Thursday, May 11, 2017
Defining and calculating genome coverage, depth and breadth of coverage
Average estimation of the whole genome coverage in a sequencing assay (i.e. depth of coverage) is calculated with the formula:
Similarly you can calculate the estimation of the coverage for each gene or gene locus:
In reality of the sequencing experiment, distribution of the mapped reads is uneven and in additon not all portions of the reads will map to the genome, therefore for each nucleotide you will calculate specific read coverage (per base read coverage), for example using bedtools genomecov:
On the other side, breadth of coverage is a different term than depth of coverage and relates to the proportion of the genome that is covered with reads. Both breadth and depth of coverage correlate to the sequencing depth i.e. the number of reads generated in the sequencing experiment.
For details see publication: