Answers.Body: <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>
  
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Answers.Text: Oh, now I get it. freebayes chose 1 genotype per samples, due to majority of the reads. thank you for your answer!
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Answers.Text: you're welcome :) happy genotyping
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Body: <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>
  
Tags: <vcf><snp>
Title: Allele count is zero
ThreadText: # 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:
  
  [![samtools tview screenshot](https://i.sstatic.net/aS63N.png)](https://i.sstatic.net/aS63N.png)
  
  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=<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
  
  > **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  
  
  ---
  
  