Figure 5. Whole-genome mutation analysis and evolutionary history of the “military” lineage of B. atrophaeus var. globigii.

A) Whole-genome shotgun sequences of the other strains were mapped to the de novo assembled contigs of the 1942 strain using Newbler. Mutations exhibiting high quality scores in both reference and query sequences and with differences from the template exhibited in >85% of the individual sequencing reads are indicated as a blackened box. In one case (position 259001 in ATCC 9372-1) an initial false-negative due to the formation of a homopolymeric tract was found by direct inspection of the assemblies. The genes whose functions are altered by the given mutation are indicated in Table 4. B) Microevolutionary history of B. atrophaeus var. globigii strains. “Enhancement” events are indicated in red.