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: 5dca14438c87e
Sample: 5dca14438c87e

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Summary
ID: 5dca14438c87e
Date: Tue Nov 12 02:15:36 2019
Strain: lineage2.2.1
Drug-resistance: MDR

Drug1ResistanceSupporting Mutations (frequency)
IsoniazidRfabG1 c.-15C>T (1.00)
RifampicinRrpoB p.Ser450Leu (1.00)
Ethambutol
PyrazinamideRpncA p.Asp49Asn (1.00)
StreptomycinRrpsL p.Lys88Arg (0.92), rrs r.799c>t (0.11)
EthionamideRfabG1 c.-15C>T (1.00)
Fluoroquinolones
AmikacinRrrs r.1484g>t (0.11)
CapreomycinRrrs r.1484g>t (0.11)
KanamycinRrrs r.1484g>t (0.11)

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>C0.188
rpoB762872p.Met1022Ile0.200
rpoB762878p.Ile1024Met0.194
rpoB762879p.Met1025Leu0.226
rpoB762896c.3090G>C0.270
rpoB762925p.Thr1040Ile0.282
rpoB762938c.3132G>C0.263
rpoB762939p.Met1045Leu0.256
rpoB762942p.Ile1046Val0.263
rpoB762953c.3147G>A0.256
rpoB762965c.3159T>C0.256
rpoB763031c.3225T>C1.000
rpoC764817p.Val483Ala1.000
rpsL781395c.-165T>C0.968
rrs1472108r.263c>t0.108
rrs1472122r.277g>t0.103
rrs1472123r.278a>t0.103
rrs1472150r.305t>a0.206
rrs1472160r.315c>t0.226
rrs1472172r.327t>c0.655
rrs1472181r.336g>a0.195
rrs1472210r.365a>t0.459
rrs1472214r.369c>g0.367
rrs1472215r.370a>g0.200
rrs1472225r.380c>a0.578
rrs1472234r.389t>c0.200
rrs1472235r.390g>c0.330
rrs1472240r.395g>c0.536
rrs1472242r.397c>t0.518
rrs1472251r.406g>c0.375
rrs1472252r.407g>a0.364
rrs1472259r.414c>a0.381
rrs1472344r.499c>t0.463
rrs1472389r.544g>a0.409
rrs1472390r.545t>a0.409
rrs1472391r.546c>t0.409
rrs1472400r.555c>t0.111
rrs1472416r.571c>t0.185
rrs1472422r.577t>c0.208
rrs1472549r.704g>a0.128
rrs1472571r.726g>c0.125
rrs1472581r.736a>c0.147
rrs1472598r.753a>c0.245
rrs1472599r.754g>t0.250
rrs1472616r.771g>a0.327
rrs1472655r.810g>t0.129
rrs1472660r.815t>c0.194
rrs1472673r.828t>g0.133
rrs1472674r.829t>g0.133
rrs1472675r.830t>a0.133
rrs1472677r.832c>a0.138
rrs1472692r.847t>c0.143
rrs1472713r.868t>c0.419
rrs1472714r.869a>g0.143
rrs1472716r.871c>t0.400
rrs1472734r.889c>t0.265
rrs1472741r.896g>a0.254
rrs1472742r.897c>t0.529
rrs1472744r.899a>g0.274
rrs1472767r.922g>a0.214
rrs1472781r.936c>t0.543
rrs1472785r.940g>t0.218
rrs1472786r.941c>g0.221
rrs1472793r.948a>t0.553
rrs1472803r.958t>a0.232
rrs1472812r.967a>c0.206
rrs1472814r.969g>a0.206
rrs1472887r.1042g>c0.740
rrs1472956r.1111t>c0.150
rrs1472957r.1112c>t0.278
rrs1472973r.1128a>t0.350
rrs1472987r.1142g>a0.190
rrs1472989r.1144g>a0.174
rrs1472990r.1145a>g0.227
rrs1473035r.1190g>a0.267
rrs1473055r.1210c>t0.154
rrs1473056r.1211a>t0.154
rrs1473066r.1221a>g0.182
rrs1473088r.1243a>g0.174
rrs1473121r.1276t>c0.214
rrs1473145r.1300c>t0.333
rrs1473163r.1318c>t0.377
rrs1473164r.1319c>g0.370
rrs1473166r.1321g>a0.185
rrs1473177r.1332g>a0.424
rrs1473192r.1347a>g0.410
rrs1473202r.1357c>t0.312
rrs1473204r.1359c>t0.312
rrs1473205r.1360t>c0.391
rrs1473226r.1381c>t0.323
rrs1473252r.1407t>c0.243
rrs1473259r.1414c>t0.216
rrs1473270r.1425g>a0.125
rrs1473276r.1431a>g0.129
rrs1473301r.1456t>c0.125
rrs1473305r.1460g>t0.118
rrs1473316r.1471c>t0.152
rrl1474197r.540c>t0.138
rrl1474249r.592g>t0.182
rrl1474760r.1103a>g0.160
rrl1474794r.1137c>t0.138
rrl1475699r.2042c>t0.138
rrl1475783r.2126t>g0.354
rrl1475791r.2134a>g0.242
rrl1475803r.2146t>c0.545
rrl1475804r.2147g>c0.552
rrl1475816r.2159c>g0.622
rrl1475817r.2160a>g0.627
rrl1475881r.2224t>c0.380
rrl1475883r.2226a>c0.404
rrl1475892r.2235a>c0.362
rrl1475894r.2237c>g0.354
rrl1475900r.2243a>g0.333
rrl1475904r.2247g>a0.340
rrl1476194r.2537a>g0.115
rrl1476200r.2543a>t0.120
rrl1476201r.2544c>t0.120
rrl1476214r.2557g>t0.136
rrl1476215r.2558c>t0.150
rrl1476224r.2567a>g0.150
rrl1476245r.2588c>t0.176
rrl1476252r.2595t>g0.167
rrl1476253r.2596a>g0.167
rrl1476256r.2599a>g0.167
rrl1476260r.2603a>g0.150
rrl1476281r.2624t>c0.136
rrl1476324r.2667g>a0.194
rrl1476336r.2679c>t0.395
rrl1476338r.2681c>t0.436
rrl1476339r.2682g>a0.179
rrl1476356r.2699c>t0.216
rrl1476357r.2700t>c0.159
rrl1476358r.2701t>c0.261
rrl1476359r.2702c>g0.457
rrl1476369r.2712c>t0.229
rrl1476381r.2724g>c0.490
rrl1476382r.2725a>g0.235
rrl1476383r.2726t>a0.364
rrl1476384r.2727g>a0.279
rrl1476408r.2751g>a0.537
rrl1476411r.2754g>a0.373
rrl1476425r.2768g>t0.323
rrl1476428r.2771c>t0.215
rrl1476429r.2772a>c0.375
rrl1476442r.2785t>a0.209
rrl1476443r.2786g>t0.462
rrl1476455r.2798c>a0.333
rrl1476456r.2799a>t0.159
rrl1476463r.2806c>t0.208
rrl1476466r.2809c>t0.431
rrl1476470r.2813c>t0.259
rrl1476481r.2824t>c0.481
rrl1476483r.2826g>a0.130
rrl1476501r.2844c>t0.250
rrl1476506r.2849t>c0.596
rrl1476515r.2858c>t0.179
rrl1476524r.2867c>t0.167
rrl1476525r.2868a>g0.167
rrl1476530r.2873c>t0.156
rrl1476536r.2879g>a0.212
rrl1476539r.2882a>g0.152
rrl1476540r.2883c>g0.156
rrl1476547r.2890c>t0.135
rpsA1834177c.636A>C1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
ald3086788c.-32T>C1.000
embC4242643c.2781C>T1.000
embA4243460c.228C>T1.000
gid4407588c.615T>C1.000
gid4407927p.Glu92Asp1.000

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;