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Table 1 Regression results for neutral substitution rates estimated from non-CpG and all sites

From: Human-macaque comparisons illuminate variation in neutral substitution rates

 

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

  1. 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