Table 1:

Correspondence between the narrow lineages used in MIRU-VNTRplus database, together with their frequencies there, and the broad lineages in TB-Insight as well as the broad and refined ones in our study.

Narrow lineage	Broad lineage	Refined lineage	# (unique)
Beijing	East-Asian	East-Asian	10 (8)
Bovis	M. bovis	M. bovis	11 (11)
Cameroon	Euro-American	Euro-American	10 (10)
Canettii	not used due to sparsity	not used	2 (2)
Caprae	not used due to sparsity	M. caprae	11 (11)
Delhi/CAS	East-African Indian	East-African Indian	10 (8)
EAI	Indo-Oceanic	Indo-Oceanic	12 (2)
Ghana	Euro-American	Euro-American	10 (6)
Haarlem	Euro-American	Euro-American	13 (12)
H37Rv	not used due to sparsity	not used	1 (1)
LAM	Euro-American	Euro-American	11 (11)
llama	not used due to sparsity	not used	4 (4)
NEW-1	not used due to sparsity	not used	3 (3)
S	Euro-American	Euro-American	12 (11)
Seal	not used due to sparsity	not used	2 (1)
TUR	not used due to sparsity	not used	4 (2)
Uganda*	Euro-American	Euro-American	20 (17)
Ural	not used due to sparsity	not used	4 (4)
vole	not used due to sparsity	not used	2 (2)
West African 1	M. africanum†	M. africanum 1	22 (21)
West African 2	M. africanum†	M. africanum 2	11 (11)
X	Euro-American	Euro-American	3 (2)

^*- includes Uganda I and II;

^†- includes West African 1 and 2.