TB-Profiler result

Run: SRR29093783
Summary

Run ID: SRR29093783

Sample name:

Date: 2025-02-11T16:30:10.178347

Number of reads: 3371998

Percentage reads mapped: 99.26

Median coverage: 114.0

Strain: lineage4.3.4.2.1

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 0.99
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.99
lineage4.3.4 Euro-American (LAM) RD174 0.99
lineage4.3.4.2 Euro-American (LAM) RD174 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Leu Assoc w R
isoniazid katG p.Leu141Phe Uncertain significance Mutation from literature
ethambutol embB p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Trp68* Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Gly88Cys Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Gly88Cys 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 7563 p.Gly88Cys missense_variant 0.99 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761140 p.His445Leu missense_variant 0.99 rifampicin Assoc w R
katG 2155689 p.Leu141Phe missense_variant 0.98 isoniazid Uncertain significance Mutation from literature
pncA 2289038 p.Trp68* stop_gained 0.99 pyrazinamide Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.99 ethambutol Uncertain significance Mutation from literature
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 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13631 c.-73T>G upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.99 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2784211 c.-169A>C upstream_gene_variant 0.29 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.99 pyrazinamide Not assoc w R
Rv3236c 3612865 p.Ser84Arg missense_variant 1.0 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.99 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.98 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246567 c.54G>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4248018 p.Val502Ala missense_variant 1.0 ethambutol
whiB6 4338411 c.64_110delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT frameshift_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338411 c.65_110delCAGTAACCGCCCTGTATGAGGTCCCGCTCGGCGTTTGCACGCAAGA frameshift_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R
gid 4408175 p.Ala10Pro missense_variant 1.0 streptomycin Uncertain significance