Below is a fragment of my VCF file:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aln.sorted.bam 11561 6 . C X 0 . DP=1;I16=1,0,0,0,38,1444,0,0,6,36,0,0,0,0,0,0;QS=1.000000,0.000000,0.000000,0.000000 PL 0,3,6 11561 7 . C X 0 . DP=1;I16=1,0,0,0,38,1444,0,0,6,36,0,0,1,1,0,0;QS=1.000000,0.000000,0.000000,0.000000 PL 0,3,6 11561 8 . A X 0 . DP=1;I16=1,0,0,0,38,1444,0,0,6,36,0,0,2,4,0,0;QS=1.000000,0.000000,0.000000,0.000000 PL 0,3,6 11561 19 . G A,X 0 . DP=2;I16=1,0,1,0,38,1444,38,1444,6,36,6,36,7,49,13,169;QS=0.500000,0.500000,0.000000,0.000000;RPB=9.668049e-01 PL 1,0,1,4,4,4 11561 337 . ca cAa 0 . INDEL;IS=1,0.200000;DP=5;I16=1,1,1,0,68,2312,40,1600,2,2,15,225,35,697,6,36;QS=0.347826,0.652174,0.000000,0.000000;VDB=6.365454e-02 PL 6,0,0 11561 375 . taaaaaaaa taaaaaaa 0 . INDEL;IS=1,0.200000;DP=5;I16=0,0,1,0,0,0,18,324,0,0,6,36,0,0,25,625;QS=0.000000,1.000000,0.000000,0.000000 PL 6,3,0 11561 390 . A T,G,X 0 . DP=4;I16=0,0,2,1,0,0,114,4332,0,0,8,38,0,0,75,1875;QS=0.000000,0.571429,0.428571,0.000000;VDB=5.227153e-02 PL 5,6,0,5,2,2,5,6,5,5 11561 740 . AC ACC 0 . INDEL;IS=4,0.102564;DP=39;I16=20,7,2,1,741,22083,49,819,457,12337,5,13,524,11426,48,866;QS=0.970732,0.029268,0.000000,0.000000;VDB=5.891593e-02 PL 0,54,149
I need to find the SNPs and INDELs, however I don't quiet understand the X under the ALT. Does it mean X-chomosome? Does the following mean that there is a SNP from G to A on chromosome X? How do I know that significance of this result? Is it the QS=0.500000 or the QUAL=0? Is there anything I need to know when collecting the SNPs and INDELs?
11561 19 . G A,X 0 . DP=2;I16=1,0,1,0,38,1444,38,1444,6,36,6,36,7,49,13,169;QS=0.500000,0.500000,0.000000,0.000000;RPB=9.668049e-01 PL 1,0,1,4,4,4
Thank you in advance!