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Table 3 Classes under negative selection compared to ancestral repeats.

From: Predicting functionally important SNP classes based on negative selection

rank

class name

p-value

q-value

1

nonsynonymous

5.0 × 10-8

1.1 × 10-3

2

constrained elements

3.6 × 10-5

2.3 × 10-3

3

constrained elements minus coding

1.4 × 10-4

3.4 × 10-3

4

coding

1.2 × 10-3

4.5 × 10-3

5

constrained elements minus genes

3.0 × 10-3

5.7 × 10-3

6

constrained elements 1 kb from genes

3.2 × 10-3

6.8 × 10-3

7

H3K79me3

8.0 × 10-3

7.9 × 10-3

8

constrained elements 100 kb from genes

1.1 × 10-2

9.0 × 10-3

9

miRanda

3.4 × 10-2

1.0 × 10-2

10

H3K36me3

4.0 × 10-2

1.1 × 10-2

11

PolII

6.3 × 10-2

1.3 × 10-2

12

H3K4me2

7.1 × 10-2

1.4 × 10-2

13

cisRED

1.0 × 10-1

1.5 × 10-2

  1. Classes with an excess of low derived alleles when compared to the ancestral repeats are shown. Bolded, italicized classes are statistically significant when we apply an FDR correction with α = 0.05. Only resequenced Perlegen SNP markers are included in this analysis to minimize ascertainment bias. For our comparisons, we rely on allele frequencies present in the AFR Perlegen population.