TABLE 2.

Lineage prediction of the Mtb reference strains by TS or WGS^a, validated with SpoTyping

Frequency	Lineage identified by:
	Targeted-SNPsb	WGS-SNPs	SpoTyping
1	Wild-typec	Wild-type	H37Rv
2	Haarlem	Haarlem	T1, H1
2	East African Indian	East African Indian	CAS1-Delhi
2	Indo Oceanic	Indo Oceanic	EAI1-SOM, EAI6-BGD1
4	LAM	LAM	LAM1, LAM6, T5-RUS1
5	East Asian	East Asian	Beijing
1	East Asian	East Asian	NDd
2	Wild-type	Not sequenced by WGS
1	East Asian	Not sequenced by WGS

^aWGS, whole genome sequencing.

^bSNPs, single nucleotide polymorphisms.

^cWild-type, strain without phylogenetic variants (identical to H37Rv).

^dND, not determined.