Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

Table 7 Comparison of the CpG transition rate between the X chromosome and the 22 autosomes

	CpG specific transition rate		CpG transition rate
Levels of the one-way ANOVA	Estimate	P-value	Estimate	P-value
Intercept	-0.0708	1.04e-03**	-0.1730	6.82e-15***
Chromosome 1	0.0638	1.58e-02*	0.1531	1.83e-08***
Chromosome 2	0.0565	3.32e-02*	0.1567	9.46e-09***
Chromosome 3	0.0870	1.21e-03**	0.1809	5.97e-11***
Chromosome 4	0.0644	2.46e-02*	0.1759	2.37e-09***
Chromosome 5	0.0437	1.20e-01	0.1374	2.03e-06***
Chromosome 6	0.0579	4.94e-02*	0.1666	3.86e-08***
Chromosome 7	0.0330	2.97e-01	0.1293	6.84e-05***
Chromosome 8	-0.0036	9.08e-01	0.1382	1.53e-05***
Chromosome 9	0.0942	2.71e-03**	0.1890	4.94e-09***
Chromosome 10	0.0871	2.95e-03**	0.1864	6.22e-10***
Chromosome 11	0.0988	1.44e-03**	0.1911	2.09e-09***
Chromosome 12	0.0555	6.11e-02	0.1345	1.03e-05***
Chromosome 13	0.0625	8.53e-02	0.1501	5.88e-05***
Chromosome 14	0.0005	8.88e-01	0.0900	9.89e-03**
Chromosome 15	0.0333	9.87e-01	0.1376	2.74e-05***
Chromosome 16	0.0630	1.13e-01	0.1707	2.92e-05***
Chromosome 17	-0.0011	9.74e-01	0.1144	1.33e-03**
Chromosome 18	0.0862	1.92e-02*	0.1901	5.02e-07***
Chromosome 19	-0.0118	8.68e-01	0.1157	1.15e-01
Chromosome 20	-0.0077	8.46e-01	0.0756	6.28e-02
Chromosome 21	0.1033	5.49e-02	0.2319	2.76e-05***
Chromosome 22	0.0288	6.00e-01	0.1228	2.99e-02*

CpG-specific transition rate is corrected for among-chromosomes variation in divergence, GC content, DNA methylation and transcription level; CpG transition rate is only corrected for variation in GC content, DNA methylation and transcription level among chromosomes. Estimates and P-values of a one-way ANOVA are listed, where the contrasts are based on the X chromosome. P-values are marked with asterisks to highlight their significance level, where single, double and triple asterisks indicate P-values below a threshold of 0.05, 0.01 and 0.001, respectively.