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: 5da95e75acad4
Sample: 5da95e75acad4

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Summary
ID: 5da95e75acad4
Date: Fri Oct 18 07:44:09 2019
Strain: lineage1.2.1
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage1Indo-OceanicEAIRD239
lineage1.2.1Indo-OceanicEAI2RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB6112p.Met291Ile1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8452p.Ala384Val1.000
gyrA9143c.1842T>C1.000
gyrA9260c.1959G>C1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpoC763531c.162G>C1.000
rpoC763884p.Ala172Val0.988
rpoC763886c.517C>A1.000
rpsL781395c.-165T>C1.000
embR1417019p.Cys110Tyr1.000
embR1417554c.-207C>G1.000
rrs1471896r.51t>c0.467
rrs1471900r.55c>t0.464
rrs1472106r.261g>a0.266
rrs1472112r.267c>t0.268
rrs1472113r.268t>c0.268
rrs1472127r.282c>t0.475
rrs1472129r.284g>c0.496
rrs1472137r.292g>a0.516
rrs1472150r.305t>a0.545
rrs1472151r.306c>a0.545
rrs1472172r.327t>c0.576
rrs1472203r.358g>a0.596
rrs1472210r.365a>c0.579
rrs1472213r.368g>c0.595
rrs1472215r.370a>g0.590
rrs1472225r.380c>a0.549
rrs1472234r.389t>c0.491
rrs1472236r.391c>g0.468
rrs1472240r.395g>a0.468
rrs1472344r.499c>t0.582
rrs1472379r.534t>g0.583
rrs1472382r.537g>a0.578
rrs1472400r.555c>t0.560
rrs1472507r.662c>g0.402
rrs1472517r.672t>a0.400
rrs1472518r.673g>c0.415
rrs1472530r.685g>a0.504
rrs1472537r.692c>t0.520
rrs1472544r.699c>g0.528
rrs1472545r.700a>t0.533
rrs1472557r.712g>a0.543
rrs1472570r.725g>a0.515
rrs1472571r.726g>c0.515
rrs1472581r.736a>t0.529
rrs1472598r.753a>c0.568
rrs1472616r.771g>a0.584
rrs1472734r.889c>t0.532
rrs1472741r.896g>a0.518
rrs1472744r.899a>g0.534
rrs1472767r.922g>a0.546
rrs1472779r.934g>a0.519
rrs1472781r.936c>t0.531
rrs1472786r.941c>t0.543
rrs1472793r.948a>t0.557
rrs1472803r.958t>a0.562
rrs1472895r.1050c>t0.605
rrs1473020r.1175t>c0.525
rrs1473035r.1190g>a0.558
rrs1473053r.1208t>a0.418
rrs1473055r.1210c>t0.418
rrs1473056r.1211a>t0.418
rrs1473062r.1217t>a0.458
rrs1473068r.1223a>g0.442
rrs1473070r.1225g>a0.452
rrs1473081r.1236c>t0.574
rrs1473089r.1244a>c0.506
rrs1473093r.1248c>a0.489
rrs1473094r.1249t>a0.479
rrs1473099r.1254t>a0.474
rrs1473110r.1265t>g0.299
rrs1473111r.1266a>g0.302
rrs1473115r.1270g>c0.302
rrs1473130r.1285g>a0.377
rrs1473145r.1300c>t0.177
rrs1473147r.1302g>c0.184
rrs1473148r.1303g>a0.182
rrs1473150r.1305t>g0.184
rrs1473161r.1316a>c0.171
rrs1473163r.1318c>t0.173
rrs1473164r.1319c>g0.173
rrs1473166r.1321g>a0.173
rrs1473177r.1332g>a0.484
rrs1473179r.1334c>t0.480
rrs1473192r.1347a>g0.508
rrs1473202r.1357c>t0.407
rrs1473205r.1360t>c0.400
rrs1473226r.1381c>t0.591
rrs1473352r.1507c>t0.446
rrl1473851r.194g>c0.169
rrl1473862r.205c>a0.186
rrl1473870r.213g>t0.180
rrl1473871r.214t>g0.175
rrl1473876r.219g>a0.197
rrl1473887r.230t>g0.243
rrl1473888r.231t>a0.246
rrl1473898r.241c>t0.284
rrl1473899r.242a>c0.284
rrl1473905r.248t>c0.311
rrl1473926r.269g>c0.295
rrl1474218r.561t>a0.435
rrl1474228r.571t>c0.356
rrl1474236r.579g>a0.290
rrl1474249r.592g>t0.167
rrl1474252r.595t>a0.164
rrl1474330r.673a>t0.338
rrl1474527r.870t>g0.290
rrl1474530r.873g>t0.299
rrl1474537r.880g>a0.300
rrl1474539r.882c>a0.304
rrl1474542r.885a>c0.309
rrl1474552r.895c>g0.304
rrl1474555r.898t>g0.313
rrl1474562r.905g>c0.313
rrl1474565r.908t>a0.304
rrl1474570r.913g>t0.304
rrl1474571r.914g>t0.310
rrl1474578r.921a>g0.347
rrl1474584r.927c>g0.338
rrl1474586r.929t>a0.338
rrl1474777r.1120t>c0.316
rrl1474779r.1122g>a0.325
rrl1474780r.1123c>t0.338
rrl1474782r.1125g>a0.338
rrl1474790r.1133c>t0.364
rrl1474798r.1141c>t0.423
rrl1474804r.1147c>t0.468
rrl1474823r.1166c>g0.543
rrl1474827r.1170c>t0.548
rrl1474831r.1174a>c0.536
rrl1474844r.1187g>t0.550
rrl1474866r.1209c>a0.631
rrl1474869r.1212g>t0.626
rrl1474896r.1239a>g0.574
rrl1474902r.1245t>c0.564
rrl1474904r.1247g>c0.559
rrl1474913r.1256t>a0.516
rrl1474920r.1263g>a0.506
rrl1475122r.1465c>t0.429
rrl1475129r.1472g>a0.426
rrl1475145r.1488c>t0.429
rrl1475154r.1497c>a0.426
rrl1475162r.1505g>a0.352
rrl1475167r.1510t>a0.365
rrl1475175r.1518g>a0.362
rrl1475182r.1525t>a0.340
rrl1475188r.1531c>t0.341
rrl1475574r.1917c>a0.512
rrl1475672r.2015c>g0.419
rrl1475673r.2016t>c0.419
rrl1475687r.2030c>t0.422
rrl1475696r.2039t>c0.407
rrl1475699r.2042c>t0.398
rrl1475703r.2046a>g0.389
rrl1475707r.2050t>a0.402
rrl1475716r.2059a>g0.465
rrl1475803r.2146t>c0.439
rrl1475804r.2147g>c0.434
rrl1475816r.2159c>g0.482
rrl1475817r.2160a>g0.491
rrl1475843r.2186g>a0.496
rrl1475849r.2192g>a0.519
rrl1475853r.2196c>t0.519
rrl1475858r.2201t>c0.510
rrl1476126r.2469c>t0.474
rrl1476128r.2471t>a0.468
rrl1476135r.2478t>c0.449
rrl1476141r.2484a>g0.449
rrl1476153r.2496t>c0.444
rrl1476164r.2507a>g0.392
rrl1476165r.2508t>a0.392
rrl1476181r.2524a>c0.406
rrl1476229r.2572c>t0.138
rrl1476251r.2594t>c0.586
rrl1476260r.2603a>g0.608
rrl1476280r.2623a>c0.566
rrl1476293r.2636c>t0.234
rrl1476294r.2637a>g0.234
rrl1476295r.2638c>g0.234
rrl1476296r.2639c>t0.231
rrl1476297r.2640c>a0.231
rrl1476301r.2644a>c0.234
rrl1476302r.2645g>a0.231
rrl1476311r.2654g>c0.227
rrl1476312r.2655t>c0.227
rrl1476313r.2656g>a0.234
rrl1476332r.2675g>c0.536
rrl1476338r.2681c>t0.556
rrl1476353r.2696g>t0.628
rrl1476358r.2701t>c0.645
rrl1476372r.2715t>c0.637
rrl1476382r.2725a>g0.656
rrl1476383r.2726t>a0.667
rrl1476408r.2751g>a0.659
rrl1476425r.2768g>a0.648
rrl1476428r.2771c>t0.669
rrl1476466r.2809c>t0.684
rrl1476481r.2824t>c0.645
rrl1476506r.2849t>c0.532
rrl1476512r.2855c>t0.147
rrl1476514r.2857c>t0.145
rrl1476517r.2860c>t0.143
rrl1476519r.2862c>g0.136
rrl1476530r.2873c>t0.139
rrl1476536r.2879g>a0.147
rrl1476537r.2880a>g0.151
rrl1476538r.2881a>g0.151
rrl1476540r.2883c>g0.158
rrl1476547r.2890c>t0.436
rrl1476567r.2910c>t0.493
rrl1476573r.2916a>t0.483
rrl1476577r.2920t>g0.479
rrl1476594r.2937c>t0.456
rrl1476603r.2946g>a0.289
rrl1476607r.2950c>t0.289
rrl1476608r.2951c>g0.292
rrl1476614r.2957a>g0.292
rrl1476619r.2962c>t0.290
rrl1476624r.2967t>a0.292
rrl1476628r.2971t>a0.290
rrl1476629r.2972c>a0.290
rrl1476630r.2973a>g0.290
rrl1476637r.2980c>g0.402
fabG11674162c.723C>T1.000
tlyA1917972c.33A>G1.000
tlyA1918286p.Gly116Val1.000
katG2154724p.Arg463Leu1.000
kasA2518132c.18C>T1.000
kasA2519048p.Gly312Ser1.000
ahpC2726211c.20 21del1.000
ald3086788c.-32T>C1.000
fbiA3640557c.15T>C1.000
alr3841662c.-242A>G0.213
alr3841663c.-243G>A0.216
embC4240671p.Thr270Ile1.000
embC4241042p.Asn394Asp1.000
embC4242643c.2781C>T1.000
embA4243580c.348G>A1.000
embA4244420c.1188G>C1.000
embA4245969p.Pro913Ser1.000
embB4247578c.1065G>A1.000
embB4247646p.Glu378Ala1.000
embB4249195c.2682C>A1.000
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;