Whole-genome approaches are becoming critical components of microbial forensics. The SNPs and indels identified in the analysis of evidentiary materials currently become the basis for higherthroughput assays to screen large numbers of samples [56, 72] . Decreasing costs of whole-genome sequencing, and the comprehensive nature of the analysis, may make this the preferred method of forensic analysis of microbial samples in the future. With recently developed techniques of allele quantitation within populations by mass spectrometry [73] , real-time PCR [74] , and census-bysequencing [68, 75] , it may be possible to quantitate accurately rare alleles within any given microbial population. We are particularly intrigued by the possibility that, given a mixture of different variants and sufficient sequencing power, ultra-high coverage sequencing may prove to be a more quantitative means of enumerating the relative populations in a sample even before the presence of variants has been established. The results from sequencing two strains of BACI051 in this study provide evidence of such hidden diversity.