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: 5dd2432116f5b
Sample: 5dd2432116f5b

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Summary
ID: 5dd2432116f5b
Date: Mon Nov 18 07:11:20 2019
Strain: lineage1.1.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6112p.Met291Ile1.000
gyrB6124c.885C>T1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8452p.Ala384Val1.000
gyrA9047c.1746C>T1.000
gyrA9143c.1842T>C1.000
gyrA9304p.Gly668Asp1.000
gyrA9443c.2142G>A1.000
rpoB759546c.-261A>G1.000
rpoB760490c.684C>T1.000
rpoB763031c.3225T>C1.000
rpoC763884p.Ala172Val1.000
rpoC763886c.517C>A1.000
rpoC765171p.Pro601Leu1.000
rpsL781395c.-165T>C1.000
embR1417019p.Cys110Tyr1.000
embR1417554c.-207C>G1.000
rrs1471896r.51t>c0.619
rrs1471900r.55c>t0.616
rrs1472094r.249t>a0.215
rrs1472106r.261g>a0.400
rrs1472112r.267c>t0.413
rrs1472113r.268t>c0.419
rrs1472127r.282c>t0.614
rrs1472129r.284g>c0.622
rrs1472137r.292g>a0.634
rrs1472150r.305t>a0.677
rrs1472151r.306c>a0.677
rrs1472172r.327t>c0.697
rrs1472203r.358g>a0.695
rrs1472210r.365a>c0.699
rrs1472213r.368g>c0.679
rrs1472215r.370a>g0.684
rrs1472225r.380c>a0.664
rrs1472234r.389t>c0.612
rrs1472236r.391c>g0.592
rrs1472240r.395g>a0.606
rrs1472344r.499c>t0.682
rrs1472379r.534t>g0.665
rrs1472382r.537g>a0.665
rrs1472400r.555c>t0.629
rrs1472507r.662c>g0.347
rrs1472517r.672t>a0.393
rrs1472518r.673g>c0.393
rrs1472530r.685g>a0.510
rrs1472537r.692c>t0.533
rrs1472544r.699c>g0.536
rrs1472545r.700a>t0.539
rrs1472557r.712g>a0.603
rrs1472570r.725g>a0.611
rrs1472571r.726g>c0.607
rrs1472581r.736a>t0.627
rrs1472598r.753a>c0.635
rrs1472616r.771g>a0.629
rrs1472734r.889c>t0.689
rrs1472741r.896g>a0.684
rrs1472744r.899a>g0.683
rrs1472767r.922g>a0.692
rrs1472779r.934g>a0.654
rrs1472781r.936c>t0.668
rrs1472786r.941c>t0.673
rrs1472793r.948a>t0.705
rrs1472803r.958t>a0.739
rrs1472895r.1050c>t0.714
rrs1473020r.1175t>c0.610
rrs1473035r.1190g>a0.633
rrs1473053r.1208t>a0.534
rrs1473055r.1210c>t0.538
rrs1473056r.1211a>t0.534
rrs1473062r.1217t>a0.558
rrs1473068r.1223a>g0.548
rrs1473070r.1225g>a0.562
rrs1473081r.1236c>t0.657
rrs1473089r.1244a>c0.593
rrs1473093r.1248c>a0.563
rrs1473094r.1249t>a0.568
rrs1473099r.1254t>a0.545
rrs1473110r.1265t>g0.372
rrs1473111r.1266a>g0.380
rrs1473115r.1270g>c0.377
rrs1473130r.1285g>a0.448
rrs1473145r.1300c>t0.243
rrs1473147r.1302g>c0.235
rrs1473148r.1303g>a0.240
rrs1473150r.1305t>g0.238
rrs1473161r.1316a>c0.237
rrs1473163r.1318c>t0.243
rrs1473164r.1319c>g0.246
rrs1473166r.1321g>a0.239
rrs1473177r.1332g>a0.618
rrs1473179r.1334c>t0.615
rrs1473192r.1347a>g0.650
rrs1473202r.1357c>t0.584
rrs1473205r.1360t>c0.580
rrs1473226r.1381c>t0.684
rrs1473352r.1507c>t0.697
rrl1473384c.-274A>T0.167
rrl1473851r.194g>c0.241
rrl1473862r.205c>a0.262
rrl1473870r.213g>t0.269
rrl1473871r.214t>g0.264
rrl1473876r.219g>a0.282
rrl1473887r.230t>g0.342
rrl1473888r.231t>a0.348
rrl1473898r.241c>t0.365
rrl1473899r.242a>c0.368
rrl1473905r.248t>c0.381
rrl1473926r.269g>c0.380
rrl1474218r.561t>a0.658
rrl1474228r.571t>c0.593
rrl1474236r.579g>a0.576
rrl1474249r.592g>t0.534
rrl1474252r.595t>a0.539
rrl1474269r.612c>t0.437
rrl1474330r.673a>t0.361
rrl1474527r.870t>g0.467
rrl1474530r.873g>t0.489
rrl1474537r.880g>a0.512
rrl1474539r.882c>a0.518
rrl1474542r.885a>c0.537
rrl1474552r.895c>g0.537
rrl1474555r.898t>g0.550
rrl1474562r.905g>c0.524
rrl1474565r.908t>a0.524
rrl1474570r.913g>t0.528
rrl1474571r.914g>t0.515
rrl1474578r.921a>g0.528
rrl1474584r.927c>g0.522
rrl1474586r.929t>a0.530
rrl1474777r.1120t>c0.525
rrl1474779r.1122g>a0.534
rrl1474780r.1123c>t0.548
rrl1474782r.1125g>a0.548
rrl1474790r.1133c>t0.595
rrl1474798r.1141c>t0.620
rrl1474804r.1147c>t0.653
rrl1474823r.1166c>g0.677
rrl1474827r.1170c>t0.669
rrl1474831r.1174a>c0.655
rrl1474844r.1187g>t0.685
rrl1474866r.1209c>a0.680
rrl1474869r.1212g>t0.676
rrl1474896r.1239a>g0.627
rrl1474902r.1245t>c0.632
rrl1474904r.1247g>c0.627
rrl1474913r.1256t>a0.579
rrl1474920r.1263g>a0.576
rrl1475122r.1465c>t0.197
rrl1475129r.1472g>a0.205
rrl1475145r.1488c>t0.187
rrl1475154r.1497c>a0.172
rrl1475162r.1505g>a0.170
rrl1475167r.1510t>a0.183
rrl1475175r.1518g>a0.182
rrl1475182r.1525t>a0.176
rrl1475188r.1531c>t0.155
rrl1475574r.1917c>a0.596
rrl1475672r.2015c>g0.613
rrl1475673r.2016t>c0.602
rrl1475687r.2030c>t0.629
rrl1475696r.2039t>c0.590
rrl1475699r.2042c>t0.588
rrl1475703r.2046a>g0.574
rrl1475707r.2050t>a0.575
rrl1475716r.2059a>g0.628
rrl1475803r.2146t>c0.510
rrl1475804r.2147g>c0.514
rrl1475816r.2159c>g0.562
rrl1475817r.2160a>g0.573
rrl1475843r.2186g>a0.563
rrl1475849r.2192g>a0.592
rrl1475853r.2196c>t0.590
rrl1475858r.2201t>c0.590
rrl1476126r.2469c>t0.548
rrl1476128r.2471t>a0.543
rrl1476135r.2478t>c0.540
rrl1476141r.2484a>g0.535
rrl1476153r.2496t>c0.548
rrl1476164r.2507a>g0.533
rrl1476165r.2508t>a0.533
rrl1476181r.2524a>c0.510
rrl1476221r.2564t>c0.177
rrl1476225r.2568t>g0.197
rrl1476229r.2572c>t0.229
rrl1476251r.2594t>c0.715
rrl1476260r.2603a>g0.727
rrl1476280r.2623a>c0.741
rrl1476293r.2636c>t0.442
rrl1476294r.2637a>g0.442
rrl1476295r.2638c>g0.447
rrl1476296r.2639c>t0.447
rrl1476297r.2640c>a0.447
rrl1476301r.2644a>c0.442
rrl1476302r.2645g>a0.429
rrl1476311r.2654g>c0.415
rrl1476312r.2655t>c0.410
rrl1476313r.2656g>a0.420
rrl1476332r.2675g>c0.692
rrl1476338r.2681c>t0.709
rrl1476353r.2696g>t0.731
rrl1476358r.2701t>c0.733
rrl1476372r.2715t>c0.714
rrl1476382r.2725a>g0.722
rrl1476383r.2726t>a0.732
rrl1476408r.2751g>a0.747
rrl1476425r.2768g>a0.749
rrl1476428r.2771c>t0.727
rrl1476466r.2809c>t0.740
rrl1476481r.2824t>c0.731
rrl1476506r.2849t>c0.653
rrl1476512r.2855c>t0.213
rrl1476514r.2857c>t0.200
rrl1476517r.2860c>t0.195
rrl1476519r.2862c>g0.192
rrl1476524r.2867c>a0.188
rrl1476525r.2868a>g0.185
rrl1476530r.2873c>t0.190
rrl1476536r.2879g>a0.200
rrl1476537r.2880a>g0.205
rrl1476538r.2881a>g0.205
rrl1476540r.2883c>g0.213
rrl1476547r.2890c>t0.577
rrl1476567r.2910c>t0.656
rrl1476573r.2916a>t0.667
rrl1476577r.2920t>g0.667
rrl1476594r.2937c>t0.644
rrl1476603r.2946g>a0.484
rrl1476607r.2950c>t0.462
rrl1476608r.2951c>g0.462
rrl1476614r.2957a>g0.474
rrl1476619r.2962c>t0.435
rrl1476624r.2967t>a0.448
rrl1476628r.2971t>a0.431
rrl1476629r.2972c>a0.431
rrl1476630r.2973a>g0.436
rrl1476637r.2980c>g0.617
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
kasA2518132c.18C>T1.000
ald3086788c.-32T>C1.000
alr3841654c.-234A>C0.205
alr3841662c.-242A>G0.260
alr3841663c.-243G>A0.217
embC4240671p.Thr270Ile1.000
embC4241042p.Asn394Asp1.000
embC4242643c.2781C>T1.000
embA4243848p.Val206Met1.000
embA4245969p.Pro913Ser1.000
embB4246584p.Arg24Pro0.500
embB4247646p.Glu378Ala1.000
gid4407588c.615T>C1.000
gid4407873c.330C>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;