TABLE 3.
Effect of fragment length on similarity-based OTU number, Shannon-Weaver diversity index, and richness estimation
| Sequence length, % similarity level | No. of unique OTUs | Shannon-Weaver index | Richness estimatea |
|---|---|---|---|
| Full lengthb | |||
| 100 | 1,183 | 7.08 | 350,169 |
| 97 | 1,031 | 6.86 | 7,452 |
| 70 | 54 | 3.01 | 67 |
| 55 | 6 | 0.67 | 6 |
| 46 | 2 | 0.01 | 2 |
| Truncatedc | |||
| 100 | 1,166 | 7.05 | 61,646 |
| 97 | 911 | 6.65 | 4,175 |
| 70 | 80 | 3.41 | 93 |
| 55 | 15 | 1.68 | 18 |
| 46 | 5 | 0.47 | 6 |
a
Based on full biased corrected Chao1 richness estimates.
b
Based on 1,184 full-length sequences.
c
Based on 1,184 truncated sequences. Truncations were created by deleting the upstream base pair region from the E. coli consensus position 536 and downstream of consensus position 906.