[ensembl-dev] unmapped/un-displayable SNP from dbsnp
bert at ebi.ac.uk
Fri Oct 8 16:10:31 BST 2010
Although it says on the mentioned dbSNP page:
RefSNP Alleles: A/G
it also says:
and further down on the page it again says:
CCG => CCA
CCG => CCC
CCG => CCT
But the in the Population diversity part again only A and G are
mentioned as alleles.
So, I get the feeling dbSNP is messing up things here ....
On Fri, Oct 8, 2010 at 3:54 PM, Kim Brugger <kim.brugger at easih.ac.uk> wrote:
> If you look at the dbsnp page for this snp it is only two alleles A/G for
> this snp, so it looks like the counting of alleles is faulty. Furthermore
> the SNP is represented in the 1000 genomes data, and other datasets I deem
> Thanks for explaining how/why this filtering is done.
> On 08/10/10 14:14, Graham Ritchie wrote:
>> Hi Kim,
>> This SNP has *more than* 3 alleles, and we have taken the decision to fail
>> all such SNPs, we debated this decision internally recently and Paul
>> concluded as follows:
>> "These are still far, far more likely to be errors than real. While some
>> probably exist, true SNPs with all four alleles require very complex
>> selection pressures to remain in the population and so this number is simply
>> never likely to grow to "many SNPs." In fact, the word quadallelic does not
>> return any results in Pubmed.
>> This does not mean that it will never happen, only that it is very, very
>> rare. Note that we don't fail triallelic SNPs, which are also rare and
>> enriched for error."
>> Hope this makes sense. If you have example of SNPs that don't appear for
>> other reasons then please let us know. We do track all SNPs we fail and the
>> reason for doing so in the failed_variation table of the variation database.
>> On 8 Oct 2010, at 13:54, Kim Brugger wrote:
>>> I am looking for the rs1053738 snp. When I do a search on the ensembl-web
>>> it is found and it exists with 2 synonyms, but if I want to display I am
>>> told it was not mapped as the variation has 3 alleles.
>>> The SNP should be located at 3:124951820-124951821. I have a large set
>>> of snps that I cannot find either with the ensembl-web or using the api.
>>> Kim Brugger
>>> EASIH, University of Cambridge
>>> Dev mailing list
>>> Dev at ensembl.org
> Kim Brugger
> EASIH, University of Cambridge
> Dev mailing list
> Dev at ensembl.org
Bert Overduin, Ph.D.
PANDA Coordination & Outreach
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
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