Table 4.
The classification of denoised sequences from the nine test data sets
| Name | Unique | Good | Bimera | Trimera | Quadramera | Unclassified |
|---|---|---|---|---|---|---|
| Divergent | ||||||
| AmpliconNoise | 79 | 56(70.9%) | 21(26.6%) | 1(1.3%) | 0 (0.0%) | 1(1.3%) |
| SLP 1% | 305 | 210 (68.9%) | 23 (7.5%) | 1 (0.3%) | 0 (0.0%) | 71(23.3%) |
| SLP 2% | 60 | 29 (48.3%) | 22 (36.7%) | 0 (0.0%) | 0 (0.0%) | 9(15.0%) |
| DeNoiser | 37 | 28 (75.7%) | 7 (18.9%) | 1 (2.7%) | 0 (0.0) | 1(2.7%) |
| Artificial | ||||||
| AmpliconNoise | 118 | 94(79.7%) | 21(17.8%) | 0 (0.0%) | 0 (0.0%) | 3(2.5%) |
| SLP 1% | 230 | 168 (73.0%) | 21 (9.1%) | 0 (0.0%) | 0 (0.0%) | 41(17.9%) |
| SLP 2% | 62 | 36 (58.1%) | 20 (32.3%) | 0 (0.0%) | 0 (0.0%) | 6(9.7%) |
| DeNoiser | 59 | 46 (78.0%) | 8 (13.6%) | 0 (0.0%) | 0 (0.0%) | 5(8.5%) |
| Even1 | ||||||
| AmpliconNoise | 2341 | 89 (3.8%) | 1847 (78.9%) | 244 (10.4%) | 4 (0.2%) | 157(6.7%) |
| SLP 1% | 2205 | 108 (4.9%) | 1631 (74.0%) | 253 (11.5%) | 4 (0.2%) | 209(9.5%) |
| SLP 2% | 894 | 38 (4.3%) | 638 (71.4%) | 142 (15.9%) | 4 (0.4%) | 72(8.1%) |
| DeNoiser | 289 | 63 (21.8%) | 161 (55.7%) | 36 (12.5%) | 3 (1.0%) | 26(9.0%) |
| Even2 | ||||||
| AmpliconNoise | 2082 | 90 (4.3%) | 1651 (79.3%) | 227 (10.9%) | 4 (0.2%) | 110(5.3%) |
| SLP 1% | 1958 | 97 (5.0%) | 1448 (74.0%) | 235 (12.0%) | 4 (0.2%) | 174(8.9%) |
| SLP 2% | 789 | 44 (5.6%) | 553 (70.1%) | 134 (17.0%) | 4 (0.5%) | 54(6.8%) |
| DeNoiser | 285 | 64 (22.5%) | 171 (60.0%) | 22 (7.7%) | 4 (1.4%) | 24(8.4%) |
| Even3 | ||||||
| AmpliconNoise | 2210 | 91 (4.1%) | 1781 (80.6%) | 188 (8.5%) | 3 (0.1%) | 147(6.7%) |
| SLP 1% | 2164 | 117 (5.4%) | 1635 (75.6%) | 194 (9.0%) | 3 (0.1%) | 215(9.9%) |
| SLP 2% | 874 | 40 (4.6%) | 649 (74.3%) | 105 (12.0%) | 1 (0.1%) | 79(9.0%) |
| Denoiser | 287 | 64 (22.3%) | 170 (59.2%) | 24 (8.4%) | 0 (0.0%) | 29(10.1%) |
| Uneven1 | ||||||
| AmpliconNoise | 1124 | 94 (8.4%) | 816 (72.6%) | 81 (7.2%) | 1 (0.1%) | 132(11.7%) |
| SLP 1% | 1040 | 90 (8.7%) | 682 (65.6%) | 88 (8.5%) | 2 (0.2%) | 178(17.1%) |
| SLP 2% | 439 | 51 (11.6%) | 278 (63.3%) | 49 (11.2%) | 1 (0.2%) | 60(13.7%) |
| Denoiser | 212 | 61 (28.8%) | 111 (52.4%) | 9 (4.2%) | 0 (0.0%) | 31(14.6%) |
| Uneven2 | ||||||
| AmpliconNoise | 859 | 77 (9.0%) | 669 (77.9%) | 71 (8.3%) | 2 (0.2%) | 40(4.7%) |
| SLP 1% | 814 | 81 (10.0%) | 570 (70.0%) | 77 (9.5%) | 2 (0.2%) | 84(10.3%) |
| SLP 2% | 330 | 36 (10.9%) | 226 (68.5%) | 36 (10.9%) | 2 (0.6%) | 30(9.1%) |
| Denoiser | 154 | 49 (31.8%) | 87 (56.5%) | 9 (5.8%) | 1 (0.6%) | 8(5.2%) |
| Uneven3 | ||||||
| AmpliconNoise | 1053 | 75 (7.1%) | 843 (80.1%) | 82 (7.8%) | 0 (0.0%) | 53(5.0%) |
| SLP 1% | 1031 | 89 (8.6%) | 745 (72.3%) | 92 (8.9%) | 0 (0.0%) | 105(10.2%) |
| SLP 2% | 399 | 45 (11.3%) | 259 (64.9%) | 49 (12.3%) | 0 (0.0%) | 46(11.5%) |
| Denoiser | 202 | 55 (27.2%) | 124 (61.4%) | 7 (3.5%) | 0 (0.0%) | 16(7.9%) |
| Titanium | ||||||
| AmpliconNoise - σs = 0.1 | 163 | 76 (46.6%) | 77 (47.2%) | 1 (0.6%) | 0 (0.0%) | 9(5.5%) |
| AmpliconNoise - σs = 0.04 | 304 | 91 (29.9%) | 174 (57.2%) | 2 (0.7%) | 0 (0.0%) | 37(12.2%) |
| SLP 1% | 765 | 520 (68.0%) | 157 (20.5%) | 1 (0.1%) | 0 (0.0%) | 87(11.4%) |
| SLP 2% | 182 | 72 (39.6%) | 92 (50.5%) | 1(0.5%) | 0 (0.0%) | 17(9.3%) |
| DeNoiser | 151 | 14 (9.3%) | 70 (46.4%) | 6(4.0%) | 0 (0.0%) | 61(40.4%) |
The number of unique denoised sequences classified into the five categories, 'Good', 'Bimera', 'Trimera', 'Quadramera' and 'Unclassified', as defined in the text are given together with percentages of the total in parentheses.