Hello Scott - This is confusing, due to the different dbSNP releases. Hopefully some information about the track and links can help.
The link from the hg18/dbSNP 130 track is based just on a SNP rs number, and the most current record at NCBI comes up, which is for build 131. There is no way around this for us. http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs9629043 Back in build 130 (and in build 129), rs9629043 did map in two locations. UCSC maps directly from dbSNP content and only realigns the flanking sequence (back to the original map location from dbSNP). We do not alter content but do add in some annotation under certain circumstances. When there are unexpected things we notice, they are included as UCSC Annotations on description page. For this SNP rs9629043, in hg18, and track dbSNP 130, two locations are noted on the item description page, below the dbSNP info. In some cases (not this one) even more UCSC annotation can be added (see the Methods section "UCSC Annotations" for the types of things we will note). Thank you and hopefully this helps with any confusion. Please contact our mailing list again if you would like more help for this or other questions, Jen UCSC Genome Browser support On 8/31/10 3:39 AM, Davidson, S. wrote: > Hi UCSC team, > > I have came across an SNP on the dbSNP 130 build that has two entries. > The SNP is rs9629043. It is shown on UCSC to be in 2 locations on different > chromosomes; chr1:554,550-554,700 and chrM:3,974-4,474. > Following the link to dbSNP, they have it solely at the chr1 location. > > Is this an error in the transfer onto the UCSC system that QC didn't catch or > is it matched here due to an alignment that dbSNP haven't made? > > Thanks very much for the help, > > Scott Davidson > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
