TB-Profiler result

Run: ERR2653199
Summary

Run ID: ERR2653199

Sample name:

Date: 2024-10-05T09:48:36.324137

Number of reads: 4282015

Percentage reads mapped: 97.46

Median coverage: 137.0

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) None 0.98
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.99
lineage4.3.4.2 Euro-American (LAM) RD174 0.99
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)
p.Ile194Thr Uncertain significance Mutation from literature
katG p.Met257Ile Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Asp12Asn Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
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
gyrA 7570 p.Ala90Val missense_variant 0.96 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.96 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)
inhA 1674782 p.Ile194Thr missense_variant 0.99 ethionamide Uncertain significance Mutation from literature
isoniazid Uncertain significance Mutation from literature
katG 2155341 p.Met257Ile missense_variant 0.7 isoniazid Uncertain significance Mutation from literature
pncA 2289208 p.Asp12Asn missense_variant 0.97 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.99 ethambutol 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
gyrB 6140 p.Val301Leu missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6737 p.Thr500Ala missense_variant 0.98 levofloxacin Uncertain significance
moxifloxacin 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.95 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.97 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 1254569 c.-35G>A upstream_gene_variant 0.99 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254623 c.-89C>T upstream_gene_variant 0.24 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854145 c.540C>T synonymous_variant 0.95 linezolid
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
ndh 2102366 p.Ala226Val missense_variant 0.97 isoniazid
delamanid
ethionamide
katG 2155607 p.Gly169Ser missense_variant 0.14 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2715225 p.Trp36* stop_gained 0.59 kanamycin Uncertain significance
amikacin Uncertain significance
eis 2715346 c.-14C>T upstream_gene_variant 0.97 kanamycin Assoc w R
amikacin Assoc w R - Interim
folC 2747386 c.213C>T synonymous_variant 0.99 para-aminosalicylic_acid
Rv2477c 2784552 c.-510C>T upstream_gene_variant 0.94 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.98 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
ald 3087531 p.Ala238Thr missense_variant 0.98 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.99 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.97 cycloserine
rpoA 3878592 c.-85C>A upstream_gene_variant 0.94 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.99 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 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 0.99 kanamycin
capreomycin
amikacin
gid 4408009 p.Val65Gly missense_variant 0.98 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R