Fig. 5: Extrapolating beyond the CN-mappable genome.
From: Most large structural variants in cancer genomes can be detected without long reads
a, Summary of SV breakends in the CN-mappable genome, including those predicted to be undetected by JaBbA v1 (Figs. 1 and 2). b, Heatmap showing the number of NAHR-eligible reference sequence position pairs, defined as pairs of reference positions >10 kb apart with ≥96% homology across 500 bp. The size of each bin in the genome-wide plot is 10 Mb (top subpanel) and 1 Mb (bottom subpanel, CN-unmappable zoom-in). CNU, CN-unmappable; CNM, CN-mappable. c, Fractional contribution of NAHR-eligible position pairs (see above) tallied across CN-unmappable and CN-mappable genome partitions. The number of position pairs with at least one site in a CN-unmappable region is expected to be ~100 times greater than the number of position pairs fully contained in CN-mappable regions. d, Alluvial plot showing the estimated fraction of SV breakends mapped by SRS across the genome. Colors stratify breakends on the basis of SRS mappability and homologous recombination versus other repair mechanisms.
