Hi Xingyi, GC Percent is computed based on the standard DNA base pairs (A,C,T,G) and not off of M,R,W,S,Y,K,V,H,D,B,X which you described below.
Do you have the "Base Position" track in "full" display mode? When you are zoomed in at the base level and have the "Base Position" track set to "full" you can see that the first line shows the DNA bases that are used in the GC percent computation. Below that the track shows three frames of translation when viewed at the base level. To read more about this track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr21&g=ruler Hopefully this makes sense. If not, feel free to contact the mailing list with any further questions you may have. Vanessa Kirkup Swing UCSC Bioinformatics Group ----- Original Message ----- From: "WOO Xing Yi" <[email protected]> To: "Vanessa Kirkup Swing" <[email protected]> Cc: [email protected] Sent: Sunday, June 20, 2010 7:38:26 PM GMT -08:00 US/Canada Pacific Subject: RE: [Genome] hg18 gc5Base Hi Vanessa, Thanks for your reply. Another question: Other than A,C,G,T and N, how does the GC-content computation considers bases M,R,W,S,Y,K,V,H,D,B,X? Thanks Xingyi -----Original Message----- From: Vanessa Kirkup Swing [mailto:[email protected]] Sent: Saturday, June 19, 2010 5:12 AM To: WOO Xing Yi Cc: [email protected] Subject: Re: [Genome] hg18 gc5Base Hi Xingyi, The reason for numbers other than 0,20,40,60,80,100 is because N bases aren't counted. So for instance, ACTNN would yield 33.3% G-C because only 1/3 are G-C instead of 1/5. Please don't hesitate to contact the mailing list if you have more questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "WOO Xing Yi" <[email protected]> To: [email protected] Sent: Thursday, June 17, 2010 9:12:50 PM GMT -08:00 US/Canada Pacific Subject: [Genome] hg18 gc5Base Hi, I'm looking at the data downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/gc5Base/ While it's mentioned that the possible values for GcPercent is 0,20,40,60,80,100, I found other values as well. How should I interpret these values? e.g. in chr1 307581 33.3 511231 50 3895126 50 13429746 25 29750666 50 103636491 25 103843836 33.3 103893836 50 120498676 50 120738216 33.3 120788216 50 121186956 50 141476956 33.3 141909281 25 142134336 25 142386046 33.3 142436046 50 142935836 33.3 142985836 50 143163101 25 143522081 50 144876006 50 144926006 33.3 146492661 50 146542661 33.3 146727981 50 146777981 33.3 147000771 25 147221081 25 147726266 50 204498841 25 221814466 50 246974831 33.3 247024831 50 247199716 50 Thanks and regards, Xingyi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
