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: 5d30f471c10b7
Sample: 5d30f471c10b7

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Summary
ID: 5d30f471c10b7
Date: Thu Jul 18 23:38:01 2019
Strain: lineage4.4.2
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpsL781395c.-165T>C1.000
rrs1471896r.51t>c0.361
rrs1471900r.55c>t0.345
rrs1472094r.249t>a0.123
rrs1472106r.261g>a0.291
rrs1472108r.263c>t0.128
rrs1472113r.268t>c0.299
rrs1472127r.282c>t0.373
rrs1472129r.284g>c0.364
rrs1472137r.292g>a0.376
rrs1472150r.305t>a0.412
rrs1472151r.306c>a0.412
rrs1472172r.327t>c0.458
rrs1472203r.358g>a0.378
rrs1472210r.365a>c0.330
rrs1472213r.368g>c0.330
rrs1472215r.370a>g0.330
rrs1472225r.380c>a0.318
rrs1472234r.389t>c0.282
rrs1472236r.391c>g0.273
rrs1472240r.395g>a0.269
rrs1472344r.499c>t0.482
rrs1472379r.534t>g0.438
rrs1472382r.537g>a0.438
rrs1472400r.555c>t0.438
rrs1472507r.662c>g0.212
rrs1472517r.672t>a0.246
rrs1472518r.673g>c0.239
rrs1472530r.685g>a0.329
rrs1472537r.692c>t0.333
rrs1472544r.699c>g0.360
rrs1472545r.700a>t0.360
rrs1472557r.712g>a0.400
rrs1472570r.725g>a0.415
rrs1472571r.726g>c0.415
rrs1472581r.736a>t0.468
rrs1472598r.753a>c0.458
rrs1472616r.771g>a0.475
rrs1472734r.889c>t0.264
rrs1472741r.896g>a0.264
rrs1472744r.899a>g0.262
rrs1472767r.922g>a0.257
rrs1472779r.934g>a0.264
rrs1472781r.936c>t0.267
rrs1472786r.941c>t0.275
rrs1472793r.948a>t0.275
rrs1472803r.958t>a0.295
rrs1472895r.1050c>t0.471
rrs1472970r.1125c>g0.114
rrs1472977r.1132g>c0.115
rrs1472982r.1137g>c0.111
rrs1472987r.1142g>t0.117
rrs1472988r.1143t>a0.117
rrs1472991r.1146g>a0.118
rrs1472992r.1147a>t0.118
rrs1473002r.1157g>t0.122
rrs1473004r.1159t>a0.123
rrs1473008r.1163c>a0.123
rrs1473009r.1164t>c0.125
rrs1473020r.1175t>c0.122
rrs1473035r.1190g>a0.136
rrs1473352r.1507c>t0.394
rrl1474777r.1120t>c0.280
rrl1474779r.1122g>a0.284
rrl1474780r.1123c>t0.284
rrl1474782r.1125g>a0.305
rrl1474790r.1133c>t0.372
rrl1474798r.1141c>t0.402
rrl1474804r.1147c>t0.427
rrl1474823r.1166c>g0.455
rrl1474827r.1170c>t0.455
rrl1474831r.1174a>c0.459
rrl1474844r.1187g>t0.479
rrl1474866r.1209c>a0.492
rrl1474869r.1212g>t0.487
rrl1474896r.1239a>g0.455
rrl1474902r.1245t>c0.457
rrl1474904r.1247g>c0.463
rrl1474913r.1256t>a0.432
rrl1474920r.1263g>a0.453
rrl1475803r.2146t>c0.333
rrl1475804r.2147g>c0.333
rrl1475816r.2159c>g0.318
rrl1475817r.2160a>g0.318
rrl1475843r.2186g>a0.344
rrl1475849r.2192g>a0.350
rrl1475853r.2196c>t0.350
rrl1475858r.2201t>c0.328
rrl1476221r.2564t>c0.133
rrl1476225r.2568t>g0.133
rrl1476229r.2572c>t0.156
rrl1476251r.2594t>c0.220
rrl1476260r.2603a>g0.233
rrl1476280r.2623a>c0.256
rrl1476293r.2636c>t0.244
rrl1476294r.2637a>g0.244
rrl1476295r.2638c>g0.244
rrl1476296r.2639c>t0.227
rrl1476297r.2640c>a0.227
rrl1476301r.2644a>c0.213
rrl1476302r.2645g>a0.213
rrl1476311r.2654g>c0.222
rrl1476312r.2655t>c0.222
rrl1476313r.2656g>a0.222
rrl1476332r.2675g>c0.507
rrl1476338r.2681c>t0.486
rrl1476353r.2696g>t0.507
rrl1476358r.2701t>c0.532
rrl1476372r.2715t>c0.541
rrl1476382r.2725a>g0.552
rrl1476383r.2726t>a0.552
rrl1476408r.2751g>a0.600
rrl1476425r.2768g>a0.562
rrl1476428r.2771c>t0.586
rrl1476466r.2809c>t0.559
rrl1476481r.2824t>c0.500
rrl1476506r.2849t>c0.444
rrl1476512r.2855c>t0.143
rrl1476514r.2857c>t0.122
rrl1476517r.2860c>t0.122
rrl1476519r.2862c>g0.122
rrl1476524r.2867c>a0.125
rrl1476525r.2868a>g0.125
rrl1476530r.2873c>t0.122
rrl1476536r.2879g>a0.125
rrl1476537r.2880a>g0.125
rrl1476538r.2881a>g0.122
rrl1476540r.2883c>g0.122
rrl1476547r.2890c>t0.116
rrl1476567r.2910c>t0.125
rrl1476573r.2916a>t0.128
rrl1476577r.2920t>g0.132
tlyA1917972c.33A>G1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.234
alr3841654c.-234A>C0.255
alr3841662c.-242A>G0.298
alr3841663c.-243G>A0.304
embC4242643c.2781C>T1.000
embA4246508c.3276G>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;