Table 3 Generalized linear mixed model analysis on clustered and non-clustered strains in the lineage2.2.2 cohort

Rv0982

1,098,417

G910A

Asp304Asn

< 0.001

2.092(1.958,2.234)

Rv1743

1,969,405

G402A

Gly134Gly

< 0.001

2.063(1.808,2.354)

Rv2027c

2,274,294

C215T

Thr72Ile

< 0.001

2.442(1.952,3.056)

Rv1747

1,973,911

C282T

Pro94Pro

< 0.001

2.442(2.081,2.866)

Rv1626

1,828,320

C141T

Gly47Gly

< 0.001

1.853(1.637,2.098)

Rv0014c

16,352

C1119T

Ala373Ala

< 0.001

2.098(1.815,2.425)

Rv2247

2,520,964

G222A

Thr74Thr

0.009

0.436(0.317,0.6)

Rv0758

852,994

G599T

Gly200Val

0.005

0.414(0.302,0.566)

Rv0014c

16,465

G1006C

Val336Leu

< 0.001

2.462(1.968,3.08)

Rv0845

942,450

C1261T

Leu421Leu

< 0.001

2.524(2.014,3.165)

Rv1266c

1,414,305

C1536G

Asp512Glu

< 0.001

2.535(2.022,3.177)

Rv0490

580,362

C1014G

Ala338Ala

0.004

0.402(0.293,0.55)

Rv3132c

3,498,065

C1201A

Arg401Arg

< 0.001

2.43(1.943,3.04)

Rv1028c

1,151,173

G514C

Asp172His

0.001

0.492(0.399,0.608)

Rv1028c

1,149,602

G2085A

Ser695Ser

< 0.001

2.838(2.199,3.662)

Rv3765c

4,211,244

A541C

Ser181Arg

0.051

0.526(0.378,0.731)

Rv0981

1,096,890

T69C

Asn23Asn

0.006

0.51(0.399,0.651)

Rv1675c

1,900,608

G368A

Gly123Glu

< 0.001

2.442(1.952,3.056)

Rv1743

1,969,938

C935T

Pro312Leu

0.008

1.505(1.289,1.758)

Rv1743

1,970,586

C1583T

Ala528Val

0.024

0.469(0.335,0.656)

Rv0845

941,473

T284A

Phe95Tyr

< 0.001

2.032(1.684,2.452)

Rv0602c

699,629

T171C

His57His

0.001

1.855(1.542,2.232)

Rv2984

3,339,998

C145G

Pro49Ala

0.031

0.487(0.349,0.679)

Rv0845

942,410

T1221C

Val407Val

0.214

1.357(1.062,1.733)

Rv1027c

1,148,482

C626A

Ser209*

0.095

0.838(0.754,0.931)

Rv1027c

1,148,459

G649T

Glu217*

0.188

1.166(1.038,1.311)

Rv0601c

698,968

C27T

Gly9Gly

< 0.001

0.532(0.452,0.626)

Rv0758

853,066

G671T

Gly224Val

0.377

1.115(0.986,1.261)

Rv0014c

16,119

G1352T

Arg451Leu

0.042

1.379(1.177,1.614)

Rv1813c

2,055,937

G176A

Gly59Glu

0.701

1.063(0.908,1.245)

Rv1747

1,974,919

C1290T

Arg430Arg

0.556

0.898(0.747,1.079)

Rv1368

1,541,426

G407T

Arg136Leu

0.538

0.893(0.743,1.074)

Rv0981

1,097,238

G417A

Pro139Pro

0.254

0.86(0.754,0.981)