Table 2.
Detected cytosine positions relative to the genome-wide cytosine positions per five biological replicates of the control line and the LR2 epiline (fourth selfing) discriminated by restriction endonuclease combination and cytosine context (CG, CHG and CHH)
| Group of biological replicates | Restriction endonuclease combination | Detected cytosine positions in genome | |||
|---|---|---|---|---|---|
| CG | CHG | CHH | C (%) | ||
| Union (collection of all covered positions in at least one replicate) | |||||
| Control | MspI-DpnII | 18,507,834 | 15,887,099 | 58,570,249 | 52.0 |
| LR2 | MspI-DpnII | 19,434,811 | 16,678,896 | 61,436,046 | 54.6 |
| Control | MspI-ApeKI | 15,715,023 | 12,901,771 | 42,018,210 | 39.5 |
| LR2 | MspI-ApeKI | 14,573,921 | 12,185,636 | 39,744,568 | 37.2 |
| Intersection (common positions in all replicates) | |||||
| Control | MspI-DpnII | 6,459,314 | 5,448,976 | 19,305,085 | 17.5 |
| LR2 | MspI-DpnII | 8,023,858 | 7,435,066 | 29,372,103 | 25.1 |
| Control | MspI-ApeKI | 7,053,953 | 6,410,114 | 19,063,516 | 18.2 |
| LR2 | MspI-ApeKI | 5,454,292 | 5,509,874 | 15,910,607 | 15.0 |
| Jaccard indexa (proportion of common on all detected positions) | |||||
| (%) | (%) | (%) | (%) | ||
| Control | MspI-DpnII | 34.9 | 34.3 | 33.0 | 33.6 |
| LR2 | MspI-DpnII | 41.3 | 44.6 | 47.8 | 46.0 |
| Control | MspI-ApeKI | 44.9 | 49.7 | 45.4 | 46.1 |
| LR2 | MspI-ApeKI | 37.4 | 45.2 | 40.0 | 40.4 |
a Jaccard index or Jaccard similarity coefficient = intersection / union