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

Lee Stopak lee.stopak at ada.com
Fri Jul 21 12:56:21 BST 2017


Ah, I understand, I misassumed the ancestral allele was the major allele,
and just looked at the reference/alternate allele + the specified allele in
the MAF when deciding which was major/minor allele. That was my wrong
assumption.

Thank you!

On Fri, Jul 21, 2017 at 1:48 PM, Emily Perry <emily at ebi.ac.uk> wrote:

> Hi Lee
>
> 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.
>
> Taking your first example, rs7636839, the minor allele is G because it's
> found in 42% of 1000 Genomes individuals:
> http://www.ensembl.org/Homo_sapiens/Variation/Population?
> db=core;r=3:189638652-189639652;v=rs7636839;vdb=variation;vf=4598592
>
> The ancestral allele is also G because that's the allele found in
> Chimpanzee and other primates:
> http://www.ensembl.org/Homo_sapiens/Variation/Compara_
> Alignments?db=core;r=3:189638652-189639652;v=rs7636839;vdb=variation;vf=
> 4598592
>
> All the best
>
> Emily
>
> 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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> --
> 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
>
>
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