Most transcription factor binding sites are in a few mosaic classes of the human genome

BMC Genomics

Table 1 Summary statistics for the mosaic classes of the human genome

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.

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