6674586 T A 163.54 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=48.28;MQ0=0;OQ=656.95;QD=12.17;SB=-109.40 GT:AD:DP:GL:GQ 0/1:27,27:47:-83.14,-14.16,-95.96:99 +chr1 4824573 rs6674680 T C 13.56 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=52.32;MQ0=0;OQ=270.57;QD=5.11;SB=-156.88 GT:AD:DP:GL:GQ 0/1:35,18:46:-44.20,-13.86,-137.80:99 +chr1 4824574 . G A 7.24 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=52.42;MQ0=0;OQ=361.86;QD=6.83;SB=-143.57 GT:AD:DP:GL:GQ 0/1:34,19:46:-53.32,-13.85,-117.68:99 +chr1 4824682 rs12135493 G A 249.33 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=51.42;MQ0=1;OQ=988.12;QD=12.83;SB=-444.35 GT:AD:DP:GL:GQ 0/1:44,32:73:-124.08,-21.99,-153.59:99 +chr1 4824703 rs6671779 A G 149.25 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=3.56;MQ=45.45;MQ0=6;OQ=857.95;QD=10.46;SB=-366.21 GT:AD:DP:GL:GQ 0/1:48,33:70:-110.16,-21.08,-158.61:99 +chr1 4824716 rs6674795 T A 84.16 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=5.06;MQ=43.80;MQ0=7;OQ=985.67;QD=11.60;SB=-441.50 GT:AD:DP:GL:GQ 0/1:51,34:73:-123.84,-21.98,-157.76:99 +chr1 4824850 rs36062377 G T 24.04 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=3;HaplotypeScore=2.62;MQ=51.81;MQ0=1;OQ=1235.06;QD=17.15;SB=-475.54 GT:AD:DP:GL:GQ 0/1:30,42:67:-146.97,-20.18,-98.26:99 +chr1 4825033 rs7529540 T C 245.46 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=39.74;MQ0=8;OQ=558.43;QD=7.55;SB=-301.05 GT:AD:DP:GL:GQ 0/1:47,27:63:-78.11,-18.99,-158.23:99 +chr1 4825352 rs4559467 G A 108.52 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=5.62;MQ=48.67;MQ0=0;OQ=560.80;QD=11.22;SB=-300.78 GT:AD:DP:GL:GQ 0/1:27,20:40:-71.42,-12.05,-75.01:99 +chr1 4825513 rs4638087 G C 326.19 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=1176.04;QD=19.60;SB=-421.03 GT:AD:DP:GL:GQ 0/1:27,33:59:-138.66,-17.78,-117.95:99 +chr1 4825553 rs4551566 C G 30.76 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.33;MQ0=0;OQ=1250.51;QD=22.33;SB=-448.38 GT:AD:DP:GL:GQ 0/1:22,34:55:-144.91,-16.57,-96.90:99 +chr1 4826034 rs7529926 A G 223.14 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=2.45;MQ=57.60;MQ0=0;OQ=1139.50;QD=13.57;SB=-533.50 GT:AD:DP:GL:GQ 0/1:44,39:83:-142.23,-25.00,-178.33:99 +chr1 4826162 rs7525613 C T 13.44 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=2;HaplotypeScore=3.45;MQ=59.36;MQ0=1;OQ=993.15;QD=10.80;SB=-409.28 GT:AD:DP:GL:GQ 0/1:59,33:90:-129.72,-27.12,-195.16:99 +chr1 4826345 rs2104305 G T 184.73 PASS AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=57.85;MQ0=1;OQ=505.67;QD=12.64;SB=-209.45 GT:AD:DP:GL:GQ 0/1:21,19:39:-65.60,-11.75,-75.98:99 +chr1 4826423 rs2093767 G A 138.65 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=58.83;MQ0=0;OQ=815.33;QD=15.68;SB=-288.73 GT:AD:DP:GL:GQ 0/1:27,25:52:-100.48,-15.67,-95.85:99 +chr1 4826585 rs2093766 C T 86.86 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=59.52;MQ0=0;OQ=705.53;QD=13.07;SB=-332.40 GT:AD:DP:GL:GQ 0/1:31,23:54:-90.10,-16.27,-110.86:99 +chr1 4826810 rs10915643 T G 203.85 PASS AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=57.12;MQ0=0;OQ=525.52;QD=11.94;SB=-258.86 GT:AD:DP:GL:GQ 0/1:23,21:42:-68.49,-12.65,-82.71:99 +chr1 4827586 rs55916988 A T 25.36 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=889.58;QD=14.35;SB=-432.48 GT:AD:DP:GL:GQ 0/1:33,29:62:-110.92,-18.68,-123.75:99 +chr1 4827658 rs10915644 C T 105.99 PASS AC=1;AF=0.50;AN=2;DB;DP=104;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=60.00;MQ0=0;OQ=1865.95;QD=17.94;SB=-912.01 GT:AD:DP:GL:GQ 0/1:46,58:101:-220.30,-30.43,-168.62:99 +chr1 4828047 rs10915645 G T 162.71 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.35;MQ0=0;OQ=1117.38;QD=13.97;SB=-570.65 GT:AD:DP:GL:GQ 0/1:41,39:77:-138.21,-23.19,-142.58:99 +chr1 4828218 rs10915646 T C 280.72 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=1.03;MQ=59.65;MQ0=0;OQ=827.35;QD=15.32;SB=-429.21 GT:AD:DP:GL:GQ 0/1:26,28:54:-102.28,-16.26,-103.92:99 +chr1 4829521 rs7525315 A G 34.89 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=2;HaplotypeScore=1.86;MQ=60.00;MQ0=0;OQ=437.24;QD=11.82;SB=-193.62 GT:AD:DP:GL:GQ 0/1:19,18:35:-57.55,-10.55,-75.26:99 +chr1 4829549 rs7511935 G C 92.43 PASS AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=60.00;MQ0=0;OQ=512.56;QD=13.85;SB=-232.38 GT:AD:DP:GL:GQ 0/1:19,18:33:-64.49,-9.95,-73.26:99 +chr1 4829662 rs7512035 G A 4.93 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=9.93;MQ=58.76;MQ0=0;OQ=838.03;QD=17.10;SB=-374.88 GT:AD:DP:GL:GQ 0/1:21,27:46:-104.45,-17.36,-74.24:99 +chr1 4830041 rs1886112 T C 323.11 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.65;MQ=58.39;MQ0=0;OQ=754.42;QD=11.79;SB=-313.28 GT:AD:DP:GL:GQ 0/1:35,29:61:-97.11,-18.38,-135.74:99 +chr1 4830111 rs2411950 A G 299.57 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=2.97;MQ=59.44;MQ0=0;OQ=788.01;QD=11.76;SB=-302.20 GT:AD:DP:GL:GQ 0/1:34,33:66:-101.98,-19.90,-134.57:99 +chr1 4831214 rs11588518 A G 386.42 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=58.39;MQ0=0;OQ=816.62;QD=14.85;SB=-422.33 GT:AD:DP:GL:GQ 0/1:26,29:53:-100.91,-15.96,-102.18:99 +chr1 4832304 rs10915647 T G 357.62 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.96;MQ=59.21;MQ0=0;OQ=992.87;QD=12.89;SB=-411.65 GT:AD:DP:GL:GQ 0/1:36,41:75:-125.17,-22.60,-131.25:99 +chr1 4833095 rs10489136 G A 381.62 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.25;MQ0=0;OQ=597.16;QD=11.94;SB=-271.12 GT:AD:DP:GL:GQ 0/1:30,20:49:-77.76,-14.76,-108.40:99 +chr1 4833385 rs11809159 G A 313.41 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.57;MQ0=0;OQ=671.57;QD=12.44;SB=-350.34 GT:AD:DP:GL:GQ 0/1:33,21:52:-86.11,-15.67,-111.35:99 +chr1 4834568 rs12691490 G A 57.53 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=59.19;MQ0=0;OQ=1072.80;QD=14.30;SB=-179.14 GT:AD:DP:GL:GQ 0/1:41,34:74:-132.86,-22.29,-148.17:99 +chr1 4834712 rs11810903 C T 299.28 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.50;MQ0=0;OQ=847.25;QD=15.99;SB=-334.31 GT:AD:DP:GL:GQ 0/1:27,26:50:-103.07,-15.06,-90.22:99 +chr1 4835505 . G A 70.11 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=57.18;MQ0=2;OQ=1406.02;QD=19.00;SB=-566.58 GT:AD:DP:GL:GQ 0/1:33,41:71:-165.27,-21.39,-109.48:99 +chr1 4835574 rs60862815 A G 389.11 PASS AC=1;AF=0.50;AN=2;DB;DP=96;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=52.44;MQ0=0;OQ=1406.97;QD=14.66;SB=-683.24 GT:AD:DP:GL:GQ 0/1:48,48:95:-172.59,-28.61,-196.25:99 +chr1 4835660 . A G 23.51 PASS AC=1;AF=0.50;AN=2;DP=96;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.01;MQ0=0;OQ=1833.96;QD=19.10;SB=-522.87 GT:AD:DP:GL:GQ 0/1:39,57:96:-215.59,-28.91,-159.74:99 +chr1 4837550 rs35283465 T G 356.52 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1133.74;QD=16.67;SB=-504.82 GT:AD:DP:GL:GQ 0/1:30,38:68:-137.14,-20.48,-110.12:99 +chr1 4837913 rs10753390 T C 137.37 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=2.60;MQ=60.00;MQ0=0;OQ=941.83;QD=14.72;SB=-459.61 GT:AD:DP:GL:GQ 0/1:30,34:62:-116.15,-18.68,-119.75:99 +chr1 4839426 rs942248 G A 447.55 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.57;MQ=60.00;MQ0=0;OQ=1139.23;QD=16.75;SB=-553.39 GT:AD:DP:GL:GQ 0/1:34,34:68:-137.70,-20.50,-108.59:99 +chr1 4841270 rs10915651 A G 240.97 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=57.66;MQ0=0;OQ=816.55;QD=11.66;SB=-378.12 GT:AD:DP:GL:GQ 0/1:39,31:68:-105.42,-20.48,-155.28:99 +chr1 4841714 rs4654463 A C 478.61 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=555.94;QD=9.75;SB=-254.73 GT:AD:DP:GL:GQ 0/1:35,22:56:-75.74,-16.86,-132.35:99 +chr1 4844074 rs10733017 T C 2.18 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=11.82;MQ=59.63;MQ0=0;OQ=699.51;QD=11.10;SB=-327.09 GT:AD:DP:GL:GQ 0/1:36,27:62:-91.91,-18.68,-144.88:99 +chr1 4844167 rs11576728 C A 571.03 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=1050.49;QD=13.64;SB=-532.68 GT:AD:DP:GL:GQ 0/1:42,35:77:-131.52,-23.19,-153.03:99 +chr1 4844702 rs7543026 G A 584.71 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.93;MQ0=0;OQ=948.11;QD=15.54;SB=-391.87 GT:AD:DP:GL:GQ 0/1:33,28:60:-116.18,-18.08,-104.09:99 +chr1 4845341 rs6658585 A C 76.93 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.00;MQ=59.18;MQ0=0;OQ=1071.52;QD=16.74;SB=-367.56 GT:AD:DP:GL:GQ 0/1:26,38:62:-129.11,-18.67,-97.88:99 +chr1 4845498 rs12057393 G A 364.71 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=12;HaplotypeScore=3.79;MQ=47.74;MQ0=0;QD=4.19;SB=-24.81 GT:AD:DP:GL:GQ 0/1:67,20:77:-62.95,-23.20,-211.18:99 +chr1 4845501 . G A 272.57 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=2;HaplotypeScore=5.43;MQ=47.58;MQ0=0;QD=3.17;SB=59.32 GT:AD:DP:GL:GQ 0/1:69,17:79:-54.34,-23.80,-226.78:99 +chr1 4845504 . G A 237.01 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=2;HaplotypeScore=5.58;MQ=47.42;MQ0=0;QD=2.79;SB=100.89 GT:AD:DP:GL:GQ 0/1:69,16:79:-50.79,-23.80,-233.92:99 +chr1 4846112 rs34320332 A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=25.56;MQ=59.10;MQ0=1;OQ=980.42;QD=12.41;SB=-508.92 GT:AD:DP:GL:GQ 0/1:43,36:73:-123.31,-21.99,-148.19:99 +chr1 4846138 rs4141866 T G 321.22 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1084.74;QD=12.91;SB=-515.88 GT:AD:DP:GL:GQ 0/1:44,39:81:-136.16,-24.40,-149.14:99 +chr1 4846537 rs2224810 C T 118.17 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=2.15;MQ=60.00;MQ0=0;OQ=819.69;QD=11.71;SB=-407.37 GT:AD:DP:GL:GQ 0/1:43,26:69:-109.19,-23.93,-141.50:99 +chr1 4846628 rs2209160 C T 102.30 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=6.02;MQ=59.71;MQ0=0;OQ=1103.05;QD=13.96;SB=-498.70 GT:AD:DP:GL:GQ 0/1:45,34:78:-137.10,-23.51,-139.74:99 +chr1 4847013 rs4654617 G A 341.44 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.65;MQ=60.12;MQ0=0;OQ=1328.73;QD=14.44;SB=-558.05 GT:AD:DP:GL:GQ 0/1:51,41:91:-163.57,-27.42,-178.46:99 +chr1 4847234 rs4654618 G A 257.57 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.79;MQ0=0;OQ=1473.23;QD=16.93;SB=-644.65 GT:AD:DP:GL:GQ 0/1:44,43:86:-176.51,-25.90,-155.83:99 +chr1 4847304 rs11576619 A C 410.62 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1115.68;QD=12.54;SB=-555.85 GT:AD:DP:GL:GQ 0/1:50,39:89:-141.65,-26.80,-188.69:99 +chr1 4848245 rs10915655 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.04;HRun=13;HaplotypeScore=40.55;MQ=53.84;MQ0=0;OQ=783.98;QD=11.53;SB=-399.49 GT:AD:DP:GL:GQ 0/1:35,30:57:-98.55,-16.87,-112.34:99 +chr1 4848259 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=13;HaplotypeScore=8.75;MQ=53.39;MQ0=0;OQ=145.61;QD=2.24;SB=43.71 GT:AD:DP:GL:GQ 0/1:50,15:51:-33.22,-15.38,-143.27:99 +chr1 4848272 rs59534952 C T 83.18 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=2.85;MQ=55.61;MQ0=0;OQ=567.99;QD=11.83;SB=-226.73 GT:AD:DP:GL:GQ 0/1:29,19:46:-73.94,-13.86,-98.14:99 +chr1 4849613 rs2224809 G T 40.55 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=5.98;MQ=59.05;MQ0=0;OQ=753.24;QD=11.77;SB=-371.10 GT:AD:DP:GL:GQ 0/1:36,28:62:-97.28,-18.68,-118.15:99 +chr1 4851425 rs4654464 C A 99.04 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=3;HaplotypeScore=1.30;MQ=59.74;MQ0=0;OQ=1201.43;QD=13.50;SB=-585.67 GT:AD:DP:GL:GQ 0/1:47,42:87:-149.63,-26.21,-164.62:99 +chr1 4851649 rs1544062 A C 506.42 PASS AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.80;MQ0=0;OQ=1031.53;QD=11.21;SB=-464.74 GT:AD:DP:GL:GQ 0/1:52,40:90:-133.54,-27.11,-194.44:99 +chr1 4852648 rs6664880 A G 404.16 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=757.37;QD=15.15;SB=-338.35 GT:AD:DP:GL:GQ 0/1:21,29:49:-93.79,-14.77,-78.78:99 +chr1 4853388 rs16839786 G T 224.38 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=53.58;MQ0=0;OQ=920.28;QD=16.43;SB=-211.55 GT:AD:DP:GL:GQ 0/1:26,30:55:-111.88,-16.57,-81.39:99 +chr1 4853673 rs61764897 T A 731.06 Indel AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=49.62;MQ0=0;QD=11.25;SB=-257.66 GT:AD:DP:GL:GQ 0/1:39,26:64:-95.67,-19.28,-148.40:99 +chr1 4854729 rs11578197 G A 258.41 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.18;MQ=59.65;MQ0=0;OQ=1050.33;QD=16.16;SB=-476.48 GT:AD:DP:GL:GQ 0/1:33,32:63:-127.30,-18.99,-107.48:99 +chr1 4855018 rs16839789 C T 363.83 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=59.33;MQ0=0;OQ=1117.05;QD=14.70;SB=-538.76 GT:AD:DP:GL:GQ 0/1:39,37:73:-136.99,-22.00,-128.05:99 +chr1 4855722 rs6426446 C T 346.09 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.43;MQ0=0;OQ=1302.13;QD=17.84;SB=-634.73 GT:AD:DP:GL:GQ 0/1:34,39:71:-154.89,-21.40,-105.41:99 +chr1 4855930 rs6426447 T C 166.41 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=57.78;MQ0=0;OQ=489.14;QD=8.58;SB=-219.87 GT:AD:DP:GL:GQ 0/1:31,26:53:-68.18,-15.98,-120.90:99 +chr1 4856415 rs7547152 G C 495.16 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=942.12;QD=15.20;SB=-441.90 GT:AD:DP:GL:GQ 0/1:35,27:61:-115.88,-18.38,-149.41:99 +chr1 4857229 rs58851741 C T 459.60 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=966.78;QD=16.67;SB=-403.91 GT:AD:DP:GL:GQ 0/1:27,31:57:-117.15,-17.19,-83.93:99 +chr1 4857438 rs6663654 A G 150.02 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.74;MQ=59.66;MQ0=0;OQ=1188.14;QD=17.73;SB=-597.99 GT:AD:DP:GL:GQ 0/1:26,41:63:-141.07,-18.98,-97.28:99 +chr1 4857938 rs4654466 T G 14.09 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=3;HaplotypeScore=2.02;MQ=60.00;MQ0=0;OQ=2439.19;QD=33.41;SB=-1032.90 GT:AD:DP:GL:GQ 1/1:0,73:72:-247.54,-21.70,-0.04:99 +chr1 4857962 rs4654620 T C 617.25 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2216.51;QD=34.63;SB=-1013.85 GT:AD:DP:GL:GQ 1/1:0,64:63:-225.26,-18.98,-0.03:99 +chr1 4858133 rs12026056 C T 160.83 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.48;MQ0=0;OQ=1391.17;QD=19.32;SB=-472.46 GT:AD:DP:GL:GQ 0/1:31,41:70:-163.49,-21.09,-105.37:99 +chr1 4858331 rs2411952 T G 714.78 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2714.55;QD=33.93;SB=-941.23 GT:AD:DP:GL:GQ 1/1:0,80:78:-275.06,-23.49,-0.02:99 +chr1 4858799 rs10915656 A G 325.06 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=541.63;QD=8.88;SB=-253.33 GT:AD:DP:GL:GQ 0/1:37,24:61:-75.83,-18.39,-146.51:99 +chr1 4859646 rs2031246 A G 219.32 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.68;MQ0=0;OQ=1950.88;QD=29.12;SB=-966.30 GT:AD:DP:GL:GQ 1/1:0,67:62:-198.73,-18.70,-0.06:99 +chr1 4859671 . T C 13.11 PASS AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=1;HaplotypeScore=3.64;MQ=59.06;MQ0=0;OQ=883.63;QD=12.81;SB=-329.17 GT:AD:DP:GL:GQ 0/1:37,32:67:-111.83,-20.19,-139.59:99 +chr1 4859954 rs34895557 G T 206.38 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.25;MQ=59.24;MQ0=0;OQ=744.21;QD=13.53;SB=-251.43 GT:AD:DP:GL:GQ 0/1:28,27:52:-93.37,-15.67,-91.09:99 +chr1 4860771 rs1998542 A G 287.69 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.36;MQ0=0;OQ=1092.68;QD=14.57;SB=-569.57 GT:AD:DP:GL:GQ 0/1:37,38:74:-134.84,-22.29,-148.74:99 +chr1 4861394 rs12564397 A T 437.24 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=1000.40;QD=17.86;SB=-441.86 GT:AD:DP:GL:GQ 0/1:25,31:56:-120.19,-16.87,-93.72:99 +chr1 4861557 rs35411636 G A 169.15 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.73;MQ=59.72;MQ0=0;OQ=1208.45;QD=18.04;SB=-440.97 GT:AD:DP:GL:GQ 0/1:30,37:64:-143.41,-19.28,-105.19:99 +chr1 4863429 . C T 229.25 PASS AC=1;AF=0.50;AN=2;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=1493.09;QD=17.36;SB=-728.57 GT:AD:DP:GL:GQ 0/1:41,45:85:-178.20,-25.60,-151.88:99 +chr1 4863497 rs7524606 G A 427.14 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=1.18;MQ=60.00;MQ0=0;OQ=1511.71;QD=17.58;SB=-634.67 GT:AD:DP:GL:GQ 0/1:42,44:85:-180.06,-25.60,-147.35:99 +chr1 4863865 rs1980722 C T 503.84 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3056.08;QD=40.21;SB=-645.86 GT:AD:DP:GL:GQ 1/1:0,76:76:-309.21,-22.89,-0.02:99 +chr1 4864428 rs11580747 G C 245.21 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.79;MQ=59.63;MQ0=0;OQ=942.97;QD=14.97;SB=-334.34 GT:AD:DP:GL:GQ 0/1:36,27:61:-115.96,-18.38,-154.60:99 +chr1 4865012 rs17345545 A C 595.58 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1349.09;QD=16.06;SB=-446.78 GT:AD:DP:GL:GQ 0/1:36,48:82:-162.89,-24.70,-132.81:99 +chr1 4865105 rs57839229 A T 93.37 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=1.14;MQ=59.34;MQ0=0;OQ=1132.50;QD=17.98;SB=-522.98 GT:AD:DP:GL:GQ 0/1:27,36:62:-135.21,-18.67,-99.92:99 +chr1 4865351 rs4654467 A G 16.96 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.01;HRun=0;HaplotypeScore=4.70;MQ=59.78;MQ0=0;OQ=2675.08;QD=31.11;SB=-1049.26 GT:AD:DP:GL:GQ 1/1:0,84:83:-271.15,-24.72,-0.06:99 +chr1 4866087 rs10915662 A T 363.81 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.38;MQ0=0;OQ=1323.19;QD=19.75;SB=-593.71 GT:AD:DP:GL:GQ 0/1:27,40:67:-155.78,-20.18,-103.30:99 +chr1 4866400 rs12064982 G A 103.40 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=3.34;MQ=60.00;MQ0=0;OQ=973.54;QD=18.03;SB=-247.54 GT:AD:DP:GL:GQ 0/1:25,29:53:-116.61,-15.97,-79.83:99 +chr1 4866918 rs12031154 A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=24.82;MQ=54.18;MQ0=0;OQ=935.81;QD=11.27;SB=-380.06 GT:AD:DP:GL:GQ 0/1:43,40:73:-118.86,-22.00,-142.88:99 +chr1 4866921 rs12026933 G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.03;HRun=18;HaplotypeScore=19.70;MQ=54.46;MQ0=0;OQ=1554.81;QD=17.87;SB=-743.33 GT:AD:DP:GL:GQ 0/1:33,51:81:-182.28,-23.51,-100.13:99 +chr1 4867019 rs11803696 A G 583.39 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1173.47;QD=12.90;SB=-430.96 GT:AD:DP:GL:GQ 0/1:48,43:89:-147.44,-26.81,-193.48:99 +chr1 4867070 rs6672145 C T 154.08 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.79;MQ=58.49;MQ0=0;OQ=2949.30;QD=37.81;SB=-1148.66 GT:AD:DP:GL:GQ 1/1:0,78:74:-298.53,-22.29,-0.02:99 +chr1 4867333 rs10737414 C T 577.78 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=3774.90;QD=40.59;SB=-1090.96 GT:AD:DP:GL:GQ 1/1:0,93:91:-376.49,-27.41,-0.02:99 +chr1 4867363 rs7533707 A T 409.29 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=3186.97;QD=36.63;SB=-1277.61 GT:AD:DP:GL:GQ 1/1:0,87:84:-322.30,-25.30,-0.02:99 +chr1 4867599 rs7520488 G C 176.88 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=3.17;MQ=58.98;MQ0=0;OQ=1260.85;QD=19.70;SB=-431.87 GT:AD:DP:GL:GQ 0/1:29,35:63:-148.35,-18.98,-119.77:99 +chr1 4867836 rs10753391 C T 252.04 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.73;MQ=58.82;MQ0=0;OQ=2192.96;QD=37.17;SB=-1090.48 GT:AD:DP:GL:GQ 1/1:0,58:57:-222.90,-17.17,-0.02:99 +chr1 4869610 rs10753392 A G 2.94 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=12.66;MQ=58.15;MQ0=0;OQ=2566.56;QD=33.77;SB=-1061.07 GT:AD:DP:GL:GQ 1/1:1,75:72:-260.27,-21.69,-0.02:99 +chr1 4869715 rs10753393 A G 57.47 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.94;MQ=55.52;MQ0=0;OQ=2164.34;QD=32.79;SB=-1098.81 GT:AD:DP:GL:GQ 1/1:0,66:62:-220.05,-18.68,-0.03:99 +chr1 4869773 rs10737415 G A 79.07 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.29;MQ=59.56;MQ0=0;OQ=867.20;QD=16.36;SB=-154.19 GT:AD:DP:GL:GQ 0/1:24,29:51:-105.37,-15.37,-83.26:99 +chr1 4869802 rs10753394 T C 256.85 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.38;MQ=60.00;MQ0=0;OQ=1715.99;QD=30.64;SB=-772.60 GT:AD:DP:GL:GQ 1/1:0,56:56:-175.25,-16.90,-0.06:99 +chr1 4869982 rs10915666 G A 210.38 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=58.75;MQ0=0;OQ=1883.17;QD=36.21;SB=-696.34 GT:AD:DP:GL:GQ 1/1:0,50:49:-191.92,-14.76,-0.02:99 +chr1 4870346 rs6675549 G A 170.55 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=4.29;MQ=57.91;MQ0=0;OQ=1211.32;QD=19.23;SB=-547.10 GT:AD:DP:GL:GQ 0/1:28,35:62:-143.11,-18.69,-84.61:99 +chr1 4870866 rs60530383 A G 40.28 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=2.54;MQ=60.00;MQ0=0;OQ=824.16;QD=14.46;SB=-305.38 GT:AD:DP:GL:GQ 0/1:28,29:56:-102.57,-16.87,-109.85:99 +chr1 4871367 rs12034557 C T 506.72 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1054.17;QD=18.82;SB=-458.82 GT:AD:DP:GL:GQ 0/1:25,31:55:-125.27,-16.57,-85.80:99 +chr1 4871442 rs11584441 T G 5.72 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=1.95;MQ=57.60;MQ0=1;OQ=392.05;QD=7.00;SB=-149.17 GT:AD:DP:GL:GQ 0/1:35,21:54:-58.76,-16.27,-123.74:99 +chr1 4871485 rs12034590 C T 165.34 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.35;MQ0=0;OQ=1273.44;QD=19.90;SB=-540.59 GT:AD:DP:GL:GQ 0/1:26,38:62:-149.30,-18.68,-91.11:99 +chr1 4871683 rs10915667 G A 252.09 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=1.13;MQ=59.56;MQ0=0;OQ=868.47;QD=16.70;SB=-440.82 GT:AD:DP:GL:GQ 0/1:26,26:50:-105.19,-15.06,-84.43:99 +chr1 4872046 rs41524347 T G 240.01 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=531.74;QD=7.28;SB=-248.55 GT:AD:DP:GL:GQ 0/1:47,26:72:-78.15,-21.69,-181.81:99 +chr1 4872269 rs7549400 A G 96.19 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=58.82;MQ0=1;OQ=894.68;QD=13.76;SB=-387.61 GT:AD:DP:GL:GQ 0/1:34,31:64:-112.04,-19.29,-126.05:99 +chr1 4872967 rs11805753 C T 385.01 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.56;MQ=59.68;MQ0=0;OQ=1214.98;QD=17.11;SB=-484.47 GT:AD:DP:GL:GQ 0/1:35,36:70:-145.88,-21.10,-111.38:99 +chr1 4873161 rs10915668 C T 676.89 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2872.25;QD=39.89;SB=-1024.38 GT:AD:DP:GL:GQ 1/1:0,72:72:-290.83,-21.69,-0.02:99 +chr1 4874423 rs10915669 T C 15.37 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=2.47;MQ=59.06;MQ0=0;OQ=1979.91;QD=28.69;SB=-648.94 GT:AD:DP:GL:GQ 1/1:0,69:62:-201.63,-18.69,-0.05:99 +chr1 4875425 rs10157835 A G 332.29 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.11;MQ0=0;OQ=1038.14;QD=16.48;SB=-539.00 GT:AD:DP:GL:GQ 0/1:28,35:63:-126.07,-18.98,-114.44:99 +chr1 4877097 rs12565275 C G 395.93 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.57;MQ0=0;OQ=611.15;QD=11.32;SB=-239.42 GT:AD:DP:GL:GQ 0/1:33,21:54:-80.69,-16.29,-144.98:99 +chr1 4877956 rs2898849 G C 124.47 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=59.05;MQ0=0;OQ=3110.04;QD=42.60;SB=-1016.57 GT:AD:DP:GL:GQ 1/1:0,72:72:-314.62,-21.70,-0.03:99 +chr1 4878047 rs12564793 G C 328.95 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.70;MQ0=0;OQ=765.57;QD=12.15;SB=-303.80 GT:AD:DP:GL:GQ 0/1:37,26:61:-98.24,-18.40,-159.57:99 +chr1 4880219 rs11585512 A G 134.50 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=3.24;MQ=59.43;MQ0=0;OQ=632.04;QD=9.58;SB=-314.90 GT:AD:DP:GL:GQ 0/1:35,31:61:-84.88,-18.39,-132.31:99 +chr1 4880279 rs11583660 G A 590.60 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=976.49;QD=13.95;SB=-412.71 GT:AD:DP:GL:GQ 0/1:40,30:69:-121.72,-20.78,-142.93:99 +chr1 4880552 rs12035499 G A 202.58 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.63;MQ0=0;OQ=1072.23;QD=21.02;SB=-458.86 GT:AD:DP:GL:GQ 0/1:20,31:50:-125.57,-15.06,-66.05:99 +chr1 4881363 rs942245 A G 135.80 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=2549.24;QD=35.41;SB=-1267.52 GT:AD:DP:GL:GQ 1/1:0,72:71:-258.53,-21.38,-0.02:99 +chr1 4882246 rs6698453 G A 17.37 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=3;HaplotypeScore=2.99;MQ=60.00;MQ0=0;OQ=1152.61;QD=20.22;SB=-564.76 GT:AD:DP:GL:GQ 0/1:24,33:57:-135.71,-17.17,-88.68:99 +chr1 4883339 rs12043326 T C 559.70 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=840.35;QD=11.84;SB=-378.86 GT:AD:DP:GL:GQ 0/1:36,35:67:-107.51,-20.19,-138.68:99 +chr1 4883603 rs10915672 C A 302.35 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=917.14;QD=15.81;SB=-477.86 GT:AD:DP:GL:GQ 0/1:28,30:58:-112.47,-17.47,-92.34:99 +chr1 4883658 rs4141867 T C 369.29 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=1888.75;QD=33.14;SB=-779.12 GT:AD:DP:GL:GQ 1/1:0,57:54:-192.48,-16.27,-0.02:99 +chr1 4883885 rs6702564 G A 362.71 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=1074.71;QD=17.62;SB=-363.86 GT:AD:DP:GL:GQ 0/1:29,32:61:-129.13,-18.37,-105.65:99 +chr1 4884232 rs1535733 T C 178.47 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.73;MQ=59.20;MQ0=1;OQ=1010.15;QD=15.08;SB=-514.02 GT:AD:DP:GL:GQ 0/1:32,35:66:-124.18,-19.88,-130.89:99 +chr1 4884527 rs6666792 C A 73.74 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=1.81;MQ=60.00;MQ0=0;OQ=1017.13;QD=16.14;SB=-354.42 GT:AD:DP:GL:GQ 0/1:29,34:62:-123.67,-18.68,-100.25:99 +chr1 4884742 rs2093765 A G 735.50 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2661.52;QD=35.97;SB=-1066.10 GT:AD:DP:GL:GQ 1/1:0,74:74:-269.76,-22.29,-0.02:99 +chr1 4885223 rs6667433 C T 727.08 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=1991.58;QD=36.21;SB=-991.61 GT:AD:DP:GL:GQ 1/1:1,54:54:-205.04,-16.28,-2.29:99 +chr1 4885428 rs10753395 A C 505.64 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.54;MQ0=0;OQ=2504.61;QD=34.79;SB=-1254.33 GT:AD:DP:GL:GQ 1/1:0,72:71:-254.07,-21.38,-0.02:99 +chr1 4885629 rs10915675 C T 373.73 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=59.20;MQ0=0;OQ=841.96;QD=14.52;SB=-410.79 GT:AD:DP:GL:GQ 0/1:31,27:56:-104.36,-16.88,-95.31:99 +chr1 4886330 rs2411956 G T 352.27 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.52;MQ=59.33;MQ0=0;OQ=915.03;QD=14.76;SB=-419.13 GT:AD:DP:GL:GQ 0/1:29,33:59:-112.57,-17.78,-93.60:99 +chr1 4886464 rs2898852 G A 427.35 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.13;MQ=59.69;MQ0=0;OQ=1311.14;QD=17.48;SB=-649.71 GT:AD:DP:GL:GQ 0/1:36,39:74:-156.69,-22.29,-124.22:99 +chr1 4887284 rs6666453 T G 591.26 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.63;MQ0=0;OQ=819.61;QD=13.22;SB=-407.64 GT:AD:DP:GL:GQ 0/1:31,31:61:-103.62,-18.37,-115.39:99 +chr1 4887891 rs61271613 G A 361.07 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=59.32;MQ0=0;OQ=1029.14;QD=15.13;SB=-413.79 GT:AD:DP:GL:GQ 0/1:37,31:68:-126.69,-20.50,-120.37:99 +chr1 4887923 rs12567162 A C 597.28 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1047.19;QD=16.36;SB=-475.28 GT:AD:DP:GL:GQ 0/1:27,37:63:-126.98,-18.97,-102.36:99 +chr1 4888122 rs11584727 G A 343.84 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=58.62;MQ0=0;OQ=960.03;QD=15.74;SB=-414.74 GT:AD:DP:GL:GQ 0/1:31,30:58:-116.76,-17.47,-107.44:99 +chr1 4888166 rs10799275 T C 449.24 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=759.70;QD=14.07;SB=-405.31 GT:AD:DP:GL:GQ 0/1:28,26:54:-95.52,-16.26,-116.08:99 +chr1 4888741 rs6667349 A G 162.92 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=2;HaplotypeScore=1.54;MQ=60.00;MQ0=0;OQ=906.44;QD=15.63;SB=-403.28 GT:AD:DP:GL:GQ 0/1:26,32:57:-111.10,-17.17,-105.01:99 +chr1 4891078 rs10915677 A C 501.83 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=791.64;QD=10.84;SB=-393.76 GT:AD:DP:GL:GQ 0/1:42,31:72:-104.14,-21.69,-153.97:99 +chr1 4891278 rs10753396 A G 48.68 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.33;MQ=59.27;MQ0=0;OQ=705.13;QD=13.83;SB=-249.29 GT:AD:DP:GL:GQ 0/1:25,26:49:-88.56,-14.77,-92.96:99 +chr1 4892541 rs6675977 C T 304.31 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.24;MQ0=0;OQ=854.23;QD=15.53;SB=-341.48 GT:AD:DP:GL:GQ 0/1:29,26:53:-104.68,-15.97,-89.47:99 +chr1 4893597 rs9426511 G A 254.52 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.65;MQ=59.63;MQ0=0;OQ=950.24;QD=15.08;SB=-473.01 GT:AD:DP:GL:GQ 0/1:32,31:60:-116.38,-18.07,-112.58:99 +chr1 4894312 rs12409253 G A 317.80 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.37;MQ0=0;OQ=1178.40;QD=17.85;SB=-478.44 GT:AD:DP:GL:GQ 0/1:31,35:66:-141.01,-19.88,-111.62:99 +chr1 4894801 rs12044092 G A 352.37 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.41;MQ=58.46;MQ0=0;OQ=1019.91;QD=14.36;SB=-390.41 GT:AD:DP:GL:GQ 0/1:36,34:67:-125.46,-20.19,-124.85:99 +chr1 4894886 rs12049256 T C 300.25 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.80;MQ=59.40;MQ0=0;OQ=829.82;QD=11.85;SB=-433.52 GT:AD:DP:GL:GQ 0/1:40,30:69:-107.05,-20.79,-158.76:99 +chr1 4895006 rs11588368 G A 587.49 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=820.91;QD=16.10;SB=-424.82 GT:AD:DP:GL:GQ 0/1:26,25:51:-100.74,-15.37,-86.84:99 +chr1 4895035 rs11591047 T C 208.88 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=60.00;MQ0=0;OQ=456.13;QD=9.70;SB=-221.38 GT:AD:DP:GL:GQ 0/1:26,21:45:-62.46,-13.57,-101.40:99 +chr1 4895453 rs10915681 C A 168.48 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=1;HaplotypeScore=1.78;MQ=58.81;MQ0=0;OQ=612.66;QD=11.14;SB=-214.30 GT:AD:DP:GL:GQ 0/1:31,24:51:-79.91,-15.36,-100.29:99 +chr1 4895802 rs10915682 G C 444.70 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.75;MQ0=0;OQ=770.78;QD=14.82;SB=-369.80 GT:AD:DP:GL:GQ 0/1:29,22:52:-98.80,-18.44,-131.37:99 +chr1 4896045 rs10915683 A G 284.67 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.68;MQ0=0;OQ=528.33;QD=8.95;SB=-128.57 GT:AD:DP:GL:GQ 0/1:38,21:56:-72.98,-16.87,-140.47:99 +chr1 4896086 rs4654470 A G 55.66 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=5.44;MQ=59.62;MQ0=0;OQ=494.74;QD=8.11;SB=-214.66 GT:AD:DP:GL:GQ 0/1:40,20:59:-73.24,-20.48,-157.99:99 +chr1 4896521 rs12037632 T C 412.13 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.62;MQ0=0;OQ=681.99;QD=11.18;SB=-282.28 GT:AD:DP:GL:GQ 0/1:32,29:59:-89.26,-17.78,-128.31:99 +chr1 4896528 . C T 86.04 PASS AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.85;MQ=59.65;MQ0=0;OQ=946.41;QD=14.34;SB=-376.12 GT:AD:DP:GL:GQ 0/1:36,30:66:-117.81,-19.89,-127.23:99 +chr1 4896632 rs12040043 G A 26.46 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=5.45;MQ=59.30;MQ0=0;OQ=1274.10;QD=19.30;SB=-654.71 GT:AD:DP:GL:GQ 0/1:28,38:65:-150.27,-19.58,-99.74:99 +chr1 4897223 rs9426467 A G 376.87 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=60.00;MQ0=0;OQ=1052.07;QD=15.47;SB=-512.94 GT:AD:DP:GL:GQ 0/1:31,37:66:-128.37,-19.88,-120.24:99 +chr1 4897430 . C G 135.89 PASS AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1675.35;QD=20.68;SB=-845.32 GT:AD:DP:GL:GQ 0/1:35,46:79:-194.65,-23.83,-135.28:99 +chr1 4898245 rs9426468 A G 643.42 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=1735.77;QD=32.14;SB=-669.84 GT:AD:DP:GL:GQ 1/1:0,54:54:-177.21,-16.28,-0.04:99 +chr1 4899159 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=3;HaplotypeScore=6.05;MQ=46.85;MQ0=0;OQ=120.33;QD=2.27;SB=65.24 GT:AD:DP:GL:GQ 0/1:32,21:41:-27.68,-12.36,-128.17:99 +chr1 4899332 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=18.81;MQ=41.26;MQ0=0;OQ=75.19;QD=0.84;SB=83.30 GT:AD:DP:GL:GQ 0/1:74,15:82:-35.50,-24.70,-289.36:99 +chr1 4899338 rs61764934 T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.00;HRun=1;HaplotypeScore=53.72;MQ=39.00;MQ0=0;OQ=98.84;QD=0.96;SB=80.29 GT:AD:DP:GL:GQ 0/1:81,22:86:-39.08,-25.91,-300.72:99 +chr1 4899353 . A G 53.98 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=1;HaplotypeScore=114.06;MQ=38.02;MQ0=0;QD=0.50;SB=80.29 GT:AD:DP:GL:GQ 0/1:92,15:73:-30.68,-22.00,-253.39:86.82 +chr1 4899362 . C T 241.59 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=82.55;MQ=36.98;MQ0=0;QD=2.20;SB=83.28 GT:AD:DP:GL:GQ 0/1:96,14:84:-52.74,-25.30,-256.82:99 +chr1 4899363 . A G 254.83 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=107;Dels=0.00;HRun=0;HaplotypeScore=89.52;MQ=36.48;MQ0=0;QD=2.38;SB=77.27 GT:AD:DP:GL:GQ 0/1:93,14:79:-52.57,-23.80,-259.03:99 +chr1 4899383 . A G 183.41 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=106;Dels=0.00;HRun=0;HaplotypeScore=35.87;MQ=33.65;MQ0=0;QD=1.73;SB=12.92 GT:AD:DP:GL:GQ 0/1:63,43:62:-40.31,-18.69,-193.47:99 +chr1 4899387 . G A 263.62 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=99;Dels=0.00;HRun=1;HaplotypeScore=43.90;MQ=33.13;MQ0=0;QD=2.66;SB=77.22 GT:AD:DP:GL:GQ 0/1:87,12:64:-48.92,-19.28,-184.60:99 +chr1 4899389 . C T 535.44 SnpCluster AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=29.97;MQ=33.38;MQ0=0;QD=5.76;SB=-42.73 GT:AD:DP:GL:GQ 0/1:50,43:64:-76.11,-19.28,-160.16:99 +chr1 4899390 . A G 274.25 SnpCluster AC=1;AF=0.50;AN=2;DP=92;Dels=0.00;HRun=0;HaplotypeScore=29.97;MQ=32.97;MQ0=0;QD=2.98;SB=-22.76 GT:AD:DP:GL:GQ 0/1:49,43:57:-47.88,-17.17,-174.44:99 +chr1 4899396 . A G 365.84 SnpCluster AC=1;AF=0.50;AN=2;DP=91;Dels=0.00;HRun=0;HaplotypeScore=37.97;MQ=32.55;MQ0=0;QD=4.02;SB=-65.46 GT:AD:DP:GL:GQ 0/1:57,34:58:-57.34,-17.48,-166.05:99 +chr1 4899406 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=33.13;MQ=34.08;MQ0=0;OQ=385.33;QD=4.76;SB=65.23 GT:AD:DP:GL:GQ 0/1:64,17:63:-60.79,-18.98,-180.67:99 +chr1 4899410 . A G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=33.12;MQ=33.37;MQ0=0;OQ=280.21;QD=3.64;SB=-127.85 GT:AD:DP:GL:GQ 0/1:61,16:68:-51.79,-20.49,-213.95:99 +chr1 4899418 rs61764937 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=24.96;MQ=35.60;MQ0=0;OQ=416.78;QD=5.56;SB=-32.80 GT:AD:DP:GL:GQ 0/1:58,17:68:-65.44,-20.48,-183.51:99 +chr1 4899454 . A G 399.94 SnpCluster AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=32.10;MQ=40.74;MQ0=0;QD=4.49;SB=-98.78 GT:AD:DP:GL:GQ 0/1:68,21:81:-67.68,-24.40,-246.97:99 +chr1 4899458 . A G 39.06 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=97;Dels=0.00;HRun=0;HaplotypeScore=68.26;MQ=40.42;MQ0=0;QD=0.40;SB=83.30 GT:AD:DP:GL:GQ 0/1:88,9:79:-30.98,-23.79,-291.61:71.90 +chr1 4899460 . A G 118.03 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=100;Dels=0.00;HRun=0;HaplotypeScore=72.96;MQ=40.46;MQ0=0;QD=1.18;SB=77.27 GT:AD:DP:GL:GQ 0/1:89,11:76:-37.98,-22.90,-265.09:99 +chr1 4899462 . C T 72.49 SnpCluster AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=1;HaplotypeScore=75.80;MQ=40.64;MQ0=0;QD=0.70;SB=-1.28 GT:AD:DP:GL:GQ 0/1:95,8:73:-32.52,-21.98,-238.14:99 +chr1 4899467 . A G 135.65 SnpCluster AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=98.40;MQ=41.18;MQ0=0;QD=1.23;SB=-29.35 GT:AD:DP:GL:GQ 0/1:96,14:86:-42.76,-25.91,-295.60:99 +chr1 4899468 rs12745382 A T 958.03 SnpCluster AC=1;AF=0.50;AN=2;DB;DP=110;Dels=0.00;HRun=0;HaplotypeScore=107.35;MQ=41.23;MQ0=0;QD=8.71;SB=-316.45 GT:AD:DP:GL:GQ 0/1:64,46:95:-127.70,-28.61,-236.36:99 +chr1 4899487 rs12745394 A G 720.77 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=218;Dels=0.00;HRun=0;HaplotypeScore=160.10;MQ=38.29;MQ0=1;QD=3.31;SB=-244.39 GT:AD:DP:GL:GQ 0/1:161,57:163:-124.48,-49.12,-501.88:99 +chr1 4899493 . T C 260.40 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=248;Dels=0.00;HRun=0;HaplotypeScore=303.17;MQ=38.85;MQ0=1;QD=1.05;SB=56.79 GT:AD:DP:GL:GQ 0/1:215,32:203:-90.48,-61.15,-713.61:99 +chr1 4899494 . G A 174.70 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=310.33;MQ=39.06;MQ0=1;QD=0.69;SB=21.87 GT:AD:DP:GL:GQ 0/1:226,26:203:-81.91,-61.15,-646.58:99 +chr1 4899498 . A G 872.52 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=250.40;MQ=38.78;MQ0=1;QD=3.46;SB=78.26 GT:AD:DP:GL:GQ 0/1:199,53:211:-154.09,-63.56,-686.66:99 +chr1 4899500 rs12724550 G A 2189.95 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=250;Dels=0.00;HRun=0;HaplotypeScore=245.89;MQ=38.85;MQ0=1;QD=8.76;SB=-1087.26 GT:AD:DP:GL:GQ 0/1:149,76:205:-341.91,-119.63,-478.96:99 +chr1 4899501 . T G 179.31 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=1;HaplotypeScore=255.20;MQ=39.12;MQ0=1;QD=0.71;SB=215.88 GT:AD:DP:GL:GQ 0/1:226,25:204:-82.66,-61.45,-660.80:99 +chr1 4899507 . A G 466.12 DPFilter;Indel;SnpCluster AC=1;AF=0.50;AN=2;DP=254;Dels=0.00;HRun=0;HaplotypeScore=236.48;MQ=39.39;MQ0=1;QD=1.84;SB=155.66 GT:AD:DP:GL:GQ 0/1:206,47:211:-113.47,-63.57,-712.04:99 +chr1 4899538 . A G 1219.52 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=258;Dels=0.00;HRun=0;HaplotypeScore=176.47;MQ=39.21;MQ0=0;QD=4.73;SB=-218.54 GT:AD:DP:GL:GQ 0/1:190,68:212:-189.10,-63.86,-642.45:99 +chr1 4899540 . A G 894.27 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=255;Dels=0.00;HRun=0;HaplotypeScore=176.74;MQ=39.03;MQ0=0;QD=3.51;SB=-184.63 GT:AD:DP:GL:GQ 0/1:181,72:195:-154.12,-61.41,-609.10:99 +chr1 4899547 rs61764939 G A 1318.72 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DB;DP=260;Dels=0.00;HRun=0;HaplotypeScore=220.06;MQ=39.48;MQ0=0;QD=5.07;SB=-35.22 GT:AD:DP:GL:GQ 0/1:180,80:174:-187.61,-52.45,-416.57:99 +chr1 4899554 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=252;Dels=0.00;HRun=0;HaplotypeScore=215.32;MQ=39.44;MQ0=0;OQ=71.48;QD=0.28;SB=245.79 GT:AD:DP:GL:GQ 0/1:233,19:178:-64.05,-53.62,-575.35:99 +chr1 4899560 . A G 527.43 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=244;Dels=0.00;HRun=0;HaplotypeScore=182.32;MQ=39.84;MQ0=0;QD=2.16;SB=62.05 GT:AD:DP:GL:GQ 0/1:191,43:207:-132.12,-76.10,-688.26:99 +chr1 4899566 . C T 228.85 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=230;Dels=0.00;HRun=0;HaplotypeScore=151.86;MQ=39.79;MQ0=0;QD=0.99;SB=29.83 GT:AD:DP:GL:GQ 0/1:207,23:173:-78.29,-52.12,-551.64:99 +chr1 4899567 . A G 591.79 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=224;Dels=0.00;HRun=0;HaplotypeScore=146.70;MQ=39.85;MQ0=0;QD=2.64;SB=-287.04 GT:AD:DP:GL:GQ 0/1:172,52:165:-112.16,-49.70,-538.18:99 +chr1 4899578 . G A 586.91 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=167;Dels=0.00;HRun=1;HaplotypeScore=122.95;MQ=41.57;MQ0=0;QD=3.51;SB=-235.54 GT:AD:DP:GL:GQ 0/1:137,30:123:-99.03,-37.05,-345.51:99 +chr1 4899580 . G A 442.86 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=161;Dels=0.00;HRun=0;HaplotypeScore=120.46;MQ=41.82;MQ0=0;QD=2.75;SB=-225.49 GT:AD:DP:GL:GQ 0/1:135,26:120:-83.72,-36.15,-349.19:99 +chr1 4899586 . T C 690.02 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=149;Dels=0.00;HRun=1;HaplotypeScore=129.55;MQ=42.82;MQ0=0;QD=4.63;SB=-75.61 GT:AD:DP:GL:GQ 0/1:103,46:129:-111.14,-38.86,-403.04:99 +chr1 4899587 . G A 484.27 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=146;Dels=0.00;HRun=0;HaplotypeScore=116.82;MQ=42.67;MQ0=0;QD=3.32;SB=137.44 GT:AD:DP:GL:GQ 0/1:119,26:124:-89.06,-37.35,-358.44:99 +chr1 4899593 . C T 11.57 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=117;Dels=0.00;HRun=0;HaplotypeScore=60.92;MQ=43.18;MQ0=0;QD=0.10;SB=158.52 GT:AD:DP:GL:GQ 0/1:100,17:99:-34.23,-29.82,-323.42:44.09 +chr1 4899594 . A G 11.09 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=116;Dels=0.00;HRun=0;HaplotypeScore=60.92;MQ=43.00;MQ0=0;QD=0.10;SB=173.58 GT:AD:DP:GL:GQ 0/1:99,17:103:-35.39,-31.03,-369.44:43.58 +chr1 4899610 . C T 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=0;HaplotypeScore=9.15;MQ=43.55;MQ0=0;OQ=197.17;QD=2.22;SB=-29.37 GT:AD:DP:GL:GQ 0/1:75,14:86:-48.93,-25.93,-238.79:99 +chr1 4899946 rs4654471 T C 43.86 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=5.91;MQ=59.14;MQ0=0;OQ=975.13;QD=18.06;SB=-440.01 GT:AD:DP:GL:GQ 0/1:20,34:52:-116.46,-15.67,-76.61:99 +chr1 4902227 rs7555212 C T 596.69 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=2926.83;QD=40.65;SB=-1218.62 GT:AD:DP:GL:GQ 1/1:0,72:72:-296.28,-21.69,-0.02:99 +chr1 4902317 rs6426367 G T 224.74 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=59.74;MQ0=0;OQ=3145.50;QD=36.16;SB=-1581.61 GT:AD:DP:GL:GQ 1/1:0,87:85:-318.15,-25.60,-0.02:99 +chr1 4902486 rs6426368 C T 717.48 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=2201.20;QD=38.62;SB=-1092.00 GT:AD:DP:GL:GQ 1/1:0,57:56:-223.72,-16.87,-0.02:99 +chr1 4902573 rs6669905 T C 700.95 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.30;MQ0=0;OQ=2165.11;QD=36.09;SB=-859.36 GT:AD:DP:GL:GQ 1/1:0,60:59:-220.11,-17.77,-0.01:99 +chr1 4903007 rs6678838 G T 279.14 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=56.35;MQ0=0;OQ=1768.51;QD=34.01;SB=-813.84 GT:AD:DP:GL:GQ 1/1:0,52:50:-180.45,-15.06,-0.02:99 +chr1 4903027 rs12142452 G T 0 FDRtranche2.00to10.00+ AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.05;HRun=16;HaplotypeScore=13.19;MQ=49.10;MQ0=0;OQ=2384.03;QD=31.37;SB=-1040.48 GT:AD:DP:GL:GQ 1/1:0,72:70:-242.01,-20.48,-0.02:99 +chr1 4903364 rs9286971 G A 258.61 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=52.70;MQ0=0;OQ=2159.66;QD=37.89;SB=-926.32 GT:AD:DP:GL:GQ 1/1:0,57:54:-219.56,-16.27,-0.01:99 +chr1 4904108 rs10799141 A G 488.42 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.61;MQ0=0;OQ=2393.63;QD=33.71;SB=-1173.70 GT:AD:DP:GL:GQ 1/1:0,71:69:-242.98,-20.79,-0.03:99 +chr1 4904115 rs10753341 C T 707.52 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.70;MQ0=0;OQ=2995.63;QD=39.42;SB=-1442.45 GT:AD:DP:GL:GQ 1/1:0,76:76:-303.17,-22.90,-0.02:99 +chr1 4904188 rs10753342 G A 611.86 PASS AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3529.10;QD=39.65;SB=-1221.14 GT:AD:DP:GL:GQ 1/1:0,89:89:-351.91,-26.82,-0.03:99 +chr1 4905340 rs7531490 A G 249.81 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.93;MQ0=0;OQ=2004.17;QD=30.83;SB=-867.03 GT:AD:DP:GL:GQ 1/1:0,65:64:-204.06,-19.31,-0.06:99 +chr1 4905635 rs7534281 T C 82.15 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=2.19;MQ=59.65;MQ0=0;OQ=2315.03;QD=35.08;SB=-1175.74 GT:AD:DP:GL:GQ 1/1:0,66:65:-235.11,-19.58,-0.02:99 +chr1 4905656 rs7542048 G A 139.59 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.78;MQ=59.63;MQ0=0;OQ=2472.89;QD=39.25;SB=-1234.03 GT:AD:DP:GL:GQ 1/1:0,62:62:-250.89,-18.68,-0.02:99 +chr1 4906196 rs6426371 T C 169.21 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=58.85;MQ0=0;OQ=1914.58;QD=30.88;SB=-835.64 GT:AD:DP:GL:GQ 1/1:0,62:59:-195.09,-17.79,-0.04:99 +chr1 4906502 rs6426372 G C 538.03 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.04;MQ0=0;OQ=3170.49;QD=42.84;SB=-1473.31 GT:AD:DP:GL:GQ 1/1:0,73:73:-320.65,-21.99,-0.02:99 +chr1 4907095 rs10915296 T C 149.48 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=1.07;MQ=58.97;MQ0=0;OQ=3030.02;QD=34.83;SB=-1495.63 GT:AD:DP:GL:GQ 1/1:0,87:84:-306.61,-25.30,-0.03:99 +chr1 4907407 rs6702058 C T 201.43 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.82;MQ=59.72;MQ0=0;OQ=3144.08;QD=38.34;SB=-1502.68 GT:AD:DP:GL:GQ 1/1:0,81:79:-318.01,-23.80,-0.02:99 +chr1 4907813 rs6677619 G T 634.30 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2646.47;QD=36.25;SB=-1071.58 GT:AD:DP:GL:GQ 1/1:0,73:72:-268.25,-21.68,-0.02:99 +chr1 4909109 rs7413385 A G 73.69 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.58;MQ=58.33;MQ0=0;OQ=950.25;QD=33.94;SB=-350.81 GT:AD:DP:GL:GQ 1/1:0,28:27:-98.62,-8.13,-0.01:81.24 +chr1 4909713 rs7413847 A G 78.92 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=58.99;MQ0=0;OQ=2491.44;QD=34.13;SB=-1130.80 GT:AD:DP:GL:GQ 1/1:0,72:69:-252.75,-20.78,-0.02:99 +chr1 4909933 rs7411727 C T 614.98 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2836.35;QD=38.85;SB=-1407.70 GT:AD:DP:GL:GQ 1/1:0,73:71:-287.24,-21.39,-0.02:99 +chr1 4910002 rs10915297 T C 288.13 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.37;MQ0=0;OQ=2563.56;QD=35.12;SB=-1064.10 GT:AD:DP:GL:GQ 1/1:0,73:72:-259.97,-21.69,-0.02:99 +chr1 4910067 rs10799142 G A 129.23 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=2.67;MQ=58.55;MQ0=0;OQ=2372.23;QD=38.89;SB=-1035.39 GT:AD:DP:GL:GQ 1/1:0,61:60:-240.82,-18.08,-0.02:99 +chr1 4910738 rs6426373 T C 29.48 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=4;HaplotypeScore=1.33;MQ=59.62;MQ0=0;OQ=2095.65;QD=34.35;SB=-1007.72 GT:AD:DP:GL:GQ 1/1:0,61:59:-213.17,-17.77,-0.02:99 +chr1 4910848 rs6664358 C T 341.96 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=2577.25;QD=39.65;SB=-933.73 GT:AD:DP:GL:GQ 1/1:0,65:64:-261.33,-19.28,-0.02:99 +chr1 4911242 rs9426489 G T 99.79 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.42;MQ=59.58;MQ0=0;OQ=1563.55;QD=28.43;SB=-641.98 GT:AD:DP:GL:GQ 1/1:2,53:45:-159.96,-13.56,-0.02:99 +chr1 4911262 rs9426490 A G 133.69 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=2076.79;QD=34.05;SB=-972.82 GT:AD:DP:GL:GQ 1/1:0,61:59:-211.29,-17.77,-0.02:99 +chr1 4911898 rs7522655 C T 592.58 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2724.61;QD=40.67;SB=-1189.07 GT:AD:DP:GL:GQ 1/1:0,67:67:-276.06,-20.18,-0.01:99 +chr1 4911961 rs7544541 G A 150.94 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=1.61;MQ=59.39;MQ0=0;OQ=2947.98;QD=38.79;SB=-1404.70 GT:AD:DP:GL:GQ 1/1:1,75:74:-298.40,-22.29,-0.02:99 +chr1 4911968 rs7544542 G A 170.72 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.72;MQ0=0;OQ=3112.64;QD=37.96;SB=-1553.08 GT:AD:DP:GL:GQ 1/1:0,82:78:-314.87,-23.50,-0.02:99 +chr1 4912150 rs9426469 G A 193 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.69;MQ0=0;OQ=2864.62;QD=38.19;SB=-1302.32 GT:AD:DP:GL:GQ 1/1:0,75:72:-290.07,-21.69,-0.02:99 +chr1 4913505 rs9426491 A G 394.38 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.04;MQ0=0;OQ=3121.73;QD=35.88;SB=-1295.55 GT:AD:DP:GL:GQ 1/1:0,87:85:-315.78,-25.60,-0.02:99 +chr1 4914443 rs6692780 T C 192.39 PASS AC=2;AF=1.00;AN=2;DB;DP=103;Dels=0.00;HRun=0;HaplotypeScore=2.33;MQ=59.62;MQ0=0;OQ=3691.18;QD=35.84;SB=-1586.36 GT:AD:DP:GL:GQ 1/1:1,102:102:-368.12,-30.72,-0.04:99 +chr1 4914588 rs6701289 G A 24.03 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=4;HaplotypeScore=1.20;MQ=58.58;MQ0=0;OQ=3206.41;QD=40.08;SB=-1396.85 GT:AD:DP:GL:GQ 1/1:0,80:78:-324.24,-23.49,-0.01:99 +chr1 4915327 rs6693486 A T 79.70 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=0.67;MQ=59.04;MQ0=0;OQ=2495.92;QD=36.70;SB=-983.49 GT:AD:DP:GL:GQ 1/1:0,68:67:-253.20,-20.19,-0.02:99 +chr1 4915704 rs6656223 G A 492.16 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1843.82;QD=39.23;SB=-720.96 GT:AD:DP:GL:GQ 1/1:0,47:46:-187.98,-13.86,-0.01:99 +chr1 4917206 rs12098076 G A 321.24 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.37;MQ0=0;OQ=1024.17;QD=17.36;SB=-411.74 GT:AD:DP:GL:GQ 0/1:27,32:58:-123.18,-17.47,-93.16:99 +chr1 4918178 rs9426470 C A 210.31 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=2272.14;QD=33.41;SB=-999.37 GT:AD:DP:GL:GQ 1/1:0,68:66:-230.83,-19.89,-0.03:99 +chr1 4918637 rs6696925 G C 480.06 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.39;MQ0=0;OQ=1020.90;QD=16.74;SB=-452.39 GT:AD:DP:GL:GQ 0/1:33,28:59:-123.15,-17.78,-134.82:99 +chr1 4920934 rs7546019 A G 7.79 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=3.94;MQ=55.17;MQ0=0;OQ=1312.69;QD=25.74;SB=-576.91 GT:AD:DP:GL:GQ 1/1:0,51:42:-134.90,-12.67,-0.04:99 +chr1 4920939 rs10799143 A G 1.06 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=9.55;MQ=55.37;MQ0=0;OQ=685.84;QD=14.29;SB=-109.82 GT:AD:DP:GL:GQ 1/1:0,38:24:-75.74,-10.17,-3.57:66.02 +chr1 4920972 rs10753343 C T 150.22 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=58.67;MQ0=0;OQ=1219.60;QD=34.85;SB=-488.14 GT:AD:DP:GL:GQ 1/1:0,34:33:-125.56,-9.95,-0.02:99 +chr1 4921030 rs10799144 A G 161.31 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=1;HaplotypeScore=1.20;MQ=58.57;MQ0=0;OQ=1984.77;QD=33.64;SB=-769.10 GT:AD:DP:GL:GQ 1/1:0,59:57:-202.08,-17.17,-0.02:99 +chr1 4921060 rs10799145 T G 245.52 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.09;MQ=58.90;MQ0=0;OQ=1759.60;QD=29.82;SB=-867.69 GT:AD:DP:GL:GQ 1/1:0,59:58:-179.61,-17.49,-0.06:99 +chr1 4921319 . C T 71.66 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=56.87;MQ0=0;OQ=1537.50;QD=20.78;SB=-754.34 GT:AD:DP:GL:GQ 0/1:29,45:71:-178.43,-21.40,-86.91:99 +chr1 4921542 . G A 297.10 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.57;MQ0=0;OQ=827.15;QD=15.32;SB=-385.90 GT:AD:DP:GL:GQ 0/1:29,25:54:-102.27,-16.28,-92.99:99 +chr1 4921651 . A G 14.60 PASS AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.42;MQ0=0;OQ=1167.54;QD=16.22;SB=-587.69 GT:AD:DP:GL:GQ 0/1:31,41:71:-141.43,-21.39,-125.09:99 +chr1 4921748 . T C 1.07 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=7.77;MQ=59.39;MQ0=0;OQ=610.60;QD=12.72;SB=-231.30 GT:AD:DP:GL:GQ 0/1:26,22:47:-78.51,-14.17,-96.88:99 +chr1 4921801 . A G 290.73 PASS AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=740.93;QD=13.98;SB=-339.17 GT:AD:DP:GL:GQ 0/1:24,29:53:-93.36,-15.98,-94.97:99 +chr1 4921915 rs12118118 A G 141.47 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.35;MQ=59.65;MQ0=0;OQ=641.25;QD=9.87;SB=-176.55 GT:AD:DP:GL:GQ 0/1:39,26:63:-86.39,-18.98,-152.81:99 +chr1 4922627 rs12119864 T C 423.73 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=58.63;MQ0=0;OQ=1289.06;QD=15.17;SB=-556.56 GT:AD:DP:GL:GQ 0/1:33,52:81:-156.60,-24.41,-132.69:99 +chr1 4923016 rs6426374 A G 591.79 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.54;MQ0=0;OQ=2408.23;QD=29.37;SB=-1057.43 GT:AD:DP:GL:GQ 1/1:0,82:76:-244.48,-22.92,-0.07:99 +chr1 4923151 . C T 132.84 PASS AC=1;AF=0.50;AN=2;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.33;MQ0=0;OQ=908.76;QD=16.23;SB=-453.45 GT:AD:DP:GL:GQ 0/1:28,28:56:-111.04,-16.88,-89.80:99 +chr1 4923249 . A G 76.65 PASS AC=1;AF=0.50;AN=2;DP=44;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=58.95;MQ0=0;OQ=491.85;QD=11.18;SB=-227.32 GT:AD:DP:GL:GQ 0/1:25,19:38:-63.92,-11.45,-77.07:99 +chr1 4923272 . A G 41.93 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=2.77;MQ=59.16;MQ0=0;OQ=549.57;QD=9.99;SB=-300.17 GT:AD:DP:GL:GQ 0/1:32,23:55:-74.82,-16.58,-127.48:99 +chr1 4923290 rs6702660 A G 624.31 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1543.54;QD=30.27;SB=-737.76 GT:AD:DP:GL:GQ 1/1:0,51:50:-157.99,-15.08,-0.05:99 +chr1 4923916 . G A 53.20 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=57.14;MQ0=0;OQ=1330.08;QD=17.97;SB=-412.89 GT:AD:DP:GL:GQ 0/1:35,39:72:-157.99,-21.70,-107.79:99 +chr1 4923977 . T C 92.93 PASS AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.60;MQ=56.31;MQ0=0;OQ=878.08;QD=13.94;SB=-397.92 GT:AD:DP:GL:GQ 0/1:29,34:62:-109.78,-18.69,-109.67:99 +chr1 4924245 rs7523398 G T 624.90 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.01;HRun=0;HaplotypeScore=0.00;MQ=52.50;MQ0=0;OQ=2976.14;QD=35.01;SB=-1222.44 GT:AD:DP:GL:GQ 1/1:0,84:82:-301.22,-24.40,-0.02:99 +chr1 4924289 . C T 145.80 Indel AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=20.35;MQ=47.42;MQ0=2;QD=1.80;SB=-17.33 GT:AD:DP:GL:GQ 0/1:69,12:76:-40.75,-22.89,-240.21:99 +chr1 4924318 . A G 303.69 PASS AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.53;MQ0=0;OQ=1150.10;QD=15.13;SB=-395.92 GT:AD:DP:GL:GQ 0/1:29,47:72:-140.00,-21.70,-115.03:99 +chr1 4924353 . A G 6.39 PASS AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=1;HaplotypeScore=4.52;MQ=59.31;MQ0=0;OQ=1199.85;QD=16.00;SB=-524.06 GT:AD:DP:GL:GQ 0/1:32,42:73:-145.26,-21.99,-127.06:99 +chr1 4924370 . T G 76.39 PASS AC=1;AF=0.50;AN=2;DP=78;Dels=0.00;HRun=0;HaplotypeScore=1.99;MQ=60.52;MQ0=0;OQ=1415.60;QD=18.15;SB=-500.81 GT:AD:DP:GL:GQ 0/1:31,47:78:-168.34,-23.49,-113.39:99 +chr1 4924651 rs140619 A C 98.30 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=1.45;MQ=58.44;MQ0=0;OQ=1008.29;QD=14.00;SB=-504.32 GT:AD:DP:GL:GQ 0/1:36,36:69:-124.90,-20.78,-122.36:99 +chr1 4924659 rs140620 C G 66.97 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=2;HaplotypeScore=3.55;MQ=58.47;MQ0=0;OQ=1278.05;QD=17.51;SB=-626.38 GT:AD:DP:GL:GQ 0/1:37,36:72:-152.80,-21.71,-149.62:99 +chr1 4924842 rs3101217 G A 427.04 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.23;MQ=60.00;MQ0=0;OQ=946.64;QD=12.46;SB=-438.36 GT:AD:DP:GL:GQ 0/1:44,31:68:-118.44,-20.49,-128.20:99 +chr1 4924889 rs3101218 G C 576.23 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=1334.27;QD=16.68;SB=-624.99 GT:AD:DP:GL:GQ 0/1:41,39:77:-159.91,-23.20,-177.20:99 +chr1 4924920 rs3101219 T C 593.97 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1041.98;QD=16.28;SB=-455.18 GT:AD:DP:GL:GQ 0/1:28,36:64:-126.76,-19.28,-110.51:99 +chr1 4924999 rs3101220 G C 298.13 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.20;MQ0=0;OQ=811.79;QD=14.00;SB=-233.01 GT:AD:DP:GL:GQ 0/1:32,26:57:-101.64,-17.18,-138.57:99 +chr1 4925039 rs3128678 A G 0.26 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=4;HaplotypeScore=3.38;MQ=59.22;MQ0=0;OQ=1744.26;QD=32.30;SB=-816.04 GT:AD:DP:GL:GQ 1/1:0,54:50:-178.03,-15.06,-0.02:99 +chr1 4925077 rs3101221 C A 25.14 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.44;MQ=58.58;MQ0=0;OQ=647.61;QD=11.56;SB=-325.00 GT:AD:DP:GL:GQ 0/1:30,26:49:-82.82,-14.77,-78.79:99 +chr1 4925169 rs3128679 A G 107.98 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.44;MQ=60.00;MQ0=0;OQ=535.15;QD=8.92;SB=-144.42 GT:AD:DP:GL:GQ 0/1:36,24:59:-74.58,-17.78,-140.21:99 +chr1 4925429 rs3128680 G A 469.33 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=766.43;QD=14.46;SB=-348.86 GT:AD:DP:GL:GQ 0/1:29,24:53:-95.89,-15.97,-104.44:99 +chr1 4925430 rs3101222 C G 427.23 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=771.83;QD=15.13;SB=-299.97 GT:AD:DP:GL:GQ 0/1:28,23:50:-95.55,-15.08,-110.57:99 +chr1 4925635 rs3101223 A G 252.82 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=59.74;MQ0=0;OQ=1091.51;QD=12.26;SB=-378.11 GT:AD:DP:GL:GQ 0/1:48,41:87:-138.64,-26.21,-194.64:99 +chr1 4926101 rs3128681 G A 350.75 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.95;MQ=59.68;MQ0=0;OQ=1174.87;QD=16.55;SB=-610.10 GT:AD:DP:GL:GQ 0/1:35,35:70:-141.86,-21.09,-114.49:99 +chr1 4926299 rs1017724 C T 190.62 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1174.58;QD=15.06;SB=-383.10 GT:AD:DP:GL:GQ 0/1:41,37:77:-143.94,-23.19,-149.98:99 +chr1 4926372 rs1017726 A G 298.07 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=887.74;QD=17.07;SB=-423.28 GT:AD:DP:GL:GQ 0/1:22,30:52:-107.72,-15.67,-84.02:99 +chr1 4926476 rs3128682 A G 470.65 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=981.70;QD=13.27;SB=-502.91 GT:AD:DP:GL:GQ 0/1:33,41:71:-122.87,-21.41,-123.57:99 +chr1 4926532 rs3128683 G T 372.36 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.69;MQ0=0;OQ=1069.82;QD=14.26;SB=-471.94 GT:AD:DP:GL:GQ 0/1:37,38:72:-131.95,-21.69,-128.03:99 +chr1 4926586 rs34841047 T C 307.90 PASS AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.74;MQ0=0;OQ=1407.30;QD=15.64;SB=-662.64 GT:AD:DP:GL:GQ 0/1:42,48:89:-170.82,-26.81,-167.25:99 +chr1 4926613 rs7547938 A C 101.18 PASS AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=59.79;MQ0=0;OQ=2670.20;QD=30.00;SB=-1246.34 GT:AD:DP:GL:GQ 1/1:1,88:87:-270.68,-26.22,-0.07:99 +chr1 4926617 . G A 38.65 PASS AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=1;HaplotypeScore=1.60;MQ=59.78;MQ0=0;OQ=1691.34;QD=19.90;SB=-782.69 GT:AD:DP:GL:GQ 0/1:36,49:84:-197.72,-25.30,-133.23:99 +chr1 4926705 rs10799146 C G 149.65 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=59.64;MQ0=0;OQ=2201.93;QD=42.34;SB=-980.37 GT:AD:DP:GL:GQ 1/1:0,52:52:-223.80,-15.67,-0.02:99 +chr1 4926719 . T C 99.55 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=59.60;MQ0=0;OQ=721.00;QD=12.65;SB=-331.93 GT:AD:DP:GL:GQ 0/1:26,31:55:-91.96,-16.58,-103.71:99 +chr1 4926770 . T G 92.62 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.63;MQ=58.93;MQ0=0;OQ=842.91;QD=13.82;SB=-346.83 GT:AD:DP:GL:GQ 0/1:28,33:58:-105.05,-17.47,-101.93:99 +chr1 4926781 rs10915300 G A 186.83 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=58.91;MQ0=0;OQ=2257.64;QD=37.63;SB=-1055.32 GT:AD:DP:GL:GQ 1/1:0,60:57:-229.37,-17.17,-0.02:99 +chr1 4927339 rs6426375 C A 293.44 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.63;MQ0=0;OQ=1104.83;QD=17.54;SB=-437.22 GT:AD:DP:GL:GQ 0/1:25,38:59:-131.54,-17.77,-79.77:99 +chr1 4927361 rs12122012 G C 449.67 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=855.62;QD=14.50;SB=-302.94 GT:AD:DP:GL:GQ 0/1:34,25:57:-106.02,-17.18,-140.73:99 +chr1 4927449 rs12129823 C A 265.42 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.57;MQ=58.95;MQ0=0;OQ=867.88;QD=14.00;SB=-380.76 GT:AD:DP:GL:GQ 0/1:32,30:60:-108.15,-18.08,-97.33:99 +chr1 4927847 rs12122183 G A 490.19 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=1239.90;QD=16.31;SB=-577.98 GT:AD:DP:GL:GQ 0/1:38,38:75:-149.87,-22.60,-137.70:99 +chr1 4928324 rs10799147 T G 316.36 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.64;MQ0=0;OQ=672.70;QD=12.94;SB=-277.80 GT:AD:DP:GL:GQ 0/1:27,25:51:-85.91,-15.36,-101.41:99 +chr1 4928782 . A T 20.70 PASS AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=58.98;MQ0=0;OQ=748.61;QD=18.26;SB=-256.98 GT:AD:DP:GL:GQ 0/1:17,24:41:-90.49,-12.35,-66.37:99 +chr1 4930115 rs10799148 T G 517.72 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=2291.16;QD=34.71;SB=-1027.09 GT:AD:DP:GL:GQ 1/1:0,66:65:-232.72,-19.58,-0.02:99 +chr1 4930427 rs34645017 G C 291.45 PASS AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=722.42;QD=16.05;SB=-202.61 GT:AD:DP:GL:GQ 0/1:25,20:45:-89.08,-13.56,-109.77:99 +chr1 4930735 rs11578909 A G 280.08 PASS AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=59.36;MQ0=0;OQ=698.77;QD=12.05;SB=-374.99 GT:AD:DP:GL:GQ 0/1:29,28:57:-90.34,-17.18,-117.72:99 +chr1 4931239 rs10799149 G A 641.63 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.08;MQ0=0;OQ=2438.74;QD=39.98;SB=-916.20 GT:AD:DP:GL:GQ 1/1:0,61:60:-247.47,-18.07,-0.01:99 +chr1 4931421 rs7518523 A G 261.63 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.88;MQ0=0;OQ=2083.34;QD=31.09;SB=-1042.40 GT:AD:DP:GL:GQ 1/1:0,67:65:-211.96,-19.60,-0.05:99 +chr1 4931997 rs10753344 T C 618.70 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2888.62;QD=33.98;SB=-1001.71 GT:AD:DP:GL:GQ 1/1:0,85:82:-292.48,-24.71,-0.04:99 +chr1 4932316 rs12127329 G A 183.50 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=60.00;MQ0=0;OQ=2411.54;QD=39.53;SB=-1136.02 GT:AD:DP:GL:GQ 1/1:0,61:61:-244.76,-18.38,-0.02:99 +chr1 4932881 rs11585724 C T 291.52 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.68;MQ=59.24;MQ0=0;OQ=985.86;QD=16.16;SB=-484.11 GT:AD:DP:GL:GQ 0/1:30,31:59:-119.65,-17.78,-92.67:99 +chr1 4932899 rs56016205 G C 205.73 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.90;MQ=58.78;MQ0=0;OQ=942.89;QD=16.54;SB=-283.52 GT:AD:DP:GL:GQ 0/1:30,27:56:-114.45,-16.88,-128.26:99 +chr1 4933102 rs56190527 G A 17.84 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=7.39;MQ=59.07;MQ0=0;OQ=754.79;QD=15.10;SB=-398.92 GT:AD:DP:GL:GQ 0/1:26,24:48:-93.22,-14.46,-90.86:99 +chr1 4933190 rs56216708 T C 104.26 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=0.32;MQ=59.13;MQ0=0;OQ=1884.00;QD=35.55;SB=-879.00 GT:AD:DP:GL:GQ 1/1:0,53:53:-192.00,-15.97,-0.02:99 +chr1 4933296 . G A 768.22 SnpCluster AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.45;MQ0=0;QD=12.59;SB=-376.12 GT:AD:DP:GL:GQ 0/1:35,26:58:-97.59,-17.48,-110.76:99 +chr1 4933297 . C T 815.45 SnpCluster AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.45;MQ0=0;QD=13.37;SB=-431.91 GT:AD:DP:GL:GQ 0/1:35,26:61:-103.20,-18.37,-126.35:99 +chr1 4933303 . G A 803.12 SnpCluster AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.37;MQ0=0;QD=13.39;SB=-365.85 GT:AD:DP:GL:GQ 0/1:35,25:58:-101.08,-17.48,-105.94:99 +chr1 4933521 rs7535462 G A 371.82 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.07;MQ0=0;OQ=1957.02;QD=39.14;SB=-986.02 GT:AD:DP:GL:GQ 1/1:0,50:49:-199.30,-14.76,-0.01:99 +chr1 4933673 . C G 6.69 PASS AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=58.23;MQ0=0;OQ=1494.10;QD=22.64;SB=-505.26 GT:AD:DP:GL:GQ 0/1:26,40:63:-171.68,-18.99,-100.63:99 +chr1 4934014 rs12128545 G A 43.64 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=59.66;MQ0=0;OQ=1421.27;QD=20.90;SB=-664.71 GT:AD:DP:GL:GQ 0/1:27,41:67:-165.59,-20.18,-95.71:99 +chr1 4934078 rs12136209 C G 149.50 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.61;MQ=60.00;MQ0=0;OQ=1636.42;QD=21.82;SB=-832.32 GT:AD:DP:GL:GQ 0/1:31,44:75:-189.53,-22.60,-132.33:99 +chr1 4934416 rs12126894 T G 441.68 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.57;MQ0=0;OQ=586.00;QD=11.49;SB=-304.83 GT:AD:DP:GL:GQ 0/1:29,22:51:-77.25,-15.36,-105.02:99 +chr1 4935048 rs10915303 A G 334.36 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.69;MQ=51.50;MQ0=0;OQ=770.15;QD=12.84;SB=-364.97 GT:AD:DP:GL:GQ 0/1:27,33:52:-95.98,-15.68,-87.76:99 +chr1 4935474 rs34001007 G A 343.02 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=962.36;QD=16.88;SB=-495.13 GT:AD:DP:GL:GQ 0/1:27,30:56:-116.40,-16.88,-86.00:99 +chr1 4935789 rs12128035 T C 226.01 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.43;MQ=58.94;MQ0=0;OQ=796.37;QD=12.64;SB=-306.28 GT:AD:DP:GL:GQ 0/1:34,29:62:-101.60,-18.68,-137.85:99 +chr1 4936034 rs6689050 G C 388.76 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1874.06;QD=42.59;SB=-652.91 GT:AD:DP:GL:GQ 1/1:0,44:44:-191.00,-13.26,-0.01:99 +chr1 4936094 rs12757902 G A 302.17 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=59.62;MQ0=0;OQ=578.28;QD=11.80;SB=-268.20 GT:AD:DP:GL:GQ 0/1:27,21:43:-74.09,-12.98,-70.80:99 +chr1 4936362 rs12126016 G T 367.30 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.41;MQ0=0;OQ=1064.42;QD=14.99;SB=-543.63 GT:AD:DP:GL:GQ 0/1:34,37:71:-131.11,-21.39,-120.19:99 +chr1 4936409 rs11581023 G A 329.13 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=58.70;MQ0=0;OQ=1088.63;QD=16.49;SB=-413.38 GT:AD:DP:GL:GQ 0/1:32,34:63:-131.13,-18.99,-102.39:99 +chr1 4936482 rs12122541 A G 353.13 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=58.04;MQ0=0;OQ=684.77;QD=12.45;SB=-247.32 GT:AD:DP:GL:GQ 0/1:27,28:52:-87.43,-15.67,-100.04:99 +chr1 4936602 rs11584985 C T 191.63 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.33;MQ=59.29;MQ0=0;OQ=1088.30;QD=18.45;SB=-387.41 GT:AD:DP:GL:GQ 0/1:25,34:57:-129.30,-17.18,-77.34:99 +chr1 4936637 rs898335 T G 589.23 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2347.69;QD=35.57;SB=-808.10 GT:AD:DP:GL:GQ 1/1:0,66:66:-238.37,-19.88,-0.02:99 +chr1 4937911 rs12739724 G A 135.48 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=59.34;MQ0=0;OQ=1173.07;QD=20.58;SB=-518.55 GT:AD:DP:GL:GQ 0/1:24,33:57:-137.76,-17.17,-89.96:99 +chr1 4937953 rs6666618 A C 126.74 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=60.00;MQ0=0;OQ=1008.55;QD=15.28;SB=-391.76 GT:AD:DP:GL:GQ 0/1:30,36:65:-123.72,-19.58,-111.64:99 +chr1 4939240 rs1841241 A G 358.83 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.81;MQ=59.68;MQ0=0;OQ=900.69;QD=12.34;SB=-390.90 GT:AD:DP:GL:GQ 0/1:37,36:72:-115.05,-21.70,-146.81:99 +chr1 4939654 rs6660626 C G 245.03 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=59.55;MQ0=0;OQ=1495.04;QD=18.01;SB=-651.03 GT:AD:DP:GL:GQ 0/1:41,42:81:-177.21,-24.42,-163.44:99 +chr1 4940611 . A G 75.27 PASS AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.50;MQ0=0;OQ=761.25;QD=16.55;SB=-322.41 GT:AD:DP:GL:GQ 0/1:18,28:44:-92.67,-13.26,-69.31:99 +chr1 4941180 rs12138041 C G 147.56 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.43;MQ0=0;OQ=1446.36;QD=22.25;SB=-675.09 GT:AD:DP:GL:GQ 0/1:27,38:64:-167.20,-19.28,-114.12:99 +chr1 4941754 rs6426376 A C 0.05 FDRtranche0.10to1.00 AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=6;HaplotypeScore=1.65;MQ=58.89;MQ0=0;OQ=2125.54;QD=33.74;SB=-942.08 GT:AD:DP:GL:GQ 1/1:0,63:61:-216.16,-18.37,-0.02:99 +chr1 4942581 . C G 69.18 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.19;MQ0=0;OQ=1081.86;QD=18.98;SB=-432.32 GT:AD:DP:GL:GQ 0/1:28,29:57:-128.65,-17.18,-121.65:99 +chr1 4942801 rs12132419 G A 594.05 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.75;MQ0=0;OQ=1256.99;QD=16.76;SB=-497.49 GT:AD:DP:GL:GQ 0/1:35,40:73:-150.98,-21.99,-126.45:99 +chr1 4943594 rs1563791 C A 403.62 PASS AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.16;MQ=58.68;MQ0=0;OQ=828.65;QD=15.63;SB=-357.20 GT:AD:DP:GL:GQ 0/1:25,28:53:-102.11,-15.96,-89.65:99 +chr1 4943942 rs10737391 T A 518.14 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.47;MQ0=0;OQ=2837.87;QD=37.84;SB=-993.50 GT:AD:DP:GL:GQ 1/1:0,75:74:-287.39,-22.29,-0.02:99 +chr1 4943949 rs6674570 C G 129.66 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.29;MQ0=0;OQ=3029.36;QD=43.28;SB=-1059.65 GT:AD:DP:GL:GQ 1/1:0,70:69:-306.54,-20.79,-0.02:99 +chr1 4943976 rs6689766 T C 365.66 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=56.77;MQ0=0;OQ=827.54;QD=14.03;SB=-391.26 GT:AD:DP:GL:GQ 0/1:29,30:57:-103.21,-17.17,-110.62:99 +chr1 4943997 rs6698166 G T 369.44 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.73;MQ0=0;OQ=860.15;QD=13.87;SB=-411.14 GT:AD:DP:GL:GQ 0/1:31,31:60:-107.37,-18.08,-104.72:99 +chr1 4943998 rs6698167 G A 353.24 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.73;MQ0=0;OQ=1051.24;QD=16.96;SB=-519.06 GT:AD:DP:GL:GQ 0/1:30,32:61:-126.79,-18.38,-103.11:99 +chr1 4944360 rs12131010 A G 342.06 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=58.85;MQ0=0;OQ=760.68;QD=9.88;SB=-317.87 GT:AD:DP:GL:GQ 0/1:43,34:75:-101.96,-22.60,-172.57:99 +chr1 4944890 rs1106586 G A 276.08 PASS AC=1;AF=0.50;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=1.40;MQ=59.59;MQ0=0;OQ=802.40;QD=14.33;SB=-392.78 GT:AD:DP:GL:GQ 0/1:30,26:55:-100.10,-16.58,-95.63:99 +chr1 4945646 rs898336 G C 25.91 PASS AC=2;AF=1.00;AN=2;DB;DP=96;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=56.72;MQ0=0;OQ=4154.41;QD=43.28;SB=-1921.01 GT:AD:DP:GL:GQ 1/1:0,96:94:-414.44,-28.32,-0.03:99 +chr1 4945654 rs7417805 T C 207.20 PASS AC=2;AF=1.00;AN=2;DB;DP=101;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=56.30;MQ0=0;OQ=3685.03;QD=36.49;SB=-1843.78 GT:AD:DP:GL:GQ 1/1:0,101:100:-367.50,-30.12,-0.02:99 +chr1 4946090 rs12046931 C T 231 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=2.55;MQ=56.28;MQ0=0;OQ=1030.23;QD=13.56;SB=-511.04 GT:AD:DP:GL:GQ 0/1:44,32:74:-128.62,-22.31,-131.20:99 +chr1 4946898 rs6679312 A G 627.33 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.42;MQ0=0;OQ=2846.93;QD=36.04;SB=-1277.52 GT:AD:DP:GL:GQ 1/1:0,79:79:-288.30,-23.79,-0.02:99 +chr1 4947277 . A C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=64;Dels=0.00;HRun=1;HaplotypeScore=4.31;MQ=58.55;MQ0=0;OQ=58.76;QD=0.92;SB=83.26 GT:AD:DP:GL:GQ 0/1:39,25:47:-23.33,-14.17,-133.19:91.60 +chr1 4947969 rs716671 G T 362.39 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=0.74;MQ=59.37;MQ0=0;OQ=959.61;QD=14.54;SB=-385.78 GT:AD:DP:GL:GQ 0/1:32,34:63:-118.22,-18.98,-106.13:99 +chr1 4948484 rs7541612 T C 301.06 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.16;MQ0=0;OQ=2459.32;QD=34.16;SB=-1006.88 GT:AD:DP:GL:GQ 1/1:0,72:70:-249.54,-21.08,-0.02:99 +chr1 4948794 rs10737392 A C 185.94 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2094.20;QD=29.50;SB=-992.36 GT:AD:DP:GL:GQ 1/1:0,71:69:-213.07,-20.80,-0.07:99 +chr1 4951092 rs12725971 A G 439.70 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.52;MQ0=0;OQ=1026.84;QD=13.16;SB=-423.90 GT:AD:DP:GL:GQ 0/1:43,35:78:-129.46,-23.49,-174.67:99 +chr1 4951570 rs6683624 C T 353.86 PASS AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=59.06;MQ0=0;OQ=1065.83;QD=15.45;SB=-486.02 GT:AD:DP:GL:GQ 0/1:35,34:67:-130.05,-20.19,-121.88:99 +chr1 4953123 rs7418901 T C 620.55 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=2650.80;QD=31.56;SB=-1309.87 GT:AD:DP:GL:GQ 1/1:0,84:83:-268.73,-25.03,-0.06:99 +chr1 4955464 rs1459754 T C 197.18 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.56;MQ0=0;OQ=2710.14;QD=31.88;SB=-1351.75 GT:AD:DP:GL:GQ 1/1:0,85:84:-274.67,-25.33,-0.07:99 +chr1 4956424 rs12566071 T C 456.39 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.68;MQ0=0;OQ=1092.05;QD=27.30;SB=-412.16 GT:AD:DP:GL:GQ 1/1:0,40:36:-112.83,-10.86,-0.04:99 +chr1 4956725 rs12047194 C T 71.14 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.61;MQ=60.00;MQ0=0;OQ=1049.88;QD=16.93;SB=-178.21 GT:AD:DP:GL:GQ 0/1:29,33:61:-126.65,-18.37,-103.04:99 +chr1 4957085 . G A 6.71 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.62;MQ0=0;OQ=1318.00;QD=21.61;SB=-441.83 GT:AD:DP:GL:GQ 0/1:23,38:60:-153.16,-18.08,-75.01:99 +chr1 4957708 rs9701766 C T 287.33 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=59.24;MQ0=0;OQ=1921.26;QD=34.93;SB=-917.67 GT:AD:DP:GL:GQ 1/1:0,55:50:-195.73,-15.07,-0.02:99 +chr1 4957732 rs12134477 T G 328.37 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.88;MQ=59.35;MQ0=0;OQ=737.05;QD=11.52;SB=-389.76 GT:AD:DP:GL:GQ 0/1:34,30:62:-95.67,-18.68,-123.44:99 +chr1 4960336 rs9286972 T C 80.40 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=3;HaplotypeScore=0.87;MQ=59.38;MQ0=0;OQ=2352.51;QD=35.11;SB=-877.01 GT:AD:DP:GL:GQ 1/1:0,67:65:-238.86,-19.58,-0.02:99 +chr1 4960363 rs9286973 A G 217.69 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.91;MQ=58.74;MQ0=0;OQ=2328.65;QD=33.27;SB=-776.20 GT:AD:DP:GL:GQ 1/1:0,68:66:-236.47,-19.88,-0.02:99 +chr1 4960544 rs10158116 T C 435.93 PASS AC=2;AF=1.00;AN=2;DB;DP=28;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=930.68;QD=33.24;SB=-423.17 GT:AD:DP:GL:GQ 1/1:0,28:27:-96.66,-8.13,-0.01:81.23 +chr1 4961077 rs1380469 C T 600.30 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=3571.25;QD=40.58;SB=-1432.72 GT:AD:DP:GL:GQ 1/1:0,88:87:-356.13,-26.20,-0.02:99 +chr1 4961379 rs10158288 T C 503.56 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=2541.28;QD=30.99;SB=-793.00 GT:AD:DP:GL:GQ 1/1:0,82:80:-257.79,-24.13,-0.07:99 +chr1 4963153 rs10915307 G A 69.93 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=1.45;MQ=59.07;MQ0=0;OQ=713.61;QD=14.27;SB=-252.29 GT:AD:DP:GL:GQ 0/1:25,25:45:-88.21,-13.57,-68.76:99 +chr1 4964065 rs10737393 G C 566.31 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1749.68;QD=40.69;SB=-797.25 GT:AD:DP:GL:GQ 1/1:0,43:42:-178.57,-12.66,-0.02:99 +chr1 4964532 rs28667637 T C 501.28 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=1316.20;QD=16.05;SB=-509.69 GT:AD:DP:GL:GQ 0/1:33,49:82:-159.62,-24.71,-131.78:99 +chr1 4964976 rs12027167 C T 376.96 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.50;MQ0=0;OQ=1085.57;QD=14.47;SB=-544.31 GT:AD:DP:GL:GQ 0/1:42,33:75:-134.44,-22.60,-148.57:99 +chr1 4965052 rs28444318 G A 401.64 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.69;MQ0=0;OQ=1204.51;QD=18.82;SB=-457.96 GT:AD:DP:GL:GQ 0/1:28,36:62:-142.42,-18.68,-88.92:99 +chr1 4965449 rs10915308 C T 686.42 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=2543.15;QD=38.53;SB=-937.28 GT:AD:DP:GL:GQ 1/1:0,66:64:-257.91,-19.28,-0.02:99 +chr1 4965556 rs12123277 C A 350.21 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=722.36;QD=9.63;SB=-338.31 GT:AD:DP:GL:GQ 0/1:48,27:74:-97.81,-22.29,-174.39:99 +chr1 4965577 rs1380470 A G 738.02 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2392.77;QD=36.25;SB=-1196.76 GT:AD:DP:GL:GQ 1/1:0,66:66:-242.88,-19.88,-0.01:99 +chr1 4965710 rs10915309 G A 204.24 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=59.60;MQ0=0;OQ=2319.12;QD=39.98;SB=-986.30 GT:AD:DP:GL:GQ 1/1:0,58:58:-235.51,-17.47,-0.02:99 +chr1 4968070 rs10915310 A G 390.05 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=59.15;MQ0=0;OQ=1179.59;QD=14.39;SB=-449.76 GT:AD:DP:GL:GQ 0/1:38,44:81:-145.65,-24.41,-157.59:99 +chr1 4968105 rs10799151 A G 154.91 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=3.73;MQ=58.89;MQ0=0;OQ=1031.60;QD=12.74;SB=-406.80 GT:AD:DP:GL:GQ 0/1:40,41:78:-129.95,-23.51,-157.15:99 +chr1 4968710 . C G 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.90;MQ=53.48;MQ0=0;OQ=64.03;QD=1.56;SB=-49.12 GT:AD:DP:GL:GQ 0/1:36,5:37:-20.84,-11.15,-143.24:96.86 +chr1 4968815 rs10915311 A C 217.55 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.03;MQ0=0;OQ=2004.53;QD=29.92;SB=-920.78 GT:AD:DP:GL:GQ 1/1:0,66:64:-204.09,-19.29,-0.06:99 +chr1 4969030 rs34951087 G T 218.41 PASS AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=59.09;MQ0=0;OQ=572.86;QD=11.23;SB=-277.34 GT:AD:DP:GL:GQ 0/1:30,21:51:-75.93,-15.36,-106.99:99 +chr1 4970267 rs10915312 A G 154.58 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=2;HaplotypeScore=1.56;MQ=58.90;MQ0=0;OQ=985.64;QD=12.32;SB=-409.96 GT:AD:DP:GL:GQ 0/1:41,39:79:-125.65,-23.81,-166.76:99 +chr1 4970523 rs12045336 A G 132 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.57;MQ=59.62;MQ0=0;OQ=1080.57;QD=17.71;SB=-383.65 GT:AD:DP:GL:GQ 0/1:25,36:60:-129.41,-18.07,-101.07:99 +chr1 4971344 . A C 49.60 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=45.73;MQ=55.38;MQ0=0;QD=0.57;SB=95.30 GT:AD:DP:GL:GQ 0/1:77,10:78:-31.75,-23.50,-240.44:82.44 +chr1 4972155 rs1870516 C T 119.50 PASS AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=2;HaplotypeScore=2.64;MQ=59.76;MQ0=0;OQ=1584.03;QD=16.67;SB=-599.54 GT:AD:DP:GL:GQ 0/1:49,46:91:-189.10,-27.42,-151.90:99 +chr1 4972838 rs1459756 T C 570.91 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=978.37;QD=13.22;SB=-505.27 GT:AD:DP:GL:GQ 0/1:38,36:72:-122.81,-21.69,-153.16:99 +chr1 4972952 rs9286975 G A 397.79 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2673.75;QD=39.91;SB=-1305.72 GT:AD:DP:GL:GQ 1/1:0,67:67:-270.98,-20.18,-0.02:99 +chr1 4973015 rs9662653 T A 589.24 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.20;MQ0=0;OQ=1272.49;QD=16.74;SB=-576.01 GT:AD:DP:GL:GQ 0/1:36,40:76:-153.42,-22.89,-135.61:99 +chr1 4973096 rs9701780 T C 360.62 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.34;MQ0=0;OQ=907.74;QD=12.97;SB=-427.52 GT:AD:DP:GL:GQ 0/1:38,32:70:-115.14,-21.08,-154.90:99 +chr1 4973099 rs1459757 A G 435.82 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.36;MQ0=0;OQ=906.72;QD=12.59;SB=-477.95 GT:AD:DP:GL:GQ 0/1:40,32:72:-115.64,-21.69,-161.61:99 +chr1 4973396 rs10753346 T C 325.42 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.65;MQ0=0;OQ=745.38;QD=11.29;SB=-293.22 GT:AD:DP:GL:GQ 0/1:39,27:65:-97.40,-19.58,-152.44:99 +chr1 4973518 rs10799152 A C 461.39 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.77;MQ0=0;OQ=1062.89;QD=13.29;SB=-461.68 GT:AD:DP:GL:GQ 0/1:43,37:80:-133.67,-24.09,-159.84:99 +chr1 4974497 rs35292186 A G 69.66 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=59.78;MQ0=0;OQ=1148.97;QD=13.84;SB=-573.87 GT:AD:DP:GL:GQ 0/1:43,40:81:-142.58,-24.40,-174.12:99 +chr1 4976182 rs10915314 G C 291.75 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.96;MQ=60.00;MQ0=0;OQ=1306.22;QD=17.65;SB=-415.30 GT:AD:DP:GL:GQ 0/1:38,36:73:-155.90,-22.00,-163.97:99 +chr1 4977412 rs12047764 T C 324.11 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.63;MQ0=0;OQ=712.65;QD=11.49;SB=-368.84 GT:AD:DP:GL:GQ 0/1:33,29:62:-93.24,-18.69,-135.85:99 +chr1 4978209 rs10915315 A G 314.02 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.17;MQ0=0;OQ=593.55;QD=8.73;SB=-263.22 GT:AD:DP:GL:GQ 0/1:42,26:67:-82.83,-20.19,-168.85:99 +chr1 4978799 rs10915316 T C 253.84 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=3.42;MQ=59.03;MQ0=0;OQ=793.88;QD=11.03;SB=-421.21 GT:AD:DP:GL:GQ 0/1:40,31:69:-103.46,-20.78,-159.70:99 +chr1 4980236 . G A 100.41 PASS AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.79;MQ0=0;OQ=1786.33;QD=21.02;SB=-886.64 GT:AD:DP:GL:GQ 0/1:34,51:83:-206.92,-25.00,-119.27:99 +chr1 4980926 rs10915317 T C 438.47 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.66;MQ0=0;OQ=838.53;QD=12.33;SB=-314.09 GT:AD:DP:GL:GQ 0/1:34,34:67:-107.33,-20.19,-138.42:99 +chr1 4981033 rs898337 G A 348.85 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.70;MQ0=0;OQ=1302.29;QD=16.91;SB=-502.50 GT:AD:DP:GL:GQ 0/1:36,41:75:-156.11,-22.60,-126.45:99 +chr1 4981597 rs7516703 C T 165.71 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=1.76;MQ=60.19;MQ0=0;OQ=561.42;QD=9.85;SB=-184.86 GT:AD:DP:GL:GQ 0/1:36,21:54:-75.71,-16.28,-112.37:99 +chr1 4982000 rs10799153 A G 596.01 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.94;MQ0=0;OQ=1157.46;QD=16.30;SB=-464.59 GT:AD:DP:GL:GQ 0/1:32,39:71:-140.42,-21.40,-120.74:99 +chr1 4983908 . G A 17.79 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=67;Dels=0.00;HRun=16;HaplotypeScore=7.18;MQ=55.71;MQ0=0;QD=0.27;SB=86.25 GT:AD:DP:GL:GQ 0/1:51,16:49:-19.83,-14.77,-145.36:50.55 +chr1 4985809 rs9439574 C T 11.86 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=4;HaplotypeScore=0.16;MQ=58.95;MQ0=0;OQ=1576.28;QD=19.70;SB=-625.03 GT:AD:DP:GL:GQ 0/1:34,46:79:-184.71,-23.79,-124.63:99 +chr1 4985815 rs9439575 A G 487 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.98;MQ0=0;OQ=1410.52;QD=17.20;SB=-545.94 GT:AD:DP:GL:GQ 0/1:36,46:82:-169.04,-24.70,-144.72:99 +chr1 4986567 rs10218468 A C 245.59 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=789.54;QD=11.78;SB=-394.67 GT:AD:DP:GL:GQ 0/1:34,33:66:-102.12,-19.88,-128.07:99 +chr1 4987124 rs10442625 A G 373.16 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=59.63;MQ0=0;OQ=720.29;QD=11.43;SB=-219.26 GT:AD:DP:GL:GQ 0/1:37,26:62:-93.99,-18.68,-145.68:99 +chr1 4988477 rs2169089 A G 373.87 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.63;MQ=59.69;MQ0=0;OQ=1114.19;QD=14.86;SB=-356.97 GT:AD:DP:GL:GQ 0/1:29,45:72:-136.41,-21.71,-118.67:99 +chr1 4988875 rs716112 A G 453.40 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=842.62;QD=12.58;SB=-426.87 GT:AD:DP:GL:GQ 0/1:33,34:66:-107.44,-19.90,-129.75:99 +chr1 4990575 rs1459764 C T 573.83 PASS AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=1234.93;QD=15.63;SB=-612.07 GT:AD:DP:GL:GQ 0/1:42,37:78:-150.28,-23.50,-132.81:99 +chr1 4990857 rs9439507 A G 285 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.35;MQ0=0;OQ=2461.09;QD=34.66;SB=-1130.69 GT:AD:DP:GL:GQ 1/1:0,71:71:-249.72,-21.39,-0.03:99 +chr1 4991092 rs10442626 G C 211.49 PASS AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.60;MQ0=0;OQ=718.97;QD=12.61;SB=-159.21 GT:AD:DP:GL:GQ 0/1:31,26:54:-91.46,-16.28,-132.88:99 +chr1 4991687 rs4949164 A G 470.49 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=60.00;MQ0=0;OQ=1103.70;QD=13.80;SB=-401.93 GT:AD:DP:GL:GQ 0/1:38,42:79:-137.46,-23.80,-155.83:99 +chr1 4993546 rs7533014 T C 526.25 PASS AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1036.32;QD=11.39;SB=-442.91 GT:AD:DP:GL:GQ 0/1:49,42:90:-134.04,-27.12,-197.59:99 +chr1 4993852 rs11580542 A G 170.64 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.73;MQ0=0;OQ=650.23;QD=9.56;SB=-317.81 GT:AD:DP:GL:GQ 0/1:43,25:66:-88.19,-19.88,-168.41:99 +chr1 4994065 . C T 20.53 PASS AC=1;AF=0.50;AN=2;DP=71;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1330.95;QD=18.75;SB=-592.09 GT:AD:DP:GL:GQ 0/1:33,38:71:-157.76,-21.38,-120.30:99 +chr1 4994295 rs6693990 G A 335.33 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=57.88;MQ0=0;OQ=1019.69;QD=16.19;SB=-465.42 GT:AD:DP:GL:GQ 0/1:31,32:60:-123.32,-18.07,-111.15:99 +chr1 4994563 rs1459763 A G 13.43 PASS AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=5.21;MQ=58.04;MQ0=0;OQ=377.66;QD=9.21;SB=-181.57 GT:AD:DP:GL:GQ 0/1:25,16:38:-52.50,-11.45,-93.25:99 +chr1 4995722 rs1459762 C T 513.24 PASS AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=1249.58;QD=19.22;SB=-511.06 GT:AD:DP:GL:GQ 0/1:27,38:64:-147.53,-19.29,-84.78:99 +chr1 4996533 . T G 102.56 PASS AC=1;AF=0.50;AN=2;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.96;MQ=59.08;MQ0=0;OQ=597.86;QD=9.80;SB=-320.69 GT:AD:DP:GL:GQ 0/1:35,26:61:-81.45,-18.38,-132.05:99 +chr1 4999697 . C G 5.71 PASS AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.53;MQ0=0;OQ=2076.06;QD=23.59;SB=-758.01 GT:AD:DP:GL:GQ 0/1:34,54:87:-237.12,-26.23,-133.95:99 +chr1 4999785 . A G 153.89 PASS AC=1;AF=0.50;AN=2;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=59.42;MQ0=0;OQ=950.41;QD=13.20;SB=-485.20 GT:AD:DP:GL:GQ 0/1:39,33:71:-119.71,-21.39,-153.18:99 +chr1 5000124 rs35565495 A G 217.11 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.82;MQ=57.68;MQ0=0;OQ=905.68;QD=12.41;SB=-443.62 GT:AD:DP:GL:GQ 0/1:40,33:73:-115.85,-22.00,-156.82:99 +chr1 5000551 rs1459761 A G 316.71 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=2.15;MQ=59.68;MQ0=0;OQ=1082.64;QD=18.35;SB=-522.18 GT:AD:DP:GL:GQ 0/1:24,35:59:-129.32,-17.77,-97.53:99 +chr1 5002004 rs12403444 A G 454.86 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.14;MQ=59.69;MQ0=0;OQ=1008.17;QD=13.62;SB=-385.25 GT:AD:DP:GL:GQ 0/1:38,36:71:-125.49,-21.39,-141.83:99 +chr1 5002384 rs12403749 A G 334.10 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.18;MQ0=0;OQ=762.42;QD=12.92;SB=-306.27 GT:AD:DP:GL:GQ 0/1:32,27:59:-97.30,-17.77,-132.93:99 +chr1 5002965 rs55998096 C T 265.85 PASS AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1237.12;QD=16.95;SB=-623.66 GT:AD:DP:GL:GQ 0/1:35,38:72:-148.68,-21.69,-128.69:99 +chr1 5003908 rs1459759 T G 287.81 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.68;MQ0=0;OQ=1018.83;QD=14.15;SB=-495.74 GT:AD:DP:GL:GQ 0/1:34,38:70:-126.25,-21.08,-125.30:99 +chr1 5004548 . C T 0.18 PASS AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=4;HaplotypeScore=0.97;MQ=55.65;MQ0=0;OQ=1952.83;QD=19.15;SB=-933.54 GT:AD:DP:GL:GQ 0/1:44,58:102:-229.30,-30.73,-156.88:99 +chr1 5004874 rs55883351 G A 211.60 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=41.17;MQ0=0;OQ=1434.24;QD=17.49;SB=-707.75 GT:AD:DP:GL:GQ 0/1:39,43:79:-170.52,-23.81,-118.83:99 +chr1 5005796 . T G 22.56 PASS AC=1;AF=0.50;AN=2;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.97;MQ=52.68;MQ0=0;OQ=1101.12;QD=15.73;SB=-417.74 GT:AD:DP:GL:GQ 0/1:29,41:66:-133.27,-19.88,-106.95:99 +chr1 5005889 rs10737394 A G 342.71 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.43;MQ0=0;OQ=434.38;QD=9.05;SB=-233.28 GT:AD:DP:GL:GQ 0/1:27,21:46:-60.59,-13.87,-106.69:99 +chr1 5006532 rs10799156 G C 195.83 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=38.14;MQ0=9;OQ=508.53;QD=10.38;SB=-226.35 GT:AD:DP:GL:GQ 0/1:19,30:34:-64.39,-10.25,-81.21:99 +chr1 5007005 rs6603829 T C 0.07 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=16.12;MQ=27.87;MQ0=17;OQ=171.08;QD=2.19;SB=-108.70 GT:AD:DP:GL:GQ 0/1:51,27:35:-30.94,-10.55,-97.26:99 +chr1 5007006 rs6603830 G A 0.04 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=18.32;MQ=27.85;MQ0=18;OQ=165.82;QD=2.13;SB=-81.55 GT:AD:DP:GL:GQ 0/1:59,19:36:-30.72,-10.85,-97.29:99 +chr1 5007287 . C G 0.46 PASS AC=1;AF=0.50;AN=2;DP=52;Dels=0.00;HRun=1;HaplotypeScore=8.19;MQ=48.27;MQ0=4;OQ=754.87;QD=14.52;SB=-244.08 GT:AD:DP:GL:GQ 0/1:26,25:44:-92.04,-13.27,-89.64:99 +chr1 5007421 . A G 0.01 FDRtranche2.00to10.00 AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=1;HaplotypeScore=5.43;MQ=22.24;MQ0=26;OQ=110.20;QD=1.12;SB=7.49 GT:AD:DP:GL:GQ 0/1:85,12:42:-26.95,-12.65,-140.65:99 +chr1 5007424 . G C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=2;HaplotypeScore=3.53;MQ=23.00;MQ0=24;OQ=143.47;QD=1.54;SB=3.27 GT:AD:DP:GL:GQ 0/1:81,12:42:-30.29,-12.66,-152.47:99 +chr1 5011084 . C G 46.29 PASS AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=45.50;MQ0=2;OQ=1885.25;QD=20.27;SB=-717.97 GT:AD:DP:GL:GQ 0/1:41,52:88:-218.32,-26.51,-163.98:99 +chr1 5011731 . C T 18.24 PASS AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=2;HaplotypeScore=0.79;MQ=54.65;MQ0=1;OQ=1577.37;QD=18.13;SB=-623.62 GT:AD:DP:GL:GQ 0/1:41,46:86:-186.92,-25.90,-147.64:99 +chr1 5012084 rs10915327 C T 347.57 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=48.94;MQ0=2;OQ=1240.99;QD=17.24;SB=-606.09 GT:AD:DP:GL:GQ 0/1:32,40:68:-147.88,-20.49,-101.20:99 +chr1 5012508 . G A 165.62 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=34.81;MQ0=2;OQ=954.73;QD=16.75;SB=-470.48 GT:AD:DP:GL:GQ 0/1:23,33:48:-113.23,-14.48,-57.23:99 +chr1 5014453 . C A 65.76 PASS AC=1;AF=0.50;AN=2;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.92;MQ=59.79;MQ0=0;OQ=1613.72;QD=18.13;SB=-734.55 GT:AD:DP:GL:GQ 0/1:38,51:88:-191.16,-26.50,-131.97:99 +chr1 5016018 . T G 165.96 PASS AC=1;AF=0.50;AN=2;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=1295.09;QD=17.50;SB=-624.73 GT:AD:DP:GL:GQ 0/1:31,43:74:-155.08,-22.29,-116.52:99 +chr1 5018516 rs4262591 A T 76.12 PASS AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.00;HRun=2;HaplotypeScore=0.94;MQ=59.27;MQ0=0;OQ=1137.62;QD=12.78;SB=-520.24 GT:AD:DP:GL:GQ 0/1:50,39:87:-143.25,-26.20,-190.22:99 +chr1 5020923 rs970119 A C 493.82 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=718.78;QD=10.27;SB=-241.77 GT:AD:DP:GL:GQ 0/1:40,30:69:-95.95,-20.78,-149.31:99 +chr1 5023267 . C G 91.77 PASS AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.92;MQ0=0;OQ=800.92;QD=19.07;SB=-315.01 GT:AD:DP:GL:GQ 0/1:20,22:41:-95.73,-12.36,-81.61:99 +chr1 5024719 rs1563792 G A 196.62 PASS AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.54;MQ0=0;OQ=1348.55;QD=16.45;SB=-599.05 GT:AD:DP:GL:GQ 0/1:42,40:80:-162.25,-24.11,-132.60:99 +chr1 5027451 rs56184292 G T 6.36 PASS AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=4;HaplotypeScore=0.58;MQ=60.00;MQ0=0;OQ=1415.10;QD=15.05;SB=-721.57 GT:AD:DP:GL:GQ 0/1:44,49:93:-172.81,-28.02,-154.91:99 +chr1 5029434 rs2061494 T A 49.68 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=59.72;MQ0=0;OQ=1567.79;QD=19.36;SB=-635.43 GT:AD:DP:GL:GQ 0/1:33,47:79:-183.86,-23.79,-122.93:99 +chr1 5029438 rs2061493 T A 66.27 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=1.72;MQ=59.72;MQ0=0;OQ=1477.11;QD=18.24;SB=-663.80 GT:AD:DP:GL:GQ 0/1:33,48:80:-175.09,-24.10,-128.48:99 +chr1 5029774 rs55724572 C A 223.76 PASS AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.17;MQ0=0;OQ=1394.44;QD=13.81;SB=-671.07 GT:AD:DP:GL:GQ 0/1:55,46:101:-173.14,-30.41,-200.20:99 +chr1 5029802 rs56297253 G A 420.62 PASS AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.18;MQ0=0;OQ=1452.74;QD=14.24;SB=-632.72 GT:AD:DP:GL:GQ 0/1:58,44:100:-178.69,-30.14,-182.65:99 +chr1 5030141 rs1459758 C G 545.16 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2835.80;QD=42.33;SB=-1264.90 GT:AD:DP:GL:GQ 1/1:0,67:65:-287.18,-19.58,-0.01:99 +chr1 5032542 rs977665 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.00;HRun=14;HaplotypeScore=4.90;MQ=58.74;MQ0=0;OQ=53.47;QD=0.58;SB=128.44 GT:AD:DP:GL:GQ 0/1:77,15:69:-29.43,-20.80,-218.90:86.30 +chr1 5036504 rs922123 T C 526.95 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.12;MQ0=0;OQ=805.20;QD=10.88;SB=-361.22 GT:AD:DP:GL:GQ 0/1:44,30:74:-106.10,-22.29,-176.34:99 +chr1 5036703 rs55875722 T A 259.30 PASS AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.65;MQ0=0;OQ=1241.65;QD=18.81;SB=-625.13 GT:AD:DP:GL:GQ 0/1:28,38:64:-146.72,-19.28,-96.42:99 +chr1 5036704 rs922124 T A 61.83 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=59.67;MQ0=0;OQ=2561.19;QD=37.12;SB=-1099.66 GT:AD:DP:GL:GQ 1/1:0,69:68:-259.72,-20.48,-0.02:99 +chr1 5036974 rs56077964 G A 617 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2268.61;QD=38.45;SB=-1080.42 GT:AD:DP:GL:GQ 1/1:0,59:56:-230.46,-16.87,-0.01:99 +chr1 5039060 rs56186517 C T 567.90 PASS AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.53;MQ0=0;OQ=3555.73;QD=39.95;SB=-1607.16 GT:AD:DP:GL:GQ 1/1:0,89:87:-354.57,-26.20,-0.02:99 +chr1 5039732 rs56347558 T C 203.59 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.44;MQ=59.06;MQ0=0;OQ=2530.73;QD=34.20;SB=-928.36 GT:AD:DP:GL:GQ 1/1:0,73:71:-256.68,-21.39,-0.02:99 +chr1 5040152 rs3128686 G T 232.26 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.70;MQ0=0;OQ=2534.37;QD=32.49;SB=-1255.28 GT:AD:DP:GL:GQ 1/1:1,77:71:-257.05,-21.39,-0.03:99 +chr1 5040933 rs12045197 A T 91.33 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=2.81;MQ=44.79;MQ0=0;OQ=1582.06;QD=35.96;SB=-689.38 GT:AD:DP:GL:GQ 1/1:0,44:44:-161.81,-13.26,-0.02:99 +chr1 5041153 rs3128687 G T 199.02 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=55.94;MQ0=0;OQ=2861.17;QD=36.22;SB=-1432.06 GT:AD:DP:GL:GQ 1/1:0,79:77:-289.72,-23.19,-0.02:99 +chr1 5041314 rs3128688 A T 418.75 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.72;MQ0=0;OQ=2724.95;QD=37.85;SB=-1190.46 GT:AD:DP:GL:GQ 1/1:0,72:72:-276.10,-21.69,-0.02:99 +chr1 5041500 rs3128689 C A 313.60 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.24;MQ=59.77;MQ0=0;OQ=2974.21;QD=36.27;SB=-1175.38 GT:AD:DP:GL:GQ 1/1:0,82:81:-301.03,-24.39,-0.02:99 +chr1 5042266 rs10915339 G A 611.24 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.20;MQ0=0;OQ=2730.95;QD=39.01;SB=-1105.02 GT:AD:DP:GL:GQ 1/1:0,70:70:-276.70,-21.09,-0.02:99 +chr1 5042286 rs10915340 T C 619.37 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.86;MQ0=0;OQ=2323.00;QD=35.20;SB=-939.39 GT:AD:DP:GL:GQ 1/1:0,65:65:-235.90,-19.58,-0.02:99 +chr1 5042412 rs10915341 T G 227.06 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.39;MQ0=0;OQ=2175.06;QD=35.66;SB=-984.12 GT:AD:DP:GL:GQ 1/1:0,61:61:-221.11,-18.37,-0.01:99 +chr1 5042489 rs12029437 C G 85.77 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=2.70;MQ=59.16;MQ0=0;OQ=2913.26;QD=40.46;SB=-1456.73 GT:AD:DP:GL:GQ 1/1:0,72:69:-294.94,-20.80,-0.03:99 +chr1 5042644 rs12047111 A G 505.22 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=1237.53;QD=28.78;SB=-430.81 GT:AD:DP:GL:GQ 1/1:0,43:41:-127.38,-12.37,-0.05:99 +chr1 5042678 rs2334263 T C 624.61 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=1911.69;QD=29.87;SB=-888.47 GT:AD:DP:GL:GQ 1/1:0,64:60:-194.81,-18.10,-0.06:99 +chr1 5043104 rs10799159 C A 257.58 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=59.14;MQ0=0;OQ=3046.41;QD=35.84;SB=-1505.91 GT:AD:DP:GL:GQ 1/1:0,85:84:-308.25,-25.30,-0.02:99 +chr1 5043177 rs10799160 G A 205.89 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.29;MQ0=0;OQ=2756.78;QD=37.25;SB=-1155.91 GT:AD:DP:GL:GQ 1/1:1,72:71:-282.75,-21.39,-3.49:99 +chr1 5043218 rs10799161 A C 127.41 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.10;MQ0=0;OQ=2285.87;QD=29.69;SB=-810.83 GT:AD:DP:GL:GQ 1/1:0,77:71:-232.22,-21.39,-0.05:99 +chr1 5048318 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=69;Dels=0.00;HRun=4;HaplotypeScore=11.35;MQ=48.17;MQ0=0;OQ=57.54;QD=0.83;SB=77.27 GT:AD:DP:GL:GQ 0/1:47,22:47:-23.20,-14.17,-150.00:90.38 +chr1 5048545 rs10915343 T C 699.40 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.89;MQ0=0;OQ=1690.53;QD=34.50;SB=-831.35 GT:AD:DP:GL:GQ 1/1:0,49:48:-172.65,-14.46,-0.01:99 +chr1 5050626 rs3101213 A G 203.57 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=59.71;MQ0=0;OQ=2864.75;QD=36.26;SB=-1335.60 GT:AD:DP:GL:GQ 1/1:0,79:79:-290.08,-23.79,-0.02:99 +chr1 5051336 rs2199215 T C 701.57 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2974.37;QD=35.84;SB=-1419.92 GT:AD:DP:GL:GQ 1/1:0,83:83:-301.05,-25.00,-0.02:99 +chr1 5052019 rs12121092 G T 639.83 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2775.75;QD=36.52;SB=-1128.45 GT:AD:DP:GL:GQ 1/1:0,76:76:-281.18,-22.89,-0.02:99 +chr1 5057740 rs55852005 G A 37.87 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=3;HaplotypeScore=1.46;MQ=59.22;MQ0=0;OQ=1090.29;QD=18.48;SB=-513.03 GT:AD:DP:GL:GQ 0/1:26,33:57:-129.48,-17.17,-87.67:99 +chr1 5058085 rs4949171 C T 168.96 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=1.62;MQ=59.33;MQ0=0;OQ=2116.23;QD=37.79;SB=-957.98 GT:AD:DP:GL:GQ 1/1:0,56:55:-215.23,-16.58,-0.02:99 +chr1 5058717 rs9803863 G A 206.60 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=59.13;MQ0=0;OQ=2766.44;QD=39.52;SB=-1272.71 GT:AD:DP:GL:GQ 1/1:0,69:70:-283.01,-23.72,-2.78:99 +chr1 5059210 rs982156 T C 60.22 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.49;MQ=59.24;MQ0=0;OQ=1823.01;QD=33.15;SB=-568.39 GT:AD:DP:GL:GQ 1/1:0,55:54:-185.91,-16.27,-0.03:99 +chr1 5060220 rs992597 C T 157.27 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.01;MQ0=0;OQ=2915.53;QD=38.36;SB=-981.32 GT:AD:DP:GL:GQ 1/1:0,76:74:-295.16,-22.30,-0.02:99 +chr1 5060522 rs2242157 G T 298.92 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.45;MQ0=0;OQ=2405.81;QD=35.38;SB=-942.03 GT:AD:DP:GL:GQ 1/1:0,68:68:-244.19,-20.49,-0.03:99 +chr1 5060591 rs1459766 T G 395.54 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.24;MQ0=0;OQ=2600.59;QD=35.14;SB=-1143.14 GT:AD:DP:GL:GQ 1/1:0,74:73:-263.67,-21.99,-0.02:99 +chr1 5061734 rs9439532 C T 112.42 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=2.81;MQ=59.34;MQ0=0;OQ=2118.20;QD=37.16;SB=-1042.39 GT:AD:DP:GL:GQ 1/1:0,57:54:-215.42,-16.27,-0.02:99 +chr1 5062366 rs6683881 C T 35.99 PASS AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=1;HaplotypeScore=1.70;MQ=59.80;MQ0=0;OQ=3619.28;QD=39.77;SB=-1734.02 GT:AD:DP:GL:GQ 1/1:0,91:89:-360.93,-26.81,-0.02:99 +chr1 5062541 rs4949170 A G 156.11 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.86;MQ=59.71;MQ0=0;OQ=2632.93;QD=33.33;SB=-1332.58 GT:AD:DP:GL:GQ 1/1:0,79:75:-266.90,-22.59,-0.03:99 +chr1 5062567 rs4949169 A T 172.52 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.83;MQ=59.68;MQ0=0;OQ=2759.54;QD=37.80;SB=-995.13 GT:AD:DP:GL:GQ 1/1:0,73:72:-279.55,-21.68,-0.01:99 +chr1 5063485 rs9439576 C G 98.90 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.17;MQ0=0;OQ=3111.26;QD=39.89;SB=-1145.60 GT:AD:DP:GL:GQ 1/1:0,77:71:-314.73,-21.39,-0.02:99 +chr1 5063671 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=60;Dels=0.00;HRun=2;HaplotypeScore=26.54;MQ=57.06;MQ0=0;OQ=128.17;QD=2.14;SB=77.28 GT:AD:DP:GL:GQ 0/1:38,22:39:-27.89,-11.79,-122.93:99 +chr1 5064284 rs2169090 T C 707.36 PASS AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.41;MQ0=0;OQ=3152.45;QD=35.42;SB=-1370.23 GT:AD:DP:GL:GQ 1/1:0,89:88:-318.85,-26.50,-0.02:99 +chr1 5066340 rs57000660 A G 484.39 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=766.60;QD=12.99;SB=-402.18 GT:AD:DP:GL:GQ 0/1:32,27:59:-97.71,-17.77,-131.87:99 +chr1 5066393 rs1037809 C T 706.58 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3074.28;QD=39.41;SB=-1449.38 GT:AD:DP:GL:GQ 1/1:0,78:78:-311.04,-23.50,-0.02:99 +chr1 5068397 rs6659363 G C 337.44 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.22;MQ0=0;OQ=768.71;QD=14.24;SB=-229.04 GT:AD:DP:GL:GQ 0/1:31,23:53:-96.12,-15.97,-137.34:99 +chr1 5068500 rs12124337 A C 365.74 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=60.00;MQ0=0;OQ=1243.29;QD=15.94;SB=-471.71 GT:AD:DP:GL:GQ 0/1:35,43:77:-150.81,-23.19,-127.77:99 +chr1 5068523 rs10733013 C T 471.58 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=1107.71;QD=14.39;SB=-422.79 GT:AD:DP:GL:GQ 0/1:43,34:75:-136.66,-22.60,-133.09:99 +chr1 5069554 rs2722789 G A 592.26 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1009.56;QD=14.02;SB=-503.00 GT:AD:DP:GL:GQ 0/1:41,31:72:-125.95,-21.71,-131.55:99 +chr1 5070551 rs4949160 A T 476.97 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.42;MQ0=0;OQ=1068.05;QD=14.83;SB=-488.53 GT:AD:DP:GL:GQ 0/1:37,35:71:-131.47,-21.38,-142.74:99 +chr1 5071819 . G A 258.71 PASS AC=1;AF=0.50;AN=2;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=1213.24;QD=16.18;SB=-353.81 GT:AD:DP:GL:GQ 0/1:39,36:75:-147.20,-22.59,-142.20:99 +chr1 5071854 . T A 81.17 PASS AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=60.00;MQ0=0;OQ=1149.23;QD=14.19;SB=-304.96 GT:AD:DP:GL:GQ 0/1:43,38:80:-142.31,-24.10,-164.66:99 +chr1 5072229 . G A 304.80 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=81;Dels=0.01;HRun=0;HaplotypeScore=64.90;MQ=44.02;MQ0=0;QD=3.76;SB=86.27 GT:AD:DP:GL:GQ 0/1:66,14:79:-57.26,-23.50,-230.57:99 +chr1 5072230 . C G 37.37 DPFilter;LowQual;SnpCluster AC=1;AF=0.50;AN=2;DP=83;Dels=0.01;HRun=2;HaplotypeScore=55.89;MQ=43.72;MQ0=0;QD=0.45;SB=80.30 GT:AD:DP:GL:GQ 0/1:67,6:72:-38.59,-31.57,-277.78:70.20 +chr1 5072236 . A G 214.30 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=80;Dels=0.08;HRun=2;HaplotypeScore=77.80;MQ=44.49;MQ0=0;QD=2.68;SB=83.29 GT:AD:DP:GL:GQ 0/1:56,12:72:-66.82,-42.10,-235.08:99 +chr1 5072261 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=81;Dels=0.05;HRun=0;HaplotypeScore=73.45;MQ=43.15;MQ0=0;OQ=399.38;QD=4.93;SB=83.29 GT:AD:DP:GL:GQ 0/1:51,25:67:-62.51,-19.29,-172.53:99 +chr1 5072278 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=86;Dels=0.01;HRun=1;HaplotypeScore=43.28;MQ=42.83;MQ0=0;OQ=260.49;QD=3.03;SB=63.28 GT:AD:DP:GL:GQ 0/1:59,19:75:-74.72,-45.39,-204.92:99 +chr1 5072305 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=82;Dels=0.04;HRun=0;HaplotypeScore=77.14;MQ=40.79;MQ0=0;OQ=744.26;QD=9.08;SB=-270.19 GT:AD:DP:GL:GQ 0/1:44,35:70:-97.91,-20.20,-140.23:99 +chr1 5072314 . C A 26.92 LowQual AC=1;AF=0.50;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=53.92;MQ=40.19;MQ0=0;QD=0.34;SB=-28.60 GT:AD:DP:GL:GQ 0/1:60,11:56:-29.71,-23.73,-169.35:59.74 +chr1 5072329 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=71;Dels=0.01;HRun=0;HaplotypeScore=74.94;MQ=38.44;MQ0=0;OQ=775.14;QD=10.92;SB=-292.22 GT:AD:DP:GL:GQ 0/1:41,28:64:-99.78,-18.98,-129.83:99 +chr1 5072338 . C G 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=63;Dels=0.02;HRun=2;HaplotypeScore=51.40;MQ=37.08;MQ0=0;OQ=162.47;QD=2.58;SB=101.36 GT:AD:DP:GL:GQ 0/1:48,8:57:-50.13,-30.60,-201.42:99 +chr1 5072354 . A G 70.72 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=68;Dels=0.01;HRun=3;HaplotypeScore=80.87;MQ=34.07;MQ0=1;QD=1.04;SB=50.19 GT:AD:DP:GL:GQ 0/1:55,12:60:-28.14,-17.78,-195.72:99 +chr1 5072357 . A G 633.36 SnpCluster AC=1;AF=0.50;AN=2;DP=67;Dels=0.01;HRun=1;HaplotypeScore=71.93;MQ=33.53;MQ0=1;QD=9.45;SB=-235.45 GT:AD:DP:GL:GQ 0/1:28,25:61:-115.70,-49.08,-135.16:99 +chr1 5072359 . A C 486.53 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=69;Dels=0.03;HRun=0;HaplotypeScore=52.12;MQ=33.41;MQ0=1;QD=7.05;SB=62.18 GT:AD:DP:GL:GQ 0/1:42,24:63:-73.40,-21.46,-136.62:99 +chr1 5072383 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=101;Dels=0.00;HRun=1;HaplotypeScore=82.78;MQ=35.86;MQ0=1;OQ=50.85;QD=0.50;SB=43.30 GT:AD:DP:GL:GQ 0/1:88,10:72:-37.48,-29.11,-217.86:83.68 +chr1 5072395 . C A 570.19 SnpCluster AC=1;AF=0.50;AN=2;DP=99;Dels=0.02;HRun=1;HaplotypeScore=88.86;MQ=38.13;MQ0=1;QD=5.76;SB=-12.89 GT:AD:DP:GL:GQ 0/1:64,28:75:-96.04,-35.74,-177.41:99 +chr1 5072402 . A G 56.63 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=98;Dels=0.00;HRun=3;HaplotypeScore=106.83;MQ=38.72;MQ0=1;QD=0.58;SB=77.28 GT:AD:DP:GL:GQ 0/1:88,10:70:-30.04,-21.10,-237.13:89.47 +chr1 5072405 . G T 211.27 DPFilter;SnpCluster AC=1;AF=0.50;AN=2;DP=95;Dels=0.03;HRun=0;HaplotypeScore=106.15;MQ=39.10;MQ0=1;QD=2.22;SB=86.26 GT:AD:DP:GL:GQ 0/1:74,17:80:-48.52,-24.11,-223.42:99 +chr1 5072419 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=93;Dels=0.00;HRun=1;HaplotypeScore=52.76;MQ=39.26;MQ0=1;OQ=413.09;QD=4.44;SB=8.43 GT:AD:DP:GL:GQ 0/1:71,20:77:-71.28,-26.69,-194.57:99 +chr1 5072442 . A G 31.37 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=65;Dels=0.00;HRun=2;HaplotypeScore=72.31;MQ=41.30;MQ0=0;QD=0.48;SB=47.17 GT:AD:DP:GL:GQ 0/1:57,8:62:-25.11,-18.69,-212.28:64.20 +chr1 5073664 rs2611423 C A 218.42 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=2432.37;QD=35.25;SB=-1208.34 GT:AD:DP:GL:GQ 1/1:0,69:67:-246.84,-20.18,-0.02:99 +chr1 5073938 rs2611424 A G 134.32 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.25;MQ0=0;OQ=2912.91;QD=35.96;SB=-1287.55 GT:AD:DP:GL:GQ 1/1:0,81:80:-294.90,-24.09,-0.02:99 +chr1 5074030 rs2611425 C T 598.88 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=57.51;MQ0=0;OQ=2372.22;QD=38.89;SB=-1023.68 GT:AD:DP:GL:GQ 1/1:0,61:60:-240.82,-18.07,-0.01:99 +chr1 5074510 rs9439534 C T 637.40 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.93;MQ0=0;OQ=2321.21;QD=36.27;SB=-1159.05 GT:AD:DP:GL:GQ 1/1:0,64:59:-235.72,-17.77,-0.02:99 +chr1 5074638 rs57003830 G C 372.48 PASS AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=43.54;MQ0=4;OQ=1370.10;QD=15.75;SB=-494.22 GT:AD:DP:GL:GQ 0/1:45,42:79:-164.10,-23.81,-179.75:99 +chr1 5075049 rs9439577 C T 95.46 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=2.23;MQ=38.28;MQ0=7;OQ=1971.59;QD=31.30;SB=-484.14 GT:AD:DP:GL:GQ 1/1:0,62:51:-200.77,-15.37,-0.03:99 +chr1 5075121 rs9439535 A G 238.22 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=43.82;MQ0=4;OQ=1529.43;QD=28.32;SB=-495.19 GT:AD:DP:GL:GQ 1/1:0,54:47:-156.56,-14.17,-0.03:99 +chr1 5075150 rs9439578 T G 135.05 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=2.71;MQ=50.05;MQ0=3;OQ=2063.78;QD=31.75;SB=-748.06 GT:AD:DP:GL:GQ 1/1:0,65:60:-209.99,-18.08,-0.02:99 +chr1 5075197 rs10915347 C T 55.81 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=2.29;MQ=47.56;MQ0=6;OQ=2171.81;QD=32.91;SB=-915.72 GT:AD:DP:GL:GQ 1/1:0,65:56:-220.79,-16.88,-0.02:99 +chr1 5075319 rs28828787 G A 102.87 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=26.02;MQ0=15;OQ=432.78;QD=8.32;SB=-48.66 GT:AD:DP:GL:GQ 0/1:29,23:28:-55.00,-8.44,-46.26:99 +chr1 5075370 rs10799164 C T 16.89 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=0.63;MQ=20.22;MQ0=13;OQ=746.84;QD=17.78;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,40:19:-78.27,-5.72,-0.00:57.19 +chr1 5075558 rs10799165 C T 9.35 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=9.90;MQ=22.74;MQ0=30;OQ=955.91;QD=12.58;SB=-324.43 GT:AD:DP:GL:GQ 1/1:31,45:25:-99.18,-7.53,-0.01:75.24 +chr1 5075601 rs10753349 C T 1.18 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=10.53;MQ=14.77;MQ0=51;OQ=525.81;QD=6.49;SB=-249.33 GT:AD:DP:GL:GQ 1/1:43,38:14:-56.17,-4.22,-0.00:42.14 +chr1 5075696 rs4949168 A G 0.23 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=5.94;MQ=11.29;MQ0=39;OQ=183.21;QD=2.91;SB=-118.05 GT:AD:DP:GL:GQ 1/1:33,30:6:-21.89,-1.81,-0.00:18.06 +chr1 5075699 rs10799166 G C 0.14 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=5.78;MQ=10.86;MQ0=38;OQ=173.64;QD=2.85;SB=-103.85 GT:AD:DP:GL:GQ 1/1:32,29:5:-20.93,-1.51,-0.00:15.05 +chr1 5075751 rs4949159 C A 0.57 PASS AC=2;AF=1.00;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=9.84;MQ=21.77;MQ0=1;OQ=523.96;QD=14.55;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,33:15:-55.98,-4.52,-0.00:45.14 +chr1 5075757 rs4949167 T C 1.62 PASS AC=2;AF=1.00;AN=2;DB;DP=42;Dels=0.00;HRun=1;HaplotypeScore=5.17;MQ=21.64;MQ0=3;OQ=605.43;QD=14.41;SB=-10.00 GT:AD:DP:GL:GQ 1/1:7,35:18:-64.13,-5.42,-0.00:54.16 +chr1 5076314 rs9439579 C G 74.36 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.92;MQ=43.71;MQ0=2;OQ=2095.83;QD=33.80;SB=-956.72 GT:AD:DP:GL:GQ 1/1:3,59:49:-213.18,-14.76,-0.01:99 +chr1 5076393 rs10915349 G A 1.75 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=6.65;MQ=47.36;MQ0=1;OQ=1988.87;QD=34.29;SB=-955.74 GT:AD:DP:GL:GQ 1/1:1,57:52:-202.50,-15.68,-0.03:99 +chr1 5076841 rs10799167 C T 211.34 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=45.50;MQ0=4;OQ=2210.86;QD=35.66;SB=-962.98 GT:AD:DP:GL:GQ 1/1:1,61:56:-224.69,-16.87,-0.02:99 +chr1 5077036 rs10799168 A G 167.61 PASS AC=2;AF=1.00;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=0.93;MQ=21.14;MQ0=7;OQ=400.64;QD=14.84;SB=-196.71 GT:AD:DP:GL:GQ 1/1:8,19:13:-43.66,-3.92,-0.01:39.11 +chr1 5077055 rs7414866 A G 123.85 PASS AC=2;AF=1.00;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.73;MQ=21.33;MQ0=4;OQ=281.43;QD=13.40;SB=-64.87 GT:AD:DP:GL:GQ 1/1:4,17:10:-31.74,-3.02,-0.01:30.04 +chr1 5077077 rs7412613 C T 3.36 PASS AC=2;AF=1.00;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=1.37;MQ=22.40;MQ0=3;OQ=333.18;QD=18.51;SB=-10.00 GT:AD:DP:GL:GQ 1/1:2,15:9:-36.90,-2.71,-0.00:27.09 +chr1 5077090 . C A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=2;HaplotypeScore=4.92;MQ=29.30;MQ0=3;OQ=51.83;QD=1.85;SB=-3.99 GT:AD:DP:GL:GQ 0/1:19,9:11:-11.79,-3.32,-22.43:84.66 +chr1 5077136 rs55919453 T G 371.05 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=38.18;MQ0=2;OQ=1590.74;QD=31.81;SB=-546.07 GT:AD:DP:GL:GQ 1/1:0,50:44:-162.67,-13.25,-0.01:99 +chr1 5077346 rs28778348 C A 55.21 PASS AC=2;AF=1.00;AN=2;DB;DP=30;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=26.70;MQ0=2;OQ=838.40;QD=27.95;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,29:24:-87.43,-7.23,-0.01:72.21 +chr1 5077349 rs28898289 T G 16.95 PASS AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=26.06;MQ0=2;OQ=780.24;QD=25.17;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,31:23:-81.62,-6.93,-0.01:69.20 +chr1 5077435 rs7415381 A T 121.52 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.10;MQ=26.22;MQ0=5;OQ=1349.62;QD=28.72;SB=-637.67 GT:AD:DP:GL:GQ 1/1:0,47:37:-138.56,-11.15,-0.01:99 +chr1 5077528 rs56184987 T C 231.69 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=24.13;MQ0=2;OQ=814.91;QD=18.95;SB=-252.77 GT:AD:DP:GL:GQ 1/1:0,43:27:-85.10,-8.15,-0.03:81.19 +chr1 5077549 rs55934905 G A 0.24 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=23.80;MQ0=7;OQ=1118.88;QD=22.38;SB=-246.01 GT:AD:DP:GL:GQ 1/1:0,50:29:-115.48,-8.74,-0.01:87.28 +chr1 5077770 rs60669416 C A 584.28 Indel AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=10;HaplotypeScore=19.78;MQ=46.83;MQ0=2;QD=11.69;SB=-270.35 GT:AD:DP:GL:GQ 0/1:25,24:45:-75.27,-13.56,-79.00:99 +chr1 5077806 rs2334261 C T 3.91 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.02;HRun=2;HaplotypeScore=6.33;MQ=31.47;MQ0=13;OQ=1098.90;QD=20.35;SB=-473.36 GT:AD:DP:GL:GQ 1/1:5,48:29:-113.48,-8.43,-0.01:84.27 +chr1 5077915 rs11582268 A T 437.65 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=22.80;MQ0=5;OQ=869.48;QD=19.32;SB=-460.68 GT:AD:DP:GL:GQ 1/1:0,44:25:-90.55,-7.54,-0.02:75.21 +chr1 5078308 rs12043988 C A 291.59 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=47.74;MQ0=0;OQ=2467.70;QD=37.39;SB=-935.67 GT:AD:DP:GL:GQ 1/1:0,66:65:-250.36,-19.57,-0.01:99 +chr1 5078509 rs9439503 T C 20.38 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=4.15;MQ=38.39;MQ0=4;OQ=1877.97;QD=28.03;SB=-657.32 GT:AD:DP:GL:GQ 1/1:1,66:53:-191.40,-15.96,-0.02:99 +chr1 5078532 rs9439504 C G 494.66 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=35.41;MQ0=3;OQ=2205.88;QD=36.16;SB=-588.53 GT:AD:DP:GL:GQ 1/1:0,61:50:-224.18,-15.06,-0.01:99 +chr1 5078612 rs10915350 C T 169.93 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=47.49;MQ0=1;OQ=2196.12;QD=36.60;SB=-847.62 GT:AD:DP:GL:GQ 1/1:1,58:57:-223.22,-17.18,-0.02:99 +chr1 5079390 rs10799170 A C 350.19 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=57.35;MQ0=0;OQ=2787.95;QD=35.29;SB=-1421.63 GT:AD:DP:GL:GQ 1/1:0,79:78:-282.40,-23.49,-0.02:99 +chr1 5079434 rs10915352 G T 571.75 PASS AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.02;MQ0=0;OQ=3162.32;QD=36.77;SB=-1557.78 GT:AD:DP:GL:GQ 1/1:0,86:86:-319.84,-25.90,-0.02:99 +chr1 5079595 rs10915353 G C 43.37 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.36;MQ0=0;OQ=2638.35;QD=40.59;SB=-999.16 GT:AD:DP:GL:GQ 1/1:0,65:61:-267.45,-18.39,-0.03:99 +chr1 5079666 rs6701939 T C 563.06 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2172.86;QD=35.05;SB=-713.27 GT:AD:DP:GL:GQ 1/1:0,62:60:-220.89,-18.07,-0.02:99 +chr1 5080376 . C T 202.08 PASS AC=1;AF=0.50;AN=2;DP=38;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.09;MQ0=0;OQ=426.51;QD=11.22;SB=-188.16 GT:AD:DP:GL:GQ 0/1:24,14:37:-57.08,-11.15,-81.03:99 +chr1 5080399 . C A 264.12 DPFilter;Indel AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=20;HaplotypeScore=11.69;MQ=57.12;MQ0=0;QD=4.63;SB=53.19 GT:AD:DP:GL:GQ 0/1:38,19:40:-41.75,-12.05,-100.11:99 +chr1 5080680 rs10753350 A G 105.81 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=2.00;MQ=58.32;MQ0=0;OQ=1525.28;QD=28.25;SB=-610.83 GT:AD:DP:GL:GQ 1/1:0,54:51:-156.18,-15.39,-0.07:99 +chr1 5080690 rs10753351 A C 1.11 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=3;HaplotypeScore=2.95;MQ=55.25;MQ0=0;OQ=2140.46;QD=31.48;SB=-1004.07 GT:AD:DP:GL:GQ 1/1:0,68:63:-217.66,-18.98,-0.03:99 +chr1 5081475 rs10737396 T C 76.32 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=3;HaplotypeScore=0.91;MQ=60.00;MQ0=0;OQ=2367.06;QD=33.34;SB=-935.73 GT:AD:DP:GL:GQ 1/1:0,71:67:-240.32,-20.19,-0.03:99 +chr1 5081878 rs2722794 T G 569.46 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.93;MQ0=0;OQ=2825.92;QD=34.89;SB=-1425.62 GT:AD:DP:GL:GQ 1/1:0,81:79:-286.20,-23.79,-0.02:99 +chr1 5081972 rs2611426 T A 81.80 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.88;MQ=59.18;MQ0=0;OQ=2310.37;QD=35.01;SB=-624.95 GT:AD:DP:GL:GQ 1/1:0,66:62:-234.64,-18.68,-0.02:99 +chr1 5083407 rs2045587 A G 34.52 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=1821.48;QD=33.73;SB=-913.93 GT:AD:DP:GL:GQ 1/1:0,54:52:-185.75,-15.67,-0.02:99 +chr1 5083733 rs4313443 C T 652.84 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2295.78;QD=39.58;SB=-913.70 GT:AD:DP:GL:GQ 1/1:0,58:58:-233.18,-17.47,-0.01:99 +chr1 5083785 rs4356099 G A 29.40 PASS AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=1676.22;QD=38.98;SB=-527.70 GT:AD:DP:GL:GQ 1/1:0,43:43:-171.22,-12.96,-0.02:99 +chr1 5083937 rs2722793 G T 729.18 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.44;MQ0=0;OQ=2771.95;QD=36.96;SB=-1328.90 GT:AD:DP:GL:GQ 1/1:0,75:75:-280.80,-22.59,-0.02:99 +chr1 5084549 rs10753352 G C 80.52 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.74;MQ0=0;OQ=3116.41;QD=42.69;SB=-1439.29 GT:AD:DP:GL:GQ 1/1:0,73:73:-315.25,-22.00,-0.03:99 +chr1 5085006 rs2722792 C A 486.51 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=3029.86;QD=36.95;SB=-1518.84 GT:AD:DP:GL:GQ 1/1:0,82:81:-306.59,-24.39,-0.02:99 +chr1 5085686 rs2611419 A C 735.40 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=2513.45;QD=35.40;SB=-1104.10 GT:AD:DP:GL:GQ 1/1:0,71:71:-254.95,-21.38,-0.02:99 +chr1 5087139 rs2611420 C G 615.49 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3365.59;QD=43.15;SB=-1251.98 GT:AD:DP:GL:GQ 1/1:0,78:76:-335.56,-22.90,-0.03:99 +chr1 5087240 rs2611421 C T 489.75 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=3117.95;QD=41.03;SB=-1433.39 GT:AD:DP:GL:GQ 1/1:0,76:76:-315.39,-22.89,-0.01:99 +chr1 5087511 rs2722791 G A 190.82 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=2.68;MQ=59.73;MQ0=0;OQ=3174.39;QD=37.35;SB=-1593.03 GT:AD:DP:GL:GQ 1/1:0,85:81:-321.05,-24.40,-0.02:99 +chr1 5088299 rs2611422 C T 24.96 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.01;HRun=4;HaplotypeScore=1.63;MQ=59.49;MQ0=0;OQ=3139.82;QD=38.29;SB=-1155.06 GT:AD:DP:GL:GQ 1/1:0,81:82:-317.60,-24.41,-0.03:99 +chr1 5088851 rs898338 G T 586.23 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1967.21;QD=32.25;SB=-901.77 GT:AD:DP:GL:GQ 1/1:0,61:55:-200.32,-16.57,-0.02:99 +chr1 5091688 rs11588537 G C 0.39 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=2;HaplotypeScore=2.02;MQ=59.44;MQ0=0;OQ=1667.23;QD=40.66;SB=-503.13 GT:AD:DP:GL:GQ 1/1:0,41:41:-170.32,-12.36,-0.02:99 +chr1 5092085 rs4245628 G A 151.82 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.46;MQ=59.41;MQ0=0;OQ=3066.13;QD=39.31;SB=-1187.61 GT:AD:DP:GL:GQ 1/1:0,78:77:-310.22,-23.19,-0.02:99 +chr1 5092563 rs6671889 C A 625.41 PASS AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.16;MQ0=0;OQ=3060.89;QD=36.88;SB=-1358.20 GT:AD:DP:GL:GQ 1/1:0,83:82:-309.69,-24.69,-0.01:99 +chr1 5092609 rs4949165 G C 633.91 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=3087.67;QD=42.88;SB=-1533.25 GT:AD:DP:GL:GQ 1/1:0,72:72:-312.37,-21.69,-0.02:99 +chr1 5092886 rs10492923 A G 560.12 PASS AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=897.90;QD=12.47;SB=-469.86 GT:AD:DP:GL:GQ 0/1:34,38:69:-113.87,-20.80,-132.03:99 +chr1 5093533 rs9439505 C T 206.84 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=2.29;MQ=59.13;MQ0=0;OQ=1236.94;QD=16.49;SB=-238.14 GT:AD:DP:GL:GQ 0/1:38,37:73:-148.98,-22.00,-117.20:99 +chr1 5093841 rs12143009 G A 1328.69 Indel AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=3;HaplotypeScore=2.85;MQ=59.81;MQ0=1;QD=15.27;SB=-676.33 GT:AD:DP:GL:GQ 0/1:46,41:84:-161.46,-25.31,-156.05:99 +chr1 5094064 rs16840020 C T 380.84 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=1.11;MQ=59.40;MQ0=0;OQ=843.58;QD=13.61;SB=-387.37 GT:AD:DP:GL:GQ 0/1:36,26:61:-106.01,-18.37,-128.57:99 +chr1 5094308 rs9439536 C G 94.57 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=-0.06;MQ=57.94;MQ0=0;OQ=2369.61;QD=43.08;SB=-1192.92 GT:AD:DP:GL:GQ 1/1:0,55:55:-240.56,-16.57,-0.02:99 +chr1 5094675 rs9439537 G A 205.12 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=56.69;MQ0=0;OQ=2327.54;QD=36.95;SB=-997.02 GT:AD:DP:GL:GQ 1/1:0,63:59:-236.35,-17.77,-0.02:99 +chr1 5095027 rs10737397 A C 379.35 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.02;HRun=2;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1853.36;QD=34.97;SB=-880.10 GT:AD:DP:GL:GQ 1/1:0,52:52:-188.93,-15.66,-0.01:99 +chr1 5095151 rs10915359 A G 343.67 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=60.00;MQ0=0;OQ=1130.12;QD=15.92;SB=-404.21 GT:AD:DP:GL:GQ 0/1:33,38:69:-137.08,-20.78,-130.21:99 +chr1 5095177 rs12122020 C T 430.32 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1196.16;QD=13.91;SB=-341.80 GT:AD:DP:GL:GQ 0/1:49,37:84:-148.20,-25.30,-177.14:99 +chr1 5095231 rs10492925 T C 590.40 PASS AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1272.89;QD=14.98;SB=-556.65 GT:AD:DP:GL:GQ 0/1:35,50:83:-155.59,-25.02,-138.70:99 +chr1 5095242 rs12045223 A T 548.90 PASS AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.56;MQ0=0;OQ=1555.76;QD=18.52;SB=-658.48 GT:AD:DP:GL:GQ 0/1:35,49:82:-183.56,-24.70,-128.89:99 +chr1 5096599 rs9439506 A G 501.16 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=607.79;QD=10.30;SB=-265.38 GT:AD:DP:GL:GQ 0/1:36,23:58:-81.54,-17.47,-140.55:99 +chr1 5097069 . C T 27.83 PASS AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.95;MQ0=0;OQ=280.61;QD=35.08;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:8:-31.64,-2.41,-0.00:24.08 +chr1 5097076 . C A 58.51 PASS AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.95;MQ0=0;OQ=242.27;QD=30.28;SB=-10.00 GT:AD:DP:GL:GQ 1/1:0,8:8:-27.81,-2.41,-0.00:24.07 +chr1 5097414 rs34593428 C T 209.20 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=915.00;QD=14.52;SB=-282.17 GT:AD:DP:GL:GQ 0/1:34,29:62:-113.46,-18.67,-123.11:99 +chr1 5097811 rs10799172 T C 730.17 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=2361.85;QD=34.73;SB=-1109.84 GT:AD:DP:GL:GQ 1/1:0,68:67:-239.79,-20.18,-0.02:99 +chr1 5097837 rs10799173 C T 610.42 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=2894.02;QD=39.64;SB=-1458.48 GT:AD:DP:GL:GQ 1/1:0,73:72:-293.00,-21.69,-0.02:99 +chr1 5098649 rs16840051 C T 466.71 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.76;MQ0=0;OQ=1115.98;QD=14.31;SB=-521.66 GT:AD:DP:GL:GQ 0/1:43,35:76:-137.77,-22.89,-150.84:99 +chr1 5099594 rs61576661 T C 2.98 PASS AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.02;HRun=0;HaplotypeScore=9.91;MQ=59.43;MQ0=0;OQ=660.15;QD=12.23;SB=-250.93 GT:AD:DP:GL:GQ 0/1:29,24:54:-85.27,-15.97,-115.92:99 +chr1 5100592 rs6681359 C T 709.39 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.69;MQ0=0;OQ=3001.23;QD=40.02;SB=-1288.71 GT:AD:DP:GL:GQ 1/1:0,75:75:-303.72,-22.59,-0.02:99 +chr1 5102008 rs7543139 A C 24.50 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=8.00;MQ=58.40;MQ0=0;OQ=1023.25;QD=14.62;SB=-311.81 GT:AD:DP:GL:GQ 0/1:35,35:67:-125.80,-20.19,-114.71:99 +chr1 5102179 rs16840055 A G 103.26 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.48;MQ=59.41;MQ0=0;OQ=1029.92;QD=14.51;SB=-438.97 GT:AD:DP:GL:GQ 0/1:36,35:69:-127.06,-20.79,-136.54:99 +chr1 5103146 rs4484964 T C 669.95 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.67;MQ0=0;OQ=2031.10;QD=32.24;SB=-774.73 GT:AD:DP:GL:GQ 1/1:0,63:62:-206.74,-18.69,-0.04:99 +chr1 5103788 . G T 167.53 PASS AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.70;MQ0=0;OQ=1064.37;QD=14.00;SB=-541.64 GT:AD:DP:GL:GQ 0/1:38,38:74:-132.01,-22.29,-131.40:99 +chr1 5106305 rs9439509 G A 600.29 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.19;MQ0=0;OQ=2218.17;QD=38.92;SB=-991.33 GT:AD:DP:GL:GQ 1/1:0,57:57:-225.42,-17.18,-0.02:99 +chr1 5106499 rs4345839 A G 149.68 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=1.56;MQ=59.43;MQ0=0;OQ=2177.60;QD=33.50;SB=-1108.75 GT:AD:DP:GL:GQ 1/1:0,64:62:-221.38,-18.68,-0.03:99 +chr1 5107407 rs4584438 T G 105.42 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=1.66;MQ=60.00;MQ0=0;OQ=2390.91;QD=33.67;SB=-961.60 GT:AD:DP:GL:GQ 1/1:0,70:70:-246.35,-24.25,-3.68:99 +chr1 5107616 rs4543848 T C 111.63 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=2.89;MQ=59.72;MQ0=0;OQ=2325.30;QD=34.71;SB=-962.92 GT:AD:DP:GL:GQ 1/1:0,67:66:-236.14,-19.88,-0.02:99 +chr1 5107713 . A C 103.40 PASS AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=1;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=1036.38;QD=12.79;SB=-351.52 GT:AD:DP:GL:GQ 0/1:44,37:81:-131.32,-24.40,-159.14:99 +chr1 5109104 rs12025231 C T 369.55 PASS AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=60.00;MQ0=0;OQ=1428.81;QD=14.73;SB=-339.81 GT:AD:DP:GL:GQ 0/1:53,44:96:-175.10,-28.94,-171.50:99 +chr1 5109781 rs9439510 C G 474.11 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3322.39;QD=44.30;SB=-1477.33 GT:AD:DP:GL:GQ 1/1:0,75:75:-331.24,-22.59,-0.02:99 +chr1 5109984 rs12121369 C A 599.91 PASS AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=1366.71;QD=15.89;SB=-516.80 GT:AD:DP:GL:GQ 0/1:40,46:85:-165.55,-25.60,-144.36:99 +chr1 5110261 rs7538704 G C 501.84 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1089.65;QD=15.35;SB=-449.75 GT:AD:DP:GL:GQ 0/1:33,38:67:-132.47,-20.22,-140.33:99 +chr1 5110586 rs4462197 C T 256.57 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=2327.86;QD=37.55;SB=-1085.00 GT:AD:DP:GL:GQ 1/1:0,62:59:-236.39,-17.78,-0.02:99 +chr1 5110994 rs10753353 T C 229.27 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.87;MQ=59.74;MQ0=0;OQ=2543.07;QD=35.32;SB=-1168.48 GT:AD:DP:GL:GQ 1/1:0,72:71:-257.91,-21.39,-0.02:99 +chr1 5111198 rs12027352 C T 56.90 PASS AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=2;HaplotypeScore=3.00;MQ=59.50;MQ0=0;OQ=1422.29;QD=15.29;SB=-680.29 GT:AD:DP:GL:GQ 0/1:47,46:88:-172.02,-26.51,-161.50:99 +chr1 5111405 rs4314925 G A 196.97 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=59.36;MQ0=0;OQ=2517.06;QD=38.72;SB=-1234.63 GT:AD:DP:GL:GQ 1/1:0,65:64:-255.31,-19.28,-0.02:99 +chr1 5112055 rs12145645 G A 578.52 PASS AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.38;MQ0=0;OQ=1010.93;QD=13.66;SB=-362.83 GT:AD:DP:GL:GQ 0/1:42,32:72:-126.06,-21.69,-149.75:99 +chr1 5112088 rs61762208 G A 38.27 PASS AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=1.85;MQ=59.44;MQ0=0;OQ=1643.08;QD=19.80;SB=-651.68 GT:AD:DP:GL:GQ 0/1:37,46:82:-192.29,-24.70,-131.13:99 +chr1 5112135 rs12741116 A G 713.71 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2397.16;QD=35.25;SB=-898.68 GT:AD:DP:GL:GQ 1/1:0,68:67:-243.32,-20.18,-0.02:99 +chr1 5113244 rs4600091 T C 489.07 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2494.81;QD=29.70;SB=-1138.12 GT:AD:DP:GL:GQ 1/1:0,84:79:-253.13,-23.82,-0.07:99 +chr1 5113507 rs10753354 C G 401.42 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2295.20;QD=42.50;SB=-1097.09 GT:AD:DP:GL:GQ 1/1:0,54:54:-233.13,-16.28,-0.02:99 +chr1 5113815 rs6698288 G A 330.13 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2134.65;QD=39.53;SB=-887.16 GT:AD:DP:GL:GQ 1/1:0,54:54:-217.07,-16.27,-0.02:99 +chr1 5114383 rs7517431 C G 606.11 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.11;MQ0=0;OQ=920.14;QD=14.61;SB=-463.75 GT:AD:DP:GL:GQ 0/1:36,27:62:-113.98,-18.68,-155.27:99 +chr1 5114445 rs7517449 C T 297.77 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.63;MQ0=0;OQ=2115.05;QD=38.46;SB=-1037.87 GT:AD:DP:GL:GQ 1/1:0,55:54:-215.11,-16.27,-0.02:99 +chr1 5114723 rs10915361 C T 120.85 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=3.02;MQ=58.20;MQ0=0;OQ=931.19;QD=19.81;SB=-478.50 GT:AD:DP:GL:GQ 0/1:19,28:46:-110.26,-13.86,-62.96:99 +chr1 5115596 rs9439538 T C 593.80 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1568.48;QD=30.16;SB=-606.93 GT:AD:DP:GL:GQ 1/1:0,52:50:-160.48,-15.08,-0.04:99 +chr1 5115679 rs12021698 A T 372.77 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.37;MQ0=0;OQ=887.17;QD=15.04;SB=-310.70 GT:AD:DP:GL:GQ 0/1:30,29:59:-109.77,-17.77,-114.78:99 +chr1 5115822 rs56173770 C G 132.01 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1600.81;QD=26.68;SB=-808.51 GT:AD:DP:GL:GQ 0/1:19,41:59:-181.14,-17.77,-78.42:99 +chr1 5115851 rs9439539 T A 636.93 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=2566.28;QD=37.74;SB=-1304.50 GT:AD:DP:GL:GQ 1/1:0,68:67:-260.22,-20.18,-0.01:99 +chr1 5117179 rs5009987 A G 1517.20 Indel AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=20.42;MQ=58.93;MQ0=0;QD=27.59;SB=-603.23 GT:AD:DP:GL:GQ 1/1:2,53:53:-162.87,-15.98,-7.57:84.15 +chr1 5117504 rs10799174 G A 14.48 PASS AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=8.52;MQ=58.73;MQ0=0;OQ=1003.11;QD=18.24;SB=-483.50 GT:AD:DP:GL:GQ 0/1:24,31:52:-119.27,-15.67,-72.69:99 +chr1 5117533 rs6672724 C T 186.08 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.58;MQ=58.63;MQ0=0;OQ=1901.56;QD=37.29;SB=-943.75 GT:AD:DP:GL:GQ 1/1:0,51:50:-193.77,-15.07,-0.02:99 +chr1 5118461 rs9439511 C T 378.94 PASS AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.83;MQ=58.91;MQ0=0;OQ=1153.56;QD=14.98;SB=-536.73 GT:AD:DP:GL:GQ 0/1:42,35:77:-141.84,-23.20,-148.03:99 +chr1 5119340 rs12401983 G A 186.94 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=2.35;MQ=52.79;MQ0=0;OQ=1320.64;QD=16.93;SB=-541.57 GT:AD:DP:GL:GQ 0/1:37,40:76:-158.24,-22.89,-135.98:99 +chr1 5119644 rs55835407 G A 140.46 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=42.95;MQ0=4;OQ=797.21;QD=12.86;SB=-199.88 GT:AD:DP:GL:GQ 0/1:35,27:56:-99.88,-16.88,-103.36:99 +chr1 5119704 rs56293801 T C 75.11 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.00;MQ=42.91;MQ0=1;OQ=434.63;QD=8.36;SB=-212.22 GT:AD:DP:GL:GQ 0/1:32,20:46:-60.61,-13.87,-109.45:99 +chr1 5119914 rs12097824 T C 114 PASS AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=3.43;MQ=39.01;MQ0=0;OQ=589.79;QD=9.51;SB=-187.41 GT:AD:DP:GL:GQ 0/1:33,29:57:-79.44,-17.18,-127.34:99 +chr1 5120013 rs56126017 C G 210.02 PASS AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.93;MQ=35.32;MQ0=0;OQ=1020.64;QD=14.38;SB=-272.51 GT:AD:DP:GL:GQ 0/1:43,28:70:-126.44,-21.09,-178.51:99 +chr1 5120085 . G A 0.02 FDRtranche1.00to2.00 AC=1;AF=0.50;AN=2;DP=101;Dels=0.01;HRun=0;HaplotypeScore=11.89;MQ=34.93;MQ0=0;OQ=541.17;QD=5.36;SB=13.62 GT:AD:DP:GL:GQ 0/1:77,23:97:-86.32,-28.91,-276.66:99 +chr1 5120089 . T A 0.03 FDRtranche0.10to1.00 AC=1;AF=0.50;AN=2;DP=102;Dels=0.00;HRun=0;HaplotypeScore=10.97;MQ=34.87;MQ0=0;OQ=894.55;QD=8.77;SB=-13.59 GT:AD:DP:GL:GQ 0/1:68,34:99:-122.56,-29.82,-255.26:99 +chr1 5120116 . A T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=117;Dels=0.02;HRun=0;HaplotypeScore=143.29;MQ=34.92;MQ0=0;OQ=962.81;QD=8.23;SB=-91.05 GT:AD:DP:GL:GQ 0/1:76,37:114:-138.10,-38.53,-297.11:99 +chr1 5120146 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=141;Dels=0.01;HRun=0;HaplotypeScore=240.33;MQ=33.11;MQ0=0;OQ=492.54;QD=3.49;SB=14.98 GT:AD:DP:GL:GQ 0/1:116,23:120:-88.08,-35.54,-336.13:99 +chr1 5120150 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=150;Dels=0.03;HRun=0;HaplotypeScore=253.70;MQ=32.31;MQ0=0;OQ=526.30;QD=3.51;SB=-209.96 GT:AD:DP:GL:GQ 0/1:122,23:125:-96.24,-40.33,-348.30:99 +chr1 5120166 rs61762214 C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.02;HRun=0;HaplotypeScore=340.16;MQ=31.74;MQ0=0;OQ=707.91;QD=4.19;SB=-238.38 GT:AD:DP:GL:GQ 0/1:128,38:158:-120.76,-46.69,-441.60:99 +chr1 5120182 . T C 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=171;Dels=0.00;HRun=0;HaplotypeScore=247.34;MQ=30.32;MQ0=1;OQ=181.12;QD=1.06;SB=99.79 GT:AD:DP:GL:GQ 0/1:146,25:160:-69.62,-48.22,-544.70:99 +chr1 5120218 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=186;Dels=0.00;HRun=0;HaplotypeScore=296.87;MQ=30.08;MQ0=1;OQ=467.02;QD=2.51;SB=-243.49 GT:AD:DP:GL:GQ 0/1:160,26:175:-102.70,-52.71,-541.07:99 +chr1 5120238 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=187;Dels=0.01;HRun=0;HaplotypeScore=156.33;MQ=31.62;MQ0=1;OQ=98.86;QD=0.53;SB=35.37 GT:AD:DP:GL:GQ 0/1:164,15:172:-86.49,-73.32,-562.87:99 +chr1 5120240 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=184;Dels=0.01;HRun=0;HaplotypeScore=148.66;MQ=31.61;MQ0=1;OQ=319.23;QD=1.73;SB=30.34 GT:AD:DP:GL:GQ 0/1:160,22:170:-85.81,-50.61,-526.60:99 +chr1 5120250 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=164;Dels=0.00;HRun=0;HaplotypeScore=149.91;MQ=33.54;MQ0=1;OQ=262.42;QD=1.60;SB=170.48 GT:AD:DP:GL:GQ 0/1:144,20:159:-77.42,-47.90,-500.91:99 +chr1 5120252 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=152;Dels=0.00;HRun=0;HaplotypeScore=134.92;MQ=34.14;MQ0=1;OQ=1590.07;QD=10.46;SB=-170.99 GT:AD:DP:GL:GQ 0/1:98,53:143:-208.80,-46.51,-329.18:99 +chr1 5121185 . T C 32.44 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.07;MQ=59.52;MQ0=0;OQ=529.93;QD=11.04;SB=-169.50 GT:AD:DP:GL:GQ 0/1:26,22:46:-70.14,-13.86,-100.33:99 +chr1 5122129 rs10915363 G C 183.28 PASS AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=2;HaplotypeScore=0.73;MQ=59.47;MQ0=0;OQ=1248.82;QD=17.84;SB=-543.72 GT:AD:DP:GL:GQ 0/1:31,39:66:-148.06,-19.89,-135.32:99 +chr1 5122156 rs10915364 G C 495.83 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=1017.04;QD=16.14;SB=-464.81 GT:AD:DP:GL:GQ 0/1:31,32:62:-123.68,-18.70,-134.13:99 +chr1 5122248 rs11804873 C T 62.77 PASS AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.39;MQ0=0;OQ=700.13;QD=18.42;SB=-213.90 GT:AD:DP:GL:GQ 0/1:16,22:37:-84.44,-11.15,-55.54:99 +chr1 5122456 rs10915365 C T 167.44 PASS AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=1;HaplotypeScore=2.45;MQ=59.52;MQ0=0;OQ=504.80;QD=12.94;SB=-201.18 GT:AD:DP:GL:GQ 0/1:22,17:38:-65.21,-11.45,-78.02:99 +chr1 5122978 rs12024162 T C 1.83 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=6.85;MQ=58.05;MQ0=0;OQ=2287.65;QD=35.19;SB=-898.04 GT:AD:DP:GL:GQ 1/1:1,64:63:-232.37,-18.97,-0.02:99 +chr1 5123042 rs12026730 G A 134.42 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=56.89;MQ0=0;OQ=1205.15;QD=19.76;SB=-414.94 GT:AD:DP:GL:GQ 0/1:25,36:58:-141.29,-17.49,-70.06:99 +chr1 5123330 rs9439540 C A 63.17 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.37;MQ0=0;OQ=975.37;QD=16.53;SB=-180.54 GT:AD:DP:GL:GQ 0/1:27,32:57:-117.99,-17.17,-89.17:99 +chr1 5124476 rs17366543 A G 248.41 PASS AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=60.00;MQ0=0;OQ=919.81;QD=12.26;SB=-428.10 GT:AD:DP:GL:GQ 0/1:42,33:74:-117.56,-22.29,-166.31:99 +chr1 5126548 rs6690311 A G 73.75 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=3.31;MQ=60.00;MQ0=0;OQ=1952.07;QD=34.25;SB=-789.11 GT:AD:DP:GL:GQ 1/1:0,56:56:-198.81,-16.87,-0.02:99 +chr1 5126612 rs6675995 G A 137.58 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=1;HaplotypeScore=2.05;MQ=59.06;MQ0=0;OQ=2638.82;QD=38.24;SB=-1319.37 GT:AD:DP:GL:GQ 1/1:0,69:67:-267.49,-20.19,-0.02:99 +chr1 5126665 rs10799176 G A 160.71 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.11;MQ0=0;OQ=2842.19;QD=38.93;SB=-1393.38 GT:AD:DP:GL:GQ 1/1:0,73:72:-287.83,-21.69,-0.02:99 +chr1 5126844 rs6685929 C T 627.62 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2295.72;QD=37.63;SB=-1082.35 GT:AD:DP:GL:GQ 1/1:0,61:59:-233.18,-17.78,-0.02:99 +chr1 5126974 . G T 128.27 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.02;MQ0=0;OQ=1169.78;QD=18.87;SB=-560.81 GT:AD:DP:GL:GQ 0/1:24,38:60:-138.33,-18.07,-79.90:99 +chr1 5129269 rs11583683 C T 146.33 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=4;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2126.34;QD=37.30;SB=-795.34 GT:AD:DP:GL:GQ 1/1:0,57:56:-216.24,-16.88,-0.02:99 +chr1 5129679 rs6603817 A G 112.83 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=1509.76;QD=32.82;SB=-474.53 GT:AD:DP:GL:GQ 1/1:0,46:43:-154.58,-12.95,-0.01:99 +chr1 5130606 rs4076635 G A 636.22 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=2562.75;QD=38.25;SB=-1303.24 GT:AD:DP:GL:GQ 1/1:0,67:65:-259.88,-19.58,-0.02:99 +chr1 5131752 rs4394703 C A 307.05 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.37;MQ=58.90;MQ0=0;OQ=2017.11;QD=34.19;SB=-1012.79 GT:AD:DP:GL:GQ 1/1:0,58:57:-208.21,-19.84,-2.91:99 +chr1 5132477 rs6692740 A G 667.43 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=2294.64;QD=31.43;SB=-1053.29 GT:AD:DP:GL:GQ 1/1:0,73:71:-233.10,-21.41,-0.05:99 +chr1 5133851 rs10492928 G T 624.11 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=2734.91;QD=36.47;SB=-1337.92 GT:AD:DP:GL:GQ 1/1:0,75:75:-277.10,-22.59,-0.02:99 +chr1 5134195 rs7545119 C A 288.26 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=2.20;MQ=59.11;MQ0=0;OQ=2691.33;QD=34.50;SB=-1000.80 GT:AD:DP:GL:GQ 1/1:0,78:75:-272.75,-22.59,-0.03:99 +chr1 5135504 rs10915369 C T 488.43 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=1900.03;QD=39.58;SB=-759.52 GT:AD:DP:GL:GQ 1/1:0,48:48:-193.60,-14.46,-0.01:99 +chr1 5135682 rs11583044 G A 156.17 PASS AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=56.88;MQ0=0;OQ=1535.65;QD=34.90;SB=-689.33 GT:AD:DP:GL:GQ 1/1:0,44:41:-157.17,-12.36,-0.02:99 +chr1 5135692 rs10915370 C T 137.61 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=56.35;MQ0=0;OQ=2137.06;QD=38.16;SB=-962.28 GT:AD:DP:GL:GQ 1/1:0,56:55:-217.31,-16.57,-0.02:99 +chr1 5138733 rs10915371 G A 186.78 PASS AC=2;AF=1.00;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=1.52;MQ=58.20;MQ0=0;OQ=3762.30;QD=40.02;SB=-1754.36 GT:AD:DP:GL:GQ 1/1:0,94:93:-375.23,-28.01,-0.02:99 +chr1 5139307 rs9439541 A T 634.34 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3003.64;QD=37.55;SB=-1255.20 GT:AD:DP:GL:GQ 1/1:0,80:79:-303.97,-23.79,-0.02:99 +chr1 5139791 rs6603818 C T 714.35 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.73;MQ0=0;OQ=2781.44;QD=39.73;SB=-1291.72 GT:AD:DP:GL:GQ 1/1:0,70:70:-281.75,-21.09,-0.02:99 +chr1 5140071 rs7547229 C T 724.83 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3128.00;QD=38.62;SB=-1344.39 GT:AD:DP:GL:GQ 1/1:0,81:78:-316.40,-23.49,-0.02:99 +chr1 5140234 . A C 162.19 PASS AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=858.81;QD=15.61;SB=-394.78 GT:AD:DP:GL:GQ 0/1:24,31:53:-105.13,-15.96,-88.06:99 +chr1 5141171 rs6688418 G A 695.26 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2832.24;QD=40.46;SB=-1208.37 GT:AD:DP:GL:GQ 1/1:0,70:70:-286.82,-21.08,-0.01:99 +chr1 5141665 . C T 43.31 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.95;MQ0=0;OQ=985.11;QD=18.24;SB=-409.92 GT:AD:DP:GL:GQ 0/1:25,29:53:-117.76,-15.96,-94.79:99 +chr1 5141935 rs6701052 C T 100.43 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=0.66;MQ=49.80;MQ0=8;OQ=1859.57;QD=32.06;SB=-869.02 GT:AD:DP:GL:GQ 1/1:8,50:47:-189.55,-14.16,-0.01:99 +chr1 5142041 rs12072516 A T 329.01 PASS AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.00;MQ0=0;OQ=266.78;QD=9.53;SB=-152.82 GT:AD:DP:GL:GQ 0/1:16,12:25:-37.49,-7.53,-57.93:99 +chr1 5142287 rs9286978 G A 22.41 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=23.68;MQ0=8;OQ=873.11;QD=24.95;SB=-85.33 GT:AD:DP:GL:GQ 1/1:3,32:23:-90.90,-6.93,-0.01:69.22 +chr1 5143205 rs6664086 T C 86.23 PASS AC=2;AF=1.00;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=3.60;MQ=58.49;MQ0=0;OQ=2734.43;QD=33.76;SB=-1255.67 GT:AD:DP:GL:GQ 1/1:1,80:78:-277.05,-23.49,-0.03:99 +chr1 5144621 rs6603819 C A 635.83 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2574.32;QD=36.78;SB=-1238.13 GT:AD:DP:GL:GQ 1/1:0,70:70:-261.03,-21.08,-0.02:99 +chr1 5146701 rs6669501 C T 700.51 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.28;MQ0=0;OQ=3011.38;QD=38.61;SB=-1500.64 GT:AD:DP:GL:GQ 1/1:0,78:76:-304.75,-22.90,-0.03:99 +chr1 5146942 rs10492930 A G 610.29 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2413.30;QD=30.17;SB=-1138.47 GT:AD:DP:GL:GQ 1/1:0,79:77:-244.99,-23.23,-0.08:99 +chr1 5147215 rs10492931 G A 723.45 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.22;MQ0=0;OQ=2807.87;QD=39.00;SB=-1216.01 GT:AD:DP:GL:GQ 1/1:0,72:71:-284.39,-21.39,-0.02:99 +chr1 5148161 . G A 24.17 PASS AC=1;AF=0.50;AN=2;DP=76;Dels=0.00;HRun=1;HaplotypeScore=1.43;MQ=59.39;MQ0=0;OQ=1450.62;QD=19.09;SB=-417.73 GT:AD:DP:GL:GQ 0/1:33,43:74:-170.64,-22.29,-112.74:99 +chr1 5148401 rs6665697 T C 269.23 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.48;MQ0=0;OQ=2231.09;QD=30.99;SB=-952.42 GT:AD:DP:GL:GQ 1/1:0,72:70:-226.75,-21.11,-0.06:99 +chr1 5150357 rs10915375 A G 529.20 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.37;MQ0=0;OQ=1555.45;QD=31.74;SB=-790.64 GT:AD:DP:GL:GQ 1/1:0,49:49:-159.17,-14.78,-0.04:99 +chr1 5150590 . G T 11.56 DPFilter;LowQual AC=1;AF=0.50;AN=2;DP=69;Dels=0.01;HRun=20;HaplotypeScore=36.67;MQ=54.55;MQ0=0;QD=0.17;SB=69.39 GT:AD:DP:GL:GQ 0/1:49,15:42:-26.08,-21.67,-128.29:44.08 +chr1 5150765 rs9439543 T C 624.17 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.33;MQ0=0;OQ=2519.73;QD=35.49;SB=-971.41 GT:AD:DP:GL:GQ 1/1:0,71:70:-255.58,-21.09,-0.03:99 +chr1 5150768 rs9439544 C T 629.96 PASS AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.35;MQ0=0;OQ=2827.18;QD=38.21;SB=-1183.08 GT:AD:DP:GL:GQ 1/1:0,74:71:-286.33,-21.39,-0.02:99 +chr1 5150948 rs11583754 A G 125.55 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=1.95;MQ=56.88;MQ0=0;OQ=1724.72;QD=34.49;SB=-813.67 GT:AD:DP:GL:GQ 1/1:0,50:49:-176.07,-14.76,-0.02:99 +chr1 5153524 rs7536712 T C 117.29 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=1.92;MQ=59.77;MQ0=0;OQ=2818.40;QD=35.23;SB=-1399.67 GT:AD:DP:GL:GQ 1/1:1,78:79:-289.59,-27.33,-4.17:99 +chr1 5155164 rs2722780 G T 611.46 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2724.16;QD=35.38;SB=-1305.24 GT:AD:DP:GL:GQ 1/1:0,77:77:-276.03,-23.20,-0.03:99 +chr1 5155635 rs2018394 C G 496.66 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.82;MQ0=0;OQ=3565.75;QD=43.48;SB=-1230.53 GT:AD:DP:GL:GQ 1/1:0,82:80:-355.57,-24.10,-0.02:99 +chr1 5156126 rs2679215 G C 570.08 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2670.60;QD=41.73;SB=-1328.91 GT:AD:DP:GL:GQ 1/1:0,64:63:-270.67,-18.98,-0.02:99 +chr1 5156634 rs1320179 T A 161.58 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=59.60;MQ0=0;OQ=1611.01;QD=34.28;SB=-497.40 GT:AD:DP:GL:GQ 1/1:0,47:44:-164.71,-13.26,-0.02:99 +chr1 5157054 . G A 104.21 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=1.46;MQ=58.03;MQ0=0;OQ=746.35;QD=13.09;SB=-370.87 GT:AD:DP:GL:GQ 0/1:33,24:57:-95.09,-17.17,-121.22:99 +chr1 5157089 rs2722781 C T 248.95 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=58.68;MQ0=0;OQ=2013.78;QD=38.00;SB=-852.01 GT:AD:DP:GL:GQ 1/1:0,53:51:-204.98,-15.36,-0.01:99 +chr1 5158014 rs2679216 A G 582.56 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.03;MQ0=0;OQ=2870.64;QD=35.01;SB=-1392.56 GT:AD:DP:GL:GQ 1/1:0,82:80:-290.67,-24.10,-0.03:99 +chr1 5158416 rs2722782 T C 292.12 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=1.91;MQ=59.74;MQ0=0;OQ=2481.35;QD=34.95;SB=-1226.71 GT:AD:DP:GL:GQ 1/1:0,71:71:-251.75,-21.39,-0.03:99 +chr1 5158842 rs2679217 A C 278.49 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=2099.17;QD=33.86;SB=-765.90 GT:AD:DP:GL:GQ 1/1:0,62:61:-213.53,-18.38,-0.03:99 +chr1 5160232 rs2722783 T C 124.50 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=59.02;MQ0=0;OQ=2420.10;QD=34.09;SB=-1200.16 GT:AD:DP:GL:GQ 1/1:1,69:68:-249.06,-23.31,-3.46:99 +chr1 5162761 rs2679218 T C 309.92 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.65;MQ0=0;OQ=2240.61;QD=34.47;SB=-957.91 GT:AD:DP:GL:GQ 1/1:0,65:65:-227.67,-19.58,-0.02:99 +chr1 5164088 rs2722786 A G 678.85 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2134.58;QD=34.99;SB=-757.97 GT:AD:DP:GL:GQ 1/1:0,61:60:-217.06,-18.07,-0.02:99 +chr1 5164377 rs2722787 T C 664.30 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1994.32;QD=31.16;SB=-946.38 GT:AD:DP:GL:GQ 1/1:0,64:63:-203.07,-19.00,-0.06:99 +chr1 5164508 . G A 21.64 PASS AC=1;AF=0.50;AN=2;DP=66;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=60.00;MQ0=0;OQ=1023.93;QD=15.51;SB=-404.39 GT:AD:DP:GL:GQ 0/1:35,31:64:-124.97,-19.29,-108.14:99 +chr1 5165252 rs2679219 A G 545.13 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2430.87;QD=31.16;SB=-1145.16 GT:AD:DP:GL:GQ 1/1:0,78:76:-246.73,-22.91,-0.06:99 +chr1 5165298 rs2722788 C T 111.92 PASS AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.52;MQ0=0;OQ=3387.05;QD=38.93;SB=-1669.69 GT:AD:DP:GL:GQ 1/1:0,87:85:-337.71,-25.61,-0.03:99 +chr1 5166378 rs2722790 C T 150.34 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=59.01;MQ0=0;OQ=2739.21;QD=39.13;SB=-1381.68 GT:AD:DP:GL:GQ 1/1:0,70:69:-277.52,-20.79,-0.02:99 +chr1 5170379 . C T 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=20;HaplotypeScore=3.49;MQ=51.63;MQ0=1;OQ=52.88;QD=0.64;SB=122.38 GT:AD:DP:GL:GQ 0/1:61,22:64:-27.86,-19.28,-197.27:85.72 +chr1 5172063 rs56164612 G A 177.93 PASS AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=2.36;MQ=59.16;MQ0=0;OQ=776.89;QD=15.54;SB=-274.16 GT:AD:DP:GL:GQ 0/1:24,26:48:-95.43,-14.46,-86.73:99 +chr1 5191577 rs471824 A G 242.55 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.16;MQ0=0;OQ=1721.79;QD=27.77;SB=-749.45 GT:AD:DP:GL:GQ 1/1:1,61:57:-179.88,-17.20,-4.11:99 +chr1 5191739 rs632051 C A 18.10 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=2;HaplotypeScore=4.23;MQ=58.83;MQ0=0;OQ=3137.26;QD=37.35;SB=-891.27 GT:AD:DP:GL:GQ 1/1:0,84:83:-317.33,-25.00,-0.02:99 +chr1 5193545 rs566114 T G 200.45 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=-0.06;MQ=60.00;MQ0=0;OQ=2400.30;QD=34.29;SB=-1100.14 GT:AD:DP:GL:GQ 1/1:0,70:68:-243.64,-20.48,-0.02:99 +chr1 5194097 rs56295354 C T 367.36 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.98;MQ0=0;OQ=896.66;QD=14.01;SB=-471.46 GT:AD:DP:GL:GQ 0/1:34,30:62:-111.63,-18.68,-121.51:99 +chr1 5195036 rs677735 A G 310.10 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=59.68;MQ0=0;OQ=2493.12;QD=34.15;SB=-981.71 GT:AD:DP:GL:GQ 1/1:0,73:71:-252.92,-21.39,-0.03:99 +chr1 5195467 rs2986186 T A 311.13 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.45;MQ0=0;OQ=2846.52;QD=37.45;SB=-1332.00 GT:AD:DP:GL:GQ 1/1:0,76:75:-288.25,-22.59,-0.02:99 +chr1 5196704 rs2353169 T C 724.90 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=2499.39;QD=34.71;SB=-983.95 GT:AD:DP:GL:GQ 1/1:0,72:72:-253.55,-21.69,-0.02:99 +chr1 5197705 rs473104 A G 598.18 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2654.56;QD=34.93;SB=-1319.89 GT:AD:DP:GL:GQ 1/1:0,76:74:-269.06,-22.29,-0.02:99 +chr1 5197747 rs586165 T C 721.60 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2710.69;QD=35.20;SB=-1278.13 GT:AD:DP:GL:GQ 1/1:0,77:76:-274.68,-22.89,-0.03:99 +chr1 5198145 rs584402 C T 717.83 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2714.09;QD=39.33;SB=-1353.02 GT:AD:DP:GL:GQ 1/1:0,69:69:-275.01,-20.79,-0.02:99 +chr1 5198627 rs679712 T A 207.32 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=1.59;MQ=59.36;MQ0=0;OQ=2332.10;QD=35.88;SB=-1044.59 GT:AD:DP:GL:GQ 1/1:0,65:63:-236.81,-18.97,-0.02:99 +chr1 5198919 rs551536 T C 66.98 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.47;MQ=59.68;MQ0=0;OQ=2254.50;QD=31.75;SB=-1121.22 GT:AD:DP:GL:GQ 1/1:0,71:70:-229.09,-21.11,-0.06:99 +chr1 5198972 rs551376 G A 527.51 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=2736.21;QD=38.54;SB=-1372.67 GT:AD:DP:GL:GQ 1/1:0,71:69:-277.22,-20.79,-0.02:99 +chr1 5199041 rs550558 G A 271.08 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.75;MQ0=0;OQ=2982.88;QD=39.25;SB=-1518.69 GT:AD:DP:GL:GQ 1/1:0,75:75:-301.89,-22.59,-0.02:99 +chr1 5199083 rs549773 C A 400.22 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2265.19;QD=35.39;SB=-1149.37 GT:AD:DP:GL:GQ 1/1:0,64:63:-230.13,-18.98,-0.02:99 +chr1 5199801 rs663998 C G 667.78 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.24;MQ0=1;OQ=2933.78;QD=41.91;SB=-1382.38 GT:AD:DP:GL:GQ 1/1:0,70:68:-296.98,-20.49,-0.02:99 +chr1 5199984 rs663142 G T 300.03 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=57.88;MQ0=0;OQ=2524.52;QD=34.58;SB=-1263.12 GT:AD:DP:GL:GQ 1/1:0,73:71:-256.06,-21.39,-0.02:99 +chr1 5200020 rs663106 T C 288.64 PASS AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.94;MQ0=0;OQ=2324.56;QD=29.06;SB=-1068.20 GT:AD:DP:GL:GQ 1/1:0,80:72:-236.10,-21.71,-0.06:99 +chr1 5201096 rs35339923 C T 25.91 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=2;HaplotypeScore=0.74;MQ=59.27;MQ0=0;OQ=2513.57;QD=39.90;SB=-919.70 GT:AD:DP:GL:GQ 1/1:0,63:63:-254.96,-18.98,-0.02:99 +chr1 5201932 rs611422 T C 369.89 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.65;MQ0=0;OQ=2205.79;QD=33.94;SB=-980.06 GT:AD:DP:GL:GQ 1/1:0,65:62:-224.19,-18.68,-0.02:99 +chr1 5201978 rs534321 A C 83.24 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.68;MQ0=0;OQ=2498.46;QD=34.23;SB=-901.19 GT:AD:DP:GL:GQ 1/1:0,73:73:-253.46,-21.99,-0.03:99 +chr1 5202029 rs534188 C T 644.23 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.84;MQ0=0;OQ=2223.00;QD=39.70;SB=-899.19 GT:AD:DP:GL:GQ 1/1:0,56:56:-225.90,-16.87,-0.02:99 +chr1 5202175 rs12125575 G A 578.75 PASS AC=2;AF=1.00;AN=2;DB;DP=47;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.13;MQ0=0;OQ=1740.25;QD=37.03;SB=-800.07 GT:AD:DP:GL:GQ 1/1:0,47:44:-177.62,-13.25,-0.01:99 +chr1 5202200 rs610133 T C 141.51 PASS AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=49.73;MQ0=0;OQ=1399.83;QD=30.43;SB=-711.63 GT:AD:DP:GL:GQ 1/1:0,46:41:-143.59,-12.36,-0.02:99 +chr1 5202222 rs511282 G T 609.56 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=50.02;MQ0=0;OQ=2299.71;QD=34.32;SB=-1138.31 GT:AD:DP:GL:GQ 1/1:0,67:64:-233.58,-19.28,-0.02:99 +chr1 5202265 rs599481 G T 595.11 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=49.58;MQ0=0;OQ=2113.87;QD=33.55;SB=-993.43 GT:AD:DP:GL:GQ 1/1:0,63:58:-214.99,-17.47,-0.02:99 +chr1 5202388 rs12066405 A G 127.75 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=51.98;MQ0=0;OQ=2322.85;QD=33.66;SB=-1080.10 GT:AD:DP:GL:GQ 1/1:0,69:65:-235.89,-19.58,-0.02:99 +chr1 5202422 . T G 419.39 Indel AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=66.39;MQ=43.53;MQ0=0;QD=7.23;SB=-202.77 GT:AD:DP:GL:GQ 0/1:38,20:51:-60.59,-15.36,-121.07:99 +chr1 5202441 rs12071111 G A 97.09 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=3.61;MQ=40.65;MQ0=0;OQ=1838.51;QD=34.69;SB=-927.74 GT:AD:DP:GL:GQ 1/1:1,52:48:-187.45,-14.46,-0.02:99 +chr1 5202467 rs12067585 T G 27.99 PASS AC=2;AF=1.00;AN=2;DB;DP=35;Dels=0.00;HRun=1;HaplotypeScore=0.10;MQ=52.14;MQ0=0;OQ=1141.50;QD=32.61;SB=-417.26 GT:AD:DP:GL:GQ 1/1:0,35:33:-117.74,-9.94,-0.01:99 +chr1 5202510 rs10915390 T C 6.38 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=45.77;MQ0=0;OQ=1492.54;QD=28.70;SB=-582.99 GT:AD:DP:GL:GQ 1/1:0,52:46:-152.88,-13.87,-0.04:99 +chr1 5202536 rs10915391 A G 576.79 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=40.09;MQ0=0;OQ=1719.08;QD=33.06;SB=-769.98 GT:AD:DP:GL:GQ 1/1:0,52:48:-175.51,-14.46,-0.01:99 +chr1 5202563 . A G 1303.98 SnpCluster AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=5.87;MQ=34.10;MQ0=0;QD=25.08;SB=-434.46 GT:AD:DP:GL:GQ 1/1:0,52:39:-134.00,-11.75,-0.02:99 +chr1 5202564 . T C 1560.70 SnpCluster AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;HRun=2;HaplotypeScore=5.87;MQ=34.10;MQ0=0;QD=30.01;SB=-450.83 GT:AD:DP:GL:GQ 1/1:1,51:44:-159.67,-13.26,-0.02:99 +chr1 5202566 . C T 1713.62 SnpCluster AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.22;MQ=34.87;MQ0=0;QD=32.95;SB=-454.10 GT:AD:DP:GL:GQ 1/1:0,51:43:-174.96,-12.95,-0.01:99 +chr1 5202576 rs12134110 C T 0.75 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=6.13;MQ=37.89;MQ0=0;OQ=1873.93;QD=33.46;SB=-544.73 GT:AD:DP:GL:GQ 1/1:1,55:47:-190.99,-14.16,-0.01:99 +chr1 5202767 rs2986185 A G 288.60 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.20;MQ0=0;OQ=2264.33;QD=34.84;SB=-1153.44 GT:AD:DP:GL:GQ 1/1:0,65:64:-230.04,-19.28,-0.02:99 +chr1 5202796 rs2945617 T C 352.06 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.10;MQ0=0;OQ=1791.40;QD=27.99;SB=-839.97 GT:AD:DP:GL:GQ 1/1:0,64:58:-182.79,-17.50,-0.06:99 +chr1 5202844 rs2986184 C G 260.78 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=52.86;MQ0=0;OQ=2380.85;QD=40.35;SB=-1080.09 GT:AD:DP:GL:GQ 1/1:0,59:56:-241.69,-16.88,-0.02:99 +chr1 5202908 . C T 49.09 PASS AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=56.41;MQ0=0;OQ=1679.71;QD=37.33;SB=-834.36 GT:AD:DP:GL:GQ 1/1:0,45:42:-171.56,-12.65,-0.01:99 +chr1 5203231 rs480807 G A 112.83 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=1.65;MQ=59.13;MQ0=0;OQ=2991.96;QD=39.89;SB=-1079.44 GT:AD:DP:GL:GQ 1/1:0,75:75:-302.81,-22.60,-0.03:99 +chr1 5203306 rs6687834 C T 621.90 PASS AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3055.40;QD=39.68;SB=-1315.34 GT:AD:DP:GL:GQ 1/1:0,77:77:-309.15,-23.20,-0.02:99 +chr1 5203354 rs584498 C T 147.71 PASS AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.38;MQ0=0;OQ=2983.67;QD=38.25;SB=-1435.37 GT:AD:DP:GL:GQ 1/1:0,78:75:-301.97,-22.59,-0.02:99 +chr1 5203671 rs582779 C A 167.92 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=60.00;MQ0=0;OQ=2146.95;QD=35.78;SB=-804.85 GT:AD:DP:GL:GQ 1/1:0,60:60:-218.30,-18.08,-0.02:99 +chr1 5203886 rs474456 G C 148.15 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=3.48;MQ=58.03;MQ0=0;OQ=2254.35;QD=39.55;SB=-1087.49 GT:AD:DP:GL:GQ 1/1:0,57:55:-229.05,-16.59,-0.04:99 +chr1 5203943 rs473685 T C 568.01 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.84;MQ0=0;OQ=1941.75;QD=35.30;SB=-734.93 GT:AD:DP:GL:GQ 1/1:0,55:55:-197.78,-16.57,-0.02:99 +chr1 5204037 rs472768 C A 257.84 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=1.57;MQ=53.49;MQ0=0;OQ=2116.13;QD=35.87;SB=-808.86 GT:AD:DP:GL:GQ 1/1:0,59:58:-215.21,-17.47,-0.01:99 +chr1 5204179 rs561169 C T 180.12 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.48;MQ=59.63;MQ0=0;OQ=1666.79;QD=32.68;SB=-839.97 GT:AD:DP:GL:GQ 1/1:0,51:44:-170.29,-13.26,-0.02:99 +chr1 5204268 rs677650 G C 32.68 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=0.58;MQ=41.36;MQ0=0;OQ=1911.63;QD=39.01;SB=-915.40 GT:AD:DP:GL:GQ 1/1:0,49:46:-194.77,-13.87,-0.02:99 +chr1 5204556 rs676589 T A 738.91 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.27;MQ0=0;OQ=2559.35;QD=36.56;SB=-1189.80 GT:AD:DP:GL:GQ 1/1:0,70:69:-259.54,-20.78,-0.02:99 +chr1 5204733 rs675738 T C 27.97 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=2;HaplotypeScore=2.20;MQ=59.17;MQ0=0;OQ=1658.38;QD=29.61;SB=-662.81 GT:AD:DP:GL:GQ 1/1:0,56:52:-169.47,-15.68,-0.05:99 +chr1 5204883 rs9439546 G A 532.03 PASS AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=2940.91;QD=38.70;SB=-1192.36 GT:AD:DP:GL:GQ 1/1:0,76:75:-297.70,-22.60,-0.03:99 +chr1 5204955 rs674820 A G 79.68 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.62;MQ0=0;OQ=2113.60;QD=34.65;SB=-990.71 GT:AD:DP:GL:GQ 1/1:0,61:60:-214.97,-18.07,-0.02:99 +chr1 5204998 rs674421 C T 11.79 PASS AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=1;HaplotypeScore=4.18;MQ=59.19;MQ0=0;OQ=2200.64;QD=38.61;SB=-746.99 GT:AD:DP:GL:GQ 1/1:0,57:55:-223.66,-16.57,-0.01:99 +chr1 5205224 rs673451 T G 405.18 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1733.87;QD=28.90;SB=-756.83 GT:AD:DP:GL:GQ 1/1:0,60:55:-177.02,-16.58,-0.05:99 +chr1 5206120 rs56397638 C T 43.03 Indel;LowQual AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=3.09;MQ=48.93;MQ0=0;QD=2.39;SB=-0.99 GT:AD:DP:GL:GQ 0/1:15,3:17:-12.71,-5.12,-48.36:75.87 +chr1 5206410 . T C 0.40 PASS AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;HRun=2;HaplotypeScore=1.63;MQ=56.77;MQ0=0;OQ=1364.10;QD=34.98;SB=-316.12 GT:AD:DP:GL:GQ 1/1:0,39:38:-140.01,-11.45,-0.01:99 +chr1 5206681 rs12121640 A C 71.98 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=58.51;MQ0=0;OQ=1679.67;QD=32.93;SB=-387.04 GT:AD:DP:GL:GQ 1/1:0,51:47:-171.57,-14.16,-0.01:99 +chr1 5206700 rs12125074 G A 98.48 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.05;MQ=58.12;MQ0=0;OQ=2000.17;QD=37.74;SB=-489.65 GT:AD:DP:GL:GQ 1/1:0,53:50:-203.61,-15.06,-0.01:99 +chr1 5208394 rs7549686 T C 327.06 PASS AC=2;AF=1.00;AN=2;DB;DP=94;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3436.97;QD=36.56;SB=-1599.67 GT:AD:DP:GL:GQ 1/1:0,94:93:-342.70,-28.01,-0.02:99 +chr1 5209527 rs12135834 C T 124.99 PASS AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=2736.25;QD=39.66;SB=-1253.04 GT:AD:DP:GL:GQ 1/1:0,69:68:-277.22,-20.48,-0.01:99 +chr1 5209757 rs12128282 G A 708.74 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2355.65;QD=38.62;SB=-1039.67 GT:AD:DP:GL:GQ 1/1:0,61:59:-239.17,-17.77,-0.02:99 +chr1 5210118 rs4465222 T C 132.90 PASS AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=58.97;MQ0=0;OQ=1268.12;QD=28.18;SB=-489.53 GT:AD:DP:GL:GQ 1/1:0,45:42:-130.45,-12.68,-0.06:99 +chr1 5210152 rs4465223 T C 176.23 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.16;MQ0=0;OQ=1621.75;QD=29.49;SB=-654.28 GT:AD:DP:GL:GQ 1/1:0,55:51:-165.81,-15.38,-0.05:99 +chr1 5210469 rs6686714 G T 712.77 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1971.04;QD=35.20;SB=-893.62 GT:AD:DP:GL:GQ 1/1:0,56:56:-200.71,-16.87,-0.02:99 +chr1 5211244 rs6603825 T C 594.56 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2173.03;QD=35.62;SB=-828.31 GT:AD:DP:GL:GQ 1/1:0,61:60:-220.91,-18.07,-0.02:99 +chr1 5211435 . C T 25.65 PASS AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.22;MQ=59.65;MQ0=0;OQ=960.07;QD=17.78;SB=-418.78 GT:AD:DP:GL:GQ 0/1:25,29:53:-115.26,-15.97,-85.03:99 +chr1 5212025 rs4475768 T G 354.90 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.37;MQ0=0;OQ=695.32;QD=14.19;SB=-234.36 GT:AD:DP:GL:GQ 0/1:24,25:49:-87.57,-14.76,-89.97:99 +chr1 5212226 rs494046 T C 148.80 PASS AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=2779.20;QD=29.88;SB=-1328.52 GT:AD:DP:GL:GQ 1/1:0,93:88:-281.58,-26.54,-0.08:99 +chr1 5213428 . A G 11.97 PASS AC=1;AF=0.50;AN=2;DP=48;Dels=0.00;HRun=0;HaplotypeScore=3.03;MQ=58.55;MQ0=0;OQ=408.80;QD=8.52;SB=-93.78 GT:AD:DP:GL:GQ 0/1:27,21:44:-57.43,-13.27,-96.36:99 +chr1 5213524 . T A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=0;HaplotypeScore=71.93;MQ=50.54;MQ0=0;OQ=502.87;QD=9.14;SB=-189.21 GT:AD:DP:GL:GQ 0/1:37,18:47:-67.73,-14.16,-102.82:99 +chr1 5213770 rs6658152 C T 45.87 PASS AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=0.33;MQ=60.00;MQ0=0;OQ=1572.39;QD=38.35;SB=-554.31 GT:AD:DP:GL:GQ 1/1:0,41:41:-160.84,-12.35,-0.02:99 +chr1 5215271 . A G 38.30 PASS AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=1.20;MQ=59.60;MQ0=0;OQ=1692.08;QD=29.17;SB=-770.59 GT:AD:DP:GL:GQ 1/1:0,57:55:-172.85,-16.59,-0.06:99 +chr1 5217813 . G C 1.18 PASS AC=1;AF=0.50;AN=2;DP=81;Dels=0.00;HRun=0;HaplotypeScore=9.11;MQ=58.35;MQ0=1;OQ=1164.43;QD=14.38;SB=-426.29 GT:AD:DP:GL:GQ 0/1:49,32:77:-142.93,-23.20,-194.98:99 +chr1 5217931 rs4847582 C G 145.68 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.66;MQ0=0;OQ=1509.42;QD=22.20;SB=-480.86 GT:AD:DP:GL:GQ 0/1:26,42:66:-174.11,-19.89,-110.01:99 +chr1 5218042 rs4847581 A T 229.68 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.31;MQ0=0;OQ=560.70;QD=9.19;SB=-151.08 GT:AD:DP:GL:GQ 0/1:39,22:59:-77.12,-17.77,-150.88:99 +chr1 5218412 rs12089315 C T 695.85 PASS AC=2;AF=1.00;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2655.40;QD=40.23;SB=-1167.53 GT:AD:DP:GL:GQ 1/1:0,66:65:-269.14,-19.58,-0.01:99 +chr1 5218922 rs55929300 C T 250.89 PASS AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=2.25;MQ=58.35;MQ0=0;OQ=749.84;QD=14.42;SB=-372.87 GT:AD:DP:GL:GQ 0/1:29,23:51:-93.64,-15.37,-91.04:99 +chr1 5218923 rs2945619 A G 55.86 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=2.25;MQ=58.42;MQ0=0;OQ=1817.82;QD=33.66;SB=-828.90 GT:AD:DP:GL:GQ 1/1:0,54:53:-185.39,-15.97,-0.03:99 +chr1 5219162 . C T 26.36 PASS AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=2;HaplotypeScore=0.93;MQ=59.78;MQ0=0;OQ=1260.89;QD=15.01;SB=-475.42 GT:AD:DP:GL:GQ 0/1:46,38:84:-154.67,-25.30,-167.04:99 +chr1 5220394 rs632798 A G 319.28 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=1931.82;QD=32.74;SB=-775.98 GT:AD:DP:GL:GQ 1/1:0,59:54:-196.78,-16.27,-0.02:99 +chr1 5221239 rs11584035 A G 510.42 PASS AC=2;AF=1.00;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2162.59;QD=34.33;SB=-1003.74 GT:AD:DP:GL:GQ 1/1:0,63:61:-219.86,-18.37,-0.02:99 +chr1 5221301 rs11585734 G C 28.93 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.47;MQ0=0;OQ=2416.76;QD=43.16;SB=-843.33 GT:AD:DP:GL:GQ 1/1:0,56:55:-245.27,-16.57,-0.01:99 +chr1 5221482 rs34835703 A T 2939.50 Indel AC=2;AF=1.00;AN=2;DB;DP=92;Dels=0.00;HRun=0;HaplotypeScore=3.98;MQ=58.65;MQ0=0;QD=31.95;SB=-1078.25 GT:AD:DP:GL:GQ 1/1:2,89:87:-306.96,-29.45,-9.42:99 +chr1 5221725 . G A 0 FDRtranche2.00to10.00+ AC=1;AF=0.50;AN=2;DP=60;Dels=0.03;HRun=18;HaplotypeScore=39.80;MQ=52.31;MQ0=0;OQ=152.15;QD=2.54;SB=47.14 GT:AD:DP:GL:GQ 0/1:40,18:43:-30.85,-12.35,-114.35:99 +chr1 5222078 rs972257 T A 639.98 PASS AC=2;AF=1.00;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=56.18;MQ0=0;OQ=3168.88;QD=37.28;SB=-1120.55 GT:AD:DP:GL:GQ 1/1:0,85:85:-320.49,-25.60,-0.02:99 +chr1 5222126 rs972256 A G 626.95 PASS AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.13;MQ0=0;OQ=2639.54;QD=35.19;SB=-1126.78 GT:AD:DP:GL:GQ 1/1:0,75:75:-267.56,-22.59,-0.03:99 +chr1 5224091 rs499416 T C 297.77 PASS AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=1.73;MQ=59.44;MQ0=0;OQ=2957.76;QD=36.07;SB=-1259.50 GT:AD:DP:GL:GQ 1/1:0,82:82:-299.39,-24.70,-0.03:99 +chr1 5224457 rs681122 A G 116.50 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=58.67;MQ0=0;OQ=2663.18;QD=31.70;SB=-1024.35 GT:AD:DP:GL:GQ 1/1:0,84:81:-269.96,-24.42,-0.06:99 +chr1 5224547 rs503246 T C 2.42 PASS AC=2;AF=1.00;AN=2;DB;DP=70;Dels=0.00;HRun=1;HaplotypeScore=6.13;MQ=59.67;MQ0=0;OQ=2425.86;QD=34.66;SB=-1136.77 GT:AD:DP:GL:GQ 1/1:0,69:69:-249.69,-23.90,-3.52:99 +chr1 5224600 rs504015 G A 107.71 PASS AC=2;AF=1.00;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=1.41;MQ=59.36;MQ0=0;OQ=3623.40;QD=38.14;SB=-1734.33 GT:AD:DP:GL:GQ 1/1:1,94:92:-361.34,-27.72,-0.04:99 +chr1 5225244 rs34916930 A G 210.97 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=2.75;MQ=59.23;MQ0=0;OQ=766.73;QD=12.78;SB=-281.64 GT:AD:DP:GL:GQ 0/1:31,29:57:-97.13,-17.17,-122.94:99 +chr1 5225286 rs1614164 A G 116.44 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=59.11;MQ0=0;OQ=1503.00;QD=28.90;SB=-584.52 GT:AD:DP:GL:GQ 1/1:0,52:49:-153.94,-14.79,-0.06:99 +chr1 5225305 rs531507 T C 127.86 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=0.63;MQ=59.05;MQ0=0;OQ=1485.28;QD=30.31;SB=-700.80 GT:AD:DP:GL:GQ 1/1:0,49:47:-152.15,-14.18,-0.04:99 +chr1 5225319 rs531541 G A 341.76 PASS AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.47;MQ=59.53;MQ0=0;OQ=776.62;QD=15.85;SB=-311.30 GT:AD:DP:GL:GQ 0/1:25,24:46:-94.81,-13.86,-73.71:99 +chr1 5225584 rs12139398 G T 64.15 PASS AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=3;HaplotypeScore=2.68;MQ=59.09;MQ0=0;OQ=1255.53;QD=16.52;SB=-636.75 GT:AD:DP:GL:GQ 0/1:35,41:76:-151.73,-22.89,-120.82:99 +chr1 5225784 rs648378 G A 217.93 PASS AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=1;HaplotypeScore=0.67;MQ=60.00;MQ0=0;OQ=3051.49;QD=38.63;SB=-1366.03 GT:AD:DP:GL:GQ 1/1:0,79:77:-308.76,-23.20,-0.02:99 +chr1 5225910 rs536995 T C 659.19 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2238.13;QD=31.52;SB=-1141.80 GT:AD:DP:GL:GQ 1/1:0,71:69:-227.45,-20.80,-0.05:99 +chr1 5226194 rs646542 C A 53.96 PASS AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=2;HaplotypeScore=2.51;MQ=59.52;MQ0=0;OQ=616.21;QD=12.84;SB=-186.21 GT:AD:DP:GL:GQ 0/1:25,23:46:-78.77,-13.86,-80.93:99 +chr1 5227007 rs17422703 C T 447.59 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=60.00;MQ0=0;OQ=653.00;QD=13.89;SB=-346.50 GT:AD:DP:GL:GQ 0/1:27,20:47:-82.75,-14.17,-88.07:99 +chr1 5227141 rs479689 T C 634.35 PASS AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2577.54;QD=35.80;SB=-1149.80 GT:AD:DP:GL:GQ 1/1:0,72:72:-261.36,-21.69,-0.02:99 +chr1 5227198 rs631837 T G 470.17 PASS AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=1038.21;QD=12.98;SB=-481.28 GT:AD:DP:GL:GQ 0/1:42,38:78:-130.60,-23.49,-142.85:99 +chr1 5227509 rs2945620 A G 463.41 PASS AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=1887.53;QD=34.95;SB=-718.20 GT:AD:DP:GL:GQ 1/1:0,54:53:-192.35,-15.96,-0.02:99 +chr1 5227512 rs2986190 C G 581.25 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.76;MQ0=0;OQ=2178.35;QD=38.90;SB=-696.39 GT:AD:DP:GL:GQ 1/1:0,56:54:-221.45,-16.29,-0.03:99 +chr1 5227592 rs484203 C G 505.04 PASS AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.30;MQ0=0;OQ=1740.53;QD=36.26;SB=-435.04 GT:AD:DP:GL:GQ 1/1:0,48:44:-177.67,-13.27,-0.03:99 +chr1 5227620 rs2945621 C T 184.65 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.15;MQ=58.52;MQ0=0;OQ=2108.36;QD=38.33;SB=-729.97 GT:AD:DP:GL:GQ 1/1:0,54:54:-216.99,-18.70,-2.57:99 +chr1 5228455 rs605572 G A 158.70 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.08;MQ0=0;OQ=2364.59;QD=38.76;SB=-1049.40 GT:AD:DP:GL:GQ 1/1:0,61:59:-240.06,-17.77,-0.01:99 +chr1 5228485 rs547366 A G 151.91 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=1.43;MQ=59.32;MQ0=0;OQ=1644.48;QD=29.90;SB=-746.94 GT:AD:DP:GL:GQ 1/1:0,55:53:-168.09,-15.99,-0.05:99 +chr1 5228494 rs547375 T C 432.28 PASS AC=2;AF=1.00;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=1148.89;QD=28.72;SB=-518.83 GT:AD:DP:GL:GQ 1/1:0,40:38:-118.51,-11.46,-0.04:99 +chr1 5228675 rs549178 A C 608.96 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=1844.59;QD=34.16;SB=-895.07 GT:AD:DP:GL:GQ 1/1:0,54:53:-188.06,-15.96,-0.02:99 +chr1 5229041 rs552154 A G 144.86 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.05;MQ=58.33;MQ0=0;OQ=2394.34;QD=35.74;SB=-1030.76 GT:AD:DP:GL:GQ 1/1:0,67:67:-243.04,-20.18,-0.02:99 +chr1 5229075 rs694316 A G 16.95 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=2.71;MQ=58.29;MQ0=0;OQ=1696.38;QD=32.62;SB=-808.31 GT:AD:DP:GL:GQ 1/1:0,52:49:-173.25,-14.76,-0.02:99 +chr1 5229079 rs574063 A C 47.22 PASS AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=1;HaplotypeScore=2.27;MQ=58.29;MQ0=0;OQ=1690.52;QD=32.51;SB=-775.03 GT:AD:DP:GL:GQ 1/1:0,52:50:-172.66,-15.06,-0.02:99 +chr1 5229195 rs2986189 T C 594.24 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1695.13;QD=33.24;SB=-849.99 GT:AD:DP:GL:GQ 1/1:0,50:49:-173.12,-14.76,-0.02:99 +chr1 5229410 rs590229 A G 533.32 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.69;MQ0=0;OQ=1626.39;QD=32.53;SB=-702.18 GT:AD:DP:GL:GQ 1/1:0,50:47:-166.24,-14.16,-0.02:99 +chr1 5229454 rs576935 T C 291.30 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2227.88;QD=34.81;SB=-1091.09 GT:AD:DP:GL:GQ 1/1:0,64:63:-226.40,-18.98,-0.03:99 +chr1 5229643 rs589314 C T 702.68 PASS AC=2;AF=1.00;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3349.31;QD=39.87;SB=-1157.05 GT:AD:DP:GL:GQ 1/1:0,84:83:-333.93,-25.00,-0.02:99 +chr1 5229725 rs579467 T C 242.79 PASS AC=2;AF=1.00;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.46;MQ=59.13;MQ0=0;OQ=1575.01;QD=29.72;SB=-809.29 GT:AD:DP:GL:GQ 1/1:0,53:51:-161.14,-15.39,-0.05:99 +chr1 5229840 rs580404 G A 618.34 PASS AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.49;MQ0=0;OQ=2841.67;QD=38.93;SB=-1151.68 GT:AD:DP:GL:GQ 1/1:0,73:73:-287.78,-22.00,-0.03:99 +chr1 5229963 rs587619 A G 627.90 PASS AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.05;MQ0=0;OQ=1527.65;QD=31.18;SB=-661.80 GT:AD:DP:GL:GQ 1/1:0,49:48:-156.40,-14.48,-0.05:99 +chr1 5230068 rs684796 A G 654.33 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1910.04;QD=31.31;SB=-776.75 GT:AD:DP:GL:GQ 1/1:0,61:59:-194.63,-17.79,-0.04:99 +chr1 5230099 rs493993 T C 52.25 PASS AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.40;MQ=60.00;MQ0=0;OQ=1531.39;QD=30.03;SB=-555.88 GT:AD:DP:GL:GQ 1/1:0,51:49:-156.77,-14.78,-0.05:99 +chr1 5230146 rs494138 C T 565.44 PASS AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1901.52;QD=38.03;SB=-812.08 GT:AD:DP:GL:GQ 1/1:0,50:49:-193.76,-14.77,-0.02:99 +chr1 5230400 rs683361 C T 576.16 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2445.96;QD=38.22;SB=-885.63 GT:AD:DP:GL:GQ 1/1:0,64:64:-248.21,-19.29,-0.03:99 +chr1 5230419 rs683326 A C 444.54 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=2097.81;QD=32.78;SB=-733.04 GT:AD:DP:GL:GQ 1/1:0,64:59:-213.39,-17.77,-0.02:99 +chr1 5230522 rs497780 C T 280.11 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.26;MQ=59.44;MQ0=0;OQ=2456.36;QD=36.66;SB=-1135.53 GT:AD:DP:GL:GQ 1/1:0,66:64:-249.25,-19.29,-0.03:99 +chr1 5230617 rs682425 A C 128.19 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=1.82;MQ=60.00;MQ0=0;OQ=2329.64;QD=34.26;SB=-803.08 GT:AD:DP:GL:GQ 1/1:1,67:66:-236.57,-19.88,-0.02:99 +chr1 5230727 rs499639 G A 152.07 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.28;MQ0=0;OQ=1710.74;QD=26.73;SB=-582.87 GT:AD:DP:GL:GQ 1/1:0,37:64:-256.74,-99.73,-82.08:99 +chr1 5230993 rs17423021 C T 275.08 PASS AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.00;HRun=0;HaplotypeScore=1.66;MQ=60.00;MQ0=0;OQ=870.39;QD=18.52;SB=-403.16 GT:AD:DP:GL:GQ 0/1:21,26:47:-104.48,-14.16,-73.19:99 +chr1 5231281 rs695100 T C 614.40 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=1962.66;QD=33.84;SB=-961.65 GT:AD:DP:GL:GQ 1/1:0,58:57:-199.88,-17.17,-0.03:99 +chr1 5231434 rs2860250 T G 608.99 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1940.74;QD=34.66;SB=-919.09 GT:AD:DP:GL:GQ 1/1:0,56:55:-197.68,-16.57,-0.02:99 +chr1 5231440 rs2353173 G T 713.73 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2174.12;QD=33.45;SB=-1013.52 GT:AD:DP:GL:GQ 1/1:0,65:62:-221.02,-18.68,-0.02:99 +chr1 5231533 rs4290073 G A 106.58 PASS AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=59.20;MQ0=0;OQ=1041.27;QD=12.86;SB=-342.41 GT:AD:DP:GL:GQ 0/1:49,32:81:-131.81,-24.39,-179.39:99 +chr1 5231729 rs2945622 G A 619.13 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=2286.02;QD=38.75;SB=-1132.51 GT:AD:DP:GL:GQ 1/1:0,59:57:-232.20,-17.17,-0.01:99 +chr1 5231775 rs4633300 T C 80.14 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=2.27;MQ=58.86;MQ0=0;OQ=2147.74;QD=35.21;SB=-1067.79 GT:AD:DP:GL:GQ 1/1:0,61:61:-218.38,-18.38,-0.02:99 +chr1 5231808 rs10799186 T C 608.79 PASS AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.88;MQ0=0;OQ=2059.90;QD=33.22;SB=-1027.00 GT:AD:DP:GL:GQ 1/1:0,62:60:-209.61,-18.08,-0.04:99 +chr1 5231809 rs10799187 G C 596.93 PASS AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=2598.74;QD=40.61;SB=-1318.71 GT:AD:DP:GL:GQ 1/1:0,64:61:-263.48,-18.38,-0.02:99 +chr1 5231833 rs530731 G C 494.40 PASS AC=2;AF=1.00;AN=2;DB;DP=58;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=2447.16;QD=42.19;SB=-1018.28 GT:AD:DP:GL:GQ 1/1:0,58:58:-248.32,-17.48,-0.02:99 +chr1 5231988 rs614111 C A 590.46 PASS AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.58;MQ0=0;OQ=1949.76;QD=35.45;SB=-809.87 GT:AD:DP:GL:GQ 1/1:0,55:54:-198.57,-16.26,-0.01:99 +chr1 5231995 rs614102 A G 590.99 PASS AC=2;AF=1.00;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.61;MQ0=0;OQ=2129.07;QD=36.09;SB=-828.32 GT:AD:DP:GL:GQ 1/1:0,59:59:-216.51,-17.77,-0.02:99 +chr1 5232537 rs558175 T A 537.54 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2470.42;QD=36.33;SB=-1158.53 GT:AD:DP:GL:GQ 1/1:0,68:67:-250.65,-20.18,-0.02:99 +chr1 5232779 rs560794 T A 637.12 PASS AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.66;MQ0=0;OQ=2459.58;QD=36.17;SB=-1165.07 GT:AD:DP:GL:GQ 1/1:0,68:66:-249.56,-19.88,-0.02:99 +chr1 5232782 rs600322 G A 160.84 PASS AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=59.65;MQ0=0;OQ=2495.29;QD=38.39;SB=-1228.15 GT:AD:DP:GL:GQ 1/1:0,65:64:-253.13,-19.28,-0.02:99 +chr1 5232864 rs599884 A G 212.34 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.98;MQ=59.42;MQ0=0;OQ=2139.99;QD=35.08;SB=-951.99 GT:AD:DP:GL:GQ 1/1:0,61:60:-217.60,-18.07,-0.02:99 +chr1 5233339 rs598031 G A 300.26 PASS AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.87;MQ=59.38;MQ0=0;OQ=2603.20;QD=38.85;SB=-1265.68 GT:AD:DP:GL:GQ 1/1:0,66:66:-263.92,-19.88,-0.02:99 +chr1 5233376 rs587228 C T 292.53 PASS AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=58.99;MQ0=0;OQ=2392.78;QD=39.88;SB=-1196.59 GT:AD:DP:GL:GQ 1/1:0,60:60:-242.88,-18.07,-0.02:99 +chr1 5233377 rs476866 A G 630.33 PASS AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2129.35;QD=34.91;SB=-1082.46 GT:AD:DP:GL:GQ 1/1:0,61:60:-216.54,-18.07,-0.02:99 +chr1 5233422 rs476993 T C 95.16 PASS AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=1;HaplotypeScore=0.89;MQ=58.92;MQ0=0;OQ=1891.61;QD=33.78;SB=-702.84 GT:AD:DP:GL:GQ 1/1:1,55:55:-192.78,-16.58,-0.03:99 +chr1 5233779 rs56260836 C T 250.27 PASS AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=59.69;MQ0=0;OQ=907.86;QD=15.13;SB=-369.08 GT:AD:DP:GL:GQ 0/1:31,29:57:-111.25,-17.18,-100.79:99 +chr1 5234072 rs504647 G A 600.46 PASS AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2853.54;QD=40.19;SB=-1415.37 GT:AD:DP:GL:GQ 1/1:0,71:71:-288.96,-21.39,-0.02:99 +chr1 5234128 rs7551166 T C 37.81 PASS AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=1;HaplotypeScore=4.51;MQ=60.00;MQ0=0;OQ=837.05;QD=13.29;SB=-326.85 GT:AD:DP:GL:GQ 0/1:34,29:63:-105.96,-18.97,-138.54:99 +chr1 5234274 rs583170 C A 510.70 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.64;MQ0=0;OQ=1124.36;QD=17.57;SB=-381.75 GT:AD:DP:GL:GQ 0/1:28,36:64:-134.99,-19.28,-100.59:99 +chr1 5234483 rs12746195 G T 448 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=1.30;MQ=60.00;MQ0=0;OQ=907.18;QD=14.87;SB=-443.17 GT:AD:DP:GL:GQ 0/1:30,31:60:-112.07,-18.07,-106.20:99 +chr1 5234497 rs12732868 T G 365.79 PASS AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.80;MQ=60.00;MQ0=0;OQ=834.65;QD=13.04;SB=-431.76 GT:AD:DP:GL:GQ 0/1:33,31:62:-105.43,-18.68,-118.96:99 +chr1 5234595 rs12747559 C T 411.30 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=1.47;MQ=59.66;MQ0=0;OQ=1103.55;QD=16.23;SB=-461.98 GT:AD:DP:GL:GQ 0/1:32,36:64:-132.93,-19.29,-98.65:99 +chr1 5234628 rs12746515 G A 395.10 PASS AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.70;MQ0=0;OQ=1407.50;QD=18.04;SB=-722.08 GT:AD:DP:GL:GQ 0/1:37,41:75:-166.64,-22.60,-112.02:99 +chr1 5234751 rs12747870 C T 314.20 PASS AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=1;HaplotypeScore=2.20;MQ=59.17;MQ0=0;OQ=991.08;QD=14.57;SB=-434.89 GT:AD:DP:GL:GQ 0/1:38,30:67:-122.57,-20.18,-136.08:99 +chr1 5234796 rs12729227 A T 285.02 PASS AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=1.60;MQ=58.68;MQ0=0;OQ=635.81;QD=9.49;SB=-240.21 GT:AD:DP:GL:GQ 0/1:44,23:66:-86.75,-19.88,-161.14:99 +chr1 5234855 rs12746867 G A 137.48 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=3;HaplotypeScore=0.48;MQ=58.86;MQ0=0;OQ=803.94;QD=13.18;SB=-392.38 GT:AD:DP:GL:GQ 0/1:35,26:59:-101.45,-17.77,-122.51:99 +chr1 5234867 rs12729373 A G 399.72 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=739.47;QD=12.12;SB=-312.22 GT:AD:DP:GL:GQ 0/1:35,26:61:-95.60,-18.37,-142.14:99 +chr1 5235030 rs55729623 C G 87.40 PASS AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=4.84;MQ=59.98;MQ0=0;OQ=961.43;QD=16.30;SB=-383.64 GT:AD:DP:GL:GQ 0/1:26,33:53:-115.42,-16.00,-99.45:99 +chr1 5235034 . G A 5.72 PASS AC=1;AF=0.50;AN=2;DP=62;Dels=0.00;HRun=0;HaplotypeScore=5.25;MQ=59.98;MQ0=0;OQ=618.09;QD=9.97;SB=-190.00 GT:AD:DP:GL:GQ 0/1:34,27:51:-82.91,-17.82,-96.99:99 +chr1 5235136 rs17457156 T C 138.33 PASS AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.41;MQ=59.24;MQ0=0;OQ=556.94;QD=9.13;SB=-82.80 GT:AD:DP:GL:GQ 0/1:34,26:58:-79.46,-20.48,-139.05:99 diff --git a/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap b/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap new file mode 100644 index 000000000..cd0a1f9ad --- /dev/null +++ b/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap @@ -0,0 +1,500 @@ +rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode NA19625 NA19700 NA19701 NA19702 NA19703 NA19704 NA19705 NA19708 NA19712 NA19711 NA19818 NA19819 NA19828 NA19835 NA19834 NA19836 NA19902 NA19901 NA19900 NA19904 NA19919 NA19908 NA19909 NA19914 NA19915 NA19916 NA19917 NA19918 NA19921 NA20129 NA19713 NA19982 NA19983 NA19714 NA19985 NA19984 NA20128 NA20126 NA20127 NA20277 NA20276 NA20279 NA20282 NA20281 NA20284 NA20287 NA20288 NA20290 NA20289 NA20291 NA20292 NA20295 NA20294 NA20297 NA20300 NA20298 NA20301 NA20302 NA20317 NA20319 NA20322 NA20333 NA20332 NA20335 NA20334 NA20337 NA20336 NA20340 NA20341 NA20343 NA20342 NA20344 NA20345 NA20346 NA20347 NA20348 NA20349 NA20350 NA20351 NA20357 NA20356 NA20358 NA20359 NA20360 NA20363 NA20364 NA20412 +rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC +rs11510103 A/G chr1 557616 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11510103:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA NN AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA +rs11240767 C/T chr1 718814 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11240767:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CT CC CC CT CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CT CC CC CC CT CC CC CC CC NN CC CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CT CC CC CT CT CC +rs3131972 A/G chr1 742584 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3131972:1 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CC CT TT CT TT CT CT TT CC TT TT CT CT CT CC CC CC TT CT CC TT CT CT CC CT CT CT TT CT TT CT CT CC TT CC CC TT CT CT CC CT CT CT CC CT TT TT TT CT CC CC CT CT TT CC CT TT CT CT CT CT CT CT CT CT CT CT CC CT CC CT CC CT CC CC CC +rs12562034 A/G chr1 758311 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12562034:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG GG GG GG GG NN GG AG GG GG GG AG AG AG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG GG GG GG GG AG GG GG AG +rs12124819 A/G chr1 766409 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12124819:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG 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