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: 5ddd6b75aa3b3
Sample: 5ddd6b75aa3b3

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Summary
ID: 5ddd6b75aa3b3
Date: Tue Nov 26 18:15:41 2019
Strain: lineage4
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8147p.Asn282Lys0.986
gyrA9304p.Gly668Asp1.000
rpsL781395c.-165T>C1.000
embR1416904c.443 443del1.000
rrs1471896r.51t>c0.155
rrs1471900r.55c>t0.155
rrs1472127r.282c>t0.216
rrs1472129r.284g>c0.211
rrs1472137r.292g>a0.240
rrs1472150r.305t>a0.214
rrs1472151r.306c>t0.214
rrs1472172r.327t>c0.198
rrs1472203r.358g>a0.168
rrs1472591r.746g>a0.118
rrs1472616r.771g>a0.113
rrs1472744r.899a>g0.126
rrs1472803r.958t>a0.128
rrs1472895r.1050c>t0.216
rrs1472957r.1112c>t0.115
rrs1472977r.1132g>t0.111
rrs1472982r.1137g>c0.120
rrs1473002r.1157g>t0.136
rrs1473004r.1159t>a0.123
rrs1473008r.1163c>a0.136
rrs1473009r.1164t>c0.136
rrs1473035r.1190g>a0.182
rrs1473053r.1208t>a0.182
rrs1473056r.1211a>t0.173
rrs1473062r.1217t>a0.173
rrs1473068r.1223a>g0.150
rrs1473080r.1235c>g0.111
rrs1473081r.1236c>t0.125
rrs1473192r.1347a>g0.115
rrs1473202r.1357c>t0.130
rrs1473205r.1360t>c0.120
rrs1473352r.1507c>t0.203
rrl1474747r.1090c>a0.156
rrl1474823r.1166c>g0.118
rrl1474827r.1170c>t0.120
rrl1474830r.1173a>t0.122
rrl1474831r.1174a>t0.122
rrl1474844r.1187g>t0.151
rrl1474866r.1209c>a0.170
rrl1474869r.1212g>t0.189
rrl1474896r.1239a>g0.184
rrl1474902r.1245t>c0.188
rrl1474904r.1247g>c0.188
rrl1474905r.1248t>c0.193
rrl1474913r.1256t>a0.190
rrl1474920r.1263g>a0.190
rrl1475687r.2030c>t0.145
rrl1475688r.2031g>c0.148
rrl1475696r.2039t>c0.149
rrl1475703r.2046a>g0.155
rrl1475707r.2050t>a0.149
rrl1475713r.2056c>g0.165
rrl1475716r.2059a>g0.186
rrl1475803r.2146t>c0.227
rrl1475804r.2147g>c0.211
rrl1475816r.2159c>g0.182
rrl1475817r.2160a>g0.177
rrl1475858r.2201t>c0.151
rrl1475866r.2209t>a0.149
rrl1476141r.2484a>g0.265
rrl1476153r.2496t>c0.271
rrl1476165r.2508t>a0.292
rrl1476194r.2537a>g0.154
rrl1476195r.2538c>a0.154
rrl1476196r.2539c>a0.150
rrl1476200r.2543a>t0.150
rrl1476201r.2544c>t0.150
rrl1476204r.2547c>a0.150
rrl1476210r.2553g>t0.133
rrl1476211r.2554g>t0.133
rrl1476212r.2555t>c0.136
rrl1476214r.2557g>t0.136
rrl1476215r.2558c>a0.174
rrl1476225r.2568t>g0.269
rrl1476251r.2594t>c0.250
rrl1476260r.2603a>g0.241
rrl1476280r.2623a>c0.232
rrl1476293r.2636c>t0.170
rrl1476294r.2637a>g0.170
rrl1476295r.2638c>g0.173
rrl1476296r.2639c>t0.173
rrl1476297r.2640c>t0.173
rrl1476301r.2644a>c0.173
rrl1476302r.2645g>a0.164
rrl1476311r.2654g>c0.164
rrl1476312r.2655t>c0.164
rrl1476313r.2656g>a0.164
rrl1476332r.2675g>c0.217
rrl1476353r.2696g>t0.186
rrl1476358r.2701t>c0.215
rrl1476372r.2715t>c0.238
rrl1476382r.2725a>g0.258
rrl1476383r.2726t>a0.258
rrl1476408r.2751g>a0.233
rrl1476425r.2768g>t0.250
rrl1476428r.2771c>t0.254
rrl1476429r.2772a>c0.254
rrl1476466r.2809c>t0.297
rrl1476481r.2824t>c0.243
rrl1476506r.2849t>c0.254
rrl1476514r.2857c>t0.194
rrl1476517r.2860c>t0.194
rrl1476519r.2862c>g0.194
rrl1476524r.2867c>a0.190
rrl1476525r.2868a>g0.190
rrl1476530r.2873c>t0.190
rrl1476536r.2879g>a0.190
rrl1476537r.2880a>g0.194
rrl1476538r.2881a>g0.190
rrl1476540r.2883c>g0.188
rrl1476547r.2890c>t0.235
rrl1476567r.2910c>t0.235
rrl1476573r.2916a>c0.212
rrl1476577r.2920t>g0.212
rrl1476584r.2927c>t0.209
tlyA1917972c.33A>G1.000
alr3841652c.-232A>T0.219
alr3841654c.-234A>C0.227
alr3841662c.-242A>G0.315
alr3841663c.-243G>A0.279
embC4242643c.2781C>T1.000
ethA4327376p.Ala33Gly1.000

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;