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3
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1 ##fileformat=VCFv4.2
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2 ##FILTER=<ID=LowQual,Description="Low quality">
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3 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
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5 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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7 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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8 ##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --input /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --emit-ref-confidence NONE --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 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations 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 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --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",Version=4.0.10.0,Date="October 29, 2018 1:03:15 PM EDT">
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9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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10 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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11 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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12 ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
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13 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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14 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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15 ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
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16 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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17 ##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">
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18 ##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">
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19 ##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">
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20 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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21 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
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22 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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23 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
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24 ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
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25 ##contig=<ID=chr1,length=248956422>
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26 ##contig=<ID=chr2,length=242193529>
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27 ##contig=<ID=chr3,length=198295559>
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28 ##contig=<ID=chr4,length=190214555>
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29 ##contig=<ID=chr5,length=181538259>
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30 ##contig=<ID=chr6,length=170805979>
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31 ##contig=<ID=chr7,length=159345973>
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32 ##contig=<ID=chr8,length=145138636>
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33 ##contig=<ID=chr9,length=138394717>
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34 ##contig=<ID=chr10,length=133797422>
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35 ##contig=<ID=chr11,length=135086622>
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36 ##contig=<ID=chr12,length=133275309>
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37 ##contig=<ID=chr13,length=114364328>
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38 ##contig=<ID=chr14,length=107043718>
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39 ##contig=<ID=chr15,length=101991189>
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40 ##contig=<ID=chr16,length=90338345>
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41 ##contig=<ID=chr17,length=83257441>
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42 ##contig=<ID=chr18,length=80373285>
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43 ##contig=<ID=chr19,length=58617616>
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44 ##contig=<ID=chr20,length=64444167>
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45 ##contig=<ID=chr21,length=46709983>
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46 ##contig=<ID=chr22,length=50818468>
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47 ##contig=<ID=chrX,length=156040895>
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48 ##contig=<ID=chrY,length=57227415>
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49 ##contig=<ID=chrM,length=16569>
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50 ##source=HaplotypeCaller
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51 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_1_fastq
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52 chr5 474989 . A G 96.03 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.01;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:124,12,0
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53 chr5 475231 . A T 66.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=22.09;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0
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54 chr5 181223744 . T C 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.544;DP=14;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.41;ReadPosRankSum=-0.756;SOR=1.863 GT:AD:DP:GQ:PL 0/1:6,8:14:99:202,0,133
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55 chr5 181224474 . G A 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=45;ExcessHet=3.0103;FS=1.237;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.77;ReadPosRankSum=0.504;SOR=0.945 GT:AD:DP:GQ:PL 0/1:28,17:45:99:378,0,717
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56 chr8 143923488 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.260;DP=78;ExcessHet=3.0103;FS=4.540;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.06;ReadPosRankSum=0.137;SOR=0.307 GT:AD:DP:GQ:PL 0/1:45,33:78:99:735,0,1132
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57 chr8 143923759 . G A 838.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.630;DP=66;ExcessHet=3.0103;FS=0.940;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.71;ReadPosRankSum=0.567;SOR=0.820 GT:AD:DP:GQ:PL 0/1:31,35:66:99:867,0,736
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58 chr8 143924001 . C T 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=60;ExcessHet=3.0103;FS=4.714;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.16;ReadPosRankSum=0.323;SOR=1.525 GT:AD:DP:GQ:PL 0/1:38,22:60:99:758,0,1811
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59 chr8 143924022 . A G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=58;ExcessHet=3.0103;FS=14.916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.13;ReadPosRankSum=0.674;SOR=2.948 GT:AD:DP:GQ:PL 0/1:40,18:58:99:616,0,1892
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60 chr12 56420869 . G A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=48;ExcessHet=3.0103;FS=4.262;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.02;ReadPosRankSum=0.096;SOR=0.674 GT:AD:DP:GQ:PL 0/1:30,18:48:99:413,0,759
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61 chr12 56420872 . A G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=46;ExcessHet=3.0103;FS=8.803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.13;ReadPosRankSum=0.656;SOR=1.232 GT:AD:DP:GQ:PL 0/1:18,28:46:99:724,0,415
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62 chr12 56422138 . C T 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.718;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.10;ReadPosRankSum=-0.816;SOR=0.693 GT:AD:DP:GQ:PL 0/1:4,4:8:96:101,0,96
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63 chr17 7673767 . C T 1848.77 . AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,61:61:99:1877,183,0
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64 chr17 7675327 . C T 32.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.37;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0
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65 chr17 7676154 . G C 2161.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=3.225;DP=80;ExcessHet=3.0103;FS=14.289;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.02;ReadPosRankSum=-2.023;SOR=0.642 GT:AD:DP:GQ:PL 1/1:4,76:80:99:2190,183,0
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66 chr17 43071077 . T C 92.03 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.01;SOR=3.258 GT:AD:DP:GQ:PL 1/1:0,4:4:12:120,12,0
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67 chr17 43082453 . A G 37.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=18.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0
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68 chr17 43091983 . T C 84.03 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.01;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,4:4:12:112,12,0
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69 chr17 43092919 . G A 33.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0
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70 chr17 43093220 . A G 278.77 . AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.88;SOR=4.804 GT:AD:DP:GQ:PL 1/1:0,10:10:30:307,30,0
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71 chr17 43093449 . G A 425.77 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.87;SOR=1.402 GT:AD:DP:GQ:PL 1/1:0,9:9:33:454,33,0
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72 chr17 43093454 . C T 425.77 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.78;SOR=1.270 GT:AD:DP:GQ:PL 1/1:0,11:11:33:454,33,0
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73 chr19 39177761 . G C 1134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.71;ReadPosRankSum=1.397;SOR=0.654 GT:AD:DP:GQ:PL 0/1:58,48:106:99:1163,0,1435
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74 chr19 39178960 . A ATG 226.77 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.40;SOR=4.174 GT:AD:DP:GQ:PL 1/1:0,7:7:21:264,21,0
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75 chr19 39179002 . T C 31.74 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=15.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0
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76 chr19 47271315 . C T 513.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.932;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.69;ReadPosRankSum=-1.045;SOR=0.264 GT:AD:DP:GQ:PL 1/1:1,19:20:30:542,30,0
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77 chr19 47271515 . T C 336.77 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.06;SOR=2.670 GT:AD:DP:GQ:PL 1/1:0,12:12:36:365,36,0
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78 chr19 47272198 . G T 21.77 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0
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79 chr20 46687147 . C T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.260;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.30;ReadPosRankSum=1.395;SOR=1.179 GT:AD:DP:GQ:PL 0/1:8,18:26:99:452,0,165
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