Hi John, The colors you see do not represent allele frequency. The colors represent SNP Features and are configurable from the track controls page. One way to navigate to the track controls is from the Genome Browser page: scroll down to the "Variation and Repeats" section and click on the track "SNPs(131)". This will take you to the track controls page, where you will find "Coloring Options" (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=snp131#colorSpec). If you expand this section, you will see default colors set for the "Function" SNP Feature for Color Specification, which is what you currently see in the browser display.
I hope this answers your question. Please contact us again at [email protected] if you require further assistance. Best, Luvina --- Luvina Guruvadoo UCSC Genome Bioinformatics Group John Kenyon wrote: > 27 Feb 2011 > > > Dear Sir or Madam: > > I have two questions regarding the Full SNP View of the UCSC Genome Browser. > Upon expanding the SNP to the full view, the different font color options > have me confused: (1) do these font color options represent the frequency of > the allele and (2) is the frequency within the specific population or the > general population? > > I look forward to your response regarding the above. > > > Regards, > -John > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
