Hi Greg, What Mary said is true: we obtain all of the class (and mapping and allele) information from dbSNP. But you might also like to know that we annotate cases like this that don't completely make sense. In the snp130Exceptions table, rs71254726 is noted to have the exception 'SingleClassZeroSpan'.
Descriptions of the all of the cases we annotate are in the snp130ExceptionDesc table. Hope this helps! -- Brooke Rhead UCSC Genome Bioinformatics Group Mary Goldman wrote on 9/21/10 10:52 AM: > 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
