##fileformat=VCFv4.2 ##ALT= ##FILTER= ##FILTER= ##FILTER= 30.0 && QUAL < 50.0 "> ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine.GenotypeGVCFs= ##GATKCommandLine.HaplotypeCaller= ##GATKCommandLine.VariantFiltration= 30.0 && QUAL < 50.0 ] filterName=[LowCoverage, VeryLowQual, LowQual] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=10 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> ##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) ##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive) ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##reference=file:///wrk/cairns/vcf_all/pseudomonas_fluorescens_sbw25_dna.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 0BVII_rep1 0BVII_rep10 0BVII_rep2 0BVII_rep3 0BVII_rep4 0BVII_rep5 0BVII_rep6 0BVII_rep7 0BVII_rep8 0BVII_rep9 Chromosome 45877 . A AG 10717.6 PASS AC=10;AF=1.00;AN=10;DP=338;FS=0.000;MLEAC=10;MLEAF=1.00;MQ=60.03;QD=32.48;SOR=2.675 GT:AD:DP:GQ:PL 1:0,24:24:99:781,0 1:0,51:51:99:1661,0 1:0,22:22:99:711,0 1:0,27:27:99:879,0 1:0,23:23:99:749,0 1:0,20:20:99:651,0 1:0,29:29:99:944,0 1:0,60:60:99:1932,0 1:0,37:37:99:1224,0 1:0,37:37:99:1220,0 Chromosome 895316 . C CGCACTTCGAACGCGCTGGATACTAAGGTGCATAGGATTGCGAGATGAATGACCTGGTCACTCAAACGCCGTTGTAGTGAGCGGGCTTGCCCCGCGCTGGGCTGCGAAGCAGCCCCAACACCTGCCACCCCGTTCTGCCTGACAAAACGCGGCGGCCTTATTGGGGCTGCTACGCAGCCCAGCGCGGGGCAAGCCCGCTCACCACACAT 2615.15 PASS AC=2;AF=0.200;AN=10;BaseQRankSum=2.53;ClippingRankSum=0.555;DP=520;FS=4.170;MLEAC=2;MLEAF=0.200;MQ=58.75;MQRankSum=0.433;QD=34.24;ReadPosRankSum=0.449;SOR=0.659 GT:AD:DP:GQ:PL 0:72,0:72:73:0,73 0:98,0:98:99:0,467 0:37,0:37:99:0,187 0:3,0:3:99:0,100 0:43,0:43:99:0,142 1:12,12:24:99:1559,0 0:68,0:68:39:0,39 0:110,0:110:99:0,227 1:32,1:59:99:1098,0 0:4,0:4:99:0,131 Chromosome 895351 . C G 2807.65 PASS AC=7;AF=0.875;AN=8;BaseQRankSum=0.600;ClippingRankSum=-5.910e-01;DP=459;FS=6.809;MLEAC=7;MLEAF=0.875;MQ=42.78;MQRankSum=0.057;QD=13.70;ReadPosRankSum=0.825;SOR=0.374 GT:AD:DP:GQ:PL 1:5,25:30:99:474,0 1:24,28:52:99:169,0 1:4,8:12:99:150,0 1:5,13:18:99:296,0 1:4,13:17:99:313,0 .:0,0:.:.:. 1:3,31:34:99:789,0 1:9,33:42:99:651,0 0:91,0:91:99:0,99 .:0,0:.:.:. Chromosome 895357 . G A 1729.68 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.75;ClippingRankSum=0.492;DP=676;FS=1.952;MLEAC=2;MLEAF=1.00;MQ=20.07;MQRankSum=0.805;QD=21.09;ReadPosRankSum=2.33;SOR=0.920 GT:AD:DP:GQ:PL .:0,0:.:.:. .:0,0:.:.:. .:0,0:.:.:. .:0,0:.:.:. .:0,0:.:.:. 1:4,24:28:99:766,0 .:0,0:.:.:. .:0,0:.:.:. 1:23,31:54:99:989,0 .:0,0:.:.:. Chromosome 943309 . C T 1407.68 PASS AC=1;AF=0.100;AN=10;DP=141;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=60.00;QD=33.52;SOR=0.788 GT:AD:DP:GQ:PL 0:11,0:11:99:0,135 0:18,0:18:99:0,135 0:6,0:6:99:0,135 0:10,0:10:99:0,127 0:6,0:6:99:0,135 0:9,0:9:99:0,180 1:0,42:42:99:1443,0 0:18,0:18:99:0,135 0:11,0:11:99:0,135 0:10,0:10:99:0,135 Chromosome 985332 . G GC 7690.64 PASS AC=10;AF=1.00;AN=10;DP=208;FS=0.000;MLEAC=10;MLEAF=1.00;MQ=60.02;QD=30.63;SOR=0.742 GT:AD:DP:GQ:PL 1:0,24:24:99:892,0 1:0,24:24:99:892,0 1:0,6:6:99:223,0 1:0,19:19:99:733,0 1:0,9:9:99:333,0 1:0,9:9:99:336,0 1:0,23:23:99:843,0 1:0,48:48:99:1807,0 1:0,24:24:99:884,0 1:0,21:21:99:782,0 Chromosome 1425210 . C T 7436.68 PASS AC=10;AF=1.00;AN=10;BaseQRankSum=1.53;ClippingRankSum=1.43;DP=214;FS=0.000;MLEAC=10;MLEAF=1.00;MQ=60.00;MQRankSum=0.612;QD=34.75;ReadPosRankSum=0.815;SOR=0.227 GT:AD:DP:GQ:PL 1:0,17:17:99:602,0 1:0,27:27:99:965,0 1:0,15:15:99:543,0 1:0,18:18:99:620,0 1:0,11:11:99:401,0 1:0,11:11:99:442,0 1:0,22:22:99:801,0 1:0,30:30:99:985,0 1:0,29:29:99:988,0 1:1,33:34:99:1115,0 Chromosome 1824289 . TG T 1936.64 PASS AC=1;AF=0.100;AN=10;DP=104;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=60.00;QD=33.39;SOR=0.836 GT:AD:DP:GQ:PL 0:3,0:3:99:0,100 0:5,0:5:99:0,121 0:4,0:4:99:0,141 0:5,0:5:99:0,111 0:5,0:5:99:0,140 0:4,0:4:99:0,104 0:4,0:4:99:0,109 1:0,58:58:99:1981,0 0:4,0:4:99:0,159 0:10,0:10:99:0,139 Chromosome 1824606 . C T 1866.68 PASS AC=1;AF=0.100;AN=10;BaseQRankSum=-5.960e-01;ClippingRankSum=0.085;DP=110;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=60.00;MQRankSum=-5.400e-01;QD=30.60;ReadPosRankSum=-2.800e-02;SOR=0.280 GT:AD:DP:GQ:PL 0:3,0:3:99:0,100 0:5,0:5:99:0,121 0:4,0:4:99:0,141 0:5,0:5:99:0,111 0:5,0:5:99:0,140 0:4,0:4:99:0,104 0:4,0:4:99:0,109 0:9,0:9:99:0,282 1:1,60:61:99:1902,0 0:10,0:10:99:0,139 Chromosome 1824626 . AG A 4864.85 PASS AC=3;AF=0.300;AN=10;DP=177;FS=0.000;MLEAC=3;MLEAF=0.300;MQ=60.00;QD=30.83;SOR=0.949 GT:AD:DP:GQ:PL 0:3,0:3:99:0,100 0:5,0:5:99:0,121 1:0,32:32:99:1136,0 0:5,0:5:99:0,111 1:0,37:37:99:1321,0 0:4,0:4:99:0,104 0:4,0:4:99:0,109 0:9,0:9:99:0,282 0:8,0:8:99:0,148 1:0,69:69:99:2463,0 Chromosome 3231429 . C T 1845.68 PASS AC=1;AF=0.100;AN=10;DP=103;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=60.00;QD=34.18;SOR=0.767 GT:AD:DP:GQ:PL 0:3,0:3:99:0,103 0:4,0:4:99:0,104 0:7,0:7:99:0,178 0:4,0:4:99:0,118 0:3,0:3:99:0,122 0:3,0:3:99:0,114 0:3,0:3:99:0,103 1:0,54:54:99:1881,0 0:11,0:11:99:0,271 0:11,0:11:99:0,132 Chromosome 3231466 . C T 3089.89 PASS AC=3;AF=0.300;AN=10;DP=112;FS=0.000;MLEAC=3;MLEAF=0.300;MQ=60.00;QD=29.67;SOR=1.218 GT:AD:DP:GQ:PL 0:3,0:3:99:0,103 0:4,0:4:99:0,104 1:0,23:23:99:807,0 0:4,0:4:99:0,118 1:0,22:22:99:862,0 0:3,0:3:99:0,114 0:3,0:3:99:0,103 0:3,0:3:99:0,100 0:5,0:5:99:0,135 1:0,42:42:99:1467,0 Chromosome 3447980 . TCC T 16529.6 PASS AC=10;AF=1.00;AN=10;BaseQRankSum=1.15;ClippingRankSum=0.335;DP=431;FS=0.000;MLEAC=10;MLEAF=1.00;MQ=60.40;MQRankSum=-2.195e+00;QD=34.04;ReadPosRankSum=1.51;SOR=0.457 GT:AD:DP:GQ:PL 1:0,46:46:99:2006,0 1:0,46:46:99:1988,0 1:0,31:31:99:1365,0 1:0,25:25:99:1090,0 1:2,27:29:99:896,0 1:0,29:29:99:1269,0 1:0,32:32:99:1414,0 1:2,68:70:99:2111,0 1:0,50:50:99:2223,0 1:0,50:50:99:2202,0 Chromosome 5218386 . C T 3015.15 PASS AC=2;AF=0.200;AN=10;BaseQRankSum=0.635;ClippingRankSum=-4.620e-01;DP=115;FS=0.000;MLEAC=2;MLEAF=0.200;MQ=60.00;MQRankSum=0.115;QD=33.50;ReadPosRankSum=-1.097e+00;SOR=0.293 GT:AD:DP:GQ:PL 0:3,0:3:99:0,100 1:1,59:60:99:2088,0 0:3,0:3:99:0,118 0:3,0:3:99:0,107 0:3,0:3:99:0,118 1:0,30:30:99:969,0 0:3,0:3:99:0,109 0:3,0:3:99:0,100 0:4,0:4:99:0,109 0:3,0:3:99:0,100 Chromosome 5218419 . G A 2184.68 PASS AC=1;AF=0.100;AN=10;DP=109;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=60.00;QD=30.77;SOR=0.779 GT:AD:DP:GQ:PL 0:3,0:3:99:0,100 0:9,0:9:99:0,135 0:3,0:3:99:0,118 0:3,0:3:99:0,107 0:3,0:3:99:0,118 0:7,0:7:99:0,110 0:3,0:3:99:0,109 1:0,71:71:99:2220,0 0:4,0:4:99:0,109 0:3,0:3:99:0,100 Chromosome 5218470 . A C 8920.89 PASS AC=7;AF=0.700;AN=10;DP=294;FS=0.000;MLEAC=7;MLEAF=0.700;MQ=60.00;QD=33.29;SOR=0.836 GT:AD:DP:GQ:PL 1:0,52:52:99:1663,0 0:9,0:9:99:0,135 1:0,37:37:99:1226,0 1:0,24:24:99:804,0 1:0,28:28:99:903,0 0:7,0:7:99:0,110 1:0,42:42:99:1377,0 0:10,0:10:99:0,214 1:0,45:45:99:1605,0 1:0,40:40:99:1389,0 Chromosome 5393487 . A G 1973.68 PASS AC=1;AF=0.100;AN=10;BaseQRankSum=0.985;ClippingRankSum=-7.080e-01;DP=118;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=60.00;MQRankSum=0.739;QD=29.90;ReadPosRankSum=0.308;SOR=0.832 GT:AD:DP:GQ:PL 0:4,0:4:99:0,105 0:9,0:9:99:0,135 0:4,0:4:99:0,105 0:3,0:3:99:0,100 0:5,0:5:99:0,131 0:4,0:4:99:0,100 0:4,0:4:99:0,109 1:3,63:66:99:2009,0 0:8,0:8:99:0,225 0:9,0:9:99:0,212