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: 5dde5d94488ca
Sample: 5dde5d94488ca

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Summary
ID: 5dde5d94488ca
Date: Wed Nov 27 11:37:06 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
RifampicinRrpoB p.Ser450Leu (1.00)
EthambutolRembB p.Met306Leu (0.90)
PyrazinamideRpncA p.Met175Arg (0.93)
StreptomycinRrpsL p.Lys43Arg (1.00)
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
gyrA8935p.Gln545Leu0.138
gyrA9304p.Gly668Asp1.000
rpoB761560p.Thr585Ile0.138
rpoB761621p.Met605Ile0.129
rpoB763031c.3225T>C1.000
rpoC764916p.Leu516Pro1.000
rpsL781395c.-165T>C1.000
rpsL781660p.Cys34Tyr0.132
embR1416222p.Phe376Leu0.291
embR1416234p.Cys372Gly0.346
embR1416431p.Ala306Val0.154
embR1416473p.Leu292Gln0.154
rrs1471896r.51t>c0.436
rrs1471900r.55c>t0.415
rrs1471983r.138c>g0.182
rrs1472127r.282c>t0.900
rrs1472129r.284g>c0.900
rrs1472137r.292g>a0.900
rrs1472150r.305t>a0.800
rrs1472151r.306c>t0.800
rrs1472172r.327t>c0.714
rrs1472203r.358g>a0.300
rrs1472344r.499c>t0.357
rrs1472379r.534t>g0.500
rrs1472382r.537g>a0.444
rrs1472400r.555c>t0.185
rrs1472464r.619a>g0.200
rrs1472517r.672t>a0.136
rrs1472518r.673g>c0.182
rrs1472530r.685g>a0.222
rrs1472537r.692c>t0.211
rrs1472539r.694g>t0.211
rrs1472541r.696t>g0.211
rrs1472544r.699c>g0.211
rrs1472545r.700a>t0.160
rrs1472557r.712g>a0.235
rrs1472570r.725g>a0.286
rrs1472571r.726g>c0.267
rrs1472573r.728c>t0.267
rrs1472581r.736a>t0.360
rrs1472598r.753a>c0.440
rrs1472616r.771g>a0.697
rrs1472655r.810g>a0.278
rrs1472683r.838t>c0.400
rrs1472734r.889c>t0.571
rrs1472741r.896g>a0.480
rrs1472744r.899a>g0.500
rrs1472767r.922g>a0.519
rrs1472779r.934g>a0.550
rrs1472781r.936c>t0.550
rrs1472786r.941c>t0.737
rrs1472793r.948a>t0.808
rrs1472803r.958t>a0.714
rrs1472895r.1050c>t0.681
rrs1473035r.1190g>a0.667
rrs1473053r.1208t>a0.188
rrs1473055r.1210c>t0.167
rrs1473056r.1211a>t0.167
rrs1473062r.1217t>a0.150
rrs1473068r.1223a>g0.167
rrs1473070r.1225g>a0.167
rrs1473089r.1244a>c0.263
rrs1473094r.1249t>a0.238
rrs1473099r.1254t>a0.238
rrs1473100r.1255g>a0.238
rrs1473110r.1265t>g0.222
rrs1473111r.1266a>g0.222
rrs1473115r.1270g>a0.250
rrs1473177r.1332g>a0.462
rrs1473179r.1334c>t0.533
rrs1473192r.1347a>g0.409
rrs1473202r.1357c>t0.281
rrs1473205r.1360t>c0.281
rrs1473226r.1381c>t0.465
rrs1473352r.1507c>t0.586
rrl1473756r.99g>t0.741
rrl1473758r.101g>t0.741
rrl1473765r.108a>g0.759
rrl1474156r.499g>t0.200
rrl1474218r.561t>a0.400
rrl1474228r.571t>c0.381
rrl1474249r.592g>t0.278
rrl1474252r.595t>a0.278
rrl1474330r.673a>t0.632
rrl1474527r.870t>g0.545
rrl1474528r.871t>c0.545
rrl1474530r.873g>c0.545
rrl1474537r.880g>a0.500
rrl1474539r.882c>g0.500
rrl1474542r.885a>c0.500
rrl1474552r.895c>g0.429
rrl1474555r.898t>g0.429
rrl1474562r.905g>c0.375
rrl1474565r.908t>a0.375
rrl1474570r.913g>t0.333
rrl1474571r.914g>t0.400
rrl1474578r.921a>g0.429
rrl1474584r.927c>g0.429
rrl1474586r.929t>a0.391
rrl1474790r.1133c>t0.500
rrl1474794r.1137c>a0.360
rrl1474798r.1141c>t0.357
rrl1474804r.1147c>t0.407
rrl1474823r.1166c>g0.647
rrl1474827r.1170c>t0.733
rrl1474831r.1174a>c0.742
rrl1474844r.1187g>t0.706
rrl1474866r.1209c>a0.676
rrl1474869r.1212g>t0.758
rrl1474896r.1239a>g0.632
rrl1474902r.1245t>c0.600
rrl1474904r.1247g>c0.600
rrl1474913r.1256t>a0.600
rrl1474920r.1263g>a0.600
rrl1475122r.1465c>t0.659
rrl1475129r.1472g>a0.636
rrl1475154r.1497c>a0.568
rrl1475167r.1510t>a0.568
rrl1475175r.1518g>a0.425
rrl1475182r.1525t>a0.400
rrl1475188r.1531c>t0.375
rrl1475218r.1561c>a0.167
rrl1475242r.1585g>a0.200
rrl1475574r.1917c>a0.714
rrl1475687r.2030c>t0.700
rrl1475696r.2039t>c0.400
rrl1475703r.2046a>g0.316
rrl1475707r.2050t>a0.316
rrl1475716r.2059a>g0.300
rrl1475803r.2146t>c0.240
rrl1475804r.2147g>c0.222
rrl1475816r.2159c>g0.276
rrl1475817r.2160a>g0.281
rrl1475843r.2186g>a0.256
rrl1475849r.2192g>a0.343
rrl1475853r.2196c>t0.343
rrl1475858r.2201t>c0.324
rrl1476031r.2374c>t0.167
rrl1476126r.2469c>t0.409
rrl1476128r.2471t>a0.409
rrl1476135r.2478t>c0.476
rrl1476141r.2484a>g0.526
rrl1476153r.2496t>c0.588
rrl1476164r.2507a>g0.737
rrl1476165r.2508t>a0.737
rrl1476225r.2568t>g0.545
rrl1476251r.2594t>c0.538
rrl1476260r.2603a>g0.571
rrl1476280r.2623a>c0.455
rrl1476332r.2675g>c0.176
rrl1476338r.2681c>t0.294
rrl1476353r.2696g>t0.429
rrl1476358r.2701t>c0.429
rrl1476372r.2715t>c0.417
rrl1476382r.2725a>g0.500
rrl1476383r.2726t>a0.500
rrl1476408r.2751g>a0.567
rrl1476425r.2768g>a0.591
rrl1476428r.2771c>t0.565
rrl1476466r.2809c>t0.444
rrl1476481r.2824t>c0.558
rrl1476506r.2849t>c0.486
rrl1476547r.2890c>t0.478
rrl1476567r.2910c>t0.458
rrl1476572r.2915g>a0.458
rrl1476573r.2916a>t0.458
rrl1476577r.2920t>g0.524
rrl1476584r.2927c>t0.579
rrl1476594r.2937c>t0.476
rrl1476603r.2946g>a0.350
rrl1476608r.2951c>a0.350
rrl1476637r.2980c>g0.667
rpsA1834177c.636A>C0.982
tlyA1917972c.33A>G1.000
tlyA1918044c.105C>T0.143
tlyA1918375p.Gly146Arg0.200
katG2154678c.1434C>A0.138
katG2154724p.Arg463Leu1.000
katG2155539p.Trp191Cys0.900
katG2155546p.Asp189Ala0.913
kasA2518574p.Ile154Val0.171
kasA2518629172S>172*0.176
eis2715206p.Asp43Tyr0.160
ahpC2726769p.Ala193Thr0.116
folC2746432c.1167G>T0.211
folC2746564c.1035T>A0.154
ribD2987091p.Val85Met0.963
thyX3067243c.703G>A0.200
thyX3067252p.Val232Met0.167
thyX3067934c.12G>T0.200
ald3086788c.-32T>C1.000
fbiA3640342c.-201C>T0.978
alr3840237p.Arg395Leu0.167
alr3841217c.204G>A0.154
alr3841652c.-232A>T0.122
alr3841654c.-234A>C0.118
alr3841662c.-242A>G0.126
embC4241907p.Val682Ala0.182
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
embA4244056p.Gly275Asp0.154
embA4244336c.1104C>T0.150
embA4244888c.1656G>A0.158
embA4245471p.Ala747Thr0.125
embB4246563p.Leu17Trp0.364
embB4246567c.54G>T0.421
embB4247289p.Ala259Val0.150
embB4247839c.1326G>A0.158
embB4248006p.Thr498Asn0.138
ethA4326065p.Arg470His0.135
ethA4326676p.Ser266Arg1.000
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;