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##fileformat=VCFv4.1
##Goby=UNKNOWN
##FieldGroupAssociations=INFO/pchi2-BH-FDR-q-value=q-value,INFO/pchi2-BH-FDR-q-value=indexed,CHROM=genomic-coordinate,CHROM=cross-sample-field,CHROM/VALUE=genomic-coordinate,CHROM/VALUE=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,POS/VALUE=genomic-coordinate,POS/VALUE=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,ID/VALUE=external-identifiers,ID/VALUE=cross-sample-field,REF=cross-sample-field,REF/VALUE=cross-sample-field,ALT=cross-sample-field,ALT/VALUE=cross-sample-field,QUAL=cross-sample-field,QUAL/VALUE=cross-sample-field,FILTER=cross-sample-field,FILTER/VALUE=cross-sample-field,
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=RP,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=pchi2-BH-FDR-q-value,Number=1,Type=Float,Description="Benjamini Hochberg FDR adjusted for column pchi2-BH-FDR-q-value.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT results/IPBKRNW/IPBKRNW-replicate.bam results/IPBKRNW/IPBKRNW-sorted.bam
0 145497099 . A G 17.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-30.8;QCHI2=1;PCHI2=0.752;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
1 29389393 . A ATG 31.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:36,3,0:42 1/1:36,3,0:42
1 44379612 . CT C 31.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:36,3,0:42 1/1:36,3,0:42
1 113304121 . C A 7.84 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.7;QCHI2=1;PCHI2=0.784;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:20,3,0:42 1/1:20,3,0:42
1 239926953 . C CGA 33.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:37,3,0:42 1/1:37,3,0:42
2 186893495 . C T 17.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-30.8;QCHI2=1;PCHI2=0.752;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
5 21610299 . C CGA 6.57 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=23;FQ=-38.3;QCHI2=1;PCHI2=0.758;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:23,3,0:42 1/1:23,3,0:42
6 48943221 . T TC 228 . INDEL;DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37;FQ=-57.3;QCHI2=0;PCHI2=0.992;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:136,21,0:87 1/1:136,21,0:87
8 36216797 . T C 17.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-30.8;QCHI2=1;PCHI2=0.752;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
9 94234 . TAA TAAA 33.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:37,3,0:42 1/1:37,3,0:42
9 114158 . A G 17.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-30.8;QCHI2=1;PCHI2=0.752;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
9 123469 . A G 3.61 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-30.7;QCHI2=1;PCHI2=0.85;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:17,3,0:42 1/1:17,3,0:42
9 181146 . A G 3.61 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.7;QCHI2=1;PCHI2=0.85;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:17,3,0:42 1/1:17,3,0:42
9 181486 . G A 15.5 . DP=4;AF1=0.5024;CI95=0.5,0.5;DP4=2,0,2,0;MQ=32;FQ=7.07;QCHI2=0;PCHI2=0.984;PC2=3,3;PV4=1,0,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:25,0,19:21 0/1:25,0,19:21
9 181567 . C G 19.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.8;QCHI2=1;PCHI2=0.75;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:26,3,0:42 1/1:26,3,0:42
9 182055 . A C 5.04 . DP=4;AF1=0.4976;CI95=0.5,0.5;DP4=2,0,2,0;MQ=37;FQ=7.07;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,0,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:19,0,25:21 0/1:19,0,25:21
9 182057 . C A 6.51 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=37;FQ=6.51;QCHI2=0;PCHI2=0.978;PC2=3,3;PV4=1,1,1,0;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:20,0,20:20 0/1:20,0,20:20
9 182271 . C A 3.79 . DP=6;AF1=0.496;CI95=0.25,0.5;DP4=4,0,2,0;MQ=37;FQ=5.73;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,4.5e-05,1,0.31;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:18,0,59:21 0/1:18,0,59:21
9 182801 . G C 3.79 . DP=4;AF1=0.4962;CI95=0.25,0.5;DP4=2,0,2,0;MQ=37;FQ=5.73;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,0,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:18,0,31:21 0/1:18,0,31:21
9 183183 . T G 11.4 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.7;QCHI2=1;PCHI2=0.763;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:22,3,0:42 1/1:22,3,0:42
9 185358 . C T 3.61 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.7;QCHI2=1;PCHI2=0.85;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:17,3,0:42 1/1:17,3,0:42
9 186159 . T C 9.8 . DP=10;AF1=0.4984;CI95=0.5,0.5;DP4=8,0,2,0;MQ=37;FQ=12.6;QCHI2=0;PCHI2=0.987;PC2=3,3;PV4=1,0.0027,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:22,0,100:25 0/1:22,0,100:25
9 188262 . A T 3.79 . DP=4;AF1=0.4962;CI95=0.25,0.5;DP4=2,0,2,0;MQ=37;FQ=5.73;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,0,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:18,0,31:21 0/1:18,0,31:21
9 188345 . T C 9.8 . DP=6;AF1=0.4984;CI95=0.5,0.5;DP4=4,0,2,0;MQ=33;FQ=12.6;QCHI2=0;PCHI2=0.987;PC2=3,3;PV4=1,0.00056,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:22,0,49:25 0/1:22,0,49:25
9 189046 . G T 17.4 . DP=6;AF1=0.4994;CI95=0.5,0.5;DP4=4,0,2,0;MQ=37;FQ=20.3;QCHI2=0;PCHI2=0.994;PC2=3,3;PV4=1,0.00031,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:26,0,59:29 0/1:26,0,59:29
9 190894 . TTCAT TCAT 33.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 1/1:37,3,0:42 1/1:37,3,0:42
9 192926 . T TC 13.9 . INDEL;DP=6;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,2,0;MQ=30;FQ=15.4;QCHI2=0;PCHI2=0.996;PC2=3,3;PV4=1,1,1,0.38;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:28,0,30:29 0/1:28,0,30:29
9 193132 . G T 15.4 . DP=4;AF1=0.4994;CI95=0.5,0.5;DP4=2,0,2,0;MQ=37;FQ=18.1;QCHI2=0;PCHI2=0.993;PC2=3,3;PV4=1,0,1,0;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:25,0,31:27 0/1:25,0,31:27
9 193133 . C T 23.3 . DP=4;AF1=0.5005;CI95=0.5,0.5;DP4=2,0,2,0;MQ=37;FQ=17.7;QCHI2=0;PCHI2=0.995;PC2=3,3;PV4=1,1,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:29,0,25:27 0/1:29,0,25:27
9 195030 . T G 9.8 . DP=10;AF1=0.4984;CI95=0.5,0.5;DP4=8,0,2,0;MQ=37;FQ=12.6;QCHI2=0;PCHI2=0.987;PC2=3,3;PV4=1,0.072,1,1;pchi2-BH-FDR-q-value=0.996 GT:PL:GQ 0/1:22,0,99:25 0/1:22,0,99:25
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