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<p>Hi Lee,<br>
</p>
<p>Thanks for the examples. These variants do have the same
ancestral and minor allele on the current web site, for example: <br>
</p>
<p>rs7636839<br>
rs7636839 SNP<br>
Most severe consequence Intron variant|See all predicted
consequences<br>
Alleles A/G | Ancestral: G | MAF: 0.42 (G) | Highest population
MAF: 0.49</p>
<p><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=3:142099508-142100508;v=rs7636839;vdb=variation;vf=4598592">http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=3:142099508-142100508;v=rs7636839;vdb=variation;vf=4598592</a><br>
</p>
<p>which version of the browser are you using?<br>
</p>
<p>Best wishes,</p>
<p>Sarah<br>
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<div class="moz-cite-prefix">On 21/07/2017 12:35, Lee Stopak wrote:<br>
</div>
<blockquote
cite="mid:CAEkDndLCdnAQWobQoY+MJ=rgbRhuownwWR8=zM_D7pe7Ncw_4w@mail.gmail.com"
type="cite">
<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>
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