Question: GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
gravatar for user31888
4.1 years ago by
United States
user3188880 wrote:


I ran DepthOfCoverage using a RefSeq interval list to use with the -genelist argument. I obtained a gene summary table displaying notably the 'total coverage' and 'mean coverage' values (see here for an example).

I annotated the file and got this kind of values:

Gene      total coverage      mean coverage
AGL       54765               5.75
AGMAT     1089                0.33

Q1: Does the 'total coverage' value is the sum of all the bases or reads (across all my samples) mapped in each RefSeq interval provided?

Q2: How is the 'mean coverage' calculated or related to the 'total coverage'? Does it takes the read length or gene length (or something else) into account? Is it the value usually reported in the papers as 100X coverage for example?

depthofcoverage gatk • 2.2k views
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