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Test-drive the GATK tools and Best Practices pipelines on Terra
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variant calling by unified genotyper
While using UnifiedGenotyper for variant calling, i am getting the following output. In altered base sometimes instead of single altered base, i am getting three or two different bases. I am unable to understand what does it means. How can i infer the result from this. plz help, i am new to this. Thanks in advance
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
phytoene_synthase1 980 . C A,G,T 553.14 . AC=2,14,2;AF=0.016,0.109,0.016;AN=128;BaseQRankSum=3.605;DP=250;Dels=0.00;FS=12.534;HaplotypeScore=109.3273;MLEAC=2,14,2;MLEAF=0.016,0.109,0.016;MQ=52.45;MQ0=1;MQRankSum=-7.667;QD=2.21;ReadPosRankSum=-7.988;SOR=2.691 GT:AD:DP:GQ
phytoene_synthase1 981 . A C,G,T 307.38 . AC=3,4,2;AF=0.023,0.031,0.016;AN=128;BaseQRankSum=0.189;DP=250;Dels=0.00;FS=10.700;HaplotypeScore=100.2929;MLEAC=3,4,2;MLEAF=0.023,0.031,0.016;MQ=52.49;MQ0=1;MQRankSum=-4.932;QD=1.23;ReadPosRankSum=-6.447;SOR=2.649 GT:AD:DP:GQ
phytoene_synthase1 982 . A G,T 80.82 . AC=2,2;AF=0.016,0.016;AN=128;BaseQRankSum=0.513;DP=248;Dels=0.00;FS=0.000;HaplotypeScore=138.2460;MLEAC=2,2;MLEAF=0.016,0.016;MQ=52.43;MQ0=1;MQRankSum=-2.482;QD=0.33;ReadPosRankSum=-2.922;SOR=0.954 GT:AD:DP:GQ
phytoene_synthase1 983 . T A,G 428.58 . AC=5,9;AF=0.039,0.070;AN=128;BaseQRankSum=-0.673;DP=249;Dels=0.00;FS=15.038;HaplotypeScore=139.6787;MLEAC=3,11;MLEAF=0.023,0.086;MQ=52.35;MQ0=1;MQRankSum=-6.785;QD=1.72;ReadPosRankSum=-7.156;SOR=3.639 GT:AD:DP:GQ
phytoene_synthase1 984 . G A 224.95 . AC=8;AF=0.063;AN=128;BaseQRankSum=3.123;DP=250;Dels=0.00;FS=6.380;HaplotypeScore=186.4846;MLEAC=8;MLEAF=0.063;MQ=51.99;MQ0=1;MQRankSum=-5.899;QD=0.90;ReadPosRankSum=-4.223;SOR=2.039 GT:AD:DP:GQ