TB-Profiler result

Run: ERR11081121
Summary

Run ID: ERR11081121

Sample name:

Date: 2024-10-05T09:17:53.778315

Number of reads: 5297537

Percentage reads mapped: 99.72

Median coverage: 150.0

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) None 1.0
lineage4 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.Leu430Arg Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.His445Tyr Assoc w R
isoniazid katG c.-7947_*17952del Assoc w R High-level resistance
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA c.495_496insAA Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.588_592dupGGTGG Assoc w R
kanamycin
cycloserine
ethionamide ethA c.878_881dupTGTG Assoc w R
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 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761095 p.Leu430Arg missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin Assoc w R
tlyA 1918521 c.588_592dupGGTGG frameshift_variant 1.0 capreomycin Assoc w R
katG 2135936 c.-7947_*17952del transcript_ablation 1.0 isoniazid Assoc w R High-level resistance
pncA 2288746 c.495_496insAA frameshift_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol Assoc w R
ethA 4326592 c.878_881dupTGTG frameshift_variant 1.0 ethionamide 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
dnaA 524 p.Asp175Ala missense_variant 0.99 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9381 p.Gly694Ser missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
Rv0565c 657040 p.Gly144Ala missense_variant 1.0 ethionamide Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775715 c.2766G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254249 p.Gly96Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834034 p.Ile165Pro missense_variant 1.0 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168439 p.Ser725Phe missense_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2784617 c.-575T>C upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ribD 2986827 c.-12G>A upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv2752c 3065059 p.Ala378Val missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyX 3067665 p.Ile94Thr missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3449003 c.503_508dupACTGGC disruptive_inframe_insertion 0.96 ethionamide Uncertain significance
alr 3841362 p.Thr20Met missense_variant 1.0 cycloserine
rpoA 3877836 c.672A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
clpC1 4040705 c.-1G>A upstream_gene_variant 1.0 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269124 p.Ala237Val missense_variant 1.0 ethambutol 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
gid 4407590 p.Ala205Thr missense_variant 1.0 streptomycin Uncertain significance
gid 4408057 p.Leu49Arg missense_variant 1.0 streptomycin Uncertain significance