Sobs and Coverage

Dear All,

I am confused about the relation between Sobs and Coverage in command “summary.single”. I got the rarefaction curve that is always increasing without plateau, while the coverage showed over 99%. I am afraid these two results are opposite to indicate the sequencing depth.

label group sobs nseqs coverage
0.03 OB1 757.593 62128 0.989413
0.03 OB10 1435.602 62128 0.984617
0.03 OB2 645 62128 0.990616
0.03 OB4 622.332 62128 0.992061

numsampled OB1 OB10 OB2 OB4
1 1 1 1 1
5000 107.822 306.91 80.163 112.51
10000 174.932 487.295 134.985 175.01
15000 239.02 636.647 187.323 232.308
20000 301.243 769.037 238.06 286.513
25000 362.123 890.383 288.016 338.488
30000 421.557 1003.461 337.29 388.625
35000 480.224 1111.169 385.799 437.417
40000 538.433 1213.717 434.236 485.172
45000 595.848 1312.189 482.733 532.165
50000 652.69 1407.22 530.409 578.464
55000 708.903 1499.559 577.996 623.514
60000 764.115 1589.9 625.019 667.959
62128 787.423 1627.284 645 686.706

Thanks,
Rain

Hello Rain

S.obs is an absolute estimation of the number of OTUs or phylotypes that are in your samples while coverage is a relative estimation (Good’s coverage I guess) of the total of OTUs that you have in your samples.


I hope It's clear Eduardo

Actually… Sobs is the total number of OTUs that have been observed (i.e. no estimation). Coverage is a measure of the number of OTUs that have been seen more than once. So if you have a coverage of 0.90, 90% of your sequences belong to OTUs that have been seen more than once

Pat