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: 5c868f2e81c7d
Sample: 5c868f2e81c7d

Summary
ID: 5c868f2e81c7d
Date: Mon Mar 11 16:42:10 2019
Strain: NA
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB 359L>359I (0.13)
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage3East-African-IndianCASRD750
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage1.2.2Indo-OceanicEAI1RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6196957C>T0.119
gyrB62681029C>G0.132
gyrB62801041T>C0.137
gyrB62861047T>C0.127
gyrB62891050C>T0.127
gyrB62921053G>C0.127
gyrB63071068T>G0.150
gyrB63191080G>C0.155
gyrB63461107C>T0.178
gyrB63621123T>C0.118
gyrB66551416T>C0.117
gyrB66701431G>C0.114
gyrB66731434A>C0.114
gyrB67001461T>C0.115
gyrB67091470A>G0.117
gyrB67121473G>C0.121
gyrB67281489C>T0.128
gyrB67421503A>G0.141
gyrB67451506T>G0.140
gyrB67511512G>C0.160
gyrB67601521G>C0.168
gyrB67631524G>C0.170
gyrB67751536G>C0.174
gyrB67931554T>C0.172
gyrB6797520G>520T0.176
gyrB68111572C>T0.174
gyrB68411602T>C0.203
gyrB68441605T>C0.192
gyrB68531614A>G0.139
gyrB68561617T>C0.141
gyrB68591620T>C0.139
gyrB68621623C>G0.149
gyrB68681629G>C0.143
gyrB71651926C>G0.114
gyrB71781939T>C0.115
gyrB71861947C>G0.114
gyrB72462007T>C0.115
gyrA736221E>21Q1.000
gyrA758595S>95T1.000
gyrA7763462T>C0.157
gyrA7775474C>A0.157
gyrA7781480G>C0.131
gyrA7784483A>G0.125
gyrA7790489G>C0.121
gyrA7793492G>C0.121
gyrA7796495G>C0.127
gyrA7799498A>G0.132
gyrA7814513C>G0.121
gyrA7823522G>C0.124
gyrA7835534A>C0.129
gyrA7853552C>G0.138
gyrA7859558A>G0.136
gyrA7865564T>C0.130
gyrA7886585T>C0.131
gyrA8111810G>C0.127
gyrA8121820T>C0.140
gyrA8129828T>C0.144
gyrA8135834C>G0.147
gyrA8156855T>C0.148
gyrA8164288A>288D0.850
gyrA8168867A>G0.133
gyrA8177876A>C0.136
gyrA8198897T>C0.149
gyrA8207906T>C0.150
gyrA8219918T>C0.160
gyrA8225924T>C0.170
gyrA8234933T>C0.157
gyrA8237936A>G0.159
gyrA8247316I>316V0.150
gyrA8264963T>C0.153
gyrA8267966G>C0.156
gyrA8270969G>C0.144
gyrA8276975G>A0.150
gyrA8283328I>328L0.136
gyrA8288987T>C0.136
gyrA8294993T>C0.208
gyrA83241023T>C0.222
gyrA83301029C>G0.246
gyrA83391038A>G0.238
gyrA8340347A>347S0.238
gyrA83721071G>C0.239
gyrA83751074G>C0.227
gyrA8382361L>361M0.214
gyrA83871086C>T0.198
gyrA8391364Y>364H0.193
gyrA83991098T>G0.200
gyrA8401367D>367A0.198
gyrA84051104C>T0.198
gyrA84201119T>C0.212
gyrA84421141C>T0.223
gyrA84531152A>C0.225
gyrA84591158G>A0.208
gyrA84621161A>T0.204
gyrA84651164C>G0.202
gyrA84711170T>C0.179
gyrA84721171C>T0.179
gyrA84801179C>A0.198
gyrA84861185T>C0.191
gyrA85041203G>C0.189
gyrA85161215T>C0.160
gyrA85191218A>C0.163
gyrA85201219C>T0.165
gyrA85281227G>C0.172
gyrA85431242C>G0.194
gyrA85461245T>C0.186
gyrA85521251C>A0.190
gyrA85611260A>G0.155
gyrA85761275C>G0.146
gyrA85791278C>T0.137
gyrA85881287G>A0.131
gyrA85971296C>G0.119
gyrA86031302A>G0.119
gyrA86361335A>C0.136
gyrA86421341A>G0.135
gyrA86931392T>C0.127
gyrA86961395G>C0.125
gyrA86991398A>G0.124
gyrA87111410A>C0.136
gyrA87141413A>G0.136
gyrA87291428T>C0.126
gyrA8730477G>477R0.124
gyrA8740480R>480H0.126
gyrA8780493D>493E0.168
gyrA87861485T>C0.172
gyrA88011500G>C0.195
gyrA88071506C>T0.200
gyrA88101509A>G0.195
gyrA88161515C>G0.189
gyrA8818506S>506N0.189
gyrA88281527T>C0.208
gyrA88371536C>T0.221
gyrA88521551T>C0.213
gyrA88581557T>C0.230
gyrA88671566A>G0.220
gyrA88701569G>C0.208
gyrA88731572A>C0.215
gyrA88911590G>A0.221
gyrA88971596T>C0.221
gyrA89031602T>C0.232
gyrA89331632G>C0.203
gyrA89391638T>C0.162
gyrA89421641G>C0.164
gyrA89461645T>C0.166
gyrA89661665C>G0.178
gyrA8967556A>556R0.177
gyrA89871686C>G0.176
gyrA89901689C>G0.164
gyrA89961695T>C0.173
gyrA8998566L>566W0.175
gyrA90171716C>G0.172
gyrA90231722A>C0.163
gyrA90291728T>C0.148
gyrA90321731T>C0.143
gyrA90351734G>C0.137
gyrA9050583D>583E0.150
gyrA90511750T>C0.144
gyrA90561755C>G0.144
gyrA90621761C>G0.145
gyrA90681767G>C0.143
gyrA90711770G>C0.136
gyrA90801779G>T0.164
gyrA90891788G>C0.164
gyrA90991798T>C0.158
gyrA91041803C>G0.158
gyrA91191818A>G0.185
gyrA91221821C>G0.185
gyrA91431842T>C0.196
gyrA91521851C>T0.175
gyrA9153618T>618E0.175
gyrA91581857C>T0.179
gyrA91611860C>G0.167
gyrA91821881T>C0.194
gyrA91911890G>C0.191
gyrA92001899A>G0.179
gyrA9204635S>635T0.177
gyrA92241923C>T0.168
gyrA92301929T>C0.157
gyrA92331932C>G0.157
gyrA92391938C>T0.173
gyrA9252651V>651I0.153
gyrA92841983T>C0.169
gyrA92911990C>T0.132
gyrA92961995T>C0.126
gyrA92991998G>C0.124
gyrA9300667A>667S0.123
gyrA9304668G>668D1.000
gyrA9308669D>669E0.122
gyrA93232022C>G0.149
gyrA93352034G>C0.161
gyrA93652064G>A0.161
gyrA93742073G>C0.161
gyrA93772076A>G0.164
gyrA93832082T>G0.157
gyrA93862085T>C0.154
gyrA93952094G>C0.138
gyrA93982097T>C0.135
gyrA94132112G>C0.136
gyrA95182217A>G0.129
gyrA96022301T>C0.159
gyrA9611770D>770E0.169
gyrA96262325T>C0.147
gyrA96292328C>G0.154
gyrA9630777V>777I0.154
gyrA96352334T>C0.152
gyrA96382337C>G0.152
gyrA96412340C>A0.151
gyrA96442343T>C0.152
gyrA96502349G>C0.182
gyrA96562355C>G0.183
gyrA96652364A>C0.183
gyrA9666789R>789G0.178
gyrA96742373T>C0.188
gyrA97042403T>G0.166
gyrA97082407T>C0.162
gyrA97162415T>C0.158
gyrA97252424G>A0.149
gyrA9727809G>809E0.146
gyrA9729810D>810N0.146
gyrA97342433A>C0.141
gyrA97492448G>C0.142
gyrA97552454C>T0.137
rpoB7598126A>T0.112
rpoB760424618C>G0.124
rpoB760430624T>C0.136
rpoB760472666C>T0.158
rpoB760475669A>G0.157
rpoB760481675G>C0.155
rpoB760484678A>G0.158
rpoB760793987A>G0.141
rpoB760805999G>C0.141
rpoB7609311125C>G0.129
rpoB7609341128C>T0.128
rpoB7609461140A>G0.165
rpoB7609821176G>C0.168
rpoB7609851179G>C0.176
rpoB7609911185G>C0.185
rpoB7610061200C>G0.178
rpoB7610151209G>C0.165
rpoB7610211215G>C0.153
rpoB7610271221A>G0.163
rpoB7610361230G>C0.167
rpoB7610371231T>C0.167
rpoB7610571251G>C0.170
rpoB7611021296A>G0.163
rpoB7615791773G>C0.126
rpoB7615881782C>T0.134
rpoB7616061800C>G0.165
rpoB7616121806G>C0.167
rpoB7616151809A>C0.171
rpoB7616361830G>T0.211
rpoB7616451839C>G0.194
rpoB7616481842T>C0.179
rpoB7616571851C>G0.194
rpoB7616751869G>C0.204
rpoB7617201914C>G0.155
rpoB761725640E>640A0.149
rpoB7617321926C>G0.150
rpoB7617351929C>G0.150
rpoB7617471941G>C0.171
rpoB7617501944G>C0.176
rpoB7617651959T>C0.168
rpoB761772656H>656A0.164
rpoB761778658N>658D0.169
rpoB761791662R>662H0.142
rpoB7618132007T>C0.140
rpoB761815670A>670E0.140
rpoB7618342028T>C0.132
rpoB761848681C>681S0.114
rpoB7618522046C>G0.114
rpoB7618582052G>C0.116
rpoB7618732067A>C0.124
rpoB7618852079T>C0.126
rpoB7619062100C>G0.119
rpoB7619122106T>C0.123
rpoB761915703D>703E0.127
rpoB761916704D>704N0.127
rpoB7619482142G>C0.160
rpoB7619542148C>G0.148
rpoB7620082202C>T0.161
rpoB7620142208C>T0.144
rpoB7620172211A>G0.147
rpoB7620832277T>C0.125
rpoB7620862280G>C0.128
rpoB7621012295C>G0.143
rpoB762114770I>770V0.154
rpoB7621312325C>G0.136
rpoB7621402334G>C0.148
rpoB7621432337T>C0.146
rpoB7621492343G>C0.153
rpoB7621672361T>C0.163
rpoB7621762370T>C0.162
rpoB7621852379G>C0.167
rpoB7622062400C>G0.164
rpoB7622332427G>C0.192
rpoB7622462440C>T0.178
rpoB7622542448T>G0.185
rpoB7622572451C>G0.186
rpoB7622662460T>C0.178
rpoB7622842478G>C0.189
rpoB7622932487T>C0.171
rpoB7623142508C>T0.160
rpoB7623172511A>G0.156
rpoB7623292523G>C0.136
rpoB7623382532T>C0.130
rpoB7623472541T>C0.142
rpoB762362852E>852D0.139
rpoB7623692563T>C0.142
rpoB7624102604T>G0.113
rpoB7624192613C>G0.115
rpoB7624342628T>G0.153
rpoB7624492643C>A0.151
rpoB7624672661C>T0.156
rpoB7624882682G>C0.113
rpoB7629293123G>C0.138
rpoB7629893183G>C0.186
rpoB7629953189G>T0.188
rpoB7630133207C>G0.191
rpoB7630283222T>C0.177
rpoB7630313225T>C0.177
rpoB7630343228C>G0.212
rpoB7630403234C>G0.228
rpoB7630673261C>G0.256
rpoB7630703264T>C0.256
rpoB7630853279C>G0.293
rpoB7631153309T>C0.269
rpoB7631363330C>T0.235
rpoB7631483342G>C0.200
rpoB7631583352C>T0.216
rpoB7631663360A>G0.222
rpoB7631903384C>T0.220
rpoB7632143408T>C0.140
rpoB7632263420A>G0.138
rpoB7632273421C>T0.148
rpoB7632383432T>C0.153
rpoB7632533447G>C0.146
rpoB7632563450G>A0.146
rpoB7632683462C>G0.148
rpoB7632833477T>C0.122
rpoB7632843478C>T0.123
rpoC76340233C>G0.120
rpoC763546177A>G0.118
rpoC763636267T>C0.139
rpoC763657288G>A0.155
rpoC763660291T>G0.155
rpoC763675306C>G0.143
rpoC763696327T>C0.153
rpoC763702333C>G0.165
rpoC763717348T>C0.174
rpoC763723354G>C0.177
rpoC763732363C>G0.184
rpoC763741372C>T0.176
rpoC763744375G>C0.174
rpoC763765396T>C0.174
rpoC763774405G>C0.191
rpoC763807438T>C0.132
rpoC763816447C>G0.138
rpoC763835156A>156M0.157
rpoC763853162V>162I0.184
rpoC763858489A>G0.186
rpoC763872168G>168A0.183
rpoC763876169E>169D0.187
rpoC763879510A>G0.194
rpoC763888519G>C0.196
rpoC763891522G>C0.194
rpoC763894525A>G0.191
rpoC763900531G>C0.198
rpoC763915546C>T0.242
rpoC763942573C>G0.253
rpoC763945576T>C0.250
rpoC763951582G>C0.253
rpoC763960591T>C0.235
rpoC763987618C>T0.253
rpoC763991208I>208L0.247
rpoC763996627T>C0.244
rpoC764002633C>G0.253
rpoC764005636G>C0.256
rpoC764020651C>T0.235
rpoC764024655T>C0.229
rpoC764032221D>221E0.189
rpoC764040224S>224T0.181
rpoC764044675T>C0.200
rpoC764059690G>T0.190
rpoC764083714A>G0.167
rpoC764098729A>G0.174
rpoC764101732C>G0.167
rpoC764102245V>245I0.165
rpoC764112248Y>248F0.168
rpoC764116747C>T0.165
rpoC764131762T>C0.160
rpoC764248879C>G0.127
rpoC764266897T>C0.120
rpoC764269900G>C0.122
rpoC764272903G>C0.123
rpoC764278909A>G0.117
rpoC764338969G>A0.163
rpoC764353984G>C0.165
rpoC764365996C>T0.183
rpoC7643801011G>C0.145
rpoC7643811012T>A0.134
rpoC7643871018T>C0.138
rpoC7644051036A>C0.149
rpoC7644191050C>G0.154
rpoC7644281059G>C0.149
rpoC7644311062G>C0.147
rpoC7644341065A>G0.147
rpoC7644461077T>C0.158
rpoC7644491080G>C0.157
rpoC7644521083T>C0.168
rpoC7644581089G>C0.160
rpoC7644611092A>G0.162
rpoC7644891120C>T0.204
rpoC7644971128A>G0.194
rpoC7645101141C>T0.161
rpoC7645211152T>C0.150
rpoC7645271158C>T0.153
rpoC7645361167G>C0.153
rpoC7645391170C>G0.155
rpoC7645481179G>A0.149
rpoC7645511182G>C0.130
rpoC7647641395T>C0.120
rpoC7648091440C>T0.123
rpoC7648271458G>C0.130
rpoC7651031734G>T0.132
rpoC7652921923G>C0.132
rpoC7652981929G>C0.139
rpoC765300644V>644A0.138
rpoC7653191950A>G0.149
rpoC765326653H>653A0.152
rpoC765330654S>654N0.152
rpoC7653461977C>G0.164
rpoC7653491980T>C0.157
rpoC7653521983G>C0.158
rpoC7653641995G>A0.126
rpoC7655292160C>T0.120
rpoC7655412172C>G0.128
rpoC7655802211G>C0.108
rpoC7657342365T>C0.128
rpoC7657392370G>T0.121
rpoC7657512382C>G0.115
rpoC765753795D>795A0.124
rpoC7657722403C>G0.125
rpoC7657842415C>G0.143
rpoC7657872418C>T0.152
rpoC7657932424C>G0.150
rpoC7657962427C>T0.150
rpoC7658112442T>C0.135
rpoC7658142445A>G0.133
rpoC7658262457T>C0.128
rpoC7658352466C>T0.126
rpoC7658502481G>C0.150
rpoC7658832514C>G0.154
rpoC7658862517C>G0.161
rpoC7658922523T>C0.164
rpoC7664083039C>G0.121
rpoC7664113042C>G0.121
rpoC7664473078T>C0.120
rpoC7664923123T>C0.118
rpoC7666573288A>G0.133
rpoC7666723303T>C0.128
rpoC7666731102G>1102N0.128
rpoC7667653396A>C0.147
rpoC7667743405T>C0.144
rpoC7667953426C>T0.193
rpoC7668013432C>G0.196
rpoC7668043435A>G0.217
rpoC7668613492G>C0.258
rpoC7668643495G>C0.258
rpoC7669003531T>C0.287
rpoC7669333564A>G0.286
rpoC7669453576A>G0.299
rpoC7669633594T>C0.245
rpoC7669723603G>C0.270
rpoC7669963627C>T0.253
rpoC7670093640T>A0.222
rpoC7670143645G>C0.213
rpoC7670333664T>A0.222
rpoC7670593690T>G0.206
rpoC7670623693C>A0.189
rpoC7670983729T>C0.178
rpoC7671193750A>G0.162
rpoC7671343765C>A0.143
rpoC7671583789T>C0.121
rpoC7671801271A>1271Q0.163
rpoC7671913822C>G0.170
rpoC7672063837C>G0.151
rpoC7672093840T>C0.159
rpoC7672123843G>C0.155
rpoC7672213852C>G0.193
rpoC7672303861G>C0.182
rpoC7672333864T>C0.186
rpoC7672633894T>C0.171
rpoC7672641299A>1299Q0.159
rpoC7672753906T>C0.165
rpoC7672783909T>C0.167
rpoC7672813912C>G0.169
rpoC7672843915C>T0.171
rpoC7672883919C>T0.173
rpsL78157112C>T0.129
rpsL78162869T>C0.149
rpsL78163172G>C0.146
rpsL78164990T>C0.156
rpsL78165596T>C0.134
rpsL781700141G>C0.144
rpsL781703144G>T0.140
rpsL781715156T>C0.125
rpsL781728169T>C0.127
rpsL781736177T>C0.129
rpsL781742183C>T0.134
rpsL781748189C>G0.140
rpsL781754195G>C0.138
rpsL781760201T>C0.136
rpsL781772213C>A0.138
rpsL781808249C>T0.156
rpsL781811252C>T0.156
rpsL781832273T>C0.133
rpsL781838279G>C0.163
rpsL781841282C>G0.163
rpsL781865306G>C0.130
rpsL781868309T>C0.133
rpsL781871312G>C0.133
rpsL781877318T>C0.129
rpsL781892333A>G0.146
rpsL781898339A>T0.141
rpsL781916357T>C0.131
rpsL781929124G>124S0.123
rplC8008146A>G0.133
rplC8008179A>T0.133
rplC80084436T>C0.158
rplC801168360C>G0.116
rplC801171363A>G0.115
rplC801180372C>G0.120
rplC801195387G>C0.127
rplC801207399C>T0.124
rplC801255447C>T0.123
rplC801300492C>G0.139
rplC801309501C>G0.143
rplC801312504G>C0.142
rplC801321513C>T0.135
rplC801367187A>187T0.118
embR1416222376F>376L0.200
embR1416234372C>372G0.213
rrs147192378T>C0.130
rrs147192580T>C0.130
rrs147193287A>G0.130
rrs147193489A>G0.130
rrs1471969124T>C0.185
rrs1471970125G>A0.185
rrs1472075230A>G0.135
rrs14731051260G>A0.114
rrs14731231278A>T0.127
rrs14731451300C>T0.153
rrs14731661321G>A0.179
rrs14732901445C>T0.165
rrl14736581T>A0.209
rrl14736592T>A0.209
rrl147366811C>T0.222
rrl147367720C>G0.254
rrl147375699G>A0.216
rrl1473758101G>T0.216
rrl1473806149C>T0.194
rrl1474093436G>T0.161
rrl1474099442G>A0.158
rrl1474103446A>T0.145
rrl1474140483C>T0.150
rrl1474151494C>T0.153
rrl1474181524C>T0.213
rrl1474249592G>T0.290
rrl1474291634TTTCCTCTCCGGAGGA>T0.328
rrl1474308651G>T0.241
rrl1474310653T>G0.236
rrl1474356699T>C0.244
rrl1474362705A>G0.244
rrl1474376719T>C0.244
rrl1474427770A>C0.147
rrl1474429772G>C0.143
rrl1474432775C>G0.139
rrl1474639982G>A0.326
rrl14747941137C>T0.236
rrl14748121155G>A0.260
rrl14748231166C>T0.234
rrl14748311174A>G0.229
rrl14749041247G>A0.282
rrl14749561299C>T0.179
rrl14749601303C>G0.179
rrl14749631306G>T0.194
rrl14749641307T>A0.194
rrl14749651308G>C0.194
rrl14749701313G>A0.200
rrl14750061349A>T0.200
rrl14750611404C>T0.159
rrl14750881431A>T0.255
rrl14751991542G>A0.273
rrl14752061549C>T0.273
rrl14752091552G>C0.273
rrl14752131556C>T0.273
rrl14752491592T>C0.271
rrl14752521595C>T0.275
rrl14752661609T>C0.244
rrl14752671610G>A0.244
rrl14752751618C>T0.229
rrl14752761619T>C0.229
rrl14752911634A>C0.239
rrl14753131656G>A0.273
rrl14753151658A>T0.273
rrl14753551698C>T0.265
rrl14753691712G>T0.280
rrl14754021745C>T0.271
rrl14754191762C>T0.282
rrl14754291772G>A0.282
rrl14754361779C>T0.297
rrl14754831826C>T0.333
rrl14755051848G>A0.387
rrl14755261869C>A0.316
rrl14755891932G>A0.778
rrl14755991942A>G0.211
rrl14756081951T>C0.238
rrl14756421985T>C0.186
rrl14756572000A>G0.184
rrl14756592002G>T0.184
rrl14758812224T>C0.425
rrl14759882331A>G0.450
rrl14760312374C>T0.318
rrl14760322375C>A0.318
rrl14760332376T>C0.318
rrl14760342377C>A0.318
rrl14760452388G>T0.304
rrl14760472390G>T0.292
rrl14760482391G>A0.292
rrl14760492392C>T0.292
rrl14760862429G>A0.324
rrl14760892432T>C0.286
rrl14760952438C>G0.256
rrl14761062449A>T0.244
rrl14761152458T>C0.262
rrl14761172460G>C0.262
rrl14762142557G>A0.190
rrl14762242567A>G0.188
rrl14762812624T>C0.220
rrl14765832926G>A0.171
rrl14765842927C>T0.171
rrl14765942937C>T0.143
rrl14765972940G>A0.140
rrl14766032946G>A0.143
rrl14766082951C>G0.128
rrl14766282971T>A0.140
fabG1167365773T>73K0.125
fabG116736671673667A>G0.123
fabG116736791673679T>G0.145
fabG116736851673685C>T0.156
fabG1167371091L>91I0.184
fabG1167371693A>93K0.182
fabG1167373398M>98I0.224
fabG116737481673748A>G0.164
fabG11673749104K>104R0.178
fabG11673758107K>107E0.184
fabG11673890151A>151S0.181
fabG116739011673901A>G0.171
fabG11673905156S>156A0.162
fabG116739161673916A>C0.155
fabG11673917160V>160L0.153
fabG116739221673922T>C0.178
fabG11673941168A>168S0.177
fabG116739461673946C>G0.167
fabG116739551673955G>C0.156
fabG116739611673961A>C0.127
inhA1674624423A>C0.133
inhA1674630429C>G0.128
inhA1674822621C>G0.118
inhA1674828627G>A0.118
inhA1674846215I>215M0.127
inhA1674870669T>C0.110
inhA1674942741T>G0.110
inhA1674960759C>G0.110
inhA1674966765T>G0.108
rpsA18335545T>5A0.167
rpsA183356827G>C0.177
rpsA183358948A>T0.158
rpsA183359554T>C0.153
rpsA1833661120A>G0.138
rpsA1833667126C>G0.144
rpsA1833748207C>G0.114
rpsA1833787246C>G0.119
rpsA1833790249T>C0.119
rpsA1833802261A>G0.123
rpsA1833811270G>T0.128
rpsA1833838297G>C0.136
rpsA1833841300C>G0.135
rpsA1833847306C>G0.129
rpsA1834177636A>C0.118
rpsA1834189648G>C0.126
rpsA1834195654G>C0.140
rpsA1834210669C>T0.151
rpsA1834222681T>C0.169
rpsA1834249708T>C0.123
rpsA1834261720A>G0.120
rpsA1834411870T>C0.127
rpsA1834417876G>C0.126
rpsA1834423882G>C0.123
rpsA1834435894G>C0.140
rpsA1834451910T>C0.143
rpsA1834465924T>C0.132
rpsA1834468927A>G0.143
rpsA1834489948T>C0.153
rpsA1834510969C>T0.149
rpsA1834513972C>G0.143
rpsA1834528987T>C0.165
rpsA1834540999G>C0.167
rpsA18345461005T>C0.169
rpsA18346091068T>C0.126
rpsA18346331092A>G0.130
rpsA18346391098T>C0.137
rpsA1834654371E>371D0.135
rpsA18346841143C>T0.143
rpsA18346901149T>C0.167
rpsA18347321191T>C0.145
rpsA1834733398A>398S0.145
rpsA18347381197A>G0.147
rpsA18347531212T>C0.141
rpsA1834765408E>408D0.157
rpsA1834775412A>412T0.155
rpsA18347801239A>G0.143
rpsA18347861245A>G0.146
rpsA18347891248T>C0.143
rpsA18347921251G>C0.141
rpsA18348491308C>G0.157
rpsA18348521311C>G0.145
tlyA191797233A>G1.000
tlyA1918236297A>C0.160
tlyA1918248309T>C0.147
tlyA1918251312T>G0.151
tlyA1918258107H>107E0.144
tlyA1918271111A>111V0.143
tlyA1918275336T>C0.143
tlyA1918278339C>G0.141
tlyA1918310124N>124S0.148
tlyA1918315126P>126A0.150
tlyA1918323384G>C0.139
tlyA1918326387G>C0.144
tlyA1918330131L>131V0.144
tlyA1918346136A>136V0.152
tlyA1918352138G>138D0.152
tlyA1918356417C>G0.152
tlyA1918359420A>G0.158
tlyA1918362423G>C0.153
tlyA1918422483T>C0.141
tlyA1918425486C>A0.137
tlyA1918434495C>G0.122
katG2154724463R>463L1.000
katG2155179933G>A0.157
katG2155185927A>G0.164
katG2155190308T>308S0.149
katG2155191921T>A0.149
katG2155200912A>G0.187
pncA2289047195G>A1.000
kasA25181213Q>3K0.161
kasA251813218C>T0.165
kasA251813824T>C0.163
kasA251817460A>G0.153
kasA251819026S>26A0.188
kasA251819929I>29V0.176
kasA2518220106C>T0.174
kasA2518234120G>A0.159
kasA251824845A>45V0.157
kasA251826149E>49D0.147
kasA251826350F>50Y0.147
kasA251826551V>51I0.147
kasA2518413100S>100N0.143
kasA2518421103V>103L0.138
kasA2518429315A>C0.128
kasA2518439109A>109S0.134
kasA2518444330T>C0.128
kasA2518447333T>G0.126
kasA2518459345T>C0.133
kasA2518462348A>C0.131
kasA2518468354A>C0.134
kasA2518474360G>A0.135
kasA2518480366T>C0.182
kasA2518483369C>G0.182
kasA2518504390T>C0.189
kasA2518506131A>131E0.186
kasA2518519405G>C0.189
kasA2518528414C>G0.187
kasA2518540426T>C0.183
kasA2518561447T>C0.190
kasA2518567453G>C0.152
kasA2518570456G>C0.152
kasA2518574154I>154V0.158
kasA2518579465T>C0.154
kasA2518588474T>C0.167
kasA2518591477G>C0.165
kasA2518609165M>165I0.165
kasA2518864750G>C0.126
kasA2518879765A>G0.138
kasA2518885771T>C0.140
kasA2518898784T>C0.135
kasA2518906792A>G0.135
kasA2518910266L>266M0.137
kasA2518921807T>C0.127
kasA2518951837G>C0.111
kasA2519008894C>G0.125
kasA2519050936C>G0.137
kasA2519053939G>C0.137
kasA2519056942G>C0.133
kasA2519062948T>G0.197
kasA2519068954C>T0.190
kasA2519072320A>320T0.179
kasA2519107993T>C0.165
kasA2519108332D>332Q0.165
kasA25191221008G>C0.159
kasA25191371023T>G0.163
kasA25191581044C>T0.171
kasA25191671053T>G0.175
kasA25191731059C>G0.183
kasA2519196361T>361S0.176
ahpC272621018T>C0.117
ahpC272621624T>C0.132
ahpC272621927A>G0.128
ahpC272623214Q>14E0.132
ahpC272624351T>G0.127
ahpC272624452C>T0.127
ahpC272625120G>20A0.129
ahpC272625563T>C0.130
ahpC272625866C>T0.161
ahpC2726303111T>C0.213
ahpC272631140S>40N0.186
ahpC272631541D>41E0.191
ahpC272631842E>42D0.194
ahpC272632244P>44A0.191
ahpC2726330138G>A0.200
ahpC2726336144G>C0.200
ahpC2726348156T>C0.224
ahpC2726357165A>G0.246
ahpC2726366174G>C0.265
ahpC2726378186T>G0.208
ahpC2726387195C>T0.164
ahpC2726390198G>C0.167
ahpC2726393201G>C0.157
ahpC272639769S>69G0.153
ahpC2726408216T>C0.141
ahpC2726414222G>A0.125
ahpC272642076E>76D0.125
ahpC2726493101N>101E0.118
ahpC2726506105T>105K0.125
ahpC2726508316T>C0.123
ahpC2726528336C>G0.113
ahpC2726540348C>G0.118
ahpC2726543351A>G0.114
ahpC2726546354C>G0.115
ahpC2726551120Q>120L0.122
ahpC2726556122A>122T0.117
ahpC2726564372C>G0.143
ahpC2726591399C>G0.131
ahpC2726593134V>134A0.133
ahpC2726600408T>C0.135
ahpC2726601137I>137L0.135
folC2747289104P>104A0.118
folC2747290309T>C0.119
folC2747293306C>T0.116
folC2747302297T>C0.133
folC2747314285T>G0.143
folC2747317282G>C0.136
folC274734386V>86I0.129
folC274735582V>82I0.131
folC2747359240G>C0.135
folC2747362237C>G0.135
folC274739469I>69V0.132
folC2747395204A>G0.128
folC2747407192A>G0.111
folC274741562R>62C0.115
folC2747419180G>C0.119
folC2747422177C>T0.120
folC2747425174G>A0.116
folC2747442157A>G0.189
folC274746744D>44E0.156
ribD2987066228A>G0.114
ribD2987069231T>C0.115
ribD298709285V>85A0.110
embC4240512217S>217T0.126
embC4240516654G>C0.126
embC4240519657T>C0.125
embC4240543681G>C0.129
embC4240651789G>A0.143
embC4240726864G>C0.147
embC4240780918T>C0.168
embC4240783921G>C0.170
embC4240789927T>C0.160
embC4240819957A>G0.167
embC4240828966G>A0.165
embC4240831969T>G0.150
embC42408671005T>C0.134
embC42408701008T>C0.133
embC42408731011C>G0.131
embC42408791017G>C0.132
embC4240880340A>340T0.132
embC42408851023T>C0.124
embC42408971035C>G0.117
embC42409451083T>G0.120
embC4240954364I>364M0.114
embC42409601098G>C0.116
embC42410891227C>G0.130
embC42410951233C>T0.143
embC42411071245G>C0.130
embC42411401278A>G0.150
embC42411461284C>G0.167
embC42411581296T>C0.167
embC42411611299C>G0.168
embC42411621300T>C0.170
embC42411701308G>C0.167
embC42411731311C>T0.163
embC42412031341T>C0.156
embC42412061344G>C0.155
embC42412181356G>C0.176
embC42412301368A>G0.158
embC42412331371G>C0.151
embC4241318486P>486T0.988
embC42414491587C>G0.190
embC4241453531I>531V0.185
embC42414791617C>G0.202
embC42414801618T>C0.202
embC42414881626G>C0.211
embC4241496545A>545G0.189
embC42415001638A>C0.191
embC4241501547S>547T0.191
embC42415061644G>C0.209
embC42415181656A>G0.211
embC42415211659T>C0.213
embC42415301668C>G0.219
embC42415361674A>G0.213
embC42415391677T>C0.213
embC42415451683T>C0.208
embC42415481686T>C0.211
embC42415511689A>G0.208
embC4241567569I>569V0.247
embC42415721710C>G0.250
embC42415781716G>C0.247
embC42415841722T>C0.247
embC42415871725C>G0.247
embC4241591577L>577V0.263
embC42416111749G>C0.304
embC42416141752A>C0.304
embC42416261764T>C0.329
embC42416351773G>C0.329
embC42416441782G>C0.299
embC42416481786T>C0.294
embC4241657599S>599P0.323
embC42416651803G>C0.313
embC42416711809T>C0.318
embC42416891827G>C0.172
embC4241691610G>610A0.169
embC4241694611A>611V0.164
embC42416981836G>C0.169
embC42417041842C>G0.169
embC42417071845G>A0.179
embC42417131851G>C0.215
embC42417191857G>C0.212
embC4241727622F>622Y0.274
embC4241741627V>627L0.244
embC4241747629V>629L0.241
embC4241750630L>630V0.241
embC42417551893C>G0.256
embC42417701908T>C0.276
embC42417911929G>C0.256
embC42417941932C>G0.259
embC42417971935C>T0.259
embC42418091947A>C0.250
embC42419952133C>G0.218
embC4242002714L>714V0.203
embC42420072145G>A0.211
embC4242011717L>717V0.211
embC4242024721V>721A0.193
embC4242036725Q>725L0.195
embC4242045728I>728T0.118
embC42420552193C>T0.149
embC42420612199G>C0.155
embC42420702208T>C0.146
embC4242075738R>738H0.851
embC42420792217T>C0.151
embC42420852223A>G0.157
embC42420912229T>G0.160
embC42420922230T>C0.160
embC4242095745A>745T0.169
embC42421062244C>G0.195
embC42421212259A>G0.179
embC4242138759L>759Q0.160
embC42421422280T>C0.160
embC42421452283C>G0.160
embC42421512289A>G0.160
embC42421602298G>C0.123
embC4242161767A>767S0.122
embC4242170770T>770G0.120
embC42421752313G>C0.123
embC4242176772P>772S0.123
embC4242179773L>773A0.123
embC42421842322C>G0.123
embC42421932331G>C0.145
embC42421962334A>C0.145
embC42422082346T>G0.156
embC42422202358A>G0.167
embC42422292367C>A0.158
embC4242245795T>795R0.129
embC4242519886T>886S0.121
embC42425322670A>T0.162
embC4242539893S>893P0.159
embC42425442682C>T0.171
embC4242552897R>897Q0.176
embC4242554898L>898V0.173
embC42425772715A>G0.178
embC4242585908A>908G0.151
embC42425892727A>G0.137
embC4242594911H>911P0.133
embC42425982736T>C0.118
embC42426012739G>C0.113
embC4242607915M>915I0.113
embC4242608916E>916Q0.113
embC42426312769G>C0.114
embC42426432781C>T0.892
embC4242689943V>943I0.156
embC4242710950Q>950E0.175
embC42427152853T>C0.174
embC42427422880C>G0.152
embC42427482886A>G0.161
embC42427542892G>C0.159
embC4242764968V>968L0.145
embC42427722910G>C0.151
embC4242779973N>973D0.132
embA42443661134C>G0.159
embA42443721140T>G0.169
embA42443781146G>A0.157
embA42443811149G>A0.148
embA42443901158G>C0.136
embA42443931161G>C0.122
embA42443961164T>C0.121
embA42444081176G>C0.118
embA4244523431P>431A0.125
embA42445341302T>C0.136
embA42445371305T>G0.136
embA42445431311C>G0.140
embA4244547439I>439V0.133
embA42445821350T>C0.118
embA42445851353A>G0.119
embA4244670480A>480L0.118
embA42446751443A>G0.118
embA42446781446G>C0.117
embA42446811449A>C0.128
embA42446901458G>A0.148
embA42447021470C>G0.155
embA42447081476C>G0.153
embA4244728499F>499W0.147
embA42450411809C>G0.120
embA42450441812G>C0.120
embA42450531821G>C0.144
embA42450601828T>C0.152
embA42450831851A>C0.189
embA42450891857G>C0.179
embA42451011869G>C0.173
embA42451371905T>C0.200
embA42451461914G>A0.194
embA42451491917C>G0.186
embA4245153641I>641V0.184
embA42451821950T>C0.180
embA42451891957C>T0.182
embA4245198656L>656I0.204
embA42452071975T>C0.200
embA42452151983A>C0.204
embA4245222664Y>664Q0.194
embA42452482016G>C0.178
embA42452572025A>G0.184
embA42452632031A>G0.188
embA4245282684I>684V0.176
embA42452852053T>C0.168
embA42452902058C>G0.162
embA42452932061T>G0.162
embA42452962064G>C0.160
embA42452992067A>G0.162
embA42454312199T>C0.119
embA42454342202G>C0.119
embA42454702238T>C0.147
embA42454732241C>G0.149
embA4245483751Q>751A0.112
embA4245490753V>753A0.115
embA4245501757A>757T0.112
embA42455122280G>C0.116
embA42455182286A>G0.116
embA42455242292G>C0.116
embA42455272295C>G0.114
embA42455302298T>C0.114
embA4245531767I>767V0.114
embA4245535768S>768N0.118
embA42455392307C>G0.130
embA42455422310C>G0.133
embA42455572325G>A0.203
embA42455752343C>G0.192
embA4245576782K>782Q0.192
embA42456592427C>G0.158
embA42456742442A>C0.205
embA42456772445G>C0.203
embA4245693821I>821V0.189
embA42457012469G>C0.192
embA42457042472G>C0.216
embA42457252493A>G0.192
embA42457262494T>C0.192
embA42457372505A>C0.188
embA42457402508T>C0.215
embA42457642532G>C0.270
embA4245772847N>847T0.265
embA42457852553G>C0.231
embA42458072575T>C0.154
embA42458122580G>C0.156
embA4245813861P>861A0.159
embA4245820863S>863T0.164
embA42458242592G>C0.164
embA42458332601G>C0.194
embA42458422610G>C0.213
embA42458452613T>C0.216
embA42458512619G>C0.224
embA42458602628C>G0.215
embA4245885885D>885T0.197
embA4245892887I>887T0.195
embA42458992667C>G0.190
embA42459022670G>A0.197
embA42459052673C>G0.200
embA42459112679A>G0.200
embA42459172685G>A0.200
embA4245930900G>900R0.170
embA42460102778G>T0.108
embA42460222790C>G0.125
embA42460402808C>G0.126
embA4246041937D>937N0.126
embA42460552823T>C0.128
embA42460642832T>C0.135
embA4246080950P>950S0.120
embA42461642932T>C0.167
embA42461842952A>C0.168
embA42461962964C>G0.173
embA42462052973A>G0.168
embA42462112979T>C0.168
embA42462172985G>A0.149
embA42462202988T>C0.149
embA42462232991C>T0.149
embA4246227999I>999V0.151
embA42462353003G>A0.196
embA42462421004Q>1004G0.188
embA42462503018G>C0.173
embA42462563024G>T0.160
embA42462593027G>C0.161
embA42462641011H>1011R0.144
embA42462923060A>G0.128
embA42463291033T>1033A0.129
embA42463493117C>G0.136
embB4246669156C>G0.140
embB4247464951C>G0.139
embB4247470957T>C0.141
embB4247491978G>C0.152
embB4247497984T>C0.175
embB4247512999T>C0.138
embB42475391026T>C0.133
embB42475541041T>C0.137
embB42475661053C>A0.144
embB42475721059A>G0.144
embB4247579356A>356F0.135
embB42475871074G>A0.131
embB42476031090C>T0.139
embB42476111098G>T0.133
embB42476141101T>C0.136
embB4247940476L>476W0.121
embB42479741461C>G0.138
embB42480071494C>G0.120
embB4248011500S>500R0.116
embB4248014501T>501A0.116
embB4248035508V>508I0.123
embB42480401527C>G0.126
embB4248041510A>510T0.125
embB4248044511K>511A0.125
embB42480701557T>C0.175
embB42480851572T>C0.177
embB42480971584C>G0.172
embB42481301617G>C0.163
embB42481421629T>C0.159
embB42481431630T>C0.157
embB42481571644A>G0.193
embB42481721659G>C0.206
embB42481991686A>G0.172
embB4248200563I>563V0.169
embB42482051692C>G0.164
embB4248206565S>565G0.169
embB42482201707A>C0.188
embB42483041791G>C0.163
embB42483161803C>G0.144
embB42483191806A>G0.144
embB42483431830G>C0.153
embB42483501837T>C0.127
embB42483551842A>G0.125
embB42483581845C>G0.128
embB42483611848A>C0.127
embB4248362617S>617A0.129
embB42483731860C>G0.174
embB42483821869C>G0.186
embB42483861873C>A0.155
embB42484571944T>C0.118
embB42484721959T>C0.115
embB42484751962G>C0.115
embB4248504664D>664G0.122
embB42485352022C>G0.124
embB42491532640G>C0.111
embB4249164884A>884D0.125
ethA43263071167G>C0.172
ethA43263101164A>G0.172
ethR4327746198A>G0.151
ethR432775569E>69D0.154
gid4407588615T>C1.000

Analysis pipeline specifications

TBProfiler Version: 0.1

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;