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Supplementary Figures Distances between breakpoints in ABL1 and ALU or L1 repeat elements Quantile-quantile plots comparing the distribution of distances from breakpoints to the nearest repeat of the given class, with that of distances of all bases in the ABL1 region to the nearest repeat. The black line is the QQ plot for the actual breakpoints, while the grey lines arise from 1000 simulations each of 308 uniformly distributed breakpoints in the ABL1 region. The QQ plots of the actual breakpoints lie within the envelopes of the random simulations.

Distance from all bases to nearest repeat (bp) Supplementary Figure 1 ALU Distance from all bases to nearest repeat (bp) Distance from breakpoint to nearest repeat (bp)

Distance from all bases to nearest repeat (bp) Supplementary Figure 2 L1 Distance from all bases to nearest repeat (bp) Distance from breakpoint to nearest repeat (bp)