Hello Carl, UCSC incorporates positional information directly from dbSNP. There are multiple genomes and dbSNP versions at UCSC. Confirming that the same data are being compared would be important - click on the dbSNP track name in the Assembly browser for full data source/credit details.
In the most recent Chicken genome, galGal3, the track group Variation and Repeats has two BGI tracks. There is no dbSNP track for this genome. I was unable to determine which genome rs24649162 is from. However, if you do have two SNP track within a genome, you can use the Table browser to compare the data with the functions "intersection" and "correlation". Or, download the data and use your own tools. http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support On 7/13/10 1:05 PM, Carl Schmidt wrote: > I am having a problem resolving discrepancies between chicken SNPs > mapped by NCBI and their locations in the chicken UCSC browser. > For example SNP rs14548959 map to the same chromosome by NCBI or when > blatting the sequence to the UCSC browser, but their different by > several million base pairs. > > Also, there are discrepancies between BGI numbers at NCBi versus ones > listed at UCSC (rs24649162) > > Are these differences arising from different versions of the genomic > sequence and SNP list at UCSC and NCBI? > > Also, is it possible to get a mapping of rs numbers to the UCSC BGI > number? > > Best regards, > Carl > > > > Carl Schmidt > Department of Animal& Food Sciences > University of Delaware > Newark, DE 19716 > 302-831-1334 > [email protected] > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
