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: 5d7664c3e13d5
Sample: 5d7664c3e13d5

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Summary
ID: 5d7664c3e13d5
Date: Mon Sep 9 15:44:08 2019
Strain: lineage4.2.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (1.00)
EthambutolRembB p.Gly406Ala (1.00)
PyrazinamideRpncA p.Val155Gly (1.00)
StreptomycinRrpsL p.Lys88Thr (1.00), rrs r.799c>t (0.51)
EthionamideRethA p.Met1Arg (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA7727c.426G>C1.000
gyrA8688p.Ala463Ser1.000
gyrA9304p.Gly668Asp1.000
rpoB761489c.1683G>A1.000
rpsL781395c.-165T>C1.000
embR1416234p.Cys372Gly0.123
rrs1471896r.51t>c0.452
rrs1472127r.282c>t0.530
rrs1472128r.283g>c0.530
rrs1472138r.293c>a0.552
rrs1472147r.302g>t0.544
rrs1472150r.305t>a0.561
rrs1472151r.306c>a0.552
rrs1472160r.315c>t0.627
rrs1472172r.327t>c0.622
rrs1472207r.362a>g0.623
rrs1472222r.377g>a0.549
rrs1472223r.378c>g0.538
rrs1472225r.380c>a0.528
rrs1472228r.383g>c0.519
rrs1472229r.384c>t0.519
rrs1472240r.395g>a0.528
rrs1472251r.406g>a0.509
rrs1472256r.411t>a0.449
rrs1472262r.417c>t0.420
rrs1472263r.418c>t0.420
rrs1472269r.424g>a0.417
rrs1472338r.493a>t0.629
rrs1472344r.499c>t0.618
rrs1472379r.534t>a0.603
rrs1472382r.537g>a0.591
rrs1472396r.551a>t0.581
rrs1472405r.560c>t0.547
rrs1472517r.672t>c0.462
rrs1472530r.685g>a0.510
rrs1472537r.692c>t0.519
rrs1472541r.696t>g0.528
rrs1472545r.700a>g0.529
rrs1472557r.712g>a0.592
rrs1472571r.726g>c0.532
rrs1472573r.728c>t0.532
rrs1472574r.729t>a0.532
rrs1472581r.736a>t0.490
rrs1472582r.737g>t0.490
rrs1472598r.753a>c0.480
rrs1472599r.754g>a0.460
rrs1472607r.762g>a0.455
rrs1472612r.767g>t0.455
rrs1472616r.771g>a0.463
rrs1472655r.810g>a0.471
rrs1472658r.813g>a0.426
rrs1472659r.814g>t0.426
rrs1472715r.870c>a0.138
rrs1472719r.874g>a0.219
rrs1472742r.897c>t0.609
rrs1472744r.899a>g0.594
rrs1472779r.934g>a0.661
rrs1472781r.936c>t0.672
rrs1472786r.941c>t0.667
rrs1472793r.948a>t0.630
rrs1472803r.958t>a0.646
rrs1472895r.1050c>t0.629
rrs1473026r.1181t>c0.297
rrs1473035r.1190g>a0.316
rrs1473047r.1202c>t0.268
rrs1473053r.1208t>a0.310
rrs1473056r.1211a>t0.293
rrs1473062r.1217t>a0.286
rrs1473068r.1223a>g0.275
rrs1473070r.1225g>a0.275
rrs1473192r.1347a>g0.185
rrs1473198r.1353g>t0.200
rrs1473202r.1357c>t0.200
rrs1473205r.1360t>c0.208
rrs1473248r.1403g>a0.268
rrs1473249r.1404t>c0.275
rrs1473254r.1409a>g0.268
rrs1473255r.1410a>g0.268
rrs1473258r.1413t>c0.275
rrs1473265r.1420c>t0.268
rrs1473274r.1429c>t0.256
rrs1473279r.1434g>a0.250
rrs1473289r.1444t>a0.200
rrs1473290r.1445c>a0.196
rrs1473298r.1453a>c0.239
rrs1473303r.1458t>c0.250
rrs1473311r.1466g>a0.250
rrs1473316r.1471c>t0.255
rrs1473322r.1477t>c0.288
rrs1473327r.1482a>g0.269
rrs1473328r.1483c>t0.269
rrs1473352r.1507c>t0.486
rrl1473899r.242a>t0.556
rrl1473923r.266c>g0.552
rrl1473928r.271t>c0.517
rrl1474228r.571t>g0.160
rrl1474812r.1155g>a0.200
rrl1474823r.1166c>g0.233
rrl1474824r.1167a>g0.233
rrl1474827r.1170c>t0.226
rrl1474831r.1174a>c0.226
rrl1474844r.1187g>t0.250
rrl1474866r.1209c>a0.219
rrl1474869r.1212g>a0.219
rrl1474896r.1239a>g0.353
rrl1475498r.1841c>g0.273
rrl1475571r.1914a>t0.455
rrl1475574r.1917c>a0.435
rrl1475586r.1929c>a0.381
rrl1475591r.1934g>a0.400
rrl1475672r.2015c>g0.469
rrl1475673r.2016t>c0.484
rrl1475687r.2030c>t0.500
rrl1475688r.2031g>c0.500
rrl1475692r.2035g>c0.500
rrl1475695r.2038g>a0.500
rrl1475704r.2047c>t0.533
rrl1475707r.2050t>a0.533
rrl1475713r.2056c>g0.533
rrl1475716r.2059a>g0.533
rrl1475722r.2065g>a0.516
rrl1475783r.2126t>g0.719
rrl1475803r.2146t>c0.768
rrl1475804r.2147g>c0.768
rrl1475816r.2159c>g0.793
rrl1475817r.2160a>g0.800
rrl1475858r.2201t>c0.769
rrl1475869r.2212c>t0.750
rrl1476141r.2484a>g0.500
rrl1476153r.2496t>c0.560
rrl1476160r.2503t>a0.538
rrl1476164r.2507a>g0.519
rrl1476165r.2508t>a0.519
rrl1476179r.2522c>t0.538
rrl1476332r.2675g>c0.652
rrl1476338r.2681c>t0.646
rrl1476358r.2701t>c0.686
rrl1476372r.2715t>c0.697
rrl1476382r.2725a>g0.641
rrl1476383r.2726t>a0.672
rrl1476408r.2751g>a0.672
rrl1476411r.2754g>a0.672
rrl1476425r.2768g>t0.604
rrl1476427r.2770g>t0.604
rrl1476428r.2771c>t0.604
rrl1476429r.2772a>c0.611
rrl1476443r.2786g>c0.650
rrl1476455r.2798c>g0.683
rrl1476463r.2806c>t0.672
rrl1476466r.2809c>t0.677
rrl1476481r.2824t>c0.656
rrl1476506r.2849t>c0.630
rrl1476512r.2855c>t0.310
rrl1476514r.2857c>t0.310
rrl1476517r.2860c>t0.321
rrl1476519r.2862c>g0.321
rrl1476523r.2866t>c0.333
rrl1476524r.2867c>a0.333
rrl1476525r.2868a>g0.333
rrl1476528r.2871a>t0.333
rrl1476530r.2873c>t0.385
rrl1476538r.2881a>g0.407
rrl1476540r.2883c>g0.379
rrl1476547r.2890c>t0.625
rrl1476567r.2910c>t0.727
rrl1476573r.2916a>c0.690
rrl1476577r.2920t>g0.659
rrl1476582r.2925t>c0.630
rrl1476637r.2980c>a0.674
tlyA1917972c.33A>G1.000
ahpC2726146c.-47G>GT1.000
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.214
alr3841654c.-234A>C0.227
alr3841662c.-242A>G0.302
alr3841663c.-243G>A0.304
embC4242643c.2781C>T1.000
embB4246584p.Arg24Pro0.333
gid4407997p.Gly69Asp1.000

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;