Getting the average coverage from the coverage counts at each depth.

Hi,

I have read quite a few posts here about coverage already. But I still had a few questions. I have a BAM file I'm trying to find the coverage of it (typically like say 30X).

So, I decided to use genomeCoverageBed for my analysis. And I used the following command:

genomeCoverageBed -ibam file.bam -g ~/refs/human_g1k_v37.fasta > coverage.txt

As many are aware, the output of the file looks something like this:

genome    0    26849578    100286070 0.26773
genome    1    30938928    100286070     0.308507
genome    2    21764479    100286070    0.217024
genome    3    11775917    100286070    0.117423
genome    4    5346208    100286070    0.0533096
genome    5    2135366    100286070    0.0212927
genome    6    785983    100286070    0.00783741
genome    7    281282    100286070    0.0028048
genome    8    106971    100286070    0.00106666
genome    9    47419    100286070    0.000472837
genome    10    27403    100286070    0.000273248

To find the coverage, I multiplied col2 (depth) with col3 (number of bases in genome with that depth) and then summed the entire column. Then, I divided it by genome length to get the coverage. In this case, col2 * col3 is:

0
30938928
43528958
35327751
21384832
10676830
4715898
1968974
855768
426771
274030

And the sum is: 150098740. Since the genome length is 100286070, the coverage is 150098740/100286070 = 1.5. That is to say it is, 1.5X. I have only considered the first 10 depth from the file here, but you get the idea. So, is this the right way to get the physical coverage?

Note: While the output file (coverage.txt) gives individual chromosome details, I only took the genome details i.e., col1 labeled as genome.