TB-Profiler result

Run: ERR4829975
Summary

Run ID: ERR4829975

Sample name:

Date: 2024-06-18T07:58:26.057046

Number of reads: 3634922

Percentage reads mapped: 99.6

Median coverage: 89.0

Strain: lineage4.5;lineage4.9

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 0.88
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 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
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Pro54Leu Assoc w R
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
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 0.16 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 0.25 rifampicin Assoc w R
pncA 2289081 p.Pro54Leu missense_variant 0.15 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.16 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
dnaA 1199 p.Arg400His missense_variant 0.85 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 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.83 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576400 c.1053C>T synonymous_variant 0.16 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ccsA 620029 c.139C>T synonymous_variant 0.9 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rpoB 759485 c.-322G>A upstream_gene_variant 0.88 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1406101 p.Pro414Ser missense_variant 0.78 streptomycin Uncertain significance
isoniazid Not assoc w R
pyrazinamide Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475395 n.1738T>C non_coding_transcript_exon_variant 0.86 capreomycin
linezolid Uncertain significance
tsnR 1853597 c.-9G>C upstream_gene_variant 0.94 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.89 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169991 p.Gly208Ser missense_variant 0.74 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.27 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.25 pyrazinamide
PPE35 2170568 p.Ile15Met missense_variant 0.77 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783502 c.541T>C synonymous_variant 0.19 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2784443 c.-401G>T upstream_gene_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3087367 p.Ala183Val missense_variant 0.2 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.76 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877536 c.972C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
clpC1 4038318 p.Pro796Leu missense_variant 0.83 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.86 ethambutol Not assoc w R
ubiA 4269124 p.Ala237Val missense_variant 0.12 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.87 capreomycin
amikacin
kanamycin
gid 4407967 p.Leu79Trp missense_variant 0.9 streptomycin Uncertain significance