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Table 4 References after Affinity Propagation clustering for nclusters = 32.

From: Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis

AP-subfamily naming

reference

Most represented subfamilies

Nb of spoligotype patterns

 

Classical subfamily naming

SIT

spoligotype (43 format)

First most represented subfamily

Second most repr. family

 
    

Subfamily

Prop.

  

Afri1

AFRI1

181

AFRI1

0.531

AFRI

32

Afri2-3

AFRI2

331

AFRI2

0.364

AFRI3

22

Beij

BEIJ

1

BEIJ

0.842

U

19

Bov1-3

BOV1

482

BOV1

0.585

BOV

159

Bov2

BOV2

683

BOV2

0.467

BOV

45

Cap

CAP

647

CAP

0.75

U

20

CAS

CAS1

26

CAS1

0.487

CAS

80

EAI1

EAI1

48

EAI1

0.804

U

46

EAI3-5 (del2-3-37-38-39)

EAI2

11

EAI5

0.383

EAI3

55

EAI2 (del3-20-21)

EAI2

19

EAI2

0.5

U

48

EAI

EAI5

236

EAI5

0.651

EAI4

86

EAI6 (del23-37)

EAI6

292

EAI6

0.5

EAI5

42

H1-2

H1

47

H1

0.790

U

62

H3

H3

50

H3

0.927

U

96

Ural

H4

262

H4

0.714

U

28

LAM5-2-1(del3-13)

LAM2

17

LAM5

0.207

U

92

LAM3

LAM3

33

LAM3

0.455

U

33

LAM

LAM9

42

LAM9

0.574

LAM11

136

Manu

MANU2

54

MANU2

0.793

U

29

Pin-Mic

PIN

637

BOV

0.391

U

23

S

S

34

S

0.678

U

59

T (T1-H3-Lam10-Cam)

T1

53

T1

0.828

H3

261

T1a (del5-40-43)

T1

833

T1

0.484

U

31

T1b (del21)

T1

291

U

0.367

T1

30

T1c (del15)

T2

118

T1

0.432

U

37

T2 (del40)

T2

52

T2

0.521

U

119

T3 (del13)

T3

37

T3

0.373

U

59

T4 (del19-23-24-38-39)

T4

39

T1

0.406

T4

32

T5 (del23)

T5

44

T5

0.561

U

41

X

X1

119

X1

0.492

U

61

X2

X2

137

X2

0.824

T1

34

SEA1 (del29-34)

U

458

U

0.955

CAS

22

  1. BEIJ = Beijing (also East Asia); afri=M. africanum; CAS = Central Asia (also East Africa and India); LAM = Latino-American and Mediterranean; H = Haarlem; EAI = East African Indian. Confirmed subfamilies are shown in bold.