Count coverage WGS data
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23 months ago
mailard • 0

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

genome qualimap BAM QC • 653 views
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23 months ago
ATpoint 65k

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.

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

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

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Okey, thanks for your time!