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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?

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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

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  • $\begingroup$ 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 at 7:49
  • $\begingroup$ you're welcome :) happy genotyping $\endgroup$ – StupidWolf Apr 2 at 19:49

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