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: 5dca1d08aec8e
Sample: 5dca1d08aec8e

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Summary
ID: 5dca1d08aec8e
Date: Tue Nov 12 02:50:23 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.799c>t (0.27), rrs r.888g>a (0.35)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.43), rrs r.1484g>t (0.31)
CapreomycinRrrs r.1402c>a (0.43), rrs r.1484g>t (0.31)
KanamycinRrrs r.1402c>a (0.43), rrs r.1484g>t (0.31)

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
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C0.989
rpsL781395c.-165T>C1.000
rrs1471866r.21c>t0.339
rrs1471896r.51t>c0.154
rrs1471900r.55c>t0.154
rrs1472102r.257g>a0.382
rrs1472106r.261g>a0.455
rrs1472112r.267c>t0.456
rrs1472113r.268t>c0.456
rrs1472137r.292g>a0.201
rrs1472150r.305t>a0.607
rrs1472151r.306c>t0.211
rrs1472172r.327t>c0.655
rrs1472203r.358g>a0.196
rrs1472251r.406g>a0.494
rrs1472344r.499c>t0.568
rrs1472379r.534t>c0.636
rrs1472400r.555c>t0.619
rrs1472416r.571c>t0.604
rrs1472422r.577t>c0.576
rrs1472494r.649a>g0.539
rrs1472496r.651t>a0.528
rrs1472498r.653c>t0.542
rrs1472517r.672t>a0.175
rrs1472518r.673g>t0.175
rrs1472530r.685g>a0.208
rrs1472537r.692c>t0.221
rrs1472544r.699c>a0.227
rrs1472545r.700a>t0.236
rrs1472558r.713g>a0.427
rrs1472566r.721g>a0.180
rrs1472569r.724g>a0.400
rrs1472571r.726g>c0.291
rrs1472579r.734g>c0.205
rrs1472580r.735c>t0.175
rrs1472581r.736a>t0.697
rrs1472597r.752g>a0.339
rrs1472598r.753a>c0.354
rrs1472599r.754g>t0.347
rrs1472607r.762g>a0.329
rrs1472616r.771g>a0.370
rrs1472655r.810g>t0.424
rrs1472660r.815t>c0.388
rrs1472673r.828t>g0.228
rrs1472674r.829t>g0.200
rrs1472675r.830t>a0.204
rrs1472677r.832c>a0.202
rrs1472692r.847t>c0.202
rrs1472713r.868t>c0.313
rrs1472714r.869a>g0.395
rrs1472716r.871c>t0.345
rrs1472742r.897c>t0.384
rrs1472744r.899a>g0.359
rrs1472755r.910g>a0.348
rrs1472781r.936c>t0.418
rrs1472790r.945t>c0.322
rrs1472793r.948a>t0.397
rrs1472803r.958t>a0.388
rrs1472895r.1050c>t0.655
rrs1472952r.1107t>c0.364
rrs1472955r.1110c>t0.466
rrs1472956r.1111t>c0.461
rrs1472957r.1112c>t0.454
rrs1472973r.1128a>t0.542
rrs1472987r.1142g>a0.446
rrs1472989r.1144g>a0.425
rrs1472990r.1145a>g0.436
rrs1473035r.1190g>a0.447
rrs1473055r.1210c>t0.406
rrs1473056r.1211a>t0.417
rrs1473066r.1221a>g0.431
rrs1473088r.1243a>g0.428
rrs1473093r.1248c>t0.431
rrs1473100r.1255g>a0.344
rrs1473102r.1257c>t0.344
rrs1473104r.1259c>t0.338
rrs1473110r.1265t>g0.344
rrs1473111r.1266a>g0.341
rrs1473115r.1270g>t0.354
rrs1473121r.1276t>c0.459
rrs1473145r.1300c>t0.487
rrs1473166r.1321g>a0.538
rrs1473177r.1332g>a0.225
rrs1473192r.1347a>g0.234
rrs1473205r.1360t>c0.231
rrs1473252r.1407t>c0.561
rrs1473259r.1414c>t0.548
rrs1473270r.1425g>a0.526
rrs1473276r.1431a>g0.526
rrs1473290r.1445c>t0.492
rrs1473301r.1456t>c0.500
rrs1473305r.1460g>t0.514
rrs1473316r.1471c>t0.545
rrs1473352r.1507c>t0.418
rrl1474140r.483c>t0.154
rrl1474141r.484g>c0.152
rrl1474142r.485c>g0.174
rrl1474151r.494c>t0.391
rrl1474155r.498g>a0.415
rrl1474164r.507c>t0.448
rrl1474171r.514c>t0.457
rrl1474181r.524c>t0.470
rrl1474184r.527c>t0.474
rrl1474185r.528g>a0.478
rrl1474197r.540c>t0.480
rrl1474199r.542g>a0.488
rrl1474202r.545t>c0.492
rrl1474218r.561t>a0.287
rrl1474228r.571t>c0.195
rrl1474249r.592g>t0.516
rrl1474252r.595t>a0.177
rrl1474269r.612c>t0.382
rrl1474275r.618t>g0.138
rrl1474348r.691c>t0.377
rrl1474351r.694g>t0.380
rrl1474353r.696a>t0.377
rrl1474354r.697c>t0.366
rrl1474362r.705a>g0.371
rrl1474383r.726g>t0.336
rrl1474387r.730c>t0.336
rrl1474476r.819c>t0.286
rrl1474488r.831g>t0.333
rrl1474496r.839c>a0.366
rrl1474497r.840g>c0.366
rrl1474506r.849c>g0.397
rrl1474507r.850g>t0.397
rrl1474516r.859c>a0.450
rrl1474529r.872a>c0.496
rrl1474530r.873g>a0.488
rrl1474537r.880g>a0.496
rrl1474539r.882c>t0.484
rrl1474540r.883t>g0.488
rrl1474558r.901g>a0.589
rrl1474584r.927c>t0.647
rrl1474627r.970g>a0.567
rrl1474632r.975g>t0.546
rrl1474636r.979a>t0.530
rrl1474637r.980c>t0.530
rrl1474638r.981c>g0.539
rrl1474639r.982g>c0.544
rrl1474672r.1015c>t0.308
rrl1474674r.1017a>c0.304
rrl1474675r.1018c>a0.304
rrl1474676r.1019t>c0.304
rrl1474677r.1020a>g0.304
rrl1474694r.1037c>t0.304
rrl1474760r.1103a>g0.255
rrl1474777r.1120t>c0.325
rrl1474779r.1122g>a0.322
rrl1474782r.1125g>a0.322
rrl1474783r.1126g>a0.336
rrl1474794r.1137c>t0.397
rrl1474823r.1166c>g0.519
rrl1474827r.1170c>t0.513
rrl1474830r.1173a>t0.506
rrl1474831r.1174a>t0.506
rrl1474864r.1207c>t0.597
rrl1474883r.1226t>c0.597
rrl1474904r.1247g>c0.593
rrl1474932r.1275c>t0.500
rrl1475129r.1472g>t0.357
rrl1475137r.1480a>g0.459
rrl1475154r.1497c>t0.146
rrl1475171r.1514c>t0.457
rrl1475175r.1518g>a0.150
rrl1475499r.1842c>t0.424
rrl1475515r.1858g>a0.491
rrl1475526r.1869c>a0.459
rrl1475531r.1874c>t0.444
rrl1475538r.1881t>a0.459
rrl1475539r.1882a>t0.459
rrl1475545r.1888t>g0.459
rrl1475548r.1891c>t0.438
rrl1475549r.1892t>c0.444
rrl1475672r.2015c>t0.326
rrl1475673r.2016t>c0.344
rrl1475699r.2042c>t0.376
rrl1475722r.2065g>t0.421
rrl1475751r.2094c>t0.238
rrl1475752r.2095c>t0.244
rrl1475753r.2096c>g0.271
rrl1475758r.2101a>g0.224
rrl1475765r.2108a>t0.218
rrl1475769r.2112t>c0.298
rrl1475775r.2118g>t0.459
rrl1475783r.2126t>g0.381
rrl1475803r.2146t>c0.422
rrl1475804r.2147g>c0.422
rrl1475816r.2159c>g0.384
rrl1475817r.2160a>g0.378
rrl1475858r.2201t>c0.332
rrl1475866r.2209t>a0.302
rrl1475869r.2212c>a0.451
rrl1475881r.2224t>c0.654
rrl1475883r.2226a>t0.641
rrl1475898r.2241a>g0.657
rrl1475899r.2242g>a0.657
rrl1475916r.2259c>g0.667
rrl1475937r.2280a>t0.662
rrl1475943r.2286g>a0.645
rrl1475952r.2295a>g0.631
rrl1475963r.2306g>t0.563
rrl1475970r.2313c>t0.560
rrl1475975r.2318c>t0.558
rrl1475977r.2320a>g0.536
rrl1475978r.2321c>t0.536
rrl1475988r.2331a>g0.510
rrl1475993r.2336c>t0.490
rrl1475997r.2340a>t0.474
rrl1475998r.2341c>t0.474
rrl1476001r.2344t>c0.479
rrl1476030r.2373a>g0.132
rrl1476130r.2473g>a0.505
rrl1476131r.2474c>t0.505
rrl1476164r.2507a>g0.579
rrl1476194r.2537a>g0.636
rrl1476200r.2543a>t0.627
rrl1476201r.2544c>t0.624
rrl1476214r.2557g>t0.585
rrl1476215r.2558c>t0.582
rrl1476224r.2567a>g0.505
rrl1476225r.2568t>g0.175
rrl1476229r.2572c>g0.174
rrl1476245r.2588c>t0.448
rrl1476251r.2594t>c0.214
rrl1476252r.2595t>g0.401
rrl1476253r.2596a>g0.397
rrl1476256r.2599a>g0.397
rrl1476260r.2603a>g0.633
rrl1476280r.2623a>c0.225
rrl1476281r.2624t>c0.331
rrl1476294r.2637a>g0.263
rrl1476295r.2638c>g0.255
rrl1476296r.2639c>t0.258
rrl1476297r.2640c>a0.216
rrl1476299r.2642c>g0.209
rrl1476300r.2643g>t0.209
rrl1476301r.2644a>t0.224
rrl1476308r.2651g>c0.227
rrl1476311r.2654g>c0.267
rrl1476312r.2655t>c0.289
rrl1476332r.2675g>c0.250
rrl1476337r.2680c>t0.374
rrl1476338r.2681c>t0.261
rrl1476353r.2696g>t0.328
rrl1476358r.2701t>c0.339
rrl1476359r.2702c>g0.368
rrl1476369r.2712c>t0.384
rrl1476372r.2715t>c0.360
rrl1476381r.2724g>c0.350
rrl1476382r.2725a>g0.383
rrl1476383r.2726t>a0.383
rrl1476408r.2751g>a0.214
rrl1476425r.2768g>t0.358
rrl1476428r.2771c>t0.738
rrl1476429r.2772a>c0.738
rrl1476466r.2809c>t0.447
rrl1476481r.2824t>c0.755
rrl1476506r.2849t>c0.695
rrl1476514r.2857c>t0.133
rrl1476515r.2858c>t0.434
rrl1476519r.2862c>g0.125
rrl1476524r.2867c>t0.479
rrl1476525r.2868a>g0.495
rrl1476530r.2873c>t0.480
rrl1476536r.2879g>a0.451
rrl1476539r.2882a>g0.380
rrl1476540r.2883c>g0.446
rrl1476547r.2890c>t0.477
inhA1674210c.9A>C0.984
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.205
alr3841654c.-234A>C0.233
alr3841662c.-242A>G0.247
alr3841663c.-243G>A0.250
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
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;