TB-Profiler result

Run: SRR24466757
Summary

Run ID: SRR24466757

Sample name:

Date: 2024-03-26T15:22:39.632918

Number of reads: 3134613

Percentage reads mapped: 99.56

Median coverage: 79.0

Strain: lineage4

Spoligotype:

Drug-resistance: Sensitive

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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
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
gyrB 6463 c.1224C>T synonymous_variant 0.98 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.16 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 576651 p.Asp435Ala missense_variant 0.18 ethionamide
isoniazid
rpoC 765150 p.Gly594Glu missense_variant 0.14 rifampicin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154980 c.1132C>T synonymous_variant 0.88 isoniazid Not assoc w R - Interim
PPE35 2170811 c.-199C>T upstream_gene_variant 0.92 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2715352 c.-20A>C upstream_gene_variant 0.94 amikacin
kanamycin
Rv2680 2995868 c.-236_-232delGGGAA upstream_gene_variant 1.0 capreomycin
thyX 3067976 c.-31T>C upstream_gene_variant 0.88 para-aminosalicylic_acid
Rv3083 3448385 c.-119C>G upstream_gene_variant 0.94 ethionamide
Rv3236c 3612290 p.Leu276Arg missense_variant 0.94 pyrazinamide
fbiB 3642615 p.Pro361Ala missense_variant 0.9 clofazimine
pretomanid
delamanid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268076 p.Met254Ala missense_variant 0.94 ethambutol Uncertain significance
ethR 4326919 c.-630T>C upstream_gene_variant 0.92 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 0.99 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338885 c.-365delA upstream_gene_variant 0.93 capreomycin
amikacin
kanamycin
gid 4407938 p.Val89Leu missense_variant 0.93 streptomycin