Table 3.
Average diversity estimates of the mock community (n = 12, rarified to 6654 sequences per sample) with and without removing low-frequency sequences
| Mock community | Actual number of OTUsa | Observed number of OTUs | Estimated total number of OTUsb | Chao diversity index | Shannon diversity index | Inverse Simpson index | Error rate (%) | File size (Gb)c |
|---|---|---|---|---|---|---|---|---|
| All sequences | 20 | 734 ± 56 | 374,770 ± 214,807 | 21,676 ± 3273 | 3.6 ± 0.1 | 18 ± 0.8 | 3.6 | 41 |
| Singletons removed | 20 | 28 ± 0.8 | 68 ± 13 | 41 ± 3 | 2.7 ± 0.02 | 12 ± 0.3 | 1.4 | 21 |
| Single and doubletons removed | 20 | 22 ± 0.3 | 22 ± 0.3 | 23 ± 0.7 | 2.6 ± 0.02 | 12 ± 0.3 | 1.3 | 3 |
Average diversity estimates: plus or minus (±) the standard error of the mean, where appropriate
a Haemophilus parasuis has two divergent copies of the 16S rRNA gene that cluster separately
bThe estimated total number of OTUs is the number of OTUs predicted to be in the sample based on the number of OTUs observed in the sequences. The program Catchall was used to make the estimates [14]
cSize of the distance matrix file