Points represent specific pairwise comparisons; popANI, SNP-based strain similarity, as calculated by inStrain. Red and blue lines show the same-strain cutoffs for SynTracker (>0.955) and inStrain (>0.99999); the same cutoffs are used in each panel. Purple points mark comparisons classified as the same strain by both tools, red points mark comparisons classified as the same strain by SynTrakcer, blue points mark comparisons classified as the same strain by inStrain and gray points are pairs marked as belonging to different strains by both tools. N. gonorrhoeae, n = 66 comparisons.
