Robin, We show SNPs from dbSNP (http://www.ncbi.nlm.nih.gov/SNP/), which includes submissions by 1000 Genomes as well as many other projects and labs. dbSNP aligns submitted flanking sequences to the genome, and when multiple submitted SNPs align to the same spot on the genome, the submitted SNPs are clustered into a reference SNP (rs# IDs). rs35362888 does not include a submission by 1000 Genomes; if you click on rs35362888 in the genome browser, and then click the link to dbSNP's report page (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs35362888), then scroll down to the "Submitter records..." section, you'll see that it was submitted only by ABI. 9 bases to the left is an indel rs71646259 (same -/T but on the other side of TTTTTTTT), but according to dbSNP that was clustered from two submissions by other non-1000 Genomes projects.
I would like to take a look at the 1000 Genomes file where you saw "Chr1 245712945", please could you send me a pointer? Thanks, Angie ----- "Robin Young" <[email protected]> wrote: > From: "Robin Young" <[email protected]> > To: [email protected] > Sent: Friday, November 19, 2010 9:42:42 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] 1000 Genomes Indels > > Sir/Madam, > > > > I've been trying to compare indel positions downloaded from 1000 Genomes > with those in the UCSC browser, however there are some differences > between the two sources, e.g in build 36 for rsid rs35362888 > > > > UCSC : Chr1 245712954 245712955 > > 1000G: Chr1 245712945 > > > > Any help/suggestions as to why there could potentially be differences, > or where the 1000Genomes positions originate from, would be greatly > appreciated. > > > > Regards > > > > Robin Young > > > > Cardiovascular Epidemiology Unit > > Department of Public Health and Primary Care > > University of Cambridge > > > > Strangeways Research Laboratory > > Worts Causeway > > Cambridge > > CB1 8RN > > United Kingdom > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
