TB-Profiler result

Run: SRR5341216
Summary

Run ID: SRR5341216

Sample name:

Date: 2024-04-15T00:58:39.664258

Number of reads: 1260039

Percentage reads mapped: 99.28

Median coverage: 36.0

Strain: lineage3;lineage4.1.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.3
lineage4.1 Euro-American None 0.59
lineage4.1.2 Euro-American None 0.66
lineage4 Euro-American None 0.68
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.102delG Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 0.63 isoniazid Assoc w R High-level resistance
gid 4408100 c.102delG frameshift_variant 0.66 streptomycin 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 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
fgd1 491591 p.Lys270Met missense_variant 0.63 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.71 rifampicin Not assoc w R
rpoB 761421 p.Asn539His missense_variant 0.28 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764263 c.894G>A synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.6 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 776100 p.Thr794Ile missense_variant 0.37 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
rplC 800200 c.-609C>G upstream_gene_variant 0.63 linezolid
Rv1129c 1253097 p.Ser480Pro missense_variant 0.81 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.31 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
PPE35 2167926 p.Leu896Ser missense_variant 0.48 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.61 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.58 pyrazinamide
Rv1979c 2221988 p.Leu393Ile missense_variant 0.25 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.52 isoniazid
thyX 3067423 c.523C>T synonymous_variant 0.36 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449566 p.Gly355Arg missense_variant 0.77 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.29 ethambutol Not assoc w R
embC 4242329 p.Glu823Lys missense_variant 0.75 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.82 ethambutol Not assoc w R
ethA 4327728 c.-255C>T upstream_gene_variant 0.58 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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.38 streptomycin Not assoc w R