#Variant position genome start Variant position genome stop Var. type Number WT base Var. base Region Gene ID Gene Name Gene start Gene stop Gene length Dir. WT AA Codon nr. Codon nr. E. coli Var. AA AA change Codon change Variant position gene start Variant position gene stop Antibiotic Reference PMID High Confidence SNP 6575 6575 SNP 1 c t coding Rv0005 gyrB 5123 7267 2145 + Arg 485 - Cys Arg485Cys cgt/tgt 1453 1453 fluoroquinolones (FQ) 19470506 6579 6579 SNP 1 c t coding Rv0005 gyrB 5123 7267 2145 + Ser 486 - Phe Ser486Phe tcc/ttc 1457 1457 fluoroquinolones (FQ) 19721073 6620 6620 SNP 1 g a coding Rv0005 gyrB 5123 7267 2145 + Asp 500 - Asn Asp500Asn gac/aac 1498 1498 fluoroquinolones (FQ) 19721073 6734 6734 SNP 1 g a coding Rv0005 gyrB 5123 7267 2145 + Asn 538 - Asp Asn538Asp aac/gac 1612 1612 fluoroquinolones (FQ) 17412727 6741 6741 SNP 1 a t coding Rv0005 gyrB 5123 7267 2145 + Glu 540 - Val Glu540Val gaa/gta 1619 1619 fluoroquinolones (FQ) 19721073 6742 6742 SNP 1 a t coding Rv0005 gyrB 5123 7267 2145 + Glu 540 - Asp Glu540Asp gaa/gat 1620 1620 fluoroquinolones (FQ) 19721073 6749 6749 SNP 1 g a coding Rv0005 gyrB 5123 7267 2145 + Ala 543 - Thr Ala543Thr gcg/acg 1627 1627 fluoroquinolones (FQ) 19470506 7566 7566 SNP 1 g a coding Rv0006 gyrA 7302 9818 2517 + Asp 89 - Asn Asp89Asn gac/aac 265 265 fluoroquinolones (FQ) 19687244 7570 7570 SNP 1 c t coding Rv0006 gyrA 7302 9818 2517 + Ala 90 - Val Ala90Val gcg/gtg 269 269 fluoroquinolones (FQ) 21300839 yes 7572 7572 SNP 1 t c coding Rv0006 gyrA 7302 9818 2517 + Ser 91 - Pro Ser91Pro tcg/ccg 271 271 fluoroquinolones (FQ) 21562102 yes 7581 7581 SNP 1 g c coding Rv0006 gyrA 7302 9818 2517 + Asp 94 - His Asp94His gac/cac 280 280 fluoroquinolones (FQ) 21562102 yes 7581 7581 SNP 1 g a coding Rv0006 gyrA 7302 9818 2517 + Asp 94 - Asn Asp94Asn gac/aac 280 280 fluoroquinolones (FQ) 21562102 yes 7581 7581 SNP 1 g t coding Rv0006 gyrA 7302 9818 2517 + Asp 94 - Tyr Asp94Tyr gac/tac 280 280 fluoroquinolones (FQ) 21562102 yes 7582 7582 SNP 1 a g coding Rv0006 gyrA 7302 9818 2517 + Asp 94 - Gly Asp94Gly gac/ggc 281 281 fluoroquinolones (FQ) 21300839 yes 7582 7582 SNP 1 a c coding Rv0006 gyrA 7302 9818 2517 + Asp 94 - Ala Asp94Ala gac/gcc 281 281 fluoroquinolones (FQ) 21300839 yes 7582 7582 SNP 1 a t coding Rv0006 gyrA 7302 9818 2517 + Asp 94 - Val Asp94Val gac/gtc 281 281 fluoroquinolones (FQ) 17434825 575729 575729 SNP 1 c t coding Rv0486 mshA 575348 576790 1443 + Gln 128 - STOP Gln128STOP cag/tag 382 382 ethionamide (ETH) 18651841 576164 576164 SNP 1 c t coding Rv0486 mshA 575348 576790 1443 + Arg 273 - Cys Arg273Cys cgc/tgc 817 817 ethionamide (ETH) 18651841 576242 576242 SNP 1 g t coding Rv0486 mshA 575348 576790 1443 + Gly 299 - Cys Gly299Cys ggc/tgc 895 895 ethionamide (ETH) 18651841 576338 576338 SNP 1 c t coding Rv0486 mshA 575348 576790 1443 + Gln 331 - STOP Gln331STOP cag/tag 991 991 ethionamide (ETH) 18651841 576414 576414 SNP 1 g a coding Rv0486 mshA 575348 576790 1443 + Gly 356 - Asp Gly356Asp ggc/gac 1067 1067 ethionamide (ETH) 18651841 576429 576429 SNP 1 a c coding Rv0486 mshA 575348 576790 1443 + Glu 361 - Ala Glu361Ala gag/gcg 1082 1082 ethionamide (ETH) 18651841 760314 760314 SNP 1 g t coding Rv0667 rpoB 759807 763325 3519 + Val 170 146 Phe Val170Phe gtc/ttc 508 508 rifampicin (RMP) 11136757 761004 761004 SNP 1 a g coding Rv0667 rpoB 759807 763325 3519 + Thr 400 481 Ala Thr400Ala acc/gcc 1198 1198 rifampicin (RMP) 22646308 761093 761093 SNP 1 g c coding Rv0667 rpoB 759807 763325 3519 + Gln 429 510 His Gln429His cag/cac 1287 1287 rifampicin (RMP) 15184414 761095 761095 SNP 1 t c coding Rv0667 rpoB 759807 763325 3519 + Leu 430 511 Pro Leu430Pro ctg/ccg 1289 1289 rifampicin (RMP) 8027320 761095 761095 SNP 1 t g coding Rv0667 rpoB 759807 763325 3519 + Leu 430 511 Arg Leu430Arg ctg/cgg 1289 1289 rifampicin (RMP) 8027320 761098 761098 SNP 1 g c coding Rv0667 rpoB 759807 763325 3519 + Ser 431 512 Thr Ser431Thr agc/acc 1292 1292 rifampicin (RMP) 8027320 761100 761100 SNP 1 c a coding Rv0667 rpoB 759807 763325 3519 + Gln 432 513 Lys Gln432Lys caa/aaa 1294 1294 rifampicin (RMP) 11136757 761101 761101 SNP 1 a c coding Rv0667 rpoB 759807 763325 3519 + Gln 432 513 Pro Gln432Pro caa/cca 1295 1295 rifampicin (RMP) 9003625 761101 761101 SNP 1 a t coding Rv0667 rpoB 759807 763325 3519 + Gln 432 513 Leu Gln432Leu caa/cta 1295 1295 rifampicin (RMP) 16672384 761108 761108 SNP 1 g t coding Rv0667 rpoB 759807 763325 3519 + Met 434 515 Ile Met434Ile atg/att 1302 1302 rifampicin (RMP) 15184414 761109 761109 SNP 1 g t coding Rv0667 rpoB 759807 763325 3519 + Asp 435 516 Tyr Asp435Tyr gac/tac 1303 1303 rifampicin (RMP) 11880449 yes 761110 761110 SNP 1 a t coding Rv0667 rpoB 759807 763325 3519 + Asp 435 516 Val Asp435Val gac/gtc 1304 1304 rifampicin (RMP) 21300839 yes 761111 761111 SNP 1 c g coding Rv0667 rpoB 759807 763325 3519 + Asp 435 516 Glu Asp435Glu gac/gag 1305 1305 rifampicin (RMP) 8027320 761117 761120 Del 3 caac c coding Rv0667 rpoB 759807 763325 3519 + Asn 438 519 - Asn438- aac/_ 1312 1314 rifampicin (RMP) 11136757 761120 761120 SNP 1 c g coding Rv0667 rpoB 759807 763325 3519 + Asn 438 519 Lys Asn438Lys aac/aag 1314 1314 rifampicin (RMP) 19721079 761128 761128 SNP 1 c t coding Rv0667 rpoB 759807 763325 3519 + Ser 441 522 Leu Ser441Leu tcg/ttg 1322 1322 rifampicin (RMP) 7759399 761128 761128 SNP 1 c g coding Rv0667 rpoB 759807 763325 3519 + Ser 441 522 Trp Ser441Trp tcg/tgg 1322 1322 rifampicin (RMP) 15814606 761139 761139 SNP 1 c a coding Rv0667 rpoB 759807 763325 3519 + His 445 526 Asn His445Asn cac/aac 1333 1333 rifampicin (RMP) 14729930 yes 761139 761139 SNP 1 c g coding Rv0667 rpoB 759807 763325 3519 + His 445 526 Asp His445Asp cac/gac 1333 1333 rifampicin (RMP) 21300839 yes 761139 761139 SNP 1 c t coding Rv0667 rpoB 759807 763325 3519 + His 445 526 Tyr His445Tyr cac/tac 1333 1333 rifampicin (RMP) 21300839 yes 761140 761140 SNP 1 a c coding Rv0667 rpoB 759807 763325 3519 + His 445 526 Pro His445Pro cac/ccc 1334 1334 rifampicin (RMP) 7759399 yes 761140 761140 SNP 1 a g coding Rv0667 rpoB 759807 763325 3519 + His 445 526 Arg His445Arg cac/cgc 1334 1334 rifampicin (RMP) 9003625 yes 761140 761140 SNP 1 a t coding Rv0667 rpoB 759807 763325 3519 + His 445 526 Leu His445Leu cac/ctc 1334 1334 rifampicin (RMP) 10921994 761141 761141 SNP 1 c a coding Rv0667 rpoB 759807 763325 3519 + His 445 526 Gln His445Gln cac/caa 1335 1335 rifampicin (RMP) 8027320 761154 761154 SNP 1 c t coding Rv0667 rpoB 759807 763325 3519 + Ser 450 531 Ala Ser450Ala tcg/gcg 1348 1348 rifampicin (RMP) 11136757 761155 761155 SNP 1 c g coding Rv0667 rpoB 759807 763325 3519 + Ser 450 531 Trp Ser450Trp tcg/tgg 1349 1349 rifampicin (RMP) 7759399 yes 761155 761155 SNP 1 c t coding Rv0667 rpoB 759807 763325 3519 + Ser 450 531 Leu Ser450Leu tcg/ttg 1349 1349 rifampicin (RMP) 21300839 yes 761161 761161 SNP 1 t c coding Rv0667 rpoB 759807 763325 3519 + Leu 452 533 Pro Leu452Pro ctg/ccg 1355 1355 rifampicin (RMP) 8913484 yes 761277 761277 SNP 1 a t coding Rv0667 rpoB 759807 763325 3519 + Ile 491 572 Phe Ile491Phe atc/ttc 1471 1471 rifampicin (RMP) 10565894 781687 781687 SNP 1 a g coding Rv0682 rpsL 781560 781934 375 + Lys 43 - Arg Lys43Arg aag/agg 128 128 streptomycin (SM) 22646308 yes 781821 781821 SNP 1 a c coding Rv0682 rpsL 781560 781934 375 + Lys 88 - Gln Lys88Gln aag/cag 262 262 streptomycin (SM) 8849220 781822 781822 SNP 1 a g coding Rv0682 rpsL 781560 781934 375 + Lys 88 - Arg Lys88Arg aag/agg 263 263 streptomycin (SM) 22646308 yes 801268 801268 SNP 1 t c coding Rv0701 rplC 800809 801462 654 + Cys 154 - Arg Cys154Arg tgt/cgt 460 460 linezolid (LZD) 22371899 1473246 1473246 SNP 1 a g ribosomal MTB000019 rrs 1471846 1473382 1537 + - - - - --- - 1401 1401 amikacin (AMK) kanamycin (KAN) capreomycin (CPR) 21300839 yes 1473247 1473247 SNP 1 c t ribosomal MTB000019 rrs 1471846 1473382 1537 + - - - - --- - 1402 1402 amikacin (AMK) kanamycin (KAN) capreomycin (CPR) 16048924 yes 1473329 1473329 SNP 1 g t ribosomal MTB000019 rrs 1471846 1473382 1537 + - - - - --- - 1484 1484 amikacin (AMK) kanamycin (KAN) capreomycin (CPR) 21562102 yes 1475956 1475956 SNP 1 g t ribosomal MTB000020 rrl 1473658 1476795 3138 + - - - - --- - 2299 2299 linezolid (LZD) 18070973 1476471 1476471 SNP 1 g t ribosomal MTB000020 rrl 1473658 1476795 3138 + - - - - --- - 2814 2814 linezolid (LZD) 18070973 1673423 1673423 SNP 1 g t intergenic Rv1483 fabG1 1673440 1674183 809 + - - - - --- - -17 -17 isoniazid (INH) 14638486 1673424 1673424 SNP 1 a g intergenic Rv1483 fabG1 1673440 1674183 809 + - - - - --- - -16 -16 isoniazid (INH) 19494067 1673425 1673425 SNP 1 c t intergenic Rv1483 fabG1 1673440 1674183 809 + - - - - --- - -15 -15 isoniazid (INH) 21300839 yes 1673432 1673432 SNP 1 t a intergenic Rv1483 fabG1 1673440 1674183 809 + - - - - --- - -8 -8 isoniazid (INH) 19494067 yes 1673432 1673432 SNP 1 t c intergenic Rv1483 fabG1 1673440 1674183 809 + - - - - --- - -8 -8 isoniazid (INH) 21300839 yes 1674782 1674782 SNP 1 t c coding Rv1484 inhA 1674202 1675011 810 + Ile 194 - Thr Ile194Thr atc/acc 581 581 isoniazid (INH) 21110864 1833909 1833909 SNP 1 a c coding Rv1630 rpsA 1833542 1834987 1446 + Asp 123 - Ala Asp123Ala gac/gcc 368 368 pyrazinamide (PZA) 21835980 1834325 1834325 SNP 1 g a coding Rv1630 rpsA 1833542 1834987 1446 + Val 262 - Met Val262Met gtg/atg 784 784 pyrazinamide (PZA) 21835980 1834852 1834855 Del 3 cgcc c coding Rv1630 rpsA 1833542 1834987 1446 + Ala 438 - - Ala438- gcc/_ 1312 1314 pyrazinamide (PZA) 21835980 1917946 1917946 SNP 1 c t coding Rv1694 tlyA 1917940 1918746 807 + Arg 3 - STOP Arg3STOP cga/tga 7 7 capreomycin (CPR) 15673735 1917979 1917979 SNP 1 c t coding Rv1694 tlyA 1917940 1918746 807 + Arg 14 - Trp Arg14Trp cgg/tgg 40 40 capreomycin (CPR) 15673735 1917991 1917991 SNP 1 c t coding Rv1694 tlyA 1917940 1918746 807 + Arg 18 - STOP Arg18STOP cga/tga 52 52 capreomycin (CPR) 15673735 1918003 1918003 SNP 1 c t coding Rv1694 tlyA 1917940 1918746 807 + Gln 22 - STOP Gln22STOP cag/tag 64 64 capreomycin (CPR) 15673735 1918139 1918139 SNP 1 c a coding Rv1694 tlyA 1917940 1918746 807 + Ala 67 - Glu Ala67Glu gcg/gag 200 200 capreomycin (CPR) 15673735 1918144 1918144 SNP 1 a g coding Rv1694 tlyA 1917940 1918746 807 + Lys 69 - Glu Lys69Glu aaa/gaa 205 205 capreomycin (CPR) 15673735 1918211 1918211 SNP 1 c a coding Rv1694 tlyA 1917940 1918746 807 + Ala 91 - Glu Ala91Glu gca/gaa 272 272 capreomycin (CPR) 15673735 1918292 1918292 SNP 1 t c coding Rv1694 tlyA 1917940 1918746 807 + Leu 118 - Pro Leu118Pro ctg/ccg 353 353 capreomycin (CPR) 15673735 1918322 1918322 SNP 1 t a coding Rv1694 tlyA 1917940 1918746 807 + Val 128 - Glu Val128Glu gtg/gag 383 383 capreomycin (CPR) 15673735 1918388 1918388 SNP 1 t c coding Rv1694 tlyA 1917940 1918746 807 + Leu 150 - Pro Leu150Pro ctg/ccg 449 449 capreomycin (CPR) 15673735 1918487 1918487 SNP 1 c t coding Rv1694 tlyA 1917940 1918746 807 + Pro 183 - Leu Pro183Leu ccg/ctg 548 548 capreomycin (CPR) 15673735 1918489 1918489 SNP 1 c a coding Rv1694 tlyA 1917940 1918746 807 + Gln 184 - Lys Gln184Lys cag/aag 550 550 capreomycin (CPR) 15673735 1918489 1918489 SNP 1 c t coding Rv1694 tlyA 1917940 1918746 807 + Gln 184 - STOP Gln184STOP cag/tag 550 550 capreomycin (CPR) 15673735 1918494 1918494 SNP 1 t g coding Rv1694 tlyA 1917940 1918746 807 + Phe 185 - Leu Phe185Leu ttt/ttg 555 555 capreomycin (CPR) 15673735 1918651 1918651 SNP 1 g a coding Rv1694 tlyA 1917940 1918746 807 + Glu 238 - Lys Glu238Lys gag/aag 712 712 capreomycin (CPR) 15673735 2102240 2102240 SNP 1 g a coding Rv1854c ndh 2103042 2101651 1392 - Arg 268 - His Arg268His cgc/cac 803 803 isoniazid (INH) 11408244 2102715 2102715 SNP 1 a g coding Rv1854c ndh 2103042 2101651 1392 - Thr 110 - Ala Thr110Ala acc/gcc 328 328 isoniazid (INH) 11408244 2155167 2155167 SNP 1 c g coding Rv1908c katG 2156111 2153889 2223 - Ser 315 - Arg Ser315Arg agc/agg 945 945 isoniazid (INH) 16870753 2155167 2155167 SNP 1 c a coding Rv1908c katG 2156111 2153889 2223 - Ser 315 - Arg Ser315Arg agc/aga 945 945 isoniazid (INH) 17403134 2155168 2155168 SNP 1 g c coding Rv1908c katG 2156111 2153889 2223 - Ser 315 - Thr Ser315Thr agc/acc 944 944 isoniazid (INH) 8878604 2155168 2155168 SNP 1 g a coding Rv1908c katG 2156111 2153889 2223 - Ser 315 - Asn Ser315Asn agc/aac 944 944 isoniazid (INH) 9210694 yes 2155168 2155168 SNP 1 g t coding Rv1908c katG 2156111 2153889 2223 - Ser 315 - Ile Ser315Ile agc/atc 944 944 isoniazid (INH) 9210694 yes 2155169 2155169 SNP 1 a g coding Rv1908c katG 2156111 2153889 2223 - Ser 315 - Gly Ser315Gly agc/ggc 943 943 isoniazid (INH) 8878604 yes 2155206 2155206 SNP 1 c g coding Rv1908c katG 2156111 2153889 2223 - Ser 302 - Arg Ser302Arg agc/agg 906 906 isoniazid (INH) 22646308 2155212 2155212 SNP 1 g c coding Rv1908c katG 2156111 2153889 2223 - Trp 300 - Cys Trp300Cys tgg/tgc 900 900 isoniazid (INH) 22646308 2155222 2155222 SNP 1 g t coding Rv1908c katG 2156111 2153889 2223 - Gly 297 - Val Gly297Val ggc/gtc 890 890 isoniazid (INH) 11796356 2155699 2155699 SNP 1 a g coding Rv1908c katG 2156111 2153889 2223 - Asn 138 - Ser Asn138Ser aac/agc 413 413 isoniazid (INH) 16870753 2288704 2288704 SNP 1 g t coding Rv2043c pncA 2289241 2288681 561 - Val 180 - Phe Val180Phe gtc/ttc 538 538 pyrazinamide (PZA) 11641519 2288727 2288727 SNP 1 t c coding Rv2043c pncA 2289241 2288681 561 - Leu 172 - Pro Leu172Pro ctg/ccg 515 515 pyrazinamide (PZA) 22646308 2288730 2288730 SNP 1 c t coding Rv2043c pncA 2289241 2288681 561 - Ala 171 - Val Ala171Val gcg/gtg 512 512 pyrazinamide (PZA) 10471589 2288757 2288757 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Gly 162 - Asp Gly162Asp ggt/gat 485 485 pyrazinamide (PZA) 22646308 2288766 2288766 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Leu 159 - Arg Leu159Arg ctg/cgg 476 476 pyrazinamide (PZA) 11641519 2288782 2288782 SNP 1 a g coding Rv2043c pncA 2289241 2288681 561 - Arg 154 - Gly Arg154Gly agg/ggg 460 460 pyrazinamide (PZA) 21300839 2288805 2288805 SNP 1 c a coding Rv2043c pncA 2289241 2288681 561 - Ala 146 - Glu Ala146Glu gcg/gag 437 437 pyrazinamide (PZA) 22646308 2288806 2288806 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Ala 146 - Thr Ala146Thr gcg/acg 436 436 pyrazinamide (PZA) 11641519 2288813 - Ins 5 _ gccag coding Rv2043c pncA 2289241 2288681 561 - Ala 143 - Ala Ala143Ala gcc/gc g cca g c 433 429 pyrazinamide (PZA) 22646308 2288820 2288820 SNP 1 a c coding Rv2043c pncA 2289241 2288681 561 - Gln 141 - Pro Gln141Pro cag/ccg 422 422 pyrazinamide (PZA) 8640557 2288821 2288821 SNP 1 c t coding Rv2043c pncA 2289241 2288681 561 - Gln 141 - STOP Gln141STOP cag/tag 421 421 pyrazinamide (PZA) 11641519 2288836 2288836 SNP 1 g t coding Rv2043c pncA 2289241 2288681 561 - Asp 136 - Tyr Asp136Tyr gat/tat 406 406 pyrazinamide (PZA) 11641519 2288836 2288836 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Asp 136 - Asn Asp136Asn gat/aat 406 406 pyrazinamide (PZA) 11641519 2288844 2288844 SNP 1 t c coding Rv2043c pncA 2289241 2288681 561 - Ile 133 - Thr Ile133Thr att/act 398 398 pyrazinamide (PZA) 10390239 2288848 2288848 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Gly 132 - Ser Gly132Ser ggt/agt 394 394 pyrazinamide (PZA) 9055989 2288859 2288859 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Val 128 - Gly Val128Gly gtc/ggc 383 383 pyrazinamide (PZA) 15616332 2288883 2288883 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Leu 120 - Arg Leu120Arg ctg/cgg 359 359 pyrazinamide (PZA) 21300839 2288885 2288885 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Trp 119 - STOP Trp119STOP tgg/tga 357 357 pyrazinamide (PZA) 11641519 2288902 2288902 SNP 1 a c coding Rv2043c pncA 2289241 2288681 561 - Thr 114 - Pro Thr114Pro acg/ccg 340 340 pyrazinamide (PZA) 9692180 2288934 2288934 SNP 1 a c coding Rv2043c pncA 2289241 2288681 561 - Tyr 103 - Ser Tyr103Ser tac/tcc 308 308 pyrazinamide (PZA) 11641519 2288953 2288953 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Gly 97 - Ser Gly97Ser ggt/agt 289 289 pyrazinamide (PZA) 10681313 2288956 2288956 SNP 1 a g coding Rv2043c pncA 2289241 2288681 561 - Lys 96 - Glu Lys96Glu aag/gag 286 286 pyrazinamide (PZA) 22646308 2288982 2288982 SNP 1 c t coding Rv2043c pncA 2289241 2288681 561 - Thr 87 - Met Thr87Met acg/atg 260 260 pyrazinamide (PZA) 10390238 2288988 2288988 SNP 1 t c coding Rv2043c pncA 2289241 2288681 561 - Leu 85 - Pro Leu85Pro ctg/ccg 254 254 pyrazinamide (PZA) 9055989 2289016 2289016 SNP 1 a c coding Rv2043c pncA 2289241 2288681 561 - Thr 76 - Pro Thr76Pro act/cct 226 226 pyrazinamide (PZA) 9056006 2289031 2289031 SNP 1 c t coding Rv2043c pncA 2289241 2288681 561 - His 71 - Tyr His71Tyr cat/tat 211 211 pyrazinamide (PZA) 16848344 2289036 2289036 SNP 1 c t coding Rv2043c pncA 2289241 2288681 561 - Pro 69 - Leu Pro69Leu cca/cta 206 206 pyrazinamide (PZA) 10390238 2289039 2289039 SNP 1 g c coding Rv2043c pncA 2289241 2288681 561 - Trp 68 - Ser Trp68Ser tgg/tcg 203 203 pyrazinamide (PZA) 11641519 2289040 2289040 SNP 1 t c coding Rv2043c pncA 2289241 2288681 561 - Trp 68 - Arg Trp68Arg tgg/cgg 202 202 pyrazinamide (PZA) 11641519 2289040 2289040 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Trp 68 - Gly Trp68Gly tgg/ggg 202 202 pyrazinamide (PZA) 11641519 2289049 - Ins 1 a at coding Rv2043c pncA 2289241 2288681 561 - Ser 65 - - Ser65- tcc/atcc 193 193 pyrazinamide (PZA) 22646308 2289052 2289052 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Tyr 64 - Asp Tyr64Asp tat/gat 190 190 pyrazinamide (PZA) 11641519 2289054 2289054 SNP 1 a g coding Rv2043c pncA 2289241 2288681 561 - Asp 63 - Gly Asp63Gly gac/ggc 188 188 pyrazinamide (PZA) 9692180 2289061 2289061 SNP 1 a c coding Rv2043c pncA 2289241 2288681 561 - Thr 61 - Pro Thr61Pro aca/cca 181 181 pyrazinamide (PZA) 10390238 2289073 2289073 SNP 1 c t coding Rv2043c pncA 2289241 2288681 561 - His 57 - Tyr His57Tyr cac/tac 169 169 pyrazinamide (PZA) 16848344 2289073 2289073 SNP 1 c g coding Rv2043c pncA 2289241 2288681 560 - His 57 - Asp His57Asp cac/gac 169 169 pyrazinamide (PZA) 19861002 2289081 2289081 SNP 1 c t coding Rv2043c pncA 2289241 2288681 561 - Pro 54 - Leu Pro54Leu ccg/ctg 161 161 pyrazinamide (PZA) 16848344 2289096 2289096 SNP 1 a g coding Rv2043c pncA 2289241 2288681 561 - Asp 49 - Gly Asp49Gly gac/ggc 146 146 pyrazinamide (PZA) 10390239 2289096 2289096 SNP 1 a c coding Rv2043c pncA 2289241 2288681 561 - Asp 49 - Ala Asp49Ala gac/gcc 146 146 pyrazinamide (PZA) 11641519 2289103 2289103 SNP 1 a g coding Rv2043c pncA 2289241 2288681 561 - Thr 47 - Ala Thr47Ala acc/gcc 139 139 pyrazinamide (PZA) 22646308 2289108 2289108 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Val 45 - Gly Val45Gly gtg/ggg 134 134 pyrazinamide (PZA) 11641519 2289159 2289159 SNP 1 c a coding Rv2043c pncA 2289241 2288681 561 - Ala 28 - Asp Ala28Asp gcc/gac 83 83 pyrazinamide (PZA) 11641519 2289201 2289201 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Cys 14 - Tyr Cys14Tyr tgc/tac 41 41 pyrazinamide (PZA) 11641519 2289204 2289204 SNP 1 t c coding Rv2043c pncA 2289241 2288681 561 - Phe 13 - Ser Phe13Ser ttc/tcc 38 38 pyrazinamide (PZA) 10390238 2289208 2289208 SNP 1 g a coding Rv2043c pncA 2289241 2288681 561 - Asp 12 - Asn Asp12Asn gac/aac 34 34 pyrazinamide (PZA) 9055989 2289213 2289213 SNP 1 a c coding Rv2043c pncA 2289241 2288681 561 - Gln 10 - Pro Gln10Pro cag/ccg 29 29 pyrazinamide (PZA) 21300839 yes 2289213 2289213 SNP 1 a g coding Rv2043c pncA 2289241 2288681 561 - Gln 10 - Arg Gln10Arg cag/cgg 29 29 pyrazinamide (PZA) 10681313 2289216 2289216 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Val 9 - Gly Val9Gly gtg/ggg 26 26 pyrazinamide (PZA) 11641519 2289216 2289216 SNP 1 t c coding Rv2043c pncA 2289241 2288681 561 - Val 9 - Ala Val9Ala gtg/gcg 26 26 pyrazinamide (PZA) 11641519 2289219 2289219 SNP 1 a g coding Rv2043c pncA 2289241 2288681 561 - Asp 8 - Gly Asp8Gly gac/ggc 23 23 pyrazinamide (PZA) 11641519 2289222 2289222 SNP 1 t a coding Rv2043c pncA 2289241 2288681 561 - Val 7 - Asp Val7Asp gtc/gac 20 20 pyrazinamide (PZA) 11641519 2289226 - Ins 1 t tg coding Rv2043c pncA 2289241 2288681 561 - Ile 6 - - Ile6- atc/catc 16 16 pyrazinamide (PZA) 22646308 2289231 2289231 SNP 1 t g coding Rv2043c pncA 2289241 2288681 561 - Leu 4 - Trp Leu4Trp ttg/tgg 11 11 pyrazinamide (PZA) 11641519 2289235 2289235 SNP 1 g c coding Rv2043c pncA 2289241 2288681 561 - Ala 3 - Pro Ala3Pro gcg/ccg 7 7 pyrazinamide (PZA) 10390238 2289239 2289239 SNP 1 g t coding Rv2043c pncA 2289241 2288681 561 - Met 1 - Ile Met1Ile atg/att 3 3 pyrazinamide (PZA) 11641519 2289252 2289252 SNP 1 a g intergenic Rv2043c pncA 2289241 2288681 561 - - - - - --- - -11 -11 pyrazinamide (PZA) 22646308 2715342 2715342 SNP 1 g a intergenic Rv2416c eis 2715332 2714124 1209 - - - - - --- - -10 -10 kanamycin (KAN) 21300839 2715346 2715346 SNP 1 c t intergenic Rv2416c eis 2715332 2714124 1209 - - - - - --- - -14 -14 kanamycin (KAN) 21300839 2726136 2726136 SNP 1 c t intergenic Rv2428 ahpC 2726193 2726780 588 + - - - - --- - -57 -57 isoniazid (INH) 22646308 2726145 2726145 SNP 1 g a intergenic Rv2428 ahpC 2726193 2726780 588 + - - - - --- - -48 -48 isoniazid (INH) 12654653 3073808 3073808 SNP 1 c g coding Rv2764c thyA 3074471 3073680 792 - Arg 222 - Gly Arg222Gly cgc/ggc 664 664 para-aminosalicylic acid (PAS) 15225321 4241078 4241078 SNP 1 a g coding Rv3793 embC 4239863 4243147 3285 + Ile 406 - Val Ile406Val atc/gtc 1216 1216 ethambutol (EMB) 20427375 4243221 4243221 SNP 1 c t intergenic Rv3794 embA 4243233 4246517 3285 + - - - - --- - -12 -12 ethambutol (EMB) 20427375 4243225 4243225 SNP 1 c a intergenic Rv3794 embA 4243233 4246517 3285 + - - - - --- - -8 -8 ethambutol (EMB) 20427375 4243242 4243242 SNP 1 g a coding Rv3794 embA 4243233 4246517 3285 + Asp 4 - Asn Asp4Asn gac/aac 10 10 ethambutol (EMB) 10639358 4243245 4243245 SNP 1 g a coding Rv3794 embA 4243233 4246517 3285 + Gly 5 - Ser Gly5Ser ggt/agt 13 13 ethambutol (EMB) 10639358 4243833 4243833 SNP 1 g a coding Rv3794 embA 4243233 4246517 3285 + Ala 201 - Thr Ala201Thr gcg/acg 601 601 ethambutol (EMB) 10639358 4244193 4244193 SNP 1 g a coding Rv3794 embA 4243233 4246517 3285 + Gly 321 - Ser Gly321Ser ggc/agc 961 961 ethambutol (EMB) 10639358 4244281 4244281 SNP 1 g a coding Rv3794 embA 4243233 4246517 3285 + Gly 350 - Asp Gly350Asp ggc/gac 1049 1049 ethambutol (EMB) 10639358 4244617 4244617 SNP 1 c t coding Rv3794 embA 4243233 4246517 3285 + Ala 462 - Val Ala462Val gcg/gtg 1385 1385 ethambutol (EMB) 10639358 4245730 4245730 SNP 1 a c coding Rv3794 embA 4243233 4246517 3285 + Asp 833 - Ala Asp833Ala gac/gcc 2498 2498 ethambutol (EMB) 10639358 4246734 4246734 SNP 1 t g coding Rv3795 embB 4246514 4249810 3297 + Leu 74 - Arg Leu74Arg ctg/cgg 221 221 ethambutol (EMB) 20427375 4247402 4247402 SNP 1 t g coding Rv3795 embB 4246514 4249810 3297 + Ser 297 - Ala Ser297Ala tcg/gcg 889 889 ethambutol (EMB) 10639358 4247429 4247429 SNP 1 a g coding Rv3795 embB 4246514 4249810 3297 + Met 306 - Val Met306Val atg/gtg 916 916 ethambutol (EMB) 21300839 yes 4247429 4247429 SNP 1 a c coding Rv3795 embB 4246514 4249810 3297 + Met 306 - Leu Met306Leu atg/ctg 916 916 ethambutol (EMB) 9257740 yes 4247430 4247430 SNP 1 t c coding Rv3795 embB 4246514 4249810 3297 + Met 306 - Thr Met306Thr atg/acg 917 917 ethambutol (EMB) 11854934 yes 4247431 4247431 SNP 1 g a coding Rv3795 embB 4246514 4249810 3297 + Met 306 - Ile Met306Ile atg/ata 918 918 ethambutol (EMB) 21300839 yes 4247431 4247431 SNP 1 g c coding Rv3795 embB 4246514 4249810 3297 + Met 306 - Ile Met306Ile atg/atc 918 918 ethambutol (EMB) 21300839 yes 4247431 4247431 SNP 1 g t coding Rv3795 embB 4246514 4249810 3297 + Met 306 - Ile Met306Ile atg/att 918 918 ethambutol (EMB) 21300839 yes 4247469 4247469 SNP 1 a c coding Rv3795 embB 4246514 4249810 3297 + Tyr 319 - Ser Tyr319Ser tat/tct 956 956 ethambutol (EMB) 16641474 4247495 4247495 SNP 1 g t coding Rv3795 embB 4246514 4249810 3297 + Asp 328 - Tyr Asp328Tyr gat/tat 982 982 ethambutol (EMB) 10639358 4247496 4247496 SNP 1 a g coding Rv3795 embB 4246514 4249810 3297 + Asp 328 - Gly Asp328Gly gat/ggt 983 983 ethambutol (EMB) 10639358 4247507 4247507 SNP 1 t c coding Rv3795 embB 4246514 4249810 3297 + Trp 332 - Arg Trp332Arg tgg/cgg 994 994 ethambutol (EMB) 22646308 4247513 4247513 SNP 1 c t coding Rv3795 embB 4246514 4249810 3297 + Tyr 334 - His Tyr334His tac/cac 1000 1000 ethambutol (EMB) 16641474 4247573 4247573 SNP 1 g a coding Rv3795 embB 4246514 4249810 3297 + Asp 354 - Asn Asp354Asn gac/aac 1060 1060 ethambutol (EMB) 20427375 4247717 4247717 SNP 1 c g coding Rv3795 embB 4246514 4249810 3297 + Leu 402 - Val Leu402Val ctg/gtg 1204 1204 ethambutol (EMB) 20427375 4247723 4247723 SNP 1 c t coding Rv3795 embB 4246514 4249810 3297 + Pro 404 - Ser Pro404Ser ccg/tcg 1210 1210 ethambutol (EMB) 20427375 4247729 4247729 SNP 1 g a coding Rv3795 embB 4246514 4249810 3297 + Gly 406 - Ser Gly406Ser ggc/agc 1216 1216 ethambutol (EMB) 20427375 4247730 4247730 SNP 1 g c coding Rv3795 embB 4246514 4249810 3297 + Gly 406 - Ala Gly406Ala ggc/gcc 1217 1217 ethambutol (EMB) 20427375 4247730 4247730 SNP 1 g a coding Rv3795 embB 4246514 4249810 3297 + Gly 406 - Asp Gly406Asp ggc/gac 1217 1217 ethambutol (EMB) 20427375 4247863 4247863 SNP 1 c g coding Rv3795 embB 4246514 4249810 3297 + Ile 450 - Met Ile450Met atc/atg 1350 1350 ethambutol (EMB) 20427375 4247873 4247873 SNP 1 g a coding Rv3795 embB 4246514 4249810 3297 + Ala 454 - Thr Ala454Thr gcg/acg 1360 1360 ethambutol (EMB) 20427375 4248002 4248002 SNP 1 c a coding Rv3795 embB 4246514 4249810 3297 + Gln 497 - Lys Gln497Lys cag/aag 1489 1489 ethambutol (EMB) 20427375 4248003 4248003 SNP 1 a g coding Rv3795 embB 4246514 4249810 3297 + Gln 497 - Arg Gln497Arg cag/cgg 1490 1490 ethambutol (EMB) 20427375 4248747 4248747 SNP 1 g a coding Rv3795 embB 4246514 4249810 3297 + Gly 745 - Asp Gly745Asp ggc/gac 2234 2234 ethambutol (EMB) 10639358 4249518 4249518 SNP 1 a g coding Rv3795 embB 4246514 4249810 3297 + His 1002 - Arg His1002Arg cac/cgc 3005 3005 ethambutol (EMB) 22646308 4326087 4326087 SNP 1 c a coding Rv3854c ethA 4327473 4326004 1470 - Arg 463 - Ser Arg463Ser cgt/agt 1387 1387 ethionamide (ETH) 14638486 4326236 4326236 SNP 1 g a coding Rv3854c ethA 4327473 4326004 1470 - Gly 413 - Asp Gly413Asp ggt/gat 1238 1238 ethionamide (ETH) 14638486 4326300 4326300 SNP 1 a g coding Rv3854c ethA 4327473 4326004 1470 - Thr 392 - Ala Thr392Ala acg/gcg 1174 1174 ethionamide (ETH) 14638486 4326320 4326320 SNP 1 g a coding Rv3854c ethA 4327473 4326004 1470 - Gly 385 - Asp Gly385Asp ggc/gac 1154 1154 ethionamide (ETH) 14638486 4326333 4326333 SNP 1 g c coding Rv3854c ethA 4327473 4326004 1470 - Ala 381 - Pro Ala381Pro gcc/ccc 1141 1141 ethionamide (ETH) 10944230 4326449 4326449 SNP 1 c a coding Rv3854c ethA 4327473 4326004 1470 - Thr 342 - Lys Thr342Lys acg/aag 1025 1025 ethionamide (ETH) 10944230 4326461 4326461 SNP 1 t g coding Rv3854c ethA 4327473 4326004 1470 - Ile 338 - Ser Ile338Ser atc/agc 1013 1013 ethionamide (ETH) 14638486 4326738 4326738 SNP 1 c t coding Rv3854c ethA 4327473 4326004 1470 - Gln 246 - STOP Gln246STOP cag/tag 736 736 ethionamide (ETH) 14638486 4326807 4326807 SNP 1 g a coding Rv3854c ethA 4327473 4326004 1470 - Glu 223 - Lys Glu223Lys gag/aag 667 667 ethionamide (ETH) 14638486 4326917 4326917 SNP 1 c a coding Rv3854c ethA 4327473 4326004 1470 - Thr 186 - Lys Thr186Lys acg/aag 557 557 ethionamide (ETH) 10944230 4327224 4327224 SNP 1 t g coding Rv3854c ethA 4327473 4326004 1470 - Tyr 84 - Asp Tyr84Asp tac/gac 250 250 ethionamide (ETH) 10944230 4327301 4327301 SNP 1 a c coding Rv3854c ethA 4327473 4326004 1470 - Asp 58 - Ala Asp58Ala gac/gcc 173 173 ethionamide (ETH) 10944230 4327307 4327307 SNP 1 a c coding Rv3854c ethA 4327473 4326004 1470 - Asp 56 - Ala Asp56Ala gac/gcc 167 167 ethionamide (ETH) 14638486 4327322 4327322 SNP 1 c t coding Rv3854c ethA 4327473 4326004 1470 - Pro 51 - Leu Pro51Leu ccc/ctc 152 152 ethionamide (ETH) 10944230 4327346 4327346 SNP 1 g a coding Rv3854c ethA 4327473 4326004 1470 - Gly 43 - Asp Gly43Asp ggc/gac 128 128 ethionamide (ETH) 14638486 4327347 4327347 SNP 1 g t coding Rv3854c ethA 4327473 4326004 1470 - Gly 43 - Cys Gly43Cys ggc/tgc 127 127 ethionamide (ETH) 10944230 4407604 4407604 SNP 1 c a coding Rv3919c gidB 4408202 4407528 675 - Ala 200 - Glu Ala200Glu gcg/gag 599 599 streptomycin (SM) 22646308 4407790 4407790 SNP 1 c t coding Rv3919c gidB 4408202 4407528 675 - Ala 138 - Val Ala138Val gcg/gtg 413 413 streptomycin (SM) 22646308 4407824 4407824 SNP 1 c t coding Rv3919c gidB 4408202 4407528 675 - Gln 127 - STOP Gln127STOP caa/taa 379 379 streptomycin (SM) 22646308 4407931 4407931 SNP 1 t c coding Rv3919c gidB 4408202 4407528 675 - Leu 91 - Pro Leu91Pro cta/cca 272 272 streptomycin (SM) 22646308 4407940 4407940 SNP 1 t c coding Rv3919c gidB 4408202 4407528 675 - Val 88 - Ala Val88Ala gta/gca 263 263 streptomycin (SM) 22646308 4407992 4407992 SNP 1 g a coding Rv3919c gidB 4408202 4407528 675 - Gly 71 - Arg Gly71Arg gga/aga 211 211 streptomycin (SM) 22646308 4408009 4408009 SNP 1 t g coding Rv3919c gidB 4408202 4407528 675 - Val 65 - Gly Val65Gly gtc/ggc 194 194 streptomycin (SM) 22646308 4408102 4408102 SNP 1 g c coding Rv3919c gidB 4408202 4407528 675 - Gly 34 - Ala Gly34Ala ggg/gcg 101 101 streptomycin (SM) 22646308 156593 156593 SNP 1 t c coding Rv0129c fbpC 157600 156578 1023 - Ala 336 - Ala Ala336Ala gct/gcc 1008 1008 phylo (M. canettii) 22768315 157129 157129 SNP 1 g a coding Rv0129c fbpC 157600 156578 1023 - Gly 158 - Ser Gly158Ser ggc/agc 472 472 phylo (Delhi/CAS) 22768315 157292 157292 SNP 1 g a coding Rv0129c fbpC 157600 156578 1023 - Glu 103 - Glu Glu103Glu gag/gaa 309 309 phylo (LAM) 22768315 273265 273265 SNP 1 g t coding Rv0228 - 273055 274278 1224 + Ala 71 - Cys Ala71Cys ggc/tgc 211 211 phylo (West African 2) 22768315 491591 491591 SNP 1 a t coding Rv0407 fgd1 490783 491793 1011 + Lys 270 - Met Lys270Met aag/atg 809 809 phylo (Haarlem) 22768315 491668 491668 SNP 1 a g coding Rv0407 fgd1 490783 491793 1011 + Lys 296 - Glu Lys296Glu aag/gag 886 886 phylo (West African 2) 22768315 491742 491742 SNP 1 t c coding Rv0407 fgd1 490783 491793 1010 + Phe 320 - Phe Phe320Phe ttt/ttc 960 960 phylo (not Euro-American, M. africanum, M. bovis, M. canettii, M. caprae, M. microti, M. pinipedii, Beijing, Delhi/CAS, EAI) 22768315 495108 495108 SNP 1 c a coding Rv0410c pknG 497314 495062 2253 - Thr 736 - Lys Thr736Lys acg/aag 2207 2207 phylo (West African 2) 22768315 495322 495322 SNP 1 g a coding Rv0410c pknG 497314 495062 2253 - Ala 665 - Thr Ala665Thr gcc/acc 1993 1993 phylo (West African 1a, West African 1b) 22768315 495473 495473 SNP 1 g a coding Rv0410c pknG 497314 495062 2253 - Ser 614 - Ser Ser614Ser tcg/tca 1842 1842 phylo (EAI) 22768315 497108 497108 SNP 1 g a coding Rv0410c pknG 497314 495062 2253 - Pro 69 - Pro Pro69Pro ccg/cca 207 207 phylo (M. bovis, M. caprae) 22768315 648756 648756 SNP 1 c t coding Rv0557 mgtA 648536 649672 1137 + Thr 74 - Ile Thr74Ile acg/atg 221 221 phylo (West African 1a, West African 1b) 22768315 648856 648856 SNP 1 t c coding Rv0557 mgtA 648536 649672 1137 + Gly 107 - Gly Gly107Gly ggt/ggc 321 321 phylo (not Euro-American, M. africanum, M. bovis, M. canettii, M. caprae, M. microti, M. pinipedii, Beijing, Delhi/CAS, EAI) 22768315 648990 648990 SNP 1 g c coding Rv0557 mgtA 648536 649672 1137 + Arg 152 - Pro Arg152Pro cgc/ccc 455 455 phylo (Haarlem) 22768315 648992 648992 SNP 1 c g coding Rv0557 mgtA 648536 649672 1137 + Leu 153 - Val Leu153Val ctg/gtg 457 457 phylo (S-type) 22768315 649067 649067 SNP 1 c g coding Rv0557 mgtA 648536 649672 1137 + Arg 178 - Gly Arg178Gly cgg/ggg 532 532 phylo (Cameroon) 22768315 649345 649345 SNP 1 c t coding Rv0557 mgtA 648536 649672 1137 + Ala 270 - Ala Ala270Ala gcc/gct 810 810 phylo (EAI) 22768315 649446 649446 SNP 1 g a coding Rv0557 pimB 648536 649672 1137 + Gly 304 - Asp Gly304Asp ggc/gac 911 911 phylo (West African 1a, West African 1b) 22768315 649585 649585 SNP 1 g a coding Rv0557 mgtA 648536 649672 1137 + Val 350 - Val Val350Val gtg/gta 1050 1050 phylo (M. caprae) 22768315 649601 649601 SNP 1 c t coding Rv0557 mgtA 648536 649672 1137 + Pro 356 - Ser Pro356Ser ccg/tcg 1066 1066 phylo (M. canettii) 22768315 1128814 1128814 SNP 1 g a coding Rv1009 rpfB 1128091 1129179 1089 + Glu 242 - Lys Glu242Lys gag/aag 724 724 phylo (EAI Manila) 22768315 1128825 1128825 SNP 1 c t coding Rv1009 rpfB 1128091 1129179 1089 + Gly 245 - Gly Gly245Gly ggc/ggt 735 735 phylo (M. microti, M. pinipedii) 22768315 1128915 1128915 SNP 1 g c coding Rv1009 rpfB 1128091 1129179 1089 + Glu 275 - Asp Glu275Asp gag/gac 825 825 phylo (M. canettii) 22768315 1128935 1128935 SNP 1 g a coding Rv1009 rpfB 1128091 1129179 1089 + Gly 282 - Glu Gly282Glu gga/gaa 845 845 phylo (M. bovis, M. caprae) 22768315 1129124 1129124 SNP 1 t a coding Rv1009 rpfB 1128091 1129179 1089 + Leu 345 - Gln Leu345Gln ctg/cag 1034 1034 phylo (M. canettii) 22768315 1129128 1129128 SNP 1 t c coding Rv1009 rpfB 1128091 1129179 1089 + Arg 346 - Arg Arg346Arg cgt/cgc 1038 1038 phylo (M. canettii) 22768315 1129160 1129160 SNP 1 c t coding Rv1009 rpfB 1128091 1129179 1089 + Ala 357 - Val Ala357Val gca/gta 1070 1070 phylo (M. bovis) 22768315 1129165 1129165 SNP 1 g a coding Rv1009 rpfB 1128091 1129179 1089 + Ala 359 - Thr Ala359Thr gcg/acg 1075 1075 phylo (TUR) 22768315 1816848 1816848 SNP 1 g t coding Rv1617 pykA 1816189 1817607 1419 + Glu 220 - Asp Glu220Asp gag/gat 660 660 phylo (M. africanum, M. caprae, M. microti, M. pinipedii) 22768315 2053454 2053454 SNP 1 g a coding Rv1811 mgtC 2053443 2054147 705 + Leu 4 - Leu Leu4Leu ctg/cta 12 12 phylo (Ural) 22768315 2053487 2053487 SNP 1 c t coding Rv1811 mgtC 2053443 2054147 705 + Val 15 - Val Val15Val gtc/gtt 45 45 phylo (M. canettii) 22768315 2053682 2053682 SNP 1 c t coding Rv1811 mgtC 2053443 2054147 705 + Ile 80 - Ile Ile80Ile atc/att 240 240 phylo (LAM) 22768315 2053726 2053726 SNP 1 c t coding Rv1811 mgtC 2053443 2054147 705 + Thr 95 - Met Thr95Met acg/atg 284 284 phylo (West African 1b) 22768315 2053762 2053762 SNP 1 c t coding Rv1811 mgtC 2053443 2054147 705 + Ala 107 - Val Ala107Val gcc/gtc 320 320 phylo (West African 2) 22768315 2053987 2053987 SNP 1 g a coding Rv1811 mgtC 2053443 2054147 705 + Arg 182 - His Arg182His cgc/cac 545 545 phylo (Haarlem) 22768315 2134258 2134258 SNP 1 c t coding Rv1884c rpfC 2134261 2133731 531 - His 2 - Tyr His2Tyr cat/tat 4 4 phylo (M. canettii) 22768315 2223896 2223896 SNP 1 t c coding Rv1980c mpt64 2224029 2223343 687 - Met 45 - Thr Met45Thr atg/acg 134 134 phylo (M. canettii) 22768315 2223902 2223902 SNP 1 t a coding Rv1980c mpt64 2224029 2223343 687 - Ile 43 - Asn Ile43Asn att/aat 128 128 phylo (West African 1a, West African 1b) 22768315 2279228 2279228 SNP 1 g t coding Rv2032 acg 2279129 2280124 996 + Ala 34 - Ser Ala34Ser gcc/tcc 100 100 phylo (M. caprae) 22768315 2279314 2279314 SNP 1 g c coding Rv2032 acg 2279129 2280124 996 + Gly 62 - Gly Gly62Gly ggg/ggc 186 186 phylo (M. canettii) 22768315 2280081 2280081 SNP 1 c t coding Rv2032 acg 2279129 2280124 996 + Pro 318 - Leu Pro318Leu cca/cta 953 953 phylo (M. bovis, M. caprae) 22768315 2726105 2726105 SNP 1 g a intergenic Rv2428 ahpC 2726193 2726780 588 + - - - - --- - -88 -88 phylo (Delhi/CAS) 22768315 2751764 2751764 SNP 1 g a coding Rv2450c rpfE 2752180 2751662 519 - Gly 139 - Gly Gly139Gly ggg/gga 417 417 phylo (M. canettii) 22768315 2751866 2751866 SNP 1 g a coding Rv2450c rpfE 2752180 2751662 519 - Ala 105 - Ala Ala105Ala gcg/gca 315 315 phylo (M. canettii) 22768315 2752122 2752122 SNP 1 c g coding Rv2450c rpfE 2752180 2751662 519 - Thr 20 - Arg Thr20Arg acg/agg 59 59 phylo (Beijing) 22768315 2752132 2752132 SNP 1 t c coding Rv2450c rpfE 2752180 2751662 519 - Leu 17 - Leu Leu17Leu ttg/ctg 49 49 phylo (West African 1a, West African 1b) 22768315 2936944 2936944 SNP 1 c g coding Rv2609c - 2937865 2936810 1056 - Gln 308 - Glu Gln308Glu cag/gag 922 922 phylo (M. canettii) 22768315 2939177 2939177 SNP 1 t c coding Rv2611c - 2939962 2939012 951 - Tyr 262 - Tyr Tyr262Tyr tat/tac 786 786 phylo (West African 2) 22768315 2939577 2939577 SNP 1 t g coding Rv2611c - 2939962 2939012 951 - Leu 129 - Arg Leu129Arg ctc/cgc 386 386 phylo (M. canettii) 22768315 2939716 2939716 SNP 1 t c coding Rv2611c - 2939962 2939012 951 - Cys 83 - Arg Cys83Arg tgc/cgc 247 247 phylo (M. canettii) 22768315 2940461 2940461 SNP 1 t c coding Rv2612c pgsA1 2940612 2939959 654 - Met 51 - Thr Met51Thr atg/acg 152 152 phylo (M. canettii) 22768315 2940562 2940562 SNP 1 c t coding Rv2612c pgsA1 2940612 2939959 654 - Thr 17 - Thr Thr17Thr acc/act 51 51 phylo (M. canettii) 22768315 2940608 2940608 SNP 1 g a coding Rv2612c pgsA1 2940612 2939959 654 - Ser 2 - Asn Ser2Asn agc/aac 5 5 phylo (EAI) 22768315 2940930 2940930 SNP 1 c t coding Rv2613c - 2941196 2940609 588 - Pro 89 - Pro Pro89Pro ccc/cct 267 267 phylo (M. canettii) 22768315 2941179 2941179 SNP 1 c t coding Rv2613c - 2941196 2940609 588 - Arg 6 - Arg Arg6Arg cgc/cgt 18 18 phylo (Delhi/CAS) 22768315 2955135 2955135 SNP 1 a c coding Rv2628 - 2955058 2955420 363 + Ile 26 - Ile Ile26Ile ata/atc 78 78 phylo (M. canettii) 22768315 2955202 2955202 SNP 1 t g coding Rv2628 - 2955058 2955420 363 + Ser 49 - Ala Ser49Ala tcc/gcc 145 145 phylo (M. canettii) 22768315 2955233 2955233 SNP 1 c t coding Rv2628 - 2955058 2955420 363 + Ser 59 - Leu Ser59Leu tcg/ttg 176 176 phylo (M.africanum, M. bovis, M. canettii, M. caprae, M. microti, M. pinipedii, EAI) 22768315 2955305 2955305 SNP 1 t g coding Rv2628 - 2955058 2955420 363 + Leu 83 - Trp Leu83Trp ttg/tgg 248 248 phylo (M. microti, M. pinipedii) 22768315 2955310 2955310 SNP 1 a g coding Rv2628 - 2955058 2955420 363 + Thr 85 - Ala Thr85Ala acc/gcc 253 253 phylo (M. canettii) 22768315 2955343 2955343 SNP 1 g a coding Rv2628 - 2955058 2955420 363 + Ala 96 - Thr Ala96Thr gcg/acg 286 286 phylo (West African 1a, West African 1b) 22768315 2955957 2955957 SNP 1 a c coding Rv2629 - 2955767 2956891 1125 + Asp 64 - Ala Asp64Ala gat/gct 191 191 phylo (Beijing) 22768315 2956731 2956731 SNP 1 c t coding Rv2629 - 2955767 2956891 1125 + Pro 322 - Leu Pro322Leu ccg/ctg 965 965 phylo (Ghana) 22768315 3296371 - Ins 7 g gccgcggc coding Rv2947c pks15 3297840 3296350 1490 - Gly 490 - - Gly490- ggc/gggccgcggc 1470 1470 phylo (not Euro-American, M. africanum, M. bovis, M. canettii, M. caprae, M. microti, M. pinipedii, Beijing, Delhi/CAS, EAI) 2447842 3986987 3986987 SNP 1 g t coding Rv3547 ddn 3986844 3987299 456 + Leu 48 - Leu Leu48Leu ctg/ctt 144 144 phylo (West African 1a, West African 1b) 22768315 3987050 3987050 SNP 1 c t coding Rv3547 ddn 3986844 3987299 456 + Asp 69 - Asp Asp69Asp gac/gat 207 207 phylo (M. canettii) 22768315 3987111 3987111 SNP 1 c g coding Rv3547 ddn 3986844 3987299 456 + Leu 90 - Val Leu90Val ctc/gtc 268 268 phylo (M. microti, M. pinipedii) 22768315 3987180 3987180 SNP 1 g a coding Rv3547 ddn 3986844 3987299 456 + Asp 113 - Asn Asp113Asn gac/aac 337 337 phylo (West African 1a, West African 1b) 22768315 3987287 3987287 SNP 1 t c coding Rv3547 ddn 3986844 3987299 456 + Val 148 - Val Val148Val gtt/gtc 444 444 phylo (M. canettii) 22768315 7539 7539 SNP 1 a g coding Rv0006 gyrA 7302 9818 2516 + Thr 80 - Ala Thr80Ala acc/gcc 238 238 phylo (Uganda I+II) 24458512 7585 7585 SNP 1 g c coding Rv0006 gyrA 7302 9818 2516 + Ser 95 - Thr Ser95Thr agc/acc 284 284 phylo (not H37Rv) 24458512 491595 491595 SNP 1 c t coding Rv0407 fgd1 490783 491793 1011 + Ala 271 - Ala Ala271Ala gcc/gct 813 813 phylo (West African 1a) 24458512 575665 575665 SNP 1 g c coding Rv0486 mshA 575348 576790 1442 + Gly 106 - Gly Gly106Gly ggg/ggc 318 318 phylo (M. canettii) 24458512 575679 575679 SNP 1 a g coding Rv0486 mshA 575348 576790 1442 + Asn 111 - Ser Asn111Ser aac/agc 332 332 phylo (Haarlem) 24458512 575907 575907 SNP 1 c t coding Rv0486 mshA 575348 576790 1442 + Ala 187 - Val Ala187Val gca/gta 560 560 phylo (Beijing) 24458512 576077 576077 SNP 1 c t coding Rv0486 mshA 575348 576790 1442 + Leu 244 - Leu Leu244Leu ctg/ttg 730 730 phylo (Tur) 24458512 1461251 1461251 SNP 1 g t coding Rv1305 atpE 1461045 1461290 245 + Ala 69 - Ala Ala69Ala gcg/gct 207 207 phylo (West African 2) 24458512 1471848 - Ins 1 t tt ribosomal MTB000019 rrs 1471846 1473382 1537 + - - - - --- - 4 4 phylo (M. canettii) 24458512 1471851 1471851 SNP 1 t g ribosomal MTB000019 rrs 1471846 1473382 1537 + - - - - --- - 6 6 phylo (M. canettii) 24458512 1473079 1473079 SNP 1 g a ribosomal MTB000019 rrs 1471846 1473382 1537 + - - - - --- - 1234 1234 phylo (M. microti) 24458512 1473094 1473094 SNP 1 t c ribosomal MTB000019 rrs 1471846 1473382 1537 + - - - - --- - 1249 1249 phylo (M. pinipedii) 24458512 1673338 1673338 SNP 1 g a intergenic Rv1483 fabG1 1673440 1674183 809 + - - - - --- - -102 -102 phylo (West African 1a, West African 1b) 24458512 1674434 1674434 SNP 1 t c coding Rv1484 inhA 1674202 1675011 809 + Val 78 - Ala Val78Ala gtg/gcg 233 233 phylo (West African 2) 24458512 1674520 1674520 SNP 1 c t coding Rv1484 inhA 1674202 1675011 809 + Pro 107 - Ser Pro107Ser ccg/tcg 319 319 phylo (M. pinipedii) 24458512 1674816 1674816 SNP 1 t c coding Rv1484 inhA 1674202 1675011 809 + Gly 205 - Gly Gly205Gly ggt/ggc 615 615 phylo (M. canettii) 24458512 1833554 1833554 SNP 1 a g coding Rv1630 rpsA 1833542 1834987 1446 + Thr 5 - Ala Thr5Ala acc/gcc 13 13 phylo (M. canettii) 24458512 1833568 1833568 SNP 1 g c coding Rv1630 rpsA 1833542 1834987 1446 + Pro 9 - Pro Pro9Pro ccg/ccc 27 27 phylo (M. canettii) 24458512 1834169 1834169 SNP 1 a g coding Rv1630 rpsA 1833542 1834987 1446 + Thr 210 - Ala Thr210Ala acc/gcc 628 628 phylo (M. canettii) 24458512 1834177 1834177 SNP 1 a c coding Rv1630 rpsA 1833542 1834987 1446 + Arg 212 - Arg Arg212Arg cga/cgc 636 636 phylo (Beijing) 24458512 1834859 1834859 SNP 1 g a coding Rv1630 rpsA 1833542 1834987 1446 + Ala 440 - Thr Ala440Thr gcg/acg 1318 1318 phylo (M. bovis, M. caprae) 24458512 1834912 1834912 SNP 1 a g coding Rv1630 rpsA 1833542 1834987 1446 + Glu 457 - Glu Glu457Glu gaa/gag 1371 1371 phylo (M. canettii) 24458512 2154724 2154724 SNP 1 g t coding Rv1908c katG 2156111 2153889 2223 - Arg 463 - Leu Arg463Leu cgg/ctg 1388 1388 phylo (not Euro-American, M. africanum, M. bovis, M . canettii, M. caprae, M. Microti, M. pinipedii, Beijing, Delhi/CAS, EAI) 9275218 2289047 2289047 SNP 1 c t coding Rv2043c pncA 2289241 2288681 560 - Ser 65 - Ser Ser65Ser tcc/tct 195 195 phylo (Delhi/CAS) 24458512 2289073 2289073 SNP 1 c g coding Rv2043c pncA 2289241 2288681 560 - His 57 - Asp His57Asp cac/gac 169 169 phylo (M. bovis) 24458512 2289104 2289104 SNP 1 a g coding Rv2043c pncA 2289241 2288681 560 - Ala 46 - Ala Ala46Ala gca/gcg 138 138 phylo (M. canettii) 24458512 2726105 2726105 SNP 1 g a intergenic Rv2428 ahpC 2726193 2726780 587 + - - - - --- - -88 -88 phylo (Delhi/CAS) 24458512 3073868 3073868 SNP 1 a g coding Rv2764c thyA 3074471 3073680 791 - Thr 202 - Ala Thr202Ala acc/gcc 604 604 phylo (LAM) 24458512 4240671 4240671 SNP 1 c t coding Rv3793 embC 4239863 4243147 3285 + Thr 270 - Ile Thr270Ile acc/atc 809 809 phylo (M. africanum, M. bovis, M. canettii, M.caprae, M. Microti, M. pinipedii, EAI) 24458512 4242075 4242075 SNP 1 g a coding Rv3793 embC 4239863 4243147 3285 + Arg 738 - Gln Arg738Gln cgg/cag 2213 2213 phylo (Delhi/CAS) 20427375 4242803 4242803 SNP 1 g c coding Rv3793 embC 4239863 4243147 3285 + Val 981 - Leu Val981Leu gtg/ctg 2941 2941 phylo (Ghana, Haarlem, X-Type) 22646308 4242970 4242970 SNP 1 c t coding Rv3793 embC 4239863 4243147 3285 + Thr 1036 Thr Thr1036Thr acc/act 3108 3108 phylo (M. bovis, M. caprae) 24458512 4243377 4243377 SNP 1 a c coding Rv3794 embA 4243233 4246517 3285 + Ser 49 - Arg Ser49Arg agc/cgc 145 145 phylo (M. canettii) 24458512 4243460 4243460 SNP 1 c t coding Rv3794 embA 4243233 4246517 3285 + Cys 76 - Cys Cys76Cys tgc/tgt 228 228 phylo (Beijing) 20427375 4243690 4243690 SNP 1 t c coding Rv3794 embA 4243233 4246517 3285 + Met 153 - Thr Met153Thr atg/acg 458 458 phylo (M. canettii) 24458512 4247590 4247590 SNP 1 a g coding Rv3795 embB 4246514 4249810 3297 + Leu 359 - Leu Leu359Leu cta/ctg 1077 1077 phylo (M. canettii) 24458512 4247646 4247646 SNP 1 a c coding Rv3795 embB 4246514 4249810 3297 + Glu 378 - Ala Glu378Ala gag/gcg 1133 1133 phylo (M. africanum, M. bovis, M. canettii, M. caprae, M. Microti, M. pinipedii, EAI) 24458512 4247815 4247815 SNP 1 c t coding Rv3795 embB 4246514 4249810 3297 + Ala 434 - Ala Ala434Ala gcc/gct 1302 1302 phylo (M. canettii) 24458512 4248195 4248195 SNP 1 a g coding Rv3795 embB 4246514 4249810 3297 + Lys 561 - Arg Lys561Arg aag/agg 1682 1682 phylo (M. canettii) 24458512 4248206 4248206 SNP 1 a g coding Rv3795 embB 4246514 4249810 3297 + Ser 565 - Gly Ser565Gly agc/ggc 1693 1693 phylo (M. canettii) 24458512 4248439 4248439 SNP 1 c t coding Rv3795 embB 4246514 4249810 3297 + Thr 642 - Thr Thr642Thr acc/act 1926 1926 phylo (M. canettii) 24458512 4407588 4407588 SNP 1 a g coding Rv3919c gidB 4408202 4407528 674 - Ala 205 - Ala Ala205Ala gca/gcg 615 615 phylo (M. africanum, M. bovis, M. canettii, M. caprae, M. Microti, M. pinipedii, Beijing, Delhi/CAS, EAI) 24458512 4407873 4407873 SNP 1 g t coding Rv3919c gidB 4408202 4407528 674 - Val 110 - Val Val110Val gtg/gtt 330 330 phylo (EAI) 24458512 4407927 4407927 SNP 1 a c coding Rv3919c gidB 4408202 4407528 674 - Glu 92 - Asp Glu92Asp gaa/gac 276 276 phylo (Beijing) 24458512 4408156 4408156 SNP 1 t g coding Rv3919c gidB 4408202 4407528 674 - Leu 16 - Arg Leu16Arg ctt/cgt 47 47 phylo (LAM) 22646308 4408185 4408185 SNP 1 c t coding Rv3919c gidB 4408202 4407528 674 - Pro 6 - Pro Pro6Pro ccc/cct 18 18 phylo (M. canettii) 24458512 4408213 4408213 SNP 1 c t intergenic Rv3919c gidB 4408202 4407528 674 - - - - - --- - -11 -11 phylo (Ural) 24458512