TB-Profiler result

Run: ERR400498
Summary

Run ID: ERR400498

Sample name:

Date: 2024-04-15T23:55:04.896564

Number of reads: 6630319

Percentage reads mapped: 99.53

Median coverage: 138.0

Strain: lineage4.6.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4.6.3 Euro-American 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8049 p.Ser250Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9146 c.1845C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620072 p.Pro61Leu missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
nusG 734562 c.309G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762375 p.Ala857Thr missense_variant 0.99 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776987 c.1493delC frameshift_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 778673 p.Pro78Leu missense_variant 1.0 clofazimine Uncertain significance
bedaquiline 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 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674090 c.-112C>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834040 p.Lys167Gln missense_variant 1.0 pyrazinamide
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626638 c.-25G>T upstream_gene_variant 0.99 bedaquiline
rifampicin
mtrB 3627477 c.-864C>G upstream_gene_variant 1.0 bedaquiline
rifampicin
embC 4240968 p.His369Arg missense_variant 1.0 ethambutol
embC 4242185 p.Asp775Asn missense_variant 0.99 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
aftB 4268573 p.Met88Ile missense_variant 1.0 ethambutol Uncertain significance
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