Coverage plots of Y. pestis chromosomes. Reads were mapped to the Y. pestis CO92 chromosome using mapreads. Each row represents a Y. pestis chromosome (strain indicated in the upper left of each plot) as described in Figure 1. The arrow in the 97A-7970 and La Paz plots indicates the deletion region depicted in detail in Figure 7. The arrowhead in the La Paz plot indicates the amplified region depicted in Figure 8.