TB-Profiler result

Run: ERR2600544
Summary

Run ID: ERR2600544

Sample name:

Date: 2024-10-04T10:52:38.167796

Number of reads: 9748084

Percentage reads mapped: 97.43

Median coverage: 296.0

Strain: lineage2.2.1;lineage4.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.09
lineage2 East-Asian RD105 0.19
lineage4.1 Euro-American None 0.69
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.18
lineage2.2 East-Asian (Beijing) RD105;RD207 0.19
lineage4 Euro-American None 0.82
lineage4.3.3 Euro-American (LAM) RD115 0.13
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Tyr147* Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 0.87 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.87 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.13 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.11 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
ethA 4327033 p.Tyr147* stop_gained 0.19 ethionamide Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 698 p.Arg233Gln missense_variant 0.12 isoniazid Uncertain significance
dnaA 1057 p.Val353Ile missense_variant 0.56 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.24 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.23 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.18 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.19 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.71 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 764438 c.1069C>T synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.7 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.16 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.72 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.16 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.18 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.16 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.2 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.69 linezolid
rplC 801019 p.Thr71Ala missense_variant 0.65 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1304962 p.Trp678Gly missense_variant 0.16 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364706 c.294G>A synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
atpE 1461209 c.165C>T synonymous_variant 0.75 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.11 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.19 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.12 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.15 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyX 3067267 p.Phe227Val missense_variant 0.23 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.1 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.18 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.22 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627390 c.-41G>A upstream_gene_variant 0.69 rifampicin Uncertain significance
bedaquiline
clpC1 4038287 c.2418C>T synonymous_variant 0.14 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.7 ethambutol Not assoc w R
embA 4243225 c.-8C>A upstream_gene_variant 0.25 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.19 ethambutol Not assoc w R
embB 4247296 c.783G>A synonymous_variant 0.68 ethambutol Not assoc w R - Interim
embB 4249408 c.2895G>A synonymous_variant 0.71 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.14 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.15 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.22 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.11 streptomycin Not assoc w R