The coverage of a given reference base is computed by counting the number of read bases mapped to it in an alignment (see Materials and methods). The mean coverage is computed by averaging this value across every base in the reference. Then the relative coverage for a particular base is computed as the ratio of these values. A relative coverage of 1 indicates that a particular base is covered at the expected average rate. A relative coverage above 1 indicates higher than expected coverage and below 1 indicates lower than expected coverage.
