Confusion about the term genome coverage

Question

[Picasa]

Hi,

For instance, if I have 3 libraries of paired end:

350: 20x

550: 10x

750: 5x

My coverage genome is 20+10+5 = 35x or (20+10+5)/3 = 11.5x ??

[Ming Tommy Tang]

are these three are replicates? if they are, then 35x is correct.

[Picasa]

What do you mean by replicates ? These are independent libraries.

[sentausa]

I believe what tangming2005 meant with replicates is that all the libraries are from the same organism. They are, right?

[Picasa]

They are from the same organism

[Ming Tommy Tang]

then, just add them up.

Answer 1

[thackl]

The sum is correct: 35x

Genome coverage in the most simple way means the mean per-base coverage of the genome given a set of reads (can be multiple libraries). I.e. if you have a genome of 1000bp in length and 10 reads of 100 bp, than you coverage is (10*100bp)/1000bp = 1. If you have 100 reads, the coverage is 100*100bp/1000bp = 10, ... Whether or not the reads derive from different libraries, does not matter. To get the coverage, just compute the total number of bases in your read libraries and divide by the genome size.