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: 5dca16b14de20
Sample: 5dca16b14de20

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Summary
ID: 5dca16b14de20
Date: Tue Nov 12 02:28:54 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.799c>t (0.24), rrs r.888g>a (0.48)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.29), rrs r.1484g>t (0.24)
CapreomycinRrrs r.1402c>a (0.29), rrs r.1484g>t (0.24)
KanamycinRrrs r.1402c>a (0.29), rrs r.1484g>t (0.24)

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
rpoB762197c.2391C>T0.174
rpoB762200c.2394C>T0.167
rpoB762212c.2406G>C0.180
rpoB762233c.2427G>C0.153
rpoB762236c.2430G>C0.145
rpoB762245c.2439G>C0.148
rpoB762254c.2448T>C0.150
rpoB762257c.2451C>A0.136
rpoB762273p.Ala823Ser0.121
rpoB762284c.2478G>T0.127
rpoB762293c.2487T>C0.114
rpoB762296c.2490G>C0.118
rpoB762879p.Met1025Leu0.109
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C1.000
rrs1471853r.8t>c0.178
rrs1471866r.21c>t0.255
rrs1471896r.51t>c0.121
rrs1471900r.55c>t0.126
rrs1472102r.257g>a0.309
rrs1472106r.261g>a0.490
rrs1472112r.267c>t0.340
rrs1472113r.268t>c0.367
rrs1472127r.282c>t0.221
rrs1472129r.284g>c0.152
rrs1472130r.285g>a0.149
rrs1472137r.292g>a0.356
rrs1472150r.305t>a0.738
rrs1472151r.306c>t0.373
rrs1472160r.315c>t0.175
rrs1472172r.327t>c0.712
rrs1472203r.358g>a0.273
rrs1472225r.380c>a0.264
rrs1472240r.395g>a0.140
rrs1472251r.406g>a0.533
rrs1472344r.499c>t0.449
rrs1472379r.534t>c0.412
rrs1472400r.555c>t0.422
rrs1472416r.571c>t0.303
rrs1472422r.577t>c0.298
rrs1472494r.649a>g0.352
rrs1472496r.651t>a0.356
rrs1472498r.653c>t0.360
rrs1472507r.662c>g0.138
rrs1472517r.672t>a0.139
rrs1472518r.673g>t0.150
rrs1472530r.685g>a0.236
rrs1472537r.692c>t0.254
rrs1472544r.699c>a0.201
rrs1472545r.700a>t0.185
rrs1472558r.713g>a0.333
rrs1472566r.721g>a0.210
rrs1472569r.724g>a0.330
rrs1472571r.726g>c0.330
rrs1472579r.734g>c0.251
rrs1472580r.735c>t0.178
rrs1472581r.736a>t0.694
rrs1472597r.752g>a0.291
rrs1472598r.753a>c0.397
rrs1472599r.754g>t0.320
rrs1472607r.762g>a0.270
rrs1472616r.771g>a0.454
rrs1472655r.810g>t0.511
rrs1472658r.813g>a0.189
rrs1472660r.815t>c0.431
rrs1472661r.816a>g0.164
rrs1472673r.828t>g0.319
rrs1472674r.829t>g0.169
rrs1472675r.830t>a0.206
rrs1472677r.832c>a0.179
rrs1472680r.835c>t0.110
rrs1472682r.837t>c0.127
rrs1472683r.838t>g0.125
rrs1472687r.842a>t0.153
rrs1472690r.845c>a0.222
rrs1472692r.847t>c0.134
rrs1472697r.852t>c0.218
rrs1472713r.868t>c0.492
rrs1472714r.869a>g0.207
rrs1472716r.871c>t0.510
rrs1472742r.897c>t0.496
rrs1472744r.899a>g0.543
rrs1472755r.910g>a0.162
rrs1472767r.922g>a0.193
rrs1472781r.936c>t0.542
rrs1472790r.945t>c0.179
rrs1472793r.948a>t0.524
rrs1472803r.958t>a0.456
rrs1472824r.979t>a0.123
rrs1472895r.1050c>t0.699
rrs1472952r.1107t>c0.333
rrs1472955r.1110c>t0.364
rrs1472956r.1111t>c0.450
rrs1472957r.1112c>t0.539
rrs1472973r.1128a>t0.531
rrs1472987r.1142g>a0.424
rrs1472989r.1144g>a0.412
rrs1472990r.1145a>g0.476
rrs1473035r.1190g>a0.533
rrs1473055r.1210c>t0.535
rrs1473056r.1211a>t0.535
rrs1473066r.1221a>g0.562
rrs1473088r.1243a>g0.474
rrs1473093r.1248c>t0.481
rrs1473100r.1255g>a0.373
rrs1473102r.1257c>t0.343
rrs1473104r.1259c>t0.385
rrs1473110r.1265t>g0.373
rrs1473111r.1266a>g0.368
rrs1473115r.1270g>t0.324
rrs1473121r.1276t>c0.469
rrs1473145r.1300c>t0.562
rrs1473163r.1318c>t0.151
rrs1473164r.1319c>a0.131
rrs1473166r.1321g>a0.558
rrs1473177r.1332g>a0.445
rrs1473192r.1347a>g0.375
rrs1473199r.1354ca>c0.436
rrs1473205r.1360t>c0.368
rrs1473252r.1407t>c0.529
rrs1473259r.1414c>t0.535
rrs1473270r.1425g>a0.340
rrs1473276r.1431a>g0.505
rrs1473290r.1445c>t0.425
rrs1473301r.1456t>c0.468
rrs1473305r.1460g>t0.395
rrs1473316r.1471c>t0.518
rrs1473352r.1507c>t0.455
rrl1474151r.494c>t0.302
rrl1474155r.498g>a0.323
rrl1474164r.507c>t0.333
rrl1474171r.514c>t0.329
rrl1474181r.524c>t0.333
rrl1474184r.527c>t0.364
rrl1474185r.528g>a0.312
rrl1474197r.540c>t0.402
rrl1474199r.542g>a0.377
rrl1474202r.545t>c0.358
rrl1474218r.561t>a0.336
rrl1474228r.571t>c0.239
rrl1474249r.592g>t0.520
rrl1474252r.595t>a0.244
rrl1474269r.612c>t0.379
rrl1474275r.618t>g0.183
rrl1474348r.691c>t0.333
rrl1474351r.694g>t0.329
rrl1474353r.696a>t0.333
rrl1474354r.697c>t0.333
rrl1474362r.705a>g0.329
rrl1474383r.726g>t0.293
rrl1474387r.730c>t0.297
rrl1474476r.819c>t0.149
rrl1474488r.831g>t0.240
rrl1474496r.839c>a0.233
rrl1474497r.840g>c0.233
rrl1474506r.849c>g0.243
rrl1474507r.850g>t0.250
rrl1474516r.859c>a0.267
rrl1474529r.872a>c0.269
rrl1474530r.873g>a0.265
rrl1474537r.880g>a0.304
rrl1474539r.882c>t0.265
rrl1474540r.883t>g0.273
rrl1474558r.901g>a0.365
rrl1474584r.927c>t0.433
rrl1474627r.970g>a0.422
rrl1474632r.975g>t0.402
rrl1474636r.979a>t0.432
rrl1474637r.980c>t0.474
rrl1474638r.981c>g0.463
rrl1474639r.982g>c0.395
rrl1474672r.1015c>t0.286
rrl1474674r.1017a>c0.294
rrl1474675r.1018c>a0.299
rrl1474676r.1019t>c0.278
rrl1474677r.1020a>g0.356
rrl1474694r.1037c>t0.260
rrl1474734r.1077g>t0.125
rrl1474760r.1103a>g0.253
rrl1474777r.1120t>c0.241
rrl1474779r.1122g>a0.325
rrl1474782r.1125g>a0.350
rrl1474783r.1126g>a0.225
rrl1474794r.1137c>t0.450
rrl1474823r.1166c>g0.536
rrl1474827r.1170c>t0.465
rrl1474830r.1173a>t0.494
rrl1474831r.1174a>t0.526
rrl1474864r.1207c>t0.570
rrl1474883r.1226t>c0.467
rrl1474904r.1247g>c0.568
rrl1474913r.1256t>c0.106
rrl1474932r.1275c>t0.380
rrl1475129r.1472g>t0.152
rrl1475137r.1480a>g0.295
rrl1475171r.1514c>t0.337
rrl1475499r.1842c>t0.340
rrl1475515r.1858g>a0.361
rrl1475526r.1869c>a0.349
rrl1475531r.1874c>t0.338
rrl1475538r.1881t>a0.375
rrl1475539r.1882a>t0.364
rrl1475545r.1888t>g0.388
rrl1475548r.1891c>t0.343
rrl1475549r.1892t>c0.362
rrl1475672r.2015c>t0.301
rrl1475673r.2016t>c0.301
rrl1475699r.2042c>t0.413
rrl1475722r.2065g>t0.423
rrl1475751r.2094c>t0.357
rrl1475752r.2095c>t0.328
rrl1475753r.2096c>g0.373
rrl1475758r.2101a>g0.339
rrl1475761r.2104c>g0.237
rrl1475769r.2112t>c0.169
rrl1475775r.2118g>t0.447
rrl1475777r.2120a>t0.106
rrl1475783r.2126t>g0.342
rrl1475803r.2146t>c0.458
rrl1475804r.2147g>c0.458
rrl1475816r.2159c>g0.460
rrl1475817r.2160a>g0.458
rrl1475858r.2201t>c0.415
rrl1475866r.2209t>a0.412
rrl1475869r.2212c>a0.258
rrl1475881r.2224t>c0.393
rrl1475883r.2226a>t0.422
rrl1475898r.2241a>g0.433
rrl1475899r.2242g>a0.443
rrl1475916r.2259c>g0.441
rrl1475937r.2280a>t0.449
rrl1475943r.2286g>a0.425
rrl1475952r.2295a>g0.425
rrl1475963r.2306g>t0.378
rrl1475970r.2313c>t0.333
rrl1475975r.2318c>t0.329
rrl1475977r.2320a>g0.307
rrl1475978r.2321c>t0.311
rrl1475988r.2331a>g0.304
rrl1475993r.2336c>t0.313
rrl1475997r.2340a>t0.303
rrl1475998r.2341c>t0.303
rrl1476001r.2344t>c0.317
rrl1476047r.2390g>t0.111
rrl1476130r.2473g>a0.467
rrl1476131r.2474c>t0.544
rrl1476164r.2507a>g0.462
rrl1476194r.2537a>g0.526
rrl1476200r.2543a>t0.477
rrl1476201r.2544c>t0.478
rrl1476214r.2557g>t0.407
rrl1476215r.2558c>t0.400
rrl1476224r.2567a>g0.453
rrl1476245r.2588c>t0.430
rrl1476252r.2595t>g0.347
rrl1476253r.2596a>g0.329
rrl1476256r.2599a>g0.347
rrl1476260r.2603a>g0.364
rrl1476281r.2624t>c0.288
rrl1476294r.2637a>g0.221
rrl1476295r.2638c>g0.224
rrl1476296r.2639c>t0.224
rrl1476297r.2640c>a0.206
rrl1476299r.2642c>g0.167
rrl1476300r.2643g>t0.181
rrl1476301r.2644a>t0.205
rrl1476308r.2651g>c0.176
rrl1476311r.2654g>c0.243
rrl1476312r.2655t>c0.239
rrl1476332r.2675g>c0.335
rrl1476337r.2680c>t0.259
rrl1476338r.2681c>t0.337
rrl1476353r.2696g>t0.362
rrl1476358r.2701t>c0.415
rrl1476359r.2702c>g0.318
rrl1476369r.2712c>t0.327
rrl1476372r.2715t>c0.422
rrl1476381r.2724g>c0.292
rrl1476382r.2725a>g0.466
rrl1476383r.2726t>a0.435
rrl1476408r.2751g>a0.210
rrl1476425r.2768g>t0.418
rrl1476428r.2771c>t0.739
rrl1476429r.2772a>c0.645
rrl1476466r.2809c>t0.468
rrl1476481r.2824t>c0.815
rrl1476506r.2849t>c0.771
rrl1476514r.2857c>t0.126
rrl1476515r.2858c>t0.447
rrl1476524r.2867c>t0.368
rrl1476525r.2868a>g0.429
rrl1476530r.2873c>t0.403
rrl1476536r.2879g>a0.392
rrl1476539r.2882a>g0.342
rrl1476540r.2883c>g0.384
rrl1476547r.2890c>t0.368
rrl1476567r.2910c>t0.108
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.214
alr3841654c.-234A>C0.217
alr3841662c.-242A>G0.239
alr3841663c.-243G>A0.239
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;