|
Lineage
|
No. training (test)
|
No. countries train (test)
|
% MDR-TB
|
No. transmission [clusters]
|
Potential barcoding SNPs*
|
Robust SNPs**
|
|---|
|
1
|
2162 (1203)
|
25 (42)
|
7.8
|
354 [130]
|
344
|
17
|
|
1.1
|
1487 (530)
|
19 (36)
|
5.5
|
218 [82]
|
23
|
2
|
|
1.1.1
|
706 (170)
|
8 (16)
|
3.8
|
60 [25]
|
41
|
5
|
|
1.1.1.1
|
358 (120)
|
5 (9)
|
2.1
|
28 [11]
|
52
|
3
|
|
1.1.2
|
459 (278)
|
15 (25)
|
9.0
|
83 [31]
|
109
|
3
|
|
1.1.3
|
299 (80)
|
11 (16)
|
3.2
|
73 [25]
|
42
|
2
|
|
1.1.3.1
|
84 (31)
|
7 (13)
|
3.5
|
10 [4]
|
68
|
2
|
|
1.1.3.2
|
155 (33)
|
7 (7)
|
1.1
|
57 [18]
|
113
|
6
|
|
1.1.3.3
|
32 (7)
|
5 (4)
|
10.3
|
4 [2]
|
36
|
2
|
|
1.2
|
309 (550)
|
13 (21)
|
7.5
|
40 [16]
|
60
|
2
|
|
1.2.1
|
28 (44)
|
3 (7)
|
6.9
|
6 [2]
|
78
|
5
|
|
1.2.2
|
277 (505)
|
13 (18)
|
7.5
|
34 [14]
|
159
|
8
|
|
1.2.2.1
|
244 (453)
|
12 (18)
|
6.9
|
34 [14]
|
34
|
1
|
|
1.3
|
366 (122)
|
16 (19)
|
18.0
|
96 [32]
|
71
|
2
|
|
1.3.1
|
88 (25)
|
7 (11)
|
10.6
|
20 [7]
|
50
|
4
|
|
1.3.2
|
278 (97)
|
16 (17)
|
20.3
|
76 [25]
|
83
|
4
|
|
2
|
4556 (4322)
|
45 (56)
|
36.2
|
1778 [413]
|
72
|
4
|
|
2.1
|
95 (41)
|
6 (9)
|
19.8
|
27 [10]
|
172
|
4
|
|
2.2
|
4461 (4281)
|
45 (56)
|
36.5
|
1751 [403]
|
79
|
17
|
|
2.2.1
|
4239 (4007)
|
45 (56)
|
35.1
|
1632 [389]
|
17
|
2
|
|
2.2.1.1
|
338 (443)
|
19 (18)
|
28.0
|
98 [40]
|
6
|
2
|
|
2.2.1.2
|
29 (21)
|
6 (9)
|
36.0
|
10 [3]
|
5
|
1
|
|
2.2.2
|
222 (273)
|
16 (15)
|
59.0
|
119 [14]
|
54
|
4
|
|
3
|
2654 (1271)
|
24 (31)
|
13.4
|
847 [242]
|
166
|
8
|
|
3.1
|
715 (362)
|
15 (22)
|
9.5
|
372 [80]
|
1
|
1
|
|
3.1.1
|
387 (280)
|
11 (16)
|
6.2
|
243 [43]
|
17
|
2
|
|
3.1.2
|
295 (69)
|
13 (8)
|
14.3
|
124 [35]
|
8
|
2
|
|
3.1.2.1
|
98 (25)
|
8 (7)
|
19.5
|
25 [12]
|
15
|
7
|
|
3.1.2.2
|
48 (0)
|
3 (0)
|
0
|
36 [2]
|
85
|
6
|
|
3.2
|
89 (31)
|
6 (9)
|
10.0
|
31 [7]
|
85
|
2
|
|
4
|
8320 (9883)
|
44 (99)
|
18.5
|
3109 [731]
|
94
|
3
|
|
4.1
|
2594 (2325)
|
35 (64)
|
18.5
|
1043 [191]
|
58
|
3
|
|
4.1.1
|
889 (482)
|
20 (27)
|
18.1
|
403 [72]
|
30
|
13
|
|
4.1.1.1
|
210 (158)
|
14 (16)
|
9.5
|
92 [20]
|
39
|
2
|
|
4.1.1.2
|
55 (44)
|
4 (6)
|
2.0
|
33 [3]
|
92
|
2
|
|
4.1.1.3
|
579 (247)
|
18 (23)
|
22.4
|
266 [44]
|
58
|
3
|
|
4.1.1.3.1
|
207 (13)
|
3 (3)
|
9.6
|
158 [5]
|
46
|
3
|
|
4.1.2
|
1612 (1743)
|
32 (61)
|
17.3
|
622 [113]
|
13
|
1
|
|
4.1.2.1
|
1383 (1087)
|
32 (60)
|
22.5
|
563 [96]
|
49
|
3
|
|
4.1.2.1.1
|
231 (18)
|
1 (1)
|
97.6
|
221 [2]
|
73
|
3
|
|
4.1.3
|
28 (70)
|
7 (10)
|
57.1
|
4 [2]
|
124
|
3
|
|
4.1.4
|
24 (12)
|
8 (7)
|
38.9
|
10 [2]
|
60
|
4
|
|
4.2
|
481 (532)
|
23 (26)
|
28.0
|
87 [32]
|
116
|
8
|
|
4.2.1
|
206 (240)
|
13 (20)
|
28.3
|
34 [13]
|
26
|
2
|
|
4.2.1.1
|
54 (148)
|
9 (10)
|
6.9
|
2 [1]
|
36
|
2
|
|
4.2.2
|
274 (288)
|
20 (18)
|
28.1
|
53 [19]
|
20
|
2
|
|
4.2.2.1
|
74 (41)
|
10 (6)
|
45.2
|
22 [7]
|
26
|
2
|
|
4.2.2.2
|
120 (139)
|
11 (14)
|
27.8
|
15 [7]
|
31
|
10
|
|
4.3
|
2507 (2928)
|
30 (75)
|
23.1
|
993 [244]
|
38
|
2
|
|
4.3.1
|
58 (67)
|
7 (15)
|
6.4
|
40 [3]
|
28
|
1
|
|
4.3.1.1
|
37 (2)
|
3 (1)
|
0.0
|
36 [1]
|
52
|
2
|
|
4.3.2
|
409 (1200)
|
16 (21)
|
7.2
|
75 [32]
|
75
|
1
|
|
4.3.2.1
|
291 (917)
|
6 (7)
|
3.7
|
50 [23]
|
55
|
4
|
|
4.3.3
|
648 (810)
|
25 (57)
|
41.3
|
210 [66]
|
33
|
1
|
|
4.3.4
|
1366 (807)
|
23 (45)
|
24.1
|
664 [142]
|
8
|
1
|
|
4.3.4.1
|
194 (170)
|
14 (30)
|
28.9
|
49 [14]
|
19
|
4
|
|
4.3.4.2
|
1170 (635)
|
22 (34)
|
23.1
|
614 [128]
|
26
|
1
|
|
4.3.4.2.1
|
877 (287)
|
13 (18)
|
5.6
|
457 [103]
|
11
|
1
|
|
4.4
|
560 (1059)
|
24 (29)
|
15.7
|
190 [63]
|
37
|
2
|
|
4.4.1
|
420 (861)
|
22 (25)
|
16.0
|
149 [48]
|
38
|
4
|
|
4.4.1.1
|
379 (755)
|
21 (24)
|
17.8
|
136 [44]
|
16
|
1
|
|
4.4.1.1.1
|
75 (206)
|
5 (4)
|
19.6
|
22 [9]
|
60
|
3
|
|
4.4.1.2
|
39 (106)
|
8 (6)
|
1.4
|
13 [4]
|
95
|
9
|
|
4.4.2
|
112 (181)
|
7 (9)
|
14.7
|
33 [13]
|
7
|
2
|
|
4.5
|
293 (357)
|
17 (17)
|
15.7
|
49 [22]
|
50
|
1
|
|
4.6
|
340 (442)
|
21 (25)
|
22.1
|
139 [39]
|
12
|
1
|
|
4.6.1
|
73 (296)
|
9 (12)
|
29.8
|
24 [8]
|
53
|
3
|
|
4.6.1.1
|
29 (126)
|
6 (7)
|
1.3
|
14 [3]
|
22
|
1
|
|
4.6.1.2
|
40 (154)
|
9 (11)
|
54.6
|
10 [5]
|
37
|
1
|
|
4.6.2
|
164 (89)
|
16 (17)
|
15.4
|
65 [20]
|
22
|
1
|
|
4.6.2.1
|
2 (0)
|
1 (0)
|
0
|
2 [1]
|
45
|
2
|
|
4.6.2.2
|
150 (89)
|
14 (17)
|
15.9
|
60 [18]
|
106
|
6
|
|
4.6.3
|
23 (9)
|
3 (4)
|
0
|
20 [3]
|
135
|
3
|
|
4.6.4
|
23 (7)
|
5 (4)
|
50.0
|
10 [2]
|
49
|
1
|
|
4.6.5
|
23 (18)
|
5 (5)
|
19.5
|
9 [3]
|
8
|
2
|
|
4.7
|
158 (200)
|
18 (23)
|
10.3
|
56 [20]
|
10
|
3
|
|
4.8
|
1051 (1807)
|
29 (55)
|
7.8
|
419 [88]
|
17
|
1
|
|
4.8.1
|
63 (90)
|
7 (4)
|
22.2
|
21 [5]
|
46
|
3
|
|
4.8.2
|
116 (5)
|
3 (2)
|
0
|
113 [1]
|
42
|
2
|
|
4.8.3
|
21 (3)
|
1 (1)
|
0
|
19 [1]
|
34
|
1
|
|
4.9
|
243 (141)
|
14 (22)
|
12.5
|
114 [24]
|
37
|
3
|
|
4.9.1
|
74 (15)
|
6 (3)
|
5.6
|
44 [1]
|
49
|
3
|
|
5
|
26 (255)
|
6 (12)
|
14.6
|
2 [1]
|
460
|
13
|
|
6
|
32 (135)
|
6 (13)
|
3.6
|
5 [2]
|
214
|
10
|
|
7
|
38 (26)
|
3 (2)
|
0
|
3 [1]
|
837
|
38
|
|
8
|
2 (0)
|
1 (0)
|
0
|
0 [0]
|
888
|
43
|
|
9
|
3 (0)
|
1 (0)
|
0
|
0 [0]
|
160
|
5
|
|
M. bovis
|
81 (281)
|
9 (12)
|
0.8
|
42 [11]
|
93
|
3
|
|
M. caprae
|
3 (7)
|
2 (3)
|
0
|
0 [0]
|
225
|
5
|
|
M. orygis
|
26 (12)
|
4 (4)
|
0
|
0 [0]
|
743
|
28
|
|
Totals
|
17,903 (17,395)
|
165 (269)
|
21.0
|
6140 [1531]
|
8128
|
421
|
- Bolded are changes from the barcode in reference [1]—either new sub-lineages or new barcoding SNPs; MDR-TB multidrug-resistant TB, which is resistant to at least rifampicin and isoniazid drugs. *All potential barcoding SNPs (FST = 1). **Final robust SNP set, based on synonymous changes in essential and non-drug resistance genes only (except 12 sub-lineages which had no informative SNPs in essential genes; see Additional file 1: Table S2)
