Hello Anna, You can read more about how the data for this track are calculated and what they mean by looking at the description page (and the references contained therein):
http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chr21&g=cons46way You can get to the description page for any track by clicking on the blue bar to the left of the track in the main display or by clicking on the track title above its pulldown menu in the browser. Note this part of the "Description" section which addresses your questions: In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 9/14/11 1:55 PM, Anna Olofsson wrote: > Hi, I'm a beginner at USCS browser and I was wondering how to get the > conservation score for a specific substitution, e.g. C/T for homo sapiens. I > tried to browse for my gene by choosing Genome and then go to Tables where I > chose option comparative genomics and then I got the conservation > automatically. And then I choose the option mammal cons > (phyloP46wayPlacental). What I don't get is the table I get when press the > output-button (with plain text). There are two columns, and I understand that > the first column is my position and I'm guessing the second i the p-value, > but I thought that phyloP was given out p-values and I'm getting a value > above 1. Why is that? Also, when I go back and choose mammal cons by > phatscons, I get a value below 1. What I'm wondering is how to interpretate > these values I get? > > Best, > Anna > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
