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: 5d807c6cc8499
Sample: 5d807c6cc8499

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Summary
ID: 5d807c6cc8499
Date: Tue Sep 17 07:28:04 2019
Strain: lineage2.2.1;lineage4.3
Drug-resistance: XDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (0.92)
EthambutolRembB p.Met306Val (0.90), embB p.His312Arg (0.11)
PyrazinamideRpncA c.-11A>G (0.99)
StreptomycinRrpsL p.Lys43Arg (0.93), rrs r.462c>t (0.18)
Ethionamide
FluoroquinolonesRgyrA p.Asp94Tyr (0.97)
AmikacinRrrs r.1401a>g (0.92)
CapreomycinRrrs r.1401a>g (0.92)
KanamycinRrrs r.1401a>g (0.92)

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
gyrB6169c.930C>G0.121
gyrB6209c.970C>T0.129
gyrB6238c.999G>A0.122
gyrB6242p.Arg335Lys0.138
gyrB6250c.1011A>G0.148
gyrB6256c.1017G>A0.133
gyrB6280c.1041T>C0.109
gyrB6286c.1047T>C0.111
gyrB7178c.1939T>C0.108
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8156c.855T>C0.138
gyrA8168c.867A>G0.121
gyrA8177c.876A>C0.120
gyrA8867c.1566A>G0.113
gyrA9182c.1881T>C0.119
gyrA9191c.1890G>C0.120
gyrA9200c.1899A>G0.115
gyrA9227c.1926C>G0.128
gyrA9242c.1941A>C0.121
gyrA9304p.Gly668Asp1.000
rpoB760307c.501T>C0.111
rpoB760328c.522G>C0.109
rpoB760331c.525G>C0.117
rpoB760340c.534G>T0.123
rpoB760361c.555T>C0.136
rpoB760370c.564C>G0.131
rpoB760376p.Asp190Glu0.154
rpoB760380p.Thr192Leu0.149
rpoB760406c.600G>C0.158
rpoB760412c.606C>G0.133
rpoB760424c.618C>G0.147
rpoB760430c.624T>C0.138
rpoB760646c.840C>G0.174
rpoB760655c.849A>G0.174
rpoB760661c.855A>C0.195
rpoB760670c.864G>C0.202
rpoB760674c.868T>C0.212
rpoB760679c.873A>G0.215
rpoB760683c.877T>C0.213
rpoB760715c.909C>G0.197
rpoB760718c.912C>T0.179
rpoB760724c.918T>C0.197
rpoB760730c.924T>C0.187
rpoB760751c.945G>C0.194
rpoB760925c.1119T>C0.135
rpoB760928c.1122G>C0.136
rpoB760934c.1128C>T0.158
rpoB760946c.1140A>G0.179
rpoB760982c.1176G>C0.189
rpoB760985c.1179G>C0.118
rpoB760991c.1185G>C0.177
rpoB761006c.1200C>G0.111
rpoB761015c.1209G>C0.154
rpoB761021c.1215G>C0.163
rpoB761027c.1221A>G0.156
rpoB761036c.1230G>C0.140
rpoB761037c.1231T>C0.138
rpoB761057c.1251G>C0.150
rpoB761102c.1296A>G0.141
rpoB761306c.1500C>G0.126
rpoB761327c.1521A>G0.141
rpoB761330c.1524G>C0.111
rpoB761354c.1548C>T0.116
rpoB761360c.1554T>C0.154
rpoB761362p.Ser519Thr0.152
rpoB761373p.Val523His0.131
rpoB761636c.1830G>T0.109
rpoB761645c.1839C>G0.103
rpoB761648c.1842T>C0.104
rpoB761657c.1851C>G0.130
rpoB761675c.1869G>C0.125
rpoB761747c.1941G>C0.118
rpoB761765c.1959T>C0.108
rpoB761834c.2028T>C0.127
rpoB761852c.2046C>G0.117
rpoB761885c.2079T>C0.121
rpoB761915p.Asp703Glu0.105
rpoB761916p.Asp704Asn0.105
rpoB761948c.2142G>C0.108
rpoB761954c.2148C>G0.108
rpoB762083c.2277T>C0.105
rpoB762086c.2280G>C0.128
rpoB762101c.2295C>G0.135
rpoB762114p.Ile770Val0.133
rpoB762131c.2325C>G0.153
rpoB762140c.2334G>C0.141
rpoB762143c.2337T>C0.143
rpoB762149c.2343G>C0.137
rpoB762167c.2361T>C0.146
rpoB762310p.His835Arg0.839
rpoB762827c.3021G>C0.132
rpoB762857c.3051C>G0.131
rpoB762860c.3054G>C0.137
rpoB762863c.3057T>C0.131
rpoB762929c.3123G>C0.112
rpoB762989c.3183G>C0.151
rpoB762995c.3189G>T0.174
rpoB763013c.3207C>G0.151
rpoB763028c.3222T>C0.141
rpoB763031c.3225T>C0.156
rpoB763034c.3228C>G0.141
rpoB763040c.3234C>G0.141
rpoB763070c.3264T>C0.111
rpoB763115c.3309T>C0.130
rpoB763190c.3384C>T0.113
rpoB763214c.3408T>C0.105
rpoB763226c.3420A>G0.117
rpoB763227c.3421C>T0.117
rpoB763238c.3432T>C0.123
rpoC763402c.33C>G0.141
rpoC763411c.42T>G0.114
rpoC763441c.72C>T0.109
rpoC763444c.75T>C0.108
rpoC763456c.87A>G0.140
rpoC763486c.117T>G0.167
rpoC763492c.123G>A0.163
rpoC763528c.159G>A0.158
rpoC763546c.177A>G0.154
rpoC763570c.201G>C0.132
rpoC763573c.204G>C0.112
rpoC763594c.225C>T0.113
rpoC763660c.291T>G0.108
rpoC763675c.306C>G0.115
rpoC763696c.327T>C0.139
rpoC763702c.333C>G0.143
rpoC763717c.348T>C0.173
rpoC763723c.354G>C0.176
rpoC763732c.363C>G0.188
rpoC763738c.369G>A0.177
rpoC763741c.372C>T0.182
rpoC763744c.375G>C0.205
rpoC763765c.396T>C0.169
rpoC763774c.405G>C0.171
rpoC763807c.438T>C0.172
rpoC763816c.447C>G0.169
rpoC763835p.Ala156Met0.164
rpoC763853p.Val162Ile0.146
rpoC763858c.489A>G0.146
rpoC763872p.Gly168Ala0.134
rpoC763876p.Glu169Asp0.124
rpoC763879c.510A>G0.118
rpoC763894c.525A>G0.115
rpoC763960c.591T>C0.135
rpoC764024c.655T>C0.118
rpoC764032p.Asp221Glu0.110
rpoC764044c.675T>C0.115
rpoC764059c.690G>T0.121
rpoC764083c.714A>G0.149
rpoC764098c.729A>G0.112
rpoC764101c.732C>G0.115
rpoC764102p.Val245Ile0.114
rpoC764116c.747C>T0.118
rpoC764131c.762T>C0.136
rpoC764188c.819A>G0.146
rpoC764195p.Ser276Ile0.111
rpoC764203c.834G>C0.110
rpoC764206c.837T>C0.123
rpoC764215c.846A>G0.126
rpoC764236c.867G>A0.151
rpoC764248c.879C>G0.156
rpoC764257c.888G>C0.160
rpoC764266c.897T>C0.118
rpoC764269c.900G>C0.113
rpoC764272c.903G>C0.105
rpoC764278c.909A>G0.110
rpoC764365c.996C>T0.124
rpoC764380c.1011G>C0.106
rpoC764381c.1012T>A0.105
rpoC764387c.1018T>C0.105
rpoC764405c.1036A>C0.112
rpoC764872c.1503A>G0.119
rpoC764911c.1542A>G0.118
rpoC764932c.1563C>A0.121
rpoC764968c.1599T>C0.119
rpoC764995c.1626C>G0.136
rpoC765007c.1638T>G0.106
rpoC765034c.1665T>C0.111
rpoC765040c.1671T>C0.123
rpoC765041c.1672T>C0.111
rpoC765047c.1678T>C0.113
rpoC765055c.1686C>G0.127
rpoC765073c.1704G>C0.128
rpoC765076c.1707A>G0.118
rpoC765079c.1710T>G0.118
rpoC765082c.1713G>C0.118
rpoC765089c.1720T>C0.120
rpoC765967c.2598C>T0.120
rpoC765982c.2613C>G0.130
rpoC765994c.2625A>T0.124
rpoC766010c.2641T>A0.125
rpoC766021c.2652G>C0.130
rpoC766027c.2658G>C0.121
rpoC766043p.Gln892Glu0.152
rpoC766054c.2685C>G0.133
rpoC766082p.Ala905Gln0.140
rpoC766096c.2727G>C0.155
rpoC766630c.3261G>C0.148
rpoC766657c.3288A>G0.141
rpoC766672c.3303T>C0.134
rpoC766673p.Gly1102Asn0.133
rpoC766726c.3357T>C0.141
rpoC766738c.3369G>C0.126
rpoC766933c.3564A>G0.133
rpoC766945c.3576A>G0.136
rpoC766963c.3594T>C0.155
rpoC766972c.3603G>C0.137
rpoC766996c.3627C>T0.137
rpoC767009c.3640T>A0.128
rpoC767014c.3645G>C0.129
rpoC767033c.3664T>A0.127
rpoC767059c.3690T>G0.122
rpoC767062c.3693C>A0.110
rpoC767098c.3729T>C0.116
rpsL781395c.-165T>C1.000
rpsL781736c.177T>C0.110
rpsL781760c.201T>C0.110
rpsL781832c.273T>C0.185
rpsL781838c.279G>C0.140
rpsL781841c.282C>G0.178
rpsL781865c.306G>C0.118
rpsL781868c.309T>C0.161
rpsL781871c.312G>C0.167
rpsL781877c.318T>C0.128
rpsL781892c.333A>G0.140
rpsL781898c.339A>T0.130
rpsL781916c.357T>C0.147
rpsL781929p.Gly124Ser0.138
rplC800814c.6A>G0.149
rplC800817c.9A>T0.135
rplC800844c.36T>C0.118
rrs1473105r.1260g>a0.173
rrs1473123r.1278a>t0.172
rrs1473145r.1300c>t0.204
rrs1473166r.1321g>a0.191
rrl1473756r.99g>a0.127
rrl1473758r.101g>t0.127
rrl1473806r.149c>t0.111
rrl1473877r.220g>a0.115
rrl1473898r.241c>t0.146
rrl1473943r.286g>t0.109
rrl1473945r.288t>a0.102
rrl1473986r.329t>c0.106
rrl1473987r.330g>a0.109
rrl1474181r.524c>t0.125
rrl1474249r.592g>t0.118
rrl1474308r.651g>t0.111
rrl1474310r.653t>g0.130
rrl1474356r.699t>c0.209
rrl1474362r.705a>g0.238
rrl1474376r.719t>c0.214
rrl1474427r.770a>c0.147
rrl1474429r.772g>c0.156
rrl1474432r.775c>g0.156
rrl1474639r.982g>a0.195
rrl1474794r.1137c>t0.167
rrl1474812r.1155g>a0.200
rrl1474823r.1166c>t0.206
rrl1474831r.1174a>g0.222
rrl1474904r.1247g>a0.261
rrl1474956r.1299c>t0.186
rrl1474960r.1303c>g0.167
rrl1474963r.1306g>t0.175
rrl1474964r.1307t>a0.167
rrl1474965r.1308g>c0.163
rrl1474970r.1313g>a0.205
rrl1475006r.1349a>t0.208
rrl1475061r.1404c>t0.109
rrl1475088r.1431a>t0.122
rrl1475315r.1658a>t0.139
rrl1475355r.1698c>t0.189
rrl1475419r.1762c>t0.147
rrl1475483r.1826c>t0.219
rrl1475505r.1848g>a0.188
rrl1475526r.1869c>a0.219
rrl1475599r.1942a>g0.129
rrl1475659r.2002g>t0.125
rrl1475763r.2106c>t0.121
rrl1475881r.2224t>c0.115
rrl1475988r.2331a>g0.256
rrl1476031r.2374c>t0.163
rrl1476032r.2375c>a0.163
rrl1476033r.2376t>c0.163
rrl1476034r.2377c>a0.163
rrl1476045r.2388g>t0.159
rrl1476047r.2390g>t0.156
rrl1476048r.2391g>a0.156
rrl1476049r.2392c>t0.167
rrl1476086r.2429g>a0.174
rrl1476089r.2432t>c0.146
rrl1476095r.2438c>g0.140
rrl1476106r.2449a>t0.116
rrl1476115r.2458t>c0.114
rrl1476117r.2460g>c0.109
rrl1476224r.2567a>g0.132
rrl1476281r.2624t>c0.216
rrl1476597r.2940g>a0.132
rrl1476603r.2946g>a0.143
rrl1476608r.2951c>g0.176
rrl1476628r.2971t>a0.154
rrl1476689r.3032a>t0.158
rrl1476690r.3033c>t0.158
rrl1476693r.3036g>a0.162
rrl1476695r.3038t>a0.158
rrl1476716r.3059a>c0.158
rrl1476726r.3069a>g0.158
fabG11673905p.Ser156Ala0.110
fabG11673916c.477A>T0.125
fabG11673917p.Val160Leu0.125
fabG11673922c.483T>C0.138
fabG11673941p.Ala168Ser0.171
fabG11673946c.507C>G0.173
fabG11673955c.516G>C0.173
fabG11673961c.522A>C0.173
fabG11673985c.546C>G0.144
fabG11674006p.Asp189Glu0.168
fabG11674079p.Pro214Ala0.135
fabG11674114c.675T>A0.130
fabG11674123c.684T>C0.138
fabG11674126c.687G>C0.136
fabG11674132c.693T>C0.127
fabG11674136p.Ser233Ala0.129
inhA1674624c.423A>C0.128
inhA1674630c.429C>G0.129
inhA1674660c.459G>C0.120
inhA1674672c.471C>G0.113
inhA1674703c.502T>C0.203
inhA1674708c.507G>A0.115
inhA1674718c.517A>C0.171
inhA1674870c.669T>C0.135
inhA1674879c.678T>C0.149
inhA1674903c.702T>C0.135
inhA1674904p.Ala235Pro0.132
inhA1674909c.708G>A0.111
rpsA1833661c.120A>G0.106
rpsA1833838c.297G>C0.109
rpsA1833841c.300C>G0.111
rpsA1833847c.306C>G0.125
rpsA1833856c.315A>G0.136
rpsA1833874c.333T>C0.141
rpsA1833928c.387G>C0.194
rpsA1833940c.399C>G0.191
rpsA1833971c.430C>T0.139
rpsA1833979c.438T>C0.137
rpsA1834000c.459G>C0.111
rpsA1834021c.480C>T0.112
rpsA1834123c.582C>G0.124
rpsA1834177c.636A>C1.000
rpsA1834189c.648G>C0.113
rpsA1834210c.669C>T0.115
rpsA1834222c.681T>C0.136
rpsA1834231c.690T>C0.136
rpsA1834234c.693G>C0.119
rpsA1834249c.708T>C0.152
rpsA1834348c.807T>C0.111
rpsA1834465c.924T>C0.120
rpsA1834468c.927A>G0.119
rpsA1834489c.948T>C0.111
rpsA1834528c.987T>C0.149
rpsA1834546c.1005T>C0.167
rpsA1834609c.1068T>C0.116
rpsA1834633c.1092A>G0.123
rpsA1834639c.1098T>C0.111
rpsA1834684c.1143C>T0.132
rpsA1834690c.1149T>C0.167
rpsA1834732c.1191T>C0.113
rpsA1834845c.1305 1307del0.988
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518199p.Ile29Val0.110
kasA2518234c.120G>A0.125
kasA2518248p.Ala45Val0.127
kasA2518265p.Val51Ile0.102
kasA2518519c.405G>C0.116
kasA2518528c.414C>G0.119
kasA2518540c.426T>C0.113
kasA2518783c.669T>C0.112
kasA2518792c.678C>A0.110
kasA2518795c.681C>G0.117
kasA2518825c.711T>C0.152
kasA2518864c.750G>C0.147
kasA2518879c.765A>G0.165
kasA2518885c.771T>C0.157
kasA2518898c.784T>C0.113
folC2747032c.567T>G0.132
folC2747059c.540A>G0.117
folC2747062c.537T>C0.108
folC2747065c.534G>A0.107
folC2747071c.528G>C0.111
folC2747086c.513T>G0.137
folC2747089c.510C>G0.135
folC2747101c.498C>G0.115
folC2747107c.492C>G0.107
folC2747110c.489A>G0.108
folC2747113c.486G>C0.110
folC2747116c.483C>G0.106
thyX3067316c.630T>C0.105
thyX3067325c.621T>C0.105
thyX3067349c.597C>G0.117
thyX3067355c.591T>G0.130
thyX3067367c.579C>G0.144
thyX3067373c.573G>C0.137
thyX3067379c.567G>A0.133
thyX3067391c.555C>G0.114
thyX3067394c.552C>G0.112
thyX3067949c.-4C>T0.945
thyA3073817219Q>219*0.914
thyA3073839c.633A>G0.101
thyA3073863c.609A>G0.118
thyA3073874p.Ile200Val0.116
thyA3073892c.580A>G0.111
thyA3074097c.375G>C0.120
thyA3074100c.372A>G0.118
thyA3074106c.366A>G0.122
thyA3074130c.342C>G0.122
thyA3074147p.Ile109Val0.110
thyA3074205p.Glu89Asp0.130
thyA3074214c.258A>G0.132
thyA3074244c.228T>C0.141
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.271
alr3841654c.-234A>C0.282
alr3841662c.-242A>G0.331
alr3841663c.-243G>A0.287
embC4240819c.957A>G0.117
embC4240831c.969T>G0.112
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
embA4245083c.1851A>C0.134
embA4245089c.1857G>C0.139
embA4245101c.1869G>C0.143
embA4245137c.1905T>C0.143
embA4245146c.1914G>A0.119
embA4245149c.1917C>G0.121
embA4245153p.Ile641Val0.112
embA4245737c.2505A>C0.113
embA4245740c.2508T>C0.112
embA4245764c.2532G>C0.137
embA4245772p.Asn847Thr0.128
embB4246563p.Leu17Trp0.148
embB4246567c.54G>T0.137
embB4247464c.951C>G0.149
embB4247470c.957T>C0.146
embB4247491c.978G>C0.139
embB4247497c.984T>C0.146
embB4247512c.999T>C0.144
embB4247539c.1026T>C0.110
embB4247951p.Ser480Ala0.110
embB4248304c.1791G>C0.130
embB4248316c.1803C>G0.110
embB4248319c.1806A>G0.112
embB4249441c.2928A>G0.113
embB4249444c.2931T>C0.113
ethA4326250408Y>408*0.986
ethA4326676p.Ser266Arg0.975
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;