Hello Abhishek, Thank you for searching the mailing list archives!
Are you referring to your own SNP predictions, or the SNPs in the SNP track on the Genome Browser (from dbSNP)? If you are referring to the SNP track, you can find information on a SNP's predicted functional role in the 'func' field of the SNP table (such as the snp129 table for the hg18 assembly). Note that non-synonymous changes are denoted by words other than "non-synonymous". A full description of the possible classifications for the 'func' field is on the SNP track details page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=snp129). Here is an excerpt: # Coding - Synonymous - no change in peptide for allele with respect to reference assembly (coding-synon) # Coding - Non-Synonymous - change in peptide for allele with respect to reference assembly (nonsense, missense, frameshift) These annotations are done by dbSnp, based on RefSeq Genes. Indel information is in the 'class' field of the SNP table. Again, more details are available on the SNP track details page. The locations of SNPs in genomic coordinates are available in the chrom, chromStart and chromEnd fields. We do not have information on the position of SNPs within genes; however, there are other annotations in the 'func' field that describe a SNP's position in a gene, such as locus region, intron, untranslated, splice site, etc. If you are instead referring to your own SNP predictions, perhaps this previous mailing list response is what you are looking for: https://lists.soe.ucsc.edu/pipermail/genome/2009-May/018897.html I hope this is helpful. If you have further questions, please feel free to email us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/07/09 08:45, Pratap, Abhishek wrote: > Hi All > > > > This might seem to be an old track question. However I was not able to > find a good answer in the mailing list archives. > > > > For all our SNP predictions we would like to know whether they are > synonymous / non-synonymous. If Non-synonymous/Exonic then find the > position on the gene where amino acid is getting changed and to what > ...Also info about indels will help. > > > > It will be great if you could give me some pointers. > > > > > > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences <http://www.igs.umaryland.edu/> > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > > Chair > RSG-Worldwide <http://iscbsc.org/rsg> > ISCB-Student Council <http://iscbsc.org/> > > > > > > > > > > > > Thanks, > > -Abhi > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
