Human-macaque comparisons illuminate variation in neutral substitution rates

Table 3 Regression results for neutral substitution rates estimated from CpG sites

	CpG sites
Predictors	t value*	Significance^†	VIF^‡	Variability explained^§
X chromosome/autosome indicator	13.99	<10^-4	1.1	0.02
GC content
Linear term	-57.37	<10^-4	2.7	0.32
Quadratic term	5.73	<10^-4	1.2
Exon density	-6.28	<10^-4	2.3	0.003
SNP density	NS	NS	NS	NS
Male recomb rate	NS	NS	NS	NS
Female recomb rate	NS	NS	NS	NS
Distance to telomeres
Linear term	NS	NS	NS	NS
Quadratic term	NS	NS	NS
Multiple R²				0.82
Adjusted R²				0.82

CpG sites were taken in ancestral repeats (without requiring orthology to mouse, rat, dog and cow) for each of 2,270 windows of size 1 Mb. *t value, test statistic of null hypothesis that each predictor's coefficient is equal to zero; ^†p-values adjusted for multiple tests (using Bonferroni correction); ^‡VIF, variance inflation factor; ^§relative contribution to explained variability computed for each predictor. NS, non-significant.

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