Placement of the ISS isolates into a core genome SNP phylogeny.

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Placement of the ISS isolates into a core genome SNP phylogeny. Placement of the ISS isolates into a core genome SNP phylogeny. We used 461 B. cereus sensu lato genomes publicly available in the NCBI database to generate a 193,732-character SNP matrix with BWA-MEM and GATK in conjunction with NASP. The tree was inferred with IQ-TREE. The SNPs were called from a 628,820-character core genome alignment. The phylogeny retention index (0.94) and the consistency index (0.31) were calculated with Phangorn. The B. cereus sensu lato phylogeny is separated into three major clades. The expanded view on the right provides a closer look at the portion of the tree within clade 1 that includes the ISS isolates. The ISS isolates are closely related to B. anthracis but are in a distinct and separate clade. Kasthuri Venkateswaran et al. mSystems 2017; doi:10.1128/mSystems.00021-17