I have 70 BAM files (1 for each of 70 complete genome samples), against which I ran mpileup
and bcftools call
to get 70 BCF variant files. I then merged all these BCF files into one large BCF file (using bcftools merge
).
The question is how to interpret lines (like the following).
For example, this line appears to say - amongst all 70 samples - there is ONE sample which had both ALT alleles (1/1:54,3,0
). The AC=2 and the AN=2...so I assumed that the multiple ./.:.
meant no matching data (or, implicitely, that all the other samples matched the reference).
1 10297 . C T 27.3033 PASS VDB=0.96;SGB=-0.453602;RPB=1;MQB=1;BQB=1;MQ0F=0.166667;MQ=40;DP=6;DP4=0,1,0,2;AN=2;AC=2 GT:PL ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. 1/1:54,3,0 ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:. ./.:.
HOWEVER, to check this I ran ...
ls ./*bcf | while read filename; do bcftools view -H -i 'POS=10297' $filename ; done
...which searched all 70 of the individual sample BCF files for data at position 10297
. I got 56 lines back.1 matching the 1/1:54,3,0
...
1 10297 . C T 27.3033 PASS DP=6;VDB=0.96;SGB=-0.453602;RPB=1;MQB=1;BQB=1;MQ0F=0.166667;AC=2;AN=2;DP4=0,1,0,2;MQ=40 GT:PL 1/1:54,3,0
(see the rest of the output below)
I notice also that 55 of the returns are annotated GL000208
, which I assume is a reference to this contig. The only return that does NOT reference GL000208
is the one that was heterozygous 1/1
(the rest here homozygous 0/1
).
So, I realize I probably just answered my own question (that GL000208
is a known SNP?? in the reference...or perhaps just IS the reference??)...but confirmation and maybe some details would be helpful :D
=== THE OTHER 55 RETURNS ===
GL000208.1 10297 . T A 222 PASS DP=81;VDB=0.0460824;SGB=-0.693145;RPB=0.487662;MQB=1;MQSB=1;BQB=0.407941;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=23,12,20,21;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=72;VDB=0.562051;SGB=-0.69312;RPB=0.998414;MQB=1;MQSB=1;BQB=0.873005;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=18,12,20,12;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=98;VDB=0.208973;SGB=-0.693145;RPB=0.702471;MQB=1;MQSB=1;BQB=0.541047;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=22,28,21,19;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 110 PASS DP=61;VDB=0.0147504;SGB=-0.670168;RPB=0.21281;MQB=1;MQSB=1;BQB=0.434287;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=23,21,6,4;MQ=60 GT:PL0/1:145,0,255
GL000208.1 10297 . T A 222 PASS DP=81;VDB=0.592406;SGB=-0.692717;RPB=0.418206;MQB=1;MQSB=1;BQB=0.129543;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=25,30,13,10;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=68;VDB=0.0306362;SGB=-0.693079;RPB=0.505598;MQB=1;MQSB=1;BQB=0.309834;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=20,16,16,13;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=90;VDB=0.889266;SGB=-0.69312;RPB=0.967791;MQB=1;MQSB=1;BQB=0.372578;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=29,27,17,15;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=98;VDB=0.0613164;SGB=-0.693079;RPB=0.999491;MQB=1;MQSB=1;BQB=0.000509874;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=31,36,14,15;MQ=60 GT:PL 0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=120;VDB=0.159068;SGB=-0.693147;RPB=0.929583;MQB=1;MQSB=1;BQB=0.063241;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=43,23,21,31;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=88;VDB=0.457547;SGB=-0.69311;RPB=0.985837;MQB=1;MQSB=1;BQB=0.133031;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=24,30,17,14;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=80;VDB=0.0588969;SGB=-0.693145;RPB=0.940626;MQB=1;MQSB=1;BQB=0.80705;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=22,16,22,18;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 118 PASS DP=13;VDB=0.136193;SGB=-0.616816;RPB=0.194278;MQB=0.961166;MQSB=0.961166;BQB=0.531709;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,2,4;MQ=6GT:PL 0/1:151,0,156
GL000208.1 10297 . T A 222 PASS DP=88;VDB=0.825491;SGB=-0.692976;RPB=0.591208;MQB=1;MQSB=1;BQB=0.00869542;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=34,25,12,14;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=105;VDB=0.322342;SGB=-0.693146;RPB=0.837101;MQB=1;MQSB=1;BQB=0.0363126;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=29,30,23,20;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=29;VDB=0.00495249;SGB=-0.690438;RPB=0.43845;MQB=1;MQSB=1;BQB=0.163206;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=8,4,9,8;MQ=60 GT:PL0/1:255,0,233
GL000208.1 10297 . T A 222 PASS DP=75;VDB=0.0750914;SGB=-0.693079;RPB=0.915284;MQB=1;MQSB=1;BQB=0.0100281;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=22,23,13,16;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 212 PASS DP=73;VDB=0.0565414;SGB=-0.69168;RPB=0.889463;MQB=1;MQSB=1;BQB=0.00821477;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=25,29,10,9;MQ=60 GT:PL0/1:246,0,255
GL000208.1 10297 . T A 222 PASS DP=101;VDB=0.0915851;SGB=-0.693097;RPB=0.999383;MQB=1;MQSB=1;BQB=0.0638933;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=33,34,14,16;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=121;VDB=0.0283351;SGB=-0.693146;RPB=0.941197;MQB=1;MQSB=1;BQB=0.00317092;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=39,32,26,18;MQ=60 GT:PL 0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=68;VDB=0.654808;SGB=-0.692914;RPB=0.276665;MQB=1;MQSB=1;BQB=0.49648;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=24,15,15,10;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=77;VDB=0.157913;SGB=-0.692352;RPB=0.968799;MQB=1;MQSB=1;BQB=0.225269;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=31,22,12,9;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=110;VDB=0.219827;SGB=-0.693139;RPB=0.777912;MQB=1;MQSB=1;BQB=0.316287;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=39,34,15,21;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=125;VDB=0.367966;SGB=-0.693147;RPB=0.666486;MQB=1;MQSB=1;BQB=0.106854;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=40,30,24,28;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=133;VDB=0.926022;SGB=-0.693147;RPB=0.313402;MQB=1;MQSB=1;BQB=0.688419;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=34,28,38,25;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=95;VDB=0.122979;SGB=-0.693147;RPB=0.863786;MQB=1;MQSB=1;BQB=0.334625;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=21,24,19,30;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 219 PASS DP=72;VDB=0.633915;SGB=-0.692067;RPB=0.911418;MQB=1;MQSB=1;BQB=0.972641;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=23,25,9,11;MQ=60 GT:PL0/1:252,0,255
GL000208.1 10297 . T A 217 PASS DP=88;VDB=0.849872;SGB=-0.692914;RPB=0.859387;MQB=1;MQSB=1;BQB=0.77073;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=28,35,17,8;MQ=60 GT:PL0/1:250,0,255
GL000208.1 10297 . T A 222 PASS DP=110;VDB=0.889949;SGB=-0.693147;RPB=0.833134;MQB=1;MQSB=1;BQB=0.0618411;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=26,25,30,28;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=114;VDB=0.0551714;SGB=-0.693147;RPB=0.992354;MQB=1;MQSB=1;BQB=0.192874;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=34,23,25,29;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=80;VDB=0.49346;SGB=-0.692352;RPB=0.835525;MQB=1;MQSB=1;BQB=0.645775;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=28,25,13,8;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=102;VDB=0.182212;SGB=-0.693079;RPB=0.946461;MQB=1;MQSB=1;BQB=0.283315;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=38,26,12,17;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=92;VDB=0.779094;SGB=-0.69311;RPB=0.904512;MQB=1;MQSB=1;BQB=0.948066;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=27,33,16,15;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=95;VDB=0.318542;SGB=-0.693127;RPB=0.927494;MQB=1;MQSB=1;BQB=0.959119;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=31,27,20,13;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=74;VDB=0.356374;SGB=-0.692831;RPB=0.575503;MQB=1;MQSB=1;BQB=0.63342;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=24,24,15,9;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=62;VDB=0.0243716;SGB=-0.692717;RPB=0.187277;MQB=1;MQSB=1;BQB=0.996656;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=20,18,13,10;MQ=60 GT:PL0/1:255,0,255
1 10297 . C T 27.3033 PASS DP=6;VDB=0.96;SGB=-0.453602;RPB=1;MQB=1;BQB=1;MQ0F=0.166667;AC=2;AN=2;DP4=0,1,0,2;MQ=40 GT:PL 1/1:54,3,0
GL000208.1 10297 . T A 222 PASS DP=85;VDB=0.112395;SGB=-0.693144;RPB=0.970041;MQB=1;MQSB=1;BQB=0.256217;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=15,30,20,19;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=94;VDB=0.142519;SGB=-0.693147;RPB=0.998392;MQB=1;MQSB=1;BQB=0.764039;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=26,20,23,25;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=113;VDB=0.212235;SGB=-0.693147;RPB=0.979879;MQB=1;MQSB=1;BQB=0.212548;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=27,34,23,29;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=123;VDB=0.478991;SGB=-0.693147;RPB=0.903964;MQB=1;MQSB=1;BQB=0.177772;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=40,34,23,24;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 187 PASS DP=54;VDB=0.10893;SGB=-0.686358;RPB=0.428026;MQB=1;MQSB=1;BQB=0.315058;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=21,19,6,8;MQ=60 GT:PL0/1:221,0,255
GL000208.1 10297 . T A 222 PASS DP=62;VDB=0.40128;SGB=-0.692717;RPB=0.299916;MQB=1;MQSB=1;BQB=0.306744;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=17,22,11,12;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=49;VDB=0.651545;SGB=-0.69168;RPB=0.325662;MQB=1;MQSB=1;BQB=0.944296;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=17,13,10,9;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=102;VDB=0.0519816;SGB=-0.693145;RPB=0.992323;MQB=1;MQSB=1;BQB=0.0857568;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=24,32,24,17;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 219 PASS DP=55;VDB=0.540591;SGB=-0.689466;RPB=0.852376;MQB=1;MQSB=1;BQB=0.0104413;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=23,16,7,9;MQ=60 GT:PL0/1:252,0,255
GL000208.1 10297 . T A 222 PASS DP=69;VDB=0.0665008;SGB=-0.692914;RPB=0.704969;MQB=1;MQSB=1;BQB=0.395949;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=22,20,13,12;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=107;VDB=0.832778;SGB=-0.693147;RPB=0.637084;MQB=1;MQSB=1;BQB=0.178158;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=30,25,28,22;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=61;VDB=0.222952;SGB=-0.692067;RPB=0.139278;MQB=1;MQSB=1;BQB=0.291918;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=23,16,12,8;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 205 PASS DP=70;VDB=0.163372;SGB=-0.691153;RPB=0.674838;MQB=1;MQSB=1;BQB=0.0225;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=28,24,11,7;MQ=60 GT:PL0/1:239,0,255
GL000208.1 10297 . T A 222 PASS DP=148;VDB=0.00266433;SGB=-0.693147;RPB=0.896319;MQB=1;MQSB=1;BQB=0.00888503;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=47,24,41,34;MQ=60 GT:PL 0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=87;VDB=0.577098;SGB=-0.69311;RPB=0.999613;MQB=1;MQSB=1;BQB=0.133484;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=28,25,16,15;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 222 PASS DP=97;VDB=0.249946;SGB=-0.693147;RPB=0.359953;MQB=1;MQSB=1;BQB=0.993045;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=15,25,31,21;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 221 PASS DP=95;VDB=0.46429;SGB=-0.692717;RPB=0.826527;MQB=1;MQSB=1;BQB=0.859249;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=36,29,12,11;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 221 PASS DP=109;VDB=0.848602;SGB=-0.692914;RPB=0.478419;MQB=1;MQSB=1;BQB=0.986804;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=41,32,15,10;MQ=60 GT:PL0/1:255,0,255
GL000208.1 10297 . T A 26.9567 PASS DP=59;VDB=0.0175011;SGB=-0.636426;RPB=0.109536;MQB=1;MQSB=1;BQB=0.689018;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=22,28,4,3;MQ=60 GT:PL0/1:63,0,255
GL000208.1 10297 . T A 166 PASS DP=56;VDB=0.0376046;SGB=-0.686358;RPB=0.991632;MQB=1;MQSB=1;BQB=0.237299;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=20,16,12,2;MQ=60 GT:PL0/1:200,0,255
I would advice you to add this to the question because it is not an answer to your question.