Hey Hiram, Sorry - am I missing something? rs12345 looks like a simple bi-allelic SNP (not an indel) which should have a length of 1. It's ref allele matches the ref genome. The annotation page also says it has length 1. I don't think this is the perfect case you were looking for....
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=248751473&o=25855458&t=25855459&g=snp135Common&i=rs12345 Yep, I've seen that link. Thanks again. Sorry - I never dreamed this would turn into such a marathon thread! -J On Fri, Mar 23, 2012 at 1:34 PM, Hiram Clawson <[email protected]> wrote: > Good Afternoon J: > > This is a perfect case to illuminate the interval notation. > Note the interval this item is declared to be in > [25855459-25855459) > Note the size of this interval: = end - start = 25855459 - 25855459 = 0 > > The length of this item is ZERO ! It doesn't exist ! > It can not be found in this sequence. It is somewhere between > actual bases: [25855458-25855459) and [25855459-25855460) > but not in this reference sequence. > > So, in one sense, you could say that the interval: [25855459-25855459) > is actually talking about the gap between two bases. The genome > browser does not show gaps at all, there are only bases and they > are directly next to each other with no intervening space. We don't > do gaps between bases. When you enter such a position, we can't > display it, we do the next best thing and display one of the bases > next to this non-existent item. > > I'm sure you have already seen our discussion: > http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms > > -Hiram > > ----- Original Message ----- > From: "J Ireland" <[email protected]> > To: "Hiram Clawson" <[email protected]> > Cc: [email protected] > Sent: Thursday, March 22, 2012 11:24:00 PM > Subject: Re: [Genome] base vs gap numbering > > Hey Hiram, > > > I'm definitely a firm believer in the interval, trust me - and I > definitely dig the UCSC data tables and the half-open, zero-start intervals. > > > So, rolling with the "everything is an interval" and looking up rs12345... > > > If I zoom into the browser here: > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr22%3A25855458-25855460 > I see rs12345 appears to be at [25855458-25855459) given the hash marks. > This is a zero-based start and end. > > > Now, I click on rs12345 and see the position as 25855459-25855459 in the > annotation page. Should I interpret this as [25855459-25855459), with a > one-based start and zero-based end or as [25855459-25855459] a fully closed > interval with start and end both one-based? > > > I know you're straddling different count-starting conventions between db > tables and the annotation pages. Maybe my misunderstanding is I thought the > browser was using the same convention as the annotation pages, but it looks > like the browser is actually more inline with the db tables... > > > Thanks for taking this trip with me down the rabbit hole of the obscure > and arcane ;) > -J > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
