Raw data for figures throughout the manuscript.

Fig 1C_SNPalignments: Data presented here are the genome wide SNP alignment sequences for each strain as determined by the PhAME alignment software. Fig 1D_RAxML bootstrapcalcs: from the RAxML bootstrap analysis. The linkages generated from each of the 100 boot strapping repetitions are listed and are the source of the boot strapping values presented in Fig 1D. The bipartitioned tree produced from these is presented in Fig 1D. Fig 1F: We have provided the means and upper/lower limits generated by the simulation code. The input sequence and code are available at the github link indicated in the manuscript to enable reproduction of our simulation. Raw data output from 1,000 simulation runs each containing 10,000 input DNA sequences across 10 different scenarios generated a huge amount of raw data output which the code processes into the observed means and error. Fig 1G: The mean Hamming distance as a function of population percentage is presented. Using the code and sequence input from https://github.com/akirpich-ap/anthrax-simulations, the mean Hamming distance and proportion of bacterial sequences acquiring a stop codon can be reproduced. The Hamming distance represents the nucleotide sequence deviation from the input. Fig 3A: OD600 measured at T = 0 and every 2 minutes and used to calculate % of starting OD600. The strains and replicates are listed. Fig 3B: Raw CFUs, spore counts, and statistical methods for calculating significance are presented. Data for all subpanels are shown. Fig 3C: Spore association with each cell type as a % of wild type are indicated. Individual data points from 2 experiments are presented with the mean and SD in the Fig 3C. Fig 3D: raw mouse survival data following intranasal challenge with 1 × 106 spores. One indicates a mouse death at a certain day, and a 0 indicates survival until study endpoint. Fig 3E: CFU counts for each mouse challenged singly with spores of the different strains. Each individual data point, the means and SD are shown in the original Fig 3E. Fig 3F: CFU counts of mutant and mutant complement bacteria in pooled organs of the same mouse are listed. Fig 3G: CFU counts for in vitro and in vivo studies and calculations of the CI for each replicate are presented. Fig 4A: raw mouse survival data following subcutaneous challenge with 1,000 spores. One indicates a mouse death at a certain day, and a 0 indicates survival until study endpoint. Fig 4B: raw Galleria mellonella survival data following spore challenge. One indicates a mouse death at a certain day, and a 0 indicates survival until study endpoint. Fig 4C–4G: Simulation code, input, and output files are available at https://github.com/jmponciano/mice. S1B and S1D Fig: The images in S1B and S1D Fig are the raw readouts from the gas chromatography mass spectrometer and were not modified in any way. From these raw readouts, data about peak area and observed mass spectra were extracted and are presented here. S2 Fig: raw mouse survival data following intranasal (left column) and subcutaneous (right column) spore challenge. One indicates a mouse death at a certain day, and a 0 indicates survival until study endpoint. S3B Fig: raw mouse survival data following vaccination with AVA and subcutaneous spore challenge of the indicated strains at the indicated doses. One indicates a mouse death at a certain day, and a 0 indicates survival until study endpoint. AVA, anthrax vaccine adsorbed.
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