Coverage is calculated based on the start and the stop position of an alignment. However, segemehl produced split reads that are very far from each other and in that case calculating coverage based on the CIGAR string (which indicates which bases between start and end are matches or mismatches) would give a clearer picture of coverage.
Coverage is calculated based on the start and the stop position of an alignment. However, segemehl produced split reads that are very far from each other and in that case calculating coverage based on the CIGAR string (which indicates which bases between start and end are matches or mismatches) would give a clearer picture of coverage.