TB-Profiler result

Run: ERR13290848
Summary

Run ID: ERR13290848

Sample name:

Date: 2025-02-11T13:14:20.164938

Number of reads: 1297036

Percentage reads mapped: 99.61

Median coverage: 37.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.93
lineage2 East-Asian RD105 0.07
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.1
lineage4 Euro-American None 0.89
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
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)
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide pncA p.Thr76Pro Assoc w R
streptomycin gid p.Glu170* Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>C Uncertain significance Mutation from literature
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid folC p.Ile43Ser Mutation from literature
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761109 p.Asp435Tyr missense_variant 0.88 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.18 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.8 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)
pncA 2289016 p.Thr76Pro missense_variant 0.97 pyrazinamide Assoc w R
eis 2715342 c.-10G>C upstream_gene_variant 0.97 kanamycin Uncertain significance Mutation from literature
folC 2747471 p.Ile43Ser missense_variant 0.85 para-aminosalicylic_acid Mutation from literature
embB 4248002 p.Gln497Lys missense_variant 0.9 ethambutol Assoc w R
gid 4407695 p.Glu170* stop_gained 0.86 streptomycin 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
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 7892 c.591G>A synonymous_variant 0.85 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.9 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rpoB 760305 p.Arg167Cys missense_variant 0.81 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 766275 p.Ala969Val missense_variant 0.85 rifampicin
rpoC 767123 p.Val1252Leu missense_variant 0.82 rifampicin Uncertain significance
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.29 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674265 p.Ala22Ser missense_variant 0.89 isoniazid Uncertain significance
ethionamide Uncertain significance
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 2154418 p.Val565Gly missense_variant 0.95 isoniazid Uncertain significance
katG 2154980 p.Leu378Met missense_variant 0.9 isoniazid Uncertain significance
PPE35 2170137 p.Ser159Leu missense_variant 0.87 pyrazinamide
PPE35 2170568 p.Ile15Met missense_variant 0.82 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
Rv2752c 3065439 c.753C>T synonymous_variant 0.88 levofloxacin Not assoc w R - Interim
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
whiB7 3568476 c.204T>C synonymous_variant 0.88 kanamycin
amikacin
streptomycin
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoA 3878580 c.-73A>G upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoA 3879070 c.-563G>A upstream_gene_variant 0.9 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.92 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin