Overview of genomic variability among the specimens included in this study. Panel (a) shows variations in read depth for the alignment of reads from the three field isolates against the chromosomes of L. borgpetersenii strain L550 (subtype A). CNVs (insertions and deletions) larger than 2 kb predicted by CNVnator are shown below the plot. Panel (b) shows nonsynonymous SNVs and short indels located within protein-coding genes, identified for the four subtype A specimens by using strain L550 as a reference. Panel (c) shows chromosome-to-chromosome comparisons among the two reference genomes for subtype A and B and the genomes of our corresponding laboratory strains. In these comparisons, red bands indicate similar regions and blue bands indicate inversions. Panel (d) is similar to panel (b) but for variants identified for the subtype B laboratory strain, using the genome of strain JB197 as reference.