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: 5d16420778a14
Sample: 5d16420778a14

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Summary
ID: 5d16420778a14
Date: Fri Jun 28 17:37:17 2019
Strain: lineage4.2.1
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
Rifampicin
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.19)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.12)
CapreomycinRrrs r.1402c>a (0.12)
KanamycinRrrs r.1402c>a (0.12)

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.1Euro-American (TUR)H3;H4None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpsL781395c.-165T>C1.000
rrs1472150r.305t>a0.189
rrs1472172r.327t>c0.258
rrs1472203r.358g>a0.123
rrs1472251r.406g>a0.137
rrs1472253r.408g>t0.132
rrs1472517r.672t>a0.119
rrs1472518r.673g>t0.123
rrs1472530r.685g>a0.159
rrs1472537r.692c>t0.156
rrs1472544r.699c>a0.143
rrs1472545r.700a>t0.137
rrs1472566r.721g>a0.145
rrs1472571r.726g>c0.191
rrs1472579r.734g>t0.176
rrs1472581r.736a>t0.297
rrs1472598r.753a>c0.205
rrs1472599r.754g>t0.176
rrs1472616r.771g>a0.132
rrs1472655r.810g>a0.149
rrs1472713r.868t>c0.125
rrs1472742r.897c>t0.308
rrs1472744r.899a>g0.239
rrs1472781r.936c>t0.314
rrs1472793r.948a>t0.282
rrs1472803r.958t>a0.152
rrs1472828r.983t>c0.120
rrs1472895r.1050c>t0.236
rrs1472957r.1112c>t0.123
rrs1472973r.1128a>t0.169
rrs1473035r.1190g>a0.301
rrs1473055r.1210c>t0.178
rrs1473056r.1211a>t0.230
rrs1473066r.1221a>g0.161
rrs1473088r.1243a>g0.149
rrs1473100r.1255g>a0.125
rrs1473102r.1257c>t0.125
rrs1473104r.1259c>t0.125
rrs1473110r.1265t>g0.119
rrs1473111r.1266a>g0.119
rrs1473121r.1276t>c0.143
rrs1473145r.1300c>t0.174
rrs1473163r.1318c>t0.118
rrs1473166r.1321g>a0.239
rrs1473177r.1332g>a0.118
rrs1473252r.1407t>c0.143
rrs1473259r.1414c>t0.155
rrs1473276r.1431a>g0.151
rrs1473314r.1469a>c0.200
rrl1474197r.540c>t0.133
rrl1474199r.542g>a0.135
rrl1474218r.561t>a0.219
rrl1474228r.571t>c0.164
rrl1474249r.592g>t0.277
rrl1474252r.595t>a0.169
rrl1474269r.612c>t0.146
rrl1474275r.618t>g0.162
rrl1474280r.623c>t0.132
rrl1474281r.624a>g0.158
rrl1474310r.653t>g0.132
rrl1474316r.659t>c0.175
rrl1474317r.660g>a0.125
rrl1474351r.694g>t0.114
rrl1474362r.705a>g0.136
rrl1474516r.859c>a0.205
rrl1474529r.872a>c0.133
rrl1474530r.873g>a0.133
rrl1474537r.880g>a0.125
rrl1474558r.901g>a0.220
rrl1474584r.927c>t0.222
rrl1474627r.970g>a0.160
rrl1474632r.975g>t0.115
rrl1474636r.979a>t0.140
rrl1474637r.980c>t0.120
rrl1474638r.981c>g0.137
rrl1474639r.982g>c0.118
rrl1474672r.1015c>t0.115
rrl1474677r.1020a>g0.115
rrl1474794r.1137c>t0.135
rrl1474864r.1207c>t0.143
rrl1474883r.1226t>c0.182
rrl1474932r.1275c>t0.118
rrl1475129r.1472g>t0.154
rrl1475171r.1514c>t0.133
rrl1475673r.2016t>c0.130
rrl1475699r.2042c>t0.130
rrl1475722r.2065g>t0.138
rrl1475775r.2118g>t0.148
rrl1475783r.2126t>g0.133
rrl1475803r.2146t>c0.184
rrl1475804r.2147g>c0.182
rrl1475816r.2159c>g0.148
rrl1475817r.2160a>g0.150
rrl1475858r.2201t>c0.139
rrl1475866r.2209t>a0.160
rrl1475869r.2212c>a0.141
rrl1475881r.2224t>c0.123
rrl1475883r.2226a>t0.137
rrl1475898r.2241a>g0.135
rrl1475899r.2242g>a0.122
rrl1475916r.2259c>g0.177
rrl1475943r.2286g>a0.164
rrl1475952r.2295a>g0.170
rrl1475970r.2313c>t0.143
rrl1475975r.2318c>t0.128
rrl1476030r.2373a>g0.125
rrl1476032r.2375c>a0.125
rrl1476034r.2377c>g0.128
rrl1476040r.2383c>t0.128
rrl1476045r.2388g>t0.125
rrl1476047r.2390g>t0.125
rrl1476049r.2392c>t0.128
rrl1476115r.2458t>c0.113
rrl1476164r.2507a>g0.141
rrl1476194r.2537a>g0.195
rrl1476200r.2543a>t0.162
rrl1476201r.2544c>t0.149
rrl1476214r.2557g>t0.171
rrl1476215r.2558c>t0.171
rrl1476224r.2567a>g0.139
rrl1476245r.2588c>t0.114
rrl1476252r.2595t>g0.233
rrl1476256r.2599a>g0.225
rrl1476260r.2603a>g0.310
rrl1476280r.2623a>c0.186
rrl1476281r.2624t>c0.143
rrl1476293r.2636c>t0.172
rrl1476294r.2637a>g0.281
rrl1476295r.2638c>g0.258
rrl1476296r.2639c>t0.281
rrl1476301r.2644a>t0.188
rrl1476311r.2654g>c0.274
rrl1476312r.2655t>c0.328
rrl1476313r.2656g>a0.213
rrl1476332r.2675g>c0.289
rrl1476338r.2681c>t0.286
rrl1476353r.2696g>t0.219
rrl1476358r.2701t>c0.293
rrl1476369r.2712c>t0.195
rrl1476372r.2715t>c0.181
rrl1476381r.2724g>c0.117
rrl1476382r.2725a>g0.240
rrl1476383r.2726t>a0.233
rrl1476408r.2751g>a0.127
rrl1476411r.2754g>a0.113
rrl1476425r.2768g>a0.145
rrl1476428r.2771c>t0.316
rrl1476429r.2772a>c0.203
rrl1476463r.2806c>t0.149
rrl1476466r.2809c>t0.270
rrl1476481r.2824t>c0.442
rrl1476506r.2849t>c0.420
rrl1476515r.2858c>t0.243
rrl1476524r.2867c>t0.189
rrl1476525r.2868a>g0.268
rrl1476530r.2873c>t0.205
rrl1476536r.2879g>a0.179
rrl1476539r.2882a>g0.154
rrl1476540r.2883c>g0.162
rrl1476547r.2890c>t0.125
fabG11673380c.-60C>G0.176
folC2747536c.63C>T1.000
ald3086788c.-32T>C1.000
ald3087168p.Tyr117His0.310
alr3841662c.-242A>G0.404
alr3841663c.-243G>A0.263
embC4242643c.2781C>T1.000
embB4249594c.3081G>A1.000

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;