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.
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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: 5d807cf0aa809
Sample: 5d807cf0aa809

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Summary
ID: 5d807cf0aa809
Date: Tue Sep 17 07:34:44 2019
Strain: lineage2.2.1;lineage4.3;lineage4.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRfabG1 c.-8T>C (1.00)
RifampicinRrpoB p.Asp435Val (0.77)
EthambutolRembB p.Ala659Thr (0.12)
Pyrazinamide
StreptomycinRrrs r.462c>t (0.26)
EthionamideRfabG1 c.-8T>C (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

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

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6100c.861G>C0.110
gyrB6115c.876A>G0.104
gyrB6123p.Ala295Gly0.107
gyrB6127c.888G>C0.111
gyrB6130c.891T>C0.113
gyrB6136c.897G>A0.151
gyrB6139c.900G>C0.149
gyrB6196c.957C>T0.137
gyrB6307c.1068T>G0.123
gyrB6319c.1080G>C0.139
gyrB6362c.1123T>C0.186
gyrB6376c.1137G>A0.158
gyrB6379c.1140C>G0.167
gyrB6382c.1143A>G0.164
gyrB6388c.1149T>C0.164
gyrB6403c.1164T>C0.154
gyrB6415c.1176G>C0.130
gyrB6670c.1431G>C0.127
gyrB6673c.1434A>C0.125
gyrB6676c.1437T>G0.122
gyrB6700c.1461T>C0.167
gyrB6703c.1464G>C0.175
gyrB6709c.1470A>G0.173
gyrB6712c.1473G>C0.173
gyrB6728c.1489C>T0.192
gyrB6742c.1503A>G0.208
gyrB6745c.1506T>G0.211
gyrB6751c.1512G>C0.211
gyrB6760c.1521G>C0.232
gyrB6763c.1524G>C0.260
gyrB6775c.1536G>C0.266
gyrB6793c.1554T>C0.212
gyrB6797p.Gly520Thr0.171
gyrB6811c.1572C>T0.174
gyrB6949c.1710A>G0.118
gyrB6952c.1713C>G0.130
gyrB6967c.1728T>C0.179
gyrB6973c.1734G>C0.181
gyrB6982c.1743A>C0.200
gyrB7007c.1768C>T0.188
gyrB7010c.1771C>T0.186
gyrB7023p.Leu595Gln0.163
gyrB7033c.1794G>C0.172
gyrB7051p.Glu604Asp0.182
gyrB7066c.1827G>C0.163
gyrB7078c.1839A>C0.165
gyrB7084c.1845A>G0.163
gyrB7090c.1851C>T0.158
gyrB7093c.1854T>G0.147
gyrB7099c.1860G>A0.147
gyrB7108c.1869G>A0.120
gyrB7114c.1875C>A0.120
gyrB7141c.1902T>C0.131
gyrB7165c.1926C>G0.165
gyrB7178c.1939T>C0.169
gyrB7186c.1947C>G0.183
gyrB7216c.1977G>C0.158
gyrB7228c.1989C>T0.135
gyrB7234c.1995C>T0.127
gyrB7246c.2007T>C0.103
gyrB7252c.2013G>C0.116
gyrA7349c.48A>G0.108
gyrA7361c.60C>T0.123
gyrA7362p.Glu21Gln1.000
gyrA7391c.90C>T0.153
gyrA7394c.93T>C0.165
gyrA7427c.126G>C0.193
gyrA7442c.141G>C0.180
gyrA7451c.150C>G0.188
gyrA7457c.156T>C0.193
gyrA7475c.174A>G0.167
gyrA7480p.Phe60Tyr0.153
gyrA7484c.183T>C0.157
gyrA7514c.213C>G0.143
gyrA7523c.222C>A0.135
gyrA7532c.231T>C0.145
gyrA7541c.240C>G0.107
gyrA7547c.246C>T0.111
gyrA7585p.Ser95Thr1.000
gyrA7673c.372G>A0.113
gyrA7683c.382A>C0.128
gyrA7694c.393A>G0.133
gyrA7697c.396C>G0.133
gyrA7710c.409T>C0.133
gyrA7721c.420G>A0.139
gyrA7725c.424C>T0.141
gyrA7728c.427A>C0.143
gyrA7739c.438C>T0.181
gyrA7763c.462T>C0.213
gyrA7784c.483A>G0.184
gyrA7793c.492G>C0.171
gyrA7796c.495G>C0.169
gyrA7799c.498A>G0.191
gyrA7814c.513C>G0.167
gyrA7823c.522G>C0.134
gyrA8090c.789C>A0.113
gyrA8096c.795T>A0.140
gyrA8099c.798T>C0.129
gyrA8106c.805C>T0.143
gyrA8111c.810G>C0.164
gyrA8121c.820T>C0.203
gyrA8129c.828T>C0.219
gyrA8135c.834C>G0.219
gyrA8156c.855T>C0.205
gyrA8168c.867A>G0.195
gyrA8177c.876A>C0.190
gyrA8189c.888G>C0.213
gyrA8198c.897T>C0.211
gyrA8207c.906T>C0.215
gyrA8219c.918T>C0.211
gyrA8225c.924T>C0.203
gyrA8234c.933T>C0.162
gyrA8237c.936A>G0.157
gyrA8247p.Ile316Val0.161
gyrA8324c.1023T>C0.109
gyrA8420c.1119T>C0.125
gyrA8453c.1152A>C0.167
gyrA8459c.1158G>A0.125
gyrA8462c.1161A>C0.121
gyrA8465c.1164C>G0.116
gyrA8471c.1170T>C0.119
gyrA8472c.1171C>T0.121
gyrA8480c.1179C>A0.110
gyrA8486c.1185T>C0.113
gyrA8489c.1188A>G0.114
gyrA8504c.1203G>C0.114
gyrA8516c.1215T>C0.116
gyrA8519c.1218A>C0.116
gyrA8520c.1219C>T0.118
gyrA8528c.1227G>C0.118
gyrA8767p.Arg489Lys0.119
gyrA8780p.Asp493Glu0.130
gyrA8786c.1485T>C0.135
gyrA8801c.1500G>C0.149
gyrA8807c.1506C>T0.149
gyrA8810c.1509A>G0.179
gyrA8818p.Ser506Asn0.186
gyrA8828c.1527T>C0.186
gyrA8829c.1528T>C0.183
gyrA8852c.1551T>C0.215
gyrA8858c.1557T>C0.212
gyrA8867c.1566A>G0.203
gyrA8870c.1569G>C0.203
gyrA8873c.1572A>C0.218
gyrA8891c.1590G>A0.195
gyrA8897c.1596T>C0.200
gyrA8903c.1602T>C0.184
gyrA8933c.1632G>C0.165
gyrA8946c.1645T>C0.141
gyrA9089c.1788G>C0.103
gyrA9099c.1798T>C0.116
gyrA9104c.1803C>G0.110
gyrA9119c.1818A>G0.123
gyrA9122c.1821C>A0.120
gyrA9143c.1842T>C0.136
gyrA9153p.Thr618Glu0.128
gyrA9158c.1857C>T0.126
gyrA9161c.1860C>G0.125
gyrA9182c.1881T>C0.184
gyrA9191c.1890G>C0.189
gyrA9200c.1899A>G0.223
gyrA9204p.Ser635Thr0.221
gyrA9218c.1917C>T0.219
gyrA9227c.1926C>G0.153
gyrA9230c.1929T>C0.155
gyrA9233c.1932C>G0.156
gyrA9267p.Asn656Gly0.243
gyrA9293c.1992G>C0.242
gyrA9296c.1995T>C0.239
gyrA9299c.1998G>C0.239
gyrA9304p.Gly668Glu1.000
gyrA9308c.2007C>T0.241
gyrA9317c.2016G>T0.258
gyrA9323c.2022C>G0.235
gyrA9335c.2034G>C0.209
gyrA9345c.2044A>C0.185
gyrA9365c.2064G>A0.152
gyrA9374c.2073G>C0.132
gyrA9377c.2076A>G0.114
gyrA9383c.2082T>C0.114
rpoB759573c.-234T>C0.127
rpoB759624c.-183G>A0.149
rpoB759644c.-163T>A0.111
rpoB759647c.-160T>C0.108
rpoB760079c.273G>A0.115
rpoB760091c.285G>C0.148
rpoB760101c.295T>C0.148
rpoB760112c.306T>C0.161
rpoB760118c.312T>G0.161
rpoB760130p.Asp108Glu0.177
rpoB760139c.333A>G0.197
rpoB760142c.336C>G0.197
rpoB760181c.375T>C0.241
rpoB760184c.378A>G0.231
rpoB760196c.390C>G0.220
rpoB760223c.417T>C0.237
rpoB760235c.429T>C0.266
rpoB760253c.447T>C0.262
rpoB760283c.477G>C0.250
rpoB760307c.501T>C0.234
rpoB760310c.504G>C0.224
rpoB760313c.507G>C0.224
rpoB760340c.534G>C0.250
rpoB760343c.537G>C0.241
rpoB760361c.555T>C0.200
rpoB760376p.Asp190Glu0.183
rpoB760380p.Thr192Leu0.173
rpoB760406c.600G>C0.167
rpoB760424c.618C>G0.167
rpoB760430c.624T>C0.175
rpoB760475c.669A>G0.263
rpoB760481c.675G>C0.247
rpoB760484c.678A>G0.237
rpoB760522p.Ser239Asn0.258
rpoB760532c.726T>C0.236
rpoB760533p.Val243His0.227
rpoB760547c.741G>C0.258
rpoB760567p.Ser254Trp0.239
rpoB760591p.Val262Ala0.288
rpoB760611c.805T>C0.221
rpoB760634c.828T>C0.215
rpoB760646c.840C>G0.230
rpoB760655c.849A>G0.246
rpoB760661c.855A>C0.254
rpoB760670c.864G>C0.232
rpoB760674c.868T>C0.232
rpoB760679c.873A>G0.222
rpoB760683c.877T>C0.232
rpoB760724c.918T>C0.206
rpoB760730c.924T>C0.203
rpoB760748c.942C>G0.167
rpoB760751c.945G>C0.167
rpoB760757c.951T>C0.172
rpoB760759p.Val318Ala0.169
rpoB760769c.963C>G0.169
rpoB760781c.975G>C0.141
rpoB760793c.987A>G0.111
rpoB760862c.1056G>C0.110
rpoB760869p.Val355Ile0.141
rpoB760886c.1080A>G0.164
rpoB760919c.1113C>G0.243
rpoB760925c.1119T>C0.241
rpoB760928c.1122G>C0.244
rpoB760946c.1140A>G0.280
rpoB760970c.1164G>C0.286
rpoB760973c.1167G>C0.282
rpoB760991c.1185G>C0.269
rpoB761015c.1209G>C0.266
rpoB761027c.1221A>G0.278
rpoB761036c.1230G>C0.241
rpoB761037c.1231T>C0.235
rpoB761060c.1254C>G0.258
rpoB761096c.1290G>C0.211
rpoB761097c.1291A>T0.211
rpoB761102c.1296A>G0.209
rpoB761132c.1326G>T0.196
rpoB761133c.1327T>C0.209
rpoB761150c.1344A>C0.193
rpoB761165c.1359G>C0.158
rpoB761168c.1362C>G0.152
rpoB761180c.1374A>C0.179
rpoB761189c.1383T>G0.180
rpoB761195c.1389G>C0.149
rpoB761198c.1392G>C0.136
rpoB761204c.1398C>G0.149
rpoB761249c.1443A>G0.158
rpoB761255c.1449T>G0.167
rpoB761261c.1455G>T0.179
rpoB761273c.1467T>C0.194
rpoB761327c.1521A>G0.206
rpoB761345c.1539G>C0.198
rpoB761354c.1548C>T0.188
rpoB761360c.1554T>C0.191
rpoB761362p.Ser519Thr0.185
rpoB761373p.Val523His0.178
rpoB761408c.1602G>C0.202
rpoB761414c.1608A>G0.195
rpoB761423c.1617T>C0.184
rpoB761435c.1629T>C0.147
rpoB761439p.Asp545Ser0.142
rpoB761444c.1638T>C0.136
rpoB761447c.1641C>G0.138
rpoB761452p.Val549Glu0.140
rpoB761457p.Pro551Ser0.139
rpoB761477c.1671C>G0.274
rpoB761483c.1677G>C0.275
rpoB761492c.1686G>C0.256
rpoB761504c.1698C>G0.240
rpoB761510c.1704T>C0.235
rpoB761531c.1725C>G0.195
rpoB761537c.1731C>G0.213
rpoB761564c.1758G>C0.267
rpoB761570c.1764T>C0.262
rpoB761573c.1767C>G0.250
rpoB761579c.1773G>C0.246
rpoB761606c.1800C>G0.237
rpoB761612c.1806G>C0.217
rpoB761615c.1809A>C0.192
rpoB761636c.1830G>C0.184
rpoB761645c.1839C>G0.192
rpoB761648c.1842T>C0.198
rpoB761657c.1851C>G0.204
rpoB761675c.1869G>C0.209
rpoB761682c.1876C>T0.207
rpoB761690c.1884G>C0.188
rpoB761705c.1899C>T0.139
rpoB761873c.2067A>G0.138
rpoB761885c.2079T>C0.143
rpoB761891c.2085G>C0.144
rpoB761906c.2100C>G0.120
rpoB761909c.2103T>C0.111
rpoB761912c.2106T>C0.112
rpoB761915p.Asp703Glu0.112
rpoB761916p.Asp704Asn0.111
rpoB761948c.2142G>C0.202
rpoB761954c.2148C>G0.221
rpoB761999c.2193G>C0.159
rpoB762053c.2247T>C0.125
rpoB762083c.2277T>C0.132
rpoB762086c.2280G>C0.115
rpoB762114p.Ile770Val0.110
rpoB762122c.2316C>T0.113
rpoB762131c.2325C>G0.110
rpoB762140c.2334G>C0.158
rpoB762143c.2337T>C0.158
rpoB762149c.2343G>C0.143
rpoB762158c.2352G>C0.143
rpoB762167c.2361T>C0.125
rpoB762176c.2370T>C0.124
rpoB762185c.2379G>C0.136
rpoB762233c.2427G>C0.146
rpoB762248c.2442G>C0.190
rpoB762254c.2448T>G0.192
rpoB762257c.2451C>G0.208
rpoB762266c.2460T>C0.200
rpoB762293c.2487T>C0.198
rpoB762317c.2511A>G0.204
rpoB762329c.2523G>C0.205
rpoB762338c.2532T>C0.193
rpoB762347c.2541T>C0.180
rpoB762362p.Glu852Asp0.174
rpoB762369c.2563T>C0.165
rpoB762380c.2574T>C0.188
rpoB762389c.2583G>A0.160
rpoB762434c.2628T>C0.148
rpoB762446c.2640C>G0.152
rpoB762486p.Pro894Ala0.171
rpoB762489p.Val895Gln0.169
rpoB762509c.2703T>G0.156
rpoB762510p.Ala902Pro0.154
rpoB762521c.2715C>G0.160
rpoB762533c.2727T>C0.155
rpoB762536c.2730T>C0.162
rpoB762537c.2731T>C0.162
rpoB762551c.2745C>G0.164
rpoB762701c.2895T>C0.161
rpoB762704c.2898G>C0.170
rpoB762730p.Gln975Arg0.220
rpoB762737c.2931C>G0.233
rpoB762749c.2943C>G0.239
rpoB762753c.2947T>C0.241
rpoB762758c.2952G>C0.241
rpoB762770c.2964C>G0.222
rpoB762776c.2970C>G0.141
rpoB762780p.Gly992Asn0.141
rpoB762785p.Asp993Glu0.136
rpoB762789p.Leu995Met0.143
rpoB762799p.Ala998Gly0.207
rpoB762812c.3006C>G0.179
rpoB762813p.Met1003Val0.175
rpoB762818c.3012C>G0.177
rpoB762827c.3021G>C0.192
rpoB762836c.3030C>T0.200
rpoB762857c.3051C>G0.145
rpoB762860c.3054G>C0.147
rpoB762863c.3057T>C0.152
rpoB762929c.3123G>C0.153
rpoB762962c.3156C>T0.133
rpoB762995c.3189G>C0.146
rpoB763028c.3222T>C0.120
rpoB763031c.3225T>C1.000
rpoB763034c.3228C>A0.133
rpoB763040c.3234C>G0.143
rpoB763070c.3264T>C0.177
rpoB763085c.3279C>G0.180
rpoB763115c.3309T>C0.197
rpoB763127c.3321G>C0.162
rpoB763169c.3363A>G0.224
rpoB763187c.3381C>G0.213
rpoB763202c.3396A>C0.155
rpoB763206c.3400A>T0.161
rpoB763214c.3408T>C0.175
rpoB763238c.3432T>C0.206
rpoB763253c.3447G>C0.200
rpoB763272c.3466C>T0.206
rpoB763283c.3477T>C0.164
rpoC763351c.-19T>C0.164
rpoC763352c.-18T>A0.164
rpoC763402c.33C>T0.177
rpoC763408c.39T>C0.169
rpoC763411c.42T>G0.159
rpoC763414c.45T>C0.175
rpoC763441c.72C>T0.147
rpoC763444c.75T>C0.162
rpoC763456c.87A>G0.153
rpoC763486c.117T>C0.187
rpoC763504c.135C>G0.167
rpoC763528c.159G>A0.179
rpoC763546c.177A>G0.165
rpoC763570c.201G>C0.207
rpoC763573c.204G>C0.224
rpoC763594c.225C>T0.200
rpoC763633c.264T>C0.182
rpoC763636c.267T>G0.171
rpoC763657c.288G>A0.177
rpoC763660c.291T>G0.179
rpoC763666c.297G>C0.200
rpoC763675c.306C>G0.189
rpoC763696c.327T>C0.197
rpoC763708c.339G>C0.157
rpoC763714c.345G>C0.143
rpoC763717c.348T>C0.143
rpoC763723c.354G>C0.136
rpoC763729c.360G>C0.156
rpoC763741c.372C>T0.153
rpoC763744c.375G>C0.153
rpoC763765c.396T>G0.197
rpoC763768c.399C>G0.231
rpoC763774c.405G>C0.219
rpoC763780c.411C>G0.225
rpoC763792p.Glu141Asp0.207
rpoC763801c.432C>G0.202
rpoC763807c.438T>C0.195
rpoC763813c.444C>G0.189
rpoC763835p.Ala156Met0.217
rpoC763855c.486C>T0.184
rpoC763858c.489A>G0.184
rpoC763872p.Gly168Ala0.152
rpoC763876p.Glu169Asp0.148
rpoC763879c.510A>G0.159
rpoC763888c.519G>C0.136
rpoC763891c.522G>C0.132
rpoC763894c.525A>G0.134
rpoC763960c.591T>G0.120
rpoC763991p.Ile208Leu0.129
rpoC763996c.627T>G0.146
rpoC764005c.636G>C0.167
rpoC764011c.642T>C0.167
rpoC764024c.655T>C0.193
rpoC764040p.Ser224Asn0.200
rpoC764044c.675T>C0.198
rpoC764059c.690G>C0.216
rpoC764083c.714A>G0.267
rpoC764098c.729A>G0.250
rpoC764110c.741C>T0.234
rpoC764131c.762T>C0.225
rpoC764188c.819A>G0.257
rpoC764194p.Glu275Asp0.268
rpoC764203c.834G>T0.257
rpoC764206c.837T>C0.274
rpoC764215c.846A>G0.250
rpoC764257c.888G>C0.184
rpoC764266c.897T>C0.169
rpoC764269c.900G>C0.165
rpoC764272c.903G>C0.165
rpoC764278c.909A>G0.165
rpoC764287c.918C>T0.170
rpoC764293c.924G>C0.135
rpoC764344c.975C>G0.127
rpoC764365c.996C>T0.138
rpoC764446c.1077T>C0.107
rpoC764449c.1080G>C0.110
rpoC764452c.1083T>C0.113
rpoC764458c.1089G>C0.105
rpoC764461c.1092A>G0.104
rpoC764497c.1128A>G0.145
rpoC764503c.1134G>C0.133
rpoC764521c.1152T>C0.156
rpoC764536c.1167G>C0.152
rpoC764539c.1170C>G0.154
rpoC764575c.1206T>G0.159
rpoC764578c.1209C>G0.176
rpoC764585c.1216C>T0.173
rpoC764611c.1242G>C0.203
rpoC764626c.1257C>T0.177
rpoC764632c.1263T>C0.190
rpoC764644c.1275G>C0.182
rpoC764650c.1281G>T0.205
rpoC764695c.1326T>G0.167
rpoC764716c.1347G>C0.152
rpoC764749c.1380G>C0.149
rpoC764752c.1383G>C0.149
rpoC764764c.1395T>C0.130
rpoC764815c.1446A>G0.145
rpoC764824c.1455T>C0.123
rpoC764827c.1458G>C0.118
rpoC764830c.1461C>G0.122
rpoC764858c.1489T>C0.141
rpoC764888c.1519T>C0.169
rpoC764893c.1524T>C0.186
rpoC764911c.1542A>G0.205
rpoC764923c.1554A>G0.176
rpoC764948c.1579T>C0.165
rpoC764962c.1593G>C0.157
rpoC764968c.1599T>C0.155
rpoC764983c.1614T>C0.171
rpoC764995c.1626C>G0.174
rpoC765007c.1638T>G0.158
rpoC765008c.1639T>C0.158
rpoC765016c.1647C>G0.158
rpoC765019c.1650A>G0.158
rpoC765034c.1665T>G0.138
rpoC765073c.1704G>C0.148
rpoC765076c.1707A>G0.145
rpoC765079c.1710T>G0.163
rpoC765085c.1716T>C0.143
rpoC765089c.1720T>C0.143
rpoC765103c.1734G>T0.146
rpoC765412c.2043T>C0.127
rpoC765421c.2052C>G0.159
rpoC765478c.2109T>C0.234
rpoC765499c.2130C>G0.274
rpoC765541c.2172C>G0.236
rpoC765553c.2184C>T0.194
rpoC765556c.2187G>C0.187
rpoC765559c.2190G>C0.184
rpoC765583c.2214G>T0.178
rpoC765625c.2256C>G0.120
rpoC765631p.Asp754Glu0.135
rpoC765658c.2289C>T0.152
rpoC765700c.2331T>C0.194
rpoC765734c.2365T>C0.174
rpoC765739c.2370G>C0.169
rpoC765751c.2382C>G0.171
rpoC765752p.Asp795Ser0.169
rpoC765772c.2403C>G0.187
rpoC765784c.2415C>G0.167
rpoC765796c.2427C>T0.141
rpoC765811c.2442T>C0.113
rpoC765814c.2445A>G0.123
rpoC765826c.2457T>C0.123
rpoC765883c.2514C>G0.279
rpoC765886c.2517C>G0.276
rpoC765892c.2523T>C0.314
rpoC765928c.2559C>G0.308
rpoC765937c.2568T>C0.342
rpoC765947c.2578T>C0.342
rpoC765967c.2598C>T0.312
rpoC765979c.2610C>G0.269
rpoC765982c.2613C>T0.275
rpoC765994c.2625A>T0.300
rpoC766010c.2641T>A0.258
rpoC766027c.2658G>C0.220
rpoC766043p.Gln892Glu0.163
rpoC766061p.Val898Leu0.182
rpoC766081c.2712T>C0.168
rpoC766082p.Ala905Gln0.167
rpoC766129c.2760C>G0.189
rpoC766141c.2772C>T0.167
rpoC766142c.2773C>T0.167
rpoC766168c.2799C>G0.153
rpoC766178p.Ile937Val0.163
rpoC766185p.Glu939Ala0.125
rpoC766189c.2820T>C0.125
rpoC766192c.2823T>C0.125
rpoC766193p.Gln942Glu0.123
rpoC766207c.2838T>C0.190
rpoC766216c.2847T>C0.182
rpoC766226c.2857T>C0.128
rpoC766231c.2862T>G0.117
rpoC766234c.2865T>G0.113
rpoC766237c.2868T>C0.103
rpoC766240c.2871T>C0.115
rpoC766243c.2874C>G0.134
rpoC766258c.2889T>C0.195
rpoC766273c.2904T>C0.182
rpoC766274p.Ala969Thr0.180
rpoC766279c.2910C>G0.180
rpoC766280p.Ser971Gly0.180
rpoC766300c.2931C>G0.235
rpoC766312c.2943T>G0.255
rpoC766321c.2952C>G0.266
rpoC766345c.2976T>C0.245
rpoC766348c.2979A>G0.245
rpoC766357c.2988C>T0.220
rpoC766363c.2994G>C0.220
rpoC766369c.3000C>G0.220
rpoC766381c.3012C>T0.186
rpoC766384c.3015A>G0.214
rpoC766387c.3018C>G0.212
rpoC766393c.3024C>G0.202
rpoC766402c.3033C>G0.188
rpoC766408c.3039C>T0.176
rpoC766426c.3057C>T0.197
rpoC766447c.3078T>C0.188
rpoC766456c.3087C>G0.179
rpoC766471c.3102G>C0.171
rpoC766486c.3117A>G0.237
rpoC766492c.3123T>C0.219
rpoC766522c.3153C>G0.207
rpoC766528c.3159T>C0.179
rpoC766530p.Arg1054Gln0.179
rpoC766573c.3204T>C0.229
rpoC766579c.3210C>T0.210
rpoC766582c.3213C>G0.210
rpoC766583p.Gly1072Ser0.207
rpoC766591c.3222A>G0.209
rpoC766594c.3225G>C0.200
rpoC766607p.Ile1080Leu0.242
rpoC766630c.3261G>T0.253
rpoC766633c.3264G>C0.256
rpoC766645c.3276A>G0.261
rpoC766651c.3282T>G0.270
rpoC766657c.3288A>G0.272
rpoC766666c.3297C>G0.264
rpoC766672c.3303T>C0.273
rpoC766708c.3339A>G0.289
rpoC766726c.3357T>C0.256
rpoC766738c.3369G>C0.247
rpoC766750c.3381C>G0.238
rpoC766765c.3396A>C0.228
rpoC766774c.3405T>C0.235
rpoC766804c.3435A>G0.193
rpoC766861c.3492G>C0.205
rpoC766864c.3495G>C0.224
rpoC766894c.3525T>C0.239
rpoC766895c.3526T>C0.239
rpoC766900c.3531T>C0.241
rpoC766933c.3564A>G0.205
rpoC766942c.3573C>T0.211
rpoC766945c.3576A>G0.208
rpoC766963c.3594T>C0.237
rpoC766972c.3603G>C0.214
rpoC766996c.3627C>T0.224
rpoC767035c.3666G>C0.173
rpoC767059c.3690T>G0.165
rpoC767062c.3693C>A0.163
rpoC767098c.3729T>C0.163
rpoC767119c.3750A>G0.129
rpoC767134c.3765C>A0.107
rpoC767180p.Ala1271Gln0.116
rpoC767191c.3822C>G0.125
rpoC767206c.3837C>G0.154
rpoC767209c.3840T>C0.159
rpoC767212c.3843G>C0.159
rpoC767221c.3852C>G0.168
rpoC767230c.3861G>C0.168
rpoC767233c.3864T>C0.174
rpoC767263c.3894T>C0.148
rpoC767264p.Ala1299Gln0.146
rpoC767275c.3906T>C0.150
rpoC767278c.3909T>C0.148
rpoC767281c.3912C>G0.146
rpoC767284c.3915C>G0.143
rpsL781395c.-165T>C1.000
rpsL781571c.12C>T0.188
rpsL781595c.36T>C0.232
rpsL781605p.Ile16Val0.232
rpsL781608p.Ser17Ala0.239
rpsL781628c.69T>C0.282
rpsL781631c.72G>C0.286
rpsL781649c.90T>C0.268
rpsL781655c.96T>C0.272
rpsL781700c.141G>C0.178
rpsL781703c.144G>T0.185
rpsL781715c.156T>C0.196
rpsL781728c.169T>C0.205
rpsL781736c.177T>C0.189
rpsL781742c.183C>T0.178
rpsL781748c.189C>G0.176
rpsL781754c.195G>C0.156
rpsL781760c.201T>C0.157
rpsL781772c.213C>A0.134
rpsL781808c.249C>T0.156
rpsL781811c.252C>T0.162
rpsL781832c.273T>G0.186
rpsL781838c.279G>C0.200
rpsL781841c.282C>G0.187
rpsL781865c.306G>C0.174
rpsL781868c.309T>C0.179
rpsL781871c.312G>C0.169
rpsL781877c.318T>C0.203
rpsL781892c.333A>G0.263
rpsL781898c.339A>T0.259
rpsL781916c.357T>C0.256
rpsL781929p.Gly124Ser0.234
rplC800794c.-15A>G0.191
rplC800796c.-13A>G0.179
rplC800814c.6A>G0.203
rplC800817c.9A>T0.217
rplC800844c.36T>C0.191
rplC800865c.57A>G0.118
rplC800875p.Val23Ile0.111
rplC800889c.81C>G0.119
rplC800892c.84G>C0.121
rplC801132c.324T>C0.114
rplC801147c.339T>C0.114
rplC801150c.342G>C0.113
rplC801153c.345G>C0.115
rplC801156c.348T>A0.113
rplC801168c.360C>G0.120
rplC801171c.363A>G0.124
rplC801174c.366T>C0.125
rplC801195c.387G>C0.129
rplC801207c.399C>T0.141
rplC801246c.438C>T0.120
rplC801249c.441T>C0.126
rplC801255c.447C>T0.114
rplC801321c.513C>T0.107
rplC801324c.516T>C0.108
rplC801339c.531T>C0.114
rplC801342c.534T>A0.105
rplC801348c.540T>G0.130
rplC801357c.549T>C0.132
rplC801367p.Ala187Thr0.133
rplC801402c.594T>C0.114
rplC801405c.597T>C0.118
embR1417397c.-50T>C0.986
rrs1471923r.78t>c0.180
rrs1471925r.80t>c0.180
rrs1471932r.87a>g0.177
rrs1471934r.89a>g0.197
rrs1471969r.124t>c0.161
rrs1471970r.125g>a0.161
rrs1472028r.183a>t0.125
rrs1472029r.184c>t0.120
rrs1472030r.185g>t0.122
rrs1472031r.186g>a0.125
rrs1472033r.188a>g0.128
rrs1472034r.189t>c0.146
rrs1472044r.199g>t0.140
rrs1472045r.200t>a0.140
rrs1472061r.216a>t0.164
rrs1472075r.230a>g0.185
rrs1472108r.263c>t0.200
rrs1472969r.1124a>g0.172
rrs1472970r.1125c>g0.172
rrs1472977r.1132g>c0.150
rrs1472978r.1133t>c0.164
rrs1473105r.1260g>a0.178
rrs1473123r.1278a>t0.152
rrs1473145r.1300c>t0.154
rrs1473166r.1321g>a0.159
rrs1473290r.1445c>t0.203
rrl1473658r.1t>a0.125
rrl1473659r.2t>a0.125
rrl1473668r.11c>t0.136
rrl1473758r.101g>t0.109
rrl1473877r.220g>a0.152
rrl1473898r.241c>t0.169
rrl1473943r.286g>t0.192
rrl1473945r.288t>a0.204
rrl1473946r.289a>t0.200
rrl1473986r.329t>c0.229
rrl1473987r.330g>a0.222
rrl1473995r.338g>t0.233
rrl1474001r.344c>t0.217
rrl1474009r.352a>g0.234
rrl1474012r.355c>t0.234
rrl1474093r.436g>t0.260
rrl1474099r.442g>a0.265
rrl1474103r.446a>t0.265
rrl1474140r.483c>t0.160
rrl1474151r.494c>t0.217
rrl1474181r.524c>t0.167
rrl1474249r.592g>t0.151
rrl1474308r.651g>t0.153
rrl1474310r.653t>g0.180
rrl1474356r.699t>c0.271
rrl1474362r.705a>g0.254
rrl1474376r.719t>c0.270
rrl1474639r.982g>a0.245
rrl1474794r.1137c>t0.125
rrl1474812r.1155g>a0.131
rrl1474823r.1166c>t0.145
rrl1474831r.1174a>g0.125
rrl1474904r.1247g>a0.233
rrl1474956r.1299c>t0.255
rrl1474960r.1303c>g0.250
rrl1474963r.1306g>t0.245
rrl1474964r.1307t>a0.245
rrl1474965r.1308g>c0.255
rrl1474970r.1313g>a0.250
rrl1475006r.1349a>t0.200
rrl1475061r.1404c>t0.136
rrl1475199r.1542g>a0.265
rrl1475206r.1549c>t0.286
rrl1475209r.1552g>c0.280
rrl1475213r.1556c>t0.275
rrl1475249r.1592t>c0.269
rrl1475252r.1595c>t0.280
rrl1475266r.1609t>c0.273
rrl1475267r.1610g>a0.250
rrl1475275r.1618c>t0.256
rrl1475276r.1619t>c0.256
rrl1475291r.1634a>c0.286
rrl1475315r.1658a>t0.211
rrl1475355r.1698c>t0.108
rrl1475369r.1712g>t0.114
rrl1475402r.1745c>t0.143
rrl1475419r.1762c>t0.130
rrl1475429r.1772g>a0.148
rrl1475436r.1779c>t0.143
rrl1475483r.1826c>t0.189
rrl1475505r.1848g>a0.154
rrl1475526r.1869c>a0.171
rrl1475599r.1942a>g0.217
rrl1475608r.1951t>c0.220
rrl1475642r.1985t>c0.261
rrl1475657r.2000a>g0.250
rrl1475659r.2002g>t0.265
rrl1475758r.2101ac>a0.344
rrl1475763r.2106c>t0.322
rrl1475765r.2108ag>a0.317
rrl1475881r.2224t>c0.204
rrl1475988r.2331a>g0.163
rrl1476031r.2374c>t0.135
rrl1476032r.2375c>a0.132
rrl1476033r.2376t>c0.128
rrl1476034r.2377c>a0.128
rrl1476045r.2388g>t0.125
rrl1476047r.2390g>t0.119
rrl1476048r.2391g>a0.119
rrl1476049r.2392c>t0.116
rrl1476086r.2429g>a0.208
rrl1476089r.2432t>c0.204
rrl1476095r.2438c>g0.204
rrl1476106r.2449a>t0.200
rrl1476108r.2451t>c0.196
rrl1476115r.2458t>c0.196
rrl1476117r.2460g>c0.200
rrl1476214r.2557g>a0.244
rrl1476224r.2567a>g0.256
rrl1476281r.2624t>c0.280
rrl1476583r.2926g>a0.176
rrl1476584r.2927c>t0.174
rrl1476594r.2937c>t0.157
rrl1476597r.2940g>a0.159
rrl1476603r.2946g>a0.159
rrl1476608r.2951c>g0.164
rrl1476628r.2971t>a0.185
rrl1476689r.3032a>t0.159
rrl1476690r.3033c>t0.145
rrl1476693r.3036g>a0.145
rrl1476695r.3038t>a0.145
rrl1476716r.3059a>c0.138
rrl1476755r.3098g>a0.111
fabG11673482p.Ser15Ala0.155
fabG11673487c.48T>C0.167
fabG11673490c.51A>G0.169
fabG11673523c.84G>T0.239
fabG11673535c.96A>G0.258
fabG11673547c.108T>C0.246
fabG11673568c.129C>G0.226
fabG11673574c.135C>G0.208
fabG11673580c.141T>G0.200
fabG11673589c.150A>G0.115
fabG11673591p.Ala51Val0.120
fabG11673633p.Ser65Asn0.113
fabG11673637p.Asp66Glu0.107
fabG11673641p.Val68Ile0.105
fabG11673679c.240T>C0.117
fabG11673685c.246C>T0.111
fabG11673710p.Leu91Ile0.143
fabG11673716p.Ala93Lys0.145
fabG11673733p.Met98Ile0.182
fabG11673748c.309A>G0.157
fabG11673749p.Lys104Arg0.157
fabG11673758p.Lys107Glu0.167
fabG11673890p.Ala151Ser0.227
fabG11673901c.462A>G0.256
fabG11673905p.Ser156Ala0.247
fabG11673916c.477A>C0.244
fabG11673917p.Val160Leu0.253
fabG11673922c.483T>C0.242
fabG11673941p.Ala168Ser0.250
fabG11673955c.516G>C0.273
fabG11673961c.522A>C0.276
fabG11673985c.546C>G0.240
fabG11674006p.Asp189Glu0.187
fabG11674015c.576C>T0.120
fabG11674018c.579G>C0.113
fabG11674021c.582G>C0.115
fabG11674024c.585T>C0.118
fabG11674033c.594T>C0.125
fabG11674037p.Gln200Ala0.113
fabG11674042c.603G>T0.114
fabG11674049p.Gln204Asp0.118
fabG11674054c.615T>C0.121
fabG11674060c.621A>G0.119
fabG11674063c.624G>C0.119
fabG11674079p.Pro214Ala0.194
fabG11674105c.666C>T0.164
fabG11674114c.675T>A0.156
fabG11674123c.684T>C0.133
fabG11674126c.687G>C0.133
fabG11674132c.693T>C0.127
fabG11674136p.Ser233Ala0.117
fabG11674141c.702T>C0.119
inhA1674471c.270G>C0.175
inhA1674480c.279T>C0.182
inhA1674486c.285T>C0.190
inhA1674504c.303C>G0.194
inhA1674507c.306G>C0.208
inhA1674537c.336C>G0.227
inhA1674542p.Ala114Glu0.230
inhA1674546c.345T>C0.239
inhA1674549c.348G>C0.258
inhA1674555c.354G>A0.270
inhA1674561c.360C>T0.270
inhA1674582c.381T>C0.222
inhA1674585c.384T>C0.212
inhA1674589p.Met130Leu0.212
inhA1674601p.Leu134Thr0.206
inhA1674624c.423A>C0.192
inhA1674660c.459G>C0.157
inhA1674672c.471C>G0.141
inhA1674703c.502T>C0.105
inhA1674828c.627G>A0.108
inhA1674846p.Ile215Met0.114
inhA1674864c.663C>T0.130
inhA1674870c.669T>C0.138
inhA1674879c.678T>C0.147
inhA1674903c.702T>C0.200
inhA1674904p.Ala235Pro0.211
inhA1674909c.708G>A0.219
inhA1674942c.741T>G0.197
inhA1674960c.759C>G0.163
inhA1674987c.786C>T0.110
rpsA1833518c.-24C>A0.125
rpsA1833532c.-10A>C0.136
rpsA1833554p.Thr5Ala0.148
rpsA1833568c.27G>C0.141
rpsA1833589c.48A>T0.133
rpsA1833595c.54T>C0.113
rpsA1833748c.207C>G0.129
rpsA1833787c.246C>G0.169
rpsA1833790c.249T>C0.177
rpsA1833802c.261A>G0.174
rpsA1833811c.270G>T0.181
rpsA1833838c.297G>C0.169
rpsA1833841c.300C>G0.159
rpsA1833847c.306C>G0.165
rpsA1833856c.315A>G0.171
rpsA1833874c.333T>C0.177
rpsA1833877c.336C>T0.163
rpsA1833928c.387G>C0.191
rpsA1833940c.399C>G0.178
rpsA1833971c.430C>T0.226
rpsA1833979c.438T>C0.256
rpsA1834000c.459G>C0.276
rpsA1834021c.480C>T0.235
rpsA1834030c.489C>G0.250
rpsA1834096c.555G>T0.129
rpsA1834099c.558C>G0.134
rpsA1834102c.561T>C0.136
rpsA1834105c.564C>G0.139
rpsA1834108c.567C>G0.159
rpsA1834123c.582C>G0.155
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C0.131
rpsA1834195c.654G>C0.133
rpsA1834210c.669C>T0.146
rpsA1834222c.681T>C0.138
rpsA1834231c.690T>C0.146
rpsA1834234c.693G>C0.163
rpsA1834249c.708T>C0.152
rpsA1834261c.720A>G0.133
rpsA1834262c.721T>A0.125
rpsA1834333c.792C>T0.116
rpsA1834366c.825A>G0.107
rpsA1834396c.855G>C0.147
rpsA1834411c.870T>C0.157
rpsA1834417c.876G>C0.159
rpsA1834423c.882G>C0.186
rpsA1834435c.894G>C0.194
rpsA1834451c.910T>C0.203
rpsA1834465c.924T>C0.162
rpsA1834468c.927A>G0.147
rpsA1834489c.948T>C0.176
rpsA1834528c.987T>C0.186
rpsA1834540c.999G>C0.188
rpsA1834546c.1005T>C0.169
rpsA1834609c.1068T>C0.204
rpsA1834618c.1077G>C0.222
rpsA1834633c.1092A>G0.196
rpsA1834639c.1098T>C0.218
rpsA1834654p.Glu371Asp0.228
rpsA1834690c.1149T>C0.262
rpsA1834732c.1191T>C0.211
rpsA1834733p.Ala398Ser0.205
rpsA1834738c.1197A>G0.197
rpsA1834753c.1212T>C0.244
rpsA1834765p.Glu408Asp0.220
rpsA1834775p.Ala412Thr0.253
rpsA1834780c.1239A>G0.253
rpsA1834786c.1245A>G0.221
rpsA1834789c.1248T>C0.215
rpsA1834792c.1251G>C0.221
rpsA1834849c.1308C>G0.134
rpsA1834852c.1311C>G0.137
tlyA1917951c.12T>C0.125
tlyA1917972c.33A>G1.000
tlyA1917975c.36C>G0.121
tlyA1917981c.42G>C0.121
tlyA1917990c.51G>C0.122
tlyA1917993c.54A>G0.121
tlyA1917996c.57A>G0.122
tlyA1918002c.63A>G0.132
katG2154724p.Arg463Leu1.000
katG2155321p.Ala264Val0.985
katG2155704c.408G>C0.120
katG2155716c.396A>C0.118
katG2155722c.390C>G0.118
katG2155728c.384C>G0.118
katG2155782c.330G>C0.120
katG2155785c.327A>G0.122
kasA2518132c.18C>T0.127
kasA2518138c.24T>C0.149
kasA2518146p.Phe11Tyr0.153
kasA2518162c.48G>A0.160
kasA2518174c.60A>G0.194
kasA2518190p.Ser26Ala0.192
kasA2518199p.Ile29Val0.194
kasA2518220c.106C>T0.192
kasA2518234c.120G>A0.175
kasA2518248p.Ala45Val0.167
kasA2518261p.Glu49Asp0.132
kasA2518263p.Phe50Tyr0.132
kasA2518265p.Val51Ile0.130
kasA2518444c.330T>C0.106
kasA2518447c.333T>G0.109
kasA2518459c.345T>C0.152
kasA2518462c.348A>C0.154
kasA2518468c.354A>C0.167
kasA2518474c.360G>A0.169
kasA2518480c.366T>C0.169
kasA2518483c.369C>G0.162
kasA2518504c.390T>C0.205
kasA2518506p.Ala131Glu0.198
kasA2518519c.405G>C0.225
kasA2518528c.414C>G0.247
kasA2518540c.426T>G0.256
kasA2518561c.447T>C0.240
kasA2518567c.453G>C0.181
kasA2518570c.456G>C0.178
kasA2518574p.Ile154Val0.176
kasA2518579c.465T>C0.176
kasA2518588c.474T>C0.253
kasA2518591c.477G>C0.244
kasA2518609p.Met165Ile0.242
kasA2518624c.510C>G0.231
kasA2518636c.522C>T0.231
kasA2518672c.558G>C0.233
kasA2518678c.564C>T0.222
kasA2518684c.570C>G0.211
kasA2518693c.579C>G0.177
kasA2518696c.582C>G0.177
kasA2518702c.588C>T0.153
kasA2518705c.591T>C0.156
kasA2518711c.597A>G0.135
kasA2518714c.600A>C0.147
kasA2518732c.618C>G0.173
kasA2518744c.630C>T0.175
kasA2518747c.633C>G0.188
kasA2518768c.654C>T0.156
kasA2518777c.663C>T0.152
kasA2518783c.669T>C0.152
kasA2518789c.675G>C0.144
kasA2518792c.678C>G0.137
kasA2518795c.681C>G0.145
kasA2518825c.711T>C0.190
kasA2518864c.750G>C0.190
kasA2518879c.765A>G0.157
kasA2518885c.771T>C0.142
kasA2518898c.784T>C0.114
kasA2518906c.792A>G0.120
kasA2518910p.Leu266Met0.120
kasA2518915c.801T>G0.125
kasA2518921c.807T>C0.125
kasA2519062c.948T>G0.130
kasA2519068c.954C>T0.124
kasA2519072p.Ala320Thr0.126
kasA2519095c.981C>G0.153
kasA2519107c.993T>C0.188
kasA2519108p.Asp332Gln0.184
kasA2519116c.1002C>G0.189
kasA2519122c.1008G>C0.185
kasA2519137c.1023T>G0.236
kasA2519158c.1044C>T0.240
kasA2519167c.1053T>G0.234
kasA2519173c.1059C>G0.223
kasA2519196p.Thr361Ser0.202
ahpC2726303c.111T>C0.113
ahpC2726312c.120T>C0.105
ahpC2726579c.387T>C0.114
ahpC2726591c.399C>G0.125
ahpC2726593p.Val134Ala0.145
ahpC2726600c.408T>C0.136
ahpC2726601p.Ile137Leu0.149
ahpC2726638p.Ala149Val0.206
ahpC2726645c.453C>G0.230
ahpC2726657c.465A>C0.222
ahpC2726669p.Asp159Glu0.197
ahpC2726672c.480G>A0.200
ahpC2726675c.483A>G0.200
ahpC2726681c.489A>C0.194
ahpC2726687c.495C>G0.188
ahpC2726693c.501C>G0.197
ahpC2726696c.504C>G0.194
ahpC2726717c.525A>G0.138
ahpC2726747c.555A>C0.115
folC2746451p.Gly383Ala0.115
folC2746478p.Phe374Tyr0.135
folC2746480c.1119T>A0.133
folC2746531c.1068C>G0.118
folC2746564c.1035T>C0.147
folC2746576c.1023G>C0.145
folC2746584c.1015A>G0.136
folC2747302c.297T>G0.114
folC2747314c.285T>G0.190
folC2747317c.282G>C0.190
folC2747335c.264C>G0.190
folC2747343p.Val86Ile0.212
folC2747355p.Val82Ile0.227
folC2747362c.237C>G0.218
folC2747394p.Ile69Val0.184
folC2747395c.204A>G0.162
ribD2987026p.Ala63Gly0.127
ribD2987033c.195C>G0.123
ribD2987042c.204A>G0.123
ribD2987046p.Val70Ile0.118
ribD2987058c.220T>C0.118
ribD2987066c.228A>G0.118
ribD2987069c.231T>C0.118
ribD2987092p.Val85Ala0.113
thyX3067223c.723C>G0.160
thyX3067232c.714G>C0.160
thyX3067246p.Thr234Ala0.150
thyX3067249p.Thr233Ser0.140
thyX3067252p.Val232Ile0.142
thyX3067274c.672G>C0.176
thyX3067277c.669G>C0.168
thyX3067281p.Val222Ala0.168
thyX3067284p.Ala221Gly0.168
thyX3067286c.660G>C0.165
thyX3067289c.657G>C0.165
thyX3067292c.654C>T0.175
thyX3067295c.651G>A0.172
thyX3067313c.633C>A0.224
thyX3067316c.630T>C0.237
thyX3067325c.621T>C0.230
thyX3067349c.597C>G0.203
thyX3067355c.591T>G0.197
thyX3067367c.579C>G0.207
thyX3067373c.573G>C0.203
thyX3067391c.555C>G0.236
thyX3067394c.552C>G0.238
thyX3067439c.507T>C0.224
thyX3067445c.501G>C0.220
thyX3067457c.489G>C0.180
thyX3067462c.484G>A0.168
thyX3067465p.Ile161Val0.160
thyX3067466c.480C>G0.160
thyX3067475c.471T>C0.189
thyX3067491p.Ala152Glu0.204
thyX3067493c.453T>C0.212
thyX3067510c.436G>A0.220
thyX3067515p.Ser144Thr0.204
thyX3067531p.Ala139Ser0.149
thyX3067545p.Glu134Ala0.161
thyX3067549p.Thr133Ala0.135
thyX3067556p.His130Gln0.138
thyX3067559c.387G>C0.135
thyX3067565p.Asp127Glu0.138
thyX3067570p.Ala126Pro0.126
thyX3067577c.369C>T0.146
thyX3067598c.348G>A0.131
thyX3067602p.Arg115His0.129
thyX3067611p.Lys112Thr0.157
thyX3067619c.327T>G0.156
thyX3067631c.315G>C0.132
thyX3067634c.312G>C0.128
thyX3067652c.294A>G0.122
thyX3067661c.285G>C0.122
thyX3067685c.261T>G0.136
thyX3067693p.Ile85Leu0.128
thyX3067694c.252C>G0.128
thyX3067718c.228G>C0.173
thyX3067721c.225A>G0.189
thyX3067727c.219T>G0.182
thyX3067736c.210G>A0.195
thyX3067739c.207A>G0.200
thyX3067762p.Arg62Lys0.171
thyX3067765p.Leu61Ile0.171
thyX3067781c.165G>C0.192
thyX3067793c.153A>G0.181
thyX3067799c.147C>T0.157
thyX3067802c.144G>C0.165
thyX3067814c.132A>G0.163
thyX3067850c.96T>G0.144
thyX3067869p.Thr26Ser0.118
thyX3067898p.Asp16Glu0.146
thyX3067935p.Thr4Ile0.112
thyX3067951c.-6A>G0.120
thyA3073892c.580A>G0.155
thyA3073898p.Ala192Ser0.147
thyA3073917c.555G>C0.169
thyA3073920c.552G>C0.176
thyA3073925c.547A>G0.174
thyA3073929c.543A>G0.161
thyA3073953c.519A>G0.144
thyA3073956c.516C>G0.143
thyA3073959c.513A>G0.135
thyA3073977c.495T>C0.149
thyA3073989c.483A>G0.153
thyA3074004c.468A>G0.172
thyA3074010c.462G>C0.167
thyA3074028c.444C>G0.137
thyA3074031c.441A>G0.118
thyA3074034c.438A>G0.117
thyA3074037c.435G>C0.125
thyA3074061c.411T>C0.116
thyA3074079c.393C>G0.181
thyA3074097c.375G>C0.185
thyA3074102p.Asp124Asn0.209
thyA3074127c.345C>G0.256
thyA3074130c.342C>G0.271
thyA3074154c.318A>G0.195
thyA3074157c.315G>C0.179
thyA3074160c.312T>C0.184
thyA3074165p.Ala103Thr0.181
thyA3074172c.300C>G0.169
thyA3074175c.297T>C0.174
thyA3074181c.291T>C0.220
thyA3074187c.285A>G0.225
thyA3074205p.Glu89Asp0.235
thyA3074214c.258A>G0.210
thyA3074244c.228T>C0.213
thyA3074254p.His73Arg0.186
thyA3074262c.210A>G0.153
thyA3074267p.Ile69Val0.143
thyA3074268c.204A>G0.143
thyA3074285c.187A>G0.101
ald3086788c.-32T>C1.000
fbiA3640278c.-265GT>G0.955
fbiA3640307c.-236C>A0.108
fbiA3640347c.-196A>G0.128
fbiA3640349c.-194A>G0.127
fbiA3640350c.-193C>T0.127
fbiA3640365c.-178C>G0.135
alr3841662c.-242A>G0.196
panD4044057c.225G>C0.128
panD4044072c.210G>C0.123
panD4044075c.207A>G0.122
panD4044081c.201A>G0.128
panD4044084c.198A>G0.127
panD4044105c.177C>G0.165
panD4044117c.165C>G0.159
panD4044120c.162T>G0.157
panD4044123c.159A>G0.159
panD4044126c.156A>G0.160
panD4044138c.144A>G0.153
panD4044150c.132T>C0.141
panD4044165c.117C>G0.140
panD4044174c.108G>C0.103
embC4240685p.Thr275Ala0.111
embC4240693c.831T>G0.111
embC4240699c.837C>G0.118
embC4240726c.864G>C0.200
embC4240780c.918T>C0.225
embC4240783c.921G>C0.212
embC4240789c.927T>C0.200
embC4240819c.957A>G0.189
embC4240828c.966G>A0.178
embC4240831c.969T>G0.167
embC4241032c.1170G>C0.106
embC4241038c.1176G>C0.114
embC4241047c.1185C>G0.114
embC4241050c.1188T>G0.111
embC4241053c.1191G>C0.114
embC4241089c.1227C>G0.181
embC4241095c.1233C>T0.186
embC4241107c.1245G>C0.212
embC4241140c.1278A>G0.191
embC4241146c.1284C>G0.202
embC4241158c.1296T>C0.183
embC4241161c.1299C>G0.175
embC4241162c.1300T>C0.177
embC4241170c.1308G>C0.190
embC4241173c.1311C>T0.190
embC4241203c.1341T>C0.189
embC4241206c.1344G>C0.170
embC4241218c.1356G>C0.148
embC4241230c.1368A>G0.130
embC4241233c.1371G>C0.114
embC4241449c.1587C>G0.189
embC4241453p.Ile531Val0.185
embC4241479c.1617C>G0.178
embC4241480c.1618T>C0.180
embC4241488c.1626G>C0.184
embC4241496p.Ala545Gly0.138
embC4241500c.1638A>C0.143
embC4241501p.Ser547Thr0.145
embC4241506c.1644G>C0.141
embC4241518c.1656A>G0.147
embC4241521c.1659T>C0.151
embC4241530c.1668C>A0.151
embC4241536c.1674A>G0.157
embC4241539c.1677T>C0.138
embC4241545c.1683T>C0.169
embC4241551c.1689A>G0.164
embC4241567p.Ile569Val0.148
embC4241572c.1710C>G0.150
embC4242643c.2781C>T1.000
embC4242710p.Gln950Glu0.146
embC4242715c.2853T>C0.146
embC4242742c.2880C>G0.143
embC4242748c.2886A>G0.140
embC4242754c.2892G>C0.135
embC4242764p.Val968Leu0.154
embC4242779p.Asn973Asp0.170
embC4242791p.Ala977Ser0.121
embC4242799c.2937T>C0.103
embC4242820c.2958G>C0.169
embC4242823c.2961G>C0.183
embC4242832c.2970A>C0.192
embC4242838c.2976C>G0.152
embC4242841c.2979C>T0.158
embC4242844c.2982A>G0.156
embC4242847c.2985C>A0.156
embC4242859c.2997C>T0.187
embC4242862c.3000A>G0.187
embC4242863p.Tyr1001Asn0.187
embC4242883c.3021C>G0.211
embC4242892c.3030G>C0.219
embC4242901c.3039G>C0.229
embC4242919c.3057A>G0.200
embC4242928c.3066A>G0.192
embC4242931c.3069G>C0.189
embC4242940c.3078T>C0.151
embC4242941p.His1027Asn0.151
embC4242946c.3084T>C0.151
embC4242952c.3090T>C0.138
embA4243460c.228C>T1.000
embA4244371p.Arg380Leu0.989
embA4245089c.1857G>C0.107
embA4245092c.1860C>G0.106
embA4245101c.1869G>C0.125
embA4245137c.1905T>C0.171
embA4245146c.1914G>A0.149
embA4245149c.1917C>T0.151
embA4245153p.Ile641Val0.149
embA4245182c.1950T>C0.192
embA4245189c.1957C>T0.197
embA4245198p.Leu656Ile0.224
embA4245207c.1975T>C0.224
embA4245215c.1983A>C0.177
embA4245222p.Tyr664Gln0.173
embA4245248c.2016G>C0.139
embA4245257c.2025A>G0.129
embA4245263c.2031A>G0.122
embA4245726c.2494T>C0.112
embA4246250c.3018G>C0.109
embA4246256c.3024G>T0.154
embA4246259c.3027G>C0.182
embA4246264p.His1011Arg0.197
embA4246292c.3060A>G0.185
embA4246305p.Ser1025Glu0.175
embA4246308p.Thr1026Ala0.173
embA4246316c.3084T>G0.183
embA4246319c.3087G>C0.181
embA4246329p.Thr1033Ala0.181
embA4246349c.3117C>G0.167
embA4246359p.Ala1043Ser0.133
embA4246367c.3135C>T0.133
embA4246373c.3141T>C0.132
embA4246376c.3144G>C0.144
embA4246379c.3147C>T0.128
embB4246544p.Thr11Pro0.187
embB4246548p.Pro12Gln0.232
embB4246555c.42G>C0.135
embB4246556p.Ala15Pro0.105
embB4247464c.951C>G0.161
embB4247470c.957T>C0.172
embB4247491c.978G>C0.205
embB4247497c.984T>C0.191
embB4247512c.999T>C0.195
embB4247539c.1026T>C0.182
embB4247554c.1041T>C0.155
embB4247566c.1053C>A0.140
embB4247572c.1059A>G0.145
embB4247746c.1233C>T0.167
embB4247761c.1248T>C0.209
embB4247773c.1260G>A0.182
embB4247776c.1263G>T0.180
embB4247797c.1284C>G0.147
embB4247800c.1287A>T0.147
embB4247803c.1290G>C0.145
embB4247815c.1302C>G0.136
embB4247819p.Val436Ile0.138
embB4247830c.1317A>G0.149
embB4247836c.1323A>G0.142
embB4247839c.1326G>C0.140
embB4247866c.1353G>C0.149
embB4247875c.1362G>C0.138
embB4247876c.1363C>T0.138
embB4247881c.1368G>C0.134
embB4247887c.1374C>T0.113
embB4247893c.1380C>T0.119
embB4247899p.Met462Ile0.122
embB4247914c.1401G>C0.119
embB4247932c.1419C>G0.139
embB4247940p.Leu476Trp0.147
embB4247945c.1432T>C0.160
embB4247951p.Ser480Ala0.170
embB4247956c.1443G>C0.183
embB4247974c.1461C>G0.203
embB4248007c.1494C>G0.119
embB4248011p.Ser500Arg0.118
embB4248014p.Thr501Ala0.118
embB4248045p.Lys511Thr0.103
embB4248070c.1557T>C0.194
embB4248085c.1572T>C0.194
embB4248097c.1584C>G0.173
embB4248130c.1617G>C0.181
embB4248142c.1629T>C0.137
embB4248143c.1630T>C0.137
embB4248157c.1644A>G0.159
embB4248172c.1659G>C0.150
embB4248220c.1707A>C0.111
embB4248304c.1791G>C0.132
embB4248316c.1803C>G0.125
embB4248319c.1806A>G0.132
embB4248343c.1830G>C0.140
embB4248350c.1837T>C0.124
embB4248358c.1845C>G0.114
embB4248361c.1848A>C0.115
embB4248362p.Ser617Ala0.115
embB4248373c.1860C>G0.139
embB4248382c.1869C>G0.140
embB4248386c.1873C>A0.141
embB4248457c.1944T>C0.138
embB4248472c.1959T>C0.105
embB4248475c.1962G>C0.110
embB4248504p.Asp664Gly0.121
embB4249417c.2904A>G0.122
embB4249423p.Asp970Glu0.120
embB4249424p.Leu971Met0.120
embB4249429c.2916C>T0.151
embB4249432c.2919A>G0.158
embB4249441c.2928A>G0.177
embB4249444c.2931T>C0.177
embB4249469p.Leu986Met0.198
embB4249486c.2973T>G0.203
embB4249498c.2985G>C0.169
embB4249521p.Ala1003Val0.111
ethA4327396c.78A>G0.138
ethA4327399p.Asp25Glu0.133
ethA4327423c.51G>C0.133
ethA4327435c.39T>G0.136
ethA4327438c.36A>G0.140
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;