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: 5d74afe070634
Sample: 5d74afe070634

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Summary
ID: 5d74afe070634
Date: Sun Sep 8 08:41:41 2019
Strain: lineage4.2.2
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRkatG p.Ser315Thr (1.00)
RifampicinRrpoB p.His445Tyr (0.92)
Ethambutol
Pyrazinamide
StreptomycinRrrs r.888g>a (0.76)
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
gyrA8688p.Ala463Ser1.000
gyrA9304p.Gly668Asp1.000
rpoB761489c.1683G>A1.000
rpoB762899c.3093G>C0.194
rpoB762929c.3123G>C0.209
rpoB762938c.3132G>T0.139
rpoB762959c.3153G>C0.143
rpoB762962c.3156C>T0.143
rpoB762971c.3165G>A0.155
rpoB762989c.3183G>C0.216
rpoB762995c.3189G>C0.159
rpoB763049c.3243G>A0.131
rpoB763070c.3264T>C0.146
rpoB763103c.3297G>C0.129
rpoB763115c.3309T>C0.135
rpoC763642c.273G>C0.139
rpsL781395c.-165T>C1.000
rrs1471852r.7t>a0.123
rrs1471878r.33c>t0.562
rrs1471896r.51t>c0.513
rrs1471900r.55c>t0.516
rrs1471923r.78t>c0.254
rrs1471929r.84c>g0.264
rrs1471980r.135g>c0.342
rrs1471981r.136c>a0.342
rrs1472017r.172c>t0.312
rrs1472078r.233c>t0.418
rrs1472106r.261g>a0.520
rrs1472108r.263c>t0.204
rrs1472112r.267c>t0.631
rrs1472122r.277g>a0.669
rrs1472123r.278a>t0.193
rrs1472127r.282c>t0.638
rrs1472129r.284g>c0.646
rrs1472137r.292g>a0.656
rrs1472150r.305t>a0.719
rrs1472151r.306c>a0.435
rrs1472160r.315c>t0.162
rrs1472164r.319g>a0.698
rrs1472172r.327t>c0.822
rrs1472177r.332c>t0.684
rrs1472203r.358g>a0.674
rrs1472210r.365a>c0.604
rrs1472213r.368g>c0.607
rrs1472215r.370a>g0.613
rrs1472225r.380c>a0.784
rrs1472234r.389t>c0.561
rrs1472236r.391c>g0.561
rrs1472240r.395g>a0.548
rrs1472251r.406g>a0.571
rrs1472344r.499c>t0.523
rrs1472378r.533g>t0.739
rrs1472379r.534t>g0.776
rrs1472382r.537g>a0.755
rrs1472389r.544g>a0.792
rrs1472400r.555c>t0.818
rrs1472412r.567a>c0.801
rrs1472415r.570t>g0.781
rrs1472422r.577t>c0.782
rrs1472435r.590t>c0.200
rrs1472438r.593t>c0.212
rrs1472439r.594c>t0.212
rrs1472447r.602c>t0.212
rrs1472448r.603t>c0.219
rrs1472450r.605a>g0.219
rrs1472451r.606c>g0.212
rrs1472461r.616g>c0.189
rrs1472462r.617t>c0.189
rrs1472464r.619a>g0.184
rrs1472471r.626g>a0.250
rrs1472485r.640g>a0.261
rrs1472489r.644a>t0.347
rrs1472494r.649a>g0.422
rrs1472498r.653c>t0.449
rrs1472507r.662c>g0.185
rrs1472517r.672t>a0.723
rrs1472518r.673g>t0.727
rrs1472530r.685g>a0.822
rrs1472541r.696t>g0.747
rrs1472544r.699c>a0.761
rrs1472545r.700a>t0.762
rrs1472557r.712g>a0.780
rrs1472570r.725g>a0.740
rrs1472571r.726g>c0.752
rrs1472573r.728c>t0.729
rrs1472579r.734g>t0.747
rrs1472581r.736a>t0.806
rrs1472596r.751g>t0.734
rrs1472598r.753a>t0.762
rrs1472614r.769g>t0.763
rrs1472616r.771g>a0.772
rrs1472655r.810g>a0.571
rrs1472658r.813g>a0.426
rrs1472661r.816a>g0.483
rrs1472665r.820g>a0.431
rrs1472678r.833t>c0.417
rrs1472679r.834t>c0.426
rrs1472690r.845c>a0.433
rrs1472695r.850c>t0.336
rrs1472697r.852t>c0.404
rrs1472713r.868t>c0.825
rrs1472716r.871c>t0.741
rrs1472742r.897c>t0.759
rrs1472744r.899a>g0.762
rrs1472767r.922g>a0.791
rrs1472781r.936c>t0.769
rrs1472793r.948a>t0.775
rrs1472803r.958t>a0.790
rrs1472824r.979t>a0.150
rrs1472828r.983t>c0.541
rrs1472836r.991g>a0.190
rrs1472837r.992c>t0.174
rrs1472873r.1028c>t0.343
rrs1472878r.1033g>a0.179
rrs1472880r.1035g>a0.179
rrs1472880r.1035g>ga0.194
rrs1472895r.1050c>t0.881
rrs1472954r.1109t>c0.138
rrs1472956r.1111t>c0.145
rrs1472957r.1112c>t0.400
rrs1472973r.1128a>t0.233
rrs1472987r.1142g>a0.180
rrs1472990r.1145a>g0.160
rrs1472992r.1147a>g0.125
rrs1473005r.1160c>t0.320
rrs1473009r.1164t>c0.254
rrs1473035r.1190g>a0.887
rrs1473055r.1210c>t0.175
rrs1473056r.1211a>t0.193
rrs1473066r.1221a>g0.133
rrs1473080r.1235c>t0.367
rrs1473081r.1236c>t0.131
rrs1473089r.1244a>c0.155
rrs1473091r.1246g>c0.153
rrs1473099r.1254t>g0.167
rrs1473100r.1255g>c0.184
rrs1473102r.1257c>t0.208
rrs1473104r.1259c>t0.259
rrs1473109r.1264t>g0.164
rrs1473111r.1266a>g0.259
rrs1473120r.1275c>g0.143
rrs1473121r.1276t>c0.328
rrs1473123r.1278a>t0.204
rrs1473130r.1285g>a0.147
rrs1473145r.1300c>t0.819
rrs1473147r.1302g>t0.688
rrs1473148r.1303g>a0.690
rrs1473163r.1318c>t0.686
rrs1473164r.1319c>a0.681
rrs1473166r.1321g>a0.826
rrs1473172r.1327t>c0.708
rrs1473173r.1328c>t0.726
rrs1473177r.1332g>a0.686
rrs1473191r.1346c>t0.702
rrs1473202r.1357c>t0.668
rrs1473206r.1361g>a0.682
rrs1473226r.1381c>t0.683
rrs1473252r.1407t>c0.386
rrs1473259r.1414c>t0.418
rrs1473290r.1445c>t0.297
rrs1473352r.1507c>t0.764
rrl1473679r.22t>c0.222
rrl1473698r.41g>a0.151
rrl1473704r.47c>t0.136
rrl1473717r.60g>t0.138
rrl1473719r.62g>t0.151
rrl1473720r.63a>g0.131
rrl1473722r.65g>c0.133
rrl1473724r.67t>c0.172
rrl1473731r.74t>g0.167
rrl1473750r.93c>a0.212
rrl1473758r.101g>t0.224
rrl1473768r.111a>g0.222
rrl1473770r.113t>g0.217
rrl1473876r.219g>a0.383
rrl1473899r.242a>t0.405
rrl1474130r.473c>t0.542
rrl1474140r.483c>t0.551
rrl1474151r.494c>t0.545
rrl1474174r.517a>g0.412
rrl1474181r.524c>a0.195
rrl1474184r.527c>a0.353
rrl1474186r.529a>t0.323
rrl1474197r.540c>t0.130
rrl1474201r.544t>g0.200
rrl1474202r.545t>g0.203
rrl1474218r.561t>a0.521
rrl1474236r.579g>a0.455
rrl1474249r.592g>t0.297
rrl1474252r.595t>a0.391
rrl1474255r.598c>t0.385
rrl1474269r.612c>t0.590
rrl1474286r.629c>g0.242
rrl1474287r.630t>c0.242
rrl1474330r.673a>t0.733
rrl1474338r.681g>a0.250
rrl1474341r.684t>g0.192
rrl1474348r.691c>t0.281
rrl1474351r.694g>c0.439
rrl1474353r.696a>g0.396
rrl1474362r.705a>g0.479
rrl1474371r.714c>a0.348
rrl1474378r.721g>t0.293
rrl1474381r.724t>g0.170
rrl1474387r.730c>t0.913
rrl1474447r.790g>a0.143
rrl1474451r.794t>c0.162
rrl1474466r.809g>a0.205
rrl1474487r.830g>t0.205
rrl1474495r.838g>a0.237
rrl1474496r.839c>g0.237
rrl1474497r.840g>c0.171
rrl1474498r.841g>t0.154
rrl1474505r.848c>g0.154
rrl1474506r.849c>g0.206
rrl1474507r.850g>t0.184
rrl1474508r.851c>t0.237
rrl1474517r.860c>g0.233
rrl1474537r.880g>a0.283
rrl1474551r.894g>a0.197
rrl1474552r.895c>t0.212
rrl1474583r.926c>t0.237
rrl1474626r.969t>c0.311
rrl1474634r.977t>c0.138
rrl1474636r.979a>c0.183
rrl1474637r.980c>t0.234
rrl1474638r.981c>g0.258
rrl1474640r.983c>t0.134
rrl1474677r.1020a>g0.149
rrl1474722r.1065t>c0.123
rrl1474734r.1077g>t0.297
rrl1474749r.1092c>t0.293
rrl1474779r.1122g>a0.143
rrl1474782r.1125g>a0.143
rrl1474794r.1137c>t0.412
rrl1474803r.1146g>a0.261
rrl1474812r.1155g>a0.281
rrl1474823r.1166c>g0.326
rrl1474824r.1167a>g0.253
rrl1474825r.1168g>a0.198
rrl1474830r.1173a>g0.317
rrl1474839r.1182c>t0.664
rrl1474844r.1187g>t0.673
rrl1474864r.1207c>t0.817
rrl1474866r.1209c>a0.708
rrl1474869r.1212g>t0.715
rrl1474892r.1235g>a0.656
rrl1474896r.1239a>g0.768
rrl1474901r.1244a>g0.136
rrl1474902r.1245t>c0.659
rrl1474903r.1246t>a0.659
rrl1474904r.1247g>c0.807
rrl1474913r.1256t>a0.743
rrl1474920r.1263g>c0.624
rrl1474932r.1275c>t0.288
rrl1475027r.1370g>t0.325
rrl1475031r.1374g>t0.293
rrl1475033r.1376g>c0.240
rrl1475124r.1467a>t0.115
rrl1475137r.1480a>t0.659
rrl1475144r.1487g>c0.611
rrl1475145r.1488c>t0.615
rrl1475163r.1506t>g0.672
rrl1475171r.1514c>t0.670
rrl1475175r.1518g>a0.750
rrl1475188r.1531c>t0.699
rrl1475307r.1650t>c0.214
rrl1475315r.1658a>t0.211
rrl1475318r.1661g>t0.214
rrl1475324r.1667g>a0.231
rrl1475498r.1841c>g0.606
rrl1475526r.1869c>a0.255
rrl1475531r.1874c>t0.207
rrl1475532r.1875a>g0.175
rrl1475538r.1881t>a0.163
rrl1475539r.1882a>t0.319
rrl1475542r.1885a>g0.152
rrl1475544r.1887a>t0.341
rrl1475545r.1888t>g0.341
rrl1475548r.1891c>t0.131
rrl1475549r.1892t>c0.131
rrl1475550r.1893a>g0.422
rrl1475552r.1895g>c0.455
rrl1475574r.1917c>a0.835
rrl1475672r.2015c>t0.149
rrl1475673r.2016t>c0.167
rrl1475686r.2029c>g0.167
rrl1475688r.2031g>a0.333
rrl1475696r.2039t>a0.324
rrl1475699r.2042c>t0.444
rrl1475703r.2046a>t0.343
rrl1475713r.2056c>g0.866
rrl1475716r.2059a>g0.816
rrl1475751r.2094c>a0.128
rrl1475753r.2096c>t0.171
rrl1475765r.2108a>c0.192
rrl1475769r.2112t>c0.172
rrl1475803r.2146t>c0.844
rrl1475804r.2147g>c0.844
rrl1475816r.2159c>g0.856
rrl1475817r.2160a>g0.857
rrl1475858r.2201t>c0.847
rrl1475866r.2209t>a0.816
rrl1475881r.2224t>c0.256
rrl1475883r.2226a>t0.256
rrl1475884r.2227a>g0.293
rrl1475897r.2240t>c0.359
rrl1475900r.2243a>g0.333
rrl1475902r.2245t>c0.359
rrl1475916r.2259c>g0.390
rrl1475975r.2318c>t0.508
rrl1475977r.2320a>g0.492
rrl1475990r.2333g>a0.417
rrl1475997r.2340a>t0.465
rrl1476046r.2389g>t0.413
rrl1476048r.2391g>t0.400
rrl1476049r.2392c>g0.406
rrl1476076r.2419a>g0.508
rrl1476086r.2429g>a0.275
rrl1476087r.2430c>t0.275
rrl1476099r.2442a>g0.289
rrl1476100r.2443a>c0.282
rrl1476103r.2446c>a0.275
rrl1476110r.2453g>t0.268
rrl1476113r.2456t>g0.286
rrl1476135r.2478t>c0.715
rrl1476141r.2484a>g0.711
rrl1476153r.2496t>c0.722
rrl1476165r.2508t>g0.795
rrl1476179r.2522c>t0.749
rrl1476194r.2537a>g0.485
rrl1476200r.2543a>t0.464
rrl1476201r.2544c>t0.426
rrl1476204r.2547c>t0.145
rrl1476215r.2558c>t0.275
rrl1476225r.2568t>g0.748
rrl1476229r.2572c>t0.756
rrl1476251r.2594t>c0.810
rrl1476260r.2603a>g0.880
rrl1476268r.2611a>t0.811
rrl1476275r.2618t>a0.774
rrl1476279r.2622g>a0.771
rrl1476280r.2623a>c0.760
rrl1476293r.2636c>t0.549
rrl1476294r.2637a>g0.551
rrl1476295r.2638c>g0.551
rrl1476296r.2639c>t0.667
rrl1476297r.2640c>t0.628
rrl1476301r.2644a>c0.620
rrl1476302r.2645g>a0.510
rrl1476309r.2652g>c0.144
rrl1476311r.2654g>c0.566
rrl1476312r.2655t>c0.566
rrl1476313r.2656g>a0.535
rrl1476332r.2675g>c0.797
rrl1476353r.2696g>t0.831
rrl1476358r.2701t>c0.822
rrl1476369r.2712c>t0.816
rrl1476372r.2715t>c0.811
rrl1476382r.2725a>g0.797
rrl1476383r.2726t>a0.800
rrl1476408r.2751g>a0.803
rrl1476425r.2768g>t0.771
rrl1476428r.2771c>t0.870
rrl1476429r.2772a>c0.816
rrl1476466r.2809c>t0.847
rrl1476481r.2824t>c0.837
rrl1476506r.2849t>c0.786
rrl1476514r.2857c>t0.593
rrl1476517r.2860c>t0.588
rrl1476519r.2862c>g0.580
rrl1476524r.2867c>a0.667
rrl1476525r.2868a>g0.590
rrl1476530r.2873c>t0.590
rrl1476536r.2879g>a0.713
rrl1476537r.2880a>g0.600
rrl1476538r.2881a>g0.603
rrl1476540r.2883c>g0.703
rrl1476547r.2890c>t0.767
rrl1476567r.2910c>t0.783
rrl1476572r.2915g>a0.753
rrl1476573r.2916a>t0.806
rrl1476584r.2927c>t0.839
rrl1476607r.2950c>t0.226
rrl1476608r.2951c>g0.235
rrl1476614r.2957a>t0.214
rrl1476616r.2959a>g0.167
rrl1476619r.2962c>t0.203
rrl1476628r.2971t>a0.158
rrl1476629r.2972c>a0.186
rrl1476630r.2973a>g0.158
rpsA1833949c.408T>C0.155
rpsA1834051c.510G>A0.156
rpsA1834102c.561T>C0.135
rpsA1834114c.573G>C0.136
tlyA1917972c.33A>G1.000
ahpC2726146c.-47G>GT0.980
ald3086788c.-32T>C1.000
alr3841652c.-232A>T0.254
alr3841654c.-234A>C0.278
alr3841662c.-242A>G0.342
alr3841663c.-243G>A0.317
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
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