##fileformat=VCFv4.1 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/data/scratch/workspace/RunFolder/Data/Intensities/BaseCalls/Alignment/2-AC-CAP17_S1.bam] read_buffer_size=null phone_home=NO_ET gatk_key=null read_filter=[] intervals=[/data/scratch/workspace/RunFolder/Data/Intensities/BaseCalls/Alignment/Segment_intervals_M1.0.picard] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=5000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=OFF log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=1.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false annotateNDA=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 max_alternate_alleles=3 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false includeGVCFData=true dbsnp=(RodBinding name= source=UNBOUND) comp=[] 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=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa ##gvcftools_version="0.12" ##gvcftools_cmdline="/opt/illumina/Isis/2.5.41.27.Enrichment/Workflows/EnrichmentWorker/gatk_to_gvcf --no-default-filters --min-qd 2.0000 --min-gqx 30.0000 --min-mq 20.0000" ##source=GATK 1.6 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 2-AC-CAP17 chr1 1470127 . T . . PASS END=1470301;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:550:99:60 chr1 1470302 . G . . PASS END=1470384;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:430:99:60 chr1 1470385 . C . . PASS END=1470405;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:334:99:60 chr1 1470406 . G . . PASS END=1470420;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:279:99:60 chr1 1470421 . A . . PASS END=1470471;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:185:99:59 chr1 1470472 . C . . PASS END=1470547;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:237:99:59 chr1 1470548 . C . . PASS END=1470581;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:309:99:60 chr1 1470582 . C . . PASS END=1470617;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:407:99:60 chr1 1470618 . C . . PASS END=1470696;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:530:99:60 chr1 1470697 . G . . PASS END=1470848;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:599:99:60 chr1 1470849 . G . . PASS END=1470917;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:528:99:60 chr1 1470938 . C . . PASS END=1471016;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:532:99:60 chr1 1471017 . C . . PASS END=1471168;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:580:99:60 chr1 1471169 . A . . PASS END=1471201;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:452:99:60 chr1 1471202 . A . . PASS END=1471207;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:438:99:60 chr1 1475033 . C . . PASS END=1475079;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:434:99:60 chr1 1475080 . G . . PASS END=1475185;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:477:99:60 chr1 1475186 . A . . PASS END=1475200;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:430:99:60 chr1 1475639 . G . . PASS END=1475734;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:278:99:60 chr1 1475735 . G . . PASS END=1475764;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:217:99:60 chr1 1475765 . C . . PASS END=1475770;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:199:99:60 chr1 19542127 . A . . PASS END=19542180;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:443:99:60 chr1 19542181 . T . . PASS END=19542209;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:342:99:60 chr1 19542210 . T . . PASS END=19542254;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:259:99:60 chr1 19542255 . C . . PASS END=19542297;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:200:99:60 chr1 19542298 . A . . PASS END=19542374;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:185:99:60 chr1 19542375 . G . . PASS END=19542407;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:242:99:60 chr1 19542408 . C . . PASS END=19542453;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:316:99:60 chr1 19542454 . A . . PASS END=19542499;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:412:99:60 chr1 19542500 . A . . PASS END=19542619;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:476:99:60 chr1 19542620 . C . . PASS END=19542734;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:471:99:60 chr1 19542735 . A . . PASS END=19542874;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:614:99:60 chr1 19542875 . T . . PASS END=19543157;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:643:99:60 chr1 19543158 . G . . PASS END=19543192;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:494:99:60 chr1 19543193 . T . . PASS END=19543229;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:373:99:60 chr1 19543230 . G . . PASS END=19543270;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:284:99:60 chr1 19543271 . A . . PASS END=19543364;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:217:99:60 chr1 19543365 . T . . PASS END=19543409;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:284:99:60 chr1 19543410 . C . . PASS END=19543453;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:372:99:60 chr1 19543454 . G . . PASS END=19543491;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:486:99:60 chr1 19543492 . T . . PASS END=19543755;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:620:99:60 chr1 19543756 . A . . PASS END=19543816;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:477:99:60 chr1 19543817 . A . . PASS END=19543858;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:358:99:60 chr1 19543859 . C . . PASS END=19543957;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:321:99:60 chr1 19543958 . C . . PASS END=19544010;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:420:99:60 chr1 19544010 . CA C 983.01 LowQD BaseQRankSum=-2.176;DP=533;FS=5.215;HRun=13;HaplotypeScore=1971.0200;MQ=60;MQ0=0;MQRankSum=0.746;QD=1.84;ReadPosRankSum=-1.831;SB=-428.46 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:366,80:533:99:1022,0,7626:60:99:0.179 chr1 19544011 . A . . LowQD . GT:DP:GQX:MQ 0:445:99:60 chr1 19544012 . A . . PASS END=19544060;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:539:99:60 chr1 19544061 . A . . PASS END=19544718;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:654:99:60 chr1 19544719 . T . . PASS END=19544870;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:696:99:60 chr1 19544871 . A . . PASS END=19545269;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:649:99:60 chr1 19545270 . C . . PASS END=19546006;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:749:99:60 chr1 19546032 . G . . PASS END=19546222;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:694:99:60 chr1 19547227 . G . . PASS END=19547372;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:719:99:60 chr1 19549087 . C . . PASS END=19549358;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:626:99:60 chr1 19549859 . C . . PASS END=19550022;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:567:99:60 chr1 19550023 . G . . PASS END=19550066;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:437:99:60 chr1 19550067 . G . . PASS END=19550093;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:358:99:60 chr1 19553776 . T . . PASS END=19553939;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:564:99:60 chr1 19553940 . A . . PASS END=19553974;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:434:99:60 chr1 19557307 . C . . PASS END=19557487;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:708:99:60 chr1 19557724 . G . . PASS END=19557946;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:641:99:60 chr1 19559087 . G . . PASS END=19559297;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:683:99:60 chr1 19559399 . G . . PASS END=19559659;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:693:99:60 chr1 19561593 . A . . PASS END=19561757;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:525:99:60 chr1 19561758 . A . . PASS END=19561776;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:461:99:60 chr1 19563605 . T . . PASS END=19563762;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:660:99:60 chr1 19564480 . G . . PASS END=19564574;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:603:99:60 chr1 19564575 . C . . PASS END=19564663;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:765:99:60 chr1 19565258 . G . . PASS END=19565381;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:699:99:60 chr1 19565694 . C . . PASS END=19565826;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:642:99:60 chr1 19566281 . A . . PASS END=19566509;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:644:99:60 chr1 19566760 . C . . PASS END=19566899;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:606:99:60 chr1 19566900 . G . . PASS END=19566970;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:668:99:60 chr1 19567479 . T . . PASS END=19567666;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:673:99:60 chr1 19568808 . G . . PASS END=19568997;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:681:99:60 chr1 19570077 . C . . PASS END=19570231;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:736:99:60 chr1 19570413 . C . . PASS END=19570539;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:718:99:60 chr1 19571369 . A . . PASS END=19571554;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:656:99:60 chr1 19577878 . T . . PASS END=19577989;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:573:99:60 chr1 19577990 . C . . PASS END=19578051;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:417:99:60 chr1 19578052 . G . . PASS END=19578083;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:346:99:60 chr1 27425269 . A . . PASS END=27425557;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:614:99:60 chr1 27425558 . A . . PASS END=27425734;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:548:99:60 chr1 27425735 . G . . PASS END=27426218;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:695:99:60 chr1 27426219 . A G 19887.95 PASS BaseQRankSum=-0.090;DP=703;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=34.1874;MQ=60;MQ0=0;MQRankSum=-0.145;QD=28.29;ReadPosRankSum=1.685;SB=-13319.19 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:4,697:702:99:19888,1343,0:60:99:0.994 chr1 27426220 . C . . PASS END=27426562;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:618:99:60 chr1 27426563 . C . . PASS END=27426773;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:495:99:60 chr1 27426774 . A . . PASS END=27426795;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:643:99:60 chr1 27426796 . T C 18604.72 PASS BaseQRankSum=0.186;DP=680;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=37.7197;MQ=60;MQ0=0;MQRankSum=0.056;QD=27.36;ReadPosRankSum=0.240;SB=-12844.38 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:2,677:680:99:18605,1264,0:60:99:0.997 chr1 27426797 . G . . PASS END=27427040;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:667:99:60 chr1 27427041 . T C 20615.27 PASS BaseQRankSum=1.718;DP=735;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=20.7721;MQ=60;MQ0=0;MQRankSum=-1.063;QD=28.05;ReadPosRankSum=0.558;SB=-14344.61 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,734:735:99:20615,1466,0:60:99:0.999 chr1 27427042 . T . . PASS END=27427165;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:667:99:60 chr1 27427663 . C . . PASS END=27427715;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:515:99:60 chr1 27427716 . C . . PASS END=27427796;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:533:99:60 chr1 27428185 . A . . PASS END=27428320;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:604:99:60 chr1 27428321 . T C 16085.21 PASS BaseQRankSum=0.552;DP=600;Dels=0.00;FS=5.623;HRun=0;HaplotypeScore=157.8974;MQ=60;MQ0=0;MQRankSum=-0.303;QD=26.81;ReadPosRankSum=-0.490;SB=-7687.10 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:3,576:600:99:16085,1091,0:60:99:0.995 chr1 27428322 . G . . PASS END=27428347;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:586:99:60 chr1 27428476 . C . . PASS END=27428651;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:613:99:60 chr1 27428845 . G . . PASS END=27429079;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:588:99:60 chr1 27429133 . T . . PASS END=27429264;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:688:99:60 chr1 27429683 . G . . PASS END=27429798;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:621:99:60 chr1 27429799 . A . . PASS END=27429833;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:536:99:60 chr1 27432345 . G . . PASS END=27432592;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:584:99:60 chr1 27432593 . A . . PASS END=27432608;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:552:99:60 chr1 27434108 . A . . PASS END=27434138;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:392:99:60 chr1 27434139 . C . . PASS END=27434172;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:510:99:60 chr1 27434173 . G . . PASS END=27434330;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:650:99:60 chr1 27434331 . G . . PASS END=27434386;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:524:99:60 chr1 27435987 . C . . PASS END=27436019;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:514:99:60 chr1 27436020 . C . . PASS END=27436135;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:671:99:60 chr1 27436136 . C . . PASS END=27436271;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:682:99:60 chr1 27436272 . G . . PASS END=27436298;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:565:99:60 chr1 27440286 . T . . PASS END=27440780;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:624:99:60 chr1 27440781 . C . . PASS END=27440807;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:508:99:60 chr1 27480443 . C . . PASS END=27480556;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:608:99:60 chr1 27480557 . G . . PASS END=27480756;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:708:99:60 chr1 27480757 . A G 20103.31 PASS BaseQRankSum=-0.235;DP=736;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=29.3666;MQ=60;MQ0=0;MQRankSum=-0.910;QD=27.31;ReadPosRankSum=-0.405;SB=-14099.57 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:7,728:736:99:20103,1279,0:60:99:0.990 chr1 27480758 . A . . PASS END=27481400;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:632:99:60 chr1 27481401 . G . . PASS END=27481516;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:492:99:60 chr1 27481517 . C . . PASS END=27481529;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:466:99:60 chr1 27481530 . A G 14052.50 PASS DP=463;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=24.3188;MQ=60;MQ0=0;QD=30.35;SB=-8842.72 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,461:462:99:14052,1029,0:60:99:1.000 chr1 27481531 . C . . PASS END=27481598;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:455:99:60 chr1 27481599 . C . . PASS END=27481651;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:545:99:60 chr1 43391015 . T . . PASS END=43391836;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:658:99:60 chr1 43391837 . C . . PASS END=43392942;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:706:99:60 chr1 43393245 . G . . PASS . GT:DP:GQX:MQ 0/0:602:99:60 chr1 43393245 . G GGGTGAGAAAT 31820.97 PASS BaseQRankSum=0.923;DP=602;FS=0.612;HRun=0;HaplotypeScore=537.9766;MQ=60;MQ0=0;MQRankSum=-0.143;QD=52.86;ReadPosRankSum=2.086;SB=-15481.99 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:352,249:602:99:31821,0,40221:60:99:0.414 chr1 43393246 . G . . PASS END=43393509;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:649:99:60 chr1 43394572 . A . . PASS END=43394734;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:634:99:60 chr1 43394850 . T . . PASS END=43395015;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:714:99:60 chr1 43395233 . G . . PASS END=43395328;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:483:99:60 chr1 43395329 . A . . PASS END=43395481;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:628:99:60 chr1 43395513 . A . . PASS END=43395736;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:629:99:60 chr1 43396266 . T . . PASS END=43396344;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:507:99:60 chr1 43396345 . C . . PASS END=43396567;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:651:99:60 chr1 43396686 . C . . PASS END=43396907;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:665:99:60 chr1 43408866 . G . . PASS END=43409022;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:631:99:60 chr1 43424274 . T . . PASS END=43424310;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:430:99:60 chr1 43424311 . G . . PASS END=43424724;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:560:99:60 chr1 43424725 . G . . PASS END=43424877;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:719:99:60 chr1 110163172 . T . . PASS END=110163711;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:652:99:60 chr1 110163712 . G . . PASS END=110163918;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:615:99:60 chr1 110167894 . C . . PASS END=110167947;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:460:99:60 chr1 110167948 . C . . PASS END=110168085;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:605:99:60 chr1 110168253 . A . . PASS END=110168444;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:604:99:60 chr1 110168751 . C . . PASS END=110168880;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:730:99:60 chr1 110168910 . T . . PASS END=110169063;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:575:99:60 chr1 110169064 . T . . PASS END=110169079;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:538:99:60 chr1 110169317 . G . . PASS END=110169564;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:620:99:60 chr1 110169766 . T . . PASS END=110169956;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:655:99:60 chr1 110169957 . A G 8229.33 PASS BaseQRankSum=1.956;DP=684;Dels=0.00;FS=3.117;HRun=0;HaplotypeScore=25.6059;MQ=60;MQ0=0;MQRankSum=-1.324;QD=12.03;ReadPosRankSum=-0.317;SB=-5291.43 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:349,335:684:99:8229,0,8504:60:99:0.490 chr1 110169958 . T . . PASS END=110169968;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:664:99:60 chr1 110170020 . C . . PASS END=110170170;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:643:99:60 chr1 110170365 . T . . PASS END=110170555;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:713:99:60 chr1 110170674 . G . . PASS END=110170895;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:705:99:60 chr1 110170896 . T C 9424.03 PASS BaseQRankSum=4.689;DP=803;Dels=0.00;FS=0.521;HRun=0;HaplotypeScore=18.4868;MQ=60;MQ0=0;MQRankSum=0.605;QD=11.74;ReadPosRankSum=0.084;SB=-6250.15 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:418,384:803:99:9424,0,9646:60:99:0.479 chr1 110170897 . G . . PASS END=110170929;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:799:99:60 chr1 110170955 . C . . PASS END=110171147;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:721:99:60 chr1 110171234 . T . . PASS END=110171451;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:609:99:60 chr1 110171452 . G . . PASS END=110171458;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:590:99:60 chr1 110171700 . T . . PASS END=110171704;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:574:99:60 chr1 110171705 . A C 7983.65 PASS BaseQRankSum=3.810;DP=594;Dels=0.00;FS=5.529;HRun=1;HaplotypeScore=19.1706;MQ=60;MQ0=0;MQRankSum=0.962;QD=13.44;ReadPosRankSum=-1.102;SB=-4929.10 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:275,319:594:99:7984,0,6719:60:99:0.537 chr1 110171706 . T . . PASS END=110171887;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:602:99:60 chr1 110171918 . C . . PASS END=110172142;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:783:99:60 chr1 110172387 . C . . PASS END=110172466;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:581:99:60 chr1 110172467 . G . . PASS END=110172568;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:718:99:60 chr1 110172824 . G . . PASS END=110172980;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:532:99:60 chr1 110172981 . A . . PASS END=110173016;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:405:99:60 chr1 110173017 . C . . PASS END=110173049;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:312:99:60 chr1 110173050 . A . . PASS END=110173058;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:266:99:60 chr1 110173274 . G . . PASS END=110173312;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:385:99:60 chr1 110173313 . G . . PASS END=110173404;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:501:99:60 chr1 110173405 . T . . PASS END=110173445;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:653:99:60 chr1 110173534 . C . . PASS END=110173964;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:715:99:60 chr1 110173965 . G . . PASS END=110174196;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:762:99:60 chr1 110174197 . G . . PASS END=110174707;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:665:99:60 chr1 150980836 . T . . PASS END=150980885;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:393:99:60 chr1 150980886 . C . . PASS END=150980974;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:512:99:60 chr1 150980975 . G . . PASS END=150981177;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:592:99:60 chr1 150990257 . T . . PASS END=150990410;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:628:99:60 chr1 150990912 . T . . PASS . GT:DP:GQX:MQ 0/0:662:99:60 chr1 150990913 . G C 7631.08 PASS BaseQRankSum=3.344;DP=660;Dels=0.00;FS=1.950;HRun=0;HaplotypeScore=11.3526;MQ=60;MQ0=0;MQRankSum=0.459;QD=11.56;ReadPosRankSum=-0.760;SB=-5122.89 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:340,319:660:99:7631,0,8194:60:99:0.484 chr1 150990914 . T . . PASS END=150991175;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:661:99:60 chr1 150997056 . T . . PASS END=150997301;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:587:99:60 chr1 150997960 . A . . PASS END=150998179;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:656:99:60 chr1 150999678 . T . . PASS END=150999833;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:647:99:60 chr1 151001231 . C . . PASS END=151001450;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:629:99:60 chr1 151006251 . T . . PASS END=151006529;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:603:99:60 chr1 151006530 . G . . PASS END=151006538;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:782:99:60 chr1 151006539 . C A 21957.18 PASS BaseQRankSum=1.728;DP=777;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=15.6337;MQ=60;MQ0=0;MQRankSum=0.679;QD=28.26;ReadPosRankSum=0.527;SB=-14828.88 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,775:777:99:21957,1562,0:60:99:0.999 chr1 151006540 . C . . PASS END=151008219;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:706:99:60 chr1 227127907 . T . . PASS END=227127940;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:276:99:60 chr1 227127941 . G . . PASS END=227127981;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:362:99:60 chr1 227127982 . C . . PASS END=227128123;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:444:99:60 chr1 227128124 . G . . PASS END=227128130;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:419:99:60 chr1 227149047 . G . . PASS END=227149202;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:575:99:60 chr1 227149203 . G A 7939.56 PASS BaseQRankSum=3.185;DP=680;Dels=0.00;FS=3.156;HRun=0;HaplotypeScore=56.4415;MQ=60;MQ0=0;MQRankSum=-0.422;QD=11.68;ReadPosRankSum=-0.850;SB=-5286.99 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:340,340:680:99:7940,0,7940:60:99:0.500 chr1 227149204 . G . . PASS END=227149262;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:527:99:60 chr1 227149263 . G . . PASS END=227149293;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:414:99:60 chr1 227152670 . C . . PASS END=227152862;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:613:99:60 chr1 227152863 . G . . PASS END=227153141;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:678:99:60 chr1 227153341 . T . . PASS END=227153468;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:579:99:60 chr1 227165119 . G . . PASS END=227165250;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:325:99:60 chr1 227165251 . G . . PASS END=227165254;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:311:99:60 chr1 227169697 . T . . PASS END=227169832;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:541:99:60 chr1 227169833 . A . . PASS END=227169871;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:416:99:60 chr1 227169872 . T . . PASS END=227169880;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:389:99:60 chr1 227170348 . G . . PASS END=227170494;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:644:99:60 chr1 227170564 . C . . PASS END=227170751;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:606:99:60 chr1 227170752 . G . . PASS END=227170765;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:549:99:60 chr1 227171222 . T . . PASS END=227171273;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:562:99:60 chr1 227171274 . A . . PASS END=227171364;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:721:99:60 chr1 227171431 . T . . PASS END=227171584;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:680:99:60 chr1 227171584 . GT G 11427.84 PASS BaseQRankSum=3.092;DP=683;FS=0.000;HRun=3;HaplotypeScore=1409.7431;MQ=60;MQ0=0;MQRankSum=0.107;QD=16.73;ReadPosRankSum=-1.019;SB=-5683.75 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:352,326:683:99:11428,0,11636:60:99:0.481 chr1 227171585 . T . 725.19 PASS DP=678;MQ=60;MQ0=0 GT:AD:DP:GQ:MQ:GQX 0:349:352:99:60:99 chr1 227171764 . G . . PASS END=227171957;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:655:99:60 chr1 227171958 . G C 8565.34 PASS BaseQRankSum=2.833;DP=653;Dels=0.00;FS=5.132;HRun=0;HaplotypeScore=17.5464;MQ=60;MQ0=0;MQRankSum=0.507;QD=13.12;ReadPosRankSum=-0.357;SB=-5484.39 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:304,348:653:99:8565,0,7456:60:99:0.534 chr1 227171959 . G . . PASS END=227171966;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:625:99:60 chr1 227172218 . G . . PASS END=227172289;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:608:99:60 chr1 227172290 . C T 8494.18 PASS BaseQRankSum=3.311;DP=732;Dels=0.00;FS=3.386;HRun=2;HaplotypeScore=24.2639;MQ=60;MQ0=0;MQRankSum=1.137;QD=11.60;ReadPosRankSum=1.484;SB=-5915.36 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:370,362:732:99:8494,0,9091:60:99:0.495 chr1 227172291 . G . . PASS END=227172386;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:656:99:60 chr1 227172546 . G . . PASS END=227172672;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:644:99:60 chr1 227172924 . G . . PASS END=227172934;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:571:99:60 chr1 227172935 . C G 7729.98 PASS BaseQRankSum=2.501;DP=598;Dels=0.00;FS=1.675;HRun=0;HaplotypeScore=25.4533;MQ=60;MQ0=0;MQRankSum=-0.791;QD=12.93;ReadPosRankSum=1.314;SB=-4786.07 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:295,301:598:99:7730,0,7099:60:99:0.505 chr1 227172936 . C . . PASS END=227173071;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:601:99:60 chr1 227174123 . G . . PASS END=227174144;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:646:99:60 chr1 227174145 . T C 8287.29 PASS BaseQRankSum=4.717;DP=702;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=24.9548;MQ=60;MQ0=0;MQRankSum=-0.089;QD=11.81;ReadPosRankSum=-1.025;SB=-5846.62 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:348,353:702:99:8287,0,8419:60:99:0.504 chr1 227174146 . T . . PASS END=227174209;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:703:99:60 chr1 227174210 . T C 8648.66 PASS BaseQRankSum=1.747;DP=734;Dels=0.00;FS=0.844;HRun=1;HaplotypeScore=29.6573;MQ=60;MQ0=0;MQRankSum=1.607;QD=11.78;ReadPosRankSum=0.213;SB=-5921.62 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:367,367:734:99:8649,0,8575:60:99:0.500 chr1 227174211 . G . . PASS END=227174823;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:706:99:60 chr1 227174823 . A AT 12774.55 PASS BaseQRankSum=-2.448;DP=816;FS=2.436;HRun=4;HaplotypeScore=614.5869;MQ=60;MQ0=0;MQRankSum=-3.308;QD=15.66;ReadPosRankSum=0.258;SB=-6361.19 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:411,403:816:99:12775,0,12615:60:99:0.495 chr1 227174824 . T . . PASS END=227175245;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:719:99:60 chr1 227175245 . C CT 9740.47 PASS BaseQRankSum=19.762;DP=719;FS=0.565;HRun=3;HaplotypeScore=1854.2764;MQ=60;MQ0=0;MQRankSum=0.085;QD=13.55;ReadPosRankSum=2.508;SB=-4714.80 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:410,300:719:99:9740,0,13254:60:99:0.423 chr1 227175246 . T . . PASS END=227175252;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:700:99:60 chr1 227175253 . C T 7537.75 PASS BaseQRankSum=3.209;DP=708;Dels=0.00;FS=0.861;HRun=0;HaplotypeScore=302.5640;MQ=60;MQ0=0;MQRankSum=-0.745;QD=10.65;ReadPosRankSum=1.753;SB=-5208.44 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:392,315:708:99:7538,0,9630:60:99:0.446 chr1 227175254 . G . . PASS END=227175276;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:647:99:60 chr2 99061290 . G . . PASS END=99061398;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:270:99:60 chr2 99061399 . G . . PASS END=99061426;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:209:99:60 chr2 99061427 . G . . PASS END=99061461;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:159:99:60 chr2 99061462 . G . . PASS END=99061479;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:122:99:60 chr2 99061480 . C . . PASS END=99061500;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:92:99:60 chr2 99061501 . C . . PASS END=99061521;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:70:99:60 chr2 99061522 . C . . PASS END=99061538;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:55:99:60 chr2 99061539 . G . . PASS END=99061554;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:41:87:60 chr2 99061555 . G . . PASS END=99061562;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:31:69:60 chr2 99061563 . C . . PASS END=99061575;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:24:57:60 chr2 99061576 . G . . PASS END=99061578;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:18:39:60 chr2 99135396 . G . . PASS END=99135518;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:611:99:60 chr2 99136378 . C . . PASS END=99136462;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:596:99:60 chr2 99136463 . A . . PASS END=99136586;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:608:99:60 chr2 99136587 . G . . PASS END=99136637;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:466:99:60 chr2 99136638 . A . . PASS END=99136647;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:441:99:60 chr2 99137119 . A . . PASS END=99137223;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:519:99:60 chr2 99137224 . A . . PASS . GT:DP:GQX:MQ 0/0:513:99:60 chr2 99149809 . G . . PASS END=99149844;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:400:99:60 chr2 99149845 . A . . PASS END=99149920;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:521:99:60 chr2 99149921 . C . . PASS END=99149945;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:667:99:60 chr2 99149946 . G A 18228.94 PASS BaseQRankSum=-0.799;DP=674;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=26.2964;MQ=60;MQ0=0;MQRankSum=0.334;QD=27.05;ReadPosRankSum=-0.927;SB=-12999.03 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:3,669:674:99:18229,1215,0:60:99:0.996 chr2 99149947 . G . . PASS END=99149988;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:670:99:60 chr2 99152161 . T . . PASS END=99152223;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:554:99:60 chr2 99152224 . T . . PASS END=99152338;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:714:99:60 chr2 99152561 . C . . PASS END=99152693;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:535:99:60 chr2 99152694 . T . . PASS END=99152701;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:508:99:60 chr2 99154295 . A . . PASS END=99154353;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:623:99:60 chr2 99154354 . A . . PASS END=99154467;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:711:99:60 chr2 99155323 . T . . PASS END=99155474;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:658:99:60 chr2 99155960 . G . . PASS END=99156158;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:609:99:60 chr2 99156159 . T . . PASS END=99156168;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:583:99:60 chr2 99160309 . A . . PASS END=99160360;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:600:99:60 chr2 99160361 . G C 8635.98 PASS BaseQRankSum=1.031;DP=706;Dels=0.00;FS=3.942;HRun=0;HaplotypeScore=24.8095;MQ=60;MQ0=0;MQRankSum=-0.930;QD=12.23;ReadPosRankSum=0.406;SB=-5419.25 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:348,358:706:99:8636,0,8159:60:99:0.507 chr2 99160362 . G . . PASS END=99160499;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:548:99:60 chr2 99160500 . A . . PASS . GT:DP:GQX:MQ 0/0:537:99:60 chr2 99162401 . G . . PASS END=99162566;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:648:99:60 chr2 99163018 . G . . PASS END=99163187;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:680:99:60 chr2 99165375 . T . . PASS END=99165475;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:682:99:60 chr2 99169218 . A . . PASS END=99169462;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:620:99:60 chr2 99170703 . C . . PASS END=99170779;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:564:99:60 chr2 99170780 . C . . PASS END=99170982;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:681:99:60 chr2 99171985 . C . . PASS END=99172177;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:579:99:60 chr2 99172178 . T . . PASS END=99172184;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:556:99:60 chr2 99175892 . T . . PASS END=99175992;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:623:99:60 chr2 99179897 . C . . PASS END=99180130;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:587:99:60 chr2 99181072 . C . . PASS END=99181256;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:602:99:60 chr2 99182072 . C . . PASS END=99182226;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:599:99:60 chr2 99182227 . T . . PASS END=99182259;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:726:99:60 chr2 99182461 . C . . PASS END=99182640;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:557:99:60 chr2 99182641 . C . . PASS END=99182662;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:501:99:60 chr2 99185003 . C . . PASS END=99185161;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:746:99:60 chr2 99189247 . C . . PASS END=99189420;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:624:99:60 chr2 99193421 . C . . PASS END=99193495;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:656:99:60 chr2 99193496 . C T 20243.75 PASS BaseQRankSum=-0.275;DP=728;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=35.4187;MQ=60;MQ0=0;MQRankSum=0.076;QD=27.81;ReadPosRankSum=1.158;SB=-14214.19 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:2,725:728:99:20244,1409,0:60:99:0.997 chr2 99193497 . G . . PASS END=99193624;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:569:99:60 chr2 99193625 . C . . PASS END=99193636;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:524:99:60 chr2 99198008 . T . . PASS END=99198043;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:607:99:60 chr2 99198044 . G . . PASS END=99198305;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:668:99:60 chr2 99198306 . A . . PASS END=99198314;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:637:99:60 chr2 241653150 . C . . PASS END=241654304;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:682:99:60 chr2 241654305 . G . . PASS END=241654706;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:651:99:60 chr2 241654707 . A . . PASS END=241655552;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:696:99:60 chr2 241655553 . C . . PASS END=241656621;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:715:99:60 chr2 241656622 . T . . PASS END=241656853;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:592:99:60 chr2 241657436 . G . . PASS END=241657615;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:582:99:60 chr2 241658392 . G . . PASS END=241658439;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:511:99:60 chr2 241658440 . G . . PASS END=241658645;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:672:99:60 chr2 241659160 . T . . PASS END=241659367;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:484:99:60 chr2 241659368 . C A 5758.83 PASS BaseQRankSum=0.820;DP=525;Dels=0.00;FS=6.711;HRun=0;HaplotypeScore=38.0124;MQ=60;MQ0=0;MQRankSum=-0.712;QD=10.97;ReadPosRankSum=1.579;SB=-3966.93 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:276,245:525:99:5759,0,6612:60:99:0.470 chr2 241659369 . C . . PASS END=241659373;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:517:99:60 chr2 241660300 . A . . PASS END=241660484;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:521:99:60 chr2 241660485 . A . . PASS . GT:DP:GQX:MQ 0/0:516:99:60 chr2 241661193 . G . . PASS END=241661318;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:468:99:60 chr2 241661319 . G . . PASS END=241661331;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:412:99:60 chr2 241661842 . T . . PASS END=241662034;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:530:99:60 chr2 241662035 . C . . PASS END=241662103;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:625:99:60 chr2 241662799 . G . . PASS END=241662966;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:555:99:60 chr2 241662967 . G . . PASS END=241663005;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:480:99:60 chr2 241663361 . C . . PASS END=241663481;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:500:99:60 chr2 241663482 . G . . PASS END=241663483;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:491:99:60 chr2 241664657 . G . . PASS END=241664840;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:627:99:60 chr2 241664841 . G . . PASS END=241664851;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:583:99:60 chr2 241666212 . T . . PASS END=241666387;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:672:99:60 chr2 241676449 . G . . PASS END=241676613;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:609:99:60 chr2 241676614 . A . . PASS END=241676615;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:599:99:60 chr2 241679444 . C . . PASS END=241679589;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:564:99:60 chr2 241679684 . C . . PASS END=241679811;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:576:99:60 chr2 241680655 . A . . PASS END=241680801;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:481:99:60 chr2 241680802 . G A 6511.61 PASS BaseQRankSum=-1.146;DP=588;Dels=0.00;FS=0.952;HRun=1;HaplotypeScore=16.0198;MQ=60;MQ0=0;MQRankSum=0.107;QD=11.07;ReadPosRankSum=-0.041;SB=-4689.35 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:300,288:588:99:6512,0,7021:60:99:0.490 chr2 241680803 . A . . PASS END=241680824;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:542:99:60 chr2 241682315 . G . . PASS END=241682431;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:585:99:60 chr2 241683328 . A . . PASS END=241683425;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:620:99:60 chr2 241683426 . T . . PASS END=241683505;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:626:99:60 chr2 241683506 . A . . PASS END=241683507;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:615:99:60 chr2 241684813 . C . . PASS END=241684964;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:544:99:60 chr2 241685124 . G . . PASS END=241685201;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:637:99:60 chr2 241685202 . C . . PASS END=241685356;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:779:99:60 chr2 241685425 . A . . PASS END=241685600;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:584:99:60 chr2 241685601 . A . . PA