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: 5dc882d73c25a
Sample: 5dc882d73c25a

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Summary
ID: 5dc882d73c25a
Date: Sun Nov 10 21:38:07 2019
Strain: lineage4.3.3
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
lineage4.3.3Euro-American (LAM)LAM;TRD115

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8040p.Gly247Ser1.000
gyrA9304p.Gly668Asp1.000
rpoC764995c.1626C>G1.000
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.136
embR1416234p.Cys372Gly0.131
rrs1472137r.292g>a0.160
rrs1472150r.305t>a0.178
rrs1472151r.306c>t0.169
rrs1472160r.315c>t0.207
rrs1472172r.327t>c0.205
rrs1472181r.336g>a0.198
rrs1472203r.358g>a0.178
rrs1472210r.365a>c0.152
rrs1472213r.368g>c0.147
rrs1472215r.370a>g0.146
rrs1472222r.377g>a0.151
rrs1472229r.384c>t0.144
rrs1472234r.389t>c0.143
rrs1472236r.391c>g0.144
rrs1472240r.395g>a0.144
rrs1472378r.533g>t0.165
rrs1472379r.534t>g0.146
rrs1472396r.551a>t0.186
rrs1472400r.555c>t0.188
rrs1472571r.726g>c0.147
rrs1472581r.736a>t0.145
rrs1472598r.753a>c0.153
rrs1472599r.754g>t0.137
rrs1472616r.771g>a0.136
rrs1472895r.1050c>t0.156
rrs1473035r.1190g>a0.193
rrs1473053r.1208t>a0.133
rrs1473055r.1210c>t0.126
rrs1473056r.1211a>t0.180
rrs1473062r.1217t>a0.147
rrs1473068r.1223a>g0.143
rrs1473121r.1276t>c0.124
rrs1473145r.1300c>t0.157
rrs1473166r.1321g>a0.157
rrs1473177r.1332g>a0.114
rrs1473192r.1347a>g0.132
rrs1473205r.1360t>c0.132
rrs1473252r.1407t>c0.123
rrs1473259r.1414c>t0.128
rrs1473352r.1507c>t0.143
rrl1474747r.1090c>a0.163
rrl1474844r.1187g>t0.128
rrl1474864r.1207c>t0.130
rrl1474866r.1209c>a0.130
rrl1474903r.1246t>c0.163
rrl1475129r.1472g>t0.184
rrl1475154r.1497c>t0.163
rrl1475175r.1518g>a0.239
rrl1475783r.2126t>g0.160
rrl1475803r.2146t>c0.167
rrl1475804r.2147g>c0.167
rrl1475816r.2159c>g0.175
rrl1475817r.2160a>g0.190
rrl1475858r.2201t>c0.167
rrl1475866r.2209t>a0.167
rrl1476141r.2484a>g0.326
rrl1476153r.2496t>c0.341
rrl1476194r.2537a>g0.184
rrl1476195r.2538c>a0.139
rrl1476196r.2539c>a0.132
rrl1476200r.2543a>t0.158
rrl1476201r.2544c>t0.184
rrl1476204r.2547c>a0.162
rrl1476210r.2553g>t0.135
rrl1476211r.2554g>t0.139
rrl1476212r.2555t>c0.167
rrl1476215r.2558c>a0.167
rrl1476225r.2568t>g0.189
rrl1476229r.2572c>g0.211
rrl1476251r.2594t>c0.217
rrl1476260r.2603a>g0.256
rrl1476280r.2623a>c0.244
rrl1476293r.2636c>t0.135
rrl1476294r.2637a>g0.162
rrl1476295r.2638c>g0.143
rrl1476296r.2639c>t0.171
rrl1476301r.2644a>t0.171
rrl1476302r.2645g>a0.143
rrl1476311r.2654g>c0.135
rrl1476312r.2655t>c0.158
rrl1476313r.2656g>a0.125
rrl1476332r.2675g>c0.152
rrl1476338r.2681c>t0.137
rrl1476353r.2696g>t0.164
rrl1476358r.2701t>c0.175
rrl1476369r.2712c>t0.186
rrl1476372r.2715t>c0.213
rrl1476382r.2725a>g0.203
rrl1476383r.2726t>a0.207
rrl1476408r.2751g>a0.209
rrl1476425r.2768g>a0.219
rrl1476428r.2771c>t0.262
rrl1476429r.2772a>c0.258
rrl1476466r.2809c>t0.209
rrl1476481r.2824t>c0.288
rrl1476506r.2849t>c0.286
rrl1476514r.2857c>t0.185
rrl1476519r.2862c>g0.182
rrl1476524r.2867c>t0.182
rrl1476525r.2868a>g0.182
rrl1476530r.2873c>t0.182
rrl1476536r.2879g>a0.179
rrl1476537r.2880a>g0.179
rrl1476538r.2881a>g0.182
rrl1476540r.2883c>g0.185
rrl1476547r.2890c>t0.226
rrl1476567r.2910c>t0.226
rrl1476572r.2915g>a0.218
rrl1476573r.2916a>c0.214
rrl1476577r.2920t>g0.232
rrl1476584r.2927c>t0.207
fabG11673450p.Thr4Ile1.000
tlyA1917972c.33A>G1.000
kasA2518919p.Gly269Ser1.000
thyA3073868p.Thr202Ala1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
gid4408156p.Leu16Arg1.000

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;