TB-Profiler result

Run: SRR10809051
Summary

Run ID: SRR10809051

Sample name:

Date: 2024-04-15T09:57:57.316224

Number of reads: 2994698

Percentage reads mapped: 99.61

Median coverage: 95.0

Strain: lineage4.3;lineage4.9

Spoligotype:

Drug-resistance: HR-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 0.13
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.85
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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
pyrazinamide pncA p.His82Arg Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 0.22 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
pncA 2288997 p.His82Arg missense_variant 0.14 pyrazinamide 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 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9074 c.1773G>A synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.14 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777182 c.1299C>T synonymous_variant 0.83 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1406785 p.Leu186Phe missense_variant 0.18 streptomycin
isoniazid
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472179 n.334C>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154350 p.Glu588Lys missense_variant 0.86 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2681 2997347 p.Glu203Asp missense_variant 0.82 capreomycin
Rv2752c 3066335 c.-144T>G upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.21 cycloserine
Rv3236c 3612176 p.Arg314Gln missense_variant 0.15 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841612 c.-193_-192insC upstream_gene_variant 0.81 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.2 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4243081 c.3219T>G synonymous_variant 0.81 ethambutol Not assoc w R - Interim
ethA 4326423 p.Gly351Trp missense_variant 0.87 ethionamide
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 0.22 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.25 streptomycin Not assoc w R