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: 5d80ac2d86bc6
Sample: 5d80ac2d86bc6

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Summary
ID: 5d80ac2d86bc6
Date: Tue Sep 17 11:52:02 2019
Strain: lineage2.2.1;lineage4.3
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (0.78), rpoC p.Ile491Thr (0.81)
EthambutolRembB p.Met306Val (0.95)
PyrazinamideRpncA p.Ser66Pro (0.99)
StreptomycinRrpsL p.Lys43Arg (0.90), rrs r.462c>t (0.12)
Ethionamide
FluoroquinolonesRgyrB p.Ile486Leu (0.95), gyrA p.Ala90Val (0.85)
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
gyrB6250c.1011A>G0.134
gyrB6256c.1017G>A0.133
gyrB6268c.1029C>G0.141
gyrB6280c.1041T>C0.136
gyrB6286c.1047T>C0.154
gyrB6289c.1050C>T0.146
gyrB6292c.1053G>C0.146
gyrB6307c.1068T>G0.157
gyrB6319c.1080G>C0.177
gyrB6362c.1123T>C0.172
gyrB6376c.1137G>A0.130
gyrB6379c.1140C>G0.133
gyrB6382c.1143A>G0.125
gyrB6388c.1149T>C0.121
gyrB6403c.1164T>C0.111
gyrB6742c.1503A>G0.108
gyrB6745c.1506T>G0.110
gyrB6751c.1512G>C0.134
gyrB6760c.1521G>C0.133
gyrB6763c.1524G>C0.136
gyrB6775c.1536G>C0.160
gyrB6793c.1554T>C0.143
gyrB6797p.Gly520Thr0.129
gyrB6811c.1572C>T0.148
gyrB6841c.1602T>C0.146
gyrB6844c.1605T>C0.144
gyrB6853c.1614A>G0.120
gyrB6856c.1617T>C0.117
gyrB6862c.1623C>G0.120
gyrB6919c.1680T>C0.114
gyrB6925c.1686T>C0.115
gyrB6931c.1692A>G0.122
gyrB6949c.1710A>G0.123
gyrB6952c.1713C>G0.125
gyrB6967c.1728T>C0.165
gyrB6973c.1734G>C0.151
gyrB6982c.1743A>C0.168
gyrB7006c.1767T>C0.161
gyrB7007c.1768C>T0.160
gyrB7010c.1771C>T0.155
gyrB7015p.Glu592Asp0.149
gyrB7023p.Leu595Gln0.150
gyrB7028p.Ala597Thr0.838
gyrB7033c.1794G>C0.141
gyrB7051p.Glu604Asp0.121
gyrA7362p.Glu21Gln1.000
gyrA7451c.150C>G0.111
gyrA7457c.156T>C0.123
gyrA7475c.174A>G0.111
gyrA7480p.Phe60Tyr0.117
gyrA7484c.183T>C0.119
gyrA7490c.189C>G0.135
gyrA7505c.204C>T0.157
gyrA7523c.222C>G0.180
gyrA7532c.231T>G0.159
gyrA7541c.240C>G0.155
gyrA7547c.246C>T0.144
gyrA7585p.Ser95Thr1.000
gyrA7595c.294C>G0.118
gyrA7601c.300C>G0.118
gyrA7763c.462T>C0.127
gyrA7775c.474C>A0.120
gyrA7814c.513C>G0.124
gyrA7823c.522G>C0.124
gyrA7832c.531G>T0.110
gyrA7835c.534A>C0.112
gyrA8156c.855T>C0.118
gyrA8168c.867A>G0.115
gyrA8198c.897T>C0.120
gyrA8207c.906T>C0.125
gyrA8219c.918T>C0.148
gyrA8225c.924T>C0.169
gyrA8234c.933T>C0.170
gyrA8237c.936A>G0.170
gyrA8247p.Ile316Val0.167
gyrA8264c.963T>C0.129
gyrA8267c.966G>C0.128
gyrA8270c.969G>C0.129
gyrA8276c.975G>A0.134
gyrA8283p.Ile328Leu0.134
gyrA8288c.987T>C0.136
gyrA8294c.993T>C0.182
gyrA8324c.1023T>C0.182
gyrA8330c.1029C>G0.178
gyrA8339c.1038A>G0.162
gyrA8340p.Ala347Ser0.162
gyrA8372c.1071G>C0.120
gyrA8375c.1074G>C0.108
gyrA8579c.1278C>T0.111
gyrA8588c.1287G>A0.145
gyrA8597c.1296C>G0.148
gyrA8603c.1302A>G0.141
gyrA8619c.1318T>C0.183
gyrA8624c.1323G>C0.177
gyrA8636c.1335A>C0.219
gyrA8642c.1341A>G0.221
gyrA8672c.1371A>G0.234
gyrA8678c.1377G>A0.231
gyrA8693c.1392T>C0.182
gyrA8696c.1395G>C0.169
gyrA8699c.1398A>G0.167
gyrA8711c.1410A>C0.151
gyrA8714c.1413A>G0.151
gyrA8729c.1428T>C0.151
gyrA8730p.Gly477Arg0.135
gyrA8828c.1527T>C0.108
gyrA8852c.1551T>C0.112
gyrA8858c.1557T>C0.124
gyrA8867c.1566A>G0.126
gyrA8870c.1569G>C0.128
gyrA8873c.1572A>C0.126
gyrA8891c.1590G>A0.160
gyrA8897c.1596T>C0.156
gyrA8903c.1602T>C0.156
gyrA8933c.1632G>C0.125
gyrA8939c.1638T>C0.118
gyrA8942c.1641G>C0.118
gyrA8946c.1645T>C0.117
gyrA9182c.1881T>C0.118
gyrA9191c.1890G>C0.130
gyrA9200c.1899A>G0.135
gyrA9204p.Ser635Thr0.141
gyrA9224c.1923C>T0.108
gyrA9230c.1929T>C0.110
gyrA9233c.1932C>G0.108
gyrA9239c.1938C>T0.110
gyrA9284c.1983T>C0.124
gyrA9304p.Gly668Asp1.000
gyrA9323c.2022C>G0.122
rpoB759606c.-201T>C0.180
rpoB759629c.-178T>C0.188
rpoB759644c.-163T>A0.177
rpoB759647c.-160T>C0.179
rpoB760091c.285G>C0.164
rpoB760101c.295T>C0.174
rpoB760112c.306T>C0.183
rpoB760118c.312T>G0.194
rpoB760121c.315T>C0.192
rpoB760130p.Asp108Glu0.239
rpoB760139c.333A>G0.230
rpoB760142c.336C>G0.230
rpoB760181c.375T>C0.211
rpoB760184c.378A>G0.208
rpoB760196c.390C>G0.198
rpoB760223c.417T>C0.205
rpoB760235c.429T>C0.157
rpoB760283c.477G>C0.149
rpoB760298c.492G>C0.136
rpoB760307c.501T>C0.150
rpoB760310c.504G>C0.153
rpoB760328c.522G>C0.121
rpoB760331c.525G>C0.116
rpoB760340c.534G>T0.114
rpoB760406c.600G>C0.104
rpoB760424c.618C>G0.111
rpoB760611c.805T>C0.117
rpoB760646c.840C>G0.129
rpoB760655c.849A>G0.114
rpoB760661c.855A>C0.100
rpoB760793c.987A>G0.148
rpoB760805c.999G>C0.138
rpoB760817c.1011A>G0.138
rpoB760820c.1014T>C0.138
rpoB760826c.1020C>G0.117
rpoB760830c.1024T>C0.119
rpoB760841c.1035T>C0.133
rpoB760845p.Thr347Pro0.117
rpoB760859c.1053T>C0.129
rpoB760862c.1056G>C0.129
rpoB760869p.Val355Ile0.132
rpoB760886c.1080A>G0.104
rpoB760946c.1140A>G0.173
rpoB760982c.1176G>C0.155
rpoB760985c.1179G>C0.157
rpoB760991c.1185G>C0.153
rpoB761006c.1200C>G0.195
rpoB761015c.1209G>C0.190
rpoB761021c.1215G>C0.193
rpoB761027c.1221A>G0.200
rpoB761036c.1230G>C0.202
rpoB761037c.1231T>C0.195
rpoB761057c.1251G>C0.237
rpoB761102c.1296A>G0.237
rpoB761129c.1323G>C0.212
rpoB761132c.1326G>T0.216
rpoB761133c.1327T>C0.214
rpoB761150c.1344A>C0.208
rpoB761153c.1347G>C0.214
rpoB761165c.1359G>C0.222
rpoB761180c.1374A>C0.198
rpoB761189c.1383T>C0.174
rpoB761195c.1389G>C0.158
rpoB761207c.1401C>T0.157
rpoB761213c.1407G>C0.174
rpoB761219c.1413G>C0.168
rpoB761249c.1443A>G0.145
rpoB761255c.1449T>G0.155
rpoB761261c.1455G>T0.152
rpoB761306c.1500C>G0.171
rpoB761327c.1521A>G0.198
rpoB761330c.1524G>C0.208
rpoB761354c.1548C>T0.165
rpoB761360c.1554T>C0.144
rpoB761362p.Ser519Thr0.140
rpoB761373p.Val523His0.130
rpoB761408c.1602G>C0.126
rpoB761411c.1605G>A0.127
rpoB761414c.1608A>G0.113
rpoB761537c.1731C>G0.108
rpoB761570c.1764T>C0.125
rpoB761579c.1773G>C0.141
rpoB761588c.1782C>T0.135
rpoB761606c.1800C>G0.149
rpoB761612c.1806G>C0.147
rpoB761615c.1809A>C0.141
rpoB761636c.1830G>T0.153
rpoB761645c.1839C>G0.155
rpoB761648c.1842T>C0.153
rpoB761657c.1851C>G0.151
rpoB761675c.1869G>C0.143
rpoB761747c.1941G>C0.111
rpoB761750c.1944G>C0.107
rpoB761765c.1959T>C0.114
rpoB761791p.Arg662His0.146
rpoB761813c.2007T>C0.141
rpoB761815p.Ala670Glu0.141
rpoB761834c.2028T>C0.176
rpoB761848p.Cys681Ser0.155
rpoB761852c.2046C>G0.157
rpoB761858c.2052G>C0.186
rpoB761873c.2067A>C0.197
rpoB761885c.2079T>C0.171
rpoB761906c.2100C>A0.167
rpoB761909c.2103T>C0.152
rpoB761912c.2106T>C0.154
rpoB761915p.Asp703Glu0.158
rpoB761916p.Asp704Asn0.158
rpoB761948c.2142G>C0.190
rpoB761954c.2148C>G0.177
rpoB762008c.2202C>T0.172
rpoB762014c.2208C>T0.167
rpoB762017c.2211A>G0.156
rpoB762053c.2247T>C0.159
rpoB762062c.2256T>C0.145
rpoB762065c.2259T>C0.145
rpoB762083c.2277T>C0.169
rpoB762086c.2280G>C0.167
rpoB762101c.2295C>G0.185
rpoB762114p.Ile770Val0.173
rpoB762131c.2325C>G0.157
rpoB762140c.2334G>C0.163
rpoB762143c.2337T>C0.160
rpoB762149c.2343G>C0.167
rpoB762167c.2361T>C0.170
rpoB762170c.2364C>G0.167
rpoB762185c.2379G>C0.163
rpoB762233c.2427G>C0.128
rpoB762246c.2440C>T0.120
rpoB762254c.2448T>G0.116
rpoB762257c.2451C>G0.117
rpoB762284c.2478G>C0.115
rpoB762293c.2487T>C0.106
rpoB762434c.2628T>C0.135
rpoB762449c.2643C>A0.144
rpoB762467c.2661C>T0.144
rpoB762863c.3057T>C0.107
rpoB762929c.3123G>C0.188
rpoB762989c.3183G>C0.206
rpoB762995c.3189G>T0.197
rpoB763013c.3207C>G0.188
rpoB763028c.3222T>C0.176
rpoB763031c.3225T>C0.169
rpoB763034c.3228C>G0.159
rpoB763040c.3234C>G0.171
rpoB763070c.3264T>C0.162
rpoB763085c.3279C>G0.134
rpoB763136c.3330C>T0.125
rpoB763148c.3342G>C0.117
rpoB763158c.3352C>T0.146
rpoB763166c.3360A>G0.172
rpoB763190c.3384C>T0.125
rpoB763202c.3396A>G0.123
rpoB763205c.3399G>C0.110
rpoB763206c.3400A>T0.110
rpoB763214c.3408T>C0.127
rpoB763226c.3420A>G0.127
rpoB763227c.3421C>T0.127
rpoB763238c.3432T>C0.125
rpoB763253c.3447G>C0.130
rpoB763256c.3450G>A0.133
rpoB763268c.3462C>G0.149
rpoB763283c.3477T>C0.127
rpoB763284c.3478C>T0.115
rpoC763351c.-19T>C0.137
rpoC763352c.-18T>A0.135
rpoC763402c.33C>G0.186
rpoC763411c.42T>G0.174
rpoC763414c.45T>C0.186
rpoC763441c.72C>T0.165
rpoC763444c.75T>C0.165
rpoC763456c.87A>G0.174
rpoC763486c.117T>G0.175
rpoC763492c.123G>A0.167
rpoC763528c.159G>A0.126
rpoC763573c.204G>C0.103
rpoC763594c.225C>T0.117
rpoC763636c.267T>C0.139
rpoC763657c.288G>A0.150
rpoC763660c.291T>G0.150
rpoC763675c.306C>G0.152
rpoC763696c.327T>C0.179
rpoC763702c.333C>G0.186
rpoC763717c.348T>C0.182
rpoC763723c.354G>C0.171
rpoC763732c.363C>G0.173
rpoC763738c.369G>A0.151
rpoC763741c.372C>T0.149
rpoC763744c.375G>C0.145
rpoC763765c.396T>C0.149
rpoC763774c.405G>C0.133
rpoC763807c.438T>C0.137
rpoC763816c.447C>G0.132
rpoC763853p.Val162Ile0.115
rpoC763858c.489A>G0.114
rpoC763872p.Gly168Ala0.122
rpoC763876p.Glu169Asp0.135
rpoC763879c.510A>G0.138
rpoC763888c.519G>C0.133
rpoC763891c.522G>C0.129
rpoC763894c.525A>G0.132
rpoC763900c.531G>C0.152
rpoC763945c.576T>C0.152
rpoC763960c.591T>C0.133
rpoC764083c.714A>G0.116
rpoC764098c.729A>G0.122
rpoC764101c.732C>G0.127
rpoC764102p.Val245Ile0.128
rpoC764112p.Tyr248Phe0.150
rpoC764116c.747C>T0.156
rpoC764131c.762T>C0.178
rpoC764188c.819A>G0.172
rpoC764195p.Ser276Ile0.127
rpoC764203c.834G>C0.121
rpoC764206c.837T>C0.119
rpoC764215c.846A>G0.156
rpoC764236c.867G>A0.129
rpoC764248c.879C>G0.121
rpoC764266c.897T>C0.118
rpoC764272c.903G>C0.114
rpoC764278c.909A>G0.113
rpoC764338c.969G>A0.162
rpoC764353c.984G>C0.169
rpoC764365c.996C>T0.179
rpoC764380c.1011G>C0.162
rpoC764381c.1012T>A0.159
rpoC764387c.1018T>C0.159
rpoC764405c.1036A>C0.182
rpoC764419c.1050C>G0.171
rpoC764428c.1059G>C0.138
rpoC764431c.1062G>C0.139
rpoC764434c.1065A>G0.141
rpoC764446c.1077T>C0.132
rpoC764449c.1080G>C0.134
rpoC764452c.1083T>C0.138
rpoC764458c.1089G>C0.136
rpoC764461c.1092A>G0.138
rpoC764489c.1120C>T0.120
rpoC764497c.1128A>G0.120
rpoC764650c.1281G>C0.141
rpoC764651c.1282T>A0.140
rpoC764752c.1383G>C0.163
rpoC764764c.1395T>C0.174
rpoC764809c.1440C>T0.210
rpoC764815c.1446A>G0.175
rpoC764827c.1458G>C0.188
rpoC764858c.1489T>C0.155
rpoC764872c.1503A>G0.135
rpoC764888c.1519T>C0.133
rpoC764932c.1563C>A0.138
rpoC764948c.1579T>C0.134
rpoC764968c.1599T>C0.156
rpoC764995c.1626C>G0.168
rpoC765007c.1638T>G0.154
rpoC765008c.1639T>C0.154
rpoC765011c.1642A>T0.160
rpoC765019c.1650A>G0.172
rpoC765034c.1665T>C0.177
rpoC765040c.1671T>C0.170
rpoC765041c.1672T>C0.174
rpoC765047c.1678T>C0.204
rpoC765055c.1686C>G0.226
rpoC765073c.1704G>C0.169
rpoC765076c.1707A>G0.163
rpoC765079c.1710T>G0.161
rpoC765082c.1713G>C0.157
rpoC765089c.1720T>C0.189
rpoC765103c.1734G>T0.178
rpoC765292c.1923G>C0.153
rpoC765298c.1929G>C0.150
rpoC765300p.Val644Ala0.144
rpoC765319c.1950A>G0.163
rpoC765326p.His653Ala0.142
rpoC765330p.Ser654Asn0.133
rpoC765346c.1977C>G0.167
rpoC765349c.1980T>C0.168
rpoC765352c.1983G>C0.170
rpoC765383p.Met672Leu0.198
rpoC765404p.Leu679Val0.206
rpoC765409c.2040T>C0.221
rpoC765421c.2052C>G0.200
rpoC765451c.2082C>A0.226
rpoC765478c.2109T>C0.205
rpoC765499c.2130C>G0.209
rpoC765529c.2160C>T0.141
rpoC765541c.2172C>G0.122
rpoC765553c.2184C>T0.107
rpoC765556c.2187G>C0.113
rpoC765559c.2190G>C0.113
rpoC765580c.2211G>C0.132
rpoC765613p.His748Gln0.138
rpoC765625c.2256C>G0.169
rpoC765631p.Asp754Glu0.183
rpoC765700c.2331T>C0.175
rpoC765734c.2365T>C0.163
rpoC765739c.2370G>T0.169
rpoC765751c.2382C>G0.157
rpoC765753p.Asp795Ala0.157
rpoC765772c.2403C>G0.149
rpoC765784c.2415C>G0.157
rpoC765787c.2418C>T0.156
rpoC765793c.2424C>G0.152
rpoC765796c.2427C>T0.156
rpoC765811c.2442T>C0.149
rpoC765814c.2445A>G0.149
rpoC765826c.2457T>C0.167
rpoC765835c.2466C>T0.172
rpoC765850c.2481G>C0.215
rpoC765883c.2514C>G0.163
rpoC765886c.2517C>G0.160
rpoC765892c.2523T>C0.154
rpoC765937c.2568T>C0.160
rpoC765947c.2578T>C0.189
rpoC765967c.2598C>T0.198
rpoC765982c.2613C>G0.189
rpoC765994c.2625A>T0.160
rpoC766010c.2641T>A0.158
rpoC766021c.2652G>C0.152
rpoC766027c.2658G>C0.160
rpoC766043p.Gln892Glu0.170
rpoC766054c.2685C>G0.187
rpoC766082p.Ala905Gln0.159
rpoC766096c.2727G>C0.161
rpoC766129c.2760C>G0.130
rpoC766135c.2766G>A0.125
rpoC766141c.2772C>T0.124
rpoC766142c.2773C>T0.125
rpoC766447c.3078T>C0.107
rpoC766462c.3093G>C0.116
rpoC766492c.3123T>C0.117
rpoC766522c.3153C>G0.101
rpoC766528c.3159T>C0.108
rpoC766531c.3162G>C0.106
rpoC766540p.Asp1057Glu0.121
rpoC766549c.3180G>C0.129
rpoC766573c.3204T>C0.113
rpoC766582c.3213C>G0.106
rpoC766583p.Gly1072Ser0.104
rpoC766591c.3222A>G0.129
rpoC766594c.3225G>C0.114
rpoC766597c.3228C>G0.110
rpoC766607p.Ile1080Leu0.183
rpoC766630c.3261G>C0.178
rpoC766657c.3288A>G0.215
rpoC766672c.3303T>C0.227
rpoC766673p.Gly1102Asn0.227
rpoC766726c.3357T>C0.196
rpoC766738c.3369G>C0.179
rpoC766765c.3396A>C0.167
rpoC766774c.3405T>C0.172
rpoC766801c.3432C>G0.174
rpoC766804c.3435A>G0.160
rpoC766861c.3492G>C0.119
rpoC766864c.3495G>C0.123
rpoC766900c.3531T>C0.122
rpoC766945c.3576A>G0.107
rpoC766963c.3594T>C0.125
rpoC766972c.3603G>C0.126
rpoC767098c.3729T>C0.108
rpoC767158c.3789T>C0.140
rpoC767180p.Ala1271Gln0.118
rpoC767191c.3822C>G0.134
rpoC767206c.3837C>G0.128
rpoC767209c.3840T>C0.128
rpoC767212c.3843G>C0.128
rpoC767221c.3852C>G0.130
rpoC767230c.3861G>C0.120
rpoC767233c.3864T>C0.118
rpsL781395c.-165T>C1.000
rpsL781571c.12C>T0.141
rpsL781595c.36T>C0.135
rpsL781605p.Ile16Val0.135
rpsL781608p.Ser17Ala0.138
rpsL781628c.69T>C0.160
rpsL781631c.72G>C0.148
rpsL781649c.90T>C0.160
rpsL781655c.96T>C0.150
rpsL781728c.169T>C0.122
rpsL781736c.177T>C0.115
rpsL781742c.183C>T0.144
rpsL781748c.189C>G0.147
rpsL781760c.201T>C0.152
rpsL781772c.213C>A0.157
rpsL781808c.249C>T0.170
rpsL781811c.252C>T0.170
rpsL781832c.273T>C0.191
rpsL781838c.279G>C0.146
rpsL781841c.282C>G0.136
rpsL781877c.318T>C0.148
rpsL781898c.339A>T0.120
rpsL781916c.357T>C0.121
rpsL781929p.Gly124Ser0.121
rplC800794c.-15A>G0.209
rplC800796c.-13A>G0.211
rplC800814c.6A>G0.225
rplC800817c.9A>T0.220
rplC800844c.36T>C0.239
rplC800865c.57A>G0.163
rplC800867p.Ser20Asn0.141
rplC800874c.66A>G0.130
rplC800875p.Val23Ile0.130
rplC800880c.72A>G0.133
rplC800889c.81C>G0.133
rplC800892c.84G>C0.132
rplC800907c.99C>G0.108
rplC801207c.399C>T0.115
rplC801300c.492C>G0.115
rplC801309c.501C>G0.112
rplC801312c.504G>C0.116
rplC801321c.513C>T0.106
rplC801324c.516T>C0.121
rplC801339c.531T>C0.140
rplC801341p.Leu178Gln0.138
rplC801348c.540T>G0.134
rplC801357c.549T>C0.149
rplC801367p.Ala187Thr0.159
rplC801402c.594T>C0.128
rplC801405c.597T>C0.125
rrs1471923r.78t>c0.229
rrs1471925r.80t>c0.229
rrs1471932r.87a>g0.212
rrs1471934r.89a>g0.212
rrs1471969r.124t>c0.216
rrs1471970r.125g>a0.222
rrs1472044r.199g>t0.137
rrs1472045r.200t>a0.146
rrs1472061r.216a>t0.173
rrs1472075r.230a>g0.175
rrs1472108r.263c>t0.203
rrs1472969r.1124a>g0.140
rrs1472970r.1125c>g0.140
rrs1472977r.1132g>c0.143
rrs1472978r.1133t>c0.143
rrs1473105r.1260g>a0.225
rrs1473123r.1278a>t0.205
rrs1473145r.1300c>t0.225
rrs1473166r.1321g>a0.190
rrs1473290r.1445c>t0.214
rrl1473668r.11c>t0.115
rrl1473756r.99g>a0.127
rrl1473758r.101g>t0.127
rrl1473806r.149c>t0.182
rrl1473877r.220g>a0.231
rrl1473898r.241c>t0.184
rrl1474001r.344c>t0.125
rrl1474009r.352a>g0.146
rrl1474012r.355c>t0.146
rrl1474093r.436g>t0.243
rrl1474099r.442g>a0.281
rrl1474103r.446a>t0.290
rrl1474140r.483c>t0.192
rrl1474151r.494c>t0.133
rrl1474181r.524c>t0.176
rrl1474249r.592g>t0.184
rrl1474308r.651g>t0.130
rrl1474310r.653t>g0.130
rrl1474356r.699t>c0.238
rrl1474362r.705a>g0.246
rrl1474376r.719t>c0.259
rrl1474427r.770a>c0.143
rrl1474429r.772g>c0.143
rrl1474432r.775c>g0.135
rrl1474639r.982g>a0.258
rrl1474794r.1137c>t0.224
rrl1474812r.1155g>a0.167
rrl1474823r.1166c>t0.167
rrl1474831r.1174a>g0.160
rrl1474904r.1247g>a0.125
rrl1474956r.1299c>t0.188
rrl1474960r.1303c>g0.188
rrl1474963r.1306g>t0.188
rrl1474964r.1307t>a0.188
rrl1474965r.1308g>c0.176
rrl1474970r.1313g>a0.167
rrl1475006r.1349a>t0.278
rrl1475061r.1404c>t0.250
rrl1475088r.1431a>t0.195
rrl1475199r.1542g>a0.149
rrl1475206r.1549c>t0.152
rrl1475209r.1552g>c0.140
rrl1475213r.1556c>t0.143
rrl1475249r.1592t>c0.125
rrl1475252r.1595c>t0.106
rrl1475402r.1745c>t0.172
rrl1475419r.1762c>t0.179
rrl1475429r.1772g>a0.233
rrl1475436r.1779c>t0.233
rrl1475483r.1826c>t0.241
rrl1475505r.1848g>a0.226
rrl1475526r.1869c>a0.231
rrl1475599r.1942a>g0.152
rrl1475608r.1951t>c0.139
rrl1475628r.1971g>a0.135
rrl1475642r.1985t>c0.158
rrl1475657r.2000a>g0.163
rrl1475659r.2002g>t0.163
rrl1475763r.2106c>t0.188
rrl1475988r.2331a>g0.108
rrl1476086r.2429g>a0.171
rrl1476089r.2432t>c0.171
rrl1476095r.2438c>g0.176
rrl1476106r.2449a>t0.132
rrl1476108r.2451t>c0.128
rrl1476115r.2458t>c0.154
rrl1476117r.2460g>c0.154
rrl1476214r.2557g>a0.333
rrl1476224r.2567a>g0.340
rrl1476281r.2624t>c0.271
rrl1476583r.2926g>a0.114
rrl1476584r.2927c>t0.133
rrl1476594r.2937c>t0.136
rrl1476597r.2940g>a0.133
rrl1476603r.2946g>a0.140
rrl1476608r.2951c>g0.143
rrl1476628r.2971t>a0.170
fabG11673568c.129C>G0.103
fabG11673580c.141T>G0.106
fabG11673607c.168T>C0.111
fabG11673641p.Val68Ile0.123
fabG11673646c.207T>C0.121
fabG11673679c.240T>G0.158
fabG11673685c.246C>T0.175
fabG11673710p.Leu91Ile0.153
fabG11673716p.Ala93Lys0.134
fabG11673733p.Met98Ile0.151
fabG11673748c.309A>G0.128
fabG11673749p.Lys104Arg0.128
fabG11673758p.Lys107Glu0.128
fabG11673890p.Ala151Ser0.108
fabG11673901c.462A>G0.147
fabG11673905p.Ser156Ala0.143
fabG11673916c.477A>C0.160
fabG11673917p.Val160Leu0.160
fabG11673922c.483T>C0.165
fabG11673941p.Ala168Ser0.165
fabG11673955c.516G>C0.187
fabG11673961c.522A>C0.197
fabG11673985c.546C>G0.181
fabG11674006p.Asp189Glu0.222
fabG11674015c.576C>T0.141
fabG11674018c.579G>C0.145
fabG11674021c.582G>C0.141
fabG11674024c.585T>C0.145
fabG11674033c.594T>C0.145
fabG11674037p.Gln200Ala0.131
fabG11674042c.603G>T0.133
fabG11674049p.Gln204Asp0.126
fabG11674054c.615T>C0.128
fabG11674060c.621A>G0.129
fabG11674063c.624G>C0.126
fabG11674079p.Pro214Ala0.200
fabG11674114c.675T>A0.165
fabG11674123c.684T>C0.146
fabG11674126c.687G>C0.141
fabG11674132c.693T>C0.152
fabG11674136p.Ser233Ala0.151
fabG11674141c.702T>C0.147
fabG11674156c.717C>G0.114
inhA1674537c.336C>G0.127
inhA1674601p.Leu134Thr0.122
inhA1674723c.522C>T0.109
inhA1674774c.573A>G0.107
inhA1674846p.Ile215Met0.137
inhA1674855c.654C>G0.143
inhA1674864c.663C>T0.143
inhA1674870c.669T>C0.134
inhA1674879c.678T>C0.162
inhA1674903c.702T>C0.132
inhA1674904p.Ala235Pro0.132
inhA1674909c.708G>A0.138
inhA1674942c.741T>G0.111
inhA1674960c.759C>G0.113
rpsA1833518c.-24C>A0.105
rpsA1833532c.-10A>C0.122
rpsA1833554p.Thr5Ala0.129
rpsA1833568c.27G>C0.156
rpsA1833589c.48A>T0.127
rpsA1833595c.54T>C0.129
rpsA1833661c.120A>G0.182
rpsA1833667c.126C>G0.189
rpsA1833721c.180A>G0.200
rpsA1833724c.183C>G0.190
rpsA1833727c.186G>C0.190
rpsA1833742c.201A>G0.191
rpsA1833745c.204G>C0.171
rpsA1833748c.207C>G0.169
rpsA1833787c.246C>G0.148
rpsA1833790c.249T>C0.157
rpsA1833802c.261A>G0.145
rpsA1833811c.270G>T0.146
rpsA1833838c.297G>C0.165
rpsA1833841c.300C>G0.165
rpsA1833847c.306C>G0.163
rpsA1833856c.315A>G0.169
rpsA1833874c.333T>C0.165
rpsA1833928c.387G>C0.196
rpsA1833940c.399C>G0.230
rpsA1833971c.430C>T0.182
rpsA1833979c.438T>C0.163
rpsA1834000c.459G>C0.189
rpsA1834021c.480C>T0.200
rpsA1834030c.489C>G0.189
rpsA1834123c.582C>G0.139
rpsA1834177c.636A>C0.987
rpsA1834333c.792C>T0.133
rpsA1834348c.807T>C0.125
rpsA1834366c.825A>G0.143
rpsA1834396c.855G>C0.167
rpsA1834411c.870T>C0.182
rpsA1834417c.876G>C0.176
rpsA1834423c.882G>C0.169
rpsA1834435c.894G>C0.182
rpsA1834451c.910T>C0.203
rpsA1834465c.924T>C0.197
rpsA1834468c.927A>G0.197
rpsA1834489c.948T>C0.176
rpsA1834510c.969C>T0.138
rpsA1834513c.972C>G0.138
rpsA1834528c.987T>C0.177
rpsA1834540c.999G>C0.167
rpsA1834546c.1005T>C0.148
rpsA1834609c.1068T>C0.141
rpsA1834633c.1092A>G0.132
rpsA1834639c.1098T>C0.136
rpsA1834654p.Glu371Asp0.188
rpsA1834684c.1143C>T0.194
rpsA1834690c.1149T>C0.197
rpsA1834732c.1191T>C0.194
rpsA1834733p.Ala398Ser0.192
rpsA1834738c.1197A>G0.205
rpsA1834753c.1212T>C0.192
rpsA1834765p.Glu408Asp0.200
rpsA1834775p.Ala412Thr0.203
rpsA1834780c.1239A>G0.197
rpsA1834786c.1245A>G0.158
rpsA1834789c.1248T>C0.156
rpsA1834792c.1251G>C0.150
tlyA1917951c.12T>C0.109
tlyA1917972c.33A>G1.000
tlyA1917975c.36C>G0.117
tlyA1917981c.42G>C0.115
tlyA1917990c.51G>C0.110
tlyA1917993c.54A>G0.110
tlyA1917996c.57A>G0.112
tlyA1918002c.63A>G0.123
katG2154724p.Arg463Leu1.000
katG2155691c.421A>G0.130
katG2155695c.417G>C0.139
katG2155704c.408G>C0.165
katG2155716c.396A>C0.155
katG2155722c.390C>G0.155
katG2155728c.384C>G0.148
katG2155742p.Gly124Gln0.133
katG2155743c.369C>G0.135
katG2155782c.330G>C0.116
katG2155785c.327A>G0.117
kasA2518190p.Ser26Ala0.115
kasA2518199p.Ile29Val0.115
kasA2518220c.106C>T0.113
kasA2518234c.120G>A0.111
kasA2518519c.405G>C0.133
kasA2518528c.414C>G0.143
kasA2518540c.426T>C0.154
kasA2518561c.447T>C0.178
kasA2518567c.453G>C0.145
kasA2518570c.456G>C0.145
kasA2518574p.Ile154Val0.136
kasA2518579c.465T>C0.141
kasA2518588c.474T>C0.125
kasA2518591c.477G>C0.127
kasA2518609p.Met165Ile0.117
kasA2518624c.510C>G0.122
kasA2518639c.525G>C0.147
kasA2518657c.543G>C0.149
kasA2518672c.558G>C0.147
kasA2518678c.564C>T0.132
kasA2518684c.570C>G0.141
kasA2518696c.582C>G0.115
kasA2518702c.588C>T0.136
kasA2518705c.591T>C0.136
kasA2518711c.597A>G0.148
kasA2518714c.600A>C0.160
kasA2518732c.618C>G0.177
kasA2518744c.630C>T0.180
kasA2518747c.633C>G0.180
kasA2518768c.654C>T0.185
kasA2518777c.663C>T0.194
kasA2518783c.669T>C0.194
kasA2518789c.675G>C0.175
kasA2518792c.678C>A0.172
kasA2518795c.681C>G0.167
kasA2518825c.711T>C0.205
kasA2518864c.750G>C0.161
kasA2518879c.765A>G0.146
kasA2518885c.771T>C0.140
kasA2518898c.784T>C0.126
kasA2518906c.792A>G0.122
kasA2518910p.Leu266Met0.114
kasA2518921c.807T>C0.119
kasA2519107c.993T>C0.129
kasA2519108p.Asp332Gln0.129
kasA2519116c.1002C>G0.141
kasA2519122c.1008G>C0.153
kasA2519137c.1023T>G0.197
kasA2519158c.1044C>T0.188
kasA2519167c.1053T>G0.176
kasA2519173c.1059C>G0.185
kasA2519196p.Thr361Ser0.131
ahpC2726591c.399C>G0.110
ahpC2726593p.Val134Ala0.110
ahpC2726600c.408T>C0.123
ahpC2726601p.Ile137Leu0.122
ahpC2726638p.Ala149Val0.133
ahpC2726645c.453C>G0.149
ahpC2726657c.465A>C0.149
ahpC2726669p.Asp159Glu0.118
ahpC2726672c.480G>A0.118
ahpC2726675c.483A>G0.118
ahpC2726681c.489A>C0.111
folC2747264p.Gly112Ala0.124
folC2747266c.333G>A0.121
folC2747275c.324A>G0.120
folC2747314c.285T>G0.125
folC2747317c.282G>C0.120
folC2747343p.Val86Ile0.151
thyX3067316c.630T>C0.115
thyX3067325c.621T>C0.125
thyX3067349c.597C>G0.150
thyX3067355c.591T>G0.153
thyX3067367c.579C>G0.162
thyX3067373c.573G>C0.160
thyX3067391c.555C>G0.184
thyX3067394c.552C>G0.182
thyX3067439c.507T>C0.186
thyX3067445c.501G>C0.194
thyX3067457c.489G>C0.165
thyX3067462c.484G>A0.155
thyX3067465p.Ile161Val0.145
thyX3067466c.480C>G0.146
thyX3067475c.471T>C0.151
thyX3067491p.Ala152Glu0.144
thyX3067493c.453T>C0.157
thyX3067510c.436G>A0.140
thyX3067515p.Ser144Thr0.157
thyX3067531p.Ala139Ser0.146
thyX3067545p.Glu134Ala0.146
thyX3067549p.Thr133Ala0.146
thyX3067556p.His130Gln0.159
thyX3067559c.387G>C0.145
thyX3067565p.Asp127Glu0.131
thyX3067570p.Ala126Pro0.136
thyX3067577c.369C>T0.136
thyX3067598c.348G>A0.134
thyX3067602p.Arg115His0.138
thyX3067611p.Lys112Thr0.169
thyX3067619c.327T>G0.148
thyX3067631c.315G>C0.136
thyX3067634c.312G>C0.125
thyX3067652c.294A>G0.176
thyX3067661c.285G>C0.197
thyX3067685c.261T>G0.200
thyX3067693p.Ile85Leu0.174
thyX3067694c.252C>G0.174
thyX3067718c.228G>C0.205
thyX3067721c.225A>G0.192
thyX3067727c.219T>G0.205
thyX3067736c.210G>A0.215
thyX3067739c.207A>G0.215
thyX3067748p.Asp66Glu0.223
thyX3067762p.Arg62Lys0.196
thyX3067765p.Leu61Ile0.202
thyX3067781c.165G>C0.227
thyX3067793c.153A>G0.194
thyX3067799c.147C>T0.186
thyX3067802c.144G>C0.189
thyX3067814c.132A>G0.170
thyX3067850c.96T>G0.177
thyX3067869p.Thr26Ser0.158
thyX3067874c.72G>C0.147
thyX3067877c.69C>G0.136
thyX3067883c.63G>C0.118
thyX3067886c.60T>G0.107
thyX3067889c.57G>C0.105
thyX3067898p.Asp16Glu0.165
thyX3067935p.Thr4Ile0.136
thyX3067951c.-6A>G0.132
thyA3073839c.633A>G0.118
thyA3073860c.612G>C0.136
thyA3073863c.609A>G0.136
thyA3073866c.606G>C0.136
thyA3073874p.Ile200Val0.132
thyA3073892c.580A>G0.132
thyA3073898p.Ala192Ser0.133
ald3086788c.-32T>C1.000
alr3841059p.Gly121Ala0.122
alr3841069p.Ile118Phe0.127
alr3841079c.342A>G0.135
alr3841652c.-232A>T0.239
alr3841654c.-234A>C0.248
alr3841662c.-242A>G0.301
alr3841663c.-243G>A0.259
panD4044081c.201A>G0.102
embC4241032c.1170G>C0.116
embC4241038c.1176G>C0.115
embC4241047c.1185C>G0.126
embC4241050c.1188T>G0.126
embC4241053c.1191G>C0.125
embC4241089c.1227C>G0.208
embC4241095c.1233C>T0.198
embC4241107c.1245G>C0.240
embC4241140c.1278A>G0.186
embC4241146c.1284C>G0.188
embC4241158c.1296T>C0.177
embC4241161c.1299C>G0.155
embC4241162c.1300T>C0.155
embC4241170c.1308G>C0.172
embC4241173c.1311C>T0.161
embC4241179c.1317G>A0.160
embC4241203c.1341T>C0.126
embC4241206c.1344G>C0.109
embC4241374c.1512T>G0.131
embC4241380c.1518A>C0.128
embC4241449c.1587C>G0.126
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
embA4244534c.1302T>C0.113
embA4244537c.1305T>G0.113
embA4244547p.Ile439Val0.118
embA4244557p.Arg442Thr0.114
embA4244582c.1350T>C0.108
embA4244585c.1353A>G0.116
embA4245041c.1809C>G0.116
embA4245044c.1812G>C0.117
embA4245053c.1821G>C0.123
embA4245060c.1828T>C0.137
embA4245083c.1851A>C0.159
embA4245089c.1857G>C0.164
embA4245101c.1869G>C0.171
embA4245137c.1905T>C0.188
embA4245146c.1914G>A0.155
embA4245149c.1917C>G0.146
embA4245153p.Ile641Val0.137
embA4245198p.Leu656Ile0.112
embA4245677c.2445G>C0.111
embA4245693p.Ile821Val0.129
embA4245701c.2469G>C0.129
embA4245704c.2472G>C0.134
embA4245725c.2493A>G0.155
embA4245726c.2494T>C0.165
embA4245737c.2505A>C0.181
embA4245740c.2508T>C0.193
embA4245764c.2532G>C0.218
embA4245772p.Asn847Thr0.222
embA4245785c.2553G>C0.192
embA4246292c.3060A>G0.148
embA42463061025S>1025*0.114
embA4246319c.3087G>C0.110
embA4246329p.Thr1033Ala0.111
embB4247491c.978G>C0.125
embB4247497c.984T>C0.139
embB4247512c.999T>C0.119
embB4247539c.1026T>C0.116
embB4247554c.1041T>C0.114
embB4247746c.1233C>T0.130
embB4247761c.1248T>C0.147
embB4247773c.1260G>A0.143
embB4247776c.1263G>T0.152
embB4247797c.1284C>G0.147
embB4247800c.1287A>T0.148
embB4247803c.1290G>C0.156
embB4247815c.1302C>G0.153
embB4247819p.Val436Ile0.136
embB4247830c.1317A>G0.155
embB4247836c.1323A>G0.168
embB4247839c.1326G>C0.151
embB4247866c.1353G>C0.193
embB4247875c.1362G>C0.168
embB4247876c.1363C>T0.176
embB4247881c.1368G>C0.179
embB4247887c.1374C>T0.185
embB4247893c.1380C>T0.187
embB4247899p.Met462Ile0.208
embB4247905c.1392G>C0.192
embB4247909c.1396T>C0.189
embB4247914c.1401G>C0.192
embB4247932c.1419C>G0.178
embB4247940p.Leu476Trp0.168
embB4247945c.1432T>C0.167
embB4247951p.Ser480Ala0.154
embB4247956c.1443G>C0.154
embB4247974c.1461C>G0.170
embB4248070c.1557T>C0.107
embB4248085c.1572T>C0.128
embB4248097c.1584C>G0.187
embB4248130c.1617G>C0.216
embB4248142c.1629T>C0.212
embB4248143c.1630T>C0.212
embB4248157c.1644A>G0.190
embB4248172c.1659G>C0.209
embB4248199c.1686A>G0.152
embB4248200p.Ile563Val0.153
embB4248205c.1692C>G0.160
embB4248206p.Ser565Gly0.159
embB4248220c.1707A>C0.177
embB4248304c.1791G>C0.165
embB4248316c.1803C>G0.139
embB4248319c.1806A>G0.141
embB4248343c.1830G>C0.133
embB4248350c.1837T>C0.105
embB4248355c.1842A>G0.118
embB4248358c.1845C>G0.114
embB4248361c.1848A>C0.113
embB4248362p.Ser617Ala0.113
embB4248373c.1860C>G0.138
embB4248382c.1869C>G0.120
embB4248386c.1873C>A0.115
embB4249417c.2904A>G0.109
embB4249423p.Asp970Glu0.110
embB4249424p.Leu971Met0.110
embB4249429c.2916C>T0.105
embB4249432c.2919A>G0.106
embB4249441c.2928A>G0.135
embB4249444c.2931T>C0.135
embB4249469p.Leu986Met0.152
embB4249486c.2973T>G0.142
ethA4326592294C>294*0.990
ethA4327396c.78A>G0.123
ethA4327399p.Asp25Glu0.121
ethA4327423c.51G>C0.135
ethA4327435c.39T>G0.121
ethA4327438c.36A>G0.127
ethA4327452p.Val8Leu0.109
ethA4327453c.21A>G0.109
ethA4327459c.15G>A0.104
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;