1##fileformat=VCFv4.2 2##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> 3##FILTER=<ID=ExcessHet,Description="ExcessHet > 54.69"> 4##FILTER=<ID=LowQual,Description="Low quality"> 5##FILTER=<ID=PASS,Description="All filters passed"> 6##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -10.6862 <= x < -6.7849"> 7##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -74824.4821"> 8##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -74824.4821 <= x < -10.6862"> 9##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -2.5"> 10##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -2.5 <= x < -2.25"> 11##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> 12##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> 13##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 14##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 15##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> 16##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> 17##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> 18##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> 19##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> 20##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> 21##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-0-g36282e4,Date="Sat Jun 18 23:52:15 UTC 2016",Epoch=1466293935858,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[broad-gotc-prod-cromwell-execution/PairedEndSingleSampleWorkflow/27402c9a-4187-4228-89f1-415027c5dfe0/call-GatherBamFiles/NWD242235.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[OverclippedRead] disable_read_filter=[] intervals=[broad-references/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=3 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.00468 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_is_too_short_value=30 do_not_require_softclips_both_ends=false min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> 22##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /cromwell_root/broad-jg-dev-cromwell-execution/JointGenotyping/5e7eb2b3-7b92-4b97-824d-5206122613f6/call-IndelsVariantRecalibrator/hg38_trio.indels.recal --tranches-file /cromwell_root/broad-jg-dev-cromwell-execution/JointGenotyping/5e7eb2b3-7b92-4b97-824d-5206122613f6/call-IndelsVariantRecalibrator/hg38_trio.indels.tranches --output tmp.indel.recalibrated.vcf --truth-sensitivity-filter-level 99.7 --mode INDEL --variant /cromwell_root/broad-jg-dev-cromwell-execution/JointGenotyping/5e7eb2b3-7b92-4b97-824d-5206122613f6/call-HardFilterAndMakeSitesOnlyVcf/shard-0/hg38_trio.0.variant_filtered.vcf.gz --create-output-variant-index true --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.1.0,Date="April 4, 2018 7:18:52 PM UTC"> 23##GATKCommandLine=<ID=ApplyVQSR,CommandLine="ApplyVQSR --recal-file /cromwell_root/broad-jg-dev-cromwell-execution/JointGenotyping/5e7eb2b3-7b92-4b97-824d-5206122613f6/call-SNPsVariantRecalibratorScattered/shard-0/hg38_trio.snps.0.recal --tranches-file /cromwell_root/broad-jg-dev-cromwell-execution/JointGenotyping/5e7eb2b3-7b92-4b97-824d-5206122613f6/call-SNPGatherTranches/hg38_trio.snps.gathered.tranches --output hg38_trio.filtered.0.vcf.gz --truth-sensitivity-filter-level 99.7 --mode SNP --variant tmp.indel.recalibrated.vcf --create-output-variant-index true --use-allele-specific-annotations false --ignore-all-filters false --exclude-filtered false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.1.0,Date="April 4, 2018 7:19:11 PM UTC"> 24##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path genomicsdb --batch-size 50 --sample-name-map /cromwell_root/broad-jg-dev-storage/CCDG/WHI.test-3.sample_map --reader-threads 5 --intervals chr1:1-248956422 --interval-padding 500 --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --consolidate false --validate-sample-name-map false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.1.0,Date="April 4, 2018 3:49:28 PM UTC"> 25##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output output.vcf.gz --use-new-qual-calculator true --annotation-group StandardAnnotation --only-output-calls-starting-in-intervals true --dbsnp gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf --variant gendb://genomicsdb --intervals chr1:1-248956422 --reference /cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.1.0,Date="April 4, 2018 4:44:26 PM UTC"> 26##GATKCommandLine=<ID=VariantFiltration,CommandLine="VariantFiltration --output hg38_trio.0.variant_filtered.vcf.gz --filter-expression ExcessHet > 54.69 --filter-name ExcessHet --variant /cromwell_root/broad-jg-dev-cromwell-execution/JointGenotyping/5e7eb2b3-7b92-4b97-824d-5206122613f6/call-GenotypeGVCFs/shard-0/output.vcf.gz --cluster-size 3 --cluster-window-size 0 --mask-extension 0 --mask-name Mask --filter-not-in-mask false --missing-values-evaluate-as-failing false --invalidate-previous-filters false --invert-filter-expression false --invert-genotype-filter-expression false --set-filtered-genotype-to-no-call false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.1.0,Date="April 4, 2018 5:33:28 PM UTC"> 27##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> 28##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> 29##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 30##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> 31##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> 32##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> 33##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> 34##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> 35##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 36##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> 37##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> 38##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> 39##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"> 40##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> 41##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> 42##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 43##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> 44##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants"> 45##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants"> 46##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> 47##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality"> 48##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> 49##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> 50##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model"> 51##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"> 52##contig=<ID=chr1,length=248956422> 53##contig=<ID=chr2,length=242193529> 54##contig=<ID=chr3,length=198295559> 55##contig=<ID=chr4,length=190214555> 56##contig=<ID=chr5,length=181538259> 57##contig=<ID=chr6,length=170805979> 58##contig=<ID=chr7,length=159345973> 59##contig=<ID=chr8,length=145138636> 60##contig=<ID=chr9,length=138394717> 61##contig=<ID=chr10,length=133797422> 62##contig=<ID=chr11,length=135086622> 63##contig=<ID=chr12,length=133275309> 64##contig=<ID=chr13,length=114364328> 65##contig=<ID=chr14,length=107043718> 66##contig=<ID=chr15,length=101991189> 67##contig=<ID=chr16,length=90338345> 68##contig=<ID=chr17,length=83257441> 69##contig=<ID=chr18,length=80373285> 70##contig=<ID=chr19,length=58617616> 71##contig=<ID=chr20,length=64444167> 72##contig=<ID=chr21,length=46709983> 73##contig=<ID=chr22,length=50818468> 74##contig=<ID=chrX,length=156040895> 75##contig=<ID=chrY,length=57227415> 76##contig=<ID=chrM,length=16569> 77##contig=<ID=chr1_KI270706v1_random,length=175055> 78##contig=<ID=chr1_KI270707v1_random,length=32032> 79##contig=<ID=chr1_KI270708v1_random,length=127682> 80##contig=<ID=chr1_KI270709v1_random,length=66860> 81##contig=<ID=chr1_KI270710v1_random,length=40176> 82##contig=<ID=chr1_KI270711v1_random,length=42210> 83##contig=<ID=chr1_KI270712v1_random,length=176043> 84##contig=<ID=chr1_KI270713v1_random,length=40745> 85##contig=<ID=chr1_KI270714v1_random,length=41717> 86##contig=<ID=chr2_KI270715v1_random,length=161471> 87##contig=<ID=chr2_KI270716v1_random,length=153799> 88##contig=<ID=chr3_GL000221v1_random,length=155397> 89##contig=<ID=chr4_GL000008v2_random,length=209709> 90##contig=<ID=chr5_GL000208v1_random,length=92689> 91##contig=<ID=chr9_KI270717v1_random,length=40062> 92##contig=<ID=chr9_KI270718v1_random,length=38054> 93##contig=<ID=chr9_KI270719v1_random,length=176845> 94##contig=<ID=chr9_KI270720v1_random,length=39050> 95##contig=<ID=chr11_KI270721v1_random,length=100316> 96##contig=<ID=chr14_GL000009v2_random,length=201709> 97##contig=<ID=chr14_GL000225v1_random,length=211173> 98##contig=<ID=chr14_KI270722v1_random,length=194050> 99##contig=<ID=chr14_GL000194v1_random,length=191469> 100##contig=<ID=chr14_KI270723v1_random,length=38115> 101##contig=<ID=chr14_KI270724v1_random,length=39555> 102##contig=<ID=chr14_KI270725v1_random,length=172810> 103##contig=<ID=chr14_KI270726v1_random,length=43739> 104##contig=<ID=chr15_KI270727v1_random,length=448248> 105##contig=<ID=chr16_KI270728v1_random,length=1872759> 106##contig=<ID=chr17_GL000205v2_random,length=185591> 107##contig=<ID=chr17_KI270729v1_random,length=280839> 108##contig=<ID=chr17_KI270730v1_random,length=112551> 109##contig=<ID=chr22_KI270731v1_random,length=150754> 110##contig=<ID=chr22_KI270732v1_random,length=41543> 111##contig=<ID=chr22_KI270733v1_random,length=179772> 112##contig=<ID=chr22_KI270734v1_random,length=165050> 113##contig=<ID=chr22_KI270735v1_random,length=42811> 114##contig=<ID=chr22_KI270736v1_random,length=181920> 115##contig=<ID=chr22_KI270737v1_random,length=103838> 116##contig=<ID=chr22_KI270738v1_random,length=99375> 117##contig=<ID=chr22_KI270739v1_random,length=73985> 118##contig=<ID=chrY_KI270740v1_random,length=37240> 119##contig=<ID=chrUn_KI270302v1,length=2274> 120##contig=<ID=chrUn_KI270304v1,length=2165> 121##contig=<ID=chrUn_KI270303v1,length=1942> 122##contig=<ID=chrUn_KI270305v1,length=1472> 123##contig=<ID=chrUn_KI270322v1,length=21476> 124##contig=<ID=chrUn_KI270320v1,length=4416> 125##contig=<ID=chrUn_KI270310v1,length=1201> 126##contig=<ID=chrUn_KI270316v1,length=1444> 127##contig=<ID=chrUn_KI270315v1,length=2276> 128##contig=<ID=chrUn_KI270312v1,length=998> 129##contig=<ID=chrUn_KI270311v1,length=12399> 130##contig=<ID=chrUn_KI270317v1,length=37690> 131##contig=<ID=chrUn_KI270412v1,length=1179> 132##contig=<ID=chrUn_KI270411v1,length=2646> 133##contig=<ID=chrUn_KI270414v1,length=2489> 134##contig=<ID=chrUn_KI270419v1,length=1029> 135##contig=<ID=chrUn_KI270418v1,length=2145> 136##contig=<ID=chrUn_KI270420v1,length=2321> 137##contig=<ID=chrUn_KI270424v1,length=2140> 138##contig=<ID=chrUn_KI270417v1,length=2043> 139##contig=<ID=chrUn_KI270422v1,length=1445> 140##contig=<ID=chrUn_KI270423v1,length=981> 141##contig=<ID=chrUn_KI270425v1,length=1884> 142##contig=<ID=chrUn_KI270429v1,length=1361> 143##contig=<ID=chrUn_KI270442v1,length=392061> 144##contig=<ID=chrUn_KI270466v1,length=1233> 145##contig=<ID=chrUn_KI270465v1,length=1774> 146##contig=<ID=chrUn_KI270467v1,length=3920> 147##contig=<ID=chrUn_KI270435v1,length=92983> 148##contig=<ID=chrUn_KI270438v1,length=112505> 149##contig=<ID=chrUn_KI270468v1,length=4055> 150##contig=<ID=chrUn_KI270510v1,length=2415> 151##contig=<ID=chrUn_KI270509v1,length=2318> 152##contig=<ID=chrUn_KI270518v1,length=2186> 153##contig=<ID=chrUn_KI270508v1,length=1951> 154##contig=<ID=chrUn_KI270516v1,length=1300> 155##contig=<ID=chrUn_KI270512v1,length=22689> 156##contig=<ID=chrUn_KI270519v1,length=138126> 157##contig=<ID=chrUn_KI270522v1,length=5674> 158##contig=<ID=chrUn_KI270511v1,length=8127> 159##contig=<ID=chrUn_KI270515v1,length=6361> 160##contig=<ID=chrUn_KI270507v1,length=5353> 161##contig=<ID=chrUn_KI270517v1,length=3253> 162##contig=<ID=chrUn_KI270529v1,length=1899> 163##contig=<ID=chrUn_KI270528v1,length=2983> 164##contig=<ID=chrUn_KI270530v1,length=2168> 165##contig=<ID=chrUn_KI270539v1,length=993> 166##contig=<ID=chrUn_KI270538v1,length=91309> 167##contig=<ID=chrUn_KI270544v1,length=1202> 168##contig=<ID=chrUn_KI270548v1,length=1599> 169##contig=<ID=chrUn_KI270583v1,length=1400> 170##contig=<ID=chrUn_KI270587v1,length=2969> 171##contig=<ID=chrUn_KI270580v1,length=1553> 172##contig=<ID=chrUn_KI270581v1,length=7046> 173##contig=<ID=chrUn_KI270579v1,length=31033> 174##contig=<ID=chrUn_KI270589v1,length=44474> 175##contig=<ID=chrUn_KI270590v1,length=4685> 176##contig=<ID=chrUn_KI270584v1,length=4513> 177##contig=<ID=chrUn_KI270582v1,length=6504> 178##contig=<ID=chrUn_KI270588v1,length=6158> 179##contig=<ID=chrUn_KI270593v1,length=3041> 180##contig=<ID=chrUn_KI270591v1,length=5796> 181##contig=<ID=chrUn_KI270330v1,length=1652> 182##contig=<ID=chrUn_KI270329v1,length=1040> 183##contig=<ID=chrUn_KI270334v1,length=1368> 184##contig=<ID=chrUn_KI270333v1,length=2699> 185##contig=<ID=chrUn_KI270335v1,length=1048> 186##contig=<ID=chrUn_KI270338v1,length=1428> 187##contig=<ID=chrUn_KI270340v1,length=1428> 188##contig=<ID=chrUn_KI270336v1,length=1026> 189##contig=<ID=chrUn_KI270337v1,length=1121> 190##contig=<ID=chrUn_KI270363v1,length=1803> 191##contig=<ID=chrUn_KI270364v1,length=2855> 192##contig=<ID=chrUn_KI270362v1,length=3530> 193##contig=<ID=chrUn_KI270366v1,length=8320> 194##contig=<ID=chrUn_KI270378v1,length=1048> 195##contig=<ID=chrUn_KI270379v1,length=1045> 196##contig=<ID=chrUn_KI270389v1,length=1298> 197##contig=<ID=chrUn_KI270390v1,length=2387> 198##contig=<ID=chrUn_KI270387v1,length=1537> 199##contig=<ID=chrUn_KI270395v1,length=1143> 200##contig=<ID=chrUn_KI270396v1,length=1880> 201##contig=<ID=chrUn_KI270388v1,length=1216> 202##contig=<ID=chrUn_KI270394v1,length=970> 203##contig=<ID=chrUn_KI270386v1,length=1788> 204##contig=<ID=chrUn_KI270391v1,length=1484> 205##contig=<ID=chrUn_KI270383v1,length=1750> 206##contig=<ID=chrUn_KI270393v1,length=1308> 207##contig=<ID=chrUn_KI270384v1,length=1658> 208##contig=<ID=chrUn_KI270392v1,length=971> 209##contig=<ID=chrUn_KI270381v1,length=1930> 210##contig=<ID=chrUn_KI270385v1,length=990> 211##contig=<ID=chrUn_KI270382v1,length=4215> 212##contig=<ID=chrUn_KI270376v1,length=1136> 213##contig=<ID=chrUn_KI270374v1,length=2656> 214##contig=<ID=chrUn_KI270372v1,length=1650> 215##contig=<ID=chrUn_KI270373v1,length=1451> 216##contig=<ID=chrUn_KI270375v1,length=2378> 217##contig=<ID=chrUn_KI270371v1,length=2805> 218##contig=<ID=chrUn_KI270448v1,length=7992> 219##contig=<ID=chrUn_KI270521v1,length=7642> 220##contig=<ID=chrUn_GL000195v1,length=182896> 221##contig=<ID=chrUn_GL000219v1,length=179198> 222##contig=<ID=chrUn_GL000220v1,length=161802> 223##contig=<ID=chrUn_GL000224v1,length=179693> 224##contig=<ID=chrUn_KI270741v1,length=157432> 225##contig=<ID=chrUn_GL000226v1,length=15008> 226##contig=<ID=chrUn_GL000213v1,length=164239> 227##contig=<ID=chrUn_KI270743v1,length=210658> 228##contig=<ID=chrUn_KI270744v1,length=168472> 229##contig=<ID=chrUn_KI270745v1,length=41891> 230##contig=<ID=chrUn_KI270746v1,length=66486> 231##contig=<ID=chrUn_KI270747v1,length=198735> 232##contig=<ID=chrUn_KI270748v1,length=93321> 233##contig=<ID=chrUn_KI270749v1,length=158759> 234##contig=<ID=chrUn_KI270750v1,length=148850> 235##contig=<ID=chrUn_KI270751v1,length=150742> 236##contig=<ID=chrUn_KI270752v1,length=27745> 237##contig=<ID=chrUn_KI270753v1,length=62944> 238##contig=<ID=chrUn_KI270754v1,length=40191> 239##contig=<ID=chrUn_KI270755v1,length=36723> 240##contig=<ID=chrUn_KI270756v1,length=79590> 241##contig=<ID=chrUn_KI270757v1,length=71251> 242##contig=<ID=chrUn_GL000214v1,length=137718> 243##contig=<ID=chrUn_KI270742v1,length=186739> 244##contig=<ID=chrUn_GL000216v2,length=176608> 245##contig=<ID=chrUn_GL000218v1,length=161147> 246##contig=<ID=chr1_KI270762v1_alt,length=354444> 247##contig=<ID=chr1_KI270766v1_alt,length=256271> 248##contig=<ID=chr1_KI270760v1_alt,length=109528> 249##contig=<ID=chr1_KI270765v1_alt,length=185285> 250##contig=<ID=chr1_GL383518v1_alt,length=182439> 251##contig=<ID=chr1_GL383519v1_alt,length=110268> 252##contig=<ID=chr1_GL383520v2_alt,length=366580> 253##contig=<ID=chr1_KI270764v1_alt,length=50258> 254##contig=<ID=chr1_KI270763v1_alt,length=911658> 255##contig=<ID=chr1_KI270759v1_alt,length=425601> 256##contig=<ID=chr1_KI270761v1_alt,length=165834> 257##contig=<ID=chr2_KI270770v1_alt,length=136240> 258##contig=<ID=chr2_KI270773v1_alt,length=70887> 259##contig=<ID=chr2_KI270774v1_alt,length=223625> 260##contig=<ID=chr2_KI270769v1_alt,length=120616> 261##contig=<ID=chr2_GL383521v1_alt,length=143390> 262##contig=<ID=chr2_KI270772v1_alt,length=133041> 263##contig=<ID=chr2_KI270775v1_alt,length=138019> 264##contig=<ID=chr2_KI270771v1_alt,length=110395> 265##contig=<ID=chr2_KI270768v1_alt,length=110099> 266##contig=<ID=chr2_GL582966v2_alt,length=96131> 267##contig=<ID=chr2_GL383522v1_alt,length=123821> 268##contig=<ID=chr2_KI270776v1_alt,length=174166> 269##contig=<ID=chr2_KI270767v1_alt,length=161578> 270##contig=<ID=chr3_JH636055v2_alt,length=173151> 271##contig=<ID=chr3_KI270783v1_alt,length=109187> 272##contig=<ID=chr3_KI270780v1_alt,length=224108> 273##contig=<ID=chr3_GL383526v1_alt,length=180671> 274##contig=<ID=chr3_KI270777v1_alt,length=173649> 275##contig=<ID=chr3_KI270778v1_alt,length=248252> 276##contig=<ID=chr3_KI270781v1_alt,length=113034> 277##contig=<ID=chr3_KI270779v1_alt,length=205312> 278##contig=<ID=chr3_KI270782v1_alt,length=162429> 279##contig=<ID=chr3_KI270784v1_alt,length=184404> 280##contig=<ID=chr4_KI270790v1_alt,length=220246> 281##contig=<ID=chr4_GL383528v1_alt,length=376187> 282##contig=<ID=chr4_KI270787v1_alt,length=111943> 283##contig=<ID=chr4_GL000257v2_alt,length=586476> 284##contig=<ID=chr4_KI270788v1_alt,length=158965> 285##contig=<ID=chr4_GL383527v1_alt,length=164536> 286##contig=<ID=chr4_KI270785v1_alt,length=119912> 287##contig=<ID=chr4_KI270789v1_alt,length=205944> 288##contig=<ID=chr4_KI270786v1_alt,length=244096> 289##contig=<ID=chr5_KI270793v1_alt,length=126136> 290##contig=<ID=chr5_KI270792v1_alt,length=179043> 291##contig=<ID=chr5_KI270791v1_alt,length=195710> 292##contig=<ID=chr5_GL383532v1_alt,length=82728> 293##contig=<ID=chr5_GL949742v1_alt,length=226852> 294##contig=<ID=chr5_KI270794v1_alt,length=164558> 295##contig=<ID=chr5_GL339449v2_alt,length=1612928> 296##contig=<ID=chr5_GL383530v1_alt,length=101241> 297##contig=<ID=chr5_KI270796v1_alt,length=172708> 298##contig=<ID=chr5_GL383531v1_alt,length=173459> 299##contig=<ID=chr5_KI270795v1_alt,length=131892> 300##contig=<ID=chr6_GL000250v2_alt,length=4672374> 301##contig=<ID=chr6_KI270800v1_alt,length=175808> 302##contig=<ID=chr6_KI270799v1_alt,length=152148> 303##contig=<ID=chr6_GL383533v1_alt,length=124736> 304##contig=<ID=chr6_KI270801v1_alt,length=870480> 305##contig=<ID=chr6_KI270802v1_alt,length=75005> 306##contig=<ID=chr6_KB021644v2_alt,length=185823> 307##contig=<ID=chr6_KI270797v1_alt,length=197536> 308##contig=<ID=chr6_KI270798v1_alt,length=271782> 309##contig=<ID=chr7_KI270804v1_alt,length=157952> 310##contig=<ID=chr7_KI270809v1_alt,length=209586> 311##contig=<ID=chr7_KI270806v1_alt,length=158166> 312##contig=<ID=chr7_GL383534v2_alt,length=119183> 313##contig=<ID=chr7_KI270803v1_alt,length=1111570> 314##contig=<ID=chr7_KI270808v1_alt,length=271455> 315##contig=<ID=chr7_KI270807v1_alt,length=126434> 316##contig=<ID=chr7_KI270805v1_alt,length=209988> 317##contig=<ID=chr8_KI270818v1_alt,length=145606> 318##contig=<ID=chr8_KI270812v1_alt,length=282736> 319##contig=<ID=chr8_KI270811v1_alt,length=292436> 320##contig=<ID=chr8_KI270821v1_alt,length=985506> 321##contig=<ID=chr8_KI270813v1_alt,length=300230> 322##contig=<ID=chr8_KI270822v1_alt,length=624492> 323##contig=<ID=chr8_KI270814v1_alt,length=141812> 324##contig=<ID=chr8_KI270810v1_alt,length=374415> 325##contig=<ID=chr8_KI270819v1_alt,length=133535> 326##contig=<ID=chr8_KI270820v1_alt,length=36640> 327##contig=<ID=chr8_KI270817v1_alt,length=158983> 328##contig=<ID=chr8_KI270816v1_alt,length=305841> 329##contig=<ID=chr8_KI270815v1_alt,length=132244> 330##contig=<ID=chr9_GL383539v1_alt,length=162988> 331##contig=<ID=chr9_GL383540v1_alt,length=71551> 332##contig=<ID=chr9_GL383541v1_alt,length=171286> 333##contig=<ID=chr9_GL383542v1_alt,length=60032> 334##contig=<ID=chr9_KI270823v1_alt,length=439082> 335##contig=<ID=chr10_GL383545v1_alt,length=179254> 336##contig=<ID=chr10_KI270824v1_alt,length=181496> 337##contig=<ID=chr10_GL383546v1_alt,length=309802> 338##contig=<ID=chr10_KI270825v1_alt,length=188315> 339##contig=<ID=chr11_KI270832v1_alt,length=210133> 340##contig=<ID=chr11_KI270830v1_alt,length=177092> 341##contig=<ID=chr11_KI270831v1_alt,length=296895> 342##contig=<ID=chr11_KI270829v1_alt,length=204059> 343##contig=<ID=chr11_GL383547v1_alt,length=154407> 344##contig=<ID=chr11_JH159136v1_alt,length=200998> 345##contig=<ID=chr11_JH159137v1_alt,length=191409> 346##contig=<ID=chr11_KI270827v1_alt,length=67707> 347##contig=<ID=chr11_KI270826v1_alt,length=186169> 348##contig=<ID=chr12_GL877875v1_alt,length=167313> 349##contig=<ID=chr12_GL877876v1_alt,length=408271> 350##contig=<ID=chr12_KI270837v1_alt,length=40090> 351##contig=<ID=chr12_GL383549v1_alt,length=120804> 352##contig=<ID=chr12_KI270835v1_alt,length=238139> 353##contig=<ID=chr12_GL383550v2_alt,length=169178> 354##contig=<ID=chr12_GL383552v1_alt,length=138655> 355##contig=<ID=chr12_GL383553v2_alt,length=152874> 356##contig=<ID=chr12_KI270834v1_alt,length=119498> 357##contig=<ID=chr12_GL383551v1_alt,length=184319> 358##contig=<ID=chr12_KI270833v1_alt,length=76061> 359##contig=<ID=chr12_KI270836v1_alt,length=56134> 360##contig=<ID=chr13_KI270840v1_alt,length=191684> 361##contig=<ID=chr13_KI270839v1_alt,length=180306> 362##contig=<ID=chr13_KI270843v1_alt,length=103832> 363##contig=<ID=chr13_KI270841v1_alt,length=169134> 364##contig=<ID=chr13_KI270838v1_alt,length=306913> 365##contig=<ID=chr13_KI270842v1_alt,length=37287> 366##contig=<ID=chr14_KI270844v1_alt,length=322166> 367##contig=<ID=chr14_KI270847v1_alt,length=1511111> 368##contig=<ID=chr14_KI270845v1_alt,length=180703> 369##contig=<ID=chr14_KI270846v1_alt,length=1351393> 370##contig=<ID=chr15_KI270852v1_alt,length=478999> 371##contig=<ID=chr15_KI270851v1_alt,length=263054> 372##contig=<ID=chr15_KI270848v1_alt,length=327382> 373##contig=<ID=chr15_GL383554v1_alt,length=296527> 374##contig=<ID=chr15_KI270849v1_alt,length=244917> 375##contig=<ID=chr15_GL383555v2_alt,length=388773> 376##contig=<ID=chr15_KI270850v1_alt,length=430880> 377##contig=<ID=chr16_KI270854v1_alt,length=134193> 378##contig=<ID=chr16_KI270856v1_alt,length=63982> 379##contig=<ID=chr16_KI270855v1_alt,length=232857> 380##contig=<ID=chr16_KI270853v1_alt,length=2659700> 381##contig=<ID=chr16_GL383556v1_alt,length=192462> 382##contig=<ID=chr16_GL383557v1_alt,length=89672> 383##contig=<ID=chr17_GL383563v3_alt,length=375691> 384##contig=<ID=chr17_KI270862v1_alt,length=391357> 385##contig=<ID=chr17_KI270861v1_alt,length=196688> 386##contig=<ID=chr17_KI270857v1_alt,length=2877074> 387##contig=<ID=chr17_JH159146v1_alt,length=278131> 388##contig=<ID=chr17_JH159147v1_alt,length=70345> 389##contig=<ID=chr17_GL383564v2_alt,length=133151> 390##contig=<ID=chr17_GL000258v2_alt,length=1821992> 391##contig=<ID=chr17_GL383565v1_alt,length=223995> 392##contig=<ID=chr17_KI270858v1_alt,length=235827> 393##contig=<ID=chr17_KI270859v1_alt,length=108763> 394##contig=<ID=chr17_GL383566v1_alt,length=90219> 395##contig=<ID=chr17_KI270860v1_alt,length=178921> 396##contig=<ID=chr18_KI270864v1_alt,length=111737> 397##contig=<ID=chr18_GL383567v1_alt,length=289831> 398##contig=<ID=chr18_GL383570v1_alt,length=164789> 399##contig=<ID=chr18_GL383571v1_alt,length=198278> 400##contig=<ID=chr18_GL383568v1_alt,length=104552> 401##contig=<ID=chr18_GL383569v1_alt,length=167950> 402##contig=<ID=chr18_GL383572v1_alt,length=159547> 403##contig=<ID=chr18_KI270863v1_alt,length=167999> 404##contig=<ID=chr19_KI270868v1_alt,length=61734> 405##contig=<ID=chr19_KI270865v1_alt,length=52969> 406##contig=<ID=chr19_GL383573v1_alt,length=385657> 407##contig=<ID=chr19_GL383575v2_alt,length=170222> 408##contig=<ID=chr19_GL383576v1_alt,length=188024> 409##contig=<ID=chr19_GL383574v1_alt,length=155864> 410##contig=<ID=chr19_KI270866v1_alt,length=43156> 411##contig=<ID=chr19_KI270867v1_alt,length=233762> 412##contig=<ID=chr19_GL949746v1_alt,length=987716> 413##contig=<ID=chr20_GL383577v2_alt,length=128386> 414##contig=<ID=chr20_KI270869v1_alt,length=118774> 415##contig=<ID=chr20_KI270871v1_alt,length=58661> 416##contig=<ID=chr20_KI270870v1_alt,length=183433> 417##contig=<ID=chr21_GL383578v2_alt,length=63917> 418##contig=<ID=chr21_KI270874v1_alt,length=166743> 419##contig=<ID=chr21_KI270873v1_alt,length=143900> 420##contig=<ID=chr21_GL383579v2_alt,length=201197> 421##contig=<ID=chr21_GL383580v2_alt,length=74653> 422##contig=<ID=chr21_GL383581v2_alt,length=116689> 423##contig=<ID=chr21_KI270872v1_alt,length=82692> 424##contig=<ID=chr22_KI270875v1_alt,length=259914> 425##contig=<ID=chr22_KI270878v1_alt,length=186262> 426##contig=<ID=chr22_KI270879v1_alt,length=304135> 427##contig=<ID=chr22_KI270876v1_alt,length=263666> 428##contig=<ID=chr22_KI270877v1_alt,length=101331> 429##contig=<ID=chr22_GL383583v2_alt,length=96924> 430##contig=<ID=chr22_GL383582v2_alt,length=162811> 431##contig=<ID=chrX_KI270880v1_alt,length=284869> 432##contig=<ID=chrX_KI270881v1_alt,length=144206> 433##contig=<ID=chr19_KI270882v1_alt,length=248807> 434##contig=<ID=chr19_KI270883v1_alt,length=170399> 435##contig=<ID=chr19_KI270884v1_alt,length=157053> 436##contig=<ID=chr19_KI270885v1_alt,length=171027> 437##contig=<ID=chr19_KI270886v1_alt,length=204239> 438##contig=<ID=chr19_KI270887v1_alt,length=209512> 439##contig=<ID=chr19_KI270888v1_alt,length=155532> 440##contig=<ID=chr19_KI270889v1_alt,length=170698> 441##contig=<ID=chr19_KI270890v1_alt,length=184499> 442##contig=<ID=chr19_KI270891v1_alt,length=170680> 443##contig=<ID=chr1_KI270892v1_alt,length=162212> 444##contig=<ID=chr2_KI270894v1_alt,length=214158> 445##contig=<ID=chr2_KI270893v1_alt,length=161218> 446##contig=<ID=chr3_KI270895v1_alt,length=162896> 447##contig=<ID=chr4_KI270896v1_alt,length=378547> 448##contig=<ID=chr5_KI270897v1_alt,length=1144418> 449##contig=<ID=chr5_KI270898v1_alt,length=130957> 450##contig=<ID=chr6_GL000251v2_alt,length=4795265> 451##contig=<ID=chr7_KI270899v1_alt,length=190869> 452##contig=<ID=chr8_KI270901v1_alt,length=136959> 453##contig=<ID=chr8_KI270900v1_alt,length=318687> 454##contig=<ID=chr11_KI270902v1_alt,length=106711> 455##contig=<ID=chr11_KI270903v1_alt,length=214625> 456##contig=<ID=chr12_KI270904v1_alt,length=572349> 457##contig=<ID=chr15_KI270906v1_alt,length=196384> 458##contig=<ID=chr15_KI270905v1_alt,length=5161414> 459##contig=<ID=chr17_KI270907v1_alt,length=137721> 460##contig=<ID=chr17_KI270910v1_alt,length=157099> 461##contig=<ID=chr17_KI270909v1_alt,length=325800> 462##contig=<ID=chr17_JH159148v1_alt,length=88070> 463##contig=<ID=chr17_KI270908v1_alt,length=1423190> 464##contig=<ID=chr18_KI270912v1_alt,length=174061> 465##contig=<ID=chr18_KI270911v1_alt,length=157710> 466##contig=<ID=chr19_GL949747v2_alt,length=729520> 467##contig=<ID=chr22_KB663609v1_alt,length=74013> 468##contig=<ID=chrX_KI270913v1_alt,length=274009> 469##contig=<ID=chr19_KI270914v1_alt,length=205194> 470##contig=<ID=chr19_KI270915v1_alt,length=170665> 471##contig=<ID=chr19_KI270916v1_alt,length=184516> 472##contig=<ID=chr19_KI270917v1_alt,length=190932> 473##contig=<ID=chr19_KI270918v1_alt,length=123111> 474##contig=<ID=chr19_KI270919v1_alt,length=170701> 475##contig=<ID=chr19_KI270920v1_alt,length=198005> 476##contig=<ID=chr19_KI270921v1_alt,length=282224> 477##contig=<ID=chr19_KI270922v1_alt,length=187935> 478##contig=<ID=chr19_KI270923v1_alt,length=189352> 479##contig=<ID=chr3_KI270924v1_alt,length=166540> 480##contig=<ID=chr4_KI270925v1_alt,length=555799> 481##contig=<ID=chr6_GL000252v2_alt,length=4604811> 482##contig=<ID=chr8_KI270926v1_alt,length=229282> 483##contig=<ID=chr11_KI270927v1_alt,length=218612> 484##contig=<ID=chr19_GL949748v2_alt,length=1064304> 485##contig=<ID=chr22_KI270928v1_alt,length=176103> 486##contig=<ID=chr19_KI270929v1_alt,length=186203> 487##contig=<ID=chr19_KI270930v1_alt,length=200773> 488##contig=<ID=chr19_KI270931v1_alt,length=170148> 489##contig=<ID=chr19_KI270932v1_alt,length=215732> 490##contig=<ID=chr19_KI270933v1_alt,length=170537> 491##contig=<ID=chr19_GL000209v2_alt,length=177381> 492##contig=<ID=chr3_KI270934v1_alt,length=163458> 493##contig=<ID=chr6_GL000253v2_alt,length=4677643> 494##contig=<ID=chr19_GL949749v2_alt,length=1091841> 495##contig=<ID=chr3_KI270935v1_alt,length=197351> 496##contig=<ID=chr6_GL000254v2_alt,length=4827813> 497##contig=<ID=chr19_GL949750v2_alt,length=1066390> 498##contig=<ID=chr3_KI270936v1_alt,length=164170> 499##contig=<ID=chr6_GL000255v2_alt,length=4606388> 500##contig=<ID=chr19_GL949751v2_alt,length=1002683> 501##contig=<ID=chr3_KI270937v1_alt,length=165607> 502##contig=<ID=chr6_GL000256v2_alt,length=4929269> 503##contig=<ID=chr19_GL949752v1_alt,length=987100> 504##contig=<ID=chr6_KI270758v1_alt,length=76752> 505##contig=<ID=chr19_GL949753v2_alt,length=796479> 506##contig=<ID=chr19_KI270938v1_alt,length=1066800> 507##contig=<ID=chrEBV,length=171823> 508##contig=<ID=chrUn_KN707606v1_decoy,length=2200> 509##contig=<ID=chrUn_KN707607v1_decoy,length=3033> 510##contig=<ID=chrUn_KN707608v1_decoy,length=3112> 511##contig=<ID=chrUn_KN707609v1_decoy,length=1642> 512##contig=<ID=chrUn_KN707610v1_decoy,length=1393> 513##contig=<ID=chrUn_KN707611v1_decoy,length=1103> 514##contig=<ID=chrUn_KN707612v1_decoy,length=1039> 515##contig=<ID=chrUn_KN707613v1_decoy,length=1619> 516##contig=<ID=chrUn_KN707614v1_decoy,length=3122> 517##contig=<ID=chrUn_KN707615v1_decoy,length=1934> 518##contig=<ID=chrUn_KN707616v1_decoy,length=3111> 519##contig=<ID=chrUn_KN707617v1_decoy,length=2545> 520##contig=<ID=chrUn_KN707618v1_decoy,length=2295> 521##contig=<ID=chrUn_KN707619v1_decoy,length=1551> 522##contig=<ID=chrUn_KN707620v1_decoy,length=2046> 523##contig=<ID=chrUn_KN707621v1_decoy,length=1222> 524##contig=<ID=chrUn_KN707622v1_decoy,length=1535> 525##contig=<ID=chrUn_KN707623v1_decoy,length=3784> 526##contig=<ID=chrUn_KN707624v1_decoy,length=1329> 527##contig=<ID=chrUn_KN707625v1_decoy,length=1238> 528##contig=<ID=chrUn_KN707626v1_decoy,length=5623> 529##contig=<ID=chrUn_KN707627v1_decoy,length=5821> 530##contig=<ID=chrUn_KN707628v1_decoy,length=2960> 531##contig=<ID=chrUn_KN707629v1_decoy,length=1848> 532##contig=<ID=chrUn_KN707630v1_decoy,length=2315> 533##contig=<ID=chrUn_KN707631v1_decoy,length=1945> 534##contig=<ID=chrUn_KN707632v1_decoy,length=1424> 535##contig=<ID=chrUn_KN707633v1_decoy,length=1274> 536##contig=<ID=chrUn_KN707634v1_decoy,length=1007> 537##contig=<ID=chrUn_KN707635v1_decoy,length=1414> 538##contig=<ID=chrUn_KN707636v1_decoy,length=1725> 539##contig=<ID=chrUn_KN707637v1_decoy,length=5354> 540##contig=<ID=chrUn_KN707638v1_decoy,length=2189> 541##contig=<ID=chrUn_KN707639v1_decoy,length=1294> 542##contig=<ID=chrUn_KN707640v1_decoy,length=1831> 543##contig=<ID=chrUn_KN707641v1_decoy,length=1647> 544##contig=<ID=chrUn_KN707642v1_decoy,length=2943> 545##contig=<ID=chrUn_KN707643v1_decoy,length=2857> 546##contig=<ID=chrUn_KN707644v1_decoy,length=1030> 547##contig=<ID=chrUn_KN707645v1_decoy,length=1070> 548##contig=<ID=chrUn_KN707646v1_decoy,length=1735> 549##contig=<ID=chrUn_KN707647v1_decoy,length=1982> 550##contig=<ID=chrUn_KN707648v1_decoy,length=1564> 551##contig=<ID=chrUn_KN707649v1_decoy,length=1775> 552##contig=<ID=chrUn_KN707650v1_decoy,length=1540> 553##contig=<ID=chrUn_KN707651v1_decoy,length=2013> 554##contig=<ID=chrUn_KN707652v1_decoy,length=1176> 555##contig=<ID=chrUn_KN707653v1_decoy,length=1890> 556##contig=<ID=chrUn_KN707654v1_decoy,length=3644> 557##contig=<ID=chrUn_KN707655v1_decoy,length=2785> 558##contig=<ID=chrUn_KN707656v1_decoy,length=1017> 559##contig=<ID=chrUn_KN707657v1_decoy,length=1068> 560##contig=<ID=chrUn_KN707658v1_decoy,length=1007> 561##contig=<ID=chrUn_KN707659v1_decoy,length=2605> 562##contig=<ID=chrUn_KN707660v1_decoy,length=8410> 563##contig=<ID=chrUn_KN707661v1_decoy,length=5534> 564##contig=<ID=chrUn_KN707662v1_decoy,length=2173> 565##contig=<ID=chrUn_KN707663v1_decoy,length=1065> 566##contig=<ID=chrUn_KN707664v1_decoy,length=8683> 567##contig=<ID=chrUn_KN707665v1_decoy,length=2670> 568##contig=<ID=chrUn_KN707666v1_decoy,length=2420> 569##contig=<ID=chrUn_KN707667v1_decoy,length=2189> 570##contig=<ID=chrUn_KN707668v1_decoy,length=2093> 571##contig=<ID=chrUn_KN707669v1_decoy,length=1184> 572##contig=<ID=chrUn_KN707670v1_decoy,length=1205> 573##contig=<ID=chrUn_KN707671v1_decoy,length=2786> 574##contig=<ID=chrUn_KN707672v1_decoy,length=2794> 575##contig=<ID=chrUn_KN707673v1_decoy,length=19544> 576##contig=<ID=chrUn_KN707674v1_decoy,length=2848> 577##contig=<ID=chrUn_KN707675v1_decoy,length=10556> 578##contig=<ID=chrUn_KN707676v1_decoy,length=9066> 579##contig=<ID=chrUn_KN707677v1_decoy,length=7267> 580##contig=<ID=chrUn_KN707678v1_decoy,length=2462> 581##contig=<ID=chrUn_KN707679v1_decoy,length=1774> 582##contig=<ID=chrUn_KN707680v1_decoy,length=1297> 583##contig=<ID=chrUn_KN707681v1_decoy,length=4379> 584##contig=<ID=chrUn_KN707682v1_decoy,length=4208> 585##contig=<ID=chrUn_KN707683v1_decoy,length=4068> 586##contig=<ID=chrUn_KN707684v1_decoy,length=2940> 587##contig=<ID=chrUn_KN707685v1_decoy,length=3938> 588##contig=<ID=chrUn_KN707686v1_decoy,length=2072> 589##contig=<ID=chrUn_KN707687v1_decoy,length=1136> 590##contig=<ID=chrUn_KN707688v1_decoy,length=4248> 591##contig=<ID=chrUn_KN707689v1_decoy,length=5823> 592##contig=<ID=chrUn_KN707690v1_decoy,length=3715> 593##contig=<ID=chrUn_KN707691v1_decoy,length=4885> 594##contig=<ID=chrUn_KN707692v1_decoy,length=4813> 595##contig=<ID=chrUn_KN707693v1_decoy,length=2899> 596##contig=<ID=chrUn_KN707694v1_decoy,length=1228> 597##contig=<ID=chrUn_KN707695v1_decoy,length=3119> 598##contig=<ID=chrUn_KN707696v1_decoy,length=3828> 599##contig=<ID=chrUn_KN707697v1_decoy,length=1186> 600##contig=<ID=chrUn_KN707698v1_decoy,length=1908> 601##contig=<ID=chrUn_KN707699v1_decoy,length=2795> 602##contig=<ID=chrUn_KN707700v1_decoy,length=3703> 603##contig=<ID=chrUn_KN707701v1_decoy,length=6722> 604##contig=<ID=chrUn_KN707702v1_decoy,length=6466> 605##contig=<ID=chrUn_KN707703v1_decoy,length=2235> 606##contig=<ID=chrUn_KN707704v1_decoy,length=2871> 607##contig=<ID=chrUn_KN707705v1_decoy,length=4632> 608##contig=<ID=chrUn_KN707706v1_decoy,length=4225> 609##contig=<ID=chrUn_KN707707v1_decoy,length=4339> 610##contig=<ID=chrUn_KN707708v1_decoy,length=2305> 611##contig=<ID=chrUn_KN707709v1_decoy,length=3273> 612##contig=<ID=chrUn_KN707710v1_decoy,length=5701> 613##contig=<ID=chrUn_KN707711v1_decoy,length=4154> 614##contig=<ID=chrUn_KN707712v1_decoy,length=1243> 615##contig=<ID=chrUn_KN707713v1_decoy,length=1308> 616##contig=<ID=chrUn_KN707714v1_decoy,length=2922> 617##contig=<ID=chrUn_KN707715v1_decoy,length=3044> 618##contig=<ID=chrUn_KN707716v1_decoy,length=2888> 619##contig=<ID=chrUn_KN707717v1_decoy,length=1742> 620##contig=<ID=chrUn_KN707718v1_decoy,length=4969> 621##contig=<ID=chrUn_KN707719v1_decoy,length=3270> 622##contig=<ID=chrUn_KN707720v1_decoy,length=6028> 623##contig=<ID=chrUn_KN707721v1_decoy,length=1105> 624##contig=<ID=chrUn_KN707722v1_decoy,length=2884> 625##contig=<ID=chrUn_KN707723v1_decoy,length=1124> 626##contig=<ID=chrUn_KN707724v1_decoy,length=1454> 627##contig=<ID=chrUn_KN707725v1_decoy,length=2565> 628##contig=<ID=chrUn_KN707726v1_decoy,length=2149> 629##contig=<ID=chrUn_KN707727v1_decoy,length=2630> 630##contig=<ID=chrUn_KN707728v1_decoy,length=14625> 631##contig=<ID=chrUn_KN707729v1_decoy,length=7431> 632##contig=<ID=chrUn_KN707730v1_decoy,length=5776> 633##contig=<ID=chrUn_KN707731v1_decoy,length=4820> 634##contig=<ID=chrUn_KN707732v1_decoy,length=1227> 635##contig=<ID=chrUn_KN707733v1_decoy,length=7503> 636##contig=<ID=chrUn_KN707734v1_decoy,length=9652> 637##contig=<ID=chrUn_KN707735v1_decoy,length=1091> 638##contig=<ID=chrUn_KN707736v1_decoy,length=2467> 639##contig=<ID=chrUn_KN707737v1_decoy,length=1270> 640##contig=<ID=chrUn_KN707738v1_decoy,length=4365> 641##contig=<ID=chrUn_KN707739v1_decoy,length=4284> 642##contig=<ID=chrUn_KN707740v1_decoy,length=10282> 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1452##contig=<ID=chrUn_JTFH01000558v1_decoy,length=1459> 1453##contig=<ID=chrUn_JTFH01000559v1_decoy,length=1458> 1454##contig=<ID=chrUn_JTFH01000560v1_decoy,length=1458> 1455##contig=<ID=chrUn_JTFH01000561v1_decoy,length=1454> 1456##contig=<ID=chrUn_JTFH01000562v1_decoy,length=1449> 1457##contig=<ID=chrUn_JTFH01000563v1_decoy,length=1449> 1458##contig=<ID=chrUn_JTFH01000564v1_decoy,length=1448> 1459##contig=<ID=chrUn_JTFH01000565v1_decoy,length=1446> 1460##contig=<ID=chrUn_JTFH01000566v1_decoy,length=1442> 1461##contig=<ID=chrUn_JTFH01000567v1_decoy,length=1441> 1462##contig=<ID=chrUn_JTFH01000568v1_decoy,length=1440> 1463##contig=<ID=chrUn_JTFH01000569v1_decoy,length=1439> 1464##contig=<ID=chrUn_JTFH01000570v1_decoy,length=1437> 1465##contig=<ID=chrUn_JTFH01000571v1_decoy,length=1436> 1466##contig=<ID=chrUn_JTFH01000572v1_decoy,length=1429> 1467##contig=<ID=chrUn_JTFH01000573v1_decoy,length=1429> 1468##contig=<ID=chrUn_JTFH01000574v1_decoy,length=1427> 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1486##contig=<ID=chrUn_JTFH01000592v1_decoy,length=1404> 1487##contig=<ID=chrUn_JTFH01000593v1_decoy,length=1404> 1488##contig=<ID=chrUn_JTFH01000594v1_decoy,length=1402> 1489##contig=<ID=chrUn_JTFH01000595v1_decoy,length=1402> 1490##contig=<ID=chrUn_JTFH01000596v1_decoy,length=1402> 1491##contig=<ID=chrUn_JTFH01000597v1_decoy,length=1402> 1492##contig=<ID=chrUn_JTFH01000598v1_decoy,length=1400> 1493##contig=<ID=chrUn_JTFH01000599v1_decoy,length=1398> 1494##contig=<ID=chrUn_JTFH01000600v1_decoy,length=1396> 1495##contig=<ID=chrUn_JTFH01000601v1_decoy,length=1395> 1496##contig=<ID=chrUn_JTFH01000602v1_decoy,length=1394> 1497##contig=<ID=chrUn_JTFH01000603v1_decoy,length=1393> 1498##contig=<ID=chrUn_JTFH01000604v1_decoy,length=1391> 1499##contig=<ID=chrUn_JTFH01000605v1_decoy,length=1389> 1500##contig=<ID=chrUn_JTFH01000606v1_decoy,length=1389> 1501##contig=<ID=chrUn_JTFH01000607v1_decoy,length=1388> 1502##contig=<ID=chrUn_JTFH01000608v1_decoy,length=1387> 1503##contig=<ID=chrUn_JTFH01000609v1_decoy,length=1384> 1504##contig=<ID=chrUn_JTFH01000610v1_decoy,length=1381> 1505##contig=<ID=chrUn_JTFH01000611v1_decoy,length=1381> 1506##contig=<ID=chrUn_JTFH01000612v1_decoy,length=1379> 1507##contig=<ID=chrUn_JTFH01000613v1_decoy,length=1377> 1508##contig=<ID=chrUn_JTFH01000614v1_decoy,length=1376> 1509##contig=<ID=chrUn_JTFH01000615v1_decoy,length=1376> 1510##contig=<ID=chrUn_JTFH01000616v1_decoy,length=1375> 1511##contig=<ID=chrUn_JTFH01000617v1_decoy,length=1374> 1512##contig=<ID=chrUn_JTFH01000618v1_decoy,length=1372> 1513##contig=<ID=chrUn_JTFH01000619v1_decoy,length=1371> 1514##contig=<ID=chrUn_JTFH01000620v1_decoy,length=1370> 1515##contig=<ID=chrUn_JTFH01000621v1_decoy,length=1370> 1516##contig=<ID=chrUn_JTFH01000622v1_decoy,length=1366> 1517##contig=<ID=chrUn_JTFH01000623v1_decoy,length=1363> 1518##contig=<ID=chrUn_JTFH01000624v1_decoy,length=1360> 1519##contig=<ID=chrUn_JTFH01000625v1_decoy,length=1356> 1520##contig=<ID=chrUn_JTFH01000626v1_decoy,length=1355> 1521##contig=<ID=chrUn_JTFH01000627v1_decoy,length=1355> 1522##contig=<ID=chrUn_JTFH01000628v1_decoy,length=1352> 1523##contig=<ID=chrUn_JTFH01000629v1_decoy,length=1345> 1524##contig=<ID=chrUn_JTFH01000630v1_decoy,length=1344> 1525##contig=<ID=chrUn_JTFH01000631v1_decoy,length=1344> 1526##contig=<ID=chrUn_JTFH01000632v1_decoy,length=1342> 1527##contig=<ID=chrUn_JTFH01000633v1_decoy,length=1342> 1528##contig=<ID=chrUn_JTFH01000634v1_decoy,length=1336> 1529##contig=<ID=chrUn_JTFH01000635v1_decoy,length=1334> 1530##contig=<ID=chrUn_JTFH01000636v1_decoy,length=1334> 1531##contig=<ID=chrUn_JTFH01000637v1_decoy,length=1333> 1532##contig=<ID=chrUn_JTFH01000638v1_decoy,length=1332> 1533##contig=<ID=chrUn_JTFH01000639v1_decoy,length=1328> 1534##contig=<ID=chrUn_JTFH01000640v1_decoy,length=1328> 1535##contig=<ID=chrUn_JTFH01000641v1_decoy,length=1328> 1536##contig=<ID=chrUn_JTFH01000642v1_decoy,length=1327> 1537##contig=<ID=chrUn_JTFH01000643v1_decoy,length=1325> 1538##contig=<ID=chrUn_JTFH01000644v1_decoy,length=1322> 1539##contig=<ID=chrUn_JTFH01000645v1_decoy,length=1320> 1540##contig=<ID=chrUn_JTFH01000646v1_decoy,length=1319> 1541##contig=<ID=chrUn_JTFH01000647v1_decoy,length=1318> 1542##contig=<ID=chrUn_JTFH01000648v1_decoy,length=1315> 1543##contig=<ID=chrUn_JTFH01000649v1_decoy,length=1314> 1544##contig=<ID=chrUn_JTFH01000650v1_decoy,length=1313> 1545##contig=<ID=chrUn_JTFH01000651v1_decoy,length=1313> 1546##contig=<ID=chrUn_JTFH01000652v1_decoy,length=1312> 1547##contig=<ID=chrUn_JTFH01000653v1_decoy,length=1310> 1548##contig=<ID=chrUn_JTFH01000654v1_decoy,length=1309> 1549##contig=<ID=chrUn_JTFH01000655v1_decoy,length=1309> 1550##contig=<ID=chrUn_JTFH01000656v1_decoy,length=1307> 1551##contig=<ID=chrUn_JTFH01000657v1_decoy,length=1307> 1552##contig=<ID=chrUn_JTFH01000658v1_decoy,length=1305> 1553##contig=<ID=chrUn_JTFH01000659v1_decoy,length=1304> 1554##contig=<ID=chrUn_JTFH01000660v1_decoy,length=1303> 1555##contig=<ID=chrUn_JTFH01000661v1_decoy,length=1302> 1556##contig=<ID=chrUn_JTFH01000662v1_decoy,length=1302> 1557##contig=<ID=chrUn_JTFH01000663v1_decoy,length=1301> 1558##contig=<ID=chrUn_JTFH01000664v1_decoy,length=1301> 1559##contig=<ID=chrUn_JTFH01000665v1_decoy,length=1300> 1560##contig=<ID=chrUn_JTFH01000666v1_decoy,length=1299> 1561##contig=<ID=chrUn_JTFH01000667v1_decoy,length=1297> 1562##contig=<ID=chrUn_JTFH01000668v1_decoy,length=1295> 1563##contig=<ID=chrUn_JTFH01000669v1_decoy,length=1294> 1564##contig=<ID=chrUn_JTFH01000670v1_decoy,length=1293> 1565##contig=<ID=chrUn_JTFH01000671v1_decoy,length=1291> 1566##contig=<ID=chrUn_JTFH01000672v1_decoy,length=1291> 1567##contig=<ID=chrUn_JTFH01000673v1_decoy,length=1289> 1568##contig=<ID=chrUn_JTFH01000674v1_decoy,length=1288> 1569##contig=<ID=chrUn_JTFH01000675v1_decoy,length=1288> 1570##contig=<ID=chrUn_JTFH01000676v1_decoy,length=1287> 1571##contig=<ID=chrUn_JTFH01000677v1_decoy,length=1287> 1572##contig=<ID=chrUn_JTFH01000678v1_decoy,length=1287> 1573##contig=<ID=chrUn_JTFH01000679v1_decoy,length=1286> 1574##contig=<ID=chrUn_JTFH01000680v1_decoy,length=1283> 1575##contig=<ID=chrUn_JTFH01000681v1_decoy,length=1281> 1576##contig=<ID=chrUn_JTFH01000682v1_decoy,length=1277> 1577##contig=<ID=chrUn_JTFH01000683v1_decoy,length=1274> 1578##contig=<ID=chrUn_JTFH01000684v1_decoy,length=1270> 1579##contig=<ID=chrUn_JTFH01000685v1_decoy,length=1267> 1580##contig=<ID=chrUn_JTFH01000686v1_decoy,length=1266> 1581##contig=<ID=chrUn_JTFH01000687v1_decoy,length=1260> 1582##contig=<ID=chrUn_JTFH01000688v1_decoy,length=1259> 1583##contig=<ID=chrUn_JTFH01000689v1_decoy,length=1258> 1584##contig=<ID=chrUn_JTFH01000690v1_decoy,length=1258> 1585##contig=<ID=chrUn_JTFH01000691v1_decoy,length=1258> 1586##contig=<ID=chrUn_JTFH01000692v1_decoy,length=1256> 1587##contig=<ID=chrUn_JTFH01000693v1_decoy,length=1255> 1588##contig=<ID=chrUn_JTFH01000694v1_decoy,length=1254> 1589##contig=<ID=chrUn_JTFH01000695v1_decoy,length=1254> 1590##contig=<ID=chrUn_JTFH01000696v1_decoy,length=1253> 1591##contig=<ID=chrUn_JTFH01000697v1_decoy,length=1250> 1592##contig=<ID=chrUn_JTFH01000698v1_decoy,length=1249> 1593##contig=<ID=chrUn_JTFH01000699v1_decoy,length=1248> 1594##contig=<ID=chrUn_JTFH01000700v1_decoy,length=1248> 1595##contig=<ID=chrUn_JTFH01000701v1_decoy,length=1247> 1596##contig=<ID=chrUn_JTFH01000702v1_decoy,length=1242> 1597##contig=<ID=chrUn_JTFH01000703v1_decoy,length=1242> 1598##contig=<ID=chrUn_JTFH01000704v1_decoy,length=1241> 1599##contig=<ID=chrUn_JTFH01000705v1_decoy,length=1241> 1600##contig=<ID=chrUn_JTFH01000706v1_decoy,length=1241> 1601##contig=<ID=chrUn_JTFH01000707v1_decoy,length=1239> 1602##contig=<ID=chrUn_JTFH01000708v1_decoy,length=1238> 1603##contig=<ID=chrUn_JTFH01000709v1_decoy,length=1237> 1604##contig=<ID=chrUn_JTFH01000710v1_decoy,length=1236> 1605##contig=<ID=chrUn_JTFH01000711v1_decoy,length=1235> 1606##contig=<ID=chrUn_JTFH01000712v1_decoy,length=1234> 1607##contig=<ID=chrUn_JTFH01000713v1_decoy,length=1234> 1608##contig=<ID=chrUn_JTFH01000714v1_decoy,length=1234> 1609##contig=<ID=chrUn_JTFH01000715v1_decoy,length=1233> 1610##contig=<ID=chrUn_JTFH01000716v1_decoy,length=1232> 1611##contig=<ID=chrUn_JTFH01000717v1_decoy,length=1232> 1612##contig=<ID=chrUn_JTFH01000718v1_decoy,length=1231> 1613##contig=<ID=chrUn_JTFH01000719v1_decoy,length=1230> 1614##contig=<ID=chrUn_JTFH01000720v1_decoy,length=1228> 1615##contig=<ID=chrUn_JTFH01000721v1_decoy,length=1227> 1616##contig=<ID=chrUn_JTFH01000722v1_decoy,length=1227> 1617##contig=<ID=chrUn_JTFH01000723v1_decoy,length=1226> 1618##contig=<ID=chrUn_JTFH01000724v1_decoy,length=1224> 1619##contig=<ID=chrUn_JTFH01000725v1_decoy,length=1224> 1620##contig=<ID=chrUn_JTFH01000726v1_decoy,length=1220> 1621##contig=<ID=chrUn_JTFH01000727v1_decoy,length=1220> 1622##contig=<ID=chrUn_JTFH01000728v1_decoy,length=1219> 1623##contig=<ID=chrUn_JTFH01000729v1_decoy,length=1217> 1624##contig=<ID=chrUn_JTFH01000730v1_decoy,length=1216> 1625##contig=<ID=chrUn_JTFH01000731v1_decoy,length=1215> 1626##contig=<ID=chrUn_JTFH01000732v1_decoy,length=1214> 1627##contig=<ID=chrUn_JTFH01000733v1_decoy,length=1214> 1628##contig=<ID=chrUn_JTFH01000734v1_decoy,length=1214> 1629##contig=<ID=chrUn_JTFH01000735v1_decoy,length=1213> 1630##contig=<ID=chrUn_JTFH01000736v1_decoy,length=1212> 1631##contig=<ID=chrUn_JTFH01000737v1_decoy,length=1209> 1632##contig=<ID=chrUn_JTFH01000738v1_decoy,length=1208> 1633##contig=<ID=chrUn_JTFH01000739v1_decoy,length=1207> 1634##contig=<ID=chrUn_JTFH01000740v1_decoy,length=1207> 1635##contig=<ID=chrUn_JTFH01000741v1_decoy,length=1207> 1636##contig=<ID=chrUn_JTFH01000742v1_decoy,length=1206> 1637##contig=<ID=chrUn_JTFH01000743v1_decoy,length=1206> 1638##contig=<ID=chrUn_JTFH01000744v1_decoy,length=1205> 1639##contig=<ID=chrUn_JTFH01000745v1_decoy,length=1205> 1640##contig=<ID=chrUn_JTFH01000746v1_decoy,length=1204> 1641##contig=<ID=chrUn_JTFH01000747v1_decoy,length=1204> 1642##contig=<ID=chrUn_JTFH01000748v1_decoy,length=1204> 1643##contig=<ID=chrUn_JTFH01000749v1_decoy,length=1203> 1644##contig=<ID=chrUn_JTFH01000750v1_decoy,length=1201> 1645##contig=<ID=chrUn_JTFH01000751v1_decoy,length=1201> 1646##contig=<ID=chrUn_JTFH01000752v1_decoy,length=1200> 1647##contig=<ID=chrUn_JTFH01000753v1_decoy,length=1200> 1648##contig=<ID=chrUn_JTFH01000754v1_decoy,length=1199> 1649##contig=<ID=chrUn_JTFH01000755v1_decoy,length=1198> 1650##contig=<ID=chrUn_JTFH01000756v1_decoy,length=1197> 1651##contig=<ID=chrUn_JTFH01000757v1_decoy,length=1196> 1652##contig=<ID=chrUn_JTFH01000758v1_decoy,length=1195> 1653##contig=<ID=chrUn_JTFH01000759v1_decoy,length=1194> 1654##contig=<ID=chrUn_JTFH01000760v1_decoy,length=1194> 1655##contig=<ID=chrUn_JTFH01000761v1_decoy,length=1191> 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3421##source=GenotypeGVCFs 3422##source=VariantFiltration 3423#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NWD242235 NWD359156 NWD666458 3424chr3 179199000 . A C,* 308.52 VQSRTrancheSNP99.90to100.00+ AC=1,1;AF=0.167,0.167;AN=6;BaseQRankSum=-1.052e+00;ClippingRankSum=-1.910e-01;DP=82;ExcessHet=4.7712;FS=24.798;MLEAC=1,1;MLEAF=0.167,0.167;MQ=34.33;MQRankSum=-2.200e+00;QD=6.43;ReadPosRankSum=-9.570e-01;SOR=2.422;VQSLOD=-1.252e+01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/0:13,0,0:13:0:.:.:0,0,146,0,146,146 0/1:19,3,0:22:43:0|1:820968_A_C:43,0,777,100,786,886 0/2:18,0,8:26:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:280,336,1093,0,757,733 3425chr3 179199001 . A C,* 308.52 VQSRTrancheSNP99.90to100.00+ AC=1,1;AF=0.167,0.167;AN=6;BaseQRankSum=-1.339e+00;ClippingRankSum=0.00;DP=82;ExcessHet=4.7712;FS=24.798;MLEAC=1,1;MLEAF=0.167,0.167;MQ=34.33;MQRankSum=-2.200e+00;QD=6.43;ReadPosRankSum=-1.148e+00;SOR=2.422;VQSLOD=-1.254e+01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/0:13,0,0:13:0:.:.:0,0,146,0,146,146 0/1:19,3,0:22:43:0|1:820968_A_C:43,0,777,100,786,886 0/2:18,0,8:26:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:280,336,1093,0,757,733 3426chr3 179199002 . A C,* 194.52 VQSRTrancheSNP99.90to100.00+ AC=1,1;AF=0.167,0.167;AN=6;BaseQRankSum=-2.991e+00;ClippingRankSum=-4.900e-02;DP=106;ExcessHet=4.7712;FS=16.473;MLEAC=1,1;MLEAF=0.167,0.167;MQ=37.30;MQRankSum=-1.470e-01;QD=2.95;ReadPosRankSum=-7.360e-01;SOR=1.435;VQSLOD=-9.044e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/0:15,0,0:15:0:.:.:0,0,273,0,273,273 0/1:23,7,0:30:49:.:.:49,0,658,118,678,796 0/2:30,0,6:36:99:0|1:820928_CTTGTCCAGCAGGTCCACCCTGTCTACACTACCTGCCTGCAAAGCAGATCCACCCTGTCTACACTACCTGG_C:160,252,1513,0,1261,1243 3427chr3 179199003 . G A,* 1706.05 VQSRTrancheSNP99.90to100.00+ AC=2,2;AF=0.500,0.500;AN=4;DB;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2,2;MLEAF=0.500,0.500;MQ=34.51;POSITIVE_TRAIN_SITE;QD=32.87;SOR=0.968;VQSLOD=-7.669e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,24,0:24:75:1|1:908920_C_G:1104,75,0,1104,75,1104 ./.:33,0,0:33:.:.:.:0,0,0,0,0,0 2/2:0,0,15:15:45:1|1:908920_C_G:627,627,627,45,45,0 3428chr3 179199004 . A G,* 1368.97 VQSRTrancheSNP99.90to100.00+ AC=2,1;AF=0.500,0.250;AN=4;DB;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2,1;MLEAF=0.500,0.250;MQ=32.71;QD=28.53;SOR=0.302;VQSLOD=-9.124e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,18,0:18:54:1|1:908920_C_G:810,54,0,810,54,810 ./.:29,0,0:29:.:.:.:0,0,0,0,0,0 0/2:1,0,15:16:59:0|1:908920_C_G:579,582,687,0,105,59 3429chr3 179199005 . A G,* 1434.91 PASS AC=2,2;AF=0.333,0.333;AN=6;BaseQRankSum=0.533;ClippingRankSum=1.60;DB;DP=88;ExcessHet=3.9794;FS=0.000;MLEAC=2,2;MLEAF=0.333,0.333;MQ=49.95;MQRankSum=1.07;NEGATIVE_TRAIN_SITE;QD=27.59;ReadPosRankSum=2.40;SOR=0.902;VQSLOD=-9.887e-01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:5,9,0:14:99:1|0:992967_GGGAGGGTCCATGTGTCCGTCATCTGA_G:264,0,168,283,195,478 0/1:7,8,0:15:99:1|0:992967_GGGAGGGTCCATGTGTCCGTCATCTGA_G:206,0,264,233,288,521 2/2:0,0,23:23:71:.:.:990,990,990,71,71,0 3430chr3 179199006 . T C,* 2248.91 PASS AC=2,2;AF=0.333,0.333;AN=6;BaseQRankSum=-9.740e-01;ClippingRankSum=0.545;DB;DP=101;ExcessHet=3.9794;FS=6.882;MLEAC=2,2;MLEAF=0.333,0.333;MQ=49.59;MQRankSum=-1.490e-01;NEGATIVE_TRAIN_SITE;QD=23.18;ReadPosRankSum=0.578;SOR=1.028;VQSLOD=-8.789e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:18,17,0:35:99:456,0,705,510,756,1266 0/1:15,17,0:32:99:467,0,579,512,630,1142 2/2:0,0,30:30:91:1351,1351,1351,91,91,0 3431chr3 179199007 . A G,* 1821.97 VQSRTrancheSNP99.90to100.00+ AC=2,1;AF=0.500,0.250;AN=4;DB;DP=92;ExcessHet=3.0103;FS=10.616;MLEAC=2,1;MLEAF=0.500,0.250;MQ=32.68;POSITIVE_TRAIN_SITE;QD=27.61;SOR=1.479;VQSLOD=-1.050e+01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL ./.:21,0,0:21:.:.:.:0,0,0,0,0,0 1/1:0,31,0:31:96:1|1:996335_C_A:1103,96,0,1103,96,1103 0/2:11,0,24:35:99:.:.:739,773,1159,0,386,316 3432chr3 179199008 . T C,* 601.66 VQSRTrancheSNP99.90to100.00+ AC=2,2;AF=0.333,0.333;AN=6;BaseQRankSum=-5.100e-01;ClippingRankSum=1.36;DB;DP=95;ExcessHet=3.9794;FS=27.935;MLEAC=2,2;MLEAF=0.333,0.333;MQ=48.12;MQRankSum=1.08;NEGATIVE_TRAIN_SITE;QD=12.53;ReadPosRankSum=0.849;SOR=2.062;VQSLOD=-3.093e+00;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:11,7,0:18:88:0|1:1611567_CT_C:88,0,187,121,208,329 2/2:1,0,12:13:16:.:.:212,216,235,16,35,0 0/1:4,13,0:17:20:0|1:1611567_CT_C:327,0,20,339,58,397 3433chr3 179199009 . A G,* 469.89 PASS AC=2,2;AF=0.333,0.333;AN=6;BaseQRankSum=2.60;ClippingRankSum=1.32;DB;DP=80;ExcessHet=3.9794;FS=2.173;MLEAC=2,2;MLEAF=0.333,0.333;MQ=53.43;MQRankSum=1.82;NEGATIVE_TRAIN_SITE;QD=6.44;ReadPosRankSum=1.70;SOR=1.002;VQSLOD=-6.972e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:33,7,0:40:84:84,0,865,180,886,1065 2/2:0,0,9:9:27:332,332,332,27,27,0 0/1:18,6,0:24:79:79,0,466,133,483,616 3434