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: 5dc3403e704f2
Sample: 5dc3403e704f2

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Summary
ID: 5dc3403e704f2
Date: Wed Nov 6 21:53:31 2019
Strain: lineage1.1;lineage1.1.2
Drug-resistance: Sensitive

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

Lineage2FamilyMain SpoligotypeRDS
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7394c.93T>C0.182
gyrA7397c.96G>C0.182
gyrA7406c.105G>A0.182
gyrA7415c.114C>T0.167
gyrA7418c.117C>T0.167
gyrA7623p.Pro108Met0.800
gyrA7631c.330G>C0.852
gyrA7850c.549C>G0.618
gyrA7859c.558A>G0.600
gyrA8964p.Val555Phe0.200
rpoB761126c.1320G>T0.756
rpoB761131p.Gly442Glu0.775
rpoB761133p.Leu443Ile0.811
rpoB761573c.1767C>G0.872
rpoB761579c.1773G>T0.872
rpoB762779p.Asp991Glu0.759
rpoB762878p.Ile1024Met0.868
rpoB762879p.Met1025Leu0.868
rpoB762888p.His1028Asn0.868
rpoB762899c.3093G>C0.912
rpoB762905c.3099C>T0.906
rpoB762911p.Ile1035Met0.848
rpoB762917c.3111C>A0.833
rpoB762920c.3114C>T0.821
rpoB762989c.3183G>T0.400
rpoC764701c.1332C>G0.907
rpoC764705p.Leu446Lys0.907
rpoC764713c.1344G>T0.907
rpoC764716c.1347G>C0.907
rpoC764863c.1494G>T0.500
rpoC764875c.1506C>G0.529
rpoC764878c.1509C>G0.529
rpoC764887c.1518G>T0.529
rpoC764888c.1519T>C0.529
rpoC764902c.1533C>G0.500
rpoC764911c.1542A>C0.500
rpoC764912p.Met515Val0.500
rpoC764918p.Val517Ile0.500
rpoC764926c.1557C>T0.500
rpoC764932c.1563C>G0.526
rpoC764941c.1572G>C0.550
rpoC764944c.1575C>T0.550
rpoC764953c.1584G>C0.500
rpoC764956c.1587T>C0.500
rpoC764958p.Glu530Ala0.500
rpoC764962c.1593G>A0.500
rpoC764964p.Phe532Tyr0.500
rpoC764968c.1599T>C0.500
rpoC764989c.1620G>A0.652
rpoC765171p.Pro601Leu1.000
rpsL781395c.-165T>C1.000
rpsL781682c.123T>G0.800
rpsL781685c.126G>T0.800
rpsL781691c.132G>A0.792
rplC801350181L>181*0.200
embR1416222p.Phe376Leu0.500
embR1416234p.Cys372Gly0.500
embR1417320c.28G>T0.200
rrs1471764c.-82C>A0.200
rrs1471786c.-60T>A0.200
rrs1471867r.22c>a0.333
rrs1471876r.31g>a0.333
rrs1471877r.32a>t0.333
rrs1471878r.33c>t0.333
rrs1471892r.47g>a0.348
rrs1471893r.48t>g0.348
rrs1471896r.51t>c0.348
rrs1472164r.319g>a0.943
rrs1472172r.327t>c0.944
rrs1472177r.332c>t0.931
rrs1472214r.369c>g0.922
rrs1472225r.380c>a0.919
rrs1472235r.390g>c0.910
rrs1472240r.395g>c0.906
rrs1472242r.397c>t0.905
rrs1472344r.499c>t0.953
rrs1472349r.504a>t0.962
rrs1472374r.529t>a0.965
rrs1472382r.537g>a0.982
rrs1472389r.544g>a0.981
rrs1472390r.545t>a0.981
rrs1472391r.546c>t0.981
rrs1472412r.567a>c0.965
rrs1472415r.570t>g0.964
rrs1472591r.746g>a0.954
rrs1472598r.753a>t0.958
rrs1472616r.771g>a0.954
rrs1472655r.810g>a0.901
rrs1472658r.813g>t0.897
rrs1472659r.814g>c0.897
rrs1472660r.815t>g0.897
rrs1472678r.833t>a0.896
rrs1472685r.840g>a0.870
rrs1472690r.845c>a0.870
rrs1472694r.849c>g0.884
rrs1472697r.852t>c0.886
rrs1472714r.869a>c0.965
rrs1472715r.870c>g0.951
rrs1472716r.871c>a0.951
rrs1472742r.897c>t0.956
rrs1472754r.909g>t0.957
rrs1472781r.936c>t0.966
rrs1472793r.948a>t0.957
rrs1472803r.958t>a0.955
rrs1472824r.979t>a0.812
rrs1472827r.982g>c0.800
rrs1472828r.983t>c0.800
rrs1472839r.994c>g0.750
rrs1472842r.997g>a0.731
rrs1472846r.1001c>t0.731
rrs1472847r.1002g>t0.731
rrs1472850r.1005t>c0.731
rrs1472857r.1012a>g0.760
rrs1472866r.1021c>a0.760
rrs1472870r.1025t>g0.680
rrs1472871r.1026g>t0.739
rrs1472876r.1031g>t0.760
rrs1472877r.1032t>c0.760
rrs1472879r.1034t>g0.760
rrs1472887r.1042g>c0.950
rrs1472936r.1091c>t0.965
rrs1472956r.1111t>c0.938
rrs1472957r.1112c>t0.938
rrs1472958r.1113a>t0.938
rrs1472959r.1114t>a0.960
rrs1472963r.1118g>a0.962
rrs1472982r.1137g>c0.976
rrs1472987r.1142g>t0.975
rrs1472988r.1143t>a0.975
rrs1472989r.1144g>a0.975
rrs1472990r.1145a>g0.975
rrs1473002r.1157g>t0.967
rrs1473004r.1159t>a0.967
rrs1473008r.1163c>a0.967
rrs1473009r.1164t>c0.967
rrs1473044r.1199c>g0.974
rrs1473051r.1206t>c0.971
rrs1473053r.1208t>g0.971
rrs1473056r.1211a>t0.971
rrs1473062r.1217t>a0.971
rrs1473068r.1223a>g0.970
rrs1473080r.1235c>t0.968
rrs1473093r.1248c>t0.964
rrs1473097r.1252g>c0.963
rrs1473099r.1254t>a0.963
rrs1473110r.1265t>g0.941
rrs1473111r.1266a>g0.941
rrs1473115r.1270g>t0.928
rrs1473121r.1276t>c0.914
rrs1473122r.1277t>a0.928
rrs1473123r.1278a>t0.928
rrs1473127r.1282g>a0.928
rrs1473131r.1286g>a0.928
rrs1473134r.1289t>g0.928
rrs1473135r.1290c>t0.928
rrs1473139r.1294t>c0.930
rrs1473147r.1302g>c0.930
rrs1473148r.1303g>a0.930
rrs1473163r.1318c>t0.935
rrs1473164r.1319c>g0.935
rrs1473177r.1332g>a0.935
rrs1473191r.1346c>t0.875
rrs1473192r.1347a>g0.875
rrs1473193r.1348g>a0.875
rrs1473202r.1357c>t0.872
rrs1473204r.1359c>t0.872
rrs1473205r.1360t>c0.872
rrs1473206r.1361g>a0.872
rrs1473352r.1507c>g0.952
rrs1473353r.1508c>g0.952
rrs1473358r.1513g>c0.952
rrs1473359r.1514g>c0.930
rrl1474573r.916c>t0.769
rrl1474580r.923a>g0.714
rrl1474584r.927c>g0.667
rrl1474586r.929t>a0.667
rrl1474602r.945c>t0.667
rrl1474738r.1081g>t0.200
rrl1474869r.1212g>t0.948
rrl1474875r.1218g>a0.932
rrl1474876r.1219t>a0.932
rrl1474892r.1235g>a0.167
rrl1475136r.1479g>t0.615
rrl1475137r.1480a>c0.615
rrl1475151r.1494c>t0.667
rrl1475154r.1497c>a0.667
rrl1475155r.1498a>g0.667
rrl1475156r.1499g>a0.667
rrl1475170r.1513a>g0.789
rrl1475171r.1514c>a0.789
rrl1475180r.1523g>a0.789
rrl1475517r.1860c>t0.973
rrl1475518r.1861a>g0.973
rrl1475526r.1869c>a0.972
rrl1475538r.1881t>c0.954
rrl1475539r.1882a>t0.953
rrl1475540r.1883c>t0.953
rrl1475545r.1888t>g0.965
rrl1475550r.1893a>c0.965
rrl1475551r.1894t>g0.965
rrl1475555r.1898t>g0.919
rrl1475564r.1907c>a0.971
rrl1475574r.1917c>g0.972
rrl1475576r.1919c>a0.964
rrl1475791r.2134a>g0.914
rrl1475803r.2146t>c0.908
rrl1475804r.2147g>c0.909
rrl1475816r.2159c>g0.922
rrl1475817r.2160a>g0.922
rrl1476141r.2484a>g0.765
rrl1476153r.2496t>c0.684
rrl1476154r.2497g>t0.722
rrl1476164r.2507a>g0.765
rrl1476165r.2508t>a0.765
rrl1476336r.2679c>t0.974
rrl1476356r.2699c>a0.970
rrl1476357r.2700t>c0.969
rrl1476358r.2701t>c0.969
rrl1476359r.2702c>g0.970
rrl1476369r.2712c>t0.971
rrl1476381r.2724g>c0.990
rrl1476382r.2725a>g0.990
rrl1476383r.2726t>g0.990
rrl1476384r.2727g>t0.990
rrl1476408r.2751g>a1.000
rrl1476411r.2754g>a1.000
rrl1476425r.2768g>a1.000
rrl1476429r.2772a>c1.000
rrl1476442r.2785t>a0.986
rrl1476443r.2786g>t0.986
rrl1476455r.2798c>a0.993
rrl1476456r.2799a>t0.993
rrl1476463r.2806c>t0.993
rrl1476466r.2809c>t0.993
rrl1476506r.2849t>c0.974
rrl1476565r.2908g>a0.333
rrl1476566r.2909a>g0.333
rrl1476567r.2910c>t0.333
inhA1674310p.Val37Leu0.182
rpsA1834309p.Asp256Glu0.200
rpsA1834379p.Gln280Lys0.200
katG2154724p.Arg463Leu1.000
katG2155410c.702C>G0.840
katG2155413c.699C>T0.840
katG2155433c.679G>A0.826
katG2155434c.678C>G0.826
pncA2289269c.-28G>T0.200
kasA2518132c.18C>T1.000
eis2714987p.Ala116Ser0.182
eis2715108c.225C>A0.200
thyA3074414p.Asp20Tyr0.200
thyA3074426p.Thr16Ala0.200
ald3086788c.-32T>C1.000
fbiA3641384p.Ala281Asp0.200
alr3841507c.-87C>A0.200
embC4242057p.Pro732Leu0.200
embC4242643c.2781C>T0.244
embA4245884c.2652C>A0.200
embB4246837p.Asp108Glu0.200
ethA4326121c.1353C>A0.200
gid4407588c.615T>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;