Hello, The scores in the browser are from compressed files which result in slight changes when uncompressed (the changes are not considered significant), as explained in the track's description. If the exact value is desired, then you are using the correct files in Downloads for this information.
We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "zhuocheng Hou" <[email protected]> wrote: > From: "zhuocheng Hou" <[email protected]> > To: [email protected] > Sent: Thursday, September 3, 2009 7:28:25 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] difference conservation score > > Hi there, > > I want to compute the conservation score (phastCon) for some > chromosome > region. However, I found different phastCon score between the genome > browser > output and direct calculate score from the phastCon wigFix file. Can > someone > give me hints to calculate these values? For example, > > human chr15: chr15:66,362,798-66,378,354 > This region is the fragment of the phastCons28wayPlacMammal: > fixedStep > chrom=chr15 start=66362798 step=1 > > If we directly calculated the average value, stdev, var, we would get > following values: > > mean: 0.4561 > var: 0.1136 > stdev: 0.3655 > min: 0 > max: 1.264 > > > Output from genome browser for human chr15: > chr15:66,362,798-66,378,354 > > * Vertebrate Multiz Alignment & PhastCons Conservation (28 Species) > (phastCons28wayPlacMammal)* > > > * Position: * chr15:66,362,798-66,378,354 > > * Total Bases in view: * 15,557 > > * Statistics on: * 15,555 * bases * (% 99.9871 coverage) > > Database: hg18 Table: phastCons28wayPlacMammal Chrom Data > start Data > end # of Data > values Each data > value spans > # bases Bases > covered Minimum Maximum Range Mean Variance Standard > deviation chr15 66362798 66378352 15,555 1 15,555 (99.99%) 0 1 > 1 0.204761 0.130526 0.361283 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
