Dear Neil, When you are using the browser search feature, it is organizing the results using the build number and then listing the dbSNP ID. When you click on that result it takes you to a zoomed out location in the browser that covers that entire build, not just the dbSNP that you were searching for. If you zoom in on that particular dbSNP that you search for, the coordinates are correct.
Please take a look at this session: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Vanessa&hgS_otherUserSessionName=dbSNP_MLQ_090210 The coordinates are: chr2:241179847-241179847 for dbSNP: rs3792267, but the browser view is zoomed in at these coordinates: chr2:241,179,841-241,179,857 If this doesn't answer your question, please don't hesitate to contact the mailing list again. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Neil Samson" <[email protected]> To: [email protected] Sent: Thursday, September 2, 2010 2:20:26 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Fwd: Incorrect coordinates for dbSNP summary search result page Sorry, I meant to say that the coordinates on the search result page seem incorrect (of course the coordinates should be the same for different dbSNP builds). The search result page lists the SNP as: rs3792267 at chr2:241179597-241180097 but the coordinates in the summary page going through the browser (and on the dbSNP website) are: dbSNP: rs3792267 Position: chr2:241179847-241179847 Or am I missing something here? This seems to be the case for other SNPs I have tried. ---------- Forwarded message ---------- From: Neil Samson <[email protected]> Date: 2 September 2010 09:31 Subject: Incorrect coordinates for dbSNP summary search result page To: [email protected] Hi I believe the results returned for a dbSNP rs ID search from the browser gateway are incorrect. For example a search for rs3792267 from the gateway (build hg18) returns the following: http://genome.ucsc.edu/cgi-bin/hgTracks?hgt.dummyEnterButton.x=0&hgt.dummyEnterButton.y=0&hgsid=168907504&clade=mammal&org=Human&db=hg18&position=rs3792267&hgt.suggest=&pix=1000 In my browser all the coordinates for the various builds of dbSNP are identical (even cross species ones) so there is definitely something not right going on. The coordinates in the actual genome browser all seem to be fine though. Sam _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
