Hi Qasim, Yes, this is probably due to strand confusion, as you suspected. We obtain our Ancestral Allele information directly from dbSNP, and in this case as C. However, if you click on the "Re-alignment of the SNP's flanking sequences to the genomic sequence" on our details page, you can see that when we realigned the flanking sequences, we actually found that it matched better to the opposite strand.
I do not know how Ensembl reports SNPs, but confusion as to the correct strand may be why it reports the Ancestral Allele as G while dbSNP reports it as C. I recommend contacting Ensembl: http://uswest.ensembl.org/common/Help/Contact?db=core and/or dbSNP: [email protected] if you have any questions about their processes. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/14/11 8:28 AM, Qasim Ayub wrote: > Hi > > > > I am trying to figure out the ancestral allele for rs2205718 > <http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2205718> . Ensembl > lists G as ancestral whereas from UCSC browser it appears to be the C > allele.Could this be related to which strand is used as the human > reference (hg19) has T allele in this position. > > > > With best wishes > > Qasim > --- > Qasim Ayub > Team 19: Human Evolution > Room Number E2-18 > The Sulston Laboratories > The Wellcome Trust Sanger Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge CB10 1SA > United Kingdom > > E-mail: [email protected] > Tel: +44-(0)-1223-834244 Ext:7652 > Fax: +44-(0)-1223-494919 > > > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
