I am interested in MuSiC. When I use CalcWigCovg function, there is a directory called gene_covg, which contain per-gene covered base counts for each sample. What is the relationship between gene length and gene covered bases? Usually gene length is longer than covered bases, does that mean for most of the bases within this gene, they cannot meet the coverage requirement, and what is the number of coverage requirement? Why this number is different between samples, does that mean during sequencing, some bases in a specific sample cannot be sequenced well? I read from some papers that, when people calculate background mutation rate, they usually divided the mutated bases by the total bases. (eg, Somatic mutations affect key pathways in lung adenocarcinoma, nature, 2008). Is the "bases" here the same with "coverage" in MuSiC? Also, in the output of total_covgs, there are overall non-overlapping coverages per sample. If I provied, say 5 genes (5 roi) in roi file, does that mean the sum of the 5 gene_covg in each sample is equal to the total_covg of this sample in total_covgs file? But results seems not. Looking forward to your explaination and appreciated for that.