How is the coverage calculated in NGS data for a specific region. My question is not how to calculate it using many tools that are available. My question is-
How percentage coverage for a specific region is calculated?
For example, I have a n reads(overlapping) mapped to a specific exon region of my target sequence. How is the coverage percentage calculated. is it calculated based on number of reads covered that region or bases covered overall within that region.
I think you are confused between "Coverage" and "percentage of reference genome sequenced or covered".
Coverage refers to the read depth. Coverage is calculated at a single nucleotide level and more the reads overlapping a region higher will be the coverage.
The percentage of reference genome sequenced is calculated as region of the reference genome that has sequences aligned to it. You can chose different thresholds of aligned reads to decide if a particular region of a genome has been covered or sequenced enough.
Convert the mean depth per bp to coverage of the bait at a well defined depth of coverage (1x, 4x, 10x, 25x), once donem you divide the coverage of the bait/ bait length x100.
chr start stop bait length depth 1x depth 4x depth 10x depth 25X % of coverage of the bait at (1x, 4x, 10x, 25x)
A 1 119 120 120 120 120 120 100%, 100%, 100%, 100%,
this implies that each bp of the bait was read > 25X
