DepthOfCoverage -genelist: 'total coverage' and 'mean coverage' explanation

user31888user31888 Member
edited April 2016 in Ask the GATK team

Hi,

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

Q1: Does the 'total coverage' make the sum of all the bases or reads 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?

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