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: 5d9cdc5f5bf07
Sample: 5d9cdc5f5bf07

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Summary
ID: 5d9cdc5f5bf07
Date: Tue Oct 8 20:02:11 2019
Strain: lineage2.2.1;lineage4.3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
EthambutolRembB p.His312Arg (0.14)
Pyrazinamide
StreptomycinRrrs r.462c>t (0.14)
Ethionamide
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

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6123p.Ala295Gly0.122
gyrB6127c.888G>C0.129
gyrB6136c.897G>A0.145
gyrB6139c.900G>C0.141
gyrB6256c.1017G>A0.136
gyrB6268c.1029C>G0.134
gyrB6286c.1047T>C0.124
gyrB6289c.1050C>T0.137
gyrB6292c.1053G>C0.143
gyrB6307c.1068T>G0.137
gyrB6319c.1080G>C0.127
gyrB6346c.1107C>T0.131
gyrB6362c.1123T>C0.135
gyrB6797p.Gly520Ser0.133
gyrB6811c.1572C>T0.136
gyrB7165c.1926C>G0.128
gyrB7178c.1939T>C0.145
gyrB7186c.1947C>G0.132
gyrA7362p.Glu21Gln1.000
gyrA7480p.Phe60Tyr0.127
gyrA7496c.195C>G0.132
gyrA7585p.Ser95Thr1.000
gyrA7835c.534A>C0.127
gyrA7853c.552C>G0.139
gyrA8207c.906T>C0.135
gyrA8420c.1119T>C0.162
gyrA8442c.1141C>T0.145
gyrA8465c.1164C>G0.134
gyrA8480c.1179C>T0.149
gyrA8486c.1185T>C0.140
gyrA8546c.1245T>C0.126
gyrA8552c.1251C>A0.125
gyrA9017c.1716C>G0.136
gyrA9032c.1731T>C0.124
gyrA9035c.1734G>C0.131
gyrA9068c.1767G>C0.140
gyrA9071c.1770G>C0.134
gyrA9080c.1779G>T0.150
gyrA9089c.1788G>C0.176
gyrA9099c.1798T>C0.175
gyrA9104c.1803C>G0.188
gyrA9119c.1818A>G0.206
gyrA9122c.1821C>G0.202
gyrA9143c.1842T>C0.217
gyrA9152c.1851C>T0.150
gyrA9153p.Thr618Glu0.153
gyrA9158c.1857C>T0.155
gyrA9161c.1860C>G0.168
gyrA9182c.1881T>C0.184
gyrA9191c.1890G>C0.176
gyrA9200c.1899A>G0.154
gyrA9204p.Ser635Thr0.151
gyrA9304p.Gly668Asp1.000
gyrA9665c.2364A>C0.144
rpoB759606c.-201T>C0.185
rpoB759629c.-178T>C0.165
rpoB760283c.477G>C0.174
rpoB760298c.492G>C0.175
rpoB760307c.501T>C0.158
rpoB760310c.504G>C0.158
rpoB760328c.522G>C0.154
rpoB760331c.525G>C0.143
rpoB760475c.669A>G0.124
rpoB760481c.675G>T0.130
rpoB760547c.741G>C0.133
rpoB760563c.757C>A0.134
rpoB760591p.Val262Ala0.194
rpoB760611c.805T>C0.171
rpoB760646c.840C>G0.187
rpoB760655c.849A>G0.175
rpoB760661c.855A>C0.171
rpoB760670c.864G>C0.168
rpoB760674c.868T>C0.163
rpoB760679c.873A>G0.182
rpoB760683c.877T>C0.197
rpoB760715c.909C>G0.172
rpoB760718c.912C>T0.174
rpoB760724c.918T>C0.173
rpoB760730c.924T>C0.164
rpoB760751c.945G>C0.160
rpoB760793c.987A>G0.171
rpoB760805c.999G>C0.183
rpoB760817c.1011A>G0.163
rpoB760820c.1014T>C0.162
rpoB760826c.1020C>G0.176
rpoB760830c.1024T>C0.184
rpoB760841c.1035T>C0.167
rpoB760845p.Thr347Pro0.169
rpoB760859c.1053T>C0.164
rpoB760862c.1056G>C0.162
rpoB760869p.Val355Ile0.183
rpoB760886c.1080A>G0.214
rpoB760925c.1119T>C0.198
rpoB760928c.1122G>C0.184
rpoB760931c.1125C>G0.188
rpoB760934c.1128C>T0.196
rpoB760946c.1140A>G0.236
rpoB760982c.1176G>C0.195
rpoB760985c.1179G>C0.196
rpoB760991c.1185G>C0.193
rpoB761006c.1200C>G0.206
rpoB761015c.1209G>C0.198
rpoB761021c.1215G>C0.202
rpoB761027c.1221A>G0.198
rpoB761036c.1230G>C0.162
rpoB761037c.1231T>C0.160
rpoB761057c.1251G>C0.170
rpoB761129c.1323G>C0.133
rpoB761133c.1327T>C0.132
rpoB761150c.1344A>C0.148
rpoB761153c.1347G>C0.129
rpoB761189c.1383T>C0.133
rpoB761195c.1389G>C0.125
rpoB761207c.1401C>T0.133
rpoB761213c.1407G>C0.139
rpoB761249c.1443A>G0.167
rpoB761255c.1449T>G0.163
rpoB761261c.1455G>T0.159
rpoB761306c.1500C>G0.146
rpoB761327c.1521A>G0.146
rpoB761330c.1524G>C0.140
rpoB761510c.1704T>C0.157
rpoB761531c.1725C>G0.145
rpoB761537c.1731C>G0.143
rpoB761573c.1767C>G0.136
rpoB761579c.1773G>C0.135
rpoB761588c.1782C>T0.140
rpoB761606c.1800C>G0.146
rpoB761612c.1806G>C0.149
rpoB761615c.1809A>C0.154
rpoB761675c.1869G>C0.151
rpoB761885c.2079T>C0.159
rpoB761948c.2142G>C0.151
rpoB761954c.2148C>G0.149
rpoB762008c.2202C>T0.151
rpoB762017c.2211A>G0.134
rpoB762053c.2247T>C0.139
rpoB762083c.2277T>C0.128
rpoB762086c.2280G>C0.145
rpoB762101c.2295C>G0.142
rpoB762143c.2337T>C0.136
rpoB762167c.2361T>C0.175
rpoB762176c.2370T>C0.171
rpoB762185c.2379G>C0.175
rpoB762206c.2400C>G0.175
rpoB762233c.2427G>C0.208
rpoB762246c.2440C>T0.172
rpoB762254c.2448T>G0.167
rpoB762257c.2451C>G0.165
rpoB762266c.2460T>C0.187
rpoB762284c.2478G>C0.168
rpoB762293c.2487T>C0.150
rpoB762317c.2511A>G0.133
rpoB762434c.2628T>C0.172
rpoB762449c.2643C>A0.161
rpoB762467c.2661C>T0.155
rpoB762509c.2703T>G0.144
rpoB762510p.Ala902Pro0.145
rpoB762521c.2715C>T0.152
rpoB762533c.2727T>C0.146
rpoB762536c.2730T>C0.143
rpoB762537c.2731T>C0.140
rpoB762551c.2745C>G0.154
rpoB762729p.Gln975Lys0.150
rpoB762827c.3021G>C0.159
rpoB762929c.3123G>C0.164
rpoB762989c.3183G>C0.175
rpoB762995c.3189G>T0.180
rpoB763013c.3207C>G0.154
rpoB763028c.3222T>C0.165
rpoB763031c.3225T>C0.161
rpoB763034c.3228C>G0.165
rpoB763040c.3234C>G0.160
rpoB763067c.3261C>G0.170
rpoB763070c.3264T>C0.165
rpoB763085c.3279C>G0.135
rpoB763115c.3309T>C0.149
rpoB763136c.3330C>T0.151
rpoB763148c.3342G>C0.144
rpoB763158c.3352C>T0.152
rpoB763166c.3360A>G0.140
rpoB763190c.3384C>T0.136
rpoB763214c.3408T>C0.123
rpoB763226c.3420A>G0.139
rpoB763227c.3421C>T0.137
rpoB763238c.3432T>C0.165
rpoB763253c.3447G>C0.160
rpoB763256c.3450G>A0.165
rpoB763268c.3462C>G0.155
rpoC763402c.33C>G0.159
rpoC763411c.42T>G0.158
rpoC763414c.45T>C0.167
rpoC763441c.72C>T0.160
rpoC763444c.75T>C0.160
rpoC763456c.87A>G0.172
rpoC763657c.288G>A0.146
rpoC763660c.291T>G0.149
rpoC763675c.306C>G0.164
rpoC763696c.327T>C0.172
rpoC763702c.333C>G0.168
rpoC763717c.348T>C0.144
rpoC763723c.354G>C0.165
rpoC763732c.363C>G0.171
rpoC763741c.372C>T0.152
rpoC763744c.375G>C0.153
rpoC763900c.531G>C0.150
rpoC763915c.546C>T0.175
rpoC763942c.573C>G0.194
rpoC763945c.576T>C0.179
rpoC763951c.582G>C0.180
rpoC763960c.591T>C0.164
rpoC763987c.618C>T0.126
rpoC763991p.Ile208Leu0.125
rpoC763996c.627T>C0.125
rpoC764002c.633C>G0.126
rpoC764005c.636G>C0.124
rpoC764236c.867G>A0.155
rpoC764248c.879C>G0.159
rpoC764257c.888G>C0.162
rpoC764266c.897T>C0.150
rpoC764269c.900G>C0.149
rpoC764272c.903G>C0.160
rpoC764278c.909A>G0.152
rpoC764338c.969G>A0.192
rpoC764353c.984G>C0.173
rpoC764365c.996C>T0.149
rpoC764489c.1120C>T0.147
rpoC764497c.1128A>G0.164
rpoC764510c.1141C>T0.150
rpoC764521c.1152T>C0.144
rpoC764527c.1158C>T0.157
rpoC764536c.1167G>C0.153
rpoC764539c.1170C>G0.156
rpoC764548c.1179G>A0.189
rpoC764551c.1182G>C0.176
rpoC764554c.1185C>T0.188
rpoC764560c.1191T>C0.194
rpoC764566c.1197C>G0.198
rpoC764575c.1206T>G0.204
rpoC764593c.1224C>T0.211
rpoC764611c.1242G>T0.215
rpoC764650c.1281G>C0.167
rpoC764651c.1282T>A0.167
rpoC764752c.1383G>C0.160
rpoC764764c.1395T>C0.162
rpoC764809c.1440C>T0.148
rpoC764815c.1446A>G0.150
rpoC764858c.1489T>C0.145
rpoC764948c.1579T>C0.150
rpoC764968c.1599T>C0.164
rpoC764995c.1626C>G0.164
rpoC765007c.1638T>G0.152
rpoC765008c.1639T>C0.151
rpoC765011c.1642A>T0.154
rpoC765019c.1650A>G0.167
rpoC765034c.1665T>C0.172
rpoC765040c.1671T>C0.155
rpoC765041c.1672T>C0.157
rpoC765047c.1678T>C0.184
rpoC765055c.1686C>G0.181
rpoC765089c.1720T>C0.137
rpoC765292c.1923G>C0.143
rpoC765319c.1950A>G0.138
rpoC765327p.His653Pro0.133
rpoC765330p.Ser654Asn0.135
rpoC765383p.Met672Leu0.142
rpoC765421c.2052C>G0.145
rpoC765451c.2082C>A0.168
rpoC765478c.2109T>C0.147
rpoC765499c.2130C>G0.146
rpoC765553c.2184C>T0.149
rpoC765556c.2187G>C0.140
rpoC765580c.2211G>C0.167
rpoC765613p.His748Gln0.152
rpoC765625c.2256C>G0.157
rpoC765631p.Asp754Glu0.144
rpoC765700c.2331T>C0.198
rpoC765734c.2365T>C0.196
rpoC765739c.2370G>T0.192
rpoC765751c.2382C>G0.175
rpoC765753p.Asp795Ala0.188
rpoC765772c.2403C>G0.151
rpoC765784c.2415C>G0.169
rpoC765787c.2418C>T0.164
rpoC765793c.2424C>G0.157
rpoC765796c.2427C>T0.146
rpoC765811c.2442T>C0.154
rpoC765814c.2445A>G0.162
rpoC765826c.2457T>C0.162
rpoC765835c.2466C>T0.173
rpoC765850c.2481G>C0.167
rpoC765883c.2514C>G0.155
rpoC765886c.2517C>G0.161
rpoC765892c.2523T>C0.167
rpoC765937c.2568T>C0.151
rpoC765947c.2578T>C0.157
rpoC765967c.2598C>T0.152
rpoC765982c.2613C>G0.152
rpoC766447c.3078T>C0.139
rpoC766726c.3357T>C0.153
rpoC766738c.3369G>C0.156
rpoC766765c.3396A>C0.167
rpoC766774c.3405T>C0.164
rpoC766801c.3432C>G0.159
rpoC766804c.3435A>G0.151
rpoC766861c.3492G>C0.198
rpoC766864c.3495G>C0.207
rpoC766900c.3531T>C0.223
rpoC766933c.3564A>G0.208
rpoC766945c.3576A>G0.200
rpoC766963c.3594T>C0.206
rpoC766972c.3603G>C0.198
rpoC766996c.3627C>T0.181
rpoC767009c.3640T>A0.160
rpoC767014c.3645G>C0.153
rpoC767033c.3664T>A0.193
rpoC767059c.3690T>G0.200
rpoC767062c.3693C>A0.205
rpoC767098c.3729T>C0.247
rpoC767119c.3750A>G0.259
rpoC767134c.3765C>A0.259
rpoC767158c.3789T>C0.226
rpoC767180p.Ala1271Gln0.207
rpoC767191c.3822C>G0.206
rpoC767206c.3837C>G0.242
rpoC767209c.3840T>C0.250
rpoC767212c.3843G>C0.256
rpoC767221c.3852C>G0.244
rpoC767230c.3861G>C0.259
rpoC767233c.3864T>C0.250
rpoC767263c.3894T>C0.227
rpoC767264p.Ala1299Gln0.215
rpoC767275c.3906T>C0.213
rpoC767278c.3909T>C0.217
rpoC767281c.3912C>G0.217
rpoC767284c.3915C>T0.210
rpoC767288c.3919C>T0.203
rpsL781395c.-165T>C1.000
rpsL781808c.249C>T0.161
rpsL781811c.252C>T0.160
rpsL781832c.273T>C0.156
rpsL781838c.279G>C0.155
rpsL781841c.282C>G0.155
rpsL781865c.306G>C0.182
rpsL781868c.309T>C0.184
rpsL781871c.312G>C0.182
rpsL781877c.318T>C0.180
rpsL781892c.333A>G0.200
rpsL781898c.339A>T0.206
rpsL781916c.357T>C0.186
rpsL781929p.Gly124Ser0.175
rplC801300c.492C>G0.124
rplC801309c.501C>G0.140
rplC801312c.504G>C0.132
rplC801423c.615G>C0.139
rrs1472969r.1124a>g0.175
rrs1472970r.1125c>g0.175
rrs1472977r.1132g>c0.182
rrs1472978r.1133t>c0.184
rrs1473166r.1321g>a0.132
rrl1473943r.286g>t0.130
rrl1473946r.289a>t0.125
rrl1473995r.338g>t0.135
rrl1474001r.344c>t0.138
rrl1474249r.592g>t0.190
rrl1474356r.699t>c0.126
rrl1474362r.705a>g0.123
rrl1474376r.719t>c0.127
rrl1474639r.982g>a0.134
rrl1474794r.1137c>t0.174
rrl1474812r.1155g>a0.164
rrl1474823r.1166c>t0.155
rrl1474831r.1174a>g0.140
rrl1475088r.1431a>t0.167
rrl1475199r.1542g>a0.167
rrl1475206r.1549c>t0.182
rrl1475209r.1552g>c0.184
rrl1475213r.1556c>t0.202
rrl1475249r.1592t>c0.163
rrl1475252r.1595c>t0.165
rrl1475266r.1609t>c0.168
rrl1475267r.1610g>a0.173
rrl1475275r.1618c>t0.200
rrl1475276r.1619t>c0.202
rrl1475291r.1634a>c0.180
rrl1475313r.1656g>a0.151
rrl1475315r.1658a>t0.168
rrl1475355r.1698c>t0.149
rrl1475369r.1712g>t0.141
rrl1475402r.1745c>t0.149
rrl1475429r.1772g>a0.153
rrl1475436r.1779c>t0.159
rrl1475483r.1826c>t0.173
rrl1475505r.1848g>a0.159
rrl1475526r.1869c>a0.173
rrl1475599r.1942a>g0.150
rrl1475608r.1951t>c0.135
rrl1475763r.2106c>t0.184
rrl1476086r.2429g>a0.125
rrl1476106r.2449a>t0.130
rrl1476115r.2458t>c0.125
rrl1476117r.2460g>c0.127
rrl1476214r.2557g>a0.170
rrl1476224r.2567a>g0.150
rrl1476281r.2624t>c0.156
rrl1476583r.2926g>a0.138
rrl1476584r.2927c>t0.140
rrl1476594r.2937c>t0.140
rrl1476597r.2940g>a0.155
rrl1476603r.2946g>a0.153
rrl1476608r.2951c>g0.143
rrl1476628r.2971t>a0.137
rrl1476750r.3093t>c0.142
rrl1476755r.3098g>a0.158
rrl1476759r.3102t>c0.150
rrl1476770r.3113t>c0.144
fabG11673568c.129C>G0.151
fabG11673574c.135C>G0.153
fabG11673580c.141T>G0.153
fabG11673589c.150A>G0.125
fabG11673641p.Val68Ile0.121
fabG11673657p.Thr73Lys0.147
fabG11673660p.Ala74Glu0.128
fabG11673664c.225A>C0.128
fabG11673667c.228A>G0.126
fabG11673679c.240T>G0.124
fabG11673941p.Ala168Ser0.154
fabG11673946c.507C>G0.151
fabG11673955c.516G>C0.151
fabG11673961c.522A>C0.143
fabG11673985c.546C>G0.195
fabG11674006p.Asp189Glu0.188
fabG11674079p.Pro214Ala0.143
fabG11674114c.675T>A0.136
inhA1674255c.54C>T0.133
inhA1674480c.279T>C0.133
inhA1674486c.285T>C0.131
inhA1674504c.303C>G0.158
inhA1674537c.336C>G0.129
inhA1674542p.Ala114Glu0.125
inhA1674546c.345T>C0.122
inhA1674774c.573A>G0.147
inhA1674789c.588G>C0.144
inhA1674801c.600T>C0.140
rpsA1833721c.180A>G0.127
rpsA1833727c.186G>C0.132
rpsA1833742c.201A>G0.140
rpsA1833787c.246C>G0.165
rpsA1833790c.249T>C0.164
rpsA1833802c.261A>G0.162
rpsA1833811c.270G>T0.158
rpsA1833838c.297G>C0.177
rpsA1833841c.300C>G0.178
rpsA1833847c.306C>G0.173
rpsA1833856c.315A>G0.172
rpsA1833874c.333T>C0.164
rpsA1833928c.387G>C0.165
rpsA1833940c.399C>G0.159
rpsA1834000c.459G>C0.159
rpsA1834021c.480C>T0.144
rpsA1834030c.489C>G0.145
rpsA1834099c.558C>G0.212
rpsA1834102c.561T>C0.181
rpsA1834105c.564C>G0.175
rpsA1834108c.567C>G0.172
rpsA1834123c.582C>G0.177
rpsA1834177c.636A>C1.000
rpsA1834195c.654G>C0.140
rpsA1834210c.669C>T0.144
rpsA1834249c.708T>C0.130
rpsA1834261c.720A>G0.135
rpsA1834264c.723G>C0.140
rpsA1834303c.762T>C0.150
rpsA1834306c.765T>C0.137
rpsA1834411c.870T>C0.140
rpsA1834417c.876G>C0.147
rpsA1834423c.882G>C0.146
rpsA1834451c.910T>C0.127
rpsA1834465c.924T>C0.135
rpsA1834468c.927A>G0.140
rpsA1834489c.948T>C0.150
rpsA1834501c.960G>C0.158
rpsA1834510c.969C>T0.152
rpsA1834513c.972C>G0.165
rpsA1834528c.987T>C0.152
rpsA1834546c.1005T>C0.131
rpsA1834690c.1149T>C0.130
rpsA1834733p.Ala398Ser0.133
rpsA1834738c.1197A>G0.136
rpsA1834753c.1212T>C0.151
rpsA1834775p.Ala412Thr0.147
rpsA1834780c.1239A>G0.140
rpsA1834849c.1308C>G0.152
rpsA1834852c.1311C>G0.155
tlyA1917972c.33A>G1.000
tlyA1918310p.Asn124Ser0.126
tlyA1918315p.Pro126Ala0.126
tlyA1918326c.387G>C0.120
tlyA1918330p.Leu131Val0.121
tlyA1918346p.Ala136Val0.143
tlyA1918352p.Gly138Asp0.146
tlyA1918356c.417C>G0.143
tlyA1918359c.420A>G0.147
tlyA1918362c.423G>C0.147
tlyA1918392c.453A>C0.126
tlyA1918422c.483T>C0.120
katG2154724p.Arg463Leu0.991
kasA2518162c.48G>A0.183
kasA2518174c.60A>G0.195
kasA2518190p.Ser26Ala0.192
kasA2518199p.Ile29Val0.200
kasA2518220c.106C>T0.222
kasA2518234c.120G>A0.195
kasA2518248p.Ala45Val0.169
kasA2518263p.Phe50Tyr0.131
kasA2518265p.Val51Ile0.128
kasA2518483c.369C>G0.135
kasA2518504c.390T>C0.153
kasA2518506p.Ala131Glu0.148
kasA2518519c.405G>C0.145
kasA2518528c.414C>G0.144
kasA2518540c.426T>C0.147
kasA2518561c.447T>C0.147
kasA2518588c.474T>C0.148
kasA2518591c.477G>C0.149
kasA2518609p.Met165Ile0.165
kasA2518624c.510C>G0.157
kasA2518639c.525G>C0.133
kasA2518672c.558G>C0.143
kasA2518678c.564C>T0.133
kasA2518768c.654C>T0.128
kasA2518777c.663C>T0.132
kasA2518825c.711T>C0.148
kasA2519107c.993T>C0.128
kasA2519108p.Asp332Gln0.125
kasA2519122c.1008G>C0.132
kasA2519158c.1044C>T0.130
kasA2519167c.1053T>G0.133
folC2747167p.Lys144Asn1.000
thyX3067355c.591T>G0.125
thyX3067652c.294A>G0.130
thyX3067685c.261T>G0.151
thyX3067691p.Ile85Met0.133
thyX3067694c.252C>G0.130
thyX3067850c.96T>G0.156
thyX3067869p.Thr26Ser0.138
thyX3067874c.72G>C0.133
thyX3067877c.69C>G0.135
thyX3067883c.63G>C0.131
thyX3067886c.60T>G0.162
thyX3067889c.57G>C0.150
thyX3067898p.Asp16Glu0.183
thyX3067935p.Thr4Ile0.173
thyA3073824c.648T>C0.143
thyA3073827c.645T>C0.144
thyA3073839c.633A>G0.139
thyA3073863c.609A>G0.128
thyA3074372p.Met34Leu0.150
thyA3074377p.Gln32Arg0.147
thyA3074391c.81G>T0.147
thyA3074397c.75T>C0.139
ald3086788c.-32T>C1.000
ald3087672p.His285Asp0.139
ald3087680c.861G>C0.138
ald3087704c.885T>C0.150
fbiA3640307c.-236C>A0.161
fbiA3640347c.-196A>G0.145
fbiA3640349c.-194A>G0.144
fbiA3640350c.-193C>T0.144
fbiA3640365c.-178C>G0.165
fbiA3640871p.Ala110Gly0.130
fbiA3640878c.336T>C0.137
alr3841652c.-232A>T0.177
alr3841654c.-234A>C0.180
alr3841662c.-242A>G0.291
alr3841663c.-243G>A0.197
panD4044084c.198A>G0.131
panD4044105c.177C>G0.144
embC4240078c.216A>G0.144
embC4240087c.225T>C0.144
embC4240105c.243C>T0.151
embC4240444c.582C>G0.143
embC4240459c.597G>C0.128
embC4240462c.600G>C0.125
embC4240505p.Ser215Ala0.143
embC4240512p.Ser217Thr0.140
embC4240516c.654G>C0.138
embC4240519c.657T>C0.143
embC4240543c.681G>C0.131
embC4240693c.831T>G0.134
embC4240699c.837C>G0.144
embC4240726c.864G>C0.141
embC4240780c.918T>C0.152
embC4240783c.921G>C0.149
embC4240789c.927T>C0.149
embC4240819c.957A>G0.150
embC4240828c.966G>A0.144
embC4240831c.969T>G0.147
embC4241179c.1317G>A0.178
embC4241203c.1341T>C0.167
embC4241206c.1344G>C0.176
embC4241218c.1356G>C0.157
embC4241230c.1368A>G0.153
embC4241233c.1371G>C0.151
embC4241383c.1521G>C0.137
embC4241394p.Lys511Ser0.157
embC4241449c.1587C>G0.165
embC4241453p.Ile531Val0.164
embC4241479c.1617C>G0.138
embC4241480c.1618T>C0.138
embC4241488c.1626G>C0.138
embC4241521c.1659T>C0.134
embC4241611c.1749G>C0.136
embC4241614c.1752A>C0.137
embC4241743c.1881C>G0.150
embC4241750p.Leu630Val0.157
embC4241755c.1893C>G0.151
embC4241770c.1908T>C0.183
embC4241794c.1932C>G0.146
embC4241797c.1935C>T0.147
embC4242220c.2358A>G0.133
embC4242229c.2367C>A0.167
embC4242245p.Thr795Arg0.165
embC4242643c.2781C>T0.956
embA4243460c.228C>T0.960
embA4244523p.Pro431Ala0.133
embA4244690c.1458G>A0.144
embA4244702c.1470C>G0.147
embA4244708c.1476C>G0.136
embA4245764c.2532G>C0.180
embA4245772p.Asn847Thr0.202
embA4245785c.2553G>C0.205
embA4245807c.2575T>C0.159
embA4245812c.2580G>C0.148
embA4245813p.Pro861Ala0.148
embA4245820p.Ser863Thr0.143
embA4245824c.2592G>C0.141
embA4245833c.2601G>C0.154
embA4245842c.2610G>C0.146
embA4245845c.2613T>C0.149
embA4245851c.2619G>C0.158
embA4245860c.2628C>G0.149
embA4246184c.2952A>C0.138
embA4246316c.3084T>G0.124
embA4246319c.3087G>C0.131
embA4246329p.Thr1033Ala0.152
embA4246349c.3117C>G0.167
embA4246359p.Ala1043Ser0.167
embA4246367c.3135C>T0.167
embA4246373c.3141T>C0.172
embA4246376c.3144G>C0.165
embA4246379c.3147C>T0.157
embA4246400c.3168G>C0.177
embA4246413p.His1061Phe0.168
embA4246419c.3187C>T0.162
embB4247050c.537C>G0.169
embB4247059c.546C>A0.174
embB4247068c.555T>C0.135
embB4247425c.912G>C0.144
embB4247446c.933C>T0.133
embB4247464c.951C>G0.173
embB4247470c.957T>C0.164
embB4247491c.978G>C0.175
embB4247497c.984T>C0.188
embB4247512c.999T>C0.206
embB4247539c.1026T>C0.185
embB4247554c.1041T>C0.159
embB4247566c.1053C>A0.157
embB4247572c.1059A>G0.143
embB4247815c.1302C>G0.129
embB4247819p.Val436Ile0.136
embB4247905c.1392G>C0.144
embB4247909c.1396T>C0.137
embB4247914c.1401G>C0.137
embB4247932c.1419C>G0.136
embB4247940p.Leu476Trp0.148
embB4247945c.1432T>C0.143
embB4247951p.Ser480Ala0.163
embB4247956c.1443G>C0.149
embB4247974c.1461C>G0.142
embB4248007c.1494C>G0.163
embB4248011p.Ser500Arg0.155
embB4248014p.Thr501Ala0.161
embB4248035p.Val508Ile0.157
embB4248044p.Lys511Glu0.139
embB4248070c.1557T>C0.188
embB4248085c.1572T>C0.185
embB4248097c.1584C>G0.192
embB4248130c.1617G>C0.172
embB4248142c.1629T>C0.167
embB4248143c.1630T>C0.170
embB4248157c.1644A>G0.198
embB4248172c.1659G>C0.209
embB4248199c.1686A>G0.139
embB4248200p.Ile563Val0.139
embB4248205c.1692C>G0.140
embB4248206p.Ser565Gly0.142
embB4248220c.1707A>C0.155
embB4248304c.1791G>C0.144
embB4248316c.1803C>G0.138
embB4248319c.1806A>G0.135
embB4248373c.1860C>G0.136
embB4248382c.1869C>G0.148
embB4248386c.1873C>A0.148
ethA4327435c.39T>G0.127
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;