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

[Emily Perry]

Hi Lee

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.

All the best

Emily

On 21/07/2017 12:48, Emily Perry 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
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-- 
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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