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: 5d9ce04ee198f
Sample: 5d9ce04ee198f

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Summary
ID: 5d9ce04ee198f
Date: Tue Oct 8 20:17:25 2019
Strain: lineage2.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.Ser450Leu (0.95)
EthambutolRembB p.Met306Ile (1.00)
Pyrazinamide
StreptomycinRrpsL p.Lys43Arg (1.00)
Ethionamide
Fluoroquinolones
AmikacinRrrs r.1402c>a (0.75), rrs r.1484g>t (0.73)
CapreomycinRrrs r.1402c>a (0.75), rrs r.1484g>t (0.73)
KanamycinRrrs r.1402c>a (0.75), rrs r.1484g>t (0.73)

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
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpoB762863c.3057T>C0.150
rpoB762879p.Met1025Leu0.457
rpoB762896c.3090G>C0.507
rpoB762899c.3093G>C0.519
rpoB762917c.3111C>T0.536
rpoB762920c.3114C>T0.556
rpoB762923c.3117C>G0.562
rpoB762926c.3120C>G0.570
rpoB762929c.3123G>C0.582
rpoB762932c.3126G>C0.603
rpoB762959c.3153G>C0.670
rpoB762983c.3177C>A0.557
rpoB762989c.3183G>C0.532
rpoB762995c.3189G>T0.464
rpoB763031c.3225T>C1.000
rpoB763038p.Thr1078Ala0.129
rpoB763053c.3247T>C0.442
rpoB763058c.3252C>G0.444
rpoB763070c.3264T>C0.476
rpoB763075p.Thr1090Ile0.484
rpoB763077p.Val1091Leu0.484
rpoB763115c.3309T>C0.568
rpoB763126p.Pro1107Gln0.568
rpoB763133c.3327G>C0.533
rpoB763148c.3342G>C0.435
rpoC764316p.Ala316Val0.472
rpoC764344c.975C>T0.481
rpoC764365c.996C>T0.468
rpoC764371c.1002G>C0.440
rpoC764377c.1008C>G0.403
rpoC764380c.1011G>C0.361
rpoC764381c.1012T>A0.373
rpoC764387c.1018T>C0.373
rpoC764405c.1036A>C0.326
rpoC764410c.1041G>C0.326
rpoC764593c.1224C>A0.339
rpoC764602c.1233C>T0.426
rpoC764605c.1236G>C0.453
rpoC764611c.1242G>C0.463
rpoC764632c.1263T>C0.553
rpoC764650c.1281G>T0.607
rpoC764677c.1308C>G0.667
rpoC764706p.Leu446Gln0.618
rpoC764713c.1344G>T0.609
rpoC764740p.Met457Ile0.436
rpoC764817p.Val483Gly1.000
rpsL781395c.-165T>C1.000
rrs1471878r.33c>t0.671
rrs1472075r.230a>g0.231
rrs1472078r.233c>t0.262
rrs1472102r.257g>a0.566
rrs1472106r.261g>a0.540
rrs1472108r.263c>t0.547
rrs1472112r.267c>t0.547
rrs1472113r.268t>c0.563
rrs1472123r.278a>t0.702
rrs1472150r.305t>a0.778
rrs1472172r.327t>c0.804
rrs1472225r.380c>g0.829
rrs1472240r.395g>a0.798
rrs1472251r.406g>a0.772
rrs1472328r.483g>c0.170
rrs1472333r.488g>a0.216
rrs1472344r.499c>t0.600
rrs1472382r.537g>a0.625
rrs1472389r.544g>a0.630
rrs1472400r.555c>t0.627
rrs1472422r.577t>c0.524
rrs1472426r.581t>c0.506
rrs1472494r.649a>g0.673
rrs1472496r.651t>g0.673
rrs1472498r.653c>t0.673
rrs1472507r.662c>t0.718
rrs1472558r.713g>a0.746
rrs1472569r.724g>a0.719
rrs1472571r.726g>a0.716
rrs1472581r.736a>c0.712
rrs1472606r.761c>g0.672
rrs1472616r.771g>a0.650
rrs1472623r.778a>c0.637
rrs1472645r.800g>c0.634
rrs1472655r.810g>t0.604
rrs1472660r.815t>a0.571
rrs1472666r.821g>t0.576
rrs1472673r.828t>g0.323
rrs1472675r.830t>c0.311
rrs1472677r.832c>t0.306
rrs1472682r.837t>a0.306
rrs1472683r.838t>c0.306
rrs1472686r.841g>a0.311
rrs1472687r.842a>t0.323
rrs1472694r.849c>a0.418
rrs1472697r.852t>c0.457
rrs1472714r.869a>t0.706
rrs1472767r.922g>a0.712
rrs1472790r.945t>c0.664
rrs1472895r.1050c>t0.685
rrs1472952r.1107t>c0.716
rrs1472955r.1110c>t0.692
rrs1472956r.1111t>c0.696
rrs1472957r.1112c>t0.711
rrs1472982r.1137g>a0.683
rrs1472987r.1142g>a0.681
rrs1472990r.1145a>g0.681
rrs1472993r.1148g>t0.683
rrs1473035r.1190g>a0.697
rrs1473055r.1210c>t0.652
rrs1473056r.1211a>t0.654
rrs1473066r.1221a>g0.675
rrs1473089r.1244a>t0.671
rrs1473100r.1255g>a0.603
rrs1473104r.1259c>t0.605
rrs1473105r.1260g>a0.605
rrs1473110r.1265t>g0.606
rrs1473111r.1266a>g0.607
rrs1473121r.1276t>c0.642
rrs1473122r.1277t>a0.648
rrs1473134r.1289t>c0.724
rrs1473145r.1300c>t0.732
rrs1473147r.1302g>a0.734
rrs1473164r.1319c>t0.723
rrs1473166r.1321g>a0.726
rrs1473226r.1381c>t0.751
rrs1473269r.1424c>t0.703
rrs1473276r.1431a>g0.689
rrs1473319r.1474c>t0.710
rrs1473320r.1475g>a0.716
rrs1473324r.1479g>a0.713
rrl1474155r.498g>a0.163
rrl1474164r.507c>t0.598
rrl1474166r.509g>a0.595
rrl1474183r.526t>c0.644
rrl1474184r.527c>a0.637
rrl1474201r.544t>c0.635
rrl1474202r.545t>a0.635
rrl1474218r.561t>a0.676
rrl1474249r.592g>t0.697
rrl1474265r.608g>t0.593
rrl1474269r.612c>t0.558
rrl1474275r.618t>a0.529
rrl1474280r.623c>t0.475
rrl1474281r.624a>g0.462
rrl1474305r.648g>t0.157
rrl1474316r.659t>c0.208
rrl1474317r.660g>a0.231
rrl1474348r.691c>t0.627
rrl1474351r.694g>t0.634
rrl1474354r.697c>t0.627
rrl1474359r.702c>g0.621
rrl1474362r.705a>g0.618
rrl1474387r.730c>t0.640
rrl1474454r.797g>a0.390
rrl1474466r.809g>a0.432
rrl1474476r.819c>t0.480
rrl1474488r.831g>c0.526
rrl1474495r.838g>a0.561
rrl1474498r.841g>t0.568
rrl1474505r.848c>a0.595
rrl1474508r.851c>t0.602
rrl1474516r.859c>g0.606
rrl1474537r.880g>a0.719
rrl1474558r.901g>a0.720
rrl1474583r.926c>t0.766
rrl1474601r.944c>t0.773
rrl1474632r.975g>t0.754
rrl1474636r.979a>t0.745
rrl1474637r.980c>t0.745
rrl1474638r.981c>g0.739
rrl1474639r.982g>c0.759
rrl1474672r.1015c>t0.742
rrl1474673r.1016t>c0.732
rrl1474676r.1019t>c0.744
rrl1474790r.1133c>t0.483
rrl1474794r.1137c>a0.516
rrl1474800r.1143t>c0.562
rrl1474812r.1155g>a0.603
rrl1474823r.1166c>g0.605
rrl1474827r.1170c>t0.603
rrl1474830r.1173a>t0.589
rrl1474831r.1174a>t0.589
rrl1474904r.1247g>c0.639
rrl1474905r.1248t>c0.647
rrl1474913r.1256t>c0.646
rrl1474920r.1263g>a0.614
rrl1474935r.1278a>g0.222
rrl1474938r.1281g>a0.146
rrl1475124r.1467a>t0.200
rrl1475129r.1472g>a0.302
rrl1475508r.1851a>t0.560
rrl1475526r.1869c>a0.538
rrl1475536r.1879c>a0.556
rrl1475538r.1881t>a0.551
rrl1475539r.1882a>t0.551
rrl1475545r.1888t>g0.563
rrl1475548r.1891c>t0.570
rrl1475549r.1892t>c0.570
rrl1475550r.1893a>g0.570
rrl1475599r.1942a>g0.163
rrl1475657r.2000a>g0.146
rrl1475659r.2002g>t0.163
rrl1475696r.2039t>a0.706
rrl1475703r.2046a>t0.722
rrl1475753r.2096c>g0.725
rrl1475759r.2102c>g0.721
rrl1475769r.2112t>c0.730
rrl1475775r.2118g>t0.772
rrl1475881r.2224t>c0.684
rrl1475896r.2239a>g0.609
rrl1475897r.2240t>c0.609
rrl1475898r.2241a>g0.613
rrl1475899r.2242g>a0.617
rrl1475916r.2259c>t0.707
rrl1475943r.2286g>a0.727
rrl1475952r.2295a>g0.718
rrl1475963r.2306g>t0.714
rrl1475970r.2313c>t0.719
rrl1475977r.2320a>g0.714
rrl1475988r.2331a>g0.690
rrl1475997r.2340a>g0.652
rrl1475998r.2341c>t0.656
rrl1476001r.2344t>c0.646
rrl1476033r.2376t>g0.553
rrl1476034r.2377c>t0.573
rrl1476045r.2388g>a0.436
rrl1476046r.2389g>c0.429
rrl1476049r.2392c>t0.462
rrl1476056r.2399g>a0.538
rrl1476076r.2419a>g0.593
rrl1476079r.2422g>a0.562
rrl1476086r.2429g>a0.550
rrl1476087r.2430c>t0.544
rrl1476095r.2438c>t0.524
rrl1476103r.2446c>g0.548
rrl1476110r.2453g>c0.580
rrl1476115r.2458t>c0.611
rrl1476131r.2474c>t0.758
rrl1476160r.2503t>c0.800
rrl1476165r.2508t>a0.812
rrl1476200r.2543a>t0.817
rrl1476201r.2544c>t0.813
rrl1476224r.2567a>g0.832
rrl1476245r.2588c>t0.832
rrl1476252r.2595t>g0.839
rrl1476256r.2599a>g0.844
rrl1476260r.2603a>g0.858
rrl1476281r.2624t>c0.853
rrl1476295r.2638c>g0.719
rrl1476296r.2639c>t0.719
rrl1476297r.2640c>g0.719
rrl1476298r.2641c>g0.719
rrl1476300r.2643g>t0.719
rrl1476301r.2644a>t0.730
rrl1476309r.2652g>c0.742
rrl1476311r.2654g>c0.756
rrl1476337r.2680c>t0.812
rrl1476359r.2702c>g0.806
rrl1476381r.2724g>c0.789
rrl1476428r.2771c>t0.753
rrl1476466r.2809c>t0.735
rrl1476506r.2849t>c0.622
rrl1476515r.2858c>t0.605
rrl1476524r.2867c>a0.228
rrl1476525r.2868a>g0.218
rrl1476529r.2872a>g0.222
rrl1476530r.2873c>t0.222
rrl1476536r.2879g>a0.235
rrl1476537r.2880a>g0.240
rrl1476538r.2881a>g0.240
rrl1476540r.2883c>t0.255
rrl1476544r.2887t>a0.315
rrl1476566r.2909a>t0.540
rrl1476567r.2910c>t0.531
rrl1476584r.2927c>t0.411
rrl1476585r.2928a>g0.418
rrl1476594r.2937c>t0.379
rrl1476603r.2946g>a0.393
rrl1476614r.2957a>t0.373
rrl1476619r.2962c>t0.393
rrl1476628r.2971t>g0.400
rrl1476629r.2972c>a0.393
rrl1476630r.2973a>t0.393
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
embA4243225c.-8C>T1.000
embA4243460c.228C>T1.000
embB4246567c.54G>T1.000
ethA4326648p.Tyr276His1.000
gid4407588c.615T>C0.963
gid4407927p.Glu92Asp0.971

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;