TGS-TB v2 demo

In silico genotype raw data are available.

Potential AMR prediction

AMR catalog version 20170718

View read mapping using JBrowse (Genome Res. 2009. 19: 1630-1638)

Isoniazid (INH)
ahpCahpC_promoterfabG1_promoterinhAkasAkatGkatG_promoterndh
Rifampicin (RIP)
rpoBrpoC
Pyrazinamide (PZA)
panDpncApncA_promoterrpsA
Streptomycin (STR)
gidrpsLrrs
Ethambutol (EMB)
embAembA_promoterembBembCembR
Ethionamide (ETH)
ethAethRfabG1_promoterinhAndh
Fluoroquinolones (FQ)
gyrAgyrB
Amikacin (AMK)
rrs
Capreomycin (CPM)
rrstlyA
Kanamycin (KM)
eis_promoterrrs
Para-aminosalisylic_acid (PAS)
folCribDthyA
Linezolid (LZD)
rplCrrl
Clofazimine (CFZ)
Rv0678
Bedaquiline (BDQ)
Rv0678

Strain INHRIPPZASTREMBETHFQAMKCPMKMPASLZDCFZBDQ Mutations in candidate genes
Strain_A fabG1_promoter (C-15T)
rpoB (c.1349C>T, S450L)
pncA Frameshift(+4 nt) found.
rpsL (c.128A>G, K43R)
embB (c.916A>G, M306V)
fabG1_promoter (C-15T)
folC (c.128T>C, I43T)
Strain_B katG Indel(s) found.
rpoB (c.1349C>T, S450L)
gyrA (c.281A>C, D94A)
gyrB (c.1496A>C, N499T)
Strain_C pncA Insertion/deletion found.
Strain_D

INH: Isoniazid; RIP: Rifampicin; PZA: Pyrazinamide; STR: Streptomycin; EMB: Ethambutol; ETH: Ethionamide; FQ: Fluoroquinolones; AMK: Amikacin; CPM: Capreomycin; KM: Kanamycin; PAS: Para-aminosalisylic_acid; LZD: Linezolid; CFZ: Clofazimine; BDQ: Bedaquiline;


TB profiler result

TB profiler AMR catalog used here is not the latest one.
Please refer to the original site for the latest information.
Reference
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Coll F, McNerney R, et al. Genome Med. 2015 May 27;7(1):51. doi: 10.1186/s13073-015-0164-0. TBprofiler website
Strain Lineage MDR XDR INH RIP PZA STR EMB ETH FQ AMK CPM KM Mutations in candidate genes
Strain_A lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181
R fabG1 (C-15T promoter) rpoB (Ser450Leu) rpsL (Lys43Arg) embB (Met306Val) fabG1 (C-15T promoter)
Strain_B lineage4 Euro-American LAM;T;S;X;H None
lineage4.5 Euro-American H;T RD122
rpoB (Ser450Leu) gyrA (Asp94Ala),
gyrB (Asn499Thr)
Strain_C lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207
rpoB (Val170Phe)
Strain_D lineage2 East-Asian Beijing RD105
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207

MDR: Multi drug resistance, INH + RFP; XDR: Extremely drug resistance, MDR + FQ + (AMK or CPM or KM); INH: Isoniazid; RIP: Rifampicin; PZA: Pyrazinamide; STR: Streptomycin; EMB: Ethambutol; ETH: Ethionamide; FQ: Fluoroquinolones; AMK: Amikacin; CPM: Capreomycin; KM: Kanamycin;

KvarQ MTBC analysis result

Reference
KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S. BMC Genomics. 2014 Oct 9;15(1):881. doi:10.1186/1471-2164-15-881. http://www.swisstph.ch/kvarq.
  • KvarQ modified version: Coverage torelance was changed: std 1.5 -> 2.0
    (Around line 446 in file genes.py, std limitation was changed to 2.0).
  • MTBC analysis version: MTBC.niid.3.20150403 about license
SamplePhyloResistance
Strain_A lineage 2/beijing sublineage
Rifampicin resistance::SNP761155CT=rpoB.S450L
Streptomycin resistance::SNP781687AG=rpsL.K43R
Isoniazid resistance::SNP1673425CT=inhA promoter mutation -15
Rifampicin resistance (compensatory)::SNP3877960AC=rpoA.V183G
Ethambutol resistance::SNP4247429AG=embB.M306V
Rifampicin resistance (RRDR) [761155CT=rpoB.S450L]
remark: mixed coverage
Strain_B lineage 4
Fluoroquinolones resistance::SNP7582AC=gyrA.D94A
Rifampicin resistance::SNP761155CT=rpoB.S450L
Rifampicin resistance (RRDR) [761155CT=rpoB.S450L]
Fluoroquinolones resistance (QRDR) [7582AC=gyrA.D94A]
Strain_C lineage 2/beijing sublineage
No resistance found
remark: mixed coverage
Strain_D lineage 2/beijing sublineage
No resistance found

Core genome phylogenetic tree

ML tree generated by RAxML ver. 8.2.0 [Strain]...[SRA ID]...[lineage]
R SVG Plot! S00007206...ERR123926...lineage 4.6.1.2 S00019843...ERR386996...lineage 4.6.1.1 S00013416...ERR278537+ERR386896...lineage 4.6.2 Bir 225...ERR046839...lineage 4.6.2.1 S00007213...ERR123915...lineage 4.6.2.2 S00017336...ERR330669...lineage 4.5 Strain B Bir 426...ERR072039...lineage 4.9 S00018378...ERR351925+ERR386857...lineage 4.4 S00013126...ERR270624...lineage 4.4.2 Bir 79...ERR038282...lineage 4.4.1.2 S00013203...ERR270701...lineage 4.4.1.1 S00013201...ERR270699...lineage 4.4.1 S00009328...ERR228183...lineage 4.2.1 S00017375...ERR330708...lineage 4.2.2 S00009367...ERR228222...lineage 4.2.2.1 L4 DY195...ERR234201...lineage 4.1 S00013476...ERR278597+ERR386956...lineage 4.1.2 7199-99...NC 020089...lineage 4.1.2.1 ATCC 35801...NC 020559...lineage 4.1.2.1 S00018390...ERR351937+ERR386869...lineage 4.1.2.1 Haarlem...NC 022350...lineage 4.1.2.1 Bir 74...ERR038277...lineage 4.1.1 MT0016...SRR058116...lineage 4.1.1.2 S00007381...ERR114477...lineage 4.1.1.1 S00007348...ERR117732...lineage 4.1.1.3 Mt256...ERR181435...lineage 7 S00013829...ERR294249...lineage 5 L6 N0091...ERR234254...lineage 6 S00019848...ERR387001...lineage BOV Bir 270...ERR046881...lineage 1.2.2 S00013408...ERR278529+ERR386888...lineage 1.2.1 EAI5...NC 021740...lineage 1.1.2 S00007273...ERR114427...lineage 1.1.2 S00007279...ERR117694...lineage 1.1.1 S00019855...ERR387008...lineage 1.1.1.1 S00018368...ERR351915+ERR386847...lineage 1.1.3 S00007361...ERR114513...lineage 3 S00007291...ERR114453...lineage 3.1.1 S00007295...ERR117696...lineage 3.1.2.1 S00018322...ERR351869+ERR386801...lineage 3.1.2 S00007298...ERR114442...lineage 3.1.2.2 GX 451017...SRR1710070...lineage 2.1 proto-Beijing GX 450708...SRR1710066...lineage 2.1 Shanghai 09-1608...SRS790114...lineage 2.2.2 MG1 10 0554...SRR1710083...lineage 2.2.2 SJ649...SRR1710111...lineage 2.2.2 MG1 Strain D Strain C 2533E...ERR234658...lineage 2.2.1 PG1 GQ366...ERR234133...lineage 2.2.1 PG1 Strain A 08 0205...SRR1710073...lineage 2.2.1 MG2 L2 GQ1164...ERR234116...lineage 2.2.1 PG2 L2 GQ-1343...ERR234121...lineage 2.2.1.1 hlj100113...SRS475367...lineage 2.2.1 0710Y...ERR117454...lineage 2.2.1 MG3 SJ432...SRR1710110...lineage 2.2.1 MG3 M08 14556...ERR015616...lineage 2.2.1 MG3 MTB GT 333...ERR234208...lineage 2.2.1 MG3 -NA-...ERR019574...lineage 2.2.1 MG3 L2 N0130...ERR234263...lineage 2.2.1.2 CCDC5180...NC 017522...lineage 2.2.1 S00013400...ERR278521+ERR386880...lineage 4.3.3 CTRI-2...NC 017524...lineage 4.3.3 KZN 4207...NC 016768...lineage 4.3.3 KZN 1435...NC 012943...lineage 4.3.3 KZN 605...NC 018078...lineage 4.3.3 S00013422...ERR278543+ERR386902...lineage 4.3.4.1 S00013762...ERR294182...lineage 4.3.4.2.1 FFUL KAUST MTB26...ERR275206...lineage 4.3.4.2 S00013459...ERR278580+ERR386939...lineage 4.3.4 S00019824...ERR386977...lineage 4.3.1 S00013789...ERR294209...lineage 4.3.2 F11...NC 009565...lineage 4.3.2.1 S00018339...ERR351886+ERR386818...lineage 4.3.2.1 S00017343...ERR330676...lineage 4.7 S00013760...ERR294180...lineage 4.8 S00017318...ERR330651...lineage 4 H37Rv...NC 000962...lineage 4 H37Ra ATCC 25177...NC 009525...lineage 4 S00018392...ERR351939+ERR386871...lineage 4.6 Root 100 100 100 100 80 100 100 100 100 100 42 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 37 100 99 100 100 100 83 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 44 81 74 39 79 77 77 100 100 100 100 100 100 100 95 100 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07

IS6110 insert positions

Depth filter:
%
Lightblue: forward. Red: reverse
Length shows % depth for average.
Dots show number of the insertions
(Neighboring dots are shown at different vertical positions)


[, ] H37Ra_ATCC_25177-NC_009525
[, ] H37Rv-NC_000962
[, ] F11-NC_009565
[, ] KZN_605-NC_018078
[, ] KZN_1435-NC_012943
[, ] KZN_4207-NC_016768
[, ] CTRI-2-NC_017524
[, ] CCDC5180-NC_017522
[, ] Strain_A
[, ] Strain_C
[, ] Strain_D
[, ] EAI5-NC_021740
[, ] Haarlem-NC_022350
[, ] ATCC_35801-NC_020559
[, ] 7199-99-NC_020089
[, ] Strain_B

Spoligotyping


H37Ra_ATCC_25177-NC_009525
H37Rv-NC_000962
F11-NC_009565
KZN_605-NC_018078
KZN_1435-NC_012943
KZN_4207-NC_016768
CTRI-2-NC_017524
CCDC5180-NC_017522
Strain_A
Strain_C
Strain_D
EAI5-NC_021740
Haarlem-NC_022350
ATCC_35801-NC_020559
7199-99-NC_020089
Strain_B

VNTR

Download our customised 43 VNTR loci list in PDF or Excel format.
Coloring setting of TRs
Min: Max:
Depth Filter: %
Gray box () indicates lower than the depth filter setting (%).
Black box () indicates no detection TR.
Stripe patterned box () indicates possible mixed number of TR.

Example
Number: Tandem repeats (TRs).
Blue horizontal line: Read depth ratio to avg. depth.
Box color: Corresponds to the TRs.
Lower than the depth filter setting.



H37Ra_ATCC_25177-NC_009525
H37Rv-NC_000962
F11-NC_009565
KZN_605-NC_018078
KZN_1435-NC_012943
KZN_4207-NC_016768
CTRI-2-NC_017524
CCDC5180-NC_017522
Strain_A
Strain_C
Strain_D
EAI5-NC_021740
Haarlem-NC_022350
ATCC_35801-NC_020559
7199-99-NC_020089
Strain_B