TABLE 2.
Number of reads used by RepeatExplorer in individual analyses and main clustering results.
| Sample ID and ploidy level | Genome size 1C (Gbp) | No. of analyzed readsa | Coverage | Reads in all clusters including small uncharacterized clusters (%) | Reads in clusters above the threshold of 0.01% (%) | Singlets (%) | No. of clusters above the threshold of 0.01% | No. of superclusters above the threshold of 0.01% |
| IntA (2x) | 3.686 | 4,349,101 | 0.18 x | 82.87 | 71.54 | 17.13 | 246 | 157 |
| IntC (2x) | 3.711 | 4,270,305 | 0.17 x | 81.69 | 69.87 | 18.31 | 224 | 145 |
| PreA (2x) | 3.531 | 4,212,792 | 0.18 x | 82.55 | 71.11 | 17.45 | 230 | 150 |
| PreC (2x) | 3.511 | 4,368,530 | 0.19 x | 81.42 | 69.48 | 18.58 | 228 | 149 |
| PalA (3x) | 5.543 | 4,278,270 | 0.12 x | 81.39 | 70.53 | 18.61 | 236 | 149 |
| PalF (3x) | 5.664 | 4,467,725 | 0.12 x | 82.19 | 70.92 | 17.81 | 242 | 158 |
| PicF (3x) | 5.580 | 3,767,752 | 0.10 x | 80.74 | 69.96 | 19.26 | 209 | 138 |
| PicB (3x) | 5.212 | 4,338,941 | 0.12 x | 81.31 | 69.60 | 18.69 | 260 | 173 |
| Hyb2 (2x) | 3.600 | 4,457,370 | 0.20 x | 82.01 | 71.22 | 17.99 | 241 | 160 |
| Hyb3 (2x) | 3.600 | 4,636,407 | 0.20 x | 81.82 | 71.06 | 18.18 | 251 | 161 |
| Hyb4 (2x) | 3.590 | 4,465,263 | 0.19 x | 81.83 | 71.11 | 18.17 | 246 | 157 |
aAfter exclusion of plastid and mitochondrial clusters.