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: 5da57d1708ea6
Sample: 5da57d1708ea6

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Summary
ID: 5da57d1708ea6
Date: Tue Oct 15 09:08:03 2019
Strain: lineage4.6.1.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.462c>t (0.14)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-AmericanT2-UgandaRD724

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB7072c.1833G>A0.165
gyrB7100c.1861T>C0.146
gyrB7108c.1869G>A0.167
gyrB7114c.1875C>G0.159
gyrB7120c.1881T>C0.153
gyrB7123c.1884C>A0.151
gyrA7362p.Glu21Gln1.000
gyrA7406c.105G>C0.140
gyrA7539p.Thr80Ala0.926
gyrA7585p.Ser95Thr1.000
gyrA7649c.348C>T0.138
gyrA7658c.357A>G0.145
gyrA7661c.360C>T0.144
gyrA7694c.393A>G0.158
gyrA7697c.396C>T0.157
gyrA7700c.399G>C0.158
gyrA7710c.409T>C0.162
gyrA7721c.420G>A0.161
gyrA7725c.424C>T0.164
gyrA7728c.427A>C0.162
gyrA7763c.462T>G0.169
gyrA7775c.474C>T0.144
gyrA7784c.483A>G0.137
gyrA7787c.486G>A0.138
gyrA7797c.496C>T0.131
gyrA7859c.558A>C0.123
gyrA7942p.Glu214Ala0.124
gyrA8294c.993T>C0.153
gyrA8324c.1023T>C0.149
gyrA8382p.Leu361Met0.131
gyrA8393c.1092T>C0.143
gyrA8399c.1098T>C0.136
gyrA8402p.Asp367Glu0.139
gyrA8417c.1116C>G0.139
gyrA8420c.1119T>C0.138
gyrA8421p.Val374Ile0.138
gyrA8426c.1125G>A0.142
gyrA8447c.1146C>A0.158
gyrA8450c.1149G>A0.159
gyrA8453c.1152A>C0.160
gyrA8456c.1155C>T0.158
gyrA8462c.1161A>G0.162
gyrA8480c.1179C>T0.130
gyrA8535p.Glu412Gln0.128
gyrA8540c.1239C>G0.138
gyrA8546c.1245T>C0.138
gyrA9304p.Gly668Asp1.000
rpoB759636c.-171C>T0.149
rpoB759956c.150C>T0.156
rpoB759986c.180T>C0.161
rpoB759991p.Pro62Gln0.164
rpoB760067c.261G>C0.141
rpoB760070c.264T>G0.140
rpoB760325c.519G>C0.174
rpoB760328c.522G>C0.174
rpoB760337c.531C>G0.160
rpoB760340c.534G>T0.155
rpoB760343c.537G>C0.160
rpoB760361c.555T>C0.170
rpoB760380p.Thr192Leu0.185
rpoB760403c.597C>T0.179
rpoB760406c.600G>C0.180
rpoB760412c.606C>T0.187
rpoB760415c.609C>T0.170
rpoB760418c.612G>T0.181
rpoB760424c.618C>G0.167
rpoB760427c.621G>A0.179
rpoB760430c.624T>C0.181
rpoB760454c.648C>G0.217
rpoB760463c.657C>T0.205
rpoB760475c.669A>G0.136
rpoB760478c.672C>T0.140
rpoB760481c.675G>C0.141
rpoB760484c.678A>G0.132
rpoB760490c.684C>T0.147
rpoB760547c.741G>T0.131
rpoB760591p.Val262Ala0.192
rpoB760601c.795C>T0.187
rpoB760611c.805T>C0.181
rpoB760646c.840C>G0.209
rpoB760655c.849A>G0.195
rpoB760661c.855A>C0.176
rpoB760670c.864G>C0.130
rpoB760674c.868T>C0.161
rpoB760679c.873A>G0.136
rpoB760683c.877T>C0.139
rpoB760715c.909C>T0.126
rpoB760721c.915C>G0.137
rpoB760727c.921C>G0.124
rpoB760730c.924T>C0.128
rpoB760820c.1014T>C0.141
rpoB760841c.1035T>C0.153
rpoB760848p.Thr348Ala0.147
rpoB760858p.Val351Ala0.174
rpoB760868c.1062C>T0.165
rpoB760883c.1077G>C0.186
rpoB760886c.1080A>G0.188
rpoB760919c.1113C>G0.138
rpoB760931c.1125C>G0.137
rpoB760934c.1128C>T0.133
rpoB760946c.1140A>G0.147
rpoB761150c.1344A>C0.156
rpoB761153c.1347G>C0.167
rpoB761168c.1362C>G0.163
rpoB761180c.1374A>C0.158
rpoB761189c.1383T>C0.167
rpoB761195c.1389G>T0.141
rpoB761204c.1398C>T0.125
rpoB761207c.1401C>T0.129
rpoB761264c.1458C>G0.147
rpoB761282c.1476C>T0.137
rpoB761408c.1602G>C0.143
rpoB761414c.1608A>G0.140
rpoB761423c.1617T>C0.161
rpoB761435c.1629T>C0.153
rpoB761439p.Asp545Gln0.152
rpoB761444c.1638T>C0.155
rpoB761477c.1671C>G0.158
rpoB761492c.1686G>C0.173
rpoB761510c.1704T>A0.179
rpoB761531c.1725C>G0.183
rpoB761537c.1731C>G0.171
rpoB761573c.1767C>G0.170
rpoB761579c.1773G>C0.179
rpoB761588c.1782C>T0.198
rpoB761600c.1794T>C0.187
rpoB761606c.1800C>G0.189
rpoB761612c.1806G>T0.172
rpoB761615c.1809A>C0.167
rpoB761636c.1830G>C0.192
rpoB761645c.1839C>G0.173
rpoB761648c.1842T>C0.163
rpoB761651p.Ser615Arg0.166
rpoB761657c.1851C>A0.175
rpoB761666c.1860G>C0.182
rpoB761669c.1863C>T0.181
rpoB761675c.1869G>T0.158
rpoB761682c.1876C>T0.153
rpoB761972c.2166C>A0.146
rpoB761990c.2184G>C0.180
rpoB762029c.2223C>G0.182
rpoB762050c.2244G>A0.178
rpoB762053c.2247T>C0.177
rpoB762062c.2256T>C0.185
rpoB762065c.2259T>G0.187
rpoB762074c.2268C>G0.188
rpoB762083c.2277T>C0.172
rpoB762086c.2280G>C0.176
rpoB762101c.2295C>G0.188
rpoB762114p.Ile770Val0.200
rpoB762122c.2316C>T0.201
rpoB762143c.2337T>C0.186
rpoB762149c.2343G>C0.178
rpoB762176c.2370T>C0.131
rpoB762185c.2379G>C0.127
rpoB762212c.2406G>C0.166
rpoB762233c.2427G>C0.170
rpoB762284c.2478G>C0.140
rpoB762293c.2487T>C0.143
rpoB762369c.2563T>C0.160
rpoB762389c.2583G>A0.162
rpoB762395c.2589G>C0.147
rpoB762398c.2592T>C0.140
rpoB762404c.2598T>C0.143
rpoB762410c.2604T>C0.188
rpoB762416c.2610A>G0.183
rpoB762449c.2643C>T0.178
rpoB762452c.2646G>T0.175
rpoB762470c.2664G>C0.161
rpoB762488c.2682G>C0.153
rpoB762490p.Val895Ala0.153
rpoB762509c.2703T>G0.138
rpoB762510p.Ala902Pro0.138
rpoB762515c.2709C>T0.137
rpoB762521c.2715C>G0.132
rpoB762527c.2721G>C0.130
rpoB762533c.2727T>C0.131
rpoB762536c.2730T>C0.123
rpoB762551c.2745C>T0.159
rpoB762575c.2769C>T0.160
rpoB762582c.2776T>C0.147
rpoB762587c.2781G>A0.146
rpoB762596c.2790G>T0.140
rpoB762728c.2922C>G0.130
rpoB762743c.2937G>C0.143
rpoB762746c.2940G>A0.143
rpoB762753c.2947T>C0.156
rpoB762759p.Cys985Ala0.164
rpoB762776c.2970C>T0.189
rpoB762782c.2976T>C0.193
rpoB762785p.Asp993Glu0.184
rpoB762791c.2985G>C0.191
rpoB762799p.Ala998Gly0.182
rpoB762814p.Met1003Lys0.189
rpoB762818c.3012C>G0.193
rpoB762824c.3018C>T0.203
rpoB762827c.3021G>C0.209
rpoB762857c.3051C>G0.197
rpoB762920c.3114C>T0.148
rpoB762929c.3123G>C0.153
rpoB762957c.3151C>T0.137
rpoB762962c.3156C>T0.144
rpoB762995c.3189G>T0.161
rpoB763040c.3234C>G0.165
rpoB763064c.3258G>A0.183
rpoB763070c.3264T>C0.177
rpoB763082c.3276C>A0.162
rpoB763115c.3309T>C0.154
rpoB763139c.3333C>T0.140
rpoB763166c.3360A>G0.145
rpoB763169c.3363A>G0.144
rpoB763175c.3369G>A0.145
rpoB763226c.3420A>G0.154
rpoB763247c.3441G>A0.144
rpoC763375c.6C>A0.136
rpoC763402c.33C>G0.140
rpoC763456c.87A>G0.141
rpoC763468c.99G>C0.145
rpoC763480c.111C>G0.145
rpoC763483c.114G>C0.145
rpoC763484c.115C>T0.141
rpoC763492c.123G>C0.147
rpoC763528c.159G>A0.141
rpoC763546c.177A>G0.133
rpoC763594c.225C>T0.151
rpoC763603c.234C>T0.160
rpoC763618c.249C>T0.152
rpoC763621c.252C>G0.175
rpoC763658c.289C>T0.143
rpoC763696c.327T>C0.141
rpoC763699c.330G>C0.141
rpoC763702c.333C>G0.140
rpoC763709c.340C>T0.154
rpoC763717c.348T>C0.169
rpoC763721c.352C>T0.148
rpoC763741c.372C>T0.157
rpoC763744c.375G>C0.152
rpoC763756c.387C>T0.174
rpoC763790p.Glu141Lys0.133
rpoC763807c.438T>C0.146
rpoC763813c.444C>G0.179
rpoC763835p.Ala156Met0.171
rpoC763858c.489A>G0.172
rpoC763870c.501C>T0.160
rpoC763872p.Gly168Ala0.163
rpoC763876p.Glu169Asp0.157
rpoC763879c.510A>G0.155
rpoC763882c.513G>A0.157
rpoC763888c.519G>T0.161
rpoC763891c.522G>C0.137
rpoC763894c.525A>G0.138
rpoC763936c.567C>G0.182
rpoC763939c.570G>A0.177
rpoC763945c.576T>C0.180
rpoC763948c.579G>A0.182
rpoC763963c.594C>T0.182
rpoC763967p.Gly200Ser0.179
rpoC763972c.603C>T0.189
rpoC763987c.618C>T0.167
rpoC763991p.Ile208Leu0.153
rpoC763996c.627T>C0.159
rpoC764002c.633C>G0.169
rpoC764005c.636G>C0.184
rpoC764024c.655T>C0.190
rpoC764044c.675T>C0.179
rpoC764059c.690G>C0.209
rpoC764083c.714A>G0.229
rpoC764095c.726C>G0.238
rpoC764101c.732C>G0.172
rpoC764102p.Val245Gln0.172
rpoC764116c.747C>T0.211
rpoC764169p.Asn267Thr0.207
rpoC764195p.Ser276Ile0.190
rpoC764206c.837T>C0.192
rpoC764212c.843C>T0.199
rpoC764215c.846A>C0.199
rpoC764218c.849C>T0.204
rpoC764242c.873C>T0.223
rpoC764254c.885G>C0.190
rpoC764266c.897T>C0.194
rpoC764269c.900G>C0.194
rpoC764272c.903G>C0.188
rpoC764278c.909A>G0.183
rpoC764291p.Ser308Ala0.165
rpoC764314c.945C>T0.168
rpoC764317c.948C>G0.147
rpoC764320c.951C>G0.138
rpoC764329c.960C>T0.162
rpoC764365c.996C>T0.191
rpoC764371c.1002G>C0.191
rpoC764380c.1011G>C0.160
rpoC764381c.1012T>A0.159
rpoC764387c.1018T>C0.156
rpoC764405c.1036A>C0.196
rpoC764428c.1059G>T0.186
rpoC764431c.1062G>C0.182
rpoC764434c.1065A>G0.176
rpoC764446c.1077T>C0.141
rpoC764449c.1080G>C0.142
rpoC764452c.1083T>C0.144
rpoC764455c.1086G>A0.148
rpoC764458c.1089G>C0.154
rpoC764461c.1092A>G0.165
rpoC764497c.1128A>G0.169
rpoC764500c.1131C>G0.178
rpoC764521c.1152T>C0.175
rpoC764527c.1158C>T0.172
rpoC764539c.1170C>G0.141
rpoC764542c.1173C>T0.139
rpoC764548c.1179G>T0.180
rpoC764554c.1185C>T0.204
rpoC764560c.1191T>C0.221
rpoC764575c.1206T>G0.200
rpoC764602c.1233C>T0.172
rpoC764611c.1242G>T0.194
rpoC764626c.1257C>T0.192
rpoC764635c.1266C>T0.170
rpoC764650c.1281G>T0.185
rpoC764656c.1287C>G0.178
rpoC764668c.1299C>T0.169
rpoC764692c.1323C>T0.134
rpoC765283c.1914C>G0.184
rpoC765286c.1917G>A0.170
rpoC765292c.1923G>T0.174
rpoC765295c.1926G>C0.179
rpoC765300p.Val644Ala0.178
rpoC765312p.Ala648Asp0.203
rpoC765315p.Glu649Ala0.188
rpoC765319c.1950A>G0.182
rpoC765330p.Ser654Asn0.196
rpoC765357p.Met663Thr0.216
rpoC765370c.2001G>C0.134
rpoC765371c.2002C>T0.134
rpoC765379c.2010G>T0.122
rpoC765383p.Met672Leu0.121
rpoC765409c.2040T>C0.164
rpoC765412c.2043T>C0.174
rpoC765413p.Pro682Ala0.168
rpoC765421c.2052C>G0.202
rpoC765454c.2085C>G0.222
rpoC765478c.2109T>C0.232
rpoC765499c.2130C>G0.211
rpoC765524p.Ala719Ser0.219
rpoC765529c.2160C>T0.210
rpoC765541c.2172C>G0.186
rpoC765550c.2181C>T0.174
rpoC765553c.2184C>T0.171
rpoC765556c.2187G>C0.170
rpoC765562c.2193G>C0.219
rpoC765611p.His748Ser0.200
rpoC765625c.2256C>G0.193
rpoC765631p.Asp754Glu0.192
rpoC765640c.2271A>G0.184
rpoC765658c.2289C>T0.155
rpoC765662c.2293T>C0.146
rpoC765670c.2301C>T0.136
rpoC765700c.2331T>C0.127
rpoC765742c.2373G>A0.132
rpoC765751c.2382C>G0.138
rpoC765753p.Asp795Ala0.136
rpoC765772c.2403C>G0.130
rpoC765850c.2481G>C0.145
rpoC765868c.2499G>A0.170
rpoC765871c.2502T>C0.165
rpoC765875p.Val836Ile0.163
rpoC765886c.2517C>G0.157
rpoC765908c.2539C>T0.164
rpoC765934c.2565C>T0.178
rpoC765937c.2568T>C0.187
rpoC765961c.2592G>A0.189
rpoC765962c.2593T>C0.188
rpoC765967c.2598C>T0.187
rpoC765994c.2625A>T0.187
rpoC766009c.2640G>C0.163
rpoC766010c.2641T>A0.164
rpoC766120c.2751A>G0.136
rpoC766315c.2946C>G0.139
rpoC766321c.2952C>G0.148
rpoC766348c.2979A>G0.124
rpoC766351c.2982C>A0.121
rpoC766738c.3369G>T0.121
rpoC766750c.3381C>G0.141
rpoC766753c.3384C>T0.140
rpoC766765c.3396A>C0.148
rpoC766769c.3400C>T0.159
rpoC766774c.3405T>C0.177
rpoC766798c.3429C>G0.166
rpoC766801c.3432C>G0.165
rpoC766804c.3435A>G0.165
rpoC766843c.3474T>G0.176
rpoC766864c.3495G>C0.122
rpoC766883p.Ser1172Ala0.114
rpoC766894c.3525T>C0.126
rpoC766895c.3526T>C0.126
rpoC766900c.3531T>C0.123
rpoC766918c.3549C>T0.170
rpoC766933c.3564A>G0.167
rpoC766945c.3576A>G0.174
rpoC766957c.3588G>A0.142
rpoC766958p.Gly1197Ser0.140
rpoC766963c.3594T>C0.151
rpoC766978c.3609C>T0.173
rpoC766996c.3627C>T0.168
rpoC767002c.3633G>C0.150
rpoC767008c.3639G>A0.167
rpoC767059c.3690T>G0.152
rpoC767062c.3693C>A0.152
rpoC767098c.3729T>C0.133
rpoC767119c.3750A>G0.130
rpoC767281c.3912C>G0.171
rpoC767284c.3915C>T0.173
rpoC767288c.3919C>T0.175
Rv0678779148c.159G>A0.114
Rv0678779184c.195G>T0.125
Rv0678779198p.Asn70Thr0.123
Rv0678779220c.231T>C0.142
Rv0678779229c.240T>C0.157
Rv0678779235c.246G>A0.155
Rv0678779286c.297T>C0.130
Rv0678779295c.306T>A0.128
rpsL781395c.-165T>C1.000
rpsL781571c.12C>T0.199
rpsL781608p.Ser17Gly0.166
rpsL781649c.90T>C0.170
rplC800844c.36T>C0.165
rplC800856c.48A>C0.156
rplC800865c.57A>G0.143
rplC800867p.Ser20Asn0.143
rplC800877c.69A>C0.145
rplC800883c.75G>T0.164
rplC800889c.81C>G0.161
rplC800901c.93C>G0.153
rplC800907c.99C>G0.140
rplC800913c.105G>T0.139
rplC800919c.111C>G0.138
rplC800922c.114C>T0.137
rplC800934c.126C>G0.127
embR1416232c.1116A>G0.187
embR1416379c.969G>C0.137
rrs1471969r.124t>c0.158
rrs1472035r.190g>t0.161
rrs1472042r.197t>c0.143
rrs1472075r.230a>g0.138
rrs1472300r.455c>t0.141
rrs1472329r.484a>g0.153
rrs1473085r.1240a>g0.187
rrs1473123r.1278a>t0.212
rrs1473126r.1281a>g0.209
rrs1473290r.1445c>t0.164
rrl1473401c.-257G>A0.160
rrl1473403c.-255C>T0.157
rrl1473408c.-250C>T0.152
rrl1473417c.-241C>T0.168
rrl1473421c.-237G>A0.160
rrl1473437c.-221T>C0.140
rrl1473541c.-117G>A0.184
rrl1473542c.-116C>T0.190
rrl1473571c.-87C>T0.229
rrl1473600c.-58A>G0.180
rrl1473612c.-46A>T0.189
rrl1473613c.-45G>T0.185
rrl1473614c.-44C>T0.185
rrl1473660r.3g>a0.224
rrl1473700r.43g>c0.244
rrl1473752r.95g>t0.304
rrl1473806r.149c>t0.255
rrl1473815r.158t>c0.282
rrl1473836r.179a>g0.234
rrl1473876r.219g>a0.222
rrl1473877r.220g>a0.236
rrl1473898r.241c>t0.253
rrl1473923r.266c>a0.209
rrl1473924r.267a>t0.217
rrl1473943r.286g>t0.211
rrl1473944r.287g>t0.211
rrl1473981r.324g>t0.254
rrl1473995r.338g>t0.303
rrl1474001r.344c>t0.269
rrl1474028r.371t>c0.261
rrl1474029r.372g>a0.261
rrl1474034r.377g>a0.257
rrl1474040r.383g>a0.269
rrl1474083r.426c>t0.203
rrl1474111r.454t>c0.222
rrl1474140r.483c>t0.206
rrl1474151r.494c>t0.200
rrl1474181r.524c>a0.333
rrl1474266r.609t>c0.203
rrl1474632r.975g>t0.274
rrl1474639r.982g>a0.274
rrl1474716r.1059a>g0.257
rrl1474753r.1096a>g0.320
rrl1474760r.1103a>g0.333
rrl1474794r.1137c>a0.279
rrl1474812r.1155g>a0.262
rrl1474831r.1174a>g0.224
rrl1475005r.1348c>t0.234
rrl1475006r.1349a>g0.234
rrl1475013r.1356g>a0.234
rrl1475028r.1371g>a0.171
rrl1475061r.1404c>t0.143
rrl1475202r.1545g>c0.278
rrl1475213r.1556c>t0.278
rrl1475252r.1595c>t0.196
rrl1475256r.1599c>t0.185
rrl1475266r.1609t>c0.204
rrl1475276r.1619t>c0.222
rrl1475289r.1632g>a0.220
rrl1475291r.1634a>c0.244
rrl1475297r.1640c>t0.233
rrl1475315r.1658a>c0.205
rrl1475333r.1676t>c0.211
rrl1475355r.1698c>t0.175
rrl1475369r.1712g>c0.225
rrl1475402r.1745c>t0.212
rrl1475419r.1762c>t0.283
rrl1475429r.1772g>a0.293
rrl1475446r.1789g>c0.279
rrl1475505r.1848g>a0.241
rrl1475518r.1861a>c0.250
rrl1475526r.1869c>a0.264
rrl1475608r.1951t>c0.212
rrl1475638r.1981c>t0.227
rrl1475657r.2000a>g0.224
rrl1475759r.2102c>t0.225
rrl1475760r.2103c>t0.230
rrl1475763r.2106c>t0.233
rrl1475881r.2224t>c0.248
rrl1475988r.2331a>g0.309
rrl1475997r.2340a>t0.268
rrl1476032r.2375c>t0.256
rrl1476033r.2376t>c0.256
rrl1476035r.2378g>a0.256
rrl1476056r.2399g>a0.224
rrl1476086r.2429g>a0.144
rrl1476089r.2432t>c0.128
rrl1476095r.2438c>g0.131
rrl1476115r.2458t>c0.160
rrl1476117r.2460g>c0.160
rrl1476214r.2557g>a0.116
rrl1476251r.2594t>c0.154
rrl1476281r.2624t>c0.140
rrl1476297r.2640c>t0.138
rrl1476299r.2642c>t0.128
rrl1476363r.2706a>g0.182
rrl1476583r.2926g>a0.154
rrl1476597r.2940g>a0.176
rrl1476628r.2971t>a0.150
rrl1476629r.2972c>a0.150
rrl1476716r.3059a>c0.153
rrl1476726r.3069a>g0.184
rrl1476746r.3089t>a0.225
rrl1476755r.3098g>t0.192
rrl1476759r.3102t>a0.165
rrl1476770r.3113t>c0.169
rrl1476771r.3114g>a0.169
fabG11673679c.240T>C0.157
fabG11673712c.273A>G0.175
fabG11673724c.285A>C0.174
fabG11673727c.288C>T0.167
fabG11673733p.Met98Ile0.167
fabG11673748c.309A>G0.164
fabG11673973c.534G>C0.146
fabG11673985c.546C>G0.166
fabG11674021c.582G>A0.189
fabG11674037p.Gln200Glu0.185
fabG11674051c.612A>G0.160
fabG11674054c.615T>C0.159
fabG11674060c.621A>G0.176
fabG11674063c.624G>C0.166
fabG11674079p.Pro214Ala0.153
inhA1674279c.78A>C0.156
inhA1674285c.84A>G0.154
inhA1674294c.93G>A0.160
inhA1674300c.99C>T0.178
inhA1674306c.105G>A0.176
inhA1674313c.112C>T0.153
inhA1674321c.120G>T0.157
inhA1674331p.Leu44Met0.154
inhA1674342c.141T>C0.142
inhA1674382p.Leu61Ile0.120
inhA1674411c.210C>T0.128
inhA1674421c.220T>C0.156
inhA1674426c.225C>G0.153
inhA1674429c.228C>T0.149
inhA1674435c.234G>C0.132
inhA1674443p.Ala81Val0.150
inhA1674452p.Ala84Glu0.159
inhA1674462p.Lys87Asn0.187
inhA1674471c.270G>C0.190
inhA1674480c.279T>C0.226
inhA1674486c.285T>C0.242
inhA1674489c.288G>C0.272
inhA1674501c.300G>A0.306
inhA1674503p.Thr101Ser0.298
inhA1674507c.306G>A0.301
inhA1674528c.327C>T0.295
inhA1674531c.330C>T0.293
inhA1674542p.Ala114Glu0.284
inhA1674546c.345T>C0.288
inhA1674549c.348G>C0.288
inhA1674570c.369G>C0.304
inhA1674579c.378G>C0.317
inhA1674589p.Met130Leu0.287
inhA1674618c.417C>T0.268
inhA1674624c.423A>C0.272
inhA1674627c.426T>C0.268
inhA1674639c.438C>T0.267
inhA1674651c.450C>T0.227
inhA1674654c.453G>C0.236
inhA1674656p.Ser152Thr0.236
inhA1674675c.474C>T0.229
inhA1674690c.489C>T0.180
inhA1674699c.498C>T0.173
inhA1674703c.502T>C0.167
inhA1674718c.517A>C0.130
inhA1674723c.522C>T0.125
inhA1674726c.525G>C0.121
inhA1674738c.537C>T0.136
inhA1674765c.564C>G0.132
inhA1674771c.570C>A0.143
inhA1674777c.576C>A0.141
inhA1674780c.579T>G0.143
inhA1674789c.588G>C0.158
inhA1674795c.594G>A0.162
inhA1674801c.600T>C0.177
inhA1674831c.630G>A0.144
inhA1674840c.639C>A0.125
inhA1674846c.645C>T0.151
inhA1674858c.657G>A0.167
inhA1674861p.Glu220Asp0.162
inhA1674873c.672G>A0.169
inhA1674876c.675C>A0.173
inhA1674883p.Ile228Val0.150
inhA1674888c.687C>A0.152
inhA1674903c.702T>C0.136
inhA1674904p.Ala235Pro0.136
inhA1674930c.729C>T0.120
inhA1674934p.Leu245Val0.127
rpsA1833589c.48A>T0.157
rpsA1833623p.Lys28Gln0.194
rpsA1833649c.108C>T0.191
rpsA1833724c.183C>G0.210
rpsA1833727c.186G>A0.214
rpsA1833742c.201A>G0.199
rpsA1833745c.204G>C0.209
rpsA1833748c.207C>G0.212
rpsA1833754c.213G>A0.225
rpsA1833772c.231C>T0.240
rpsA1833782p.Ser81Thr0.231
rpsA1833787c.246C>G0.227
rpsA1833790c.249T>C0.231
rpsA1833802c.261A>G0.236
rpsA1833811c.270G>T0.231
rpsA1833820c.279G>A0.229
rpsA1833832p.Glu97Asp0.235
rpsA1833856c.315A>G0.239
rpsA1833862c.321G>A0.243
rpsA1833874c.333T>C0.244
rpsA1833887p.Ile116Val0.247
rpsA1833928c.387G>C0.270
rpsA1833940c.399C>G0.245
rpsA1833952c.411C>T0.244
rpsA1833973c.432G>T0.248
rpsA1833976c.435C>T0.242
rpsA1833979c.438T>C0.250
rpsA1833988c.447C>T0.237
rpsA1834000c.459G>C0.226
rpsA1834015c.474G>T0.227
rpsA1834018c.477C>T0.223
rpsA1834021c.480C>T0.212
rpsA1834030c.489C>G0.220
rpsA1834051c.510G>A0.182
rpsA1834261c.720A>G0.124
rpsA1834528c.987T>C0.133
rpsA1834546c.1005T>C0.140
rpsA1834555c.1014T>C0.131
rpsA1834562p.Gly341Cys0.145
rpsA1834609c.1068T>C0.124
rpsA1834633c.1092A>G0.137
rpsA1834639c.1098T>C0.131
rpsA1834654p.Glu371Asp0.155
rpsA1834669c.1128G>C0.145
rpsA1834690c.1149T>C0.169
rpsA1834699p.Glu386Asp0.174
rpsA1834733p.Ala398Pro0.194
rpsA1834751p.Leu404Met0.185
rpsA1834756c.1215G>A0.182
rpsA1834765p.Glu408Asp0.197
rpsA1834767p.Lys409Thr0.185
rpsA1834774c.1233C>T0.228
rpsA1834789c.1248T>C0.245
rpsA1834792c.1251G>C0.245
rpsA1834829p.Ala430Thr0.261
tlyA1917972c.33A>G1.000
kasA2518282c.168A>G0.111
kasA2518283p.Ala57Pro0.112
kasA2518318c.204C>G0.125
kasA2518323p.Ser70Asn0.152
kasA2518336c.222A>G0.174
kasA2518339c.225C>G0.169
kasA2518351c.237C>G0.178
kasA2518360c.246C>T0.182
kasA2518369c.255G>C0.230
kasA2518374p.Gly87Ala0.246
kasA2518381p.Leu89Phe0.250
kasA2518385p.Gly91Ser0.250
kasA2518390c.276A>G0.256
kasA2518393c.279G>A0.234
kasA2518396c.282A>C0.246
kasA2518417c.303G>C0.271
kasA2518429c.315A>G0.227
kasA2518438c.324C>T0.150
kasA2518439p.Ala109Thr0.150
kasA2518444c.330T>C0.140
kasA2518447c.333T>G0.138
kasA2518450c.336C>T0.136
kasA2518453c.339C>T0.136
kasA2518462c.348A>G0.145
kasA2518468c.354A>C0.140
kasA2518475c.361A>C0.140
kasA2518480c.366T>C0.139
kasA2518483c.369C>T0.143
kasA2518504c.390T>C0.195
kasA2518506p.Ala131Glu0.184
kasA2518513c.399C>G0.185
kasA2518519c.405G>T0.185
kasA2518535p.Ala141Thr0.163
kasA2518573c.459G>C0.160
kasA2518574p.Ile154Val0.163
kasA2518588c.474T>G0.188
kasA2518591c.477G>C0.186
kasA2518609p.Met165Ile0.175
kasA2518612c.498C>T0.185
kasA2518624c.510C>G0.182
kasA2518634p.Gly174Ser0.157
kasA2518642c.528A>G0.157
kasA2518645c.531G>C0.165
kasA2518657c.543G>A0.179
kasA2518672c.558G>C0.176
kasA2518678c.564C>T0.165
kasA2518681c.567C>T0.165
kasA2518702c.588C>T0.163
kasA2518705c.591T>C0.140
kasA2518714c.600A>C0.147
kasA2518765c.651G>C0.121
kasA2518780c.666G>A0.137
kasA2518783c.669T>C0.137
kasA2518789c.675G>C0.146
kasA2518795c.681C>G0.134
kasA2518807c.693C>T0.141
kasA2518816c.702C>T0.137
kasA2518819c.705C>T0.148
kasA2518822c.708C>T0.138
kasA2518825c.711T>C0.138
kasA2519188c.1074G>C0.110
kasA2519218c.1104G>A0.168
kasA2519221c.1107G>C0.168
kasA2519225c.1111C>T0.189
ahpC2726288c.96C>T0.154
ahpC2726408c.216T>C0.127
ahpC2726432c.240C>G0.119
ahpC2726444c.252G>T0.115
ahpC2726447c.255T>C0.116
ahpC2726591c.399C>G0.119
ahpC2726600c.408T>C0.131
ahpC2726624c.432C>T0.153
folC2746699c.900G>A0.124
folC2746705c.894C>T0.163
folC2746708c.891G>A0.151
folC2746728c.871A>G0.165
thyX3067247c.699G>C0.155
thyX3067250c.696C>G0.154
thyX3067274c.672G>T0.153
thyX3067277c.669G>C0.157
thyX3067283c.663G>C0.144
thyX3067287p.Ala220Val0.145
thyX3067295c.651G>A0.155
thyX3067304c.642T>C0.132
thyX3067316c.630T>C0.133
thyX3067325c.621T>C0.130
thyX3067331c.615G>A0.138
thyX3067337c.609G>A0.139
thyX3067355c.591T>G0.118
thyX3067619c.327T>C0.139
thyX3067793c.153A>G0.138
thyX3067814c.132A>G0.183
thyX3067823c.123C>G0.154
thyX3067849p.Pro33Glu0.137
thyX3067850c.96T>G0.138
thyX3067853c.93G>T0.141
thyX3067885p.Pro21Ser0.127
thyX3067886c.60T>G0.141
thyX3067889c.57G>C0.137
thyX3067898p.Asp16Glu0.158
thyX3067916c.30T>C0.140
thyX3067919c.27C>T0.142
thyX3067925c.21C>T0.134
thyX3067934c.12G>A0.147
thyA3074397c.75T>C0.192
thyA3074423p.Pro17Ala0.162
thyA3074424c.48C>G0.163
thyA3074427c.45A>G0.163
thyA3074444p.Phe10Arg0.118
thyA3074450c.22G>A0.116
thyA3074454c.18G>A0.126
thyA3074463c.9T>A0.129
thyA3074470p.Val1Ala0.136
fbiA3640365c.-178C>G0.133
fbiA3640749c.207G>C0.148
fbiA3640758c.216G>C0.142
fbiA3640785p.Gln81His0.157
fbiA3640788c.246T>A0.157
fbiA3640797c.255T>C0.160
fbiA3640879c.337C>T0.132
fbiA3640901p.Gln120Arg0.189
fbiA3640914c.372C>G0.179
fbiA3640918p.Ser126Ala0.176
fbiA3640930p.Glu130Thr0.173
fbiA3640935c.393C>A0.166
fbiA3640938c.396A>G0.177
alr3840248c.1173G>C0.178
alr3840254c.1167T>C0.197
alr3840275c.1146A>C0.239
alr3840293c.1128A>C0.198
alr3840296c.1125C>G0.209
alr3840302c.1119C>T0.208
alr3840308c.1113C>G0.196
alr3840312p.Ile370Thr0.189
alr3840314c.1107G>A0.194
alr3840328c.1093A>G0.191
alr3840356c.1065A>G0.156
alr3840362c.1059C>T0.162
alr3840374c.1047G>A0.153
alr3840382p.Met347Leu0.158
alr3840436c.985G>A0.128
alr3840437c.984C>G0.127
alr3840446c.975C>G0.153
alr3840467c.954C>A0.131
alr3840470c.951G>C0.137
alr3840476c.945T>G0.135
alr3840482c.939A>G0.138
alr3840493c.928G>A0.130
alr3841662c.-242A>G0.227
panD4043933p.Met117Val0.149
panD4043941p.Pro114Gln0.161
panD4043943c.339T>C0.159
panD4043951p.Tyr111Asp0.165
panD4043961c.321A>G0.166
panD4044057c.225G>C0.125
panD4044072c.210G>C0.123
panD4044075c.207A>G0.136
panD4044078c.204C>T0.128
panD4044081c.201A>G0.144
panD4044087c.195G>A0.193
panD4044108c.174G>A0.170
panD4044111c.171G>C0.168
panD4044119c.163G>A0.182
panD4044120c.162T>G0.187
panD4044132c.150G>A0.258
panD4044138c.144A>G0.283
panD4044150c.132T>C0.310
panD4044159c.123G>A0.366
panD4044165c.117C>G0.365
panD4044171c.111G>A0.376
panD4044174c.108G>C0.370
panD4044210c.72G>C0.384
panD4044237c.45C>G0.208
panD4044240c.42C>G0.204
panD4044252c.30G>A0.217
panD4044266c.16G>A0.231
panD4044270c.12C>T0.219
embC4240420c.558T>C0.144
embC4240423c.561G>A0.144
embC4240444c.582C>G0.150
embC4240450c.588G>A0.148
embC4240471c.609C>T0.141
embC4240475p.Ala205Thr0.143
embC4240489c.627A>G0.136
embC4240495c.633T>C0.137
embC4240815p.Gly318Ala0.143
embC4240819c.957A>G0.165
embC4240828c.966G>A0.173
embC4240831c.969T>G0.154
embC4240853c.991C>T0.125
embC4240954c.1092T>C0.131
embC4240957c.1095C>G0.132
embC4241017c.1155T>C0.143
embC4241023c.1161T>G0.152
embC4241039p.Asp393Asn0.148
embC4241095c.1233C>T0.156
embC4241101c.1239G>C0.155
embC4241107c.1245G>A0.159
embC4241146c.1284C>G0.151
embC4241162c.1300T>C0.131
embC4241313p.Ala484Val0.183
embC4241319p.Pro486Leu0.159
embC4241326c.1464T>C0.155
embC4241332c.1470T>C0.167
embC4241351p.Ile497Val0.126
embC4241361p.Asn500Ser0.126
embC4241374c.1512T>C0.136
embC4241377c.1515C>G0.128
embC4241380c.1518A>C0.141
embC4241383c.1521G>C0.135
embC4241392c.1530G>C0.174
embC4241401c.1539C>T0.175
embC4241425c.1563G>A0.143
embC4241584c.1722T>C0.152
embC4241587c.1725C>G0.156
embC4241591c.1729C>T0.160
embC4241614c.1752A>C0.168
embC4241617c.1755G>A0.177
embC4241626c.1764T>C0.178
embC4241644c.1782G>C0.162
embC4241648c.1786T>C0.162
embC4241656c.1794G>C0.165
embC4241665c.1803G>A0.172
embC4241671c.1809T>G0.156
embC4241677c.1815G>C0.158
embC4241683c.1821G>C0.148
embC4241689c.1827G>C0.131
embC4241692c.1830C>G0.129
embC4241695c.1833T>G0.129
embC4241710c.1848G>A0.155
embC4241713c.1851G>C0.146
embC4241719c.1857G>C0.144
embC4242070c.2208T>G0.172
embC4242076c.2214G>T0.152
embC4242079c.2217T>C0.147
embC4242085c.2223A>G0.156
embC4242091c.2229T>G0.156
embC4242092c.2230T>C0.160
embC4242095p.Ala745Thr0.169
embC4242105p.Thr748Ser0.194
embC4242109c.2247C>T0.197
embC4242146p.Asn762Asp0.214
embC4242151c.2289A>G0.213
embC4242154c.2292C>A0.215
embC4242161p.Ala767Pro0.189
embC4242171p.Thr770Ser0.193
embC4242175c.2313G>T0.188
embC4242179p.Leu773Val0.198
embC4242187c.2325C>T0.142
embC4242190c.2328C>G0.124
embC4242196c.2334A>C0.126
embC4242343c.2481G>T0.118
embC4242355c.2493A>C0.138
embC4242361c.2499C>T0.130
embC4242367c.2505C>G0.129
embC4242373c.2511C>G0.130
embC4242384p.Tyr841Phe0.123
embC4242391c.2529G>C0.127
embC4242394c.2532C>T0.130
embC4242400c.2538C>G0.140
embC4242403c.2541T>C0.146
embC4242406c.2544A>G0.143
embC4242428p.Ala856Ser0.226
embC4242434p.Val858Ile0.188
embC4242445c.2583C>T0.167
embC4242452c.2590C>T0.163
embC4242643c.2781C>T0.985
embC4242721c.2859G>T0.147
embC4242742c.2880C>G0.132
embC4242745c.2883A>C0.140
embC4242748c.2886A>G0.129
embC4242826c.2964G>C0.146
embC4242832c.2970A>C0.135
embC4242838c.2976C>G0.132
embC4242916c.3054C>G0.147
embC4242928c.3066A>G0.146
embC4242931c.3069G>C0.120
embA4243262p.His10Gln0.146
embA4244474c.1242G>C0.123
embA4244479p.Thr416Met0.136
embA4244483c.1251T>C0.136
embA4244504c.1272G>A0.128
embA4244507c.1275G>T0.127
embA4244517p.Leu429Val0.145
embA4244523p.Pro431Ala0.132
embA4244534c.1302T>C0.126
embA4244537c.1305T>G0.124
embA4244636c.1404G>C0.119
embA4244645c.1413T>C0.117
embA4244648c.1416G>C0.119
embA4244649p.Asp473Asn0.119
embA4244666c.1434G>C0.181
embA4244675c.1443A>G0.182
embA4244676p.Ser482Ala0.182
embA4244681c.1449A>G0.204
embA4244684c.1452C>G0.200
embA4244714c.1482C>G0.195
embA4244747c.1515T>G0.151
embA4244868p.Ser546Arg0.130
embA4244897c.1665T>C0.132
embA4244900c.1668G>C0.125
embA4244906c.1674C>T0.140
embA4244909c.1677C>T0.143
embA4244921c.1689C>G0.144
embA4244924c.1692G>C0.158
embA4244933c.1701A>G0.158
embA4244960c.1728A>C0.193
embA4245063c.1831C>T0.148
embA4245083c.1851A>T0.154
embA4245173c.1941G>C0.146
embA4245182c.1950T>C0.192
embA4245188c.1956G>C0.203
embA4245200c.1968C>G0.169
embA4245206c.1974A>G0.168
embA4245207c.1975T>C0.166
embA4245215c.1983A>C0.176
embA4245224c.1992T>C0.171
embA4245443c.2211C>T0.152
embA4245464c.2232C>T0.189
embA4245476c.2244C>G0.189
embA4245488c.2256G>A0.153
embA4245489p.Val753Leu0.150
embA4245497c.2265C>G0.136
embA4245501p.Ala757Thr0.135
embA4245509c.2277A>G0.136
embA4245569c.2337G>A0.275
embA4245594c.2362T>A0.206
embA4245599c.2367A>G0.196
embA4245605c.2373G>C0.186
embA4245620c.2388T>C0.173
embA4245623c.2391G>A0.170
embA4245635c.2403A>G0.144
embA4245652p.Thr807Ser0.136
embA4245662c.2430G>C0.145
embA4245674c.2442A>C0.159
embA4245677c.2445G>C0.164
embA4245688p.Val819Ala0.182
embA4245692c.2460G>C0.174
embA4245701c.2469G>A0.177
embA4245704c.2472G>C0.188
embA4245726c.2494T>C0.196
embA4245737c.2505A>C0.191
embA4245742p.Thr837Ile0.143
embA4245758c.2526C>T0.116
embA4246220c.2988T>C0.139
embA4246229c.2997T>C0.139
embB4246642c.129G>C0.111
embB4246652c.139C>T0.115
embB4246657c.144C>G0.130
embB4246814p.Thr101Ala0.212
embB4246828c.315A>G0.224
embB4246843c.330T>C0.230
embB4246844c.331T>C0.230
embB4246853c.340T>C0.231
embB4246869p.Ser119Asn0.258
embB4246871p.Ala120Ser0.240
embB4246874p.Gln121Lys0.234
embB4246882c.369G>C0.251
embB4246883p.Asp124Asn0.253
embB4246910c.397T>C0.266
embB4246915c.402C>G0.276
embB4246921c.408G>A0.276
embB4246981c.468C>T0.143
embB4246992p.Asn160Thr0.153
embB4246996c.483C>T0.172
embB4247002c.489G>C0.171
embB4247011c.498C>T0.157
embB4247014c.501G>C0.162
embB4247017c.504G>C0.162
embB4247023c.510G>C0.165
embB4247029c.516G>A0.163
embB4247035c.522C>T0.172
embB4247040p.Phe176Tyr0.185
embB4247044c.531C>G0.184
embB4247047c.534C>T0.163
embB4247062c.549G>T0.165
embB4247068c.555T>C0.166
embB4247077c.564G>C0.181
embB4247086c.573C>T0.190
embB4247095c.582G>A0.196
embB4247105p.Pro198Asp0.197
embB4247114p.Ala201Arg0.193
embB4247117p.Val202Leu0.191
embB4247125c.612G>C0.211
embB4247150p.Arg213Thr0.174
embB4247155c.642G>C0.179
embB4247167c.654A>G0.180
embB4247168c.655C>T0.180
embB4247185c.672G>T0.160
embB4247192p.Val227Leu0.151
embB4247201p.Val230Thr0.126
embB4247209c.696A>G0.122
embB4247830c.1317A>G0.120
embB4247848c.1335G>A0.161
embB4247851c.1338C>G0.155
embB4247857c.1344C>G0.163
embB4247887c.1374C>T0.154
embB4247948p.Val479Leu0.137
embB4247965c.1452C>G0.127
embB4247975p.Val488Ile0.142
embB4248013c.1500A>G0.150
embB4248022p.Leu503Phe0.141
embB4248032c.1519A>C0.144
embB4248037c.1524T>G0.131
embB4248085c.1572T>G0.146
embB4248232c.1719G>C0.171
embB4248277c.1764G>C0.230
embB4248301c.1788C>T0.195
embB4248316c.1803C>G0.208
embB4248319c.1806A>G0.202
embB4248322c.1809G>A0.198
embB4248334c.1821C>G0.211
embB4248349c.1836G>A0.190
embB4248355c.1842A>G0.166
embB4248358c.1845C>T0.165
embB4248362p.Ser617Thr0.154
embB4248448c.1935C>G0.127
embB4249168c.2655C>A0.166
embB4249174c.2661C>T0.163
embB4249186c.2673G>C0.155
embB4249198c.2685G>A0.157
embB4249204c.2691T>C0.156
embB4249216c.2703A>G0.162
embB4249400p.Val963Leu0.149
embB4249417c.2904A>G0.158
embB4249432c.2919A>G0.134
embB4249459c.2946G>A0.144
ethA4326847c.627G>C0.143
ethA4326850c.624T>C0.158
ethA4326877c.597G>T0.144
ethA4326880c.594G>C0.160
ethA4326888p.Asp196Asn0.148
ethA4327041p.Glu145Gln0.183
ethR4327862p.Thr105Asn0.136
ethR4327893c.345G>A0.133
ethR4328070c.522G>A0.128

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;