Anthrax is a zoonotic disease that occurs naturally in wild and domestic animals but has been used by both state-sponsored programs and terrorists as a biological weapon. The 2001 anthrax letter attacks involved less than gram quantities of Bacillus anthracis spores while the earlier Soviet weapons program produced tons. A Soviet industrial production facility in Sverdlovsk proved deficient in 1979 when a plume of spores was accidentally released and resulted in one of the largest known human anthrax outbreak. In order to understand this outbreak and others, we have generated a B. anthracis population genetic database based upon whole genome analysis to identify all SNPs across a reference genome. Only ~12,000 SNPs were identified in this low diversity species and represents the breadth of its known global diversity. Phylogenetic analysis has defined three major clades (A, B and C) with B and C being relatively rare compared to A. The A clade has numerous subclades including a major polytomy named the Trans-Eurasian (TEA) group. The TEA radiation is a dominant evolutionary feature of B. anthracis, many contemporary populations, and must have resulted from large-scale dispersal of spores from a single source. Two autopsy specimens from the Sverdlovsk outbreak were deeply sequenced to produce draft B. anthracis genomes. This allowed the phylogenetic placement of the Sverdlovsk strain into a clade with two Asian live vaccine strains, including the Russian Tsiankovskii strain. The genome was examined for evidence of drug resistance manipulation or other genetic engineering, but none was found. Only 13 SNPs differentiated the virulent Sverdlovsk strain from its common ancestor with two vaccine strains. The Soviet Sverdlovsk strain genome is consistent with a wild type strain from Russia that had no evidence of genetic manipulation during its industrial production. This work provides insights into the world's largest biological weapons program and provides an extensive B. anthracis phylogenetic reference valuable for future anthrax investigations.