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Coverage (read or sequencing depth)

Depth of coverage

How strong is a genome "covered" by sequenced fragments (short reads)?

Per-base coverage is the average number of times a base of a genome is sequenced. The coverage depth of a genome is calculated as the number of bases of all short reads that match a genome divided by the length of this genome. It is often expressed as 1X, 2X, 3X,... (1, 2, or, 3 times coverage).

Breadth of coverage

How much of a genome is "covered" by short reads? Are there regions that are not covered, even not by a single read?

Breadth of coverage is the percentage of bases of a reference genome that are covered with a certain depth. For example: 90% of a genome is covered at 1X depth; and still 70% is covered at 5X depth. 

See also:

 → Calculating breadth of coverage using bowtie2 and samtools