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

<pre><code>##INFO=&lt;ID=AC,Number=A,Type=Integer,Description="Total number of 
alternate alleles in called genotypes
</code></pre>

<p>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.</p>

<p>If you look at your genotype calls, all are 0, so AC = 0</p>

CC BY-SA 4.0
2020-04-02T07:49:42.267Z
Oh, now I get it. freebayes chose 1 genotype per samples, due to majority of the reads. thank you for your answer!
Itai Roth
CC BY-SA 4.0
2020-04-02T19:49:01.680Z
you're welcome :) happy genotyping
StupidWolf
CC BY-SA 4.0
2020-04-01T14:42:24.680Z
2020-04-01T14:42:24.680Z
StupidWolf
<p>I ran freebayes on bacterial data and got a vcf file. Some of the SNPs found have <code>AC=0</code>, but in the bam file I can see that there are alternative alleles, so in my understanding it supposed to be <code>AC&gt;0</code>.</p>

<p>example:
in vcf file:</p>

<pre><code>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
</code></pre>

<p>but with samtools tview:</p>

<p><a href="https://i.sstatic.net/aS63N.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/aS63N.png" alt="samtools tview screenshot"></a></p>

<p>Can someone tell me if this makes sense and why it happens?</p>

<vcf><snp>
Allele count is zero
# Allele count is zero

(Asked by: username_0 on 2020-04-01)

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:

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

**Tags:** vcf, snp

---

## 1 answers

### Answer by username_1 on 2020-04-01. Score: 3 | Accepted answer

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

> **Comments:**
> **username_0**: Oh, now I get it. freebayes chose 1 genotype per samples, due to majority of the reads. thank you for your answer!  
> **username_1**: you're welcome :) happy genotyping  

---

