Samtools coverage results
Hii, I have run the samtools coverage command for calculation of gene coverage. I got this results:
#rname startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq
1 1 249250621 5267569 43635507 17.5067 3.25543 36.1 55
2 1 243199373 3735452 38023900 15.6349 2.36581 36.1 56.7
3 1 198022430 2876635 29511402 14.9031 2.24146 36.1 59.1
4 1 191154276 2120864 24624225 12.8819 1.70427 36.1 54.1
5 1 180915260 2339470 25323867 13.9976 1.99639 36.1 57.5
6 1 171115067 2710441 25385971 14.8356 2.44034 36.1 58
7 1 159138663 2524920 25711041 16.1564 2.43605 36.1 54.9
8 1 146364022 1716145 20358945 13.9098 1.80446 36.1 57.1
9 1 141213431 2185054 20803062 14.7316 2.38488 36.1 55
10 1 135534747 2104547 22107195 16.3111 2.39094 36.1 55.4
11 1 135006516 2923941 23462880 17.3791 3.33113 36.1 58.4
12 1 133851895 2562215 23469760 17.5341 2.94676 36.1 59
13 1 115169878 943925 12223004 10.613 1.26315 36.1 58.7
14 1 107349540 1610115 14890978 13.8715 2.31553 36.1 58.4
15 1 102531392 1950910 16489158 16.0821 2.92665 36.1 51.8
16 1 90354753 2338564 17753639 19.6488 3.96056 36.1 51.9
17 1 81195210 2951173 20431476 25.1634 5.59499 36.1 56.6
18 1 78077248 819720 10195226 13.0579 1.61619 36.1 57.2
19 1 59128983 2968003 18049860 30.5262 7.70268 36.1 58.5
20 1 63025520 1165330 11315216 17.9534 2.84952 36.1 59.4
21 1 48129895 561354 5884798 12.2269 1.79324 36.1 58.3
22 1 51304566 1134209 9023051 17.5872 3.40329 36.1 56
X 1 155270560 1305748 14555083 9.37401 1.29082 36.1 55.6
Y 1 59373566 205755 3473216 5.84977 0.516154 36 26.7
MT 1 16569 16217 16569 100 148.003 36 57.8
I want to understand what the coverage column is saying? Is 17 is the percentage (17%) or anything else? How to interpret the data? How do you know how much coverage of gene is there?
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