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
