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: 5dde77379a43c
Sample: 5dde77379a43c

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Summary
ID: 5dde77379a43c
Date: Wed Nov 27 13:18:43 2019
Strain: lineage4.2.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (0.99)
EthambutolRembB p.Gly406Ala (1.00), embB p.Asp1024Asn (1.00)
PyrazinamideRpncA p.Val130Gly (1.00)
StreptomycinRrpsL p.Lys88Thr (0.99)
EthionamideRethA p.Met1Arg (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8688p.Ala463Ser1.000
gyrA9304p.Gly668Asp1.000
rpoB761489c.1683G>A1.000
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.183
embR1416234p.Cys372Gly0.220
rrs1472137r.292g>a0.143
rrs1472150r.305t>a0.162
rrs1472151r.306c>t0.162
rrs1472172r.327t>c0.183
rrs1472203r.358g>a0.154
rrs1472259r.414c>a0.120
rrs1472379r.534t>c0.145
rrs1472400r.555c>t0.155
rrs1472530r.685g>a0.116
rrs1472537r.692c>t0.123
rrs1472566r.721g>a0.120
rrs1472571r.726g>c0.127
rrs1472655r.810g>a0.125
rrs1472660r.815t>c0.119
rrs1472714r.869a>g0.169
rrs1472790r.945t>c0.140
rrs1472895r.1050c>t0.237
rrs1472956r.1111t>c0.134
rrs1472990r.1145a>g0.208
rrs1473035r.1190g>a0.290
rrs1473055r.1210c>t0.190
rrs1473056r.1211a>t0.306
rrs1473066r.1221a>g0.194
rrs1473081r.1236c>t0.125
rrs1473177r.1332g>a0.143
rrs1473192r.1347a>g0.185
rrs1473205r.1360t>c0.186
rrs1473252r.1407t>c0.155
rrs1473259r.1414c>t0.158
rrs1473352r.1507c>t0.117
rrl1474249r.592g>t0.228
rrl1474310r.653t>g0.145
rrl1474348r.691c>t0.137
rrl1474351r.694g>t0.143
rrl1474362r.705a>g0.130
rrl1474387r.730c>t0.122
rrl1474626r.969t>c0.123
rrl1474634r.977t>c0.170
rrl1474636r.979a>c0.184
rrl1474637r.980c>t0.200
rrl1474638r.981c>g0.204
rrl1474640r.983c>t0.192
rrl1474675r.1018c>g0.148
rrl1474677r.1020a>g0.150
rrl1474709r.1052g>a0.138
rrl1474734r.1077g>t0.140
rrl1474779r.1122g>a0.123
rrl1474780r.1123c>t0.123
rrl1474782r.1125g>a0.123
rrl1474794r.1137c>t0.164
rrl1474802r.1145t>c0.154
rrl1474823r.1166c>g0.176
rrl1474830r.1173a>g0.161
rrl1474831r.1174a>g0.167
rrl1474832r.1175a>t0.164
rrl1474864r.1207c>t0.237
rrl1474901r.1244a>g0.194
rrl1474904r.1247g>c0.274
rrl1474913r.1256t>c0.203
rrl1474933r.1276a>g0.175
rrl1474934r.1277c>t0.161
rrl1475129r.1472g>t0.149
rrl1475499r.1842c>t0.135
rrl1475526r.1869c>t0.157
rrl1475539r.1882a>t0.163
rrl1475545r.1888t>g0.163
rrl1475548r.1891c>t0.125
rrl1475573r.1916g>t0.167
rrl1475777r.2120a>t0.133
rrl1475803r.2146t>c0.162
rrl1475804r.2147g>c0.149
rrl1475816r.2159c>g0.153
rrl1475817r.2160a>g0.172
rrl1475858r.2201t>c0.149
rrl1475866r.2209t>a0.141
rrl1475883r.2226a>c0.157
rrl1475884r.2227a>g0.138
rrl1475896r.2239a>g0.119
rrl1475898r.2241a>g0.200
rrl1475899r.2242g>a0.203
rrl1475916r.2259c>g0.170
rrl1475937r.2280a>t0.184
rrl1475943r.2286g>a0.243
rrl1475945r.2288c>a0.216
rrl1475952r.2295a>g0.200
rrl1475970r.2313c>t0.148
rrl1475975r.2318c>t0.148
rrl1476131r.2474c>t0.174
rrl1476179r.2522c>t0.222
rrl1476194r.2537a>g0.257
rrl1476200r.2543a>t0.289
rrl1476201r.2544c>t0.211
rrl1476204r.2547c>t0.222
rrl1476221r.2564t>c0.167
rrl1476224r.2567a>g0.250
rrl1476227r.2570c>t0.211
rrl1476245r.2588c>t0.175
rrl1476260r.2603a>g0.175
rrl1476359r.2702c>g0.262
rrl1476372r.2715t>c0.123
rrl1476381r.2724g>c0.302
rrl1476425r.2768g>t0.151
rrl1476428r.2771c>t0.306
rrl1476429r.2772a>t0.200
rrl1476466r.2809c>t0.234
rrl1476481r.2824t>c0.464
rrl1476506r.2849t>c0.500
rrl1476567r.2910c>t0.132
tlyA1917972c.33A>G1.000
ahpC2726146c.-47G>GT0.949
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.294
alr3841654c.-234A>C0.333
alr3841662c.-242A>G0.406
alr3841663c.-243G>A0.377
embC4242643c.2781C>T1.000
gid4407997p.Gly69Asp1.000

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;