Hi Teresita, I think this is another case where dbSNP could do better when aggregating information from multiple submissions; specifically, I think they should tally the "+" counts as G, so rs3216792 would have 24.74% G, 75.26% -.
Clicking through the UCSC details page for rs3216792 to dbSNP's (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3216792), indeed the genotype summary at the bottom of the page includes genotypes like "+/+" and "+/-" but the corresponding allele counts are all for - or G which makes more sense. Clicking through to the submitted SNPs whose genotype info dbSNP combined for rs3216792 (http://www.ncbi.nlm.nih.gov/SNP/snp_ss.cgi?subsnp_id=6310628 and http://www.ncbi.nlm.nih.gov/SNP/snp_ss.cgi?subsnp_id=48294469), it looks like EGP_SNPS's submission used genotypes -/-, -/G and G/G but SNP500CANCER's submission used -/-, +/- and +/+ -- I think SNP500CANCER should have used G instead of +. I suggest reporting this to dbSNP <[email protected]> so they can detect and fix these cases (looks like there are 273 SNPs in build 132 with allele counts for "+"). Hope that helps, Angie ----- "Teresita Diaz De Ståhl" <[email protected]> wrote: > From: "Teresita Diaz De Ståhl" <[email protected]> > To: [email protected] > Sent: Tuesday, May 31, 2011 1:56:39 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] allele frequency dbSNP > > Hi, > I wonder about allele frequency for SNPs. > For example rs3216792 (a deletion SNP). > Observed alleles are -/G and reference is G. > But allele frequencies reported are G:6.529%; -:75.258%; and > +:18.213%. What does + means in this case? G is as the reference, - a > deletion and +? An extra G? > A would appreciate if you can clarify this point. > Kind regards > > Teresita Ståhl > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
