Table 2 Generalized linear mixed model analysis on clustered and non-clustered isolates in the lineage2 cohort

Rv0104

123,454

C1138T

Gln380*

0.798

0.783(0.119–5.127)

Rv0104

123,520

T1204C

Tyr402His

0.568

2.324(0.129–41.945)

Rv0197

233,016

C786T

Ala262Ala

0.969

0.98(0.367–2.618)

Rv0197

234,477

T2247G

Tyr749*

1.910E-10

8.339(4.341–16.021)

Rv0211

252,900

C1119T

Asp373Asp

0.232

0.494(0.155–1.572)

Rv0233

278,681

C97G

His33Asp

0.599

1.892(0.176–20.389)

Rv0252

304,923

A2058G

Lys686Lys

0.836

0.737(0.041–13.318)

Rv0252

305,188

G2323T

Val775Leu

0.807

0.762(0.086–6.776)

Rv0338c

403,980

C1862T

Ala621Val

0.043

0.011(0-0.871)

Rv0338c

404,130

A1712G

Glu571Gly

0.987

-

Rv0338c

404,326

A1516G

Arg506Gly

0.227

9.612(0.245-377.692)

Rv1175c

1,306,259

T1968C

Ala656Ala

0.871

1.197(0.137–10.478)

Rv1175c

1,307,598

G629C

Cys210Ser

0.199

0.231(0.025–2.158)

Rv1207

1,351,407

C217G

Arg73Gly

0.094

1.267(0.961–1.67)

Rv1469

1,657,249

T287C

Leu96Pro

0.213

1.243(0.883–1.749)

Rv1469

1,657,942

T980G

Val327Gly

0.989

-

Rv1553

1,759,521

C87T

Leu29Leu

2.230E-04

4.655(2.057–10.535)

Rv1937

2,189,829

C1334T

Ala445Val

0.330

1.361(0.732–2.531)

Rv1937

2,190,771

T2276C

Val759Ala

0.377

0.448(0.076–2.656)

Rv2331A

2,604,740

A1G

Met1?

0.987

-

Rv2564

2,884,068

A727C

Met243Leu

0.808

0.858(0.251–2.932)

Rv2633c

2,959,618

A203G

His68Arg

0.219

0.664(0.346–1.275)

Rv2711

3,024,021

C457A

Arg153Arg

0.096

23.477(0.572-963.141)

Rv2776c

3,084,195

C109A

Pro37Thr

0.252

1.78(0.663–4.774)

Rv2869c

3,180,806

C957T

Phe319Phe

0.037

6.666(1.12–39.67)

Rv2869c

3,180,988

G775T

Val259Phe

0.007

31.249(2.508-389.366)

Rv2869c

3,181,479

A284C

Lys95Thr

0.766

0.944(0.645–1.381)

Rv3224

3,600,035

A185G

Gln62Arg

0.107

1.372(0.934–2.017)

Rv3224

3,600,576

C726T

Cys242Cys

0.987

0.972(0.038–24.925)

Rv3239c

3,614,982

A2622G

Leu874Leu

0.781

1.434(0.112–18.293)

Rv3252c

3,631,457

A532C

Thr178Pro

0.880

1.048(0.567–1.939)

Rv3571

4,013,010

G594A

Leu198Leu

0.698

0.956(0.762–1.199)

Rv3674c

4,115,890

C5G

Pro2Arg

0.289

3.494(0.346–35.297)

Rv3703c

4,145,737

T1155C

Tyr385Tyr

0.379

2.869(0.274–30.026)

Rv3703c

4,146,047

C845T

Ala282Val

0.988

-

Rv3728

4,175,847

G975A

Trp325*

0.590

1.482(0.354–6.197)

Rv3728

4,176,081

C1209T

Gly403Gly

0.091

1.271(0.963–1.678)

Rv3743c

4,194,501

C873T

Phe291Phe

0.983

1.01(0.408–2.501)

Rv3743c

4,195,074

C300T

Ala100Ala

0.706

0.906(0.544–1.511)

Rv3841

4,314,645

A468G

Leu156Leu

0.110

0.031(0-2.205)