Table 11:

Rules used by RuleTB for each SNP cluster, in order.

	M. bovis	M. africanum 2	LVIII	M. africanum 1	LI	LV
Rule 1	MIRU04 ≥ 3	ETRC ≥ 5	MIRU40 ≤ 1	MIRU04 ≤ 3	MIRU24 ≥ 2	MIRU23 ≤ 5
Rule 2	Mtub30 ≥ 3	ETRA = 6	Mtub04 ≤ 3	MIRU23 ≤ 6	MIRU26 ≤ 4	MIRU40 ≤ 3
Rule 3	QUB4156 ≤ 1	Mtub30 ≥ 4	Mtub21 ≤ 2	MIRU24 ≥ 2		Mtub04 ≥ 3
Rule 4		QUB26 ≥ 6	QUB11b ≥ 3	MIRU26 ≤ 4		ETRC = 3
Rule 5			Mtub30 = 2	QUB11b ≤ 6		Mtub21 ≥ 3
Rule 6				ETRA ≤ 7		2 ≤ QUB11b ≤ 4
Rule 7				QUB26 ≤ 6		Mtub34 ≥ 3
	LII	LIIa	LIV	LIII	LVII	LVI
Rule 1	MIRU04 ≤ 3	MIRU10 ≥ 4	MIRU10 ≤ 5	Mtub30 ≥ 3	MIRU40 ≥ 1	MIRU04 ≤ 3
Rule 2	MIRU10 ≤ 5	MIRU24 ≤ 1	ETRC ≥ 4	QUB26 ≤ 10	ETRA ≤ 3	MIRU26 ≥ 2
Rule 3	MIRU39 ≥ 3	MIRU31 ≥ 4	Mtub30 ≥ 3		Mtub30 ≥ 2	Mtub04 ≥ 3
Rule 4	MIRU40 ≤ 5	Mtub21 ≥ 2			Mtub34 ≥ 2
Rule 5	ETRC ≥ 3	Mtub29 ≥ 3			QUB26 ≥ 2
Rule 6		Mtub30 ≥ 2
Rule 7		Mtub39 ≤ 6