I am running this command, using the UCSC utilities:

bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1

to get phastCons77way coverage from 25526708 to 25528708 on chromosome 4 of the chicken genome.

The file I am using can be downloaded from here. I assumed "coverage" would be the ratio of loci with phastCons scores (so if a region of 2,000 bp has phastCons for every bp, the coverage should be 1). I think the phastCons was calculated vis multi-alignment, so it's not like each of the 77 species would have a score for that locus on the chicken genome, but rather they together has one score calculated for each bp when available.

However, I got 1.1345 as output. I am confused, 'cause I thought coverage cannot be more than 1, aka 100%.



Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.