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: 5dd02104a2374
Sample: 5dd02104a2374

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Summary
ID: 5dd02104a2374
Date: Sat Nov 16 16:19:21 2019
Strain: lineage4.8
Drug-resistance: Sensitive

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

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

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
rpsL781395c.-165T>C1.000
rrs1472150r.305t>a0.156
rrs1472172r.327t>c0.146
rrs1472895r.1050c>t0.167
rrs1473035r.1190g>a0.152
rrs1473056r.1211a>t0.139
rrs1473093r.1248c>t0.147
rrs1473104r.1259c>t0.158
rrs1473111r.1266a>g0.122
rrs1473121r.1276t>c0.174
rrs1473145r.1300c>t0.174
rrs1473166r.1321g>a0.176
rrs1473192r.1347a>g0.121
rrs1473252r.1407t>c0.125
rrs1473259r.1414c>t0.130
rrs1473276r.1431a>g0.118
rrl1474001r.344c>t1.000
rrl1474218r.561t>a0.208
rrl1474228r.571t>c0.176
rrl1474249r.592g>t0.161
rrl1474252r.595t>a0.156
rrl1474903r.1246t>c0.115
rrl1474913r.1256t>c0.131
rrl1475124r.1467a>t0.148
rrl1475171r.1514c>t0.151
rrl1475574r.1917c>a0.152
rrl1475699r.2042c>t0.132
rrl1475783r.2126t>g0.118
rrl1475803r.2146t>c0.129
rrl1475816r.2159c>g0.129
rrl1475817r.2160a>g0.129
rrl1475858r.2201t>c0.134
rrl1475866r.2209t>a0.120
rrl1475881r.2224t>c0.122
rrl1475883r.2226a>t0.138
rrl1475898r.2241a>g0.190
rrl1475899r.2242g>a0.179
rrl1475943r.2286g>a0.171
rrl1475945r.2288c>a0.133
rrl1475952r.2295a>g0.155
rrl1475970r.2313c>t0.161
rrl1475975r.2318c>t0.148
rrl1475977r.2320a>g0.126
rrl1476126r.2469c>t0.119
rrl1476130r.2473g>a0.161
rrl1476135r.2478t>c0.119
rrl1476141r.2484a>g0.138
rrl1476153r.2496t>c0.145
rrl1476164r.2507a>g0.114
rrl1476165r.2508t>g0.194
rrl1476179r.2522c>t0.123
rrl1476194r.2537a>g0.197
rrl1476200r.2543a>t0.172
rrl1476201r.2544c>t0.109
rrl1476214r.2557g>t0.115
rrl1476224r.2567a>g0.127
rrl1476250r.2593c>g0.122
rrl1476251r.2594t>c0.125
rrl1476257r.2600g>c0.132
rrl1476260r.2603a>g0.224
rrl1476280r.2623a>c0.156
rrl1476294r.2637a>g0.141
rrl1476297r.2640c>t0.113
rrl1476311r.2654g>c0.139
rrl1476312r.2655t>c0.151
rrl1476313r.2656g>a0.117
rrl1476332r.2675g>c0.182
rrl1476338r.2681c>t0.169
rrl1476353r.2696g>t0.189
rrl1476358r.2701t>c0.195
rrl1476369r.2712c>t0.146
rrl1476372r.2715t>c0.187
rrl1476382r.2725a>g0.182
rrl1476383r.2726t>a0.186
rrl1476425r.2768g>t0.172
rrl1476428r.2771c>t0.282
rrl1476429r.2772a>c0.244
rrl1476466r.2809c>t0.193
rrl1476481r.2824t>c0.306
rrl1476506r.2849t>c0.307
rrl1476515r.2858c>t0.203
rrl1476524r.2867c>t0.175
rrl1476525r.2868a>g0.215
rrl1476530r.2873c>t0.179
rrl1476536r.2879g>a0.154
rrl1476539r.2882a>g0.197
rrl1476540r.2883c>g0.167
rrl1476547r.2890c>t0.149
rrl1476584r.2927c>t0.212
rrl1476585r.2928a>g0.192
rrl1476594r.2937c>a0.140
rrl1476607r.2950c>t0.113
rrl1476608r.2951c>g0.157
rrl1476614r.2957a>t0.154
rrl1476619r.2962c>t0.160
rrl1476628r.2971t>g0.122
rrl1476629r.2972c>a0.157
rrl1476630r.2973a>g0.180
tlyA1917972c.33A>G1.000
embC4242643c.2781C>T1.000
ethA4326313c.1161G>A1.000

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;