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Hi Lee<br>
<br>
Major does not mean ancestral. The major allele is the allele which
is the most frequent. The ancestral allele is the allele found in
the aligned region in related species. In most cases the ancestral
allele will be the major one, but not always.<br>
<br>
Taking your first example, rs7636839, the minor allele is G because
it's found in 42% of 1000 Genomes individuals:<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:189638652-189639652;v=rs7636839;vdb=variation;vf=4598592">http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:189638652-189639652;v=rs7636839;vdb=variation;vf=4598592</a><br>
<br>
The ancestral allele is also G because that's the allele found in
Chimpanzee and other primates:<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Variation/Compara_Alignments?db=core;r=3:189638652-189639652;v=rs7636839;vdb=variation;vf=4598592">http://www.ensembl.org/Homo_sapiens/Variation/Compara_Alignments?db=core;r=3:189638652-189639652;v=rs7636839;vdb=variation;vf=4598592</a><br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 21/07/2017 12:35, Lee Stopak wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAEkDndLCdnAQWobQoY+MJ=rgbRhuownwWR8=zM_D7pe7Ncw_4w@mail.gmail.com">
<div dir="ltr">Hi all,
<div><br>
</div>
<div>I am doing a number of calls to fetch ancestral allele,
minor allele, and allele frequency data. Overall, I have about
35000 SNPs to fetch. I have no problem doing the calls, but
about 15% of them return an identical base as both the minor
allele and the ancestral allele. When I then lookup that SNP
on the ensembl webpage, they are NOT the same allele, but are
different. Here are a few SNPs where the minor and ancestral
allele are returned the same: </div>
<div><br>
</div>
<div>rs7636839<br>
</div>
<div>rs2495239<br>
</div>
<div>rs11705932<br>
</div>
<div>rs6999859<br>
</div>
<div>rs7432328<br>
</div>
<div>rs546131<br>
</div>
<div>rs6003982<br>
</div>
<div>rs2203205<br>
</div>
<div>rs10101158<br>
</div>
<div>rs7366282<br>
</div>
<div><br>
</div>
<div>Does anybody know why this is? I don't think it is a bug in
my code, considering the rest of the calls are returned
correctly. </div>
<div><br>
</div>
<div>Thanks!</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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