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. (XLSX)

Fig 1C_SNP比对：本部分展示的是经PhAME比对软件分析得到的各菌株的全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）比对序列。Fig 1D_RAxML自举分析：数据源自RAxML自举分析。本部分列出了100次自举重复实验得到的连锁关系，这些即为图1D中展示的自举值的来源；基于此构建的二分分枝树亦展示于图1D中。Fig 1F：本部分展示了由模拟代码生成的均值及上下限。输入序列与代码可通过论文中提及的GitHub链接获取，以支持实验重现。本次模拟共开展1000次运行，每次运行包含10种不同场景下的10000条输入DNA序列，由此产生的海量原始输出数据经代码处理后得到观测均值与误差值。Fig 1G：本部分展示了作为种群百分比函数的平均汉明距离（Hamming distance）。通过使用https://github.com/akirpich-ap/anthrax-simulations 提供的代码与输入序列，可重现平均汉明距离与获得终止密码子的细菌序列比例。汉明距离用于表征核苷酸序列与输入序列之间的偏差。Fig 3A：本部分展示了在T=0时刻及每2分钟测定的OD600（光密度600nm，optical density at 600 nm）值，用于计算相对于初始OD600的百分比；同时列出了所用菌株与生物学重复样本信息。Fig 3B：本部分展示了原始菌落形成单位（Colony-Forming Unit, CFU）计数、孢子计数以及用于计算显著性的统计方法，所有子面板的数据均已给出。Fig 3C：本部分展示了各细胞类型的孢子结合率（以野生型菌株的百分比表示）；同时呈现了2次独立实验的单个数据点，以及均值与标准差（standard deviation, SD）。Fig 3D：本部分展示了经1×10^6个孢子鼻内攻毒后的小鼠存活原始数据：1代表小鼠在某一日死亡，0代表小鼠存活至实验终点。Fig 3E：本部分展示了每只单独接受不同菌株孢子攻毒的小鼠的CFU计数；原始图3E中呈现了所有单个数据点、均值与标准差。Fig 3F：本部分列出了同一小鼠混合器官中突变株与互补突变株的CFU计数。Fig 3G：本部分展示了体外与体内实验的CFU计数，以及各重复样本的置信区间（confidence interval, CI）计算结果。Fig 4A：本部分展示了经1000个孢子皮下攻毒后的小鼠存活原始数据：1代表小鼠在某一日死亡，0代表小鼠存活至实验终点。Fig 4B：本部分展示了经孢子攻毒后的大蜡螟（Galleria mellonella）存活原始数据：1代表受试个体在某一日死亡，0代表存活至实验终点。Fig 4C–4G：模拟代码、输入文件与输出文件可通过https://github.com/jmponciano/mice 获取。补充图S1B与S1D：本部分展示的图像为气相色谱-质谱联用仪的原始读数，未经过任何修改；从这些原始读数中提取得到的峰面积与观测质谱数据亦一并呈现。补充图S2：本部分展示了经鼻内攻毒（左列）与皮下攻毒（右列）孢子后的小鼠存活原始数据：1代表小鼠在某一日死亡，0代表存活至实验终点。补充图S3B：本部分展示了经吸附炭疽疫苗（anthrax vaccine adsorbed, AVA）免疫后，以指定剂量的指定菌株孢子进行皮下攻毒的小鼠存活原始数据：1代表小鼠在某一日死亡，0代表存活至实验终点。其中AVA为吸附炭疽疫苗。（XLSX）