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: 5cc54fce6c8c4
Sample: 5cc54fce6c8c4

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Summary
ID: 5cc54fce6c8c4
Date: Sun Apr 28 08:04:50 2019
Strain: lineage2.2.1
Drug-resistance: Sensitive

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

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
rrs1471896r.51t>c0.978
rrs1471900r.55c>t0.978
rrs1472102r.257g>a0.200
rrs1472106r.261g>a0.200
rrs1472127r.282c>t0.750
rrs1472129r.284g>c0.760
rrs1472137r.292g>a0.818
rrs1472150r.305t>a0.818
rrs1472151r.306c>a0.824
rrs1472172r.327t>c0.875
rrs1472203r.358g>a0.913
rrs1472344r.499c>t0.727
rrs1472379r.534t>g0.741
rrs1472382r.537g>a0.741
rrs1472400r.555c>t0.714
rrs1472557r.712g>a0.840
rrs1472570r.725g>a0.857
rrs1472571r.726g>c0.889
rrs1472581r.736a>t0.956
rrs1472598r.753a>c0.941
rrs1472616r.771g>a0.941
rrs1472713r.868t>c0.688
rrs1472715r.870c>t0.688
rrs1472716r.871c>t0.706
rrs1472744r.899a>g0.944
rrs1472767r.922g>a0.943
rrs1472779r.934g>a0.923
rrs1472781r.936c>t0.935
rrs1472786r.941c>t0.927
rrs1472793r.948a>t0.902
rrs1472803r.958t>a0.956
rrs1472895r.1050c>t0.929
rrs1472954r.1109t>a0.762
rrs1472957r.1112c>t0.688
rrs1472958r.1113a>t0.688
rrs1472959r.1114t>a0.688
rrs1472970r.1125c>g0.636
rrs1472975r.1130t>g0.733
rrs1472977r.1132g>c0.636
rrs1472982r.1137g>c0.733
rrs1472987r.1142g>t0.846
rrs1472988r.1143t>a0.846
rrs1472992r.1147a>t0.846
rrs1473002r.1157g>t0.800
rrs1473004r.1159t>a0.800
rrs1473008r.1163c>a0.800
rrs1473009r.1164t>c0.800
rrs1473035r.1190g>a0.824
rrs1473053r.1208t>a0.737
rrs1473056r.1211a>t0.688
rrs1473062r.1217t>a0.688
rrs1473068r.1223a>g0.692
rrs1473070r.1225g>a0.692
rrs1473089r.1244a>c0.692
rrs1473093r.1248c>a0.692
rrs1473094r.1249t>a0.692
rrs1473099r.1254t>a0.692
rrs1473110r.1265t>g0.643
rrs1473111r.1266a>g0.643
rrs1473122r.1277t>g0.545
rrs1473352r.1507c>t0.900
rrl1473384c.-274A>T0.733
rrl1474777r.1120t>c0.667
rrl1474779r.1122g>a0.727
rrl1474780r.1123c>t0.667
rrl1474782r.1125g>a0.667
rrl1474790r.1133c>t0.850
rrl1474798r.1141c>t0.880
rrl1474804r.1147c>t0.893
rrl1474823r.1166c>g0.900
rrl1474827r.1170c>t0.905
rrl1474831r.1174a>c0.886
rrl1474844r.1187g>t0.909
rrl1474866r.1209c>a0.926
rrl1474869r.1212g>t0.926
rrl1474896r.1239a>g0.919
rrl1474902r.1245t>c0.903
rrl1474904r.1247g>c0.900
rrl1474913r.1256t>a0.871
rrl1474920r.1263g>a0.839
rrl1475672r.2015c>g0.857
rrl1475673r.2016t>c0.857
rrl1475687r.2030c>t0.800
rrl1475696r.2039t>c0.750
rrl1475703r.2046a>g0.750
rrl1475707r.2050t>a0.750
rrl1475716r.2059a>g0.846
rrl1475747r.2090a>g0.500
rrl1475803r.2146t>c0.786
rrl1475804r.2147g>c0.786
rrl1475816r.2159c>g0.786
rrl1475817r.2160a>g0.786
rrl1475843r.2186g>a0.688
rrl1475849r.2192g>a0.688
rrl1475853r.2196c>t0.688
rrl1475858r.2201t>c0.688
rrl1476332r.2675g>c0.885
rrl1476338r.2681c>t0.893
rrl1476353r.2696g>t0.889
rrl1476358r.2701t>c0.911
rrl1476372r.2715t>c0.925
rrl1476382r.2725a>g0.929
rrl1476383r.2726t>a0.912
rrl1476408r.2751g>a0.910
rrl1476425r.2768g>a0.917
rrl1476428r.2771c>t0.917
rrl1476466r.2809c>t0.925
rrl1476481r.2824t>c0.918
rrl1476506r.2849t>c0.854
rrl1476512r.2855c>t0.400

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;