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: 5dd3aee4870a3
Sample: 5dd3aee4870a3

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Summary
ID: 5dd3aee4870a3
Date: Tue Nov 19 09:01:59 2019
Strain: lineage4.6.2.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Ile (1.00)
RifampicinRrpoB p.Ser450Leu (1.00)
EthambutolRembB p.Met306Val (1.00)
Pyrazinamide
Streptomycin
Ethionamide
FluoroquinolonesRgyrA p.Asp94Gly (1.00)
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB762896c.3090G>T0.207
rpoB762899c.3093G>C0.200
rpoB762917c.3111C>T0.167
rpoB762923c.3117C>G0.148
rpoB762925p.Thr1040Ile0.167
rpoB762929c.3123G>T0.167
rpoB762932c.3126G>T0.208
rpoB762941p.Met1045Ile0.154
rpoB762944c.3138C>T0.160
rpoB762965c.3159T>C0.242
rpoB762980c.3174T>C0.207
rpoB762983c.3177C>A0.188
rpoB762989c.3183G>C0.241
rpoB762998c.3192G>A0.222
rpoC764363p.Gly332Ser0.367
rpoC764479c.1110G>A0.163
rpoC764503c.1134G>C0.163
rpoC764566c.1197C>G0.214
rpoC764575c.1206T>C0.286
rpoC764581c.1212T>C0.333
rpoC764582p.Leu405Met0.333
rpoC764605c.1236G>C0.385
rpoC764611c.1242G>C0.385
rpoC764620c.1251G>T0.366
rpoC764632c.1263T>C0.415
rpoC764641c.1272C>T0.316
rpoC764644c.1275G>C0.289
rpoC764650c.1281G>T0.316
rpoC764664p.Val432Ala0.171
rpoC764668c.1299C>T0.207
rpoC764672p.Gln435Glu0.207
rpoC764677c.1308C>G0.207
rpoC764695c.1326T>C0.406
rpoC764701c.1332C>G0.214
rpoC764705p.Leu446Lys0.310
rpoC764716c.1347G>C0.241
rpoC764719c.1350G>A0.219
rpoC764908c.1539G>A0.139
rpoC764911c.1542A>C0.135
rpoC764968c.1599T>C0.178
rpsL781395c.-165T>C1.000
rrs1471876r.31g>a0.494
rrs1471892r.47g>a0.468
rrs1471893r.48t>g0.436
rrs1472094r.249t>a0.171
rrs1472106r.261g>a0.595
rrs1472108r.263c>a0.595
rrs1472127r.282c>t0.273
rrs1472128r.283g>c0.273
rrs1472129r.284g>c0.273
rrs1472130r.285g>a0.267
rrs1472135r.290c>t0.255
rrs1472138r.293c>t0.250
rrs1472147r.302g>a0.255
rrs1472150r.305t>a0.255
rrs1472151r.306c>t0.255
rrs1472153r.308g>a0.255
rrs1472160r.315c>t0.598
rrs1472172r.327t>c0.716
rrs1472181r.336g>a0.649
rrs1472214r.369c>g0.723
rrs1472235r.390g>c0.675
rrs1472240r.395g>c0.656
rrs1472242r.397c>t0.659
rrs1472251r.406g>a0.569
rrs1472253r.408g>t0.569
rrs1472259r.414c>a0.577
rrs1472266r.421c>a0.541
rrs1472277r.432c>g0.505
rrs1472338r.493a>c0.598
rrs1472344r.499c>t0.669
rrs1472349r.504a>t0.633
rrs1472374r.529t>a0.684
rrs1472379r.534t>g0.669
rrs1472382r.537g>t0.706
rrs1472391r.546c>t0.712
rrs1472412r.567a>c0.327
rrs1472415r.570t>a0.213
rrs1472557r.712g>a0.444
rrs1472579r.734g>t0.162
rrs1472584r.739a>t0.196
rrs1472598r.753a>t0.780
rrs1472616r.771g>a0.761
rrs1472697r.852t>c0.185
rrs1472712r.867g>a0.280
rrs1472713r.868t>c0.317
rrs1472714r.869a>t0.188
rrs1472715r.870c>t0.354
rrs1472716r.871c>t0.417
rrs1472734r.889c>t0.699
rrs1472741r.896g>a0.702
rrs1472742r.897c>t0.782
rrs1472781r.936c>t0.788
rrs1472793r.948a>t0.788
rrs1472803r.958t>a0.784
rrs1472812r.967a>c0.672
rrs1472887r.1042g>c0.833
rrs1472982r.1137g>c0.152
rrs1472987r.1142g>t0.149
rrs1472988r.1143t>a0.146
rrs1472989r.1144g>a0.137
rrs1472990r.1145a>g0.140
rrs1473002r.1157g>t0.137
rrs1473004r.1159t>a0.135
rrs1473009r.1164t>c0.140
rrs1473038r.1193a>c0.694
rrs1473044r.1199c>g0.759
rrs1473051r.1206t>c0.149
rrs1473053r.1208t>g0.163
rrs1473056r.1211a>t0.152
rrs1473062r.1217t>a0.149
rrs1473068r.1223a>g0.146
rrs1473163r.1318c>t0.146
rrs1473164r.1319c>g0.192
rrs1473173r.1328c>t0.635
rrs1473177r.1332g>a0.722
rrs1473199r.1354ca>c0.754
rrs1473202r.1357c>t0.732
rrs1473352r.1507c>g0.559
rrs1473353r.1508c>g0.536
rrs1473358r.1513g>c0.541
rrs1473359r.1514g>c0.541
rrl1473922r.265a>c0.658
rrl1474199r.542g>a0.506
rrl1474201r.544t>c0.481
rrl1474202r.545t>a0.481
rrl1474218r.561t>a0.613
rrl1474228r.571t>c0.576
rrl1474235r.578g>c0.539
rrl1474249r.592g>t0.581
rrl1474252r.595t>a0.566
rrl1474264r.607t>g0.541
rrl1474265r.608g>a0.541
rrl1474558r.901g>c0.589
rrl1474584r.927c>g0.598
rrl1474586r.929t>a0.598
rrl1474587r.930g>a0.605
rrl1474602r.945c>g0.597
rrl1474609r.952g>c0.200
rrl1474610r.953c>t0.171
rrl1474828r.1171g>c0.477
rrl1474844r.1187g>t0.543
rrl1474864r.1207c>t0.500
rrl1474866r.1209c>a0.478
rrl1474869r.1212g>t0.522
rrl1474875r.1218g>a0.507
rrl1474876r.1219t>a0.500
rrl1474883r.1226t>c0.458
rrl1475499r.1842c>g0.593
rrl1475526r.1869c>t0.692
rrl1475538r.1881t>c0.634
rrl1475539r.1882a>t0.638
rrl1475540r.1883c>t0.638
rrl1475545r.1888t>g0.619
rrl1475553r.1896g>t0.592
rrl1475555r.1898t>g0.604
rrl1475571r.1914a>t0.625
rrl1475575r.1918c>a0.585
rrl1475577r.1920c>g0.574
rrl1475589r.1932g>a0.593
rrl1475672r.2015c>t0.574
rrl1475673r.2016t>c0.587
rrl1475685r.2028t>g0.549
rrl1475687r.2030c>t0.549
rrl1475688r.2031g>c0.549
rrl1475697r.2040c>a0.659
rrl1475702r.2045g>t0.652
rrl1475707r.2050t>c0.656
rrl1475713r.2056c>g0.670
rrl1475716r.2059a>t0.653
rrl1475803r.2146t>c0.752
rrl1475804r.2147g>c0.752
rrl1475816r.2159c>g0.772
rrl1475817r.2160a>g0.776
rrl1475881r.2224t>c0.407
rrl1475883r.2226a>c0.312
rrl1475884r.2227a>g0.184
rrl1475892r.2235a>c0.205
rrl1475894r.2237c>a0.200
rrl1475904r.2247g>a0.159
rrl1475906r.2249c>t0.163
rrl1476141r.2484a>g0.507
rrl1476153r.2496t>c0.569
rrl1476160r.2503t>g0.441
rrl1476164r.2507a>g0.554
rrl1476165r.2508t>a0.545
rrl1476252r.2595t>g0.648
rrl1476260r.2603a>g0.630
rrl1476266r.2609g>a0.648
rrl1476279r.2622g>t0.375
rrl1476280r.2623a>c0.375
rrl1476281r.2624t>a0.375
rrl1476293r.2636c>t0.375
rrl1476294r.2637a>g0.349
rrl1476295r.2638c>g0.349
rrl1476296r.2639c>t0.349
rrl1476301r.2644a>t0.365
rrl1476311r.2654g>c0.377
rrl1476312r.2655t>c0.377
rrl1476313r.2656g>a0.377
rrl1476336r.2679c>g0.724
rrl1476356r.2699c>g0.766
rrl1476357r.2700t>a0.759
rrl1476358r.2701t>c0.709
rrl1476382r.2725a>g0.740
rrl1476384r.2727g>t0.774
rrl1476404r.2747g>a0.673
rrl1476408r.2751g>a0.806
rrl1476442r.2785t>a0.679
rrl1476443r.2786g>t0.758
rrl1476455r.2798c>a0.729
rrl1476456r.2799a>t0.643
rrl1476466r.2809c>t0.745
rrl1476470r.2813c>t0.667
rrl1476474r.2817c>t0.596
rrl1476481r.2824t>c0.659
rrl1476506r.2849t>c0.677
rrl1476512r.2855c>t0.217
rrl1476567r.2910c>t0.475
rrl1476573r.2916a>t0.455
rrl1476575r.2918c>t0.461
rrl1476584r.2927c>g0.264
rrl1476586r.2929c>t0.216
rrl1476588r.2931a>t0.204
rrl1476596r.2939c>t0.200
rrl1476645r.2988a>g0.356
tlyA1917972c.33A>G1.000
ahpC2726118c.-75T>C1.000
alr3841652c.-232A>T0.256
alr3841654c.-234A>C0.263
alr3841662c.-242A>G0.268
alr3841663c.-243G>A0.298
embC4239887p.Arg9Cys1.000
embC4242643c.2781C>T1.000
ethA4326739c.735G>C1.000
ethR4328004c.456G>A1.000
gid4407756p.Ser149Arg1.000

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;