Table 2 The number of raw and valid reads sequenced for each sample, number of species and OTUs found, and subsequent alpha diversity measures.
Sample ID | Raw reads | Valid reads | No. of reads identified at the species level | No. of species found | No. of OTUs found in the sample | Good’s coverage of library(%) | Alpha diversity indices | Jackknife | Shannon | Simpson | NPShannon | Phylogenetic diversity | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ACE | Chao1 | ||||||||||||
P1 | 111,825 | 66,731 (66.7%) | 40,356 (60.5%) | 1,753 | 3747 | 99.1 | 4,142 | ##### | 4,373.00 | 5.713 | 0.026 | 5.803 | 3,663.00 |
P2 | 113,528 | 68,110 (68.1%) | 41,004 (60.2%) | 1,693 | 3302 | 99 | ##### | ##### | 3,958.00 | 5.286 | 0.038 | 5.366 | 3,469.00 |
P3 | 137,636 | 61,590 (61.6%) | 37,474 (60.8%) | 1,518 | 3461 | 99.1 | ##### | ##### | 4,044.00 | 5.669 | 0.024 | 5.76 | 3,102.00 |
P5 | 361,826 | 64,056 (64.1%) | 50,269 (78.5%) | 1,730 | 2978 | 99 | 3,463 | ##### | 3,638.00 | 5.251 | 0.046 | 5.325 | 3,245.00 |
P6 | 187,729 | 70,130 (70.1%) | 57,596 (82.1%) | 1,740 | 2924 | 99.2 | 3,333 | ##### | 3,502.00 | 5.229 | 0.048 | 5.298 | 3,253.00 |
P7 | 364,534 | 65,799 (65.8%) | 52,920 (80.4%) | 1,591 | 2685 | 99.1 | ##### | ##### | 3,283.00 | 5.139 | 0.028 | 5.208 | 3,031.00 |
P8 | 181,507 | 62,000 (62.0%) | 43,977 (70.9%) | 1,528 | 2983 | 99.1 | ##### | ##### | 3,517.00 | 5.495 | 0.023 | 5.573 | 2,995.00 |
P9 | 226,645 | 69,846 (69.8%) | 58,839 (84.2%) | 1,687 | 2761 | 99.2 | ##### | ##### | 3,353.00 | 4.914 | 0.073 | 4.981 | 3,196.00 |
P10 | 330,664 | 64,563 (64.6%) | 51,004 (79.0%) | 1,663 | 2940 | 99.1 | ##### | ##### | 3,551.00 | 5.185 | 0.046 | 5.262 | 3,145.00 |
P11 | 339,109 | 62,112 (62.1%) | 48,849 (78.6%) | 1,552 | 2690 | 99.1 | 3,085 | ##### | 3,249.00 | 5.018 | 0.055 | 5.092 | 3,009.00 |
P12 | 357,452 | 76,152 (76.2%) | 63,547 (83.4%) | 1,761 | 2928 | 99.2 | ##### | ##### | 3,559.00 | 5.041 | 0.064 | 5.105 | 3,211.00 |
