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
