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.
Back to results page.
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: 5dca1667d0fb4
Sample: 5dca1667d0fb4

Download results

Summary
ID: 5dca1667d0fb4
Date: Tue Nov 12 02:22:47 2019
Strain: lineage2.2.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage2East-AsianBeijingRD105
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB759801c.-6T>C1.000
rpoB762863c.3057T>C0.395
rpoB762872p.Met1022Ile0.460
rpoB762878p.Ile1024Met0.451
rpoB762879p.Met1025Leu0.451
rpoB762896c.3090G>C0.500
rpoB762925p.Thr1040Ile0.483
rpoB762938c.3132G>C0.415
rpoB762939p.Met1045Leu0.415
rpoB762942p.Ile1046Val0.423
rpoB762953c.3147G>A0.333
rpoB762965c.3159T>C0.339
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C0.976
rrs1472160r.315c>t0.139
rrs1472172r.327t>c0.395
rrs1472181r.336g>a0.127
rrs1472210r.365a>t0.243
rrs1472214r.369c>g0.226
rrs1472215r.370a>g0.118
rrs1472225r.380c>a0.293
rrs1472234r.389t>c0.116
rrs1472235r.390g>c0.134
rrs1472240r.395g>c0.256
rrs1472242r.397c>t0.256
rrs1472251r.406g>c0.145
rrs1472252r.407g>a0.145
rrs1472259r.414c>a0.143
rrs1472344r.499c>t0.294
rrs1472389r.544g>a0.319
rrs1472390r.545t>a0.319
rrs1472391r.546c>t0.312
rrs1472598r.753a>c0.188
rrs1472599r.754g>t0.184
rrs1472616r.771g>a0.232
rrs1472713r.868t>c0.286
rrs1472716r.871c>t0.302
rrs1472734r.889c>t0.270
rrs1472741r.896g>a0.286
rrs1472742r.897c>t0.446
rrs1472744r.899a>g0.159
rrs1472767r.922g>a0.118
rrs1472781r.936c>t0.429
rrs1472785r.940g>t0.120
rrs1472786r.941c>g0.122
rrs1472793r.948a>t0.392
rrs1472803r.958t>a0.219
rrs1472812r.967a>c0.159
rrs1472887r.1042g>c0.380
rrl1475783r.2126t>g0.204
rrl1475791r.2134a>g0.182
rrl1475803r.2146t>c0.357
rrl1475804r.2147g>c0.357
rrl1475816r.2159c>g0.383
rrl1475817r.2160a>g0.397
rrl1475881r.2224t>c0.256
rrl1475883r.2226a>c0.238
rrl1475892r.2235a>c0.200
rrl1475894r.2237c>g0.205
rrl1475900r.2243a>g0.200
rrl1475904r.2247g>a0.186
rrl1476336r.2679c>t0.278
rrl1476338r.2681c>t0.283
rrl1476339r.2682g>a0.109
rrl1476356r.2699c>t0.179
rrl1476357r.2700t>c0.138
rrl1476358r.2701t>c0.138
rrl1476359r.2702c>g0.302
rrl1476369r.2712c>t0.157
rrl1476381r.2724g>c0.268
rrl1476382r.2725a>g0.139
rrl1476383r.2726t>a0.161
rrl1476384r.2727g>a0.190
rrl1476408r.2751g>a0.321
rrl1476411r.2754g>a0.209
rrl1476425r.2768g>t0.158
rrl1476429r.2772a>c0.169
rrl1476442r.2785t>a0.159
rrl1476443r.2786g>t0.284
rrl1476455r.2798c>a0.164
rrl1476463r.2806c>t0.120
rrl1476466r.2809c>t0.173
rrl1476470r.2813c>t0.154
rrl1476506r.2849t>c0.150
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
tlyA1918671c.732C>T1.000
katG2154724p.Arg463Leu1.000
thyX3067562c.384C>T0.977
ald3086788c.-32T>C1.000
alr3841654c.-234A>C0.204
alr3841662c.-242A>G0.267
alr3841663c.-243G>A0.267
embC4241922p.Gly687Glu0.973
embC4242643c.2781C>T1.000
embC4242761p.Arg967Trp0.977
embA4243460c.228C>T1.000
embB4246544p.Thr11Pro0.170
embB4246548p.Pro12Gln0.159
embB4246563p.Leu17Trp0.105
ethA4326676p.Ser266Arg0.981
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;