[ensembl-dev] Errors in minor allele and ancestral allele

[Lee Stopak]

Hi all,

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:

rs7636839
rs2495239
rs11705932
rs6999859
rs7432328
rs546131
rs6003982
rs2203205
rs10101158
rs7366282

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.

Thanks!
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