Alignment of reads from a heterogeneous sequencing sample. Total counts of soft-clipped reads and spanning reads at the structural variation breakpoints are different between the cases of (a) deletion, (b) tandem duplication, and (c) inversion. All examples have 10 × depth of coverage, with 20% of the sample coming from the variant sequence (i.e. 2 × depth) on the bottom and 80% from the reference-like sequence (i.e. 8 × depth) on top. Arrows indicate how reads from the variant sequence will be aligned against the reference genome, with soft-clipping indicated by dotted line borders. A indicates the total number of reads that span either breakpoint, and B indicates the total number of reads that are soft-clipped at either breakpoint in each of the examples. A and B are used by SHEAR to estimate the heterogeneity of SVs.