Hello, Xiaojun. One of our engineers had this to say:
dbSNP's allele frequencies in our snp135 table don't necessarily reflect more than one population. It all depends on what data were submitted by various labs/projects, and combined by dbSNP. Each dbSNP reference SNP (rs#) is composed of one or more submitted SNPs (which have ss# IDs that you can see on dbSNP's web pages). Each submitted SNP may or may not include frequency data and population data. The frequencies that dbSNP reports for a reference SNP are tallied from frequencies reported from all submitted SNPs that were clustered into that reference SNP. UCSC shows reference SNPs only, not submitted SNPs. In order to determine what populations are represented in a particular reference SNP, you can click on the dbSNP link at the top of the details page for the SNP. At the bottom of dbSNP's reference SNP report page is a summary of population and genotype data, if available. If you need population data for a large number of SNPs, then you can download data directly from dbSNP's FTP site in various formats: ASN, XML, or flatfile database table dumps (those are what UCSC uses when building snp* tables). Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Xiaojun Zhao Sent: Wednesday, January 25, 2012 1:47 PM To: [email protected] Subject: [Genome] Allele frequencies Are allele frequencies (hg19.snp135) based on all ethnicity group? Thanks. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
