Question: How Coverage percentage is calculated in NGS data
1
gravatar for crivenster
6.0 years ago by
crivenster50
India
crivenster50 wrote:

Hi,

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.

Thank you

ADD COMMENTlink modified 6.0 years ago by Kizuna800 • written 6.0 years ago by crivenster50
7
gravatar for Ashutosh Pandey
6.0 years ago by
Philadelphia
Ashutosh Pandey12k wrote:

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.

ADD COMMENTlink modified 5 months ago by RamRS27k • written 6.0 years ago by Ashutosh Pandey12k
0
gravatar for Kizuna
6.0 years ago by
Kizuna800
France, Paris
Kizuna800 wrote:

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

ADD COMMENTlink modified 5 months ago by RamRS27k • written 6.0 years ago by Kizuna800
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