Hi Stewart, > I tried using the table browser to retrieve all of them in a bed and > got 893! I wonder where the others come from.
The mappings in snp130 are all directly from dbSNP. I don't know why Entrez would not return all of the dbSNP items (but as a programmer, I wonder if Entrez needs to be updated for the latest dbSNP release, or if there is a keyword issue somewhere). The dbSNP folks can give a more authoritative answer: [email protected] Thanks for chiming in, Angie ----- "Stewart Stevens" <[email protected]> wrote: > From: "Stewart Stevens" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: "David Gordon" <[email protected]>, [email protected] > Sent: Thursday, December 3, 2009 1:23:46 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] mitochondrial snps > > Hi, > > If you do a search at Entrez for "mt[CHR] AND homo sapiens" you get > back 872 SNPs. If you search for one of these on the UCSC browser I'm > seeing plenty of mitochondrial SNPs. > > I tried using the table browser to retrieve all of them in a bed and > got 893! I wonder where the others come from. Putting chrM in the > position field and requesting snp130 data as a bed did this. > > Cheers, > > Stewart > > > > On 4/12/2009, at 9:46 AM, Jennifer Jackson wrote: > > > Hi - > > > > I double checked the browser and found the Affy array with some SNP > > data (in hg18). I didn't find it in any other tracks. hg19 has > > nothing. > > > > What is interesting is that some tracks have a note that says "no > > chrM data" instead of the pull-down menu for display - and some > > don't - even when both sets have no chrM data. Would be nice to have > > > this be consistent, especially for tracks that get a lot of use, > > like dbSNP. > > > > Thoughts? Am I missing any other SNP tracks with data? I double > > checked but could be wrong. > > > > Thanks, > > Jen > > > > ------------------------------------------------ > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > ----- "David Gordon" <[email protected]> wrote: > > > >> From: "David Gordon" <[email protected]> > >> To: [email protected] > >> Sent: Thursday, December 3, 2009 11:58:38 AM GMT -08:00 US/Canada > > >> Pacific > >> Subject: [Genome] mitochondrial snps > >> > >> Human mitochondria is known to contain many snps. However, the > >> Genome > >> Browser as well as the downloaded file snp130.txt show no > >> mitochondrial snps. Am I mistaken? Is there somewhere else on > the > >> UCSC website where human mitochondrial snps may be downloaded? > >> > >> > >> Thanks in advance, > >> David Gordon > >> > >> > >> _______________________________________________ > >> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
