SVs are identified in lrWGS as enrichments of breakpoint-spanning read clouds. (A) Schematic illustration of read clouds spanning a chromosome 4 (chr4) to chr8 translocation breakpoint and the pair-end reads constituting the read clouds. (B) Heat map showing the enrichment of shared read cloud (barcodes) between regions on chr4 and chr8 fused by a reciprocal translocation. As the enrichment of shared read clouds progressively increases closer to the breakpoint, the signals in the heat map resemble 2 arrowheads pointing toward the breakpoint. Effectively, this allows for determining that the reciprocal translocation results in the fusion of the chr4 β-region with the chr8 a-region (i) and the chr4 α-region with the chr8 b-region (ii). The connected green and orange arrows schematically indicate the areas joined by events i and ii. (C) Schematic illustration of the derivate chromosomes generated by the reciprocal translocation. Supplemental Figure 4 provides additional details on the interpretation of read-cloud data and examples of other SVs.