|
spoligotype pattern
|
SpolDB4
|
Recent litterature
|
Deletions
|
Domain Walls
|
SpotClust subfamily
|
---|
SIT
| |
family
|
Sub-family
|
assignation
|
family
|
family
|
SpolDB3-based
|
RIM
|
41
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM9
|
N19
|
186
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM9
|
N19
|
367
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM9
|
N19
|
930
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM1
|
N19
|
1261
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM9
|
N19
|
1589
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM3
|
N2
|
1924
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM9
|
N19
|
1937
|
|
LAM
|
LAM7
|
T-TUR
|
T
|
LAM
|
LAM9
|
N19
|
35
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
262
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
361
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
399
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
T2
|
N34
|
596
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
597
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
656
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
762
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
777
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
817
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
920
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
921
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
922
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1117
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1134
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1165
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1174
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1242
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
U
|
N34
|
1269
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1276
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1281
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1292
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1447
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1448
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1457
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1568
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1581
|
|
H
|
H4
|
T-Ural
|
T
|
H
|
H3
|
N34
|
1384
|
|
H
|
H4
|
T-Ural
|
T
|
U
|
T3
|
N40
|
1446
|
|
H
|
H4
|
T-Ural
|
T
|
U
|
H3
|
N34
|
1452
|
|
H
|
H4
|
T-Ural
|
T
|
U
|
H3
|
N34
|
1455
|
|
H
|
H4
|
T-Ural
|
T
|
U
|
U
|
N34
|
1456
|
|
H
|
H4
|
T-Ural
|
T
|
U
|
H3
|
N34
|
1461
|
|
H
|
H4
|
T-Ural
|
T
|
U
|
H3
|
N34
|
1480
|
|
H
|
H4
|
T-Ural
|
T
|
U
|
LAM9
|
N19
|
105
|
|
U
|
U
|
H
|
U
|
Afri
|
LAM7
|
N29
|
1274
|
|
U
|
U
|
LAM
|
U
|
Afri
|
H1
|
N5
|
1531
|
|
U
|
U
|
X
|
X
|
X
|
X1
|
N44
|
- "Recent literature assignation" represents the standard, and refers to studies using loci other than the CRISPR locus: T-TUR classification has been suggested both by Millet et al. [35] and Abadia et al. [34] based respectively on VNTR signature and SNPs signatures. T-Ural classification has been suggested by Kovalev et al. [36] as they clustered with H37Rv strains and Abadia et al. [34]. RIM: Randomly Initialized Model. N ... families as defined by Spotclust are described on their web-site based on what SpolDB4 families/sub-families are mostly represented: N2 family is described as LAM3-rich; N5 as H1-rich; N19 as LAM-rich; N29 as LAM+EAI-rich; N34 as H3+S-rich; N40 as T3-africanum-rich; N4 as X1-H37Rv-rich. The assignations matching the standard are shown in bold characters. Assignations failures are shown in italic. Note that the "Deletions" method provides the highest number of exact assignations and the least assignation failures.