Skip to main content
. Author manuscript; available in PMC: 2011 May 24.
Published in final edited form as: Cell. 2010 Nov 24;143(5):837–847. doi: 10.1016/j.cell.2010.10.027

Figure 4. Variant breakpoint analyses.

Figure 4

Class-I variants (A–D) are defined as those without additional nucleotides at the breakpoint. (A) A histogram of the extent of matching breakpoint sequence (black) and extended breakpoint homology (gray) is shown for 590 class-I insertion/deletion events. The red line corresponds to the expected distribution of breakpoint match lengths found from 100 random permutations. Note that bin sizes are not equal. The increase in extended homology segments 250–299 bp in length corresponds to variants having Alus at their breakpoints. (B) As in (A) zoomed in to show variants having 20 bp or less matching sequence. (C) Box plot of variant size partitioned by length of extended breakpoint homology for 590 class-I insertion-deletion variants (red line : median; blue box : interquartile range; whiskers : within 1.5X interquartile range). (D) Breakpoint density map within a consensus Alu repeat sequence based on 269 copy-number variant events (blue box : RNA pol III promoter, black boxes : AT-rich segment between the two monomers that make up the Alu element and the poly A tail, purple box : position of motif (CCNCCNTNNCCNC) found in some Alus and associated with recombination hotspots (Myers et al., 2008)). Class-II variants (E–G) contain additional sequence across the breakpoint junction. (A) A class-II variant containing a 55 nucleotide-long stretch of additional sequence (in blue) that is not found at either breakpoint. (B) Histogram of the length of additional sequence found at variant breakpoints (black) and the length of detected extended homology between breakpoint sequences (gray) for 153 class-II insertion/deletion variants. (C) Genomic location for class-II unmatched sequences (>20 bp) associated with deletions. The black lines connect the positions of a class-II deletion variant (relative to the genome assembly) and the corresponding location where the additional sequence across the variant breakpoint can be found. The relationship for 31 deletion variants is depicted. One event involves a match to unlocalized sequence on chromosome 1 (chr1_rand). See also Figure S2, Table S4, and Table S5.