Coverage definition in MuSigCV
After playing with MutSigCV 1.4 example data (LUSC dataset), I am now puzzled on the definition of coverage in MutSigCV. Does it refer to the number of "bases" that are adequately sequenced or the depth at each variant location?
If it's "the depth at each variant location", you would imagine in coverage table, there will be many "0"s indicating "wild type" of a sample for that specific type of variant. I checked LUSC coverage table, it rarely has any "0"s. I also checked some highly mutated genes and less frequently mutated genes (defined in LUSC.MAF table), and compared their coverage, and found the difference seems quite small.
Any comments are welcome.