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Table 2 Classes under negative selection compared to the genome.

From: Predicting functionally important SNP classes based on negative selection

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
  1. 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.