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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.