Table 1.
Class pair | A | C | G | T | Length | CpG proportion | Proportion of genome |
---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
1 | 0.169 | 0.234 | 0.104 | 0.492 | 5.4 | 0.006 | 0.143 |
2 | 0.230 | 0.220 | 0.243 | 0.307 | 84.7 | 0.011 | 0.134 |
3 | 0.314 | 0.139 | 0.118 | 0.428 | 71.5 | 0.003 | 0.132 |
4 | 0.235 | 0.281 | 0.133 | 0.351 | 64.9 | 0.005 | 0.120 |
5 | 0.279 | 0.175 | 0.185 | 0.361 | 55.3 | 0.004 | 0.116 |
6 | 0.215 | 0.165 | 0.188 | 0.432 | 504.7 | 0.005 | 0.092 |
7 | 0.183 | 0.336 | 0.205 | 0.276 | 55.6 | 0.009 | 0.069 |
8 | 0.177 | 0.392 | 0.194 | 0.237 | 33.6 | 0.029 | 0.044 |
9 | 0.167 | 0.379 | 0.236 | 0.218 | 48.2 | 0.027 | 0.042 |
10 | 0.145 | 0.242 | 0.309 | 0.303 | 18.2 | 0.017 | 0.022 |
11 | 0.199 | 0.453 | 0.240 | 0.108 | 14.4 | 0.056 | 0.017 |
12 | 0.175 | 0.021 | 0.079 | 0.725 | 14.4 | 0.000 | 0.014 |
13 | 0.252 | 0.359 | 0.126 | 0.263 | 10.5 | 0.003 | 0.012 |
14 | 0.125 | 0.454 | 0.252 | 0.169 | 25.8 | 0.096 | 0.009 |
15 | 0.217 | 0.357 | 0.124 | 0.301 | 71.4 | 0.010 | 0.008 |
16 | 0.223 | 0.045 | 0.261 | 0.471 | 14.0 | 0.007 | 0.007 |
17 | 0.003 | 0.066 | 0.006 | 0.925 | 11.9 | 0.000 | 0.006 |
18 | 0.099 | 0.402 | 0.071 | 0.429 | 5.1 | 0.024 | 0.006 |
19 | 0.021 | 0.434 | 0.023 | 0.522 | 33.5 | 0.003 | 0.005 |
Each row refers to two classes, which we refer to as the a and b classes, each with the reverse complement properties of the other. The a class is the one with the higher percentage of T+C, and the base frequencies for this class are shown in columns 2-3-4-5. The frequencies for the b class are the same but with the A/T and C/G frequencies interchanged. Column 6 gives the mean length of the class in bases and column 7 gives the proportion of doublets within the class that are CpG: these two quantities are the same for both the a and b classes. Column 8 gives the proportion of bases in the genome within both classes of the class pair: the total of column 8 is therefore 1.0. The class pairs have been numbered by the proportion of bases they contain. All values have been calculated from the fitted HMM: the parameters of this model are given in Additional File 1.