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: 5dc388200433b
Sample: 5dc388200433b

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Summary
ID: 5dc388200433b
Date: Thu Nov 7 02:59:10 2019
Strain: lineage2.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.799c>t (0.12), rrs r.888g>a (0.37)
Ethionamide
FluoroquinolonesRgyrA p.Asp94Asn (1.00)
AmikacinRrrs r.1402c>a (0.18)
CapreomycinRrrs r.1402c>a (0.18)
KanamycinRrrs r.1402c>a (0.18)

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
rpoB762926c.3120C>G0.158
rpoB762929c.3123G>C0.162
rpoB762947c.3141C>G0.140
rpoB762989c.3183G>C0.132
rpoB763031c.3225T>C1.000
rpoC764566c.1197C>G0.111
rpoC764575c.1206T>C0.109
rpoC764578c.1209C>G0.109
rpoC764581c.1212T>C0.116
rpoC764582p.Leu405Met0.116
rpoC764602c.1233C>T0.143
rpoC764605c.1236G>T0.143
rpoC764611c.1242G>T0.128
rpoC764626c.1257C>T0.139
rpoC764632c.1263T>C0.132
rpoC764647c.1278C>T0.128
rpoC764653c.1284G>C0.125
rpsL781395c.-165T>C1.000
rrs1471853r.8t>c0.192
rrs1471866r.21c>t0.157
rrs1471896r.51t>c0.138
rrs1471900r.55c>t0.134
rrs1472106r.261g>a0.135
rrs1472127r.282c>t0.127
rrs1472137r.292g>a0.209
rrs1472150r.305t>a0.559
rrs1472151r.306c>t0.244
rrs1472160r.315c>t0.177
rrs1472172r.327t>c0.547
rrs1472203r.358g>a0.206
rrs1472225r.380c>a0.200
rrs1472251r.406g>a0.607
rrs1472338r.493a>g0.316
rrs1472344r.499c>t0.478
rrs1472379r.534t>c0.468
rrs1472400r.555c>t0.440
rrs1472412r.567a>g0.333
rrs1472416r.571c>t0.449
rrs1472422r.577t>c0.400
rrs1472427r.582t>g0.280
rrs1472494r.649a>g0.250
rrs1472496r.651t>a0.250
rrs1472498r.653c>t0.265
rrs1472513r.668t>c0.143
rrs1472530r.685g>a0.167
rrs1472537r.692c>t0.184
rrs1472544r.699c>a0.137
rrs1472545r.700a>t0.125
rrs1472549r.704g>a0.167
rrs1472557r.712g>a0.174
rrs1472558r.713g>a0.198
rrs1472569r.724g>a0.198
rrs1472570r.725g>a0.130
rrs1472571r.726g>c0.272
rrs1472579r.734g>t0.256
rrs1472581r.736a>t0.577
rrs1472584r.739a>t0.149
rrs1472597r.752g>a0.132
rrs1472598r.753a>c0.337
rrs1472599r.754g>t0.272
rrs1472607r.762g>a0.144
rrs1472612r.767g>t0.157
rrs1472616r.771g>a0.284
rrs1472655r.810g>t0.312
rrs1472658r.813g>a0.161
rrs1472660r.815t>c0.268
rrs1472661r.816a>g0.161
rrs1472670r.825g>t0.161
rrs1472673r.828t>g0.195
rrs1472675r.830t>c0.214
rrs1472677r.832c>t0.209
rrs1472690r.845c>a0.196
rrs1472692r.847t>c0.109
rrs1472697r.852t>c0.268
rrs1472707r.862a>t0.116
rrs1472713r.868t>c0.323
rrs1472714r.869a>g0.281
rrs1472716r.871c>t0.343
rrs1472742r.897c>t0.383
rrs1472744r.899a>g0.398
rrs1472755r.910g>a0.131
rrs1472767r.922g>a0.209
rrs1472781r.936c>t0.449
rrs1472790r.945t>c0.241
rrs1472793r.948a>t0.421
rrs1472803r.958t>a0.356
rrs1472824r.979t>a0.114
rrs1472895r.1050c>t0.589
rrs1472952r.1107t>c0.151
rrs1472954r.1109t>c0.153
rrs1472955r.1110c>t0.167
rrs1472956r.1111t>c0.358
rrs1472957r.1112c>t0.434
rrs1472973r.1128a>t0.309
rrs1472987r.1142g>a0.232
rrs1472989r.1144g>a0.179
rrs1472990r.1145a>g0.339
rrs1472992r.1147a>g0.153
rrs1473005r.1160c>t0.172
rrs1473035r.1190g>a0.471
rrs1473055r.1210c>t0.415
rrs1473056r.1211a>t0.446
rrs1473066r.1221a>g0.406
rrs1473088r.1243a>g0.373
rrs1473093r.1248c>t0.345
rrs1473100r.1255g>a0.273
rrs1473102r.1257c>t0.259
rrs1473104r.1259c>t0.273
rrs1473110r.1265t>g0.288
rrs1473111r.1266a>g0.302
rrs1473115r.1270g>t0.211
rrs1473121r.1276t>c0.429
rrs1473123r.1278a>t0.175
rrs1473130r.1285g>a0.154
rrs1473145r.1300c>t0.464
rrs1473166r.1321g>a0.487
rrs1473172r.1327t>g0.179
rrs1473173r.1328c>t0.184
rrs1473177r.1332g>a0.185
rrs1473192r.1347a>g0.141
rrs1473205r.1360t>c0.137
rrs1473221r.1376c>t0.212
rrs1473252r.1407t>c0.537
rrs1473259r.1414c>t0.519
rrs1473276r.1431a>c0.375
rrs1473277r.1432g>a0.304
rrs1473288r.1443c>g0.127
rrs1473290r.1445c>t0.145
rrs1473300r.1455c>t0.218
rrs1473301r.1456t>g0.273
rrs1473305r.1460g>t0.150
rrs1473316r.1471c>t0.467
rrs1473352r.1507c>t0.417
rrl1473384c.-274A>G0.110
rrl1474181r.524c>a0.205
rrl1474184r.527c>t0.256
rrl1474197r.540c>t0.327
rrl1474199r.542g>c0.222
rrl1474202r.545t>c0.113
rrl1474218r.561t>a0.311
rrl1474228r.571t>a0.203
rrl1474249r.592g>t0.405
rrl1474252r.595t>a0.135
rrl1474269r.612c>t0.237
rrl1474271r.614a>g0.107
rrl1474272r.615c>t0.107
rrl1474275r.618t>g0.220
rrl1474348r.691c>t0.149
rrl1474351r.694g>t0.128
rrl1474353r.696a>t0.130
rrl1474354r.697c>t0.133
rrl1474362r.705a>g0.130
rrl1474476r.819c>t0.154
rrl1474488r.831g>t0.161
rrl1474496r.839c>a0.172
rrl1474497r.840g>c0.172
rrl1474506r.849c>g0.172
rrl1474507r.850g>t0.169
rrl1474516r.859c>a0.169
rrl1474529r.872a>c0.190
rrl1474530r.873g>a0.190
rrl1474537r.880g>a0.196
rrl1474539r.882c>t0.200
rrl1474540r.883t>g0.214
rrl1474558r.901g>a0.241
rrl1474584r.927c>t0.246
rrl1474626r.969t>c0.222
rrl1474627r.970g>a0.173
rrl1474632r.975g>t0.157
rrl1474634r.977t>c0.170
rrl1474636r.979a>c0.205
rrl1474637r.980c>t0.340
rrl1474638r.981c>g0.340
rrl1474639r.982g>c0.170
rrl1474640r.983c>t0.174
rrl1474677r.1020a>g0.282
rrl1474709r.1052g>a0.143
rrl1474722r.1065t>c0.135
rrl1474734r.1077g>t0.225
rrl1474749r.1092c>t0.238
rrl1474760r.1103a>g0.283
rrl1474779r.1122g>a0.302
rrl1474780r.1123c>t0.208
rrl1474782r.1125g>a0.308
rrl1474794r.1137c>t0.379
rrl1474801r.1144g>a0.172
rrl1474802r.1145t>c0.172
rrl1474823r.1166c>g0.358
rrl1474827r.1170c>t0.209
rrl1474830r.1173a>t0.246
rrl1474831r.1174a>t0.250
rrl1474832r.1175a>t0.127
rrl1474864r.1207c>t0.427
rrl1474883r.1226t>c0.267
rrl1474901r.1244a>g0.143
rrl1474904r.1247g>c0.402
rrl1474913r.1256t>c0.146
rrl1474932r.1275c>t0.195
rrl1474933r.1276a>g0.110
rrl1474934r.1277c>t0.111
rrl1475129r.1472g>t0.192
rrl1475137r.1480a>g0.175
rrl1475154r.1497c>t0.150
rrl1475171r.1514c>t0.172
rrl1475175r.1518g>a0.155
rrl1475499r.1842c>t0.192
rrl1475515r.1858g>a0.250
rrl1475526r.1869c>a0.233
rrl1475531r.1874c>t0.226
rrl1475538r.1881t>a0.233
rrl1475539r.1882a>t0.233
rrl1475545r.1888t>g0.280
rrl1475548r.1891c>t0.280
rrl1475549r.1892t>c0.280
rrl1475672r.2015c>t0.277
rrl1475673r.2016t>c0.277
rrl1475699r.2042c>t0.294
rrl1475722r.2065g>t0.190
rrl1475753r.2096c>g0.109
rrl1475769r.2112t>c0.105
rrl1475775r.2118g>t0.159
rrl1475777r.2120a>t0.270
rrl1475783r.2126t>g0.284
rrl1475803r.2146t>c0.337
rrl1475804r.2147g>c0.340
rrl1475816r.2159c>g0.357
rrl1475817r.2160a>g0.354
rrl1475858r.2201t>c0.341
rrl1475866r.2209t>a0.333
rrl1475881r.2224t>c0.122
rrl1475883r.2226a>c0.385
rrl1475884r.2227a>g0.326
rrl1475896r.2239a>g0.235
rrl1475897r.2240t>c0.152
rrl1475898r.2241a>g0.424
rrl1475899r.2242g>a0.412
rrl1475906r.2249c>t0.116
rrl1475916r.2259c>g0.415
rrl1475937r.2280a>t0.368
rrl1475943r.2286g>a0.350
rrl1475952r.2295a>g0.316
rrl1475963r.2306g>t0.200
rrl1475970r.2313c>t0.211
rrl1475975r.2318c>t0.171
rrl1475977r.2320a>g0.167
rrl1475978r.2321c>t0.167
rrl1475988r.2331a>g0.179
rrl1475993r.2336c>t0.179
rrl1475997r.2340a>t0.179
rrl1475998r.2341c>t0.175
rrl1476001r.2344t>c0.175
rrl1476130r.2473g>a0.123
rrl1476131r.2474c>t0.316
rrl1476164r.2507a>g0.189
rrl1476179r.2522c>t0.255
rrl1476194r.2537a>g0.429
rrl1476200r.2543a>t0.378
rrl1476201r.2544c>t0.378
rrl1476204r.2547c>t0.182
rrl1476214r.2557g>t0.222
rrl1476215r.2558c>t0.205
rrl1476224r.2567a>g0.265
rrl1476225r.2568t>g0.184
rrl1476229r.2572c>g0.184
rrl1476245r.2588c>t0.245
rrl1476251r.2594t>c0.178
rrl1476252r.2595t>g0.217
rrl1476253r.2596a>g0.196
rrl1476256r.2599a>g0.196
rrl1476260r.2603a>g0.404
rrl1476280r.2623a>c0.235
rrl1476281r.2624t>c0.176
rrl1476294r.2637a>g0.220
rrl1476295r.2638c>g0.220
rrl1476296r.2639c>t0.214
rrl1476297r.2640c>a0.150
rrl1476299r.2642c>g0.116
rrl1476300r.2643g>t0.116
rrl1476301r.2644a>t0.163
rrl1476308r.2651g>c0.114
rrl1476311r.2654g>c0.209
rrl1476312r.2655t>c0.209
rrl1476332r.2675g>c0.267
rrl1476337r.2680c>t0.125
rrl1476338r.2681c>t0.284
rrl1476353r.2696g>t0.299
rrl1476358r.2701t>c0.311
rrl1476359r.2702c>g0.314
rrl1476369r.2712c>t0.308
rrl1476372r.2715t>c0.306
rrl1476381r.2724g>c0.359
rrl1476382r.2725a>g0.360
rrl1476383r.2726t>a0.306
rrl1476408r.2751g>a0.261
rrl1476425r.2768g>t0.368
rrl1476428r.2771c>t0.677
rrl1476429r.2772a>c0.587
rrl1476466r.2809c>t0.518
rrl1476481r.2824t>c0.732
rrl1476506r.2849t>c0.710
rrl1476514r.2857c>t0.182
rrl1476515r.2858c>t0.296
rrl1476519r.2862c>g0.151
rrl1476524r.2867c>t0.273
rrl1476525r.2868a>g0.358
rrl1476530r.2873c>t0.231
rrl1476536r.2879g>a0.340
rrl1476538r.2881a>g0.216
rrl1476539r.2882a>g0.240
rrl1476540r.2883c>g0.320
rrl1476547r.2890c>t0.220
rrl1476567r.2910c>t0.163
rrl1476584r.2927c>t0.186
rrl1476585r.2928a>g0.140
rrl1476594r.2937c>a0.140
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
ethA4327087c.387G>C1.000
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;