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: 5d3602fbab2ed
Sample: 5d3602fbab2ed

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Summary
ID: 5d3602fbab2ed
Date: Mon Jul 22 19:41:17 2019
Strain: lineage3
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Met126Ile (1.00)
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.799c>t (0.34)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.31), rrs r.1484g>t (0.33)
CapreomycinRrrs r.1402c>a (0.31), rrs r.1484g>t (0.33)
KanamycinRrrs r.1402c>a (0.31), rrs r.1484g>t (0.33)

Lineage2FamilyMain SpoligotypeRDS
lineage3East-African-IndianCASRD750

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB759746c.-61C>T1.000
rpoB761207c.1401C>T0.200
rpoB761213c.1407G>C0.200
rpoB761234c.1428G>C0.353
rpoB761243c.1437G>C0.188
rpoB761249c.1443A>G0.353
rpoB761252c.1446C>G0.176
rpoB761261c.1455G>C0.312
rpoB761264c.1458C>G0.278
rpoB762053c.2247T>C0.148
rpoB762057p.Ile751Val0.138
rpoB762062c.2256T>C0.133
rpoB762434c.2628T>G1.000
rpoB762896c.3090G>C0.195
rpoB762920c.3114C>G0.171
rpoB762923c.3117C>G0.186
rpoB762929c.3123G>C0.200
rpoB762947c.3141C>G0.125
rpoB762980c.3174T>C0.104
rpoB763031c.3225T>C1.000
rpoB763115c.3309T>C0.119
rpoB763126p.Pro1107Gln0.138
rpoB763133c.3327G>C0.117
rpoC763546c.177A>G0.131
rpoC763570c.201G>C0.160
rpoC763622p.Ala85Ser0.179
rpoC763630c.261G>C0.195
rpoC763633c.264T>C0.195
rpoC763660c.291T>C0.232
rpoC763666c.297G>C0.290
rpoC763675c.306C>G0.224
rpoC763686p.Tyr106Phe0.121
rpoC763696c.327T>C0.155
rpoC763708c.339G>C0.137
rpoC763714c.345G>C0.137
rpoC763717c.348T>C0.137
rpoC764536c.1167G>C0.116
rpoC764539c.1170C>G0.119
rpoC764545c.1176C>G0.119
rpoC764548c.1179G>T0.125
rpoC764551c.1182G>C0.116
rpoC764560c.1191T>C0.128
rpoC764566c.1197C>G0.122
rpoC764632c.1263T>C0.174
rpoC764650c.1281G>T0.170
rpoC764662c.1293G>C0.146
rpoC764706p.Leu446Gln0.143
rpsL781395c.-165T>C0.979
rpsL781802c.243G>C0.140
rpsL781817c.258G>T0.128
rpsL781829c.270G>C0.130
rpsL781832c.273T>C0.130
rrs1471866r.21c>t0.200
rrs1472106r.261g>a0.267
rrs1472113r.268t>c0.283
rrs1472148r.303t>c0.273
rrs1472150r.305t>a0.358
rrs1472172r.327t>c0.385
rrs1472251r.406g>a0.354
rrs1472259r.414c>a0.318
rrs1472338r.493a>g0.226
rrs1472344r.499c>t0.275
rrs1472379r.534t>c0.302
rrs1472382r.537g>a0.291
rrs1472400r.555c>t0.250
rrs1472422r.577t>c0.213
rrs1472494r.649a>g0.320
rrs1472496r.651t>g0.320
rrs1472498r.653c>t0.307
rrs1472558r.713g>a0.446
rrs1472569r.724g>a0.424
rrs1472581r.736a>c0.415
rrs1472583r.738t>c0.333
rrs1472607r.762g>a0.386
rrs1472655r.810g>t0.414
rrs1472660r.815t>c0.391
rrs1472673r.828t>g0.236
rrs1472674r.829t>c0.236
rrs1472677r.832c>a0.232
rrs1472682r.837t>a0.241
rrs1472683r.838t>c0.236
rrs1472685r.840g>a0.236
rrs1472687r.842a>t0.241
rrs1472697r.852t>c0.349
rrs1472701r.856t>a0.338
rrs1472714r.869a>g0.368
rrs1472730r.885a>g0.556
rrs1472755r.910g>a0.329
rrs1472790r.945t>c0.348
rrs1472895r.1050c>t0.341
rrs1472952r.1107t>c0.350
rrs1472956r.1111t>c0.342
rrs1472957r.1112c>t0.346
rrs1472969r.1124a>g0.167
rrs1472970r.1125c>g0.167
rrs1472973r.1128a>c0.177
rrs1472977r.1132g>c0.172
rrs1472978r.1133t>c0.172
rrs1472987r.1142g>a0.231
rrs1472989r.1144g>a0.169
rrs1472990r.1145a>g0.234
rrs1473035r.1190g>a0.256
rrs1473055r.1210c>t0.282
rrs1473056r.1211a>t0.282
rrs1473066r.1221a>g0.309
rrs1473100r.1255g>a0.231
rrs1473110r.1265t>g0.230
rrs1473111r.1266a>g0.233
rrs1473121r.1276t>c0.265
rrs1473122r.1277t>a0.268
rrs1473145r.1300c>t0.310
rrs1473166r.1321g>a0.329
rrs1473252r.1407t>c0.240
rrs1473276r.1431a>g0.347
rrs1473283r.1438t>c0.271
rrs1473288r.1443c>t0.200
rrs1473290r.1445c>t0.257
rrs1473292r.1447g>a0.203
rrs1473294r.1449a>g0.200
rrs1473301r.1456t>c0.317
rrs1473315r.1470t>c0.256
rrs1473316r.1471c>t0.265
rrl1473770r.113t>g0.235
rrl1473788r.131a>c0.190
rrl1473797r.140g>c0.185
rrl1473806r.149c>t0.176
rrl1473807r.150t>g0.176
rrl1473815r.158t>c0.176
rrl1473832r.175c>t0.203
rrl1473845r.188g>c0.191
rrl1474201r.544t>c0.263
rrl1474202r.545t>a0.278
rrl1474218r.561t>a0.339
rrl1474249r.592g>t0.403
rrl1474281r.624a>g0.373
rrl1474290r.633t>c0.270
rrl1474305r.648g>c0.279
rrl1474316r.659t>c0.293
rrl1474348r.691c>t0.200
rrl1474351r.694g>t0.200
rrl1474353r.696a>g0.156
rrl1474354r.697c>t0.200
rrl1474356r.699t>c0.174
rrl1474359r.702c>g0.196
rrl1474362r.705a>g0.205
rrl1474381r.724t>a0.159
rrl1474387r.730c>t0.186
rrl1474466r.809g>a0.278
rrl1474476r.819c>g0.306
rrl1474483r.826c>g0.267
rrl1474488r.831g>t0.298
rrl1474516r.859c>a0.339
rrl1474527r.870t>c0.348
rrl1474529r.872a>g0.348
rrl1474537r.880g>a0.424
rrl1474540r.883t>c0.371
rrl1474542r.885a>g0.365
rrl1474551r.894g>c0.408
rrl1474558r.901g>t0.456
rrl1474583r.926c>t0.425
rrl1474624r.967g>c0.188
rrl1474626r.969t>c0.186
rrl1474632r.975g>t0.246
rrl1474636r.979a>t0.226
rrl1474637r.980c>t0.226
rrl1474638r.981c>g0.226
rrl1474639r.982g>c0.222
rrl1474660r.1003g>a0.237
rrl1474676r.1019t>c0.242
rrl1474690r.1033c>t0.200
rrl1474722r.1065t>c0.192
rrl1474725r.1068c>g0.176
rrl1474734r.1077g>t0.293
rrl1474760r.1103a>g0.377
rrl1474777r.1120t>c0.356
rrl1474779r.1122g>a0.356
rrl1474782r.1125g>a0.348
rrl1474794r.1137c>t0.420
rrl1474801r.1144g>a0.357
rrl1474823r.1166c>g0.403
rrl1474827r.1170c>t0.397
rrl1474831r.1174a>c0.339
rrl1474904r.1247g>c0.304
rrl1474905r.1248t>c0.289
rrl1474913r.1256t>c0.283
rrl1474932r.1275c>t0.125
rrl1474934r.1277c>t0.125
rrl1475090r.1433a>t0.255
rrl1475104r.1447t>a0.296
rrl1475114r.1457c>t0.333
rrl1475116r.1459g>a0.347
rrl1475124r.1467a>t0.417
rrl1475129r.1472g>a0.417
rrl1475508r.1851a>t0.130
rrl1475526r.1869c>a0.148
rrl1475538r.1881t>a0.148
rrl1475539r.1882a>t0.140
rrl1475545r.1888t>g0.145
rrl1475548r.1891c>t0.138
rrl1475549r.1892t>c0.138
rrl1475550r.1893a>g0.140
rrl1475649r.1992a>g0.141
rrl1475655r.1998t>g0.149
rrl1475659r.2002g>a0.141
rrl1475753r.2096c>g0.184
rrl1475755r.2098t>g0.151
rrl1475757r.2100a>c0.159
rrl1475759r.2102c>g0.186
rrl1475769r.2112t>c0.186
rrl1475775r.2118g>t0.198
rrl1475776r.2119g>c0.143
rrl1475883r.2226a>c0.288
rrl1475884r.2227a>g0.288
rrl1475896r.2239a>g0.323
rrl1475897r.2240t>c0.323
rrl1475898r.2241a>g0.323
rrl1475899r.2242g>a0.333
rrl1475943r.2286g>a0.348
rrl1475952r.2295a>g0.330
rrl1475970r.2313c>t0.342
rrl1475975r.2318c>t0.293
rrl1475977r.2320a>g0.324
rrl1475988r.2331a>g0.275
rrl1475997r.2340a>g0.217
rrl1476001r.2344t>c0.217
rrl1476131r.2474c>t0.344
rrl1476160r.2503t>c0.132
rrl1476164r.2507a>g0.129
rrl1476165r.2508t>a0.129
rrl1476179r.2522c>t0.284
rrl1476194r.2537a>g0.279
rrl1476197r.2540t>g0.597
rrl1476200r.2543a>t0.409
rrl1476201r.2544c>t0.409
rrl1476221r.2564t>c0.289
rrl1476224r.2567a>g0.413
rrl1476245r.2588c>t0.375
rrl1476252r.2595t>g0.375
rrl1476256r.2599a>g0.365
rrl1476260r.2603a>g0.361
rrl1476279r.2622g>a0.246
rrl1476281r.2624t>c0.321
rrl1476295r.2638c>g0.115
rrl1476296r.2639c>t0.118
rrl1476297r.2640c>g0.120
rrl1476298r.2641c>g0.125
rrl1476300r.2643g>t0.125
rrl1476301r.2644a>t0.122
rrl1476309r.2652g>c0.122
rrl1476311r.2654g>c0.125
rrl1476359r.2702c>g0.429
rrl1476381r.2724g>c0.425
rrl1476428r.2771c>t0.470
rrl1476466r.2809c>t0.506
rrl1476506r.2849t>c0.500
rrl1476515r.2858c>t0.500
rrl1476523r.2866t>c0.351
rrl1476524r.2867c>a0.377
rrl1476525r.2868a>g0.377
rrl1476536r.2879g>a0.392
rrl1476538r.2881a>g0.392
rrl1476539r.2882a>g0.392
rrl1476540r.2883c>g0.392
rrl1476584r.2927c>t0.444
rrl1476585r.2928a>g0.438
rrl1476594r.2937c>t0.410
rrl1476603r.2946g>a0.373
rrl1476608r.2951c>g0.316
rrl1476614r.2957a>t0.283
rrl1476616r.2959a>g0.231
rrl1476619r.2962c>t0.288
rrl1476628r.2971t>a0.245
rrl1476629r.2972c>a0.288
rrl1476630r.2973a>g0.245
rrl1476661r.3004a>g0.229
rrl1476665r.3008t>g0.213
rrl1476668r.3011c>t0.217
rrl1476675r.3018c>g0.200
rpsA1833646c.105T>C0.130
rpsA1833661c.120A>G0.130
rpsA1833676c.135A>G0.130
rpsA1833679c.138G>C0.133
rpsA1833685c.144G>T0.128
rpsA1833694c.153G>C0.125
rpsA1833697c.156C>G0.128
rpsA1833721c.180A>G0.122
rpsA1833727c.186G>C0.130
rpsA1833733c.192C>G0.106
rpsA1833734p.Ala65Ser0.128
rpsA1833742c.201A>G0.130
rpsA1833970c.429G>C0.129
rpsA1833979c.438T>C0.139
rpsA1833988c.447C>G0.143
rpsA1833994c.453G>C0.114
rpsA1833997c.456G>C0.118
rpsA1834000c.459G>C0.143
rpsA1834012c.471G>C0.162
rpsA1834015c.474G>C0.162
rpsA1834024c.483G>C0.158
rpsA1834030c.489C>G0.216
rpsA1834034p.Ile165Val0.194
rpsA1834054c.513C>G0.222
rpsA1834069c.528G>C0.205
rpsA1834093c.552G>C0.132
rpsA1834099c.558C>G0.135
rpsA1834102c.561T>C0.132
rpsA1834108c.567C>G0.122
rpsA1834114c.573G>C0.114
rpsA1834123c.582C>G0.119
rpsA1834210c.669C>T0.139
rpsA1834222c.681T>C0.143
rpsA1834225c.684C>G0.139
rpsA1834231c.690T>C0.139
rpsA1834240c.699T>G0.121
rpsA1834243c.702G>C0.147
rpsA1834249c.708T>C0.152
rpsA1834261c.720A>G0.194
rpsA1834264c.723G>C0.188
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
pncA2289047c.195G>A1.000
ahpC2726105c.-88G>A1.000
ald3086788c.-32T>C1.000
alr3841662c.-242A>G0.221
alr3841663c.-243G>A0.182
embC4242075p.Arg738Gln1.000
embC4242643c.2781C>T1.000
gid4407588c.615T>C1.000

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;