Table 3.
Generalized linear mixed model analysis on clustered and non-clustered strains in the lineage2.2.2 cohort
| Gene | Position | SNP | Amino acid changes | P value | OR(95%CI) | |
|---|---|---|---|---|---|---|
| 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) | |
OR, odds ratio; CI, confidence interval