Indels in repetitive sequence contexts. (A) Relative abundance of genomic context classified as repetitive (HR, TR, and PR; see text for definitions) and nonrepetitive (NR) across the genome (top) and among indel sites (bottom). Nonrepetitive indel sites were further divided into copy-number-changing (CCC) and non-CCC indels. (B) Histogram of insertion (right) and deletion (left) counts by variant length (solid gray), and separately by genomic context (superimposed lines). Counts were adjusted within each context category to account for the fraction of polarizable calls. (C,D) Fraction of polymorphic repeat tracts (C) and relative per-nucleotide indel rates (thin lines) and model fit (D), by length of tandem repeat unit (color) and tract length (horizontal axis). Shading indicates ±2 standard errors of the mean observed polymorphic fraction or indel rate.
