Table 1

Regression results for neutral substitution rates estimated from non-CpG and all sites

Non-CpG sites
 All sites

Predictors
 t value*
 Significance†
 VIF‡
 Variability explained§
 t value*
 Significance†
 VIF‡
 Variability explained§
X chromosome/autosome indicator
 13.94
 <10-4
 1.2
 0.08
 15.25
 <10-4
 1.3
 0.09
GC content







     Linear term
 -10.34
 <10-4
 3.7
 0.12
 -5.08
 <10-4
 3.4
 0.14
     Quadratic term
 15.85
 <10-4
 1.3
18.78
 <10-4
 1.2
Exon density
 -7.03
 <10-4
 2.4
 0.02
 -9.37
 <10-4
 2.4
 0.03
SNP density
 6.25
 <10-4
 1.2
 0.02
 6.85
 <10-4
 1.2
 0.02
Male recombination rate
 3.69
 0.003
 1.6
 0.01
 4.46
 <10-4
 1.6
 0.01
Female recombination rate
 NS
 NS
 NS
 NS
 NS
 NS
 NS
 NS
Distance to telomere







     Linear term
 -12.33
 <10-4
 2.5
 0.06
 -16.78
 <10-4
 2.5
 0.11
     Quadratic term
 7.63
 <10-4
 2.0
10.77
 <10-4
 2.0
Mouse-rat orthologous neutral rate
 7.95
 <10-4
 1.8
 0.09
 6.64
 <10-4
 1.4
 0.07
Dog-cow orthologous neutral rate
 10.56
 <10-4
 1.3
10.41
 <10-4
 1.4
Multiple R2


0.52


0.53
Adjusted R2


0.52


0.52

Non-CpG and all sites were taken in ancestral repeats orthologous 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

Tyekucheva et al. Genome Biology 2008 9:R76   doi:10.1186/gb-2008-9-4-r76

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