I ran freebayes on bacterial data and got a vcf file. Some of the SNPs found have AC=0, but in the bam file I can see that there are alternative alleles, so in my understanding it supposed to be AC>0.

example: in vcf file:

CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  55509   55508   55506   55507
scaffold1       78      .       A       C       9.27683e-13     .       AB=0;ABP=0;AC=0;AF=0;AN=3;AO=466;CIGAR=1X;DP=2254;DPB=2254;DPRA=0;EPP=20.9226;EPPR=29.3274;GTI=0;LEN=1;MEANALT=2;MQM=50.3412;MQMR=45.5379;NS=3;NUMALT=1;ODDS=2080.75;PAIRED=0.899142;PAIREDR=0.533932;PAO=0;PQA=0;PQR=0;PRO=0;QA=16347;QR=63107;RO=1783;RPL=203;RPP=19.7856;RPPR=291.853;RPR=263;RUN=1;SAF=465;SAP=1006.25;SAR=1;SRF=894;SRP=3.04075;SRR=889;TYPE=snp       GT:GQ:DP:AD:RO:QR:AO:QA:GL      .       0:126.704:776:626,149:626:22118:149:5255:0,-1217.7      0:126.704:834:663,170:663:23671:170:6004:0,-1224.79     0:126.704:644:494,147:494:17318:147:5088:0,-770.853

but with samtools tview:

samtools tview screenshot

Can someone tell me if this makes sense and why it happens?


The AC is the number of alternate alleles from called genotypes, you can see this in the vcf header:

##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of 
alternate alleles in called genotypes

Assuming diploid, if we have 3 individuals, 0/0 , 0/1, 0/0, AC will be 1, because it detects 1 count of alternate allele.

If you look at your genotype calls, all are 0, so AC = 0

  • $\begingroup$ Oh, now I get it. freebayes chose 1 genotype per samples, due to majority of the reads. thank you for your answer! $\endgroup$
    – Itai Roth
    Apr 2 '20 at 7:49
  • $\begingroup$ you're welcome :) happy genotyping $\endgroup$
    – StupidWolf
    Apr 2 '20 at 19:49

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