TB Profiler
This tool processes raw sequence data to infer strain type and identify known drug resistance markers.
A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.



This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.
Back to results page.
Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).
Name: 5d2fb676e03a2
Sample: 5d2fb676e03a2

Download results

Summary
ID: 5d2fb676e03a2
Date: Thu Jul 18 01:00:40 2019
Strain: lineage2.2.1;lineage4.3;lineage4.1.1.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Asp435Val (0.79)
EthambutolRembB p.His312Arg (0.26), embB p.Gln497Pro (0.89)
Pyrazinamide
StreptomycinRrpsL p.Lys43Arg (0.64), rrs r.462c>t (0.20)
EthionamideRethA c.639 640del (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage4.1.1.1Euro-American (X-type)X2RD183

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6086p.Thr283Pro0.244
gyrB6091c.852G>C0.233
gyrB6100c.861G>C0.227
gyrB6115c.876A>G0.244
gyrB6123p.Ala295Gly0.238
gyrB6127c.888G>C0.222
gyrB6130c.891T>C0.233
gyrB6133c.894G>C0.233
gyrB6136c.897G>A0.239
gyrB6169c.930C>G0.319
gyrB6190c.951A>G0.327
gyrB6209c.970C>T0.220
gyrB6214c.975G>C0.195
gyrB6217c.978G>C0.175
gyrB6223c.984G>C0.184
gyrB6242p.Arg335Lys0.212
gyrB6250c.1011A>G0.229
gyrB6253c.1014G>C0.222
gyrB6280c.1041T>C0.265
gyrB6286c.1047T>C0.250
gyrB6292c.1053G>C0.207
gyrB6295c.1056A>G0.207
gyrB6298c.1059C>A0.207
gyrB6299c.1060C>T0.194
gyrB6307c.1068T>G0.250
gyrB6319c.1080G>C0.200
gyrB6325c.1086C>G0.200
gyrB6361c.1122G>A0.208
gyrB6362c.1123T>C0.250
gyrB6379c.1140C>G0.138
gyrB6382c.1143A>G0.138
gyrB6670c.1431G>C0.207
gyrB6673c.1434A>C0.207
gyrB6700c.1461T>C0.206
gyrB6703c.1464G>C0.176
gyrB6706c.1467G>A0.182
gyrB6709c.1470A>G0.188
gyrB6712c.1473G>C0.188
gyrB6727c.1488G>T0.250
gyrB6730c.1491A>G0.242
gyrB6745c.1506T>G0.229
gyrB6760c.1521G>C0.179
gyrB6778c.1539C>T0.216
gyrB6793c.1554T>C0.135
gyrB6797p.Gly520Thr0.135
gyrB6824c.1585C>T0.200
gyrB6841c.1602T>C0.156
gyrB6844c.1605T>G0.163
gyrB6853c.1614A>G0.146
gyrB6856c.1617T>C0.150
gyrB6859c.1620T>C0.128
gyrB6862c.1623C>G0.128
gyrB6878c.1639T>C0.122
gyrB6881c.1642T>C0.125
gyrB6904c.1665C>G0.125
gyrB6910c.1671G>A0.132
gyrB6911p.Asn558His0.135
gyrB6919c.1680T>C0.139
gyrB6925c.1686T>C0.114
gyrB6931c.1692A>C0.118
gyrB6934c.1695A>G0.114
gyrB6937c.1698G>A0.114
gyrA7355c.54T>C0.269
gyrA7362p.Glu21Gln1.000
gyrA7391c.90C>T0.219
gyrA7394c.93T>C0.212
gyrA7427c.126G>C0.160
gyrA7442c.141G>C0.160
gyrA7451c.150C>G0.200
gyrA7457c.156T>C0.200
gyrA7523c.222C>G0.152
gyrA7532c.231T>C0.147
gyrA7541c.240C>G0.139
gyrA7571c.270G>C0.147
gyrA7585p.Ser95Thr1.000
gyrA7595c.294C>G0.147
gyrA7607c.306C>G0.167
gyrA7626c.325C>T0.133
gyrA7631c.330G>C0.133
gyrA7637c.336C>G0.167
gyrA7646c.345C>T0.167
gyrA7649c.348C>T0.174
gyrA7658c.357A>G0.182
gyrA7664c.363T>C0.190
gyrA7670c.369A>G0.200
gyrA7676c.375G>C0.200
gyrA7683c.382A>C0.182
gyrA7694c.393A>G0.250
gyrA7697c.396C>G0.286
gyrA7710c.409T>C0.308
gyrA7715c.414G>C0.320
gyrA7728c.427A>C0.321
gyrA7760c.459C>T0.296
gyrA7763c.462T>C0.286
gyrA7799c.498A>G0.194
gyrA7835c.534A>G0.182
gyrA8069c.768T>C0.147
gyrA8078c.777A>G0.158
gyrA8090c.789C>G0.179
gyrA8096c.795T>C0.184
gyrA8099c.798T>C0.189
gyrA8156c.855T>C0.179
gyrA8168c.867A>G0.148
gyrA8174c.873C>G0.192
gyrA8177c.876A>C0.200
gyrA8198c.897T>C0.200
gyrA8207c.906T>C0.207
gyrA8219c.918T>C0.179
gyrA8225c.924T>C0.192
gyrA8234c.933T>G0.174
gyrA8235c.934T>C0.174
gyrA8253p.Ile318Leu0.174
gyrA8264c.963T>C0.174
gyrA8267c.966G>C0.208
gyrA8270c.969G>C0.192
gyrA8283p.Ile328Leu0.214
gyrA8288c.987T>C0.207
gyrA8294c.993T>C0.207
gyrA8324c.1023T>C0.156
gyrA8339c.1038A>G0.261
gyrA8342c.1041G>C0.261
gyrA8366c.1065G>C0.217
gyrA8375c.1074G>C0.208
gyrA8391p.Tyr364His0.148
gyrA8603c.1302A>G0.176
gyrA8619c.1318T>C0.194
gyrA8624c.1323G>C0.200
gyrA8627c.1326C>G0.200
gyrA8636c.1335A>C0.194
gyrA8642c.1341A>G0.194
gyrA8645c.1344C>G0.207
gyrA8672c.1371A>G0.200
gyrA8693c.1392T>C0.130
gyrA8858c.1557T>C0.129
gyrA8867c.1566A>G0.138
gyrA8870c.1569G>C0.154
gyrA8873c.1572A>C0.185
gyrA8888c.1587C>G0.200
gyrA8897c.1596T>C0.148
gyrA8903c.1602T>C0.154
gyrA8915c.1614A>G0.160
gyrA8987c.1686C>G0.130
gyrA8990c.1689C>G0.130
gyrA8996c.1695T>C0.136
gyrA8998p.Leu566Trp0.136
gyrA9200c.1899A>G0.125
gyrA9204p.Ser635Thr0.125
gyrA9227c.1926C>G0.130
gyrA9230c.1929T>C0.150
gyrA9233c.1932C>T0.125
gyrA9242c.1941A>C0.174
gyrA9252p.Val651Ile0.192
gyrA9275c.1974G>A0.154
gyrA9278c.1977G>C0.148
gyrA9281c.1980C>G0.148
gyrA9284c.1983T>C0.148
gyrA9291c.1990C>T0.161
gyrA9296c.1995T>C0.167
gyrA9304p.Gly668Glu1.000
gyrA9311c.2010C>T0.194
gyrA9323c.2022C>G0.226
gyrA9335c.2034G>C0.182
gyrA9345c.2044A>C0.161
gyrA9374c.2073G>C0.147
gyrA9377c.2076A>G0.139
gyrA9383c.2082T>C0.161
gyrA9386c.2085T>C0.133
rpoB760059p.Tyr85Asp0.111
rpoB760088c.282C>A0.200
rpoB760091c.285G>C0.240
rpoB760101c.295T>C0.310
rpoB760106c.300G>T0.310
rpoB760112c.306T>C0.300
rpoB760118c.312T>C0.290
rpoB760121c.315T>C0.300
rpoB760130p.Asp108Glu0.300
rpoB760139c.333A>G0.333
rpoB760142c.336C>G0.323
rpoB760181c.375T>C0.323
rpoB760184c.378A>G0.323
rpoB760196c.390C>G0.300
rpoB760223c.417T>C0.310
rpoB760235c.429T>C0.233
rpoB760283c.477G>C0.185
rpoB760307c.501T>C0.259
rpoB760328c.522G>C0.222
rpoB760331c.525G>C0.231
rpoB760337c.531C>G0.240
rpoB760340c.534G>C0.240
rpoB760361c.555T>C0.259
rpoB760376p.Asp190Glu0.250
rpoB760406c.600G>C0.308
rpoB760418c.612G>C0.269
rpoB760424c.618C>G0.240
rpoB760430c.624T>C0.217
rpoB760475c.669A>G0.208
rpoB760481c.675G>C0.208
rpoB760484c.678A>G0.208
rpoB760522p.Ser239Asn0.190
rpoB760532c.726T>C0.136
rpoB760533p.Val243Thr0.136
rpoB760547c.741G>C0.222
rpoB760563p.Arg253Met0.231
rpoB760591p.Val262Ala0.308
rpoB760611c.805T>C0.258
rpoB760634c.828T>C0.300
rpoB760646c.840C>G0.321
rpoB760655c.849A>G0.310
rpoB760661c.855A>C0.286
rpoB760670c.864G>C0.310
rpoB760674c.868T>C0.310
rpoB760679c.873A>G0.296
rpoB760683c.877T>C0.321
rpoB760718c.912C>G0.321
rpoB760721c.915C>G0.321
rpoB760724c.918T>C0.321
rpoB760730c.924T>C0.269
rpoB760751c.945G>C0.273
rpoB760757c.951T>C0.211
rpoB760759p.Val318Ala0.211
rpoB760763c.957C>T0.190
rpoB760769c.963C>G0.190
rpoB760775c.969G>C0.174
rpoB760776c.970T>A0.174
rpoB760793c.987A>G0.143
rpoB760805c.999G>C0.185
rpoB760817c.1011A>G0.179
rpoB760820c.1014T>C0.207
rpoB760826c.1020C>G0.200
rpoB760830c.1024T>C0.176
rpoB760835c.1029C>T0.182
rpoB760845p.Thr347Pro0.138
rpoB760859c.1053T>C0.229
rpoB760869p.Val355Ile0.235
rpoB760886c.1080A>G0.235
rpoB760919c.1113C>G0.243
rpoB760925c.1119T>C0.257
rpoB760928c.1122G>C0.306
rpoB760934c.1128C>T0.343
rpoB760946c.1140A>G0.371
rpoB760970c.1164G>C0.333
rpoB760982c.1176G>C0.414
rpoB760985c.1179G>C0.379
rpoB760991c.1185G>C0.379
rpoB761015c.1209G>C0.346
rpoB761021c.1215G>C0.333
rpoB761027c.1221A>G0.346
rpoB761036c.1230G>C0.321
rpoB761037c.1231T>C0.333
rpoB761051c.1245G>T0.360
rpoB761054c.1248G>C0.360
rpoB761057c.1251G>C0.360
rpoB761060c.1254C>G0.333
rpoB761063c.1257C>G0.333
rpoB761097c.1291A>T0.190
rpoB761102c.1296A>G0.190
rpoB761133c.1327T>C0.269
rpoB761150c.1344A>C0.269
rpoB761165c.1359G>C0.292
rpoB761168c.1362C>G0.304
rpoB761171c.1365C>T0.304
rpoB761180c.1374A>C0.280
rpoB761183c.1377T>G0.292
rpoB761189c.1383T>G0.273
rpoB761222c.1416G>C0.286
rpoB761249c.1443A>G0.273
rpoB761255c.1449T>G0.261
rpoB761261c.1455G>T0.240
rpoB761306c.1500C>G0.167
rpoB761327c.1521A>G0.214
rpoB761360c.1554T>C0.267
rpoB761362p.Ser519Thr0.267
rpoB761373p.Val523His0.267
rpoB761414c.1608A>G0.333
rpoB761423c.1617T>C0.353
rpoB761435c.1629T>C0.172
rpoB761437p.Ala544Asp0.179
rpoB761439p.Asp545Lys0.179
rpoB761444c.1638T>C0.179
rpoB761447c.1641C>G0.185
rpoB761452p.Val549Ala0.192
rpoB761457p.Pro551Ala0.208
rpoB761462c.1656C>G0.200
rpoB761492c.1686G>C0.296
rpoB761510c.1704T>C0.231
rpoB761531c.1725C>G0.226
rpoB761537c.1731C>G0.194
rpoB761570c.1764T>C0.241
rpoB761573c.1767C>G0.241
rpoB761579c.1773G>C0.231
rpoB761606c.1800C>G0.276
rpoB761612c.1806G>C0.276
rpoB761615c.1809A>C0.276
rpoB761636c.1830G>T0.214
rpoB761645c.1839C>G0.214
rpoB761648c.1842T>C0.222
rpoB761657c.1851C>G0.222
rpoB761675c.1869G>C0.258
rpoB761687c.1881C>T0.286
rpoB761690c.1884G>C0.286
rpoB761725p.Glu640Gly0.231
rpoB761732c.1926C>G0.231
rpoB761735c.1929C>G0.240
rpoB761747c.1941G>C0.250
rpoB761750c.1944G>C0.250
rpoB761765c.1959T>C0.219
rpoB761772p.His656Ala0.212
rpoB761778p.Asn658Asp0.226
rpoB761791p.Arg662His0.161
rpoB761864c.2058G>C0.138
rpoB761873c.2067A>G0.154
rpoB761948c.2142G>C0.174
rpoB761954c.2148C>G0.174
rpoB762114p.Ile770Val0.136
rpoB762131c.2325C>G0.200
rpoB762140c.2334G>C0.250
rpoB762143c.2337T>C0.263
rpoB762149c.2343G>C0.250
rpoB762167c.2361T>C0.333
rpoB762176c.2370T>C0.318
rpoB762185c.2379G>C0.333
rpoB762218c.2412T>G0.333
rpoB762254c.2448T>C0.312
rpoB762266c.2460T>C0.303
rpoB762284c.2478G>C0.294
rpoB762293c.2487T>C0.278
rpoB762317c.2511A>G0.343
rpoB762329c.2523G>C0.306
rpoB762338c.2532T>C0.308
rpoB762347c.2541T>C0.261
rpoB762362p.Glu852Asp0.239
rpoB762369c.2563T>C0.222
rpoB762374c.2568G>C0.196
rpoB762380c.2574T>G0.182
rpoB762395c.2589G>C0.186
rpoB762398c.2592T>C0.186
rpoB762401c.2595G>C0.186
rpoB762404c.2598T>C0.186
rpoB762410c.2604T>C0.186
rpoB762416c.2610A>G0.200
rpoB762443c.2637G>C0.200
rpoB762470c.2664G>C0.182
rpoB762489p.Val895Gln0.163
rpoB762509c.2703T>G0.216
rpoB762510p.Ala902Pro0.222
rpoB762521c.2715C>G0.209
rpoB762533c.2727T>C0.200
rpoB762536c.2730T>C0.171
rpoB762537c.2731T>C0.171
rpoB762551c.2745C>T0.163
rpoB762582c.2776T>C0.111
rpoB762782c.2976T>C0.160
rpoB762785p.Asp993Glu0.160
rpoB762788c.2982G>C0.154
rpoB762789p.Leu995Met0.154
rpoB762794c.2988C>G0.160
rpoB762799p.Ala998Gly0.154
rpoB762812c.3006C>G0.174
rpoB762813p.Met1003Val0.174
rpoB762818c.3012C>G0.174
rpoB762827c.3021G>C0.182
rpoB762830c.3024C>G0.182
rpoB762831c.3025A>T0.167
rpoB762836c.3030C>G0.154
rpoB762857c.3051C>G0.276
rpoB762860c.3054G>C0.308
rpoB762863c.3057T>C0.296
rpoB762929c.3123G>C0.160
rpoB762989c.3183G>C0.133
rpoB762995c.3189G>T0.154
rpoB763031c.3225T>C1.000
rpoB763070c.3264T>C0.308
rpoB763076c.3270C>G0.308
rpoB763085c.3279C>G0.273
rpoB763115c.3309T>C0.308
rpoB763136c.3330C>T0.357
rpoB763148c.3342G>C0.333
rpoB763158c.3352C>T0.364
rpoB763166c.3360A>G0.364
rpoB763169c.3363A>G0.364
rpoB763214c.3408T>C0.300
rpoB763220c.3414G>C0.250
rpoB763226c.3420A>G0.214
rpoB763238c.3432T>C0.214
rpoB763268c.3462C>G0.182
rpoC763402c.33C>G0.292
rpoC763411c.42T>G0.280
rpoC763414c.45T>C0.231
rpoC763441c.72C>G0.192
rpoC763444c.75T>C0.185
rpoC763456c.87A>G0.179
rpoC763468c.99G>C0.241
rpoC763486c.117T>C0.226
rpoC763528c.159G>A0.345
rpoC763546c.177A>G0.321
rpoC763570c.201G>C0.385
rpoC763594c.225C>T0.455
rpoC763633c.264T>C0.368
rpoC763636c.267T>C0.412
rpoC763642c.273G>C0.389
rpoC763658c.289C>T0.348
rpoC763675c.306C>G0.273
rpoC763696c.327T>C0.160
rpoC763702c.333C>G0.160
rpoC763735c.366G>C0.121
rpoC763744c.375G>C0.118
rpoC763765c.396T>C0.118
rpoC763768c.399C>G0.143
rpoC763780c.411C>G0.147
rpoC763783c.414G>C0.171
rpoC763801c.432C>G0.231
rpoC763807c.438T>C0.237
rpoC763819c.450G>C0.237
rpoC763831c.462A>G0.225
rpoC763835p.Ala156Met0.237
rpoC763858c.489A>G0.294
rpoC763872p.Gly168Ala0.324
rpoC763876p.Glu169Asp0.343
rpoC763879c.510A>G0.353
rpoC763888c.519G>C0.333
rpoC763891c.522G>C0.344
rpoC763894c.525A>G0.344
rpoC763903c.534G>A0.314
rpoC763945c.576T>C0.211
rpoC763960c.591T>C0.158
rpoC763967p.Gly200Ser0.150
rpoC763978c.609C>G0.184
rpoC763996c.627T>C0.214
rpoC764005c.636G>C0.233
rpoC764011c.642T>C0.220
rpoC764024c.655T>C0.184
rpoC764040p.Ser224Asn0.179
rpoC764044c.675T>C0.179
rpoC764059c.690G>C0.200
rpoC764083c.714A>G0.212
rpoC764098c.729A>G0.200
rpoC764101c.732C>G0.200
rpoC764116c.747C>T0.216
rpoC764131c.762T>C0.184
rpoC764257c.888G>C0.184
rpoC764266c.897T>C0.184
rpoC764269c.900G>C0.194
rpoC764278c.909A>G0.200
rpoC764282c.913T>A0.212
rpoC764320c.951C>G0.156
rpoC764365c.996C>T0.182
rpoC764380c.1011G>C0.190
rpoC764381c.1012T>A0.200
rpoC764387c.1018T>C0.200
rpoC764405c.1036A>C0.167
rpoC764431c.1062G>C0.208
rpoC764434c.1065A>G0.217
rpoC764446c.1077T>C0.300
rpoC764449c.1080G>C0.300
rpoC764458c.1089G>C0.318
rpoC764461c.1092A>G0.333
rpoC764497c.1128A>G0.333
rpoC764521c.1152T>C0.286
rpoC764536c.1167G>C0.300
rpoC764539c.1170C>G0.290
rpoC764560c.1191T>C0.296
rpoC764566c.1197C>G0.286
rpoC764573c.1204C>T0.214
rpoC764576c.1207T>A0.207
rpoC764581c.1212T>C0.200
rpoC764626c.1257C>T0.235
rpoC764632c.1263T>C0.219
rpoC764650c.1281G>T0.233
rpoC764681c.1312C>T0.303
rpoC764695c.1326T>C0.314
rpoC764716c.1347G>C0.262
rpoC764746c.1377G>C0.250
rpoC764752c.1383G>C0.262
rpoC764764c.1395T>C0.263
rpoC764779c.1410G>A0.216
rpoC764791c.1422C>G0.263
rpoC764809c.1440C>T0.200
rpoC764812c.1443C>G0.200
rpoC764815c.1446A>G0.206
rpoC764824c.1455T>C0.194
rpoC764830c.1461C>G0.176
rpoC764858c.1489T>C0.156
rpoC764872c.1503A>G0.194
rpoC764893c.1524T>C0.200
rpoC764911c.1542A>G0.179
rpoC764923c.1554A>G0.185
rpoC764932c.1563C>A0.185
rpoC764995c.1626C>G0.154
rpoC765007c.1638T>G0.136
rpoC765019c.1650A>G0.160
rpoC765034c.1665T>C0.174
rpoC765040c.1671T>C0.160
rpoC765041c.1672T>C0.160
rpoC765047c.1678T>C0.154
rpoC765052c.1683C>G0.143
rpoC765073c.1704G>C0.129
rpoC765076c.1707A>G0.129
rpoC765079c.1710T>G0.133
rpoC765082c.1713G>C0.133
rpoC765085c.1716T>C0.129
rpoC765089c.1720T>C0.118
rpoC765103c.1734G>A0.125
rpoC765319c.1950A>G0.130
rpoC765326p.His653Ala0.136
rpoC765330p.Ser654Asn0.143
rpoC765349c.1980T>C0.182
rpoC765352c.1983G>C0.182
rpoC765383p.Met672Leu0.214
rpoC765404p.Leu679Val0.241
rpoC765409c.2040T>C0.233
rpoC765412c.2043T>C0.258
rpoC765421c.2052C>G0.276
rpoC765451c.2082C>G0.233
rpoC765452p.Ala695Ser0.233
rpoC765478c.2109T>C0.189
rpoC765499c.2130C>G0.184
rpoC765508c.2139C>G0.158
rpoC765541c.2172C>G0.125
rpoC765553c.2184C>T0.129
rpoC765556c.2187G>C0.129
rpoC765559c.2190G>C0.133
rpoC765578c.2209C>T0.161
rpoC765583c.2214G>T0.152
rpoC765613p.His748Gln0.192
rpoC765625c.2256C>G0.240
rpoC765628c.2259G>C0.231
rpoC765631p.Asp754Glu0.231
rpoC765649c.2280C>T0.267
rpoC765658c.2289C>T0.273
rpoC765700c.2331T>C0.206
rpoC765734c.2365T>C0.194
rpoC765739c.2370G>C0.167
rpoC765751c.2382C>G0.257
rpoC765753p.Asp795Ala0.270
rpoC765772c.2403C>G0.250
rpoC765784c.2415C>G0.250
rpoC765796c.2427C>T0.231
rpoC765811c.2442T>C0.237
rpoC765814c.2445A>G0.250
rpoC765826c.2457T>C0.250
rpoC765835c.2466C>T0.265
rpoC765871c.2502T>C0.273
rpoC765883c.2514C>G0.281
rpoC765886c.2517C>G0.265
rpoC765892c.2523T>C0.242
rpoC765928c.2559C>G0.200
rpoC765967c.2598C>T0.250
rpoC765970c.2601C>T0.241
rpoC765979c.2610C>G0.267
rpoC765982c.2613C>T0.267
rpoC765985c.2616C>T0.267
rpoC765994c.2625A>T0.345
rpoC766009c.2640G>C0.323
rpoC766010c.2641T>A0.333
rpoC766021c.2652G>C0.312
rpoC766043p.Gln892Glu0.321
rpoC766054c.2685C>G0.333
rpoC766069c.2700G>A0.308
rpoC766081c.2712T>C0.200
rpoC766082p.Ala905Gln0.200
rpoC766096c.2727G>T0.227
rpoC766105c.2736C>T0.217
rpoC766258c.2889T>C0.174
rpoC766270c.2901G>C0.240
rpoC766273c.2904T>C0.240
rpoC766274p.Ala969Thr0.240
rpoC766279c.2910C>G0.250
rpoC766280p.Ser971Gly0.240
rpoC766288c.2919C>G0.296
rpoC766309c.2940G>C0.276
rpoC766312c.2943T>G0.276
rpoC766315c.2946C>G0.286
rpoC766327c.2958C>G0.276
rpoC766345c.2976T>C0.258
rpoC766348c.2979A>G0.258
rpoC766363c.2994G>C0.265
rpoC766381c.3012C>T0.222
rpoC766384c.3015A>G0.207
rpoC766390c.3021C>T0.241
rpoC766408c.3039C>T0.269
rpoC766426c.3057C>T0.167
rpoC766447c.3078T>C0.182
rpoC766483c.3114G>C0.182
rpoC766484p.Val1039Ile0.182
rpoC766492c.3123T>C0.190
rpoC766495c.3126C>T0.190
rpoC766528c.3159T>G0.304
rpoC766543c.3174C>T0.280
rpoC766573c.3204T>C0.286
rpoC766583p.Gly1072Ser0.238
rpoC766591c.3222A>G0.217
rpoC766594c.3225G>C0.217
rpoC766597c.3228C>G0.208
rpoC766607p.Ile1080Leu0.300
rpoC766630c.3261G>C0.217
rpoC766645c.3276A>G0.208
rpoC766651c.3282T>C0.214
rpoC766657c.3288A>G0.233
rpoC766672c.3303T>C0.194
rpoC766726c.3357T>C0.156
rpoC766738c.3369G>T0.148
rpoC766750c.3381C>G0.214
rpoC766765c.3396A>C0.240
rpoC766774c.3405T>C0.240
rpoC766804c.3435A>G0.125
rpoC766861c.3492G>C0.250
rpoC766864c.3495G>C0.241
rpoC766894c.3525T>C0.156
rpoC766895c.3526T>C0.156
rpoC766900c.3531T>C0.156
rpoC766903c.3534C>T0.161
rpoC766918c.3549C>T0.172
rpoC766933c.3564A>G0.206
rpoC766945c.3576A>G0.200
rpoC766963c.3594T>C0.219
rpoC766972c.3603G>C0.200
rpoC766978c.3609C>G0.207
rpoC766996c.3627C>T0.185
rpoC767059c.3690T>G0.158
rpoC767062c.3693C>A0.190
rpoC767074c.3705T>C0.190
rpoC767098c.3729T>C0.188
rpoC767119c.3750A>G0.231
rpoC767134c.3765C>G0.231
rpoC767158c.3789T>C0.300
rpoC767167c.3798C>G0.214
rpoC767180p.Ala1271Gln0.154
rpoC767191c.3822C>G0.188
rpoC767212c.3843G>C0.222
rpoC767221c.3852C>G0.278
rpoC767233c.3864T>C0.278
rpoC767263c.3894T>C0.250
rpoC767264p.Ala1299Gln0.250
rpoC767275c.3906T>C0.250
rpoC767278c.3909T>C0.250
rpoC767281c.3912C>G0.250
rpoC767284c.3915C>G0.263
rpsL781395c.-165T>C1.000
rpsL781571c.12C>T0.407
rpsL781608p.Ser17Gly0.462
rpsL781631c.72G>C0.481
rpsL781649c.90T>C0.517
rpsL781655c.96T>C0.536
rpsL781682c.123T>C0.346
rpsL781715c.156T>C0.200
rpsL781728c.169T>C0.211
rpsL781736c.177T>C0.211
rpsL781751c.192G>C0.222
rpsL781754c.195G>C0.222
rpsL781760c.201T>C0.167
rpsL781832c.273T>C0.211
rpsL781841c.282C>G0.211
rpsL781859c.300T>C0.190
rpsL781868c.309T>C0.182
rpsL781871c.312G>C0.167
rpsL781892c.333A>G0.160
rpsL781898c.339A>T0.160
rpsL781916c.357T>C0.208
rpsL781929p.Gly124Ser0.200
rplC801147c.339T>C0.133
rplC801156c.348T>A0.133
rplC801171c.363A>G0.139
rplC801174c.366T>C0.139
rplC801222c.414T>C0.258
rplC801228c.420T>C0.286
rplC801246c.438C>G0.267
rplC801249c.441T>G0.294
rplC801255c.447C>T0.286
rplC801267c.459A>C0.257
rplC801270c.462T>C0.257
rplC801276c.468G>C0.235
rplC801279c.471G>C0.235
rplC801282c.474G>C0.257
rplC801301c.493C>A0.188
rplC801312c.504G>C0.188
rplC801324c.516T>C0.222
rplC801336c.528C>G0.115
rplC801341p.Leu178Gln0.125
rplC801348c.540T>G0.167
rplC801357c.549T>C0.167
rplC801367p.Ala187Thr0.143
rplC801396c.588T>C0.138
rrs1471923r.78t>c0.235
rrs1471969r.124t>c0.158
rrs1471970r.125g>a0.158
rrs1472061r.216a>t0.154
rrs1473104r.1259c>t0.214
rrs1473105r.1260g>a0.231
rrs1473123r.1278a>t0.167
rrs1473145r.1300c>t0.154
rrl1473806r.149c>t0.286
rrl1473813r.156c>t0.357
rrl1473839r.182g>t0.286
rrl1473877r.220g>a0.429
rrl1473898r.241c>t0.312
rrl1473899r.242a>c0.312
rrl1473937r.280c>t0.364
rrl1473944r.287g>a0.304
rrl1473945r.288t>c0.273
rrl1473949r.292c>t0.286
rrl1473981r.324g>t0.250
rrl1473995r.338g>t0.263
rrl1474001r.344c>t0.263
rrl1474009r.352a>g0.250
rrl1474012r.355c>t0.250
rrl1474051r.394t>c0.188
rrl1474054r.397t>c0.188
rrl1474056r.399t>c0.188
rrl1474249r.592g>t0.158
rrl1474306r.649a>c0.200
rrl1474310r.653t>g0.200
rrl1474356r.699t>c0.222
rrl1474362r.705a>g0.263
rrl1474376r.719t>c0.316
rrl1474429r.772g>c0.133
rrl1474432r.775c>g0.133
rrl1474639r.982g>a0.167
rrl1474794r.1137c>t0.286
rrl1474812r.1155g>a0.235
rrl1474823r.1166c>t0.235
rrl1474831r.1174a>g0.222
rrl1474904r.1247g>a0.286
rrl1475199r.1542g>a0.294
rrl1475206r.1549c>t0.294
rrl1475209r.1552g>c0.333
rrl1475213r.1556c>t0.263
rrl1475249r.1592t>c0.294
rrl1475252r.1595c>t0.294
rrl1475266r.1609t>c0.200
rrl1475271r.1614a>c0.190
rrl1475273r.1616t>a0.190
rrl1475275r.1618c>t0.190
rrl1475276r.1619t>c0.190
rrl1475291r.1634a>c0.238
rrl1475313r.1656g>a0.143
rrl1475638r.1981c>t0.182
rrl1475642r.1985t>c0.182
rrl1475657r.2000a>g0.231
rrl1475659r.2002g>t0.231
rrl1475881r.2224t>c0.154
rrl1476086r.2429g>a0.250
rrl1476089r.2432t>c0.250
rrl1476095r.2438c>g0.235
rrl1476106r.2449a>t0.235
rrl1476115r.2458t>c0.250
rrl1476117r.2460g>c0.250
rrl1476224r.2567a>g0.190
rrl1476281r.2624t>c0.240
rrl1476628r.2971t>a0.214
rrl1476689r.3032a>t0.222
rrl1476690r.3033c>t0.222
rrl1476693r.3036g>a0.222
rrl1476695r.3038t>a0.222
rrl1476716r.3059a>c0.286
rrl1476723r.3066t>a0.214
rrl1476725r.3068c>t0.214
rrl1476726r.3069a>g0.214
rrl1476732r.3075t>c0.214
rrl1476755r.3098g>a0.167
rrl1476770r.3113t>c0.154
fabG11673535c.96A>C0.125
fabG11673547c.108T>C0.125
fabG11673574c.135C>G0.160
fabG11673580c.141T>C0.167
fabG11673589c.150A>G0.148
fabG11673595c.156A>C0.120
fabG11673596p.Lys53Asp0.120
fabG11673607c.168T>C0.125
fabG11673610c.171C>T0.125
fabG11673616c.177A>G0.130
fabG11673619c.180T>C0.120
fabG11673633p.Ser65Asn0.179
fabG11673646c.207T>C0.172
fabG11673658c.219G>A0.148
fabG11673660p.Ala74Glu0.143
fabG11673664c.225A>G0.148
fabG11673667c.228A>G0.148
fabG11673679c.240T>G0.125
inhA1674199c.-3C>G0.130
inhA1674205p.Thr2Ala0.115
inhA1674216c.15G>C0.125
inhA1674231c.30T>C0.111
inhA1674237c.36T>C0.111
inhA1674239p.Ser13Thr0.115
inhA1674279c.78A>C0.138
inhA1674315c.114C>G0.143
inhA1674321c.120G>C0.133
inhA1674342c.141T>C0.138
inhA1674352p.Thr51Val0.143
inhA1674368p.Ala56Glu0.148
inhA1674379c.178C>T0.161
inhA1674382p.Leu61Ile0.161
inhA1674399c.198A>G0.194
inhA1674415p.Ala72Asn0.179
inhA1674419p.Ser73Thr0.172
inhA1674427p.Gly76Gln0.179
inhA1674440p.Glu80Ala0.200
inhA1674443p.Ala81Glu0.200
inhA1674450c.249G>C0.208
inhA1674452p.Ala84Glu0.217
inhA1674480c.279T>C0.387
inhA1674486c.285T>C0.400
inhA1674489c.288G>C0.400
inhA1674507c.306G>C0.471
inhA1674537c.336C>G0.520
inhA1674542p.Ala114Glu0.480
inhA1674549c.348G>C0.429
inhA1674555c.354G>A0.407
inhA1674558c.357C>A0.407
inhA1674561c.360C>T0.379
inhA1674582c.381T>C0.188
inhA1674585c.384T>C0.188
inhA1674589p.Met130Leu0.194
inhA1674624c.423A>C0.278
inhA1674627c.426T>G0.278
inhA1674630c.429C>G0.257
inhA1674636c.435C>G0.235
inhA1674654c.453G>C0.242
inhA1674693c.492C>G0.250
inhA1674703c.502T>C0.267
inhA1674718c.517A>C0.280
inhA1674732c.531C>G0.318
inhA1674741c.540C>G0.143
inhA1674742p.Lys181Pro0.143
inhA1674745p.Tyr182His0.150
inhA1674750c.549T>C0.150
inhA1674756c.555T>C0.130
inhA1674903c.702T>C0.121
inhA1674904p.Ala235Pro0.125
inhA1674909c.708G>C0.133
inhA1674915c.714C>G0.143
rpsA1833589c.48A>T0.125
rpsA1833619c.78A>C0.167
rpsA1833661c.120A>G0.222
rpsA1833667c.126C>G0.222
rpsA1833724c.183C>G0.190
rpsA1833727c.186G>C0.174
rpsA1833742c.201A>G0.212
rpsA1833745c.204G>C0.212
rpsA1833787c.246C>G0.194
rpsA1833790c.249T>A0.188
rpsA1833799c.258C>G0.171
rpsA1833811c.270G>C0.175
rpsA1833838c.297G>C0.149
rpsA1833841c.300C>G0.130
rpsA1833847c.306C>G0.130
rpsA1833856c.315A>G0.191
rpsA1833862c.321G>T0.174
rpsA1833874c.333T>C0.200
rpsA1833928c.387G>C0.275
rpsA1833940c.399C>G0.275
rpsA1833952c.411C>A0.308
rpsA1833970c.429G>C0.333
rpsA1833979c.438T>C0.343
rpsA1834000c.459G>C0.344
rpsA1834015c.474G>C0.276
rpsA1834021c.480C>T0.296
rpsA1834097c.556T>A0.182
rpsA1834102c.561T>C0.190
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C0.111
rpsA1834195c.654G>C0.111
rpsA1834222c.681T>C0.115
rpsA1834261c.720A>C0.111
rpsA1834297c.756C>G0.143
rpsA1834303c.762T>G0.150
rpsA1834348c.807T>C0.143
rpsA1834375c.834G>A0.160
rpsA1834396c.855G>C0.240
rpsA1834411c.870T>C0.269
rpsA1834417c.876G>C0.296
rpsA1834423c.882G>C0.286
rpsA1834435c.894G>C0.286
rpsA1834451c.910T>C0.300
rpsA1834465c.924T>C0.345
rpsA1834468c.927A>G0.345
rpsA1834474c.933C>G0.345
rpsA1834489c.948T>C0.321
rpsA1834498c.957C>T0.280
rpsA1834528c.987T>C0.333
rpsA1834546c.1005T>C0.350
rpsA1834555c.1014T>C0.409
rpsA1834558c.1017C>G0.381
rpsA1834606c.1065C>G0.333
rpsA1834609c.1068T>C0.357
rpsA1834622c.1081T>A0.357
rpsA1834633c.1092A>G0.400
rpsA1834639c.1098T>C0.353
rpsA1834666c.1125G>C0.273
rpsA1834669c.1128G>A0.273
rpsA1834688c.1147A>T0.200
rpsA1834726c.1185C>A0.167
rpsA1834732c.1191T>C0.167
rpsA1834733p.Ala398Pro0.176
rpsA1834753c.1212T>C0.176
rpsA1834765c.1224A>G0.188
rpsA1834780c.1239A>G0.176
rpsA1834852c.1311C>G0.231
tlyA1917943p.Ala2Ser0.158
tlyA1917951c.12T>C0.320
tlyA1917972c.33A>G1.000
tlyA1917981c.42G>C0.348
tlyA1917990c.51G>C0.348
tlyA1917993c.54A>G0.348
tlyA1917996c.57A>G0.333
tlyA1917999c.60T>C0.348
tlyA1918002c.63A>G0.348
tlyA1918015c.76T>C0.308
tlyA1918036p.Arg33Ser0.304
tlyA1918048p.Leu37Met0.250
katG2154724p.Arg463Leu1.000
katG2155572c.540C>G0.222
katG2155581c.531G>T0.267
katG2155590c.522T>C0.250
katG2155616p.Val166Ile0.211
katG2155617c.495A>G0.211
katG2155632c.480T>G0.200
katG2155637p.Leu159Ile0.200
katG2155641p.Lys157Asn0.190
katG2155677c.435G>C0.190
katG2155680c.432C>G0.182
katG2155716c.396A>G0.179
katG2155722c.390C>G0.172
katG2155742p.Gly124Gln0.172
katG2155747p.Ala122Gly0.192
katG2155782c.330G>C0.174
katG2155785c.327A>G0.174
katG2155788c.324G>A0.174
katG2155796p.Ala106Ser0.182
katG2155806c.306A>G0.182
katG2155847p.Pro89Asp0.167
kasA2518459c.345T>C0.150
kasA2518462c.348A>C0.150
kasA2518468c.354A>T0.136
kasA2518475c.361A>C0.136
kasA2518480c.366T>C0.136
kasA2518483c.369C>G0.136
kasA2518504c.390T>C0.120
kasA2518506p.Ala131Glu0.125
kasA2518519c.405G>C0.167
kasA2518528c.414C>G0.167
kasA2518540c.426T>G0.174
kasA2518561c.447T>C0.200
kasA2518567c.453G>C0.167
kasA2518570c.456G>C0.160
kasA2518574p.Ile154Val0.125
kasA2518588c.474T>C0.182
kasA2518591c.477G>C0.182
kasA2518609p.Met165Ile0.208
kasA2518621c.507G>A0.208
kasA2518642c.528A>G0.200
kasA2518663c.549T>C0.172
kasA2518672c.558G>C0.161
kasA2518687c.573C>T0.231
kasA2518696c.582C>G0.231
kasA2518702c.588C>T0.225
kasA2518711c.597A>G0.184
kasA2518714c.600A>C0.189
kasA2518717c.603C>T0.189
kasA2518732c.618C>G0.167
kasA2518741c.627G>C0.205
kasA2518747c.633C>G0.205
kasA2518768c.654C>G0.225
kasA2518783c.669T>C0.270
kasA2518792c.678C>G0.314
kasA2518795c.681C>G0.306
kasA2518816c.702C>A0.324
kasA2518822c.708C>G0.343
kasA2518825c.711T>C0.324
kasA2518855c.741C>G0.276
kasA2518864c.750G>C0.276
kasA2518879c.765A>G0.267
kasA2518885c.771T>C0.250
kasA2518888c.774C>T0.258
kasA2518898c.784T>C0.207
kasA2518906c.792A>G0.222
kasA2518910p.Leu266Met0.231
kasA2518921c.807T>C0.154
kasA2519068c.954C>T0.167
kasA2519072p.Ala320Thr0.156
kasA2519077c.963G>C0.167
kasA2519095c.981C>G0.161
kasA2519098c.984C>G0.167
kasA2519104c.990T>A0.179
kasA2519108p.Asp332Gln0.179
kasA2519111p.Gln333Glu0.179
kasA2519116c.1002C>G0.185
kasA2519125c.1011C>T0.269
kasA2519137c.1023T>C0.259
kasA2519146c.1032C>A0.267
kasA2519173c.1059C>G0.229
kasA2519176c.1062G>A0.206
kasA2519197c.1083G>C0.185
kasA2519215c.1101C>T0.148
kasA2519221c.1107G>C0.120
kasA2519225c.1111C>T0.120
ahpC2726579c.387T>C0.143
ahpC2726582c.390G>C0.143
ahpC2726591c.399C>G0.148
ahpC2726593p.Val134Ala0.154
ahpC2726600c.408T>C0.154
ahpC2726612c.420C>G0.154
ahpC2726638p.Ala149Val0.188
ahpC2726645c.453C>G0.235
ahpC2726657c.465A>C0.250
ahpC2726669p.Asp159Glu0.259
ahpC2726672c.480G>A0.259
ahpC2726675c.483A>G0.269
ahpC2726681c.489A>G0.192
ahpC2726687c.495C>G0.192
ahpC2726693c.501C>G0.167
ahpC2726696c.504C>G0.167
ahpC2726717c.525A>G0.179
ahpC2726735c.543C>T0.148
folC2747317c.282G>C0.182
folC2747355p.Val82Ile0.222
folC2747359c.240G>C0.222
folC2747362c.237C>G0.222
folC2747394p.Ile69Val0.200
folC2747395c.204A>G0.200
folC2747401c.198C>G0.192
folC2747407c.192A>G0.208
folC2747412p.Ser63Ala0.192
folC2747416c.183T>C0.200
folC2747419c.180G>C0.200
folC2747430c.169G>A0.192
folC2747439p.Met54Leu0.172
folC2747442c.157A>G0.161
thyX3067304c.642T>C0.217
thyX3067316c.630T>C0.250
thyX3067325c.621T>C0.273
thyX3067355c.591T>G0.296
thyX3067367c.579C>G0.345
thyX3067376c.570C>G0.357
thyX3067391c.555C>G0.345
thyX3067394c.552C>G0.357
thyX3067412c.534G>C0.407
thyX3067439c.507T>C0.400
thyX3067445c.501G>C0.368
thyX3067451c.495C>T0.350
thyX3067457c.489G>C0.389
thyX3067465p.Ile161Val0.312
thyX3067466c.480C>G0.312
thyX3067470p.Asn159Ser0.312
thyX3067493c.453T>C0.238
thyX3067500p.Lys149Arg0.263
thyX3067515p.Ser144Thr0.188
thyX3067601c.345C>G0.121
thyX3067604c.342C>G0.118
thyX3067610p.Lys112Asn0.128
thyX3067613c.333C>T0.125
thyX3067619c.327T>C0.136
thyX3067640c.306C>G0.190
thyX3067652c.294A>G0.190
thyX3067661c.285G>C0.195
thyX3067682c.264C>G0.225
thyX3067685c.261T>C0.225
thyX3067688c.258C>G0.211
thyX3067694c.252C>G0.184
thyX3067718c.228G>C0.135
thyX3067721c.225A>G0.135
thyX3067724c.222C>T0.135
thyX3067727c.219T>G0.139
thyX3067739c.207A>G0.132
thyX3067742c.204T>G0.143
thyX3067765p.Leu61Ile0.143
thyX3067781c.165G>C0.192
thyX3067787c.159C>T0.125
thyX3067799c.147C>T0.115
thyX3067802c.144G>C0.120
thyX3067814c.132A>G0.115
thyX3067850c.96T>G0.179
thyX3067869p.Thr26Ser0.185
thyX3067874c.72G>C0.172
thyX3067883c.63G>C0.172
thyX3067886c.60T>C0.167
thyX3067889c.57G>C0.161
thyX3067894c.52A>G0.156
thyA3073800c.672C>G0.200
thyA3073812c.660G>C0.217
thyA3073824c.648T>G0.208
thyA3073827c.645T>C0.208
thyA3073839c.633A>G0.231
thyA3073874p.Ile200Val0.226
thyA3073878c.594C>T0.219
thyA3073892c.580A>G0.143
thyA3073893c.579G>C0.143
thyA3073899c.573C>T0.179
thyA3073925c.547A>G0.167
thyA3073926c.546C>G0.167
thyA3073929c.543A>G0.167
thyA3073953c.519A>G0.226
thyA3073977c.495T>C0.226
thyA3073989c.483A>G0.200
thyA3074001c.471G>C0.167
thyA3074004c.468A>G0.172
thyA3074010c.462G>C0.172
thyA3074031c.441A>G0.300
thyA3074037c.435G>C0.303
thyA3074057p.Glu139Pro0.214
thyA3074061c.411T>C0.241
thyA3074076c.396G>C0.269
thyA3074082c.390C>G0.280
thyA3074097c.375G>C0.286
thyA3074100c.372A>G0.296
thyA3074106c.366A>G0.296
thyA3074117c.355G>A0.296
thyA3074120c.352A>G0.286
thyA3074130c.342C>G0.296
ald3086788c.-32T>C1.000
fbiA3640291c.-252T>C0.188
fbiA3640307c.-236C>A0.136
fbiA3640347c.-196A>G0.172
fbiA3640349c.-194A>G0.172
fbiA3640350c.-193C>T0.172
fbiA3640365c.-178C>G0.179
alr3841041p.Asp127Gly0.143
alr3841060p.Gly121Arg0.135
alr3841652c.-232A>T0.318
alr3841654c.-234A>C0.318
alr3841662c.-242A>G0.375
alr3841663c.-243G>A0.333
panD4044120c.162T>C0.129
panD4044123c.159A>G0.129
panD4044126c.156A>G0.133
panD4044138c.144A>G0.143
panD4044150c.132T>C0.154
panD4044162c.120T>C0.200
panD4044165c.117C>G0.208
panD4044188c.94A>G0.200
panD4044195c.87A>G0.179
panD4044213c.69G>C0.200
embC4240183c.321A>G0.172
embC4240204c.342T>C0.179
embC4240210c.348C>G0.179
embC4240216c.354T>C0.179
embC4240229p.Leu123Ile0.185
embC4240232p.Gln124Val0.185
embC4240258c.396T>G0.267
embC4240267c.405T>C0.276
embC4240270c.408T>C0.286
embC4240277p.Leu139Val0.280
embC4240282c.420C>G0.250
embC4240285c.423C>G0.261
embC4240297c.435T>C0.231
embC4240306c.444C>G0.190
embC4240444c.582C>G0.158
embC4240459c.597G>C0.167
embC4240462c.600G>C0.167
embC4240475p.Ala205Ser0.158
embC4240480c.618G>A0.200
embC4240489c.627A>G0.200
embC4240495c.633T>C0.200
embC4240512p.Ser217Thr0.154
embC4240514p.Val218Ile0.154
embC4240519c.657T>C0.143
embC4240543c.681G>C0.172
embC4240561c.699C>G0.235
embC4240573c.711G>C0.172
embC4240574p.Val238Leu0.172
embC4240578p.Ala239Val0.172
embC4240582c.720C>G0.172
embC4240585c.723C>G0.179
embC4240591c.729C>G0.219
embC4240594c.732C>G0.219
embC4240600c.738G>C0.265
embC4240632p.Met257Thr0.273
embC4240642c.780G>C0.273
embC4240645c.783G>C0.273
embC4240657c.795G>C0.312
embC4240671p.Thr270Ile0.385
embC4240678c.816T>G0.370
embC4240685p.Thr275Ala0.346
embC4240693c.831T>C0.310
embC4240706p.Val282Thr0.250
embC4240726c.864G>C0.217
embC4240780c.918T>C0.200
embC4240783c.921G>C0.200
embC4240789c.927T>C0.259
embC4240819c.957A>G0.320
embC4240831c.969T>G0.308
embC4240867c.1005T>G0.296
embC4240870c.1008T>C0.296
embC4240879c.1017G>C0.269
embC4240880p.Ala340Thr0.259
embC4240885c.1023T>C0.276
embC4240897c.1035C>G0.276
embC4240900c.1038A>G0.286
embC4240919c.1057C>T0.308
embC4240936c.1074A>G0.370
embC4240945c.1083T>C0.261
embC4240951c.1089C>G0.280
embC4240954p.Ile364Met0.269
embC4240957c.1095C>G0.269
embC4240979p.Thr373Gln0.269
embC4240983p.Ser374Asn0.304
embC4240990c.1128A>G0.280
embC4241017c.1155T>C0.222
embC4241023c.1161T>G0.241
embC4241026c.1164C>G0.250
embC4241035c.1173G>A0.214
embC4241050c.1188T>G0.207
embC4241137c.1275G>C0.121
embC4241140c.1278A>G0.129
embC4241141p.Ile427Val0.129
embC4241158c.1296T>C0.148
embC4241161c.1299C>G0.148
embC4241162c.1300T>C0.148
embC4241203c.1341T>C0.160
embC4241230c.1368A>G0.136
embC4241233c.1371G>C0.125
embC4241236c.1374C>G0.125
embC4241374c.1512T>C0.300
embC4241380c.1518A>C0.273
embC4241394p.Lys511Ser0.333
embC4241443c.1581C>G0.304
embC4241449c.1587C>G0.280
embC4241453p.Ile531Val0.261
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
embA4244366c.1134C>G0.132
embA4244372c.1140T>G0.132
embA4244378c.1146G>A0.132
embA4244885c.1653A>G0.143
embA4244897c.1665T>C0.143
embA4244900c.1668G>C0.143
embA4244903c.1671G>C0.148
embA4244919c.1687C>T0.167
embA4244933c.1701A>G0.174
embA4244945c.1713C>G0.190
embA4244948c.1716G>C0.190
embA4244960c.1728A>C0.211
embA4244980p.Val583Ala0.250
embA4244982c.1750T>C0.167
embA4244987c.1755T>C0.167
embA4244991p.Val587Leu0.167
embA4245003p.Thr591Ala0.167
embA4245038c.1806C>T0.133
embA4245137c.1905T>C0.114
embA4245431c.2199T>C0.194
embA4245461c.2229C>G0.200
embA4245465p.Pro745Ala0.200
embA4245470c.2238T>C0.207
embA4245485c.2253A>G0.188
embA4245489p.Val753Leu0.194
embA4245501p.Ala757Thr0.182
embA4245518c.2286A>G0.176
embA4245524c.2292G>C0.147
embA4245643p.Ala804Val0.167
embA4245648p.Ile806Tyr0.167
embA4245652p.Thr807Ser0.192
embA4245659c.2427C>G0.208
embA4245674c.2442A>C0.227
embA4245677c.2445G>C0.227
embA4245683c.2451C>G0.217
embA4245689c.2457C>G0.227
embA4245692c.2460G>C0.227
embA4245693p.Ile821Val0.217
embA4245701c.2469G>C0.227
embA4245725c.2493A>C0.217
embA4245726c.2494T>C0.208
embA4245737c.2505A>C0.227
embA4245740c.2508T>C0.227
embA4245764c.2532G>C0.231
embA4245771p.Asn847Tyr0.130
embA4245807c.2575T>C0.172
embA4245820p.Ser863Thr0.172
embA4245830c.2598G>C0.226
embA4245845c.2613T>G0.212
embA4245848c.2616C>G0.206
embA4245860c.2628C>G0.212
embA4245885p.Asp885Thr0.222
embA4245892p.Ile887Thr0.231
embA4245905c.2673C>G0.250
embA4245926c.2694C>G0.130
embA4245927p.Thr899Ala0.125
embA4245983c.2751A>C0.125
embA4245989c.2757A>G0.130
embA4245992c.2760C>G0.136
embA4246010c.2778G>C0.182
embA4246013c.2781T>C0.182
embA4246041p.Asp937Asn0.154
embA4246055c.2823T>C0.160
embA4246250c.3018G>C0.261
embA4246264p.His1011Arg0.261
embA4246274c.3042G>C0.231
embA4246292c.3060A>G0.259
embA4246316c.3084T>G0.222
embA4246329p.Thr1033Leu0.211
embA4246355c.3123G>C0.200
embA4246359p.Ala1043Pro0.171
embA4246364c.3132G>C0.171
embA4246367c.3135C>T0.171
embA4246373c.3141T>C0.182
embA4246376c.3144G>C0.182
embB4247317c.804G>C0.364
embB4247326c.813A>G0.364
embB4247328p.Ser272Asn0.364
embB4247338c.825C>G0.333
embB4247348p.Thr279Ala0.308
embB4247355p.Ala281Val0.286
embB4247358p.Val282Ala0.286
embB4247365c.852A>C0.375
embB4247371c.858C>G0.375
embB4247375p.Leu288Val0.375
embB4247380c.867C>T0.375
embB4247386c.873T>C0.353
embB4247389c.876C>G0.333
embB4247395c.882C>G0.353
embB4247401c.888T>C0.316
embB4247437c.924A>G0.316
embB4247440c.927C>G0.294
embB4247464c.951C>G0.200
embB4247470c.957T>C0.211
embB4247491c.978G>C0.190
embB4247497c.984T>C0.200
embB4247500c.987C>G0.200
embB4247536c.1023C>G0.167
embB4247554c.1041T>C0.188
embB4247746c.1233C>A0.174
embB4247776c.1263G>T0.214
embB4247779c.1266C>G0.219
embB4247785c.1272G>C0.233
embB4247800c.1287A>C0.233
embB4247806c.1293G>C0.241
embB4247819p.Val436Ile0.161
embB4247824c.1311C>G0.179
embB4247830c.1317A>C0.185
embB4247836c.1323A>G0.172
embB4247842c.1329T>C0.161
embB4247876c.1363C>T0.172
embB4247881c.1368G>C0.138
embB4247887c.1374C>T0.133
embB4247890c.1377C>T0.129
embB4247899p.Met462Ile0.118
embB4248035p.Val508Ile0.130
embB4248041p.Ala510Thr0.143
embB4248044p.Lys511Ala0.136
embB4248052c.1539G>A0.176
embB4248055c.1542G>C0.188
embB4248064c.1551G>C0.200
embB4248070c.1557T>C0.176
embB4248085c.1572T>C0.227
embB4248097c.1584C>G0.208
embB4248118c.1605T>C0.222
embB4248127c.1614G>C0.192
embB4248133c.1620C>G0.148
embB4248142c.1629T>C0.148
embB4248143c.1630T>C0.148
embB4248157c.1644A>G0.148
embB4248206p.Ser565Gly0.125
embB4248220c.1707A>G0.167
embB4248241c.1728C>T0.130
embB4248265c.1752C>T0.143
embB4248266c.1753C>T0.143
embB4248277c.1764G>C0.217
embB4248304c.1791G>C0.238
embB4248316c.1803C>G0.250
embB4248319c.1806A>G0.250
embB4248322c.1809G>C0.250
embB4248343c.1830G>C0.167
embB4248346c.1833G>C0.150
embB4248350c.1837T>C0.158
embB4248355c.1842A>G0.150
embB4248358c.1845C>G0.150
embB4248361c.1848A>G0.158
embB4248362p.Ser617Ala0.158
embB4249276c.2763A>G0.161
embB4249282c.2769A>C0.167
embB4249297c.2784G>C0.161
embB4249321c.2808A>C0.179
embB4249322p.Ala937Ser0.179
embB4249325p.Lys938Asp0.179
embB4249336c.2823C>G0.185
embB4249339c.2826T>C0.185
embB4249340p.Ala943Thr0.185
embB4249345c.2832C>G0.161
embB4249348c.2835G>C0.167
embB4249351c.2838C>G0.172
embB4249369c.2856T>C0.222
embB4249381c.2868A>G0.240
embB4249469p.Leu986Met0.121
embB4249486c.2973T>G0.125
embB4249487c.2974T>C0.125
embB4249521p.Ala1003Val0.161
embB4249525c.3012T>C0.152
embB4249528c.3015C>G0.152
embB4249529p.Ile1006Val0.152
embB4249532p.Ala1007Thr0.147
embB4249537c.3024A>G0.152
embB4249543c.3030G>C0.167
embB4249558c.3045A>C0.179
embB4249564c.3051C>T0.192
embB4249568p.Ser1019Thr0.227
embB4249573c.3060T>C0.190
embB4249580p.Leu1023Met0.190
embB4249594c.3081G>C0.182
embB4249600c.3087A>G0.130
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

AnalysisProgram
Mappingbwa
Variant CallingBCFtools


Log

Drug Details
The estimated accuracy of drug resistance predictions is:

Drug1Sensitivity (%)Specificity (%)
Isoniazid 92.8 (89.9-95.7)100 (100-100)
Rifampicin 96.2 (93.9-98.5)98.1 (96.8-99.4)
Ethambutal 88.7 (83.6-93.8)81.7 (77.6-85.8)
Pyrazinamide70.9 (62.4-79.4)93.9 (90.6-97.2)
Streptomycin87.1 (82.7-91.5)89.7 (86.0-93.4)
Ethionamide 73.6 (66.7-80.5)93.3 (89.6-97.0)
Moxifloxacin60.0 (29.6-90.4)68.7 (52.6-84.8)
Ofloxacin 85.5 (79.1-91.9)94.9 (91.8-98.0)
Amikacin 82.9 (74.4-91.4)98.3 (96.0-100)
Capreomycin 60.7 (50.6-70.8)90.7 (87.2-94.2)
Kanamycin 87.3 (81.3-93.3)93.4 (89.9-96.9)
Para-aminosalisylic acidNot determinedNot determined
Linezolid Not determinedNot determined
Clofazimine Not determinedNot determined
Bedaquiline Not determinedNot determined
Multi drug resistance91.2 (87.8-94.6)98.4 (97.2-99.6)
Extremely drug resistance75.9 (64.5-87.3)98.4 (97.3-99.5)

Lineages
Lineage2LocationStrainRD type
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.1.1.1Indo-OceanicEAI4;ZERORD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239
lineage1.1.3Indo-OceanicEAI6RD239
lineage1.2Indo-OceanicEAI1;EAI2RD239
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.2.2Indo-OceanicEAI1RD239
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.2East-Asian (Beijing)Beijing-RD142RD105;RD207;RD181;RD142
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.1East-African-IndianCAS1-KiliRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage3.1.2.1East-African-IndianCAS2RD750
lineage3.1.2.2East-African-IndianCASRD750
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage4.1.1.2Euro-American (X-type)X1None
lineage4.1.1.1Euro-American (X-type)X2RD183
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone
lineage4.2.2.1Euro-AmericanLAM7-TURNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.1Euro-American (LAM)LAM9None
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174
lineage4.3.2Euro-American (LAM)LAM3None
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None
lineage4.4.1.1Euro-AmericanS;OrphansNone
lineage4.5Euro-AmericanH;TRD122
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-American T2-UgandaRD724
lineage4.6.1.2Euro-AmericanT2RD724
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.1Euro-AmericanT3RD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.9Euro-American (H37Rv-like)T1None
lineage5West-Africa 1AFRI_2;AFRI_3RD711
lineage6West-Africa 2AFRI_1RD702
lineage7Lineage 7NoneNone
lineageBOVM. bovisBOV_1;BOV_2None

Citations
1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer
This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.
© 2019 London School of Hygiene and Tropical Medicine;