Table 3 Generalized linear mixed model analysis on cross-country transmission clades

Rv0069c

77,058

A565G

Ile189Val

0.144

2.361(0.745–7.481)

Rv0073

81,963

G288A

Leu96Leu

4.34E-07

0.145(0.069–0.307)

Rv0104

122,483

T167G

Ile56Ser

9.73E-05

3.647(1.902–6.993)

Rv0104

122,794

T478G

Phe160Val

2.830E-04

29.725(0.624-1415.389)

Rv0104

123,454

C1138T

Gln380*

1.060E-04

-

Rv0104

123,520

T1204C

Tyr402His

1.390E-04

-

Rv0104

123,745

G1429A

Gly477Arg

9.80E-05

-

Rv0197

232,574

G344T

Gly115Val

6.19E-05

-

Rv0197

233,016

C786T

Ala262Ala

1.000

-

Rv0197

233,751

A1521G

Lys507Lys

1.000

-

Rv0197

234,051

G1821A

Pro607Pro

0.999

-

Rv0197

234,477

T2247G

Tyr749*

0.977

1.009(0.535–1.903)

Rv0211

252,083

A302C

Asn101Thr

2.830E-04

7.308(2.498–21.385)

Rv0211

252,900

C1119T

Asp373Asp

1.060E-04

-

Rv0211

253,388

C1607G

Ala536Gly

1.390E-04

-

Rv0233

278,681

C97G

His33Asp

0.405

0.665(0.254–1.738)

Rv0233

278,755

C171T

Ala57Ala

0.086

2.079(0.902–4.79)

Rv0252

303,414

C549T

Phe183Phe

1.000

-

Rv0252

304,679

G1814T

Gly605Val

0.989

-

Rv0252

304,902

C2037T

Arg679Arg

1.000

-

Rv0252

304,923

A2058G

Lys686Lys

0.999

-

Rv0252

305,106

C2241T

Asp747Asp

0.999

-

Rv0252

305,188

G2323T

Val775Leu

1.000

-

Rv0283

344,288

C267G

Ser89Ser

1.000

-

Rv0283

344,444

C423T

Ser141Ser

0.038

4.349(1.085–17.428)

Rv0338c

403,364

C2478T

Pro826Pro

0.286

3.114(0.387–25.064)

Rv0338c

403,920

G1922A

Arg641His

0.043

0.089(0.008–0.93)

Rv0338c

403,980

C1862T

Ala621Val

1.060E-04

0.044(0.009–0.215)

Rv0338c

404,130

A1712G

Glu571Gly

0.999

-

Rv0338c

404,326

A1516G

Arg506Gly

0.072

0.075(0.004–1.261)

Rv0338c

405,812

A30C

Ile10Ile

0.777

0.79(0.154–4.053)

Rv1175c

1,306,259

T1968C

Ala656Ala

0.999

-

Rv1175c

1,306,615

C1612G

Pro538Ala

1.000

-

Rv1175c

1,307,598

G629C

Cys210Ser

0.442

4.826(0.087-266.177)

Rv1207

1,351,407

C217G

Arg73Gly

0.454

1.18(0.765–1.822)

Rv1229c

1,372,301

C649G

Leu217Val

0.627

1.462(0.316–6.764)

Rv1436

1,613,927

C621A

Ala207Ala

0.998

-

Rv1436

1,613,960

G654T

Ala218Ala

0.002

6.606(1.962–22.243)

Rv1469

1,657,249

T287C

Leu96Pro

0.032

0.372(0.15–0.92)

Rv1469

1,657,720

C758T

Ala253Val

0.018

4.831(1.316–17.734)

Rv1469

1,657,942

T980G

Val327Gly

0.999

-

Rv1469

1,658,312

C1350T

Ala450Ala

1.000

-

Rv1937

2,190,771

T2276C

Val759Ala

0.998

-

Rv2564

2,883,997

A656G

Gln219Arg

0.997

-

Rv2564

2,884,068

A727C

Met243Leu

0.998

-

Rv2633c

2,959,714

A107G

Asp36Gly

0.999

-

Rv2869c

3,180,806

C957T

Phe319Phe

0.998

-

Rv2869c

3,180,988

G775T

Val259Phe

0.999

-

Rv3025c

3,383,912

C1155G

Ala385Ala

0.998

-

Rv3239c

3,614,982

A2622G

Leu874Leu

0.803

1.408(0.096–20.599)

Rv3252c

3,631,160

C829T

Leu277Leu

1.000

-

Rv3571

4,012,954

G538A

Ala180Thr

0.998

-

Rv3571

4,013,010

G594A

Leu198Leu

0.197

1.316(0.867–1.995)

Rv3703c

4,145,770

G1122T

Glu374Asp

0.999

-

Rv3703c

4,146,047

C845T

Ala282Val

0.998

-

Rv3703c

4,146,314

C578A

Pro193Gln

1.390E-04

5.641(2.317–13.734)

Rv3703c

4,146,330

T562C

Leu188Leu

0.999

-

Rv3728

4,175,847

G975A

Trp325*

0.999

-

Rv3728

4,176,081

C1209T

Gly403Gly

0.005

0.238(0.087–0.65)

Rv3728

4,177,264

C2392T

Arg798Cys

0.997

-

Rv3728

4,177,280

C2408A

Ser803Tyr

1.000

-

Rv3743c

4,194,501

C873T

Phe291Phe

0.125

3.04(0.735–12.579)

Rv3743c

4,194,698

G676C

Ala226Pro

0.998

-

Rv3818

4,282,707

C259G

Pro87Ala

9.80E-05

0.125(0.044–0.355)

Rv3818

4,282,821

G373A

Ala125Thr

0.999

-

Rv3818

4,283,319

G871A

Ala291Thr

9.80E-05

0.042(0.009–0.198)

Rv3841

4,314,645

A468G

Leu156Leu

0.999

-