Table 1. Cluster- and isolate-level concordance between SNP distances estimated by CSP2, CSP2, and NCBI Pathogen Detection.

For each species, the lowest average SNP differences came from the CSP2/CSP1 comparison, followed by CSP2/NCBI, then CSP1/NCBI. Mean slopes and correlation values were high across comparisons, and distances for E. coli were consistently higher at NCBI.

		Mean value across clusters (range of cluster values)			Mean SNP difference across isolates [95% CI]
Comparison	Species	Slope	Correlation	SNP difference	Contig inlier	Contig outlier
CSP1 vs. CSP2	E. coli	1.00 (0.87–1.22)	0.99 (0.97–1.0)	−0.12 (−2.58–2.53)	−0.18 [−3.25 to 2.89]	2.34 [−4.57 to 9.26]
	Listeria	1.00 (0.93–1.06)	0.99 (0.96–1.0)	−0.28 (−3.16–1.20)	−0.35 [−2.80 to 2.10]	0.12 [−3.57 to 3.81]
	Salmonella	1.00 (0.91–1.28)	0.99 (0.93–1.0)	−0.07 (−1.50–1.32)	−0.09 [−2.32 to 2.15]	0.38 [−4.61 to 5.37]
NCBI vs. CSP2	E. coli	1.02 (0.80–1.36)	0.98 (0.95–1.0)	1.87 (−3.64–5.59)	1.80 [−3.19 to 6.78]	8.45 [−4.43 to 21.3]
	Listeria	1.00 (0.93–1.12)	0.99 (0.96–1.0)	0.49 (−2.23–4.04)	0.40 [−2.22 to 3.01]	3.64 [−3.97 to 11.2]
	Salmonella	1.00 (0.72–1.06)	0.99 (0.88–1.0)	0.44 (−2.30–1.78)	0.44 [−2.19 to 3.08]	2.59 [−3.81 to 9.0]
NCBI vs. CSP1	E. coli	1.01 (0.71–1.13)	0.98 (0.91–1.0)	1.99 (−3.87–6.64)	1.98 [−3.22 to 7.17]	6.56 [−4.78 to 17.9]
	Listeria	1.00 (0.90–1.11)	0.99 (0.93–1.0)	0.77 (−0.62–3.94)	0.75 [−2.22 to 3.71]	3.52 [−4.40 to 11.5]
	Salmonella	0.99 (0.42–1.05)	0.98 (0.70–1.0)	0.52 (−1.68–2.52)	0.53 [−2.64 to 3.69]	2.21 [−3.53 to 7.96]