Imported Upstream version 0.7

[pysam.git] / tests / vcf-examples / 2.vcf

##fileformat=VCFv4.0
##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL"
##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true"
##FILTER=<ID=BothStrands,Description="Variant not seen on both strands">
##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1">
##FILTER=<ID=HP10,Description="Variant occurs in long homopolymer run (>10)">
##FILTER=<ID=HaplotypeScore,Description="HaplotypeScore>20.0">
##FILTER=<ID=HighCoverage,Description="Coverage at variant site is > 7500">
##FILTER=<ID=HomopolymerRun,Description="HRun>=15">
##FILTER=<ID=LongRepeat,Description="Variant occurs in long tandem repeat (as defined by 1kg phase one filters)">
##FILTER=<ID=LowQual,Description="QUAL<30.0">
##FILTER=<ID=PP20,Description="Variant posterior phred is < 20">
##FILTER=<ID=QualByDepth,Description="QD<1.0">
##FILTER=<ID=StrandBias,Description="SB>=-1.0">
##FILTER=<ID=TruthSensitivityTranche93.00to94.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.9628 <= x < 4.1824">
##FILTER=<ID=TruthSensitivityTranche94.00to95.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.7129 <= x < 3.9628">
##FILTER=<ID=TruthSensitivityTranche95.00to96.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.3717 <= x < 3.7129">
##FILTER=<ID=TruthSensitivityTranche96.00to97.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.8762 <= x < 3.3717">
##FILTER=<ID=TruthSensitivityTranche97.00to98.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.2618 <= x < 2.8762">
##FILTER=<ID=TruthSensitivityTranche98.00to99.00+,Description="Truth sensitivity tranche level at VQS Lod < 1.2907">
##FILTER=<ID=TruthSensitivityTranche98.00to99.00,Description="Truth sensitivity tranche level at VSQ Lod: 1.2907 <= x < 2.2618">
##FORMAT=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample Genotype Filter">
##FORMAT=<ID=GL,Number=3,Type=Integer,Description="Genotype Likelihood, log-scaled likeilhoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=HQ,Number=.,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##FORMAT=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
##FORMAT=<ID=SA,Number=1,Type=Integer,Description="Number of alternate observations by strand, delimited by |: [forward]|[reverse]">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of reference observations by strand, delimited by |: [forward]|[reverse]">
##INFO=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
##INFO=<ID=AB,Number=1,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##INFO=<ID=ABA,Number=1,Type=Integer,Description="Alternate allele balance count: the number of sequence reads from apparent heterozygotes supporting the alternate allele">
##INFO=<ID=ABP,Number=1,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=ABR,Number=1,Type=Integer,Description="Reference allele balance count: the number of sequence reads from apparent heterozygotes supporting the reference allele">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BL,Number=1,Type=Integer,Description="Base Pairs Left: number of base pairs in reads supporting the alternate to the left (5') of the alternate allele">
##INFO=<ID=BR,Number=1,Type=Integer,Description="Base Pairs Right: number of base pairs in reads supporting the alternate to the right (3') of the alternate allele">
##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DEL,Number=0,Type=Flag,Description="deletion allele">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=EL,Number=1,Type=Integer,Description="Allele End Left: number of observations of the alternate where the alternate occurs in the left end of the read">
##INFO=<ID=EPP,Number=1,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=ER,Number=1,Type=Integer,Description="Allele End Right: number of observations of the alternate where the alternate occurs in the right end of the read">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability that sample chromosomes are not all the same">
##INFO=<ID=FR,Number=0,Type=Float,Description="Estimated population frequency">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HETAR,Number=1,Type=Integer,Description="Number of individuals heterozygous alternate / reference">
##INFO=<ID=HOMA,Number=1,Type=Integer,Description="Number of individuals homozygous for the alternate">
##INFO=<ID=HOMR,Number=1,Type=Integer,Description="Number of individuals homozygous for the reference">
##INFO=<ID=HP,Number=1,Type=Integer,Description="Homopolmer run length">
##INFO=<ID=HPLen,Number=1,Type=Integer,Description="Homopolymer length">
##INFO=<ID=HR,Number=1,Type=Integer,Description="Homopolymer run length">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HU,Number=1,Type=String,Description="Homopolymer run unit (stranded)">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Not provided in original VCF header">
##INFO=<ID=INS,Number=0,Type=Flag,Description="insertion allele">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=IndelType,Number=1,Type=String,Description="Indel type description">
##INFO=<ID=KGPilot123,Number=0,Type=Flag,Description="1000 Genome discovery all pilots 2010(1,2,3)">
##INFO=<ID=LEN,Number=1,Type=Integer,Description="allele length">
##INFO=<ID=LRB,Number=1,Type=Float,Description="((max(BR, BL) / (BR + BL)) - 0.5) * 2 : The proportion of base pairs in reads on one side of the alternate allele relative to total bases, scaled from [0.5,1] to [0,1]">
##INFO=<ID=LRBP,Number=1,Type=Float,Description="Left-Right Balance Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between BL and BR given E(BR/BL) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=MNP,Number=0,Type=Flag,Description="MNP allele">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQ0Fraction,Number=1,Type=Float,Description="Fraction of Mapping Quality Zero Reads">
##INFO=<ID=MQM,Number=1,Type=Float,Description="Mean mapping quality of observed alternate alleles">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=NF,Number=0,Type=Integer,Description="Total number of forward reads containing this variant">
##INFO=<ID=NR,Number=0,Type=Integer,Description="Total number of reads containing this variant">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=PP,Number=0,Type=Float,Description="Posterior probability (phred scaled) that this variant segregates">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
##INFO=<ID=RL,Number=1,Type=Integer,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
##INFO=<ID=RPP,Number=1,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RR,Number=1,Type=Integer,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
##INFO=<ID=RUN,Number=1,Type=Integer,Description="Homopolymer run length: the number of consecutive nucleotides in the reference genome matching the alternate allele prior to the current position">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SAB,Number=1,Type=Float,Description="Strand bias for the alternate allele: SAF / ( SAF + SAR )">
##INFO=<ID=SAF,Number=1,Type=Integer,Description="Number of alternate observations on the forward strand">
##INFO=<ID=SAP,Number=1,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SAR,Number=1,Type=Integer,Description="Number of alternate observations on the reverse strand">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=SC,Number=1,Type=String,Description="Genomic sequence 10 bases either side of variant position">
##INFO=<ID=SNP,Number=0,Type=Flag,Description="SNP allele">
##INFO=<ID=SRB,Number=1,Type=Float,Description="Strand bias for the reference allele: SRF / ( SRF + SRR )">
##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##INFO=<ID=TC,Number=0,Type=Integer,Description="Total coverage">
##INFO=<ID=TR,Number=1,Type=Integer,Description="Tandem repeat run length (bp)">
##INFO=<ID=TS,Number=0,Type=Flag,Description="transition SNP">
##INFO=<ID=TU,Number=1,Type=String,Description="tandem repeat run unit (stranded)">
##INFO=<ID=TV,Number=0,Type=Flag,Description="transversion SNP">
##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated.  This bit is set if the snp has 2+ minor allele count based on frequency or genotype data.">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=dbSNP,Number=1,Type=Integer,Description="First SNP Build for RS">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true"
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]"
##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./ALL.chr20.vqsr_2of5_union_sites_for_validation_boosted.vcf] rodToIntervalTrackName=variant BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[IndelType] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false"
##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa"
##fileDate=2011-03-28
##filedate=2011-02-08
##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500"
##phasing=none
##platypusOptions={'bamFiles': ['/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06984', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06985', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06986', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06989', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07000', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07037', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07048', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07051', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07056', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07346', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10847', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10851', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11831', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11832', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11881', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11892', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11893', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11894', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11918', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11919', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11920', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11930', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11931', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11932', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11933', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11992', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11993', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11995', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12003', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12004', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12005', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12006', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12043', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12044', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12045', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12046', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12058', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12144', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12154', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12155', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12156', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12234', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12249', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12272', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12273', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12275', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12282', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12283', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12286', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12287', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12340', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12341', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12348', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12399', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12400', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12413', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12414', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12716', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12717', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12718', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12748', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12749', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12750', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12751', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12761', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12763', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12775', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12776', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12777', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12778', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12813', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12827', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12828', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12842', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12889', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12890', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18486', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18487', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18499', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18501', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18502', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18504', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18505', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18507', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18508', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18510', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18511', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18517', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18520', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18523', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18526', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18530', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18532', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18533', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18534', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18535', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18536', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18537', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18538', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18539', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18541', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18542', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18543', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18544', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18545', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18547', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18548', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18549', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18552', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18553', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18555', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18557', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18558', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18559', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18560', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18561', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18562', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18563', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18564', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18565', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18566', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18567', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18570', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18571', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18572', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18573', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18574', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18576', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18577', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18579', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18582', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18592', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18593', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18595', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18596', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18597', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18599', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18602', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18603', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18605', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18606', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18608', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18609', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18610', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18611', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18612', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18613', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18614', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18615', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18616', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18617', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18618', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18619', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18620', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18621', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18622', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18623', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18624', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18625', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18626', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18627', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18628', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18630', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18631', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18632', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18633', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18634', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18635', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18636', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18637', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18638', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18853', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18856', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18858', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18861', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18867', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18868', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18870', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18871', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18873', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18874', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18907', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18908', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18909', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18910', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18912', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18916', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18917', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18923', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18924', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18933', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18934', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18940', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18941', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18942', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18943', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18944', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18945', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18947', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18948', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18949', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18950', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18951', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18952', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18953', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18956', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18959', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18960', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18961', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18963', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18964', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18965', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18967', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18968', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18971', 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'/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01113', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01124', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01125', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01133', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01134', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01136', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01137', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01140', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01148', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01149', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01167', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01168', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01170', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01171', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01173', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01174', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01176', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01177', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01182', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01183', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01187', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01188', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01190', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01191', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01197', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01198', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01204', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01250', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01251', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01253', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01254', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01334', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01350', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01351', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01353', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01354', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01356', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01359', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01360', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01365', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01366', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01374', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01375', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01377', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01378', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01384', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01389', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01390', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01437', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01440', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01441', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01455', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01456', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01461', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01462', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01464', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01465', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01491', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01492', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01494', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01495', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01497', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01515', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01518', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01521', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01551'], 'minReads': 2, 'refFile': '/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 64, 'maxSize': 100, 'ploidy': 2, 'maxRegionSize': 10000, 'nCPU': 1, 'minFlank': 3, 'logFileName': 'LogsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.log', 'regions': ['20:1-100001'], 'maxVariants': 6, 'genIndels': 1, 'labels': None, 'dataType': 'population', 'minMapQual': 20, 'rlen': 100, 'nInd': 994, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'minReadQual': 20, 'maxCoverage': 1000000.0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 1, 'output': 'VariantCallsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.vcf'}
##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
##source=Dindel2
##source=SelectVariants
##source_20110031.1=/nfs/users/nfs_p/pd3/cvs/vcftools/perl/vcf-annotate -d /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.desc -a /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.tab.gz -c CHROM,FROM,INFO/VLD,INFO/KGPilot123,INFO/dbSNP
##vcfCTools=filter
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freebayes.20:54500000-54600000.baq.20110328.vcf, freebayes.20:54600000-54700000.baq.20110328.vcf, freebayes.20:54700000-54800000.baq.20110328.vcf, freebayes.20:54800000-54900000.baq.20110328.vcf, freebayes.20:54900000-55000000.baq.20110328.vcf, freebayes.20:55000000-55100000.baq.20110328.vcf, freebayes.20:55100000-55200000.baq.20110328.vcf, freebayes.20:55200000-55300000.baq.20110328.vcf, freebayes.20:55300000-55400000.baq.20110328.vcf, freebayes.20:55400000-55500000.baq.20110328.vcf, freebayes.20:55500000-55600000.baq.20110328.vcf, freebayes.20:55600000-55700000.baq.20110328.vcf, freebayes.20:55700000-55800000.baq.20110328.vcf, freebayes.20:55800000-55900000.baq.20110328.vcf, freebayes.20:55900000-56000000.baq.20110328.vcf, freebayes.20:56000000-56100000.baq.20110328.vcf, freebayes.20:56100000-56200000.baq.20110328.vcf, freebayes.20:56200000-56300000.baq.20110328.vcf, freebayes.20:56300000-56400000.baq.20110328.vcf, freebayes.20:56400000-56500000.baq.20110328.vcf, freebayes.20:56500000-56600000.baq.20110328.vcf, freebayes.20:56600000-56700000.baq.20110328.vcf, freebayes.20:56700000-56800000.baq.20110328.vcf, freebayes.20:56800000-56900000.baq.20110328.vcf, freebayes.20:56900000-57000000.baq.20110328.vcf, freebayes.20:57000000-57100000.baq.20110328.vcf, freebayes.20:57100000-57200000.baq.20110328.vcf, freebayes.20:57200000-57300000.baq.20110328.vcf, freebayes.20:57300000-57400000.baq.20110328.vcf, freebayes.20:57400000-57500000.baq.20110328.vcf, freebayes.20:57500000-57600000.baq.20110328.vcf, freebayes.20:57600000-57700000.baq.20110328.vcf, freebayes.20:57700000-57800000.baq.20110328.vcf, freebayes.20:57800000-57900000.baq.20110328.vcf, freebayes.20:57900000-58000000.baq.20110328.vcf, freebayes.20:58000000-58100000.baq.20110328.vcf, freebayes.20:58100000-58200000.baq.20110328.vcf, freebayes.20:58200000-58300000.baq.20110328.vcf, freebayes.20:58300000-58400000.baq.20110328.vcf, freebayes.20:58400000-58500000.baq.20110328.vcf, freebayes.20:58500000-58600000.baq.20110328.vcf, freebayes.20:58600000-58700000.baq.20110328.vcf, freebayes.20:58700000-58800000.baq.20110328.vcf, freebayes.20:58800000-58900000.baq.20110328.vcf, freebayes.20:58900000-59000000.baq.20110328.vcf, freebayes.20:59000000-59100000.baq.20110328.vcf, freebayes.20:59100000-59200000.baq.20110328.vcf, freebayes.20:59200000-59300000.baq.20110328.vcf, freebayes.20:59300000-59400000.baq.20110328.vcf, freebayes.20:59400000-59500000.baq.20110328.vcf, freebayes.20:59500000-59600000.baq.20110328.vcf, freebayes.20:59600000-59700000.baq.20110328.vcf, freebayes.20:59700000-59800000.baq.20110328.vcf, freebayes.20:59800000-59900000.baq.20110328.vcf, freebayes.20:59900000-60000000.baq.20110328.vcf, freebayes.20:60000000-60100000.baq.20110328.vcf, freebayes.20:60100000-60200000.baq.20110328.vcf, freebayes.20:60200000-60300000.baq.20110328.vcf, freebayes.20:60300000-60400000.baq.20110328.vcf, freebayes.20:60400000-60500000.baq.20110328.vcf, freebayes.20:60500000-60600000.baq.20110328.vcf, freebayes.20:60600000-60700000.baq.20110328.vcf, freebayes.20:60700000-60800000.baq.20110328.vcf, freebayes.20:60800000-60900000.baq.20110328.vcf, freebayes.20:60900000-61000000.baq.20110328.vcf, freebayes.20:61000000-61100000.baq.20110328.vcf, freebayes.20:61100000-61200000.baq.20110328.vcf, freebayes.20:61200000-61300000.baq.20110328.vcf, freebayes.20:61300000-61400000.baq.20110328.vcf, freebayes.20:61400000-61500000.baq.20110328.vcf, freebayes.20:61500000-61600000.baq.20110328.vcf, freebayes.20:61600000-61700000.baq.20110328.vcf, freebayes.20:61700000-61800000.baq.20110328.vcf, freebayes.20:61800000-61900000.baq.20110328.vcf, freebayes.20:61900000-62000000.baq.20110328.vcf, freebayes.20:62000000-62100000.baq.20110328.vcf, freebayes.20:62100000-62200000.baq.20110328.vcf, freebayes.20:62200000-62300000.baq.20110328.vcf, freebayes.20:62300000-62400000.baq.20110328.vcf, freebayes.20:62400000-62500000.baq.20110328.vcf, freebayes.20:62500000-62600000.baq.20110328.vcf, freebayes.20:62600000-62700000.baq.20110328.vcf, freebayes.20:62700000-62800000.baq.20110328.vcf, freebayes.20:62800000-62900000.baq.20110328.vcf, freebayes.20:62900000-63000000.baq.20110328.vcf, freebayes.20:63000000-63025520.baq.20110328.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    
20      458502  .       G       GA      4567.01 PASS    AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94
20      573764  .       TA      T       591.51  PASS    AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;VQSLOD=5.2458;set=VQSR
20      766143  .       C       CATCTGGTA       5521.70 PASS    AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;IndelType=INS.NumRepetitions_1.EventLength_8.;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23
20      997076  rs11467490      CTG     C       15379.78        PASS    AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TG.;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76
20      1042261 rs10597473      CCCTG   C       168658.05       PASS    AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79
20      1046297 rs33956316      C       CT,CTT,CTTT     17698   PASS    ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection
20      1405740 .       T       TA      257.28  PASS    AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94
20      1690501 .       TC      T       27928   PASS    AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07
20      1991285 rs113891396     TAA     T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA     39235.36        PASS    AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;IndelType=MULTIALLELIC_INDEL;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45
20      2355911 .       TA      T       11723   PASS    AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88
20      2771621 rs11479849      GT      G,GTT   1605.60 PASS    AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92
20      2891235 .       G       GT,GTTT 2869.87 PASS    AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;IndelType=MULTIALLELIC_INDEL;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;VQSLOD=5.4379;set=VQSR
20      3033550 .       TGAG    T       2005.90 PASS    AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;IndelType=DEL.NumRepetitions_1.EventLength_3.;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41
20      3873327 rs61519218      A       AAG     683.85  PASS    AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;IndelType=INS.NOVEL_2.;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;VQSLOD=6.1858;set=VQSR
20      4028835 .       GC      G       2511.30 PASS    AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71
20      4039609 rs67812039      G       GA      43457   PASS    AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79
20      4390056 .       TC      T       49312   PASS    AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53
20      4474622 .       TA      T,TAA,TAAA,TAAAA        94522.28        PASS    ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;IndelType=MULTIALLELIC_INDEL;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79
20      4824911 .       AC      A       41998.70        PASS    AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR
20      4839897 rs35881880      TAA     T,TA,TAAA,TAAAAA        3906.80 PASS    AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;IndelType=MULTIALLELIC_INDEL;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77
20      5507414 .       G       GCC     439.08  PASS    AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR
20      5609676 .       GA      G,GAA   799.89  PASS    AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95
20      5736211 rs35303106      CT      C,CTT   4384.40 PASS    AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66
20      5898626 rs34483659      CAAA    C,CA,CAA,CAAAAA 1140.16 PASS    ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;IndelType=MULTIALLELIC_INDEL;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5
20      5975126 rs10541892      C       CAG     504.78  PASS    AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;IndelType=INS.NOVEL_2.;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR
20      6040983 rs11087710      A       AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG       66894.55        PASS    ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72
20      7024548 .       G       GAT     5041.27 PASS    AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;IndelType=INS.NumRepetitions_5.EventLength_2.RepeatExpansion_AT.;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;VQSLOD=5.9332;set=VQSR
20      7484554 .       A       AT      5.09    PASS    AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR
20      7632194 rs77286341      GAA     AAA,G   5324    PASS    AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;IndelType=MIXED;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5
20      7767508 rs71329674      G       GA      17914   PASS    AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09
20      7920261 .       TA      T,TAA   802.15  PASS    AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37
20      8012465 rs10595338      TATGA   T       2104.41 PASS    AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53
20      8573999 .       CGTGT   C,CGT,CGTGTGT,TGTGT     45865.96        PASS    AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;IndelType=MIXED;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53
20      8610455 rs10571111      TTTTC   T       11763.51        PASS    AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;IndelType=DEL.NumRepetitions_2.EventLength_4.;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;VQSLOD=5.0554;set=VQSR
20      9139079 .       ATT     A,AT,ATTT,ATTTT,ATTTTT  8777.90 PASS    AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;IndelType=MULTIALLELIC_INDEL;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection
20      9862448 .       CT      C       49312   PASS    AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84
20      9863736 rs73618103      G       GT      50570.21        PASS    AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20
20      10926959        .       AG      A       12239   PASS    AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10
20      11299648        .       TG      T       49315   PASS    AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00
20      11561096        .       CTA     C       999     PASS    AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89
20      11723671        .       C       CA      1096.60 PASS    AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;IndelType=INS.NumRepetitions_7.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30
20      12238835        rs113904674     CTCTTCATGGTCT   C       1813.44 PASS    AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48
20      12602812        .       AT      A       12344   PASS    AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67
20      13600884        .       CTG     C,CTGTG 1278.10 PASS    AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;IndelType=MULTIALLELIC_INDEL;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23
20      13666265        .       T       TATAG   556.88  PASS    AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;IndelType=INS.NOVEL_4.;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;VQSLOD=7.3380;set=VQSR
20      13861245        rs72422273      C       CTCA    2685.46 PASS    AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;IndelType=INS.NumRepetitions_1.EventLength_3.;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR
20      13865746        .       T       TA,TAA  1416.23 PASS    AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77
20      13881703        .       CTT     C       152.85  PASS    AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_T.;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;VQSLOD=5.3874;set=VQSR
20      14260090        rs73619828      A       AT      27935   PASS    AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82
20      14260558        .       AC      A       238     PASS    AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65
20      14425481        .       GTA     G,GTATA 148.85  PASS    AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;IndelType=MULTIALLELIC_INDEL;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5
20      14943522        rs11478299      GA      AA,G    1761.24 PASS    AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;IndelType=MIXED;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81
20      14974486        .       A       AG      4101.40 PASS    AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60
20      15111137        .       GA      G       13533   PASS    AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06
20      15283028        .       A       AC,ACACACACACACAC       140844.83       PASS    AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36
20      15361056        .       ATAACT  A       4892.81 PASS    AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38
20      15579507        .       AATTAGTC        A,TATTAGTC      1936.38 PASS    AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;IndelType=MIXED;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57
20      15752535        .       CT      C,GT    3775.20 PASS    AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;IndelType=MIXED;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70
20      15883060        rs73619850      A       AT      1325.60 PASS    AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69
20      16122099        .       GA      G       12914   PASS    AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97
20      16828509        .       G       GT      843.62  PASS    AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77
20      17470034        .       GC      G       46975   PASS    AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06
20      17471374        .       AGCGGC  A       850.03  PASS    AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;IndelType=DEL.NumRepetitions_1.EventLength_5.;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85
20      18433202        rs35582929      G       GA      2506.90 PASS    AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10
20      18551314        rs10659122      CA      C,CAA,CAAA,CAAAA,CAAAAA 18810.74        PASS    ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;IndelType=MULTIALLELIC_INDEL;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection
20      18785519        .       G       GTC     415.55  PASS    AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;IndelType=INS.NOVEL_2.;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;VQSLOD=4.9313;set=VQSR
20      20301041        rs35451634      ATATG   A       200.42  PASS    AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;VQSLOD=5.0981;set=VQSR
20      20378174        .       TC      T       245.55  PASS    AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR
20      20809160        rs10571503      TAA     AAA,T   3496    PASS    AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;IndelType=MIXED;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5
20      22508765        .       CT      C       53877.84        PASS    AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;IndelType=DEL.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15
20      22555082        rs11477526      AT      A       11503   PASS    AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27
20      22590907        .       A       AC      4204.88 PASS    AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69
20      22806326        rs11468890      ATTCCATCAC      A       105320.99       PASS    AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;IndelType=DEL.NumRepetitions_2.EventLength_9.;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81
20      22999898        rs55966257      CAGGA   C       8019.97 PASS    AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43
20      23385964        rs57723772      GAA     G       8170.95 PASS    AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR
20      23534530        .       TA      T       3542.10 PASS    AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49
20      23976810        rs5841018       A       ATATTAAT        1782.38 PASS    AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;IndelType=INS.NumRepetitions_1.EventLength_7.;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98
20      24222100        .       CTTTTA  C       4219.36 PASS    AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;IndelType=DEL.NumRepetitions_2.EventLength_5.;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08
20      24395018        .       AT      A       49310   PASS    AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80
20      24411517        .       C       CA      246.18  PASS    AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56
20      24421169        .       AG      A       27480   PASS    AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91
20      24765537        rs71841337      ATTT    A,AT,ATT,ATTTT,ATTTTT   37852   PASS    AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;IndelType=MULTIALLELIC_INDEL;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection
20      25500689        .       A       AATTT   84980.72        PASS    AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;IndelType=INS.NumRepetitions_1.EventLength_4.;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;VQSLOD=4.6038;set=VQSR
20      25550373        .       GA      G       11251.31        PASS    AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58
20      25903865        .       TTC     T       7459.23 PASS    AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TC.;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR
20      25934237        .       C       CCACTT  771.36  PASS    AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;IndelType=INS.NOVEL_5.;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR
20      26054751        rs112967123     TATC    T       33244   PASS    AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;IndelType=DEL.NumRepetitions_2.EventLength_3.;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54
20      26120452        .       CAG     C       7863.19 PASS    AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06
20      26185812        .       AG      A       322.58  PASS    AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;IndelType=DEL.NumRepetitions_6.EventLength_1.RepeatExpansion_G.;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46
20      30963468        .       AGTTT   A       2041.12 PASS    AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03
20      31963212        .       AAAAAAAAAAAAG   A       727.15  PASS    AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR
20      31997272        .       CT      C,CTT,CTTT      1837.10 PASS    AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66
20      33446974        rs113250263     TAA     T,TA,TAAA       17130.16        PASS    AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;IndelType=MULTIALLELIC_INDEL;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78
20      33877149        .       C       CT      1784.40 PASS    AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84
20      34387589        rs112431805     CT      C,CTT   4039.10 PASS    AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64
20      34493409        rs73621682      C       CAG     62288.93        PASS    AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;IndelType=INS.NumRepetitions_2.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82
20      35957317        .       CTGACT  C,CGACT 4370.96 PASS    ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;IndelType=MULTIALLELIC_INDEL;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45
20      36136198        .       GTGTC   G       2078.76 PASS    AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66
20      36250522        .       CA      C       37933   PASS    AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29
20      36285033        rs34715186      AT      A       39417   PASS    AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15
20      36384872        .       CTG     C       43532.41        PASS    AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;IndelType=DEL.NumRepetitions_7.EventLength_2.RepeatExpansion_TG.;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR
20      36542802        .       GTA     G       31310.15        PASS    AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49
20      36985025        .       CCA     C       4.57    PASS    AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_CA.;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR
20      37139725        .       CAG     C       250.77  PASS    AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13
20      37213224        .       G       GTA     3230.05 PASS    AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69
20      37282014        .       ATGG    A       2518.52 PASS    AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;IndelType=DEL.NumRepetitions_5.EventLength_3.;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05
20      37532218        .       GTCCGTCCA       ATCCGTCCA,G     76120.88        PASS    AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;IndelType=MIXED;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection
20      37712193        .       AAG     A       2670.33 PASS    AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20
20      37739002        .       T       TCA     1395.38 PASS    AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_CA.;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32
20      38395256        .       TTGAG   T       633.19  PASS    AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83
20      39345038        .       CTGAACCATAATGTG C,CCCATAATGTG   60744.52        PASS    AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;IndelType=MULTIALLELIC_INDEL;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43
20      39418008        .       AG      A       46796   PASS    AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06
20      39876961        .       GT      G,GTT,GTTT      2302.10 PASS    ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;IndelType=MULTIALLELIC_INDEL;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39
20      41013333        .       TC      T       20681   PASS    AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14
20      41659532        .       GC      G       40544   PASS    AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22
20      41845580        .       GA      G       49310   PASS    AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65
20      42209428        .       GC      G       13163   PASS    AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48
20      42281109        .       T       TAG     2321.12 PASS    AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;IndelType=INS.NOVEL_2.;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;VQSLOD=4.8926;set=VQSR
20      42436117        .       TC      T       38933   PASS    AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04
20      42682214        .       C       A,CAT   3904.51 PASS    AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;IndelType=MIXED;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75
20      42973456        .       CA      C,CAA,CAAA      2675    PASS    AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05
20      43091870        .       TC      T       2455.60 PASS    AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09
20      43233648        rs74585029      GA      G,GAA   1504.40 PASS    AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22
20      43246548        .       AC      A,CC    41579.13        PASS    AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;IndelType=MIXED;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22
20      43258646        .       T       TT      1107.17 PASS    AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR
20      43718299        .       ATTACT  A       5497.06 PASS    AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60
20      43981749        .       A       AAAAAAC,AC      20899.71        PASS    ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;IndelType=MULTIALLELIC_INDEL;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33
20      43999274        .       TCAAA   T       2948.85 PASS    AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09
20      44098622        .       C       CG      1092.40 PASS    AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04
20      44327637        .       A       AG,AGGGGGG      14351.23        PASS    AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;IndelType=MULTIALLELIC_INDEL;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR
20      45202636        .       GA      G       13269   PASS    AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90
20      45417828        .       TGAGC   T,TGC   4672.90 PASS    ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;IndelType=MULTIALLELIC_INDEL;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5
20      45525657        rs66759083      TA      AA,T    49315   PASS    AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;IndelType=MIXED;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51
20      45783456        .       T       TG      2355.68 PASS    AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03
20      46517110        .       C       CT      868.55  PASS    AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;IndelType=INS.NOVEL_1.Novel_T.;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;VQSLOD=6.7740;set=VQSR
20      46629361        .       TTTCTTTC        T,TTTTC 13000.91        PASS    AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;IndelType=MULTIALLELIC_INDEL;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR
20      46951099        .       G       GT      1662.30 PASS    AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49
20      47201076        rs58052846      C       CT      982.16  PASS    AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;IndelType=INS.NOVEL_1.Novel_T.;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR
20      47965974        rs60011158      G       GA      999     PASS    AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83
20      48402974        rs57331436      GA      G       27741   PASS    AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86
20      49101936        .       C       CT      404.46  PASS    AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR
20      49731218        .       ATTTTATTTTTTATT A,ATTTTATT      8398.93 PASS    AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;IndelType=MULTIALLELIC_INDEL;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27
20      49894989        .       TA      T       172.25  PASS    AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60
20      50010923        rs66516522      C       CT,CTGG 35851   PASS    ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;IndelType=MULTIALLELIC_INDEL;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection
20      50228709        rs71192536      TG      T       20517   PASS    AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35
20      50236115        .       AGG     A,ACGGG,AG,AGGG 7429.57 PASS    AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;IndelType=MULTIALLELIC_INDEL;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;VQSLOD=8.3762;set=VQSR
20      51589568        .       TAAAC   AAAAC,T 12477.52        PASS    AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;IndelType=MIXED;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43
20      51617742        .       TGC     T,TGCGC 1374.91 PASS    AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97
20      51770354        .       AG      A       1010.90 PASS    AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60
20      51848430        .       AT      A,ATT   999     PASS    AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57
20      51897203        .       T       TG      8427.20 PASS    AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99
20      52274070        .       AAG     A       1400.37 PASS    AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11
20      52351501        .       TAC     T       199.59  PASS    AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_AC.;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5
20      52447173        .       CA      C       503.89  PASS    AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR
20      52498650        .       GT      G       24069   PASS    AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90
20      52823602        rs11469056      CAAA    C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA 14515.17        PASS    AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;IndelType=MULTIALLELIC_INDEL;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection
20      53308906        .       CT      C,CTT   2276    PASS    AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42
20      53334602        .       T       TG,TGG  905.13  PASS    ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;IndelType=MULTIALLELIC_INDEL;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5
20      53729115        .       T       TG      15.48   PASS    AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;VQSLOD=4.8071;set=VQSR
20      54033830        .       GTATTTTAAAATCA  G       2220.86 PASS    AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65
20      54375236        .       GT      G       626.13  PASS    AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77
20      54457331        .       G       GA      1793.40 PASS    AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90
20      54469810        .       CA      C       1697.62 PASS    AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;IndelType=DEL.NumRepetitions_8.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90
20      54542453        .       GTATA   G,GTA   5109.66 PASS    ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53
20      54629773        .       CA      C       1799.50 PASS    AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54
20      54710245        .       TA      T       999     PASS    AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02
20      54968173        .       A       AAT,AATAT,AT,ATAT       89535.82        PASS    ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33
20      55176688        .       TA      T       421.84  PASS    AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15
20      55664086        .       GTT     ATT,G,GT,GTTT   5622.44 PASS    AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;IndelType=MIXED;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09
20      56045006        .       TG      T       342.15  PASS    AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;IndelType=DEL.NumRepetitions_7.EventLength_1.RepeatExpansion_G.;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR
20      56158711        .       AG      A       922.47  PASS    AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22
20      56258618        rs113670927     T       C,TGC,TGTGC,TGTGTGC     37834.99        PASS    ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;IndelType=MIXED;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27
20      56395857        .       T       TAGGCAG 6614.22 PASS    AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;IndelType=INS.NumRepetitions_2.EventLength_6.;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22
20      56969289        .       GTTTGT  G       600.69  PASS    AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;IndelType=DEL.NumRepetitions_3.EventLength_5.;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51
20      57187557        .       AG      A,AGG   1486.69 PASS    AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85
20      57282771        .       T       TG      506.43  PASS    AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95
20      57419740        rs11481507      A       AT      82613.57        PASS    AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78
20      57558194        .       CT      C,CTT,CTTT      6470.30 PASS    ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;IndelType=MULTIALLELIC_INDEL;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection
20      57693627        .       AG      A       1991.90 PASS    AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55
20      57716287        .       A       AT      66.47   PASS    AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;VQSLOD=4.2080;set=VQSR
20      58121928        rs73625057      T       TGG     6649.17 PASS    AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19
20      58468826        .       ACAAG   A       999     PASS    AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17
20      58731262        .       TC      T       999     PASS    AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11
20      59181229        rs11476579      CTT     C,CT,CTTT,CTTTT 7787.17 PASS    AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;IndelType=MULTIALLELIC_INDEL;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02
20      59213979        rs112141381     G       GC      9068    PASS    AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58
20      59252945        .       CT      C,CTT   557.18  PASS    AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47
20      60016966        .       CT      C       42650   PASS    AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27
20      60188651        .       AG      A       17624.52        PASS    AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81
20      60195570        .       GTACATACATACA   ATACATACATACA,G,GTACATACA       20140   PASS    ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;IndelType=MIXED;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14
20      60670601        rs72127450      AT      A,ATT   6401.59 PASS    AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80
20      60685780        .       TC      T       1123.58 PASS    AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR
20      60744906        rs113528167     CG      C       422.53  PASS    AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR
20      60848742        .       CGT     C,CGTGT 999     PASS    AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;IndelType=MULTIALLELIC_INDEL;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39
20      61023668        rs57452309      G       GAGC    6896.67 PASS    AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;IndelType=INS.NOVEL_3.;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR
20      61180519        .       C       CA,CT   1774.30 PASS    ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5
20      61184281        .       AC      A       9798.10 PASS    AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55
20      62074219        .       C       CTAT,CTGT       2328    PASS    ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;IndelType=MULTIALLELIC_INDEL;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5
20      62304449        .       CA      C,CAA   6680.17 PASS    AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36
20      62804895        rs57769591      CCTT    C       1148    PASS    AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_3.;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;VQSLOD=6.4881;dbSNP=126;set=Intersection
20      62907688        .       AAT     A       6629.57 PASS    AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;IndelType=DEL.NumRepetitions_2.EventLength_2.RepeatExpansion_AT.;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;VQSLOD=6.1473;set=VQSR