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: 5d8070b0b0348
Sample: 5d8070b0b0348

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Summary
ID: 5d8070b0b0348
Date: Tue Sep 17 06:45:04 2019
Strain: lineage2.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00)
EthambutolRembB p.Met306Ile (1.00)
Pyrazinamide
StreptomycinRrpsL p.Lys43Arg (0.93)
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.Ser95Thr0.994
gyrA9304p.Gly668Asp0.995
rpoB761441p.Asp545Glu1.000
rpoB763031c.3225T>C1.000
rpoC763477c.108C>T0.286
rpoC763478c.109C>A0.284
rpoC763484c.115C>T0.284
rpoC763498c.129G>A0.360
rpoC763501p.Asp44Glu0.364
rpoC763505c.136C>T0.378
rpoC763519c.150G>A0.325
rpoC763522c.153C>A0.323
rpoC763528c.159G>T0.324
rpoC763534c.165T>A0.312
rpoC763535p.Arg56Lys0.306
rpoC763550p.Tyr61His0.364
rpoC763570c.201G>C0.271
rpoC763573c.204G>T0.264
rpoC763578p.Phe70Tyr0.256
rpoC763582c.213G>A0.253
rpoC763586p.Ile73Val0.262
rpoC763589p.Ile74Val0.268
rpoC763597p.Glu76Asp0.265
rpoC764377c.1008C>G0.131
rpoC764387c.1018T>C0.150
rpoC764405c.1036A>C0.151
rpoC764410c.1041G>C0.171
rpoC764419c.1050C>G0.172
rpoC764428c.1059G>C0.141
rpoC764429c.1060C>T0.146
rpoC764434c.1065A>G0.144
rpoC764435c.1066A>C0.144
rpoC764441p.Ile358Leu0.139
rpoC764446c.1077T>C0.137
rpoC764449c.1080G>C0.157
rpoC764461p.Glu364Asp0.231
rpoC764470c.1101C>T0.227
rpoC764471p.Asn368Gln0.226
rpoC764498p.Ser377Ala0.278
rpoC764503c.1134G>C0.286
rpoC764509c.1140G>A0.286
rpoC764513p.Phe382Ile0.288
rpoC764521c.1152T>C0.324
rpoC764536c.1167G>T0.351
rpoC764539c.1170C>G0.353
rpoC764548c.1179G>A0.392
rpoC764575c.1206T>C0.275
rpoC764576c.1207T>A0.275
rpoC764579p.Asp404His0.280
rpoC764582p.Leu405Met0.279
rpoC764587c.1218C>G0.251
rpoC764605c.1236G>C0.289
rpoC764614c.1245G>A0.266
rpoC764623c.1254C>T0.278
rpoC764632c.1263T>C0.265
rpoC764644c.1275G>C0.240
rpoC764650c.1281G>T0.194
rpoC764653c.1284G>C0.175
rpoC764656c.1287C>T0.171
rpoC764662c.1293G>C0.169
rpoC764817p.Val483Gly1.000
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.423
rrs1471900r.55c>t0.425
rrs1472127r.282c>t0.248
rrs1472129r.284g>c0.271
rrs1472137r.292g>a0.323
rrs1472150r.305t>a0.358
rrs1472151r.306c>t0.360
rrs1472172r.327t>c0.476
rrs1472203r.358g>a0.555
rrs1472210r.365a>c0.535
rrs1472213r.368g>c0.544
rrs1472215r.370a>g0.550
rrs1472225r.380c>a0.555
rrs1472234r.389t>c0.526
rrs1472236r.391c>g0.510
rrs1472240r.395g>a0.494
rrs1472379r.534t>g0.278
rrs1472382r.537g>a0.268
rrs1472400r.555c>t0.305
rrs1472517r.672t>a0.176
rrs1472518r.673g>c0.187
rrs1472530r.685g>a0.207
rrs1472537r.692c>t0.206
rrs1472541r.696t>g0.189
rrs1472544r.699c>g0.204
rrs1472545r.700a>t0.190
rrs1472557r.712g>a0.283
rrs1472571r.726g>c0.319
rrs1472573r.728c>t0.320
rrs1472579r.734g>a0.339
rrs1472581r.736a>t0.348
rrs1472598r.753a>c0.409
rrs1472616r.771g>a0.524
rrs1472655r.810g>a0.194
rrs1472697r.852t>a0.490
rrs1472700r.855c>t0.490
rrs1472708r.863t>a0.494
rrs1472713r.868t>c0.492
rrs1472716r.871c>t0.502
rrs1472733r.888g>c0.525
rrs1472734r.889c>t0.525
rrs1472741r.896g>a0.521
rrs1472742r.897c>g0.519
rrs1472744r.899a>g0.524
rrs1472767r.922g>a0.570
rrs1472779r.934g>a0.577
rrs1472781r.936c>t0.582
rrs1472786r.941c>t0.604
rrs1472793r.948a>t0.625
rrs1472803r.958t>a0.639
rrs1472895r.1050c>t0.362
rrs1473035r.1190g>a0.490
rrs1473053r.1208t>a0.479
rrs1473056r.1211a>t0.475
rrs1473062r.1217t>a0.484
rrs1473068r.1223a>g0.470
rrs1473070r.1225g>a0.467
rrs1473088r.1243a>g0.445
rrs1473093r.1248c>a0.429
rrs1473094r.1249t>a0.416
rrs1473099r.1254t>a0.433
rrs1473110r.1265t>g0.410
rrs1473111r.1266a>g0.402
rrs1473121r.1276t>c0.295
rrs1473122r.1277t>a0.285
rrs1473127r.1282g>a0.284
rrs1473128r.1283c>g0.289
rrs1473145r.1300c>t0.201
rrs1473147r.1302g>c0.201
rrs1473148r.1303g>a0.202
rrs1473150r.1305t>g0.203
rrs1473161r.1316a>c0.286
rrs1473163r.1318c>t0.300
rrs1473164r.1319c>g0.297
rrs1473166r.1321g>a0.356
rrs1473177r.1332g>a0.436
rrs1473179r.1334c>t0.443
rrs1473192r.1347a>g0.472
rrs1473202r.1357c>t0.465
rrs1473205r.1360t>c0.477
rrs1473226r.1381c>t0.516
rrs1473327r.1482a>g0.158
rrs1473328r.1483c>t0.171
rrs1473352r.1507c>t0.388
rrl1474578r.921a>g0.173
rrl1474584r.927c>g0.188
rrl1474586r.929t>a0.236
rrl1474782r.1125g>a0.173
rrl1474790r.1133c>t0.194
rrl1474798r.1141c>t0.228
rrl1474804r.1147c>t0.271
rrl1474823r.1166c>g0.371
rrl1474827r.1170c>t0.391
rrl1474830r.1173a>g0.400
rrl1474831r.1174a>c0.488
rrl1474844r.1187g>t0.531
rrl1474866r.1209c>a0.592
rrl1474869r.1212g>c0.609
rrl1474896r.1239a>g0.732
rrl1474902r.1245t>c0.714
rrl1474904r.1247g>c0.713
rrl1474913r.1256t>a0.673
rrl1474920r.1263g>a0.632
rrl1475122r.1465c>t0.659
rrl1475129r.1472g>t0.690
rrl1475154r.1497c>a0.740
rrl1475167r.1510t>a0.694
rrl1475175r.1518g>a0.624
rrl1475182r.1525t>a0.600
rrl1475188r.1531c>t0.571
rrl1475574r.1917c>a0.241
rrl1475672r.2015c>g0.284
rrl1475673r.2016t>c0.291
rrl1475687r.2030c>t0.386
rrl1475688r.2031g>a0.394
rrl1475696r.2039t>c0.414
rrl1475703r.2046a>g0.388
rrl1475707r.2050t>a0.386
rrl1475713r.2056c>t0.394
rrl1475716r.2059a>g0.400
rrl1475803r.2146t>c0.455
rrl1475804r.2147g>c0.446
rrl1475816r.2159c>g0.494
rrl1475817r.2160a>g0.514
rrl1475843r.2186g>a0.562
rrl1475849r.2192g>a0.542
rrl1475853r.2196c>t0.567
rrl1475858r.2201t>c0.571
rrl1476141r.2484a>g0.387
rrl1476153r.2496t>c0.403
rrl1476164r.2507a>g0.411
rrl1476165r.2508t>c0.408
rrl1476181r.2524a>c0.341
rrl1476221r.2564t>c0.227
rrl1476225r.2568t>g0.258
rrl1476229r.2572c>g0.347
rrl1476251r.2594t>c0.570
rrl1476252r.2595t>g0.590
rrl1476260r.2603a>g0.612
rrl1476280r.2623a>c0.636
rrl1476293r.2636c>t0.530
rrl1476294r.2637a>g0.527
rrl1476295r.2638c>g0.524
rrl1476296r.2639c>t0.517
rrl1476297r.2640c>a0.502
rrl1476302r.2645g>a0.514
rrl1476311r.2654g>c0.534
rrl1476312r.2655t>c0.529
rrl1476313r.2656g>a0.534
rrl1476332r.2675g>c0.646
rrl1476338r.2681c>t0.657
rrl1476353r.2696g>t0.679
rrl1476358r.2701t>c0.727
rrl1476372r.2715t>c0.726
rrl1476382r.2725a>g0.675
rrl1476383r.2726t>a0.694
rrl1476408r.2751g>a0.746
rrl1476425r.2768g>a0.758
rrl1476428r.2771c>t0.771
rrl1476466r.2809c>t0.841
rrl1476481r.2824t>c0.847
rrl1476506r.2849t>c0.792
rrl1476512r.2855c>t0.600
rrl1476514r.2857c>t0.619
rrl1476519r.2862c>g0.606
rrl1476524r.2867c>a0.578
rrl1476525r.2868a>g0.569
rrl1476530r.2873c>t0.583
rrl1476536r.2879g>a0.561
rrl1476537r.2880a>g0.556
rrl1476538r.2881a>g0.497
rrl1476540r.2883c>g0.472
rrl1476547r.2890c>t0.689
rrl1476567r.2910c>t0.703
rrl1476573r.2916a>t0.706
rrl1476577r.2920t>g0.704
rrl1476584r.2927c>t0.718
rrl1476595r.2938c>t0.698
rrl1476602r.2945g>a0.650
rrl1476607r.2950c>t0.603
rrl1476608r.2951c>g0.601
rrl1476621r.2964c>a0.532
rrl1476624r.2967t>a0.543
rrl1476628r.2971t>a0.507
rrl1476629r.2972c>a0.480
rrl1476630r.2973a>g0.487
rrl1476637r.2980c>g0.553
rpsA1833540c.-2A>G1.000
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
alr3841208c.213A>T0.356
alr3841652c.-232A>T0.211
alr3841654c.-234A>C0.219
alr3841662c.-242A>G0.261
alr3841663c.-243G>A0.255
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
ethA4326676p.Ser266Arg1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp0.994

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;