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: 5cc554b11888e
Sample: 5cc554b11888e

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Summary
ID: 5cc554b11888e
Date: Sun Apr 28 08:25:39 2019
Strain: lineage4.3.1;lineage3.1.2.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage4.3.1Euro-American (LAM)LAM9None
lineage3.1.2.2East-African-IndianCASRD750

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7412c.111C>G1.000
gyrA7442c.141G>C1.000
gyrA7480p.Phe60Tyr1.000
gyrA7484c.183T>C1.000
gyrA7499c.198G>C1.000
gyrA7526c.225G>C1.000
gyrA7532c.231T>G1.000
gyrA7541c.240C>G1.000
gyrA7547c.246C>T0.909
rpoB760235c.429T>C1.000
rpoB760244c.438G>C1.000
rpoB760457c.651C>T1.000
rpoB760463c.657C>T1.000
rpoB761579c.1773G>C1.000
rpoB761588p.Asp594Glu0.200
rpoB761600c.1794T>C1.000
rpoB761606c.1800C>G1.000
rpoB761612c.1806G>T1.000
rpoB761615c.1809A>C1.000
rpoB761636c.1830G>T1.000
rpoB761645c.1839C>G1.000
rpoB762995c.3189G>T1.000
rpoB763004c.3198G>A1.000
rpoB763007c.3201C>T1.000
rpoC764575c.1206T>G1.000
rpoC764605c.1236G>C1.000
rpoC764611c.1242G>T0.909
rpoC764650c.1281G>T1.000
rpoC764701c.1332C>G1.000
rpoC764707c.1338G>C1.000
rpoC764713c.1344G>T1.000
rpoC764716c.1347G>C1.000
rpoC764746c.1377G>T1.000
rpoC764752c.1383G>C1.000
rpoC764758c.1389C>G1.000
rpoC764764c.1395T>C1.000
rpoC764809c.1440C>T1.000
rpsL781808c.249C>T1.000
rpsL781929p.Gly124Ser1.000
rrs1471922r.77gt>g1.000
rrs1471925r.80t>c1.000
rrs1471931r.86ga>g1.000
rrs1471934r.89a>g1.000
rrs1471986r.141c>t1.000
rrs1472019r.174g>a1.000
rrs1472023r.178g>t1.000
rrs1472031r.186g>c1.000
rrs1472033r.188a>c1.000
rrs1472035r.190g>t1.000
rrs1472040r.195t>g1.000
rrs1472041r.196c>t1.000
rrs1472042r.197t>g1.000
rrs1472053r.208agc>a1.000
rrs1472061r.216a>t1.000
rrs1472075r.230a>g1.000
rrs1472106r.261g>a1.000
rrs1472108r.263c>t1.000
rrs1472150r.305t>a1.000
rrs1472251r.406g>a1.000
rrs1472337r.492c>g1.000
rrs1472380r.535g>c1.000
rrs1472446r.601t>a1.000
rrs1472452r.607g>a1.000
rrs1472464r.619a>g1.000
rrs1472846r.1001c>a0.977
rrs1472847r.1002g>c0.977
rrs1472849r.1004c>g0.977
rrs1472850r.1005t>c0.977
rrs1472857r.1012a>g0.977
rrs1472858r.1013g>t0.977
rrs1472860r.1015c>g1.000
rrs1472861r.1016g>t0.978
rrs1472973r.1128a>t1.000
rrs1473104r.1259c>t1.000
rrs1473110r.1265t>g0.989
rrs1473111r.1266a>g1.000
rrs1473120r.1275c>ct0.966
rrs1473123r.1278a>c1.000
rrs1473276r.1431a>g1.000
rrs1473290r.1445c>t1.000
rrs1473291r.1446g>gt1.000
rrs1473301r.1456t>c1.000
rrl1473668r.11c>t1.000
rrl1473696r.39t>c1.000
rrl1473697r.40c>t1.000
rrl1473699r.42a>g1.000
rrl1473717r.60g>t1.000
rrl1473746r.89t>c1.000
rrl1473758r.101g>t1.000
rrl1473770r.113t>g1.000
rrl1473788r.131a>g1.000
rrl1473806r.149c>t1.000
rrl1473807r.150t>c1.000
rrl1473814r.157at>a1.000
rrl1473823r.166t>c1.000
rrl1473829r.172g>t1.000
rrl1473830r.173t>g1.000
rrl1473831r.174g>t1.000
rrl1473832r.175c>a1.000
rrl1473876r.219g>a1.000
rrl1473887r.230t>a1.000
rrl1473898r.241c>t1.000
rrl1473899r.242a>g1.000
rrl1473916r.259c>a1.000
rrl1473922r.265a>g1.000
rrl1473923r.266c>g1.000
rrl1473935r.278c>t1.000
rrl1473937r.280c>t1.000
rrl1473943r.286g>t1.000
rrl1473945r.288t>a1.000
rrl1473946r.289a>t1.000
rrl1474083r.426c>t1.000
rrl1474091r.434c>t1.000
rrl1474093r.436g>a1.000
rrl1474096r.439c>t1.000
rrl1474099r.442g>a1.000
rrl1474108r.451c>g1.000
rrl1474135r.478g>a1.000
rrl1474140r.483c>t1.000
rrl1474151r.494c>t1.000
rrl1474174r.517a>g1.000
rrl1474181r.524c>t1.000
rrl1474183r.526t>c0.981
rrl1474185r.528g>a1.000
rrl1474186r.529a>g0.981
rrl1474249r.592g>t1.000
rrl1474266r.609t>c1.000
rrl1474269r.612c>t1.000
rrl1474289r.632c>t0.969
rrl1474292r.635t>g0.969
rrl1474308r.651g>t1.000
rrl1474310r.653t>g1.000
rrl1474362r.705a>g1.000
rrl1474414r.757c>t1.000
rrl1474426r.769t>c1.000
rrl1474428r.771c>g1.000
rrl1474429r.772g>t1.000
rrl1474430r.773c>a1.000
rrl1474432r.775c>t1.000
rrl1474438r.781a>t1.000
rrl1474439r.782a>g1.000
rrl1474446r.789c>t1.000
rrl1474626r.969t>c0.962
rrl1474627r.970g>a1.000
rrl1474629r.972g>a1.000
rrl1474632r.975g>t1.000
rrl1474636r.979a>t1.000
rrl1474637r.980c>t1.000
rrl1474638r.981c>g1.000
rrl1474639r.982g>t1.000
rrl1474640r.983c>t1.000
rrl1474673r.1016t>c1.000
rrl1474676r.1019t>a1.000
rrl1474677r.1020a>g1.000
rrl1474710r.1053t>a1.000
rrl1474711r.1054g>c0.950
rrl1474712r.1055g>a0.950
rrl1474713r.1056t>a1.000
rrl1474715r.1058t>tcca1.000
rrl1474717r.1060a>g1.000
rrl1474720r.1063c>t1.000
rrl1474753r.1096a>g1.000
rrl1474760r.1103a>g1.000
rrl1474794r.1137c>t1.000
rrl1474803r.1146g>a1.000
rrl1474812r.1155g>a1.000
rrl1474830r.1173a>g1.000
rrl1474932r.1275c>t1.000
rrl1475031r.1374g>t1.000
rrl1475061r.1404c>a1.000
rrl1475062r.1405a>t1.000
rrl1475120r.1463g>t1.000
rrl1475315r.1658a>t1.000
rrl1475353r.1696a>t1.000
rrl1475354r.1697a>g1.000
rrl1475355r.1698c>t1.000
rrl1475363r.1706c>t1.000
rrl1475419r.1762c>t1.000
rrl1475429r.1772g>t1.000
rrl1475452r.1795c>a1.000
rrl1475479r.1822c>g1.000
rrl1475483r.1826c>t1.000
rrl1475505r.1848g>a1.000
rrl1475526r.1869c>a1.000
rrl1475531r.1874c>t1.000
rrl1475544r.1887a>t1.000
rrl1475545r.1888t>g0.982
rrl1475647r.1990g>c1.000
rrl1475659r.2002g>a1.000
rrl1475753r.2096c>t1.000
rrl1475762r.2105g>t0.972
rrl1475763r.2106c>t1.000
rrl1475764r.2107a>c1.000
rrl1475765r.2108a>g1.000
rrl1475775r.2118g>a1.000
rrl1475988r.2331a>g1.000
rrl1475991r.2334t>c1.000
rrl1475995r.2338g>a1.000
rrl1476030r.2373a>g1.000
rrl1476032r.2375c>a1.000
rrl1476033r.2376t>g1.000
rrl1476035r.2378g>c1.000
rrl1476044r.2387t>g1.000
rrl1476046r.2389g>t1.000
rrl1476047r.2390g>t1.000
rrl1476049r.2392c>t1.000
rrl1476088r.2431a>c1.000
rrl1476099r.2442a>g1.000
rrl1476103r.2446c>g1.000
rrl1476105r.2448g>a1.000
rrl1476106r.2449a>t1.000
rrl1476110r.2453g>c1.000
rrl1476115r.2458t>c1.000
rrl1476131r.2474c>t1.000
rrl1476160r.2503t>c1.000
rrl1476214r.2557g>t1.000
rrl1476215r.2558c>t1.000
rrl1476224r.2567a>g1.000
rrl1476251r.2594t>g1.000
rrl1476256r.2599a>t1.000
rrl1476260r.2603a>g1.000
rrl1476281r.2624t>c1.000
rrl1476297r.2640c>t1.000
rrl1476299r.2642c>t1.000
rrl1476529r.2872a>g1.000
rrl1476540r.2883c>t1.000
rrl1476583r.2926g>a1.000
rrl1476584r.2927c>t1.000
rrl1476594r.2937c>t1.000
rrl1476597r.2940g>a1.000
rrl1476603r.2946g>a1.000
rrl1476628r.2971t>a1.000
rrl1476664r.3007t>c1.000
rrl1476665r.3008t>c1.000
rrl1476674r.3017t>c1.000
rrl1476679r.3022t>c1.000
rrl1476689r.3032a>t1.000
rrl1476690r.3033c>t1.000
rrl1476693r.3036g>a1.000
rrl1476695r.3038t>a1.000
rrl1476716r.3059a>c1.000

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;