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) | |||||
| Â | Â | (%) | (%) | (%) | (%) |
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 |