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: 5d9bb564db51f
Sample: 5d9bb564db51f

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Summary
ID: 5d9bb564db51f
Date: Mon Oct 7 23:03:35 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
gyrA7637c.336C>G0.325
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.222
embR1416234p.Cys372Gly0.218
rrs1471896r.51t>c0.187
rrs1472138r.293c>t0.248
rrs1472147r.302g>a0.284
rrs1472150r.305t>a0.329
rrs1472153r.308g>a0.295
rrs1472164r.319g>a0.590
rrs1472172r.327t>c0.639
rrs1472177r.332c>t0.627
rrs1472240r.395g>c0.677
rrs1472242r.397c>t0.672
rrs1472251r.406g>t0.643
rrs1472252r.407g>a0.632
rrs1472253r.408g>t0.638
rrs1472256r.411t>a0.629
rrs1472259r.414c>a0.647
rrs1472344r.499c>t0.745
rrs1472349r.504a>c0.734
rrs1472374r.529t>g0.743
rrs1472382r.537g>a0.756
rrs1472389r.544g>a0.742
rrs1472390r.545t>a0.733
rrs1472391r.546c>t0.735
rrs1472517r.672t>a0.770
rrs1472530r.685g>a0.784
rrs1472537r.692c>t0.796
rrs1472541r.696t>g0.774
rrs1472545r.700a>t0.791
rrs1472553r.708c>t0.778
rrs1472571r.726g>c0.787
rrs1472572r.727t>c0.768
rrs1472574r.729t>c0.765
rrs1472579r.734g>a0.774
rrs1472582r.737g>a0.771
rrs1472583r.738t>a0.771
rrs1472584r.739a>g0.777
rrs1472594r.749g>c0.777
rrs1472598r.753a>t0.798
rrs1472616r.771g>a0.793
rrs1472655r.810g>a0.307
rrs1472658r.813g>t0.197
rrs1472659r.814g>c0.192
rrs1472660r.815t>g0.189
rrs1472664r.819a>t0.173
rrs1472679r.834t>c0.188
rrs1472697r.852t>g0.191
rrs1472707r.862a>g0.252
rrs1472714r.869a>c0.224
rrs1472715r.870c>g0.222
rrs1472716r.871c>a0.238
rrs1472742r.897c>t0.699
rrs1472754r.909g>t0.694
rrs1472781r.936c>t0.713
rrs1472793r.948a>t0.699
rrs1472887r.1042g>c0.693
rrs1472912r.1067c>t0.735
rrs1472917r.1072g>a0.736
rrs1473044r.1199c>g0.689
rrs1473051r.1206t>c0.172
rrs1473053r.1208t>a0.233
rrs1473054r.1209c>g0.176
rrs1473055r.1210c>t0.176
rrs1473062r.1217t>a0.236
rrs1473068r.1223a>g0.239
rrs1473145r.1300c>t0.252
rrs1473148r.1303g>a0.239
rrs1473163r.1318c>t0.592
rrs1473166r.1321g>a0.609
rrs1473177r.1332g>a0.620
rrs1473191r.1346c>t0.623
rrs1473202r.1357c>t0.650
rrs1473206r.1361g>a0.650
rrs1473346r.1501g>a0.383
rrs1473352r.1507c>g0.434
rrs1473353r.1508c>g0.386
rrs1473358r.1513g>c0.402
rrs1473359r.1514g>c0.395
rrs1473365r.1520c>t0.386
rrl1474001r.344c>t1.000
rrl1474218r.561t>a0.307
rrl1474221r.564t>c0.246
rrl1474228r.571t>a0.274
rrl1474249r.592g>a0.256
rrl1474252r.595t>a0.293
rrl1474582r.925t>c0.715
rrl1474583r.926c>g0.710
rrl1474584r.927c>g0.726
rrl1474586r.929t>a0.739
rrl1474837r.1180a>g0.672
rrl1474844r.1187g>t0.681
rrl1474864r.1207c>t0.697
rrl1474866r.1209c>a0.673
rrl1474869r.1212g>t0.682
rrl1474875r.1218g>a0.695
rrl1474876r.1219t>a0.708
rrl1475154r.1497c>a0.340
rrl1475526r.1869c>a0.779
rrl1475538r.1881t>c0.723
rrl1475539r.1882a>t0.723
rrl1475540r.1883c>t0.723
rrl1475545r.1888t>g0.719
rrl1475550r.1893a>c0.723
rrl1475551r.1894t>g0.737
rrl1475555r.1898t>g0.722
rrl1475564r.1907c>a0.823
rrl1475574r.1917c>g0.845
rrl1475575r.1918c>t0.820
rrl1475576r.1919c>g0.821
rrl1475735r.2078t>c0.134
rrl1475791r.2134a>g0.745
rrl1475803r.2146t>c0.788
rrl1475804r.2147g>c0.784
rrl1475816r.2159c>g0.813
rrl1475817r.2160a>g0.820
rrl1475874r.2217c>t0.268
rrl1476126r.2469c>t0.527
rrl1476131r.2474c>t0.481
rrl1476141r.2484a>g0.543
rrl1476194r.2537a>g0.130
rrl1476260r.2603a>g0.141
rrl1476280r.2623a>c0.130
rrl1476336r.2679c>t0.754
rrl1476356r.2699c>a0.689
rrl1476357r.2700t>c0.686
rrl1476358r.2701t>c0.705
rrl1476359r.2702c>g0.711
rrl1476369r.2712c>t0.714
rrl1476381r.2724g>c0.702
rrl1476382r.2725a>g0.711
rrl1476383r.2726t>g0.708
rrl1476384r.2727g>t0.693
rrl1476408r.2751g>a0.738
rrl1476411r.2754g>a0.739
rrl1476425r.2768g>a0.711
rrl1476428r.2771c>t0.714
rrl1476442r.2785t>a0.711
rrl1476443r.2786g>t0.714
rrl1476455r.2798c>a0.742
rrl1476456r.2799a>t0.746
rrl1476463r.2806c>t0.749
rrl1476466r.2809c>t0.766
rrl1476506r.2849t>c0.745
tlyA1917972c.33A>G1.000
alr3841652c.-232A>T0.302
alr3841654c.-234A>C0.295
alr3841662c.-242A>G0.329
alr3841663c.-243G>A0.319
embC4242643c.2781C>T1.000
embB4247395c.882C>T1.000

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;