##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
##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">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs --output all.vcf.gz --variant ERR10466327_1_marked_duplicates.bam.raw.vcf --variant ERR10466729_marked_duplicates.bam.raw.vcf --variant ERR1102659_1_marked_duplicates.bam.raw.vcf --variant ERR1102660_1_marked_duplicates.bam.raw.vcf --variant ERR1102661_1_marked_duplicates.bam.raw.vcf --variant ERR1102662_1_marked_duplicates.bam.raw.vcf --variant ERR1102663_1_marked_duplicates.bam.raw.vcf --variant ERR1102664_1_marked_duplicates.bam.raw.vcf --variant ERR2004531_marked_duplicates.bam.raw.vcf --variant ERR2004532_marked_duplicates.bam.raw.vcf --variant ERR2004533_marked_duplicates.bam.raw.vcf --variant ERR2004535_1_marked_duplicates.bam.raw.vcf --variant ERR2004536_1_marked_duplicates.bam.raw.vcf --variant ERR2764717_1_marked_duplicates.bam.raw.vcf --variant ERR2764718_1_marked_duplicates.bam.raw.vcf --variant ERR2764719_1_marked_duplicates.bam.raw.vcf --variant ERR2764720_1_marked_duplicates.bam.raw.vcf --variant ERR2764721_1_marked_duplicates.bam.raw.vcf --variant ERR2764722_1_marked_duplicates.bam.raw.vcf --variant ERR2764723_1_marked_duplicates.bam.raw.vcf --variant ERR2764724_1_marked_duplicates.bam.raw.vcf --variant ERR2764725_1_marked_duplicates.bam.raw.vcf --variant ERR2764726_1_marked_duplicates.bam.raw.vcf --variant ERR2764727_1_marked_duplicates.bam.raw.vcf --variant ERR2764728_1_marked_duplicates.bam.raw.vcf --variant ERR2764729_1_marked_duplicates.bam.raw.vcf --variant ERR2764730_1_marked_duplicates.bam.raw.vcf --variant ERR2764731_1_marked_duplicates.bam.raw.vcf --variant ERR2764732_1_marked_duplicates.bam.raw.vcf --variant ERR2764733_1_marked_duplicates.bam.raw.vcf --variant ERR2764734_1_marked_duplicates.bam.raw.vcf --variant ERR2764735_1_marked_duplicates.bam.raw.vcf --variant ERR2764736_1_marked_duplicates.bam.raw.vcf --variant ERR2764737_1_marked_duplicates.bam.raw.vcf --variant ERR2764738_1_marked_duplicates.bam.raw.vcf --variant ERR2764739_1_marked_duplicates.bam.raw.vcf --variant ERR2764740_1_marked_duplicates.bam.raw.vcf --variant ERR2764741_1_marked_duplicates.bam.raw.vcf --variant ERR2764742_1_marked_duplicates.bam.raw.vcf --variant ERR2764743_1_marked_duplicates.bam.raw.vcf --variant ERR2764744_1_marked_duplicates.bam.raw.vcf --variant ERR2764745_1_marked_duplicates.bam.raw.vcf --variant ERR2764746_1_marked_duplicates.bam.raw.vcf --variant ERR2764747_1_marked_duplicates.bam.raw.vcf --variant ERR2764748_1_marked_duplicates.bam.raw.vcf --variant ERR2764749_1_marked_duplicates.bam.raw.vcf --variant ERR2764750_1_marked_duplicates.bam.raw.vcf --variant ERR2764751_1_marked_duplicates.bam.raw.vcf --variant ERR2764752_1_marked_duplicates.bam.raw.vcf --variant ERR2764753_1_marked_duplicates.bam.raw.vcf --variant ERR2764754_1_marked_duplicates.bam.raw.vcf --variant ERR2764755_1_marked_duplicates.bam.raw.vcf --variant ERR2764756_1_marked_duplicates.bam.raw.vcf --variant ERR2764757_1_marked_duplicates.bam.raw.vcf --variant ERR2764758_1_marked_duplicates.bam.raw.vcf --variant ERR2764759_1_marked_duplicates.bam.raw.vcf --variant ERR2764760_1_marked_duplicates.bam.raw.vcf --variant ERR2764761_1_marked_duplicates.bam.raw.vcf --variant ERR2764762_1_marked_duplicates.bam.raw.vcf --variant ERR2764763_1_marked_duplicates.bam.raw.vcf --variant ERR2764764_1_marked_duplicates.bam.raw.vcf --variant ERR2764765_1_marked_duplicates.bam.raw.vcf --variant ERR2764766_1_marked_duplicates.bam.raw.vcf --variant ERR2764775_marked_duplicates.bam.raw.vcf --variant ERR2764777_marked_duplicates.bam.raw.vcf --variant ERR4624298_marked_duplicates.bam.raw.vcf --variant ERR4624299_1_marked_duplicates.bam.raw.vcf --variant ERR4800930_marked_duplicates.bam.raw.vcf --variant ERR4801062_1_marked_duplicates.bam.raw.vcf --variant ERR4802172_marked_duplicates.bam.raw.vcf --variant ERR4802173_marked_duplicates.bam.raw.vcf --variant ERR4802174_marked_duplicates.bam.raw.vcf --variant ERR4802175_marked_duplicates.bam.raw.vcf --variant ERR4802176_marked_duplicates.bam.raw.vcf --reference ./Bbrux_WGS_reference.fasta --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --input-is-somatic false --drop-somatic-filtering-annotations false --call-genotypes false --ignore-variants-starting-outside-interval false --combine-variants-distance 0 --max-distance 2147483647 --ref-padding 1 --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 --max-variants-per-shard 0 --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 --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.4.0.0",Date="November 15, 2023, 12:48:32?PM PST">
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --emit-ref-confidence GVCF --output ERR10466327_1_marked_duplicates.bam.raw.vcf --input ERR10466327_1_marked_duplicates.bam --reference /mnt/data0/refdata/Ref_genomes/Bbrux_CBS11270/Bbrux_WGS_reference.fasta --use-posteriors-to-calculate-qual false --dont-use-dragstr-priors false --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotype-assignment-method USE_PLS_TO_ASSIGN --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --flow-use-t0-tag false --flow-probability-threshold 0.003 --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --flow-number-of-uncertain-flows-to-clip 0 --flow-nucleotide-of-first-uncertain-flow T --keep-boundary-flows false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --dragen-mode false --flow-mode NONE --apply-bqd false --apply-frd false --disable-spanning-event-genotyping false --transform-dragen-mapping-quality false --mapping-quality-threshold-for-genotyping 20 --max-effective-depth-adjustment-for-frd 0 --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --use-flow-aligner-for-stepwise-hc-filtering false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --pileup-detection-enable-indel-pileup-calling false --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.5 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman JAVA --max-mnp-distance 0 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming 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 --max-variants-per-shard 0 --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 --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.4.0.0",Date="November 12, 2023 at 1:22:56 PM PST">
##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)
##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)
##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)
##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive)
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=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">
##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">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##contig=<ID=LS990926.1,length=3978575>
##contig=<ID=LS990927.1,length=3325195>
##contig=<ID=LS990928.1,length=3706654>
##contig=<ID=LS990929.1,length=2209880>
##contig=<ID=LS990930.1,length=75320>
##source=CombineGVCFs
##source=HaplotypeCaller
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LS990926.1	1	.	N	<NON_REF>	.	.	END=105400	GT:DP:GQ:MIN_DP:PL	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0
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LS990926.1	105570	.	C	T,<NON_REF>	.	.	BaseQRankSum=-6.700e-02;DP=3979;ExcessHet=0.00;MQRankSum=-1.391e+00;RAW_MQandDP=3705964,1034;ReadPosRankSum=-2.300e-01	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:29:81:28:.:.:0,81,942,81,942,942	./.:.:3:9:3:.:.:0,9,57,9,57,57	./.:.:423:99:57:.:.:0,100,1800,100,1800,1800	./.:.:172:99:52:.:.:0,120,1800,120,1800,1800	./.:.:142:0:135:.:.:0,0,3978,0,3978,3978	./.:.:159:87:159:.:.:0,87,5572,87,5572,5572	./.:.:192:0:183:.:.:0,0,5170,0,5170,5170	./.:.:7:18:7:.:.:0,18,270,18,270,270	./.:.:12:33:12:.:.:0,33,495,33,495,495	./.:.:8:23:8:.:.:0,23,122,23,122,122	./.:.:5:14:5:.:.:0,14,62,14,62,62	./.:.:86:99:52:.:.:0,120,1800,120,1800,1800	./.:.:136:99:56:.:.:0,120,1800,120,1800,1800	./.:.:75:99:56:.:.:0,120,1800,120,1800,1800	./.:.:94:99:52:.:.:0,120,1800,120,1800,1800	./.:.:32:81:31:.:.:0,81,1173,81,1173,1173	./.:.:90:99:52:.:.:0,120,1800,120,1800,1800	./.:.:73:99:47:.:.:0,120,1800,120,1800,1800	./.:.:70:99:54:.:.:0,120,1800,120,1800,1800	./.:.:66:99:43:.:.:0,105,1575,105,1575,1575	./.:.:93:99:52:.:.:0,120,1800,120,1800,1800	./.:.:112:99:52:.:.:0,111,1800,111,1800,1800	./.:.:90:99:53:.:.:0,120,1800,120,1800,1800	./.:.:79:99:54:.:.:0,120,1800,120,1800,1800	./.:.:87:99:52:.:.:0,120,1800,120,1800,1800	./.:.:76:99:53:.:.:0,120,1800,120,1800,1800	./.:.:94:99:51:.:.:0,120,1800,120,1800,1800	./.:.:85:99:54:.:.:0,120,1800,120,1800,1800	./.:.:67:99:47:.:.:0,117,1755,117,1755,1755	./.:.:69:99:53:.:.:0,120,1800,120,1800,1800	./.:.:64:99:50:.:.:0,120,1800,120,1800,1800	.|.:62,26,0:88:99:.:0|1:105562_C_G:900,0,2522,1087,2600,3687:105562:41,21,16,10	.|.:67,35,0:102:99:.:0|1:105562_C_G:1252,0,2698,1454,2803,4257:105562:44,23,26,9	./.:.:70:99:52:.:.:0,120,1800,120,1800,1800	.|.:0,85,0:85:99:.:0|1:105562_C_G:3793,256,0,3793,256,3793:105562:0,0,56,29	./.:.:90:99:51:.:.:0,120,1800,120,1800,1800	./.:.:90:99:49:.:.:0,120,1800,120,1800,1800	./.:.:103:99:52:.:.:0,120,1800,120,1800,1800	.|.:60,30,0:90:99:.:0|1:105562_C_G:1076,0,2426,1256,2516,3773:105562:40,20,23,7	./.:.:84:99:50:.:.:0,120,1800,120,1800,1800	./.:.:73:99:53:.:.:0,120,1800,120,1800,1800	./.:.:83:99:49:.:.:0,120,1800,120,1800,1800	./.:.:85:99:53:.:.:0,120,1800,120,1800,1800	./.:.:75:99:53:.:.:0,120,1800,120,1800,1800	./.:.:117:99:54:.:.:0,120,1800,120,1800,1800	.|.:58,25,0:83:99:.:0|1:105562_C_G:863,0,2360,1038,2435,3473:105562:37,21,12,13	./.:.:117:99:57:.:.:0,120,1800,120,1800,1800	.|.:57,62,0:119:99:.:0|1:105562_C_G:2431,0,2194,2602,2380,4982:105562:45,12,49,13	./.:.:93:99:58:.:.:0,120,1800,120,1800,1800	./.:.:91:99:53:.:.:0,116,1800,116,1800,1800	./.:.:67:99:48:.:.:0,111,1800,111,1800,1800	./.:.:83:99:52:.:.:0,120,1800,120,1800,1800	./.:.:86:99:54:.:.:0,120,1800,120,1800,1800	.|.:47,38,0:85:99:.:0|1:105562_C_G:1454,0,1856,1596,1970,3566:105562:37,10,31,7	./.:.:93:99:52:.:.:0,120,1800,120,1800,1800	./.:.:74:99:51:.:.:0,120,1800,120,1800,1800	.|.:53,36,0:89:99:.:0|1:105562_C_G:1352,0,2117,1512,2225,3737:105562:40,13,28,8	.|.:44,45,0:89:99:.:0|1:105562_C_G:1751,0,1712,1883,1848,3731:105562:34,10,37,8	.|.:20,18,0:38:99:.:0|1:105562_C_G:696,0,786,756,840,1596:105562:15,5,15,3	.|.:61,19,0:80:99:.:0|1:105562_C_G:614,0,2501,798,2558,3356:105562:40,21,15,4	./.:.:57:99:43:.:.:0,102,1530,102,1530,1530	./.:.:62:99:40:.:.:0,108,1620,108,1620,1620	.|.:59,22,0:81:99:.:0|1:105562_C_G:745,0,2408,923,2474,3397:105562:44,15,16,6	./.:.:21:0:14:.:.:0,0,0,0,0,0	./.:.:36:0:33:.:.:0,0,198,0,198,198	./.:.:54:74:54:.:.:0,74,987,74,987,987	./.:.:23:48:23:.:.:0,48,720,48,720,720	./.:.:53:17:53:.:.:0,17,1002,17,1002,1002	./.:.:24:0:23:.:.:0,0,738,0,738,738	./.:.:45:78:45:.:.:0,78,965,78,965,965	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:8:0:8:.:.:0,0,60,0,60,60	./.:.:1:3:1:.:.:0,3,16,3,16,16	./.:.:4:0:4:.:.:0,0,10,0,10,10
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LS990926.1	105641	.	C	T,<NON_REF>	.	.	BaseQRankSum=-3.590e-01;DP=4183;ExcessHet=0.00;MQRankSum=-1.547e+00;RAW_MQandDP=4126480,1151;ReadPosRankSum=-4.440e-01	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:24:60:23:.:.:0,60,900,60,900,900	./.:.:3:9:3:.:.:0,9,66,9,66,66	./.:.:423:99:57:.:.:0,100,1800,100,1800,1800	./.:.:172:99:52:.:.:0,120,1800,120,1800,1800	./.:.:173:8:173:.:.:0,8,5932,8,5932,5932	./.:.:189:0:164:.:.:0,0,4670,0,4670,4670	./.:.:244:0:181:.:.:0,0,5028,0,5028,5028	./.:.:18:12:18:.:.:0,12,604,12,604,604	./.:.:13:0:13:.:.:0,0,67,0,67,67	./.:.:8:23:8:.:.:0,23,117,23,117,117	./.:.:4:0:4:.:.:0,0,0,0,0,0	./.:.:86:99:52:.:.:0,120,1800,120,1800,1800	./.:.:136:99:56:.:.:0,120,1800,120,1800,1800	./.:.:75:99:56:.:.:0,120,1800,120,1800,1800	./.:.:94:99:52:.:.:0,120,1800,120,1800,1800	./.:.:57:99:36:.:.:0,99,1485,99,1485,1485	./.:.:90:99:52:.:.:0,120,1800,120,1800,1800	./.:.:73:99:47:.:.:0,120,1800,120,1800,1800	./.:.:70:99:54:.:.:0,120,1800,120,1800,1800	./.:.:66:99:43:.:.:0,105,1575,105,1575,1575	./.:.:93:99:52:.:.:0,120,1800,120,1800,1800	./.:.:112:99:52:.:.:0,111,1800,111,1800,1800	./.:.:90:99:53:.:.:0,120,1800,120,1800,1800	./.:.:79:99:54:.:.:0,120,1800,120,1800,1800	./.:.:87:99:52:.:.:0,120,1800,120,1800,1800	./.:.:76:99:53:.:.:0,120,1800,120,1800,1800	./.:.:94:99:51:.:.:0,120,1800,120,1800,1800	./.:.:85:99:54:.:.:0,120,1800,120,1800,1800	./.:.:67:99:47:.:.:0,117,1755,117,1755,1755	./.:.:69:99:53:.:.:0,120,1800,120,1800,1800	./.:.:64:99:50:.:.:0,120,1800,120,1800,1800	.|.:69,28,0:97:99:.:0|1:105625_C_T:961,0,2805,1169,2889,4058:105625:45,24,20,8	.|.:73,36,0:109:99:.:0|1:105625_C_T:1292,0,2957,1512,3065,4577:105625:59,14,26,10	./.:.:70:99:52:.:.:0,120,1800,120,1800,1800	.|.:0,90,0:90:99:.:0|1:105625_C_T:4050,271,0,4050,271,4050:105625:0,0,76,14	./.:.:90:99:51:.:.:0,120,1800,120,1800,1800	./.:.:90:99:49:.:.:0,120,1800,120,1800,1800	./.:.:103:99:52:.:.:0,120,1800,120,1800,1800	.|.:69,28,0:97:99:.:0|1:105625_C_T:968,0,2813,1176,2897,4073:105625:52,17,21,7	./.:.:84:99:50:.:.:0,120,1800,120,1800,1800	./.:.:73:99:53:.:.:0,120,1800,120,1800,1800	./.:.:83:99:49:.:.:0,120,1800,120,1800,1800	./.:.:85:99:53:.:.:0,120,1800,120,1800,1800	./.:.:75:99:53:.:.:0,120,1800,120,1800,1800	./.:.:117:99:54:.:.:0,120,1800,120,1800,1800	.|.:61,31,0:92:99:.:0|1:105625_C_T:1118,0,2460,1302,2553,3855:105625:45,16,13,18	./.:.:117:99:57:.:.:0,120,1800,120,1800,1800	.|.:60,70,0:130:99:.:0|1:105625_C_T:2759,0,2309,2939,2519,5459:105625:56,4,58,12	./.:.:93:99:58:.:.:0,120,1800,120,1800,1800	./.:.:91:99:53:.:.:0,116,1800,116,1800,1800	./.:.:67:99:48:.:.:0,111,1800,111,1800,1800	./.:.:83:99:52:.:.:0,120,1800,120,1800,1800	./.:.:86:99:54:.:.:0,120,1800,120,1800,1800	.|.:57,33,0:90:99:.:0|1:105625_C_T:1214,0,2294,1386,2393,3779:105625:53,4,29,4	./.:.:93:99:52:.:.:0,120,1800,120,1800,1800	./.:.:74:99:51:.:.:0,120,1800,120,1800,1800	.|.:62,37,0:99:99:.:0|1:105625_C_T:1367,0,2492,1554,2603,4157:105625:56,6,33,4	.|.:54,45,0:99:99:.:0|1:105625_C_T:1723,0,2132,1885,2267,4153:105625:48,6,39,6	.|.:25,19,0:44:99:.:0|1:105625_C_T:723,0,993,798,1050,1848:105625:22,3,15,4	.|.:76,24,0:100:99:.:0|1:105625_C_T:779,0,3119,1008,3191,4199:105625:68,8,22,2	./.:.:57:99:43:.:.:0,102,1530,102,1530,1530	./.:.:62:99:40:.:.:0,108,1620,108,1620,1620	.|.:65,28,0:93:99:.:0|1:105625_C_T:976,0,2645,1171,2729,3901:105625:56,9,22,6	./.:.:27:66:27:.:.:0,66,418,66,418,418	./.:.:39:99:39:.:.:0,102,1097,102,1097,1097	./.:.:54:99:54:.:.:0,110,1294,110,1294,1294	./.:.:20:23:20:.:.:0,23,661,23,661,661	./.:.:54:22:54:.:.:0,22,1205,22,1205,1205	./.:.:37:70:37:.:.:0,70,1146,70,1146,1146	./.:.:47:0:47:.:.:0,0,0,0,0,0	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:9:7:9:.:.:0,7,196,7,196,196	./.:.:1:3:1:.:.:0,3,12,3,12,12	./.:.:5:0:5:.:.:0,0,50,0,50,50
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LS990926.1	105808	.	T	C,<NON_REF>	.	.	DP=5837;ExcessHet=0.00;RAW_MQandDP=126000,35	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:37:99:34:.:.:0,102,1012,102,1012,1012	./.:.:3:9:3:.:.:0,9,74,9,74,74	./.:.:523:99:417:.:.:0,120,1800,120,1800,1800	./.:.:244:99:196:.:.:0,120,1800,120,1800,1800	./.:.:160:0:149:.:.:0,0,3871,0,3871,3871	./.:.:183:0:164:.:.:0,0,0,0,0,0	./.:.:220:0:178:.:.:0,0,4708,0,4708,4708	./.:.:19:0:17:.:.:0,0,496,0,496,496	./.:.:14:40:14:.:.:0,40,208,40,208,208	./.:.:8:23:8:.:.:0,23,130,23,130,130	./.:.:4:12:4:.:.:0,12,64,12,64,64	./.:.:107:99:91:.:.:0,120,1800,120,1800,1800	./.:.:185:99:139:.:.:0,120,1800,120,1800,1800	./.:.:106:99:80:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:60:99:46:.:.:0,111,1665,111,1665,1665	./.:.:121:99:97:.:.:0,120,1800,120,1800,1800	./.:.:110:99:80:.:.:0,120,1800,120,1800,1800	./.:.:106:99:89:.:.:0,120,1800,120,1800,1800	./.:.:101:99:51:.:.:0,120,1800,120,1800,1800	./.:.:121:99:101:.:.:0,120,1800,120,1800,1800	./.:.:160:99:108:.:.:0,120,1800,120,1800,1800	./.:.:125:99:102:.:.:0,120,1800,120,1800,1800	./.:.:110:99:86:.:.:0,120,1800,120,1800,1800	./.:.:111:99:75:.:.:0,120,1800,120,1800,1800	./.:.:92:99:86:.:.:0,120,1800,120,1800,1800	./.:.:138:99:91:.:.:0,120,1800,120,1800,1800	./.:.:98:99:84:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:111:99:93:.:.:0,120,1800,120,1800,1800	./.:.:83:99:64:.:.:0,120,1800,120,1800,1800	./.:.:104:99:95:.:.:0,120,1800,120,1800,1800	./.:.:110:99:95:.:.:0,120,1800,120,1800,1800	./.:.:94:99:76:.:.:0,120,1800,120,1800,1800	./.:.:97:99:75:.:.:0,120,1800,120,1800,1800	./.:.:121:99:103:.:.:0,120,1800,120,1800,1800	./.:.:126:99:93:.:.:0,120,1800,120,1800,1800	./.:.:143:99:105:.:.:0,120,1800,120,1800,1800	./.:.:98:99:88:.:.:0,120,1800,120,1800,1800	./.:.:112:99:88:.:.:0,120,1800,120,1800,1800	./.:.:90:99:74:.:.:0,120,1800,120,1800,1800	./.:.:105:99:90:.:.:0,120,1800,120,1800,1800	./.:.:89:99:80:.:.:0,120,1800,120,1800,1800	./.:.:121:99:81:.:.:0,120,1800,120,1800,1800	./.:.:142:99:114:.:.:0,120,1800,120,1800,1800	./.:.:103:99:98:.:.:0,120,1800,120,1800,1800	./.:.:162:99:135:.:.:0,120,1800,120,1800,1800	./.:.:107:99:82:.:.:0,120,1800,120,1800,1800	./.:.:119:99:88:.:.:0,120,1800,120,1800,1800	./.:.:115:99:102:.:.:0,120,1800,120,1800,1800	./.:.:88:99:82:.:.:0,120,1800,120,1800,1800	./.:.:113:99:84:.:.:0,120,1800,120,1800,1800	./.:.:134:99:104:.:.:0,120,1800,120,1800,1800	./.:.:61:99:54:.:.:0,117,1755,117,1755,1755	./.:.:123:99:95:.:.:0,120,1800,120,1800,1800	./.:.:105:99:82:.:.:0,120,1800,120,1800,1800	./.:.:95:99:91:.:.:0,120,1800,120,1800,1800	./.:.:82:99:74:.:.:0,120,1800,120,1800,1800	./.:.:22:45:22:.:.:0,45,675,45,675,675	./.:.:93:99:83:.:.:0,120,1800,120,1800,1800	./.:.:81:99:53:.:.:0,120,1800,120,1800,1800	./.:.:85:99:51:.:.:0,120,1800,120,1800,1800	./.:.:78:99:73:.:.:0,120,1800,120,1800,1800	./.:.:20:0:13:.:.:0,0,0,0,0,0	./.:.:40:0:32:.:.:0,0,303,0,303,303	./.:.:44:0:42:.:.:0,0,381,0,381,381	./.:.:39:93:38:.:.:0,93,1395,93,1395,1395	./.:.:48:0:41:.:.:0,0,524,0,524,524	.|.:0,34,0:34:99:.:0|1:105808_T_C:1477,102,0,1477,102,1477:105808:0,0,18,16	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:8:0:7:.:.:0,0,0,0,0,0	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:5:15:5:.:.:0,15,108,15,108,108
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LS990926.1	105898	.	ATTTT	ATT,AT,A,ATTT,ATTTTT,<NON_REF>	.	.	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LS990926.1	105899	.	T	*,<NON_REF>	.	.	DP=5906	GT:DP:GQ:MIN_DP:PL	./.:33:90:33:0,90,1350,90,1350,1350	./.:3:0:3:0,0,0,0,0,0	./.:523:99:417:0,120,1800,120,1800,1800	./.:244:99:196:0,120,1800,120,1800,1800	./.:138:60:138:0,60,4915,60,4915,4915	./.:204:0:195:0,0,5807,0,5807,5807	./.:203:0:200:0,0,5835,0,5835,5835	./.:19:15:19:0,15,698,15,698,698	./.:15:0:15:0,0,0,0,0,0	./.:7:0:7:0,0,0,0,0,0	./.:4:0:4:0,0,0,0,0,0	./.:111:99:81:0,120,1800,120,1800,1800	./.:185:99:139:0,120,1800,120,1800,1800	./.:106:99:80:0,120,1800,120,1800,1800	./.:134:99:96:0,120,1800,120,1800,1800	./.:60:99:46:0,111,1665,111,1665,1665	./.:121:99:97:0,120,1800,120,1800,1800	./.:110:99:80:0,120,1800,120,1800,1800	./.:106:99:89:0,120,1800,120,1800,1800	./.:101:99:51:0,120,1800,120,1800,1800	./.:121:99:101:0,120,1800,120,1800,1800	./.:160:99:108:0,120,1800,120,1800,1800	./.:125:99:102:0,120,1800,120,1800,1800	./.:110:99:86:0,120,1800,120,1800,1800	./.:111:99:75:0,120,1800,120,1800,1800	./.:104:99:83:0,120,1800,120,1800,1800	./.:138:99:91:0,120,1800,120,1800,1800	./.:98:99:84:0,120,1800,120,1800,1800	./.:92:99:71:0,120,1800,120,1800,1800	./.:111:99:93:0,120,1800,120,1800,1800	./.:83:99:64:0,120,1800,120,1800,1800	./.:119:99:85:0,120,1800,120,1800,1800	./.:112:99:98:0,120,1800,120,1800,1800	./.:94:99:76:0,120,1800,120,1800,1800	./.:97:99:75:0,120,1800,120,1800,1800	./.:121:99:103:0,120,1800,120,1800,1800	./.:126:99:93:0,120,1800,120,1800,1800	./.:143:99:105:0,120,1800,120,1800,1800	./.:109:99:88:0,120,1800,120,1800,1800	./.:112:99:88:0,120,1800,120,1800,1800	./.:90:99:74:0,120,1800,120,1800,1800	./.:105:99:90:0,120,1800,120,1800,1800	./.:124:99:94:0,120,1800,120,1800,1800	./.:121:99:81:0,120,1800,120,1800,1800	./.:142:99:114:0,120,1800,120,1800,1800	./.:100:99:65:0,120,1800,120,1800,1800	./.:162:99:135:0,120,1800,120,1800,1800	./.:153:99:81:0,120,1800,120,1800,1800	./.:119:99:88:0,120,1800,120,1800,1800	./.:115:99:102:0,120,1800,120,1800,1800	./.:85:99:71:0,120,1800,120,1800,1800	./.:113:99:84:0,120,1800,120,1800,1800	./.:134:99:104:0,120,1800,120,1800,1800	./.:108:99:64:0,120,1800,120,1800,1800	./.:123:99:95:0,120,1800,120,1800,1800	./.:105:99:82:0,120,1800,120,1800,1800	./.:124:99:94:0,120,1800,120,1800,1800	./.:112:99:73:0,120,1800,120,1800,1800	./.:41:89:41:0,89,1672,89,1672,1672	./.:113:99:68:0,120,1800,120,1800,1800	./.:81:99:53:0,120,1800,120,1800,1800	./.:85:99:51:0,120,1800,120,1800,1800	./.:116:99:85:0,120,1800,120,1800,1800	./.:30:0:27:0,0,0,0,0,0	./.:45:0:43:0,0,0,0,0,0	./.:59:0:58:0,0,0,0,0,0	./.:30:75:29:0,75,1125,75,1125,1125	./.:57:0:57:0,0,0,0,0,0	./.:31:75:31:0,75,1125,75,1125,1125	./.:.:.:.:0,0,0,0,0,0	./.:0:0:0:0,0,0,0,0,0	./.:11:0:11:0,0,2,0,2,2	./.:1:0:1:0,0,0,0,0,0	./.:5:0:5:0,0,17,0,17,17
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LS990926.1	106244	.	A	*,<NON_REF>	.	.	DP=5873	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:38:96:37:.:.:0,96,1440,96,1440,1440	./.:.:3:9:3:.:.:0,9,77,9,77,77	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:247:0:222:.:.:0,0,0,0,0,0	.|.:21,1,0:22:21:.:0|1:106242_CTA_C:0,21,900,63,903,945:106242:9,12,1,0	./.:.:15:25:15:.:.:0,25,179,25,179,179	./.:.:7:0:7:.:.:0,0,52,0,52,52	./.:.:4:12:4:.:.:0,12,65,12,65,65	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:32:87:31:.:.:0,87,1305,87,1305,1305	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:23:29:23:.:.:0,29,247,29,247,247	./.:.:39:64:39:.:.:0,64,634,64,634,634	./.:.:57:99:47:.:.:0,120,1800,120,1800,1800	./.:.:42:96:42:.:.:0,96,1440,96,1440,1440	./.:.:53:99:48:.:.:0,108,836,108,836,836	./.:.:41:81:39:.:.:0,81,1215,81,1215,1215	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:8:23:8:.:.:0,23,157,23,157,157	./.:.:1:3:1:.:.:0,3,11,3,11,11	./.:.:6:18:6:.:.:0,18,122,18,122,122
LS990926.1	106245	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:38:96:37:0,96,1440	./.:3:9:3:0,9,77	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:247:0:222:0,0,0	./.:21:57:21:0,57,855	./.:15:43:15:0,43,221	./.:7:20:7:0,20,102	./.:4:12:4:0,12,65	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:34:96:34:0,96,1440	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:14:39:14:0,39,186	./.:39:51:39:0,51,606	./.:57:99:47:0,120,1800	./.:42:96:42:0,96,1440	./.:53:99:48:0,108,836	./.:41:81:39:0,81,1215	./.:1:3:1:0,3,13	./.:0:0:0:0,0,0	./.:8:23:8:0,23,157	./.:1:3:1:0,3,11	./.:5:15:5:0,15,103
LS990926.1	106246	.	G	GTCTCTT,<NON_REF>	.	.	BaseQRankSum=0.251;DP=5881;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=104400,29;ReadPosRankSum=-4.750e-01	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:38:96:37:.:.:0,96,1440,96,1440,1440	./.:.:3:9:3:.:.:0,9,77,9,77,77	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:247:0:222:.:.:0,0,0,0,0,0	.|.:21,1,0:22:21:.:0|1:106242_CTA_C:0,21,900,63,903,945:106242:9,12,1,0	./.:.:15:42:15:.:.:0,42,630,42,630,630	./.:.:7:20:7:.:.:0,20,102,20,102,102	./.:.:4:12:4:.:.:0,12,65,12,65,65	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:24:67:24:.:.:0,67,328,67,328,328	./.:.:42:99:41:.:.:0,120,901,120,901,901	./.:.:57:99:47:.:.:0,120,1800,120,1800,1800	./.:.:45:99:44:.:.:0,102,1530,102,1530,1530	./.:.:53:99:48:.:.:0,108,836,108,836,836	./.:.:41:81:39:.:.:0,81,1215,81,1215,1215	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:8:23:8:.:.:0,23,157,23,157,157	./.:.:1:3:1:.:.:0,3,11,3,11,11	./.:.:6:18:6:.:.:0,18,139,18,139,139
LS990926.1	106247	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:38:96:37:0,96,1440	./.:3:9:3:0,9,77	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:247:0:222:0,0,0	./.:22:54:22:0,54,810	./.:15:8:15:0,8,169	./.:7:20:7:0,20,102	./.:4:12:4:0,12,65	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:48:99:36:0,99,1485	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:27:6:27:0,6,269	./.:42:99:41:0,120,901	./.:57:99:47:0,120,1800	./.:45:99:44:0,102,1530	./.:53:99:48:0,108,836	./.:37:78:37:0,78,1170	./.:1:3:1:0,3,13	./.:0:0:0:0,0,0	./.:8:21:8:0,21,315	./.:1:3:1:0,3,11	./.:6:18:6:0,18,139
LS990926.1	106248	.	T	A,<NON_REF>	.	.	BaseQRankSum=0.712;DP=5880;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=144000,40;ReadPosRankSum=0.820	GT:AD:DP:GQ:MIN_DP:PL:SB	./.:.:38:96:37:0,96,1440,96,1440,1440	./.:.:3:9:3:0,9,77,9,77,77	./.:.:456:99:401:0,120,1800,120,1800,1800	./.:.:232:99:201:0,120,1800,120,1800,1800	./.:.:194:0:180:0,0,5016,0,5016,5016	./.:.:219:0:182:0,0,0,0,0,0	./.:.:247:0:222:0,0,0,0,0,0	./.:.:22:54:22:0,54,810,54,810,810	./.:.:15:8:15:0,8,169,8,169,169	./.:.:7:18:7:0,18,270,18,270,270	./.:.:4:9:4:0,9,135,9,135,135	./.:.:86:99:76:0,120,1800,120,1800,1800	./.:.:171:99:134:0,120,1800,120,1800,1800	./.:.:107:99:68:0,120,1800,120,1800,1800	./.:.:115:99:83:0,120,1800,120,1800,1800	./.:.:57:99:40:0,102,1530,102,1530,1530	./.:.:114:99:81:0,120,1800,120,1800,1800	./.:.:104:99:75:0,120,1800,120,1800,1800	./.:.:109:99:89:0,120,1800,120,1800,1800	./.:.:117:99:89:0,120,1800,120,1800,1800	./.:.:106:99:90:0,120,1800,120,1800,1800	./.:.:161:99:119:0,120,1800,120,1800,1800	./.:.:132:99:92:0,120,1800,120,1800,1800	./.:.:102:99:78:0,120,1800,120,1800,1800	./.:.:104:99:77:0,120,1800,120,1800,1800	./.:.:98:99:79:0,120,1800,120,1800,1800	./.:.:134:99:85:0,120,1800,120,1800,1800	./.:.:112:99:83:0,120,1800,120,1800,1800	./.:.:92:99:71:0,120,1800,120,1800,1800	./.:.:123:99:77:0,120,1800,120,1800,1800	./.:.:86:99:62:0,120,1800,120,1800,1800	./.:.:108:99:89:0,120,1800,120,1800,1800	./.:.:108:99:98:0,120,1800,120,1800,1800	./.:.:89:99:72:0,120,1800,120,1800,1800	./.:.:95:99:78:0,120,1800,120,1800,1800	./.:.:116:99:75:0,120,1800,120,1800,1800	./.:.:126:99:92:0,120,1800,120,1800,1800	./.:.:140:99:113:0,120,1800,120,1800,1800	./.:.:101:99:94:0,120,1800,120,1800,1800	./.:.:117:99:87:0,120,1800,120,1800,1800	./.:.:96:99:72:0,120,1800,120,1800,1800	./.:.:108:99:86:0,120,1800,120,1800,1800	./.:.:134:99:96:0,120,1800,120,1800,1800	./.:.:121:99:98:0,120,1800,120,1800,1800	./.:.:153:99:113:0,120,1800,120,1800,1800	./.:.:68:99:59:0,120,1800,120,1800,1800	./.:.:137:99:112:0,120,1800,120,1800,1800	./.:.:126:99:97:0,120,1800,120,1800,1800	./.:.:109:99:84:0,120,1800,120,1800,1800	./.:.:120:99:91:0,120,1800,120,1800,1800	./.:.:92:99:80:0,120,1800,120,1800,1800	./.:.:113:99:79:0,120,1800,120,1800,1800	./.:.:132:99:98:0,113,1800,113,1800,1800	./.:.:105:99:79:0,120,1800,120,1800,1800	./.:.:114:99:98:0,120,1800,120,1800,1800	./.:.:98:99:68:0,120,1800,120,1800,1800	./.:.:111:99:92:0,120,1800,120,1800,1800	./.:.:110:99:87:0,120,1800,120,1800,1800	./.:.:48:99:36:0,99,1485,99,1485,1485	./.:.:86:99:73:0,120,1800,120,1800,1800	./.:.:80:99:47:0,111,1606,111,1606,1606	./.:.:83:99:50:0,120,1800,120,1800,1800	./.:.:120:99:100:0,120,1800,120,1800,1800	./.:.:29:0:25:0,0,224,0,224,224	./.:.:44:59:44:0,59,796,59,796,796	./.:.:57:99:47:0,120,1800,120,1800,1800	./.:.:45:99:44:0,102,1530,102,1530,1530	./.:.:53:99:48:0,108,836,108,836,836	./.:35,1,0:36:67:.:0,67,1229,105,1232,1270:14,21,0,1	./.:.:1:3:1:0,3,13,3,13,13	./.:.:0:0:0:0,0,0,0,0,0	./.:.:9:24:9:0,24,360,24,360,360	./.:.:1:3:1:0,3,11,3,11,11	./.:.:6:12:6:0,12,180,12,180,180
LS990926.1	106249	.	A	C,<NON_REF>	.	.	BaseQRankSum=0.822;DP=5897;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=140400,39;ReadPosRankSum=1.74	GT:AD:DP:GQ:MIN_DP:PL:SB	./.:.:38:99:36:0,99,1485,99,1485,1485	./.:.:3:9:3:0,9,77,9,77,77	./.:.:456:99:401:0,120,1800,120,1800,1800	./.:.:232:99:201:0,120,1800,120,1800,1800	./.:.:194:0:180:0,0,5016,0,5016,5016	./.:.:219:0:182:0,0,0,0,0,0	./.:.:247:0:222:0,0,0,0,0,0	./.:.:23:57:23:0,57,855,57,855,855	./.:.:15:0:15:0,0,134,0,134,134	./.:.:7:20:7:0,20,109,20,109,109	./.:.:4:12:4:0,12,67,12,67,67	./.:.:86:99:76:0,120,1800,120,1800,1800	./.:.:171:99:134:0,120,1800,120,1800,1800	./.:.:107:99:68:0,120,1800,120,1800,1800	./.:.:115:99:83:0,120,1800,120,1800,1800	./.:.:57:99:40:0,102,1530,102,1530,1530	./.:.:114:99:81:0,120,1800,120,1800,1800	./.:.:104:99:75:0,120,1800,120,1800,1800	./.:.:109:99:89:0,120,1800,120,1800,1800	./.:.:117:99:89:0,120,1800,120,1800,1800	./.:.:106:99:90:0,120,1800,120,1800,1800	./.:.:161:99:119:0,120,1800,120,1800,1800	./.:.:132:99:92:0,120,1800,120,1800,1800	./.:.:102:99:78:0,120,1800,120,1800,1800	./.:.:104:99:77:0,120,1800,120,1800,1800	./.:.:98:99:79:0,120,1800,120,1800,1800	./.:.:134:99:85:0,120,1800,120,1800,1800	./.:.:112:99:83:0,120,1800,120,1800,1800	./.:.:92:99:71:0,120,1800,120,1800,1800	./.:.:123:99:77:0,120,1800,120,1800,1800	./.:.:86:99:62:0,120,1800,120,1800,1800	./.:.:108:99:89:0,120,1800,120,1800,1800	./.:.:108:99:98:0,120,1800,120,1800,1800	./.:.:89:99:72:0,120,1800,120,1800,1800	./.:.:95:99:78:0,120,1800,120,1800,1800	./.:.:116:99:75:0,120,1800,120,1800,1800	./.:.:126:99:92:0,120,1800,120,1800,1800	./.:.:140:99:113:0,120,1800,120,1800,1800	./.:.:101:99:94:0,120,1800,120,1800,1800	./.:.:117:99:87:0,120,1800,120,1800,1800	./.:.:96:99:72:0,120,1800,120,1800,1800	./.:.:108:99:86:0,120,1800,120,1800,1800	./.:.:134:99:96:0,120,1800,120,1800,1800	./.:.:121:99:98:0,120,1800,120,1800,1800	./.:.:153:99:113:0,120,1800,120,1800,1800	./.:.:68:99:59:0,120,1800,120,1800,1800	./.:.:137:99:112:0,120,1800,120,1800,1800	./.:.:126:99:97:0,120,1800,120,1800,1800	./.:.:109:99:84:0,120,1800,120,1800,1800	./.:.:120:99:91:0,120,1800,120,1800,1800	./.:.:92:99:80:0,120,1800,120,1800,1800	./.:.:113:99:79:0,120,1800,120,1800,1800	./.:.:132:99:98:0,113,1800,113,1800,1800	./.:.:105:99:79:0,120,1800,120,1800,1800	./.:.:114:99:98:0,120,1800,120,1800,1800	./.:.:98:99:68:0,120,1800,120,1800,1800	./.:.:111:99:92:0,120,1800,120,1800,1800	./.:.:110:99:87:0,120,1800,120,1800,1800	./.:.:48:99:36:0,99,1485,99,1485,1485	./.:.:86:99:73:0,120,1800,120,1800,1800	./.:.:80:99:47:0,111,1606,111,1606,1606	./.:.:83:99:50:0,120,1800,120,1800,1800	./.:.:120:99:100:0,120,1800,120,1800,1800	./.:.:29:0:25:0,0,224,0,224,224	./.:.:46:0:46:0,0,568,0,568,568	./.:.:61:7:61:0,7,1163,7,1163,1163	./.:.:37:30:37:0,30,1073,30,1073,1073	./.:.:57:0:57:0,0,1033,0,1033,1033	./.:33,1,0:34:61:.:0,61,1155,99,1158,1196:12,21,1,0	./.:.:1:3:1:0,3,13,3,13,13	./.:.:0:0:0:0,0,0,0,0,0	./.:.:9:0:9:0,0,126,0,126,126	./.:.:1:3:1:0,3,11,3,11,11	./.:.:6:18:6:0,18,152,18,152,152
LS990926.1	106250	.	A	C,<NON_REF>	.	.	BaseQRankSum=1.37;DP=5885;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=111600,31;ReadPosRankSum=0.076	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:38:99:36:.:.:0,99,1485,99,1485,1485	./.:.:3:9:3:.:.:0,9,77,9,77,77	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:247:0:222:.:.:0,0,0,0,0,0	.|.:22,1,0:23:24:.:0|1:106242_CTA_C:0,24,945,66,948,990:106242:10,12,1,0	./.:.:15:0:15:.:.:0,0,134,0,134,134	./.:.:7:20:7:.:.:0,20,109,20,109,109	./.:.:4:12:4:.:.:0,12,67,12,67,67	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:30:54:30:.:.:0,54,565,54,565,565	./.:.:46:68:46:.:.:0,68,1321,68,1321,1321	./.:.:58:99:45:.:.:0,120,1800,120,1800,1800	./.:.:41:90:41:.:.:0,90,1350,90,1350,1350	./.:.:54:99:48:.:.:0,104,807,104,807,807	./.:.:36:84:35:.:.:0,84,1260,84,1260,1260	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:9:27:9:.:.:0,27,256,27,256,256	./.:.:1:3:1:.:.:0,3,11,3,11,11	./.:.:6:18:6:.:.:0,18,152,18,152,152
LS990926.1	106251	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:38:99:36:0,99,1485	./.:3:9:3:0,9,77	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:247:0:222:0,0,0	./.:21:57:21:0,57,855	./.:15:0:15:0,0,134	./.:7:20:7:0,20,109	./.:4:12:4:0,12,67	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:48:99:36:0,99,1485	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:34:27:34:0,27,396	./.:45:99:45:0,99,1082	./.:58:99:45:0,120,1800	./.:41:90:41:0,90,1350	./.:54:99:48:0,104,807	./.:36:84:35:0,84,1260	./.:1:3:1:0,3,13	./.:0:0:0:0,0,0	./.:9:13:9:0,13,174	./.:1:3:1:0,3,11	./.:5:15:5:0,15,107
LS990926.1	106252	.	G	C,<NON_REF>	.	.	BaseQRankSum=1.34;DP=5866;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=111600,31;ReadPosRankSum=0.00	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:38:99:36:.:.:0,99,1485,99,1485,1485	./.:.:3:6:3:.:.:0,6,90,6,90,90	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:247:0:222:.:.:0,0,0,0,0,0	.|.:22,1,0:23:24:.:0|1:106242_CTA_C:0,24,945,66,948,990:106242:10,12,1,0	./.:.:15:8:15:.:.:0,8,175,8,175,175	./.:.:7:18:7:.:.:0,18,270,18,270,270	./.:.:4:11:4:.:.:0,11,59,11,59,59	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:26:2:26:.:.:0,2,216,2,216,216	./.:.:44:47:44:.:.:0,47,745,47,745,745	./.:.:58:99:45:.:.:0,120,1800,120,1800,1800	./.:.:33:81:31:.:.:0,81,1215,81,1215,1215	./.:.:54:99:48:.:.:0,104,807,104,807,807	./.:.:36:90:36:.:.:0,90,1350,90,1350,1350	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:9:26:9:.:.:0,26,151,26,151,151	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:3:9:3:.:.:0,9,67,9,67,67
LS990926.1	106253	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:35:86:35:0,86,1049	./.:3:0:3:0,0,8	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:247:0:222:0,0,0	./.:21:57:21:0,57,855	./.:15:8:15:0,8,175	./.:7:0:7:0,0,53	./.:4:12:4:0,12,66	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:48:99:36:0,99,1485	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:31:0:26:0,0,0	./.:45:51:45:0,51,999	./.:56:0:55:0,0,811	./.:33:81:31:0,81,1215	./.:57:86:57:0,86,1072	./.:36:87:36:0,87,1305	./.:1:3:1:0,3,13	./.:0:0:0:0,0,0	./.:9:26:9:0,26,151	./.:0:0:0:0,0,0	./.:5:15:5:0,15,119
LS990926.1	106254	.	A	T,<NON_REF>	.	.	BaseQRankSum=1.15;DP=5879;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=108000,30;ReadPosRankSum=0.579	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:32:96:32:.:.:0,96,1013,96,1013,1013	./.:.:3:0:3:.:.:0,0,8,0,8,8	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:247:0:222:.:.:0,0,0,0,0,0	.|.:21,1,0:22:21:.:0|1:106242_CTA_C:0,21,900,63,903,945:106242:10,11,1,0	./.:.:15:0:15:.:.:0,0,52,0,52,52	./.:.:7:0:7:.:.:0,0,53,0,53,53	./.:.:4:11:4:.:.:0,11,60,11,60,60	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:31:0:26:.:.:0,0,0,0,0,0	./.:.:45:52:45:.:.:0,52,977,52,977,977	./.:.:56:0:55:.:.:0,0,811,0,811,811	./.:.:33:81:31:.:.:0,81,1215,81,1215,1215	./.:.:54:90:54:.:.:0,90,1097,90,1097,1097	./.:.:34:61:34:.:.:0,61,1160,61,1160,1160	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:8:24:8:.:.:0,24,194,24,194,194	./.:.:1:3:1:.:.:0,3,12,3,12,12	./.:.:6:18:6:.:.:0,18,129,18,129,129
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LS990926.1	106256	.	A	T,<NON_REF>	.	.	BaseQRankSum=1.14;DP=5885;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=108000,30;ReadPosRankSum=0.416	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:33:99:33:.:.:0,99,1055,99,1055,1055	./.:.:3:9:3:.:.:0,9,69,9,69,69	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:247:0:222:.:.:0,0,0,0,0,0	.|.:22,1,0:23:24:.:0|1:106242_CTA_C:0,24,945,66,948,990:106242:10,12,1,0	./.:.:15:30:15:.:.:0,30,214,30,214,214	./.:.:7:20:7:.:.:0,20,100,20,100,100	./.:.:4:11:4:.:.:0,11,60,11,60,60	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:32:22:32:.:.:0,22,405,22,405,405	./.:.:46:99:45:.:.:0,109,946,109,946,946	./.:.:60:99:53:.:.:0,109,1392,109,1392,1392	./.:.:33:81:31:.:.:0,81,1215,81,1215,1215	./.:.:56:99:55:.:.:0,120,1800,120,1800,1800	./.:.:34:81:34:.:.:0,81,1215,81,1215,1215	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:9:27:9:.:.:0,27,210,27,210,210	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:6:18:6:.:.:0,18,129,18,129,129
LS990926.1	106257	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:33:87:33:0,87,1305	./.:3:9:3:0,9,69	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:263:17:263:0,17,8961	./.:21:60:21:0,60,900	./.:15:42:15:0,42,630	./.:7:20:7:0,20,100	./.:4:12:4:0,12,66	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:48:99:36:0,99,1485	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:23:0:22:0,0,149	./.:46:99:45:0,109,946	./.:60:99:53:0,109,1392	./.:33:81:31:0,81,1215	./.:56:99:55:0,120,1800	./.:32:75:29:0,75,1125	./.:1:3:1:0,3,13	./.:0:0:0:0,0,0	./.:9:27:9:0,27,210	./.:0:0:0:0,0,0	./.:6:18:6:0,18,129
LS990926.1	106258	.	C	G,<NON_REF>	.	.	BaseQRankSum=1.13;DP=5913;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=108000,30;ReadPosRankSum=0.415	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:35:90:34:.:.:0,90,1350,90,1350,1350	./.:.:3:9:3:.:.:0,9,69,9,69,69	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:267:0:265:.:.:0,0,7446,0,7446,7446	.|.:22,1,0:23:24:.:0|1:106242_CTA_C:0,24,945,66,948,990:106242:10,12,1,0	./.:.:15:42:15:.:.:0,42,630,42,630,630	./.:.:7:20:7:.:.:0,20,100,20,100,100	./.:.:4:11:4:.:.:0,11,56,11,56,56	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:23:0:22:.:.:0,0,149,0,149,149	./.:.:44:73:44:.:.:0,73,832,73,832,832	./.:.:60:99:53:.:.:0,109,1392,109,1392,1392	./.:.:33:81:31:.:.:0,81,1215,81,1215,1215	./.:.:56:99:55:.:.:0,120,1800,120,1800,1800	./.:.:32:75:29:.:.:0,75,1125,75,1125,1125	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:9:11:9:.:.:0,11,186,11,186,186	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:6:18:6:.:.:0,18,129,18,129,129
LS990926.1	106259	.	A	ATGTGT,<NON_REF>	.	.	BaseQRankSum=1.26;DP=5925;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=104400,29;ReadPosRankSum=0.414	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:35:90:34:.:.:0,90,1350,90,1350,1350	./.:.:3:9:3:.:.:0,9,69,9,69,69	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:267:0:265:.:.:0,0,7446,0,7446,7446	.|.:21,1,0:22:21:.:0|1:106242_CTA_C:0,21,900,63,903,945:106242:10,11,1,0	./.:.:15:42:15:.:.:0,42,630,42,630,630	./.:.:7:20:7:.:.:0,20,100,20,100,100	./.:.:4:11:4:.:.:0,11,56,11,56,56	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:34:83:34:.:.:0,83,494,83,494,494	./.:.:46:99:46:.:.:0,102,1139,102,1139,1139	./.:.:60:99:53:.:.:0,109,1392,109,1392,1392	./.:.:33:81:31:.:.:0,81,1215,81,1215,1215	./.:.:56:99:55:.:.:0,120,1800,120,1800,1800	./.:.:32:75:29:.:.:0,75,1125,75,1125,1125	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:8:24:8:.:.:0,24,210,24,210,210	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:6:18:6:.:.:0,18,129,18,129,129
LS990926.1	106260	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:35:90:34:0,90,1350	./.:3:9:3:0,9,69	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:267:0:265:0,0,7446	./.:22:63:22:0,63,945	./.:15:42:15:0,42,630	./.:7:20:7:0,20,100	./.:4:11:4:0,11,56	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:48:99:36:0,99,1485	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:27:31:27:0,31,336	./.:45:76:45:0,76,1010	./.:60:99:53:0,109,1392	./.:33:81:31:0,81,1215	./.:56:99:55:0,120,1800	./.:32:75:29:0,75,1125	./.:1:3:1:0,3,13	./.:0:0:0:0,0,0	./.:8:24:8:0,24,210	./.:1:3:1:0,3,12	./.:5:15:5:0,15,123
LS990926.1	106261	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.28;DP=5904;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=104400,29;ReadPosRankSum=0.947	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:35:90:34:.:.:0,90,1350,90,1350,1350	./.:.:3:9:3:.:.:0,9,69,9,69,69	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:267:0:265:.:.:0,0,7446,0,7446,7446	.|.:21,1,0:22:21:.:0|1:106242_CTA_C:0,21,900,63,903,945:106242:10,11,1,0	./.:.:15:39:15:.:.:0,39,585,39,585,585	./.:.:7:20:7:.:.:0,20,100,20,100,100	./.:.:4:11:4:.:.:0,11,56,11,56,56	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:19:4:19:.:.:0,4,158,4,158,158	./.:.:43:0:40:.:.:0,0,542,0,542,542	./.:.:60:99:53:.:.:0,109,1392,109,1392,1392	./.:.:33:81:31:.:.:0,81,1215,81,1215,1215	./.:.:55:58:55:.:.:0,58,1024,58,1024,1024	./.:.:32:75:29:.:.:0,75,1125,75,1125,1125	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:8:24:8:.:.:0,24,210,24,210,210	./.:.:1:3:1:.:.:0,3,12,3,12,12	./.:.:5:15:5:.:.:0,15,123,15,123,123
LS990926.1	106262	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:35:90:34:0,90,1350	./.:3:9:3:0,9,69	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:267:0:265:0,0,7446	./.:22:54:22:0,54,810	./.:15:0:15:0,0,174	./.:7:20:7:0,20,100	./.:4:11:4:0,11,56	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:48:99:36:0,99,1485	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:30:0:28:0,0,168	./.:43:0:40:0,0,542	./.:60:99:53:0,109,1392	./.:33:81:31:0,81,1215	./.:56:0:56:0,0,1083	./.:32:75:29:0,75,1125	./.:1:3:1:0,3,13	./.:0:0:0:0,0,0	./.:8:24:8:0,24,210	./.:1:3:1:0,3,12	./.:5:15:5:0,15,123
LS990926.1	106263	.	A	AG,<NON_REF>	.	.	BaseQRankSum=1.02;DP=5921;ExcessHet=0.00;MQRankSum=0.00;RAW_MQandDP=108000,30;ReadPosRankSum=0.948	GT:AD:DP:GQ:MIN_DP:PGT:PID:PL:PS:SB	./.:.:35:90:34:.:.:0,90,1350,90,1350,1350	./.:.:3:9:3:.:.:0,9,69,9,69,69	./.:.:456:99:401:.:.:0,120,1800,120,1800,1800	./.:.:232:99:201:.:.:0,120,1800,120,1800,1800	./.:.:194:0:180:.:.:0,0,5016,0,5016,5016	./.:.:219:0:182:.:.:0,0,0,0,0,0	./.:.:267:0:265:.:.:0,0,7446,0,7446,7446	.|.:22,1,0:23:24:.:0|1:106242_CTA_C:0,24,945,66,948,990:106242:10,12,1,0	./.:.:15:42:15:.:.:0,42,630,42,630,630	./.:.:7:20:7:.:.:0,20,100,20,100,100	./.:.:4:11:4:.:.:0,11,56,11,56,56	./.:.:86:99:76:.:.:0,120,1800,120,1800,1800	./.:.:171:99:134:.:.:0,120,1800,120,1800,1800	./.:.:107:99:68:.:.:0,120,1800,120,1800,1800	./.:.:115:99:83:.:.:0,120,1800,120,1800,1800	./.:.:57:99:40:.:.:0,102,1530,102,1530,1530	./.:.:114:99:81:.:.:0,120,1800,120,1800,1800	./.:.:104:99:75:.:.:0,120,1800,120,1800,1800	./.:.:109:99:89:.:.:0,120,1800,120,1800,1800	./.:.:117:99:89:.:.:0,120,1800,120,1800,1800	./.:.:106:99:90:.:.:0,120,1800,120,1800,1800	./.:.:161:99:119:.:.:0,120,1800,120,1800,1800	./.:.:132:99:92:.:.:0,120,1800,120,1800,1800	./.:.:102:99:78:.:.:0,120,1800,120,1800,1800	./.:.:104:99:77:.:.:0,120,1800,120,1800,1800	./.:.:98:99:79:.:.:0,120,1800,120,1800,1800	./.:.:134:99:85:.:.:0,120,1800,120,1800,1800	./.:.:112:99:83:.:.:0,120,1800,120,1800,1800	./.:.:92:99:71:.:.:0,120,1800,120,1800,1800	./.:.:123:99:77:.:.:0,120,1800,120,1800,1800	./.:.:86:99:62:.:.:0,120,1800,120,1800,1800	./.:.:108:99:89:.:.:0,120,1800,120,1800,1800	./.:.:108:99:98:.:.:0,120,1800,120,1800,1800	./.:.:89:99:72:.:.:0,120,1800,120,1800,1800	./.:.:95:99:78:.:.:0,120,1800,120,1800,1800	./.:.:116:99:75:.:.:0,120,1800,120,1800,1800	./.:.:126:99:92:.:.:0,120,1800,120,1800,1800	./.:.:140:99:113:.:.:0,120,1800,120,1800,1800	./.:.:101:99:94:.:.:0,120,1800,120,1800,1800	./.:.:117:99:87:.:.:0,120,1800,120,1800,1800	./.:.:96:99:72:.:.:0,120,1800,120,1800,1800	./.:.:108:99:86:.:.:0,120,1800,120,1800,1800	./.:.:134:99:96:.:.:0,120,1800,120,1800,1800	./.:.:121:99:98:.:.:0,120,1800,120,1800,1800	./.:.:153:99:113:.:.:0,120,1800,120,1800,1800	./.:.:68:99:59:.:.:0,120,1800,120,1800,1800	./.:.:137:99:112:.:.:0,120,1800,120,1800,1800	./.:.:126:99:97:.:.:0,120,1800,120,1800,1800	./.:.:109:99:84:.:.:0,120,1800,120,1800,1800	./.:.:120:99:91:.:.:0,120,1800,120,1800,1800	./.:.:92:99:80:.:.:0,120,1800,120,1800,1800	./.:.:113:99:79:.:.:0,120,1800,120,1800,1800	./.:.:132:99:98:.:.:0,113,1800,113,1800,1800	./.:.:105:99:79:.:.:0,120,1800,120,1800,1800	./.:.:114:99:98:.:.:0,120,1800,120,1800,1800	./.:.:98:99:68:.:.:0,120,1800,120,1800,1800	./.:.:111:99:92:.:.:0,120,1800,120,1800,1800	./.:.:110:99:87:.:.:0,120,1800,120,1800,1800	./.:.:48:99:36:.:.:0,99,1485,99,1485,1485	./.:.:86:99:73:.:.:0,120,1800,120,1800,1800	./.:.:80:99:47:.:.:0,111,1606,111,1606,1606	./.:.:83:99:50:.:.:0,120,1800,120,1800,1800	./.:.:120:99:100:.:.:0,120,1800,120,1800,1800	./.:.:30:0:28:.:.:0,0,168,0,168,168	./.:.:46:55:46:.:.:0,55,1051,55,1051,1051	./.:.:60:99:53:.:.:0,109,1392,109,1392,1392	./.:.:33:81:31:.:.:0,81,1215,81,1215,1215	./.:.:54:57:54:.:.:0,57,1303,57,1303,1303	./.:.:32:75:29:.:.:0,75,1125,75,1125,1125	./.:.:1:3:1:.:.:0,3,13,3,13,13	./.:.:0:0:0:.:.:0,0,0,0,0,0	./.:.:9:27:9:.:.:0,27,278,27,278,278	./.:.:1:3:1:.:.:0,3,12,3,12,12	./.:.:6:18:6:.:.:0,18,161,18,161,161
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LS990926.1	106267	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:35:90:34:0,90,1350	./.:3:9:3:0,9,69	./.:456:99:401:0,120,1800	./.:232:99:201:0,120,1800	./.:194:0:180:0,0,5016	./.:219:0:182:0,0,0	./.:265:0:230:0,0,6018	./.:23:51:23:0,51,765	./.:15:36:15:0,36,540	./.:7:7:7:0,7,78	./.:4:3:4:0,3,45	./.:86:99:76:0,120,1800	./.:171:99:134:0,120,1800	./.:107:99:68:0,120,1800	./.:115:99:83:0,120,1800	./.:57:99:40:0,102,1530	./.:114:99:81:0,120,1800	./.:104:99:75:0,120,1800	./.:109:99:89:0,120,1800	./.:117:99:89:0,120,1800	./.:106:99:90:0,120,1800	./.:161:99:119:0,120,1800	./.:132:99:92:0,120,1800	./.:102:99:78:0,120,1800	./.:104:99:77:0,120,1800	./.:98:99:79:0,120,1800	./.:134:99:85:0,120,1800	./.:112:99:83:0,120,1800	./.:92:99:71:0,120,1800	./.:123:99:77:0,120,1800	./.:86:99:62:0,120,1800	./.:108:99:89:0,120,1800	./.:108:99:98:0,120,1800	./.:89:99:72:0,120,1800	./.:95:99:78:0,120,1800	./.:116:99:75:0,120,1800	./.:126:99:92:0,120,1800	./.:140:99:113:0,120,1800	./.:101:99:94:0,120,1800	./.:117:99:87:0,120,1800	./.:96:99:72:0,120,1800	./.:108:99:86:0,120,1800	./.:134:99:96:0,120,1800	./.:121:99:98:0,120,1800	./.:153:99:113:0,120,1800	./.:68:99:59:0,120,1800	./.:137:99:112:0,120,1800	./.:126:99:97:0,120,1800	./.:109:99:84:0,120,1800	./.:120:99:91:0,120,1800	./.:92:99:80:0,120,1800	./.:113:99:79:0,120,1800	./.:132:99:98:0,113,1800	./.:105:99:79:0,120,1800	./.:114:99:98:0,120,1800	./.:98:99:68:0,120,1800	./.:111:99:92:0,120,1800	./.:110:99:87:0,120,1800	./.:48:99:36:0,99,1485	./.:86:99:73:0,120,1800	./.:80:99:47:0,111,1606	./.:83:99:50:0,120,1800	./.:120:99:100:0,120,1800	./.:20:0:20:0,0,170	./.:37:74:37:0,74,730	./.:46:0:46:0,0,579	./.:32:55:32:0,55,1030	./.:52:31:52:0,31,939	./.:32:75:29:0,75,1125	./.:1:3:1:0,3,16	./.:0:0:0:0,0,0	./.:9:27:9:0,27,198	./.:2:6:2:0,6,28	./.:5:15:5:0,15,105
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