lineage Position Gene coord. Allele change Codon number Codon change Amino-acid change LocusId Gene name lineage1 615938 1104 G/A 368 GAG/GAA E/E Rv0524 hemL lineage1.1 4404247 1056 G/A 352 CTG/CTA L/L Rv3915 - lineage1.1.1 3021283 711 G/A 237 CGG/CGA R/R Rv2707 - lineage1.1.1.1 3216553 339 G/A 113 GTC/GTT V/V Rv2907c rimM lineage1.1.2 2622402 51 G/A 17 GCC/GCT A/A Rv2343c dnaG lineage1.1.3 1491275 1038 G/A 346 CAC/CAT H/H Rv1326c glgB lineage1.2.1 3479545 375 C/A 125 GCC/GCA A/A Rv3111 moaC1 lineage1.2.2 3470377 303 C/T 101 CAG/CAA Q/Q Rv3101c ftsX lineage2 497491 810 G/A 270 GAC/GAT D/D Rv0411c glnH lineage2.1 1881090 5787 C/T 1929 GGC/GGT G/G Rv1661 pks7 lineage2.2 2505085 615 G/A 205 GCC/GCT A/A Rv2231c cobC lineage2.2.1 346693 1059 G/T 353 S/S Rv0284 lineage2.2.2 886115 532 T/C 178 T/A Rv0792c lineage2.2.3 1477522 110 C/A 37 R/L Rv1316c ogt lineage2.2.4 782634 150 A/G 50 A/A Rv0684 fusA1 lineage2.2.5 1059643 1384 G/A 462 G/S Rv0949 uvrD1 lineage2.2.7 2532616 372 G/A 124 E/E Rv2259 adhE2 lineage2.2.8_RD142 1692069 180 A/G 60 A/A Rv1501 lineage2.2.6_RD150 4248115 1602 C/T 534 D/D Rv3795 embB lineage2.2.9 4086 807 G/T 269 G/G Rv0003 recF lineage2.2.10 1364706 294 G/A 98 L/L Rv1221 sigE lineage3 3273107 894 C/A 298 GCC/GCA A/A Rv2936 drrA lineage3.1.1 1084911 840 G/A 280 TAC/TAT Y/Y Rv0973c accA2 lineage3.1.2 3722702 930 G/C 310 CTC/CTG L/L Rv3336c trpS lineage3.1.2.1 1237818 375 C/G 125 CTG/CTC L/L Rv1111c - lineage3.1.2.2 2874344 2142 G/A 714 CGC/CGT R/R Rv2555c alaS lineage4 931123 171 C/T 57 TAT/TAC Y/Y Rv0835 lpqQ lineage4.1 62657 2262 G/A 754 CCG/CCA P/P Rv0058 dnaB lineage4.1.1 3798451 C/G 350 Rv3383c idsB lineage4.1.1.1 1850119 1917 C/T 639 ACG/ACA T/T Rv1640c lysX lineage4.1.1.2 541048 444 T/G 148 TCA/TCC S/S Rv0450c mmpL4 lineage4.1.1.3 4229087 741 C/T 247 AAC/AAT N/N Rv3782 glfT1 lineage4.1.2 891756 514 A/G 172 TTG/CTG L/L Rv0798c cfp29 lineage4.1.2.1 107794 195 C/T 65 GCC/GCT A/A Rv0098 fcoT lineage4.1.3 4409231 T/G lineage4.2 2411730 393 G/C 131 TCC/TCG S/S Rv2152c murC lineage4.2.1 783601 1117 A/C 373 AGG/CGG R/R Rv0684 fusA1 lineage4.2.2 1487796 636 C/A 212 ATC/ATA I/I Rv1324 - lineage4.2.2.1 1455780 286 T/C 96 TTG/CTG L/L Rv1299 prfA lineage4.3 1480024 C/T 541 Rv1318 - lineage4.3.1 615614 780 C/A 260 GCC/GCA A/A Rv0524 hemL lineage4.3.2 4316114 483 G/A 161 GCC/GCT A/A Rv3843c - lineage4.3.2.1 3388166 705 C/G 235 ACG/ACC T/T Rv3029c fixA lineage4.3.3 403364 2478 G/A 826 CCC/CCT P/P Rv0338c - lineage4.3.4 3977226 165 G/A 55 TTG/TTA L/L Rv3538 - lineage4.3.4.1 4398141 1545 G/A 515 TCG/TCA S/S Rv3910 - lineage4.3.4.2 1132368 744 C/T 248 ACC/ACT T/T Rv1013 pks16 lineage4.3.4.2.1 1502120 522 C/A 174 ACC/ACA T/T Rv1333 - lineage4.4 4307886 1029 G/A 343 CGC/CGT R/R Rv3834c serS lineage4.4.1 4151558 660 G/A 220 GGC/GGT G/G Rv3708c asd lineage4.4.1.1 355181 684 G/A 228 AAG/AAA K/K Rv0291 mycP3 lineage4.4.1.2 2694560 405 G/C 135 CTC/CTG L/L Rv2397c cysA1 lineage4.4.2 4246508 3276 G/A 1092 GCG/GCA A/A Rv3794 embA lineage4.5 1719757 1032 G/T 344 CCG/CCT P/P Rv1524 - lineage4.6 3466426 666 G/A 222 GTC/GTT V/V Rv3097c lipY lineage4.6.1 4260268 879 G/C 293 GCC/GCG A/A Rv3800c pks13 lineage4.6.1.1 874787 555 G/A 185 CCG/CCA P/P Rv0781 ptrBa lineage4.6.1.2 1501468 543 G/C 181 CCG/CCC P/P Rv1332 - lineage4.6.2 4125058 642 G/C 214 CGG/CGC R/R Rv3683 - lineage4.6.2.1 3570528 684 C/G 228 CGG/CGC R/R Rv3198c uvrD2 lineage4.6.2.2 2875883 603 C/T 201 CTG/CTA L/L Rv2555c alaS lineage4.10 1692141 C/A lineage5 1799921 339 C/A 113 GGC/GGA G/G Rv1599 hisD lineage6 1816587 399 C/G 133 GTC/GTG V/V Rv1617 pykA lineage7 1137518 543 G/A 181 AAC/AAT N/N Rv1018c glmU lineageBovis 1492605 C/T 701 Rv1327c glgE lineageCaprae 649585 G/A lineage_AnimalA3 154276 T/G Rv0127 lineage_AnimalA2 1831253 C/T Rv1629 lineage_AnimalA1 2873278 G/T Rv2554c