Figure 1.
Examples of SCONE p-Value Scores for Coding (A), Highly Conserved Noncoding (B), and Nonconserved Regions
Positions likely to be conserved (p < 0.05) are in light green; other positions are dark. Below each plot is the portion of the multiple sequence used to generate scores for each sequence region. Deviations from human sequence (green) are indicated in red.
(A) A portion of an exon from the MET gene (chr7:115,933,744–115,933,793). The pattern of conserved positions is indicative of the triplet structure of the genetic code.
(B) A highly conserved intronic sequence in the FOXP2 gene (chr7:113,646,877–113,646,926).
(C) An intergenic region near the AXIN1 gene (chr16:343,046–343,095) showing little overall conservation, but containing a significant number of individually conserved positions.
Figure 2.
Rare Derived Allele Frequency in Conserved versus Nonconserved Sites
Positions are partitioned according to (i) ENCODE MCS elements for all ENCODE positions, (ii) SCONE conservation score for all ENCODE positions, and (iii) SCONE conservation score for all ENCODE positions outside of MCS elements. p-Values are calculated using Fisher's exact test.
Figure 3.
Conservation in Various Functional Classes
For each functional class, the fraction of positions with SCONE p-value ≤ 0.005 is shown, both including (dark) and excluding (light) positions falling within MCS elements. Ancestral repeats are included as a control.
Figure 4.
Islands of Conservation in Functionally Annotated Regions
(A) Localization of short (5–12 bp) conserved islands in functionally annotated regions. Shown is the fraction of all islands that fall within a particular region. Nongenic transcribed regions were omitted to preserve scale, but contain 93% of short conserved islands.
(B) Fold excess of short (5–12 bp) conserved islands in functionally annotated regions compared to ancestral repeat regions. Shown is the ratio of the density in each region (number of clusters divided by total number of positions in the region) to the density in ancestral repeat positions.