Hello,
I have samples sequenced at BGI using NimbleGen target enrichment kit which shows 55% of targeted sequence was covered 20x and an average coverage depth of 28X.
What does this indicate, does this mean the variant calling may not be reliable ? What is the "normal" average coverage for exome sequenced samples?
Thank you
Well it indicates exactly what it says - the mean target coverage for your exome was 28x and 55% of the targeted bases have a coverage of 20x or greater (and presumably 45% is therefore covered at <20x).
The coverage profile of a captured exon is not uniform, so you will have to assess on a base by base basis whether there is enough read support for any given variant.
What was your originally requested coverage? 28x sounds like you were going for 30x coverage, which apparently the BGI have not delivered.
There's no 'normal' average coverage. People sequence the depths that they can afford. We stopped doing 30x projects a long time ago, mostly everything we do is 50x and this is generally upped to 100x or more for whole exome on cancer.
At 55x on a SureSelect V5 exome capture experiment (analysed fresh this morning) we get coverage of 80% of bases at >20x and 76% of bases at >30x. This for me is 'normal'.
From my experience an average 30x coverage has been a standard minimum for single sample sequencing. But as has been mentioned, it depends on your budget and it's common for exome sequencing to be deeper. I would be suspicious of variant calls coming from 55% at 20x, but depending on your specific application that may be sufficient.
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We were going for 30x coverage and these samples were sequenced way back in 2010 , I think 55% of the targeted bases covered at 20x is low and therefore the variant calling wouldn't be reliable