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

[Sarah Hunt]

Hi Lee,

Thanks for the examples. These variants do have the same ancestral and 
minor allele on the current web site, for example:

rs7636839
rs7636839 SNP
Most severe consequence Intron variant|See all predicted consequences
Alleles  A/G |  Ancestral: G | MAF: 0.42 (G) | Highest population MAF: 0.49

http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=3:142099508-142100508;v=rs7636839;vdb=variation;vf=4598592

which version of the browser are you using?

Best wishes,

Sarah

On 21/07/2017 12:35, Lee Stopak wrote:
> 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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