Figure 1.

Effects of a transposition on short-read mapping. Chromosomes are horizontal bars and read pairs are pairs of horizontal lines linked by curves. Upper panel: a population ancestor corresponding to the reference genome (left) undergoing a transposition (right), in which a segment $s$ at source locus $L$ with haplotype context $\alpha$ is copied to $s^{\prime }$ at recipient sink locus $M$ with haplotype context $\beta .$ Lower panel: all four possible combinations (A–D) of source $L$ and sink $M$ haplotype in descendants. On left are shown the alignment of reads to the true haplotypes, where there are no read-mapping anomalies. On right are shown the read-mapping anomalies that arise, depending on the true haplotype backgrounds at source and sink, upon alignment to the reference genome.