Hello Dmitry, The snp129 table has average heterozygosity (avHet) and standard error (avHetSE) columns that contain values calculated by dbSNP as described here: http://www.ncbi.nlm.nih.gov/SNP/Hetfreq.html
Also see this previously-answered mailing list question regarding the abundance of zeros in these columns: http://www.soe.ucsc.edu/pipermail/genome/2008-April/016014.html A more detailed source (although it is a smaller set) for allele frequency data is the HapMap SNPs track. In particular, I think the hapmapAllelesSummary table contains the information you are looking for. To see a description of the fields in the table, select the following in the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables): clade: mammal genome: human assembly: Mar. 2006 group: variation and repeats track: HapMap SNPs table: select any of the tables in the drop-down menu Now hit "describe table schema". Scroll down to the "Connected Tables and Joining Fields" section, and click on the hapmapAllelesSummary link. I hope this is helpful. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/16/09 16:44, Dmitry Pushkarev wrote: > Hi, > > > > I'm currently wringing short reads aligned that I want to assign error > probabilities based on prior dbSNP information. In simple probabilistic > model I use I need to have priors for all positions in the genome, that is > probability that randomly chosen individual will have base N at position X. > Is there an obvious way to do so using dbSNP database from your web-site? > (i.e. to get some approximation for allele frequencies for given RS# > cluster) > > > > Thanks. > > > > --- > > Dmitry Pushkarev > > +1-650-644-8988 > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
