Table 2

Classes under negative selection compared to the genome.

rank

class name

p-value

q-value


1

coding

<1 × 10-8

1.5 × 10-3


2

nonsynonymous

<1 × 10-8

3.1 × 10-3


3

constrained elements

<1 × 10-8

4.7 × 10-3


4

constrained elements minus coding

<1 × 10-8

6.3 × 10-3


5

constrained elements minus genes

<1 × 10-8

7.8 × 10-3


6

constrained elements 1 kb from genes

<1 × 10-8

9.4 × 10-3


7

regulatory features extended

<1 × 10-8

1.1 × 10-2


8

H3K36me3

<1 × 10-8

1.3 × 10-2


9

H3K79me3

<1 × 10-8

1.4 × 10-2


10

constrained elements 100 kb from genes

1.0 × 10-8

1.6 × 10-2


11

splice site

8.0 × 10-4

1.7 × 10-2


12

DnaseI

4.5 × 10-3

1.9 × 10-2


13

H3K4me3

5.1 × 10-3

2.0 × 10-2


14

H3K4me2

8.6 × 10-3

2.2 × 10-2


15

PolII

1.1 × 10-2

2.3 × 10-2


16

miRanda

1.5 × 10-2

2.5 × 10-2


17

cisRED

2.4 × 10-2

2.7 × 10-2


Classes with a statistically significant excess of low derived alleles when compared to the genome as a whole are shown. In order to adjust for the multiplicity of testing, 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.

Levenstien and Klein BMC Bioinformatics 2011 12:26   doi:10.1186/1471-2105-12-26

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