Table 3

Classes under negative selection compared to ancestral repeats.

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


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.

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

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