Organism Z-score Non-mapping Non-Reference Base Fraction (mapped reads) Mapped Read Fraction Unmapped Reference Bases SNP calls B.globigii* 0.02 0.018 0.99 0 0 Y.pesis 0.12 0.019 0.93 134,750 47 B.mallei 3.06 0.025 0.94 166,439 431 B.pseudomallei 2.87 0.027 0.98 859 365 Representative Mapping Statistics: 10,000,000 Illumina reads, 100bp *Calibrant

Table 5: Mapping statistics for three threat agents and our Bgcalibrant. Nonalignment Z values are included for comparison. The higher Z values for Bukholderia is reflective of the higher fraction of non-reference-matching base calls in these samples and is indicative of a greater population diversity compared to Bg. Bukholderia had much higher SNP calls (Pipeline B) compared to the Y. pestis. The larger unmapped base counts along the reference genomes (column 5) for Yp and Bm are due to insertion elements that are highly mobile within these genomes and promote re-arrangements. The BFAST default parameters for assigning candidate locations to reads when there is a high multiplicity of candidate alignments across the reference genome resulted in these gaps.