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
