Massive contribution of transposable elements to ASCs. (A) Percent of human genome annotated as TE-derived compared to percent of lineage-specific constrained base pairs derived from TEs. TE contributions to eutherian- and mammal-specific constrained elements were estimated in previous studies (Lowe et al. 2007; Mikkelsen et al. 2007). (B) Derived allele frequency spectrum of AFR SNPs within TE-derived ASC subregions shows a similar enrichment at low frequencies, indicating that TE-ASCs are not noticeably enriched for false positives. (C) Enrichment was defined as the fraction of constrained (ASC or AC) base pairs attributable to a TE family divided by the fraction of the aligned genome attributable to the same family. TE family names were assigned by RepeatMasker. Family size was defined as the total size in base pairs of all TEs within the family.
