Unique coverage plots of B. anthracis genomes. Reads were mapped to the B. anthracis Ames ancestor chromosome using mapreads. Each row represents a B. anthracis chromosome (strain indicated at the upper right of each plot). Grey dots indicate coverage values at each position and red lines indicate the running mean with a window size of 1,000. Cyan tick marks near the × axis indicate the location of non-unique 35-mers in the chromosome: no reads can map uniquely to these sequences. The arrow in the A0377 plot indicates the amplified genomic region depicted in detail in Figure 4. The V-shaped profile of the coverage plot is due to the fact that replicating bacteria initiate a second round of chromosomal replication before the completion of the ongoing round, resulting in higher copy number at the origin of replication (at the ends of the plot) and lower copy number at the terminus (center of the plot).