Table 5. Summary statistics of the 454 pyrosequencing reads and effect of bioinformatic filtering strategies.
| A) Sample | # reads | # singletons (%) | # unique reads | # (%) chimeras after Initial Filtering |
| DNA-Hap454 | 12170 | 3986 (40%) | 4684 | 591 (5%) |
| DNA-Prym454 | 17532 | 4313 (25%) | 5113 | 306 (2%) |
| cDNA-Hap454 | 20503 | 8924 (44%) | 10263 | 4263 (23%) |
| cDNA-Prym454 | 17788 | 8230 (46%) | 9513 | 3093 (20%) |
| DNApool | 11778 | 3516 (30%) | 4250 | 795 (9%) |
| B) Sample | % reads remaining after filtering. IF, QS, PN, AN | # OTU99%. IF, QS, PN, AN | % unclassified* sequences. IF, QS, PN, AN | Error rate. IF, QS, PN, AN |
| DNA-Hap454 | 85, 50, 78, 83 | 858, 233, 130,11 | 0.20, 0.20, 0.30, 0.01 | 0.010, 0.008, 0.003, 0.002 |
| DNA-Prym454 | 88, 56, 67, 68 | 769, 152, 88, 10 | 0.07, 0.06, 0.09, 0.00 | 0.006, 0.005, 0.005, 0.003 |
| cDNA-Hap454 | 69, 45, 63, 71 | 1935, 721, 543, 42 | 4.29, 5.68, 2.89, 1.07 | 0.008, 0.006, 0.003, 0.004 |
| cDNA-Prym454 | 68, 39, 58, 51 | 1958, 628, 557, 15 | 8.39, 8.29, 7.17, 0.13 | 0.009, 0.006, 0.005, 0.003 |
| DNApool | 79, 42, 72, 76 | 864, 176, 124, 12 | 1.10, 1.87, 1.19, 0.49 | 0.011, 0.009, 0.009, 0.008 |
(A) Number of reads, number of singletons, number of unique reads before any filtering, and proportion of chimeras detected by Perseus in the different samples. (B) Effect of filtering procedures on proportion of reads remaining after filtering, number of OTU99%, proportion of unclassified sequences, and error rate. ‘Unclassified’ reads are reads that could not be assigned to species level.