TB-Profiler result

Run: SRR6824642
Summary

Run ID: SRR6824642

Sample name:

Date: 2024-04-14T20:07:22.661446

Number of reads: 11686221

Percentage reads mapped: 99.05

Median coverage: 344.0

Strain: lineage4.4.2

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 Euro-American None 1.0
lineage4.4 Euro-American None 1.0
lineage4.4.2 Euro-American None 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.His445Asn Assoc w R
p.Leu452Pro Assoc w R
isoniazid ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg 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
rpoB 761139 p.His445Asn missense_variant 0.17 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.15 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.15 streptomycin Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 0.18 pyrazinamide Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 0.16 isoniazid Uncertain significance Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.17 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.21 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 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
mshA 575906 p.Ala187Thr missense_variant 0.16 ethionamide Uncertain significance
isoniazid Uncertain significance
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
Rv1129c 1254651 c.-117C>T upstream_gene_variant 0.8 moxifloxacin
levofloxacin
rifampicin
isoniazid
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
katG 2156110 p.Val1Gly missense_variant 0.16 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783026 p.Asp339Glu missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2752c 3065437 p.Ala252Val missense_variant 0.83 ethambutol Uncertain significance
moxifloxacin
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3066099 p.Met31Ile missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448727 p.Leu75Arg missense_variant 0.99 ethionamide Uncertain significance
Rv3083 3449107 p.Gly202Cys missense_variant 0.14 ethionamide
Rv3083 3449921 p.Leu473Arg missense_variant 0.81 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641333 p.Gly264Glu missense_variant 0.84 clofazimine
pretomanid
delamanid
alr 3840947 c.474G>A synonymous_variant 0.83 cycloserine
clpC1 4039058 p.Phe549Leu missense_variant 0.17 pyrazinamide
clpC1 4039291 p.Asp472Tyr missense_variant 0.86 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4239221 c.-642C>T upstream_gene_variant 0.82 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243991 c.759T>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embA 4246508 c.3276G>A synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.99 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 1.0 ethambutol Not assoc w R
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