On 1/19/11 4:19 PM, Luvina Guruvadoo wrote: > Hello D., > > Thanks for your inquiry. The letters (A, C, T, G) refer to bases that > do not match the reference assembly. "N" means "nucleotide" (unknown), > so it is always a mismatch. By default, mismatching bases are > highlighted red in the display.
Hi Luvina, Thanks for your response. I am still confused. If A, C, T, G are bases that do not match the reference, then are they mismatches? If they are mismatches, then why they are in white (please see http://img4.imageshack.us/img4/4976/screenshot20110119at301.png) instead of red? Also, if all those letters (A, C, T, G, N) are mismatches, it even confuses me more since the track shown in the screenshot was aligned with Bowtie and two mismatches max per read (where as there are some reads with 5 mismatches). Please advise, Thanks, D. _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
