Using the de novo assembled draft sequence from the 1942 isolate as a template for subsequent analysis of SNPs and small indels in the other ''military'' isolates, we generated a list of highconfidence, discriminatorymutations that differentiate the strains ( Figure 5A ). The nature and annotation of the mutations are found in Table 4 and can be assigned an approximate temporal order in which they occurred ( Figure 5B ). Based on this analysis, 1942 is the most likely parental strain for all of the isolates in this study, with the 1013 lineage diverging earliest, followed by 49822, then the ''military'' lineage prior to the transfer to Camp Detrick. This conclusion is based on the observation that 49822 shares three SNPs with Detrick-1. The latter is the most likely progenitor of the other ''military'' isolates, since it has the fewest mutations relative to strain 1942. Detrick-1 can be differentiated from other ''military'' isolates by possessing the parental allele of spo0F rather than the H101R allele (position 3231470) that is characteristic of all of the other ''military'' BGisolatesand the ATCC9372 strains. The two colony morphology variants of ATCC9372 each exhibited distinct mutation profiles indicating that the reference strain is in fact a mixed population of at least two genetically distinct substrains.