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Hi Lee<br>
<br>
Another place I think you might have gotten mixed up is the
reference allele. The reference allele is the allele found in the
reference genome. It is neither necessarily the major allele or the
ancestral (though it often is). For rs7636839 the reference allele
is A because that's what was found in the reference genome.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 21/07/2017 12:48, Emily Perry wrote:<br>
</div>
<blockquote type="cite"
cite="mid:e38ca10b-c75b-ee58-a2f4-06ec755ebdc8@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
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"
moz-do-not-send="true">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"
moz-do-not-send="true">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>
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</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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</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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