Coverage is an indication of how well a nucleotide is represented in a sequencing read.

Coverage is used to describe nucleotides in shotgun sequencing (where sequence fragments are generated and then aligned to give the sequence of DNA). Coverage refers to number of times a given base appears in the fragments.

It can be calculated using the following formula:

N* L/G where N is the number of reads, L is the average read length and G is the length of the genome.

To look at an example: there is a genome of 1,000 bp. Fragments are generated and the average length of reads is 500 nucleotides. The number of reads completed is 10. Therefore the coverage of a given nucleotide would be around 5. Meaning that that specific base should appear 5 times within the DNA fragments.