TB-Profiler result

Run: SRR29016980
Summary

Run ID: SRR29016980

Sample name:

Date: 2025-02-11T12:34:57.431040

Number of reads: 670440

Percentage reads mapped: 99.7

Median coverage: 21.0

Strain: lineage4.3.4.1

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 0.97
lineage4.3.4.1 Euro-American (LAM) RD174 0.95
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.94
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 katG p.Ser315Asn Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.95 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
gyrA 7362 p.Glu21Gln 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
rpoC 764840 p.Ile491Val missense_variant 0.97 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.9 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 778994 p.Ser2Ile missense_variant 0.92 bedaquiline Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.98 capreomycin Not assoc w R
katG 2154279 c.1833C>T synonymous_variant 0.92 isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.86 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3064692 c.1498_1499dupGA frameshift_variant 0.95 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3087014 p.Trp65* stop_gained 0.92 cycloserine
Rv3083 3449070 c.567G>A synonymous_variant 0.96 ethionamide Not assoc w R - Interim
Rv3236c 3612009 p.Ala370Thr missense_variant 0.96 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.92 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.97 ethambutol Not assoc w R
embA 4243218 c.-15C>G upstream_gene_variant 0.97 ethambutol Uncertain significance
gid 4407848 p.Ala119Thr missense_variant 0.89 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.92 streptomycin Not assoc w R