Table 4 Sensitivities and specificities of the WGS tools to predict resistance to first-line drugs compared with phenotypic DST.

Drug	DST		CASTB		KvarQ		Mykr. Pred. TB		PhyResSE		TBProfiler
Drug	#R	#S	Sens	Spec	Sens	Spec	Sens	Spec	Sens	Spec	Sens	Spec
INH	29	62	0.83 (0.64, 0.94)	0.98 (0.91, 1.00)	0.79 (0.60, 0.92)	0.98 (0.91, 1.00)	0.79 (0.60, 0.92)¹	0.95 (0.87, 0.99)	0.93 (0.77, 0.99)	0.97 (0.89, 1.00)²	0.90 (0.73, 0.98)	0.84 (0.72, 0.92)²
RMP	14	77	1.00 (0.68, 1.00)	0.96 (0.89, 0.99)	0.93 (0.66, 1.00)	0.95 (0.87, 0.99)	1.00 (0.68, 1.00)	0.94 (0.85, 0.98)^2,3	1.00 (0.68, 1.00)	0.94 (0.85, 0.98)	1.00 (0.68, 1.00)	0.94 (0.85, 0.98)
SM	37	54	0.30 (0.16, 0.47)	1.00 (0.90, 1.00)	0.57 (0.39, 0.73)	1.00 (0.90, 1.00)	0.57 (0.39, 0.73)	1.00 (0.90, 1.00)	0.84 (0.68, 0.94)	0.98 (0.90, 1.00)	0.57 (0.39, 0.73)	1.00 (0.90, 1.00)
EMB	14	77	0.57 (0.29, 0.82)	1.00 (0.93, 1.00)	0.50 (0.23, 0.77)	0.99 (0.93, 1.00)	0.50 (0.23, 0.77)³	0.99 (0.93, 1.00)	0.86 (0.57, 0.98)	0.97 (0.91, 1.00)	0.86 (0.57, 0.98)	0.96 (0.89, 0.99)
PZA	9	82	0.44 (0.14, 0.79)	0.99 (0.93, 1.00)	0.22 (0.03, 0.60)	0.96 (0.90, 0.99)	n.a.	n.a.	0.67 (0.30, 0.93)	0.96 (0.90, 0.99)	0.44 (0.14, 0.79)	0.96 (0.90, 0.99)

The numbers in parentheses represent 95% confidence intervals. The equivalent table with Sanger sequencing as comparator can be found in Supplementary Table S4.
INH, isoniazid; RMP, rifampicin; SM, streptomycin; EMB, ethambutol; PZA, pyrazinamid; R, resistant; S, susceptible; sens, sensitivity; spec, specificity; n.a., not applicable.
¹Mutations that were merely reported but not interpreted were excluded from the analysis.
²kasA and inhA were not Sanger sequenced for some strains.
³Low-frequency variants that were only observed upon re-examination of the Sanger sequences were treated as wild-type since these mutations would not have been called unless the WGS data had been available.

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