Question: Is genome coverage same as k-mer coverage for that genome?
gravatar for mrj
2 days ago by
mrj20 wrote:

I am submitting a fungal sequence to NCBI. There, I need to specify the genome coverage. I have 21-mer coverage of 78.4. Does that mean my genome coverage is 78.4X?

ADD COMMENTlink written 2 days ago by mrj20

No. What do you mean by 21-mer coverage of 78.4?

Genomic coverage can be of different types. e.g. it can be theoretical. If your genome is 3 gbp and you have 30 gpb of total sequence then you have a theoretical coverage of 10x but more than likely the coverage is not uniform 10x everywhere. You may even not have all the genome covered by at least one read.

You can look at some of the suggestions here to calculate that :
Tools To Calculate Average Coverage For A Bam File?
How To Calculate Coverage

ADD REPLYlink modified 2 days ago • written 2 days ago by genomax85k
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