TB-Profiler result

Run: ERR1465948
Summary

Run ID: ERR1465948

Sample name:

Date: 2025-05-04T11:27:38.028402

Number of reads: 6155774

Percentage reads mapped: 99.73

Median coverage: 127.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: Sensitive

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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
isoniazid
ethambutol
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
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
mmaA3 738145 p.Ser2Tyr missense_variant 1.0 isoniazid 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
mmpL5 776592 p.Leu630Pro missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
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 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2101807 c.1236C>T synonymous_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
whiB7 3568758 c.-79C>G upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
alr 3841546 c.-126C>A upstream_gene_variant 1.0 cycloserine Uncertain significance
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0 cycloserine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245420 c.2188C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338647 c.-126C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407590 p.Ala205Thr missense_variant 0.99 streptomycin Uncertain significance