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: 5cff7c13b8e6e
Sample: 5cff7c13b8e6e

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Summary
ID: 5cff7c13b8e6e
Date: Tue Jun 11 11:04:38 2019
Strain: lineageBOV
Drug-resistance: Drug-resistant

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
PyrazinamideRpncA p.His57Asp (1.00)
StreptomycinRrrs r.888g>a (0.30)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineageBOVM. bovisBOV 1;BOV 2None
lineageBOV AFRI???

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrB5752c.513G>A1.000
gyrB6406c.1167C>T1.000
gyrB6446p.Ala403Ser1.000
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA8285c.984C>T1.000
gyrA9143c.1842T>C1.000
gyrA9217p.Asp639Ala1.000
gyrA9304p.Gly668Asp1.000
rpoB763031c.3225T>C1.000
rpsL781395c.-165T>C1.000
embR1416222p.Phe376Leu0.303
embR1416234p.Cys372Gly0.303
embR1417554c.-207C>G1.000
rrs1472106r.261g>a0.161
rrs1472127r.282c>t0.172
rrs1472129r.284g>c0.167
rrs1472130r.285g>a0.167
rrs1472137r.292g>a0.161
rrs1472150r.305t>a0.147
rrs1472151r.306c>t0.147
rrs1472172r.327t>c0.316
rrs1472203r.358g>a0.250
rrs1472566r.721g>a0.179
rrs1472571r.726g>c0.172
rrs1472579r.734g>c0.185
rrs1472580r.735c>t0.161
rrs1472581r.736a>t0.290
rrs1472598r.753a>c0.310
rrs1472599r.754g>t0.310
rrs1472616r.771g>a0.310
rrs1472655r.810g>a0.290
rrs1472658r.813g>a0.290
rrs1472661r.816a>g0.273
rrs1472670r.825g>t0.207
rrs1472673r.828t>g0.148
rrs1472675r.830t>c0.133
rrs1472677r.832c>t0.143
rrs1472690r.845c>a0.300
rrs1472697r.852t>c0.212
rrs1472713r.868t>c0.237
rrs1472716r.871c>t0.237
rrs1472742r.897c>t0.333
rrs1472744r.899a>g0.286
rrs1472781r.936c>t0.300
rrs1472793r.948a>t0.258
rrs1472803r.958t>a0.200
rrs1472895r.1050c>t0.212
rrs1473035r.1190g>a0.149
rrs1473053r.1208t>a0.158
rrs1473055r.1210c>t0.139
rrs1473056r.1211a>t0.194
rrs1473062r.1217t>a0.135
rrs1473068r.1223a>g0.139
rrl1474218r.561t>a0.119
rrl1474584r.927c>g0.160
rrl1474586r.929t>a0.154
rrl1474864r.1207c>t0.160
rrl1474866r.1209c>a0.250
rrl1474869r.1212g>t0.217
rrl1474875r.1218g>a0.150
rrl1474876r.1219t>a0.150
rrl1475545r.1888t>g0.143
rrl1475574r.1917c>a0.296
rrl1475783r.2126t>g0.222
rrl1475803r.2146t>c0.227
rrl1475804r.2147g>c0.227
rrl1475816r.2159c>g0.182
rrl1475817r.2160a>g0.186
rrl1476165r.2508t>g0.167
rrl1476194r.2537a>g0.156
rrl1476201r.2544c>t0.152
rrl1476359r.2702c>g0.152
rrl1476381r.2724g>c0.158
rrl1476425r.2768g>t0.119
rrl1476428r.2771c>t0.244
rrl1476429r.2772a>t0.162
rrl1476463r.2806c>t0.140
rrl1476466r.2809c>t0.167
rrl1476481r.2824t>c0.225
rrl1476506r.2849t>c0.205
rrl1476513r.2856g>t0.147
rrl1476515r.2858c>t0.147
rrl1476517r.2860c>t0.147
rrl1476523r.2866t>c0.114
rrl1476524r.2867c>a0.143
rrl1476525r.2868a>g0.143
rrl1476530r.2873c>t0.118
rrl1476538r.2881a>g0.125
rrl1476539r.2882a>g0.125
rrl1476540r.2883c>g0.125
rrl1476542r.2885t>c0.156
rrl1476567r.2910c>t0.265
rrl1476584r.2927c>t0.161
rrl1476585r.2928a>g0.161
rrl1476594r.2937c>a0.156
rpsA1834859p.Ala440Thr1.000
tlyA1917972c.33A>G1.000
katG2154724p.Arg463Leu1.000
katG2155503c.609G>A1.000
katG2156025c.87G>T1.000
kasA2518132c.18C>T1.000
ald3086788c.-32T>C1.000
ald3087084c.266 266del1.000
embC4240671p.Thr270Ile1.000
embC4242643c.2781C>T1.000
embC4242970c.3108C>T1.000
embA4244220c.988C>T1.000
embA4244260p.Val343Ala1.000
embB4246551p.Asn13Ser0.960
embB4246864c.351C>T1.000
embB4247646p.Glu378Ala1.000
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;