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: 5c94d66fe987e
Sample: 5c94d66fe987e

Summary
ID: 5c94d66fe987e
Date: Fri Mar 22 12:36:50 2019
Strain: lineage4.3
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB67781539C>T0.107
gyrB68241585C>T0.179
gyrB68411602T>C0.175
gyrB68441605T>G0.175
gyrB68531614A>G0.113
gyrB68561617T>C0.113
gyrB68591620T>C0.111
gyrB68621623C>G0.125
gyrB68781639T>C0.137
gyrB68811642T>C0.137
gyrB69041665C>G0.140
gyrB69101671G>A0.140
gyrB6911558N>558H0.140
gyrB69191680T>C0.146
gyrB69251686T>C0.149
gyrB69311692A>C0.121
gyrB69701731C>T0.120
gyrB72161977G>C0.108
gyrA736221E>21Q1.000
gyrA7451150C>G0.121
gyrA84531152A>C0.114
gyrA84621161A>G0.130
gyrA84711170T>C0.129
gyrA84801179C>T0.138
gyrA84861185T>C0.157
gyrA84891188A>G0.157
gyrA84981197C>T0.169
gyrA85041203G>C0.169
gyrA85161215T>C0.150
gyrA85191218A>C0.143
gyrA85371236G>A0.154
gyrA85461245T>C0.150
gyrA85521251C>G0.154
gyrA8556419A>419Q0.148
gyrA85611260A>C0.152
gyrA85621261C>T0.152
gyrA86031302A>G0.118
rpoB760591262V>262A0.122
rpoB760611805T>C0.124
rpoB760634828T>C0.120
rpoB760646840C>G0.114
rpoB760655849A>G0.118
rpoB760661855A>C0.129
rpoB760670864G>C0.131
rpoB760674868T>C0.129
rpoB760679873A>G0.129
rpoB760683877T>C0.110
rpoB760751945G>C0.120
rpoB760757951T>C0.110
rpoB760759318V>318A0.113
rpoB760763957C>T0.118
rpoB760793987A>G0.113
rpoB760805999G>C0.110
rpoB7608171011A>G0.129
rpoB7608201014T>C0.116
rpoB7608261020C>G0.118
rpoB7608301024T>C0.123
rpoB760845347T>347P0.146
rpoB7608591053T>C0.146
rpoB7608621056G>C0.148
rpoB760869355V>355I0.152
rpoB7608861080A>G0.160
rpoB7609191113C>G0.171
rpoB7609251119T>C0.164
rpoB7609281122G>C0.164
rpoB7609341128C>T0.182
rpoB7609461140A>G0.207
rpoB7609701164G>C0.205
rpoB7609821176G>C0.182
rpoB7609851179G>C0.187
rpoB7609911185G>C0.184
rpoB7610151209G>C0.173
rpoB7610211215G>C0.175
rpoB7610271221A>G0.171
rpoB7610361230G>C0.161
rpoB7610371231T>C0.167
rpoB7610511245G>T0.118
rpoB7610541248G>A0.120
rpoB7610571251G>C0.120
rpoB7610601254C>G0.120
rpoB7610631257C>G0.114
rpoB7618582052G>C0.111
rpoB7628573051C>G0.132
rpoB7628603054G>C0.128
rpoB7628633057T>C0.123
rpoB7629953189G>T0.125
rpoC76340233C>G0.129
rpoC76341142T>G0.112
rpoC76341445T>C0.112
rpoC76344172C>G0.123
rpoC76344475T>C0.114
rpoC76345687A>G0.112
rpoC76346899G>C0.112
rpoC7644051036A>C0.119
rpoC7644311062G>C0.143
rpoC7644341065A>G0.143
rpoC7644461077T>C0.129
rpoC7644491080G>C0.127
rpoC7644521083T>C0.132
rpoC7644581089G>C0.134
rpoC7644611092A>G0.134
rpoC7644971128A>G0.127
rpoC7645031134G>C0.132
rpoC7646261257C>T0.133
rpoC7646321263T>C0.133
rpoC7647161347G>C0.118
rpoC7647641395T>C0.117
rpoC7653191950A>G0.128
rpoC765326653H>653A0.115
rpoC765383672M>672L0.117
rpoC765404679L>679V0.117
rpoC7654092040T>C0.118
rpoC7654122043T>C0.121
rpoC7654212052C>G0.118
rpoC7655782209C>T0.113
rpoC765613748H>748Q0.116
rpoC7656252256C>G0.113
rpoC765631754D>754E0.110
rpoC7657002331T>C0.118
rpoC7657342365T>C0.135
rpoC7657392370G>C0.124
rpoC7658862517C>G0.112
rpoC7658922523T>C0.117
rpoC7667653396A>C0.112
rpoC7667743405T>C0.115
rpoC7668043435A>G0.113
rpoC7668613492G>C0.127
rpoC7668643495G>C0.129
rpoC7668943525T>C0.113
rpoC7668953526T>C0.113
rpoC7669003531T>C0.114
rpoC7669033534C>T0.114
rpoC7669633594T>C0.116
rpoC7669723603G>C0.111
rpoC7669783609C>G0.112
rpoC7669963627C>T0.126
rpoC7670333664T>A0.128
rpoC7670593690T>G0.137
rpoC7670623693C>A0.137
rpoC7670743705T>C0.137
rpoC7670983729T>C0.146
rpoC7671193750A>G0.161
rpoC7671343765C>G0.161
rpoC7671583789T>G0.163
rpoC7671673798C>G0.148
rpoC7671801271A>1271Q0.146
rpoC7671913822C>G0.150
rpoC7672213852C>G0.116
rpoC7672303861G>C0.116
rpoC7672333864T>C0.121
rpsL78163172G>C0.117
embR1416222376F>376L0.182
embR1416234372C>372G0.179
rrs1471969124T>C0.116
rrs1471970125G>A0.116
rrs14729691124A>G0.137
rrs14729701125C>G0.138
rrs14729771132G>C0.135
rrs14729781133T>C0.135
rrl1474001344C>T1.000
rrl1474639982G>A0.149
rrl14747941137C>T0.172
rrl14748121155G>A0.163
rrl14748231166C>T0.150
rrl14748311174A>G0.158
rrl14749041247G>A0.147
rrl14749561299C>T0.143
rrl14749591302C>T0.139
rrl14749701313G>A0.176
rrl14749911334T>C0.164
rrl14750061349A>T0.153
rrl14752711614A>C0.122
rrl14752731616T>A0.125
rrl14752751618C>T0.127
rrl14752761619T>C0.127
rrl14752911634A>C0.139
rrl14753131656G>A0.188
rrl14753151658A>T0.185
rrl14753331676T>C0.183
rrl14753551698C>T0.170
rrl14753691712G>C0.176
rrl14754191762C>T0.205
rrl14754831826C>T0.172
rrl14755051848G>A0.165
rrl14755261869C>A0.146
rrl14755991942A>G0.109
rrl14756081951T>C0.110
rrl14757632106C>T0.128
rrl14767163059A>C0.153
rrl14767233066T>A0.119
rrl14767253068C>T0.116
rrl14767263069A>G0.115
rrl14767323075T>C0.127
rrl14767553098G>A0.130
rrl14767593102T>C0.134
rrl14767703113T>C0.138
rrl14767713114G>A0.138
fabG1167363365S>65N0.111
inhA1674915714C>G0.120
inhA1674942741T>C0.127
inhA1674957756G>C0.132
inhA1674963762G>C0.133
inhA1674966765T>C0.137
inhA1674967256D>256T0.133
inhA1674993792G>C0.128
inhA1674994265H>265S0.128
inhA1675008807C>G0.119
rpsA1834249708T>C0.124
rpsA1834261720A>C0.117
rpsA1834264723G>C0.126
rpsA1834297756C>G0.156
rpsA1834303762T>G0.156
rpsA1834306765T>C0.163
rpsA1834348807T>C0.172
rpsA1834366825A>G0.165
rpsA1834375834G>A0.172
rpsA1834396855G>C0.200
rpsA1834411870T>C0.185
rpsA1834417876G>C0.187
rpsA1834423882G>C0.190
rpsA1834435894G>C0.183
rpsA1834451910T>C0.152
rpsA1834465924T>C0.143
rpsA1834468927A>G0.142
rpsA1834474933C>G0.130
rpsA1834489948T>C0.127
rpsA1834498957C>T0.131
tlyA191797233A>G1.000
ahpC272628896C>T0.194
ahpC2726303111T>C0.164
ahpC2726312120T>C0.158
ahpC272631541D>41E0.158
ahpC272631842E>42D0.158
ahpC272632244P>44A0.155
ahpC2726336144G>C0.172
ahpC2726348156T>C0.186
ahpC2726354162G>C0.190
ahpC2726357165A>G0.200
ahpC2726366174G>C0.172
ahpC2726372180G>C0.167
ahpC2726378186T>C0.159
ahpC2726390198G>C0.149
ahpC272639167A>67T0.149
ahpC272639769S>69G0.147
ahpC2726408216T>C0.141
panD4044057225G>T0.111
panD4044072210G>C0.113
panD4044075207A>G0.114
panD4044081201A>C0.110
panD4044084198A>G0.113
panD4044090192G>A0.114
panD4044093189T>C0.114
panD4044120162T>C0.125
panD4044123159A>G0.125
panD4044126156A>G0.123
panD4044138144A>G0.127
panD4044162120T>C0.118
panD4044165117C>G0.118
panD404418894A>G0.113
embC4240789927T>C0.118
embC4240819957A>G0.125
embC4240825963G>A0.108
embC42408671005T>G0.143
embC42408701008T>C0.156
embC42408791017G>C0.171
embC4240880340A>340T0.169
embC42408851023T>C0.158
embC42408971035C>G0.154
embC42409001038A>G0.158
embC42409191057C>T0.160
embC42409361074A>G0.159
embC42409511089C>G0.143
embC4240954364I>364M0.145
embC42409571095C>G0.141
embC42409661104G>T0.147
embC4240979373T>373P0.143
embC42426432781C>T1.000
embA42449191687C>T0.143
embA42449331701A>G0.122
embA42449451713C>G0.120
embA42449481716G>C0.120
embB42476031090C>T0.119
embB42477761263G>T0.123
embB42477791266C>G0.125
embB42477851272G>C0.125
embB42494562943G>C0.125
embB4249469986L>986M0.145
embB42494832970C>G0.129
embB42494862973T>G0.125
embB42494872974T>C0.125
embB42494982985G>C0.125

Analysis pipeline specifications

TBProfiler Version: 0.1

AnalysisProgram
Mappingbwa
Variant CallingBCFtools


Log

Drug Details
The estimated accuracy of drug resistance predictions is:

Drug1Sensitivity (%)Specificity (%)
Isoniazid 92.8 (89.9-95.7)100 (100-100)
Rifampicin 96.2 (93.9-98.5)98.1 (96.8-99.4)
Ethambutal 88.7 (83.6-93.8)81.7 (77.6-85.8)
Pyrazinamide70.9 (62.4-79.4)93.9 (90.6-97.2)
Streptomycin87.1 (82.7-91.5)89.7 (86.0-93.4)
Ethionamide 73.6 (66.7-80.5)93.3 (89.6-97.0)
Moxifloxacin60.0 (29.6-90.4)68.7 (52.6-84.8)
Ofloxacin 85.5 (79.1-91.9)94.9 (91.8-98.0)
Amikacin 82.9 (74.4-91.4)98.3 (96.0-100)
Capreomycin 60.7 (50.6-70.8)90.7 (87.2-94.2)
Kanamycin 87.3 (81.3-93.3)93.4 (89.9-96.9)
Para-aminosalisylic acidNot determinedNot determined
Linezolid Not determinedNot determined
Clofazimine Not determinedNot determined
Bedaquiline Not determinedNot determined
Multi drug resistance91.2 (87.8-94.6)98.4 (97.2-99.6)
Extremely drug resistance75.9 (64.5-87.3)98.4 (97.3-99.5)

Lineages
Lineage2LocationStrainRD type
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.1.1.1Indo-OceanicEAI4;ZERORD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239
lineage1.1.3Indo-OceanicEAI6RD239
lineage1.2Indo-OceanicEAI1;EAI2RD239
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.2.2Indo-OceanicEAI1RD239
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.2East-Asian (Beijing)Beijing-RD142RD105;RD207;RD181;RD142
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.1East-African-IndianCAS1-KiliRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage3.1.2.1East-African-IndianCAS2RD750
lineage3.1.2.2East-African-IndianCASRD750
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage4.1.1.2Euro-American (X-type)X1None
lineage4.1.1.1Euro-American (X-type)X2RD183
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone
lineage4.2.2.1Euro-AmericanLAM7-TURNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.1Euro-American (LAM)LAM9None
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174
lineage4.3.2Euro-American (LAM)LAM3None
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None
lineage4.4.1.1Euro-AmericanS;OrphansNone
lineage4.5Euro-AmericanH;TRD122
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-American T2-UgandaRD724
lineage4.6.1.2Euro-AmericanT2RD724
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.1Euro-AmericanT3RD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.9Euro-American (H37Rv-like)T1None
lineage5West-Africa 1AFRI_2;AFRI_3RD711
lineage6West-Africa 2AFRI_1RD702
lineage7Lineage 7NoneNone
lineageBOVM. bovisBOV_1;BOV_2None

Citations
1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer
This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.
© 2019 London School of Hygiene and Tropical Medicine;