Allele count is zero 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&gt;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:



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=&lt;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