Count coverage WGS data

Question

[mailard]

Hello! I aligned my WGS data to the reference genome. And now I want to see whats coverage I have (50X or 60X)? I run Qualimap and have these results: https://drive.google.com/drive/folders/1pGB7F6521dKOHylvAzZZMfWHKsPXS6LM?usp=sharing

Can you help me to understand the report? Thanks for your time

Answer 1

[ATpoint]

The genome_coverage_quotes.png tells you how how many % of your genome are covered by at least x-fold. If you want to calculate an average value then see whether there is a text file in qualimap that allows to get the values from that graph and calculate a mean. Looks like roughly 90% are covered at least 20x, 55% are 30x, 25% are 40x, will probably average out at something between 20x and 30x.

[mailard]

Thanks for your answer! I find "mean coverage", but it looks strange: mean coverageData = 348.3323X

[ATpoint]

Cannot comment to that, sounds wrong based on the plots.

[mailard]

Okey, thanks for your time!