Extended Data Fig. 7: Support for homeologous junctions.
From: Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers
a, Comparison of mapping quality for reads supporting homeologous and non-homeologous junctions. Left, density plot showing mapping quality for junction-supporting reads realigned to hg19, from a subsample of 500 non-homeologous junctions and 500 homeologous junctions. Middle, bar plot of the fraction of reads with high mapping quality (MQ = 60). Error bars represent 95% confidence interval on the Bernoulli trial parameter calculated using the fraction of non-homeologous (73,871/95,934) or homeologous (16,954/31,078) junction-supporting reads that had MQ of 60. Right, bar plot of the fraction of reads stacked by intervals of mapping quality. The number of reads in each MAPQ range for homeologous junctions (31078 total) is: MAPQ 0–29: 12,025, MAPQ 30–39: 626, MAPQ 40–49: 676, MAPQ 50–59: 797, MAPQ 60: 16,954. The number of reads in each MAPQ range for homeologous junctions (95,934 total) is: MAPQ 0–29: 19,201, MAPQ 30–39: 1,052, MAPQ 40–49: 868, MAPQ 50–59: 942, MAPQ 60: 73,871. b, Left, reference 150-mer BWA mapping quality in the neighbourhood of homeologous and non-homeologous break ends. Reference mapping quality determined by realigning sliding window of 150-mers from hg19 stepping by 1 base to hg19 and averaging across each base pair. Right, plot of alternate mappability scores calculated as the average of the reciprocal of the number of unique locations that each 150-mer overlapping a break-end-associated base pair aligns.
