Hi Greg, We obtain class information directly from dbSNP. As you can see on the details page for this SNP (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs71254726), dbSNP classifies this SNP as a single nucelotide polymorphism (or "single"). If you have questions about their classifications please contact dbSNP ([email protected]).
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 9/21/10 7:42 AM, Gregory Dougherty wrote: > Hi Brooke, > > Thank you. The insertions part was what I didn't get (there's a problem with > only looking at certain fields from a table, you end up missing out on things > like "class" = "insertion" :-( ). > > Could you explain SNP rs71254726 to me? It says it's of class "single", but > (over at dbSNPs) it looks like it's a deletion (AC -> C/G), and it has a 0 > range (on seven different chromosome! :-) ). > > Thanks! > > Greg > > ----- Original Message ----- > From: "Brooke Rhead"<[email protected]> > To: "Gregory Dougherty"<[email protected]> > Cc: [email protected] > Sent: Monday, September 20, 2010 5:15:14 PM GMT -06:00 US/Canada Central > Subject: Re: [Genome] Questions about SNP130 > > Hi Greg, > > Here is a nice discussion of chromosome positions used in our tables on > genomewiki: > http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms > > Note that we add one to the start coordinate for display in the Genome > Browser: > http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 > > To answer your specific question: > If start = 5 and end = 6, then you do indeed have a 1 bp feature at > position 5, in BED coordinates. The feature is at position 6 in Genome > Browser display coordinates. > > (You can actually paste BED coordinates directly into the Genome Browser > position/search box, and they will automatically be changed to GB > coordinates. For instance, "chr1 5 6" turns into "chr1:6-6" when you > hit "jump".) > > The SNPs whose lengths are zero are insertions, which don't cover any > bases of the reference sequence. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 09/20/10 13:48, Gregory Dougherty wrote: > >> I've loaded SNP130 into a local database (thank you very much for the >> data files, etc.) and have some questions about the data. >> >> To start, my understanding is that chromosome positions are [start, >> > end), i.e. from start (inclusive) to stop (exclusive). Or, to put it > another way if start - 5 and end = 6, then you have a 1 bp feature at > position 5. > > >> No? >> >> Because I got these results from some searches: >> mysql> select count(*) from snp130 where chromStart = chromEnd; >> +----------+ >> | count(*) | >> +----------+ >> | 2,632,502| >> +----------+ >> >> mysql> select count(*) from snp130 where chromStart = chromEnd - 1; >> +----------+ >> | count(*) | >> +----------+ >> |15,322,316| >> +----------+ >> >> The fact that you have roughly 6x SNPs where chromEnd - chromStart = >> 1 says to me that my understanding should be correct, but that leaves me >> > wondering why there are 2.6 million "SNPs" that don't cover any bases. > >> Also, IIRC, the first base of a chromosome is base 0, yes? >> >> TIA, >> >> Greg >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
