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: 5dcb7f105285e
Sample: 5dcb7f105285e

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Summary
ID: 5dcb7f105285e
Date: Wed Nov 13 03:59:40 2019
Strain: lineage4.4.1.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Ile (1.00)
RifampicinRrpoB p.His445Asp (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
FluoroquinolonesRgyrA p.Ala90Val (1.00)
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.4Euro-AmericanS;TNone
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.179
rrs1471900r.55c>t0.183
rrs1472127r.282c>t0.194
rrs1472129r.284g>c0.200
rrs1472137r.292g>a0.197
rrs1472150r.305t>a0.211
rrs1472151r.306c>a0.214
rrs1472172r.327t>c0.280
rrs1472203r.358g>a0.278
rrs1472210r.365a>c0.275
rrs1472213r.368g>c0.269
rrs1472215r.370a>g0.269
rrs1472225r.380c>a0.246
rrs1472234r.389t>c0.154
rrs1472236r.391c>g0.151
rrs1472240r.395g>a0.154
rrs1472344r.499c>t0.244
rrs1472379r.534t>g0.227
rrs1472382r.537g>a0.209
rrs1472400r.555c>t0.238
rrs1472530r.685g>a0.164
rrs1472537r.692c>t0.164
rrs1472544r.699c>g0.155
rrs1472545r.700a>t0.155
rrs1472557r.712g>a0.183
rrs1472570r.725g>a0.179
rrs1472571r.726g>c0.185
rrs1472581r.736a>t0.203
rrs1472598r.753a>c0.197
rrs1472616r.771g>a0.206
rrs1472734r.889c>t0.161
rrs1472741r.896g>a0.154
rrs1472744r.899a>g0.186
rrs1472767r.922g>a0.219
rrs1472779r.934g>a0.234
rrs1472781r.936c>t0.238
rrs1472786r.941c>t0.242
rrs1472793r.948a>t0.262
rrs1472803r.958t>a0.273
rrs1472895r.1050c>t0.271
rrs1473020r.1175t>c0.125
rrs1473035r.1190g>a0.135
rrs1473081r.1236c>t0.135
rrs1473093r.1248c>a0.125
rrs1473177r.1332g>a0.175
rrs1473179r.1334c>t0.177
rrs1473192r.1347a>g0.204
rrs1473352r.1507c>t0.214
rrl1474777r.1120t>c0.125
rrl1474780r.1123c>t0.152
rrl1474782r.1125g>a0.128
rrl1474790r.1133c>t0.150
rrl1474798r.1141c>t0.205
rrl1474804r.1147c>t0.239
rrl1474823r.1166c>g0.224
rrl1474827r.1170c>t0.216
rrl1474831r.1174a>c0.216
rrl1474844r.1187g>t0.182
rrl1474866r.1209c>a0.208
rrl1474869r.1212g>t0.200
rrl1474896r.1239a>g0.184
rrl1474902r.1245t>c0.173
rrl1474904r.1247g>c0.176
rrl1474913r.1256t>a0.163
rrl1475574r.1917c>a0.154
rrl1475716r.2059a>g0.152
rrl1475817r.2160a>g0.150
rrl1476251r.2594t>c0.151
rrl1476260r.2603a>g0.173
rrl1476280r.2623a>c0.170
rrl1476332r.2675g>c0.298
rrl1476338r.2681c>t0.304
rrl1476353r.2696g>t0.323
rrl1476358r.2701t>c0.306
rrl1476372r.2715t>c0.269
rrl1476382r.2725a>g0.267
rrl1476383r.2726t>a0.267
rrl1476408r.2751g>a0.300
rrl1476425r.2768g>a0.304
rrl1476428r.2771c>t0.273
rrl1476466r.2809c>t0.224
rrl1476481r.2824t>c0.231
rrl1476506r.2849t>c0.229
rrl1476547r.2890c>t0.148
rrl1476567r.2910c>t0.194
rrl1476573r.2916a>t0.222
rrl1476577r.2920t>g0.231
rrl1476594r.2937c>t0.246
rrl1476603r.2946g>a0.158
rrl1476607r.2950c>t0.161
rrl1476608r.2951c>g0.155
rrl1476614r.2957a>g0.158
rrl1476619r.2962c>t0.133
rrl1476637r.2980c>g0.243
tlyA1917972c.33A>G1.000
ald3086788c.-32T>C1.000
panD4044141c.141G>A1.000
embC4242643c.2781C>T1.000
embB4246584p.Arg24Pro0.464
embB4247008c.495G>A1.000
embB4249012c.2499G>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;