TABLE 1.

Topological comparisons of B. cereus sensu lato ST 26 phylogenies constructed using various SNP calling pipeline/reference genome combinations

Reference genome					Kendall-Colijn test raw P valuesc
Strain	NCBI RefSeq accession	Assembly level	MLST STa	ANI range (mean)b	BactSNP	Lyve-SET	Parsnp	Snippy
AH187	NC_011658.1	Complete genome	26	99.8–100.0 (99.9)	0/0	0/0	0/0	0/0
IS195	GCF_000399225.1	Scaffold	26	99.6–100.0 (99.7)	0/0	0/0	0/0	0/0
AND1407	GCF_000290995.1	Scaffold	164	98.9–99.2 (99.1)	0/0	0/0	0/0	0/0
MB.17	GCF_001566445.1	Contigs	144	98.8–99.1 (99.0)	0/0	3.0 × 10–4/0	0/1.0	0/1.0
MB.18	GCF_001566385.1	Contigs	2056	97.4–97.8 (97.6)	NAd	2.0 × 10–4/0	0/0	0/0
MB.22	GCF_001566535.1	Contigs	869	97.4–97.7 (97.6)	NAe	3.0 × 10–4/0	0/0	NAe

^aSeven-gene multilocus sequence typing (MLST) sequence types (ST) were determined in silico using BTyper v2.3.3.

^bRange and mean average nucleotide identity (ANI) values were calculated between the respective reference genome and 64 group III B. cereus sensu lato genomes assigned to ST 26 using FastANI v1.0.

^cData are presented as “AH187 Reference Tree/AH187 Query Tree.” For each reference-based SNP calling pipeline (i.e., BactSNP, Lyve-SET, Parsnp, and Snippy), the phylogeny produced using SNPs identified among 64 B. cereus sensu lato ST 26 isolates using the respective SNP calling pipeline and the chromosome of B. cereus sensu lato ST 26 strain AH187 as a reference genome was used as a (i) reference tree and (ii) query tree for the Kendall-Colijn test, since the chromosome of strain AH187 has been shown to be an adequate reference genome for reference-based SNP calling among ST 26 genomes (7). NA, not applicable.

^dNo SNPs identified among the 64 B. cereus sensu lato ST 26 genomes using the respective SNP calling pipeline/reference genome combination.

^eSNPs identified using the respective SNP calling pipeline/reference genome combination were not diverse enough for use with Gubbins/IQ-TREE.