Table 1. The number of potential methylation sites, DMSs and CMSs in each of three sequence contexts (CG, CHG and CHH) throughout the entire brachypodium genome and also for three features separately (Genes, Promoters and TEs).
| Region | CG | CHG | CHH | Total |
|---|---|---|---|---|
| Potential methylation sites | ||||
| Genic | 5,945,276 | 6,261,258 | 17,109,118 | 29,315,652 |
| TE | 7,066,299 | 5,524,931 | 17,168,841 | 29,760,071 |
| Promoter | 2,201,304 | 1,833,675 | 5,378,012 | 9,412,991 |
| Whole Genome | 21,814,767 | 19,722,162 | 58,692,551 | 100,229,480 |
| Differentially Methylated Sites (DMSs) | ||||
| Genic | 30,396 (0.51) | 17,059 (0.27) | 6,009 (0.04) | 53,464 (0.18) |
| TE | 29,981 (0.42) | 144,779 (2.62) | 39,990 (0.23) | 214,750 (0.72) |
| Promoter | 12,658 (0.58) | 17,276 (0.94) | 15,500 (0.29) | 45,434 (0.48) |
| Whole Genome | 120,744 (0.55) | 282,440 (1.43) | 9,7061 (0.17) | 500,245 (0.50) |
| Conserved Methylated Sites (CMSs) | ||||
| Genic | 1,537,550 (25.86) | 216,844 (3.46) | 88,467 (0.52) | 1,842,861 (6.29) |
| TE | 6,736,090 (95.33) | 3,560,407 (64.44) | 663,269 (3.86) | 10,959,766 (36.83) |
| Promoter | 568,236 (25.81) | 265,069 (14.46) | 232,488 (4.32) | 1,065,793 (11.32) |
| Whole Genome | 11,776,244 (52.98) | 5,590,834 (28.35) | 1,413,604 (2.41) | 18,780,682 (18.74) |
Numbers in parentheses represent the percentage of sites in context that are methylated. Those sites that are not DMSs or CMSs either lack evidence of methylation in both tissues or do not have a significant FET.