Hello Terence, There is no way to tell if the SNP is a reference match or not by examining the Genome Variants (or any variation) track alone. Only by examining the raw data can it be determined whether there was any/enough coverage in the area to call a SNP.
This data is not always available, but you could try contacting the original data authors to see what they have. Be warned that these datasets can be very large and require special tools to view/analysis the data. Adding in a confidence/coverage score of some kind associated for all of the comparison genome's bases (not only SNP bases) sounds like a great idea. This is another topic you could bring up with the groups that are generating the variation data. Hopefully this helps a bit, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/11/10 1:59 PM, Terence Dante Capellini wrote: > Hi, > I am currently using the genome variants tracks on the genome browser and am > wondering the following: > If no variant is displayed for a given individual (e.g., YRI NA18507) at a > particular SNP does this mean that the individual has the same allele as the > human reference individual? Alternatively, does it mean there is no data > available for that individual due to some technical difficulty? > Thank you kindly, > Terence > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
