TB-Profiler result

Run: ERR12544387
Summary

Run ID: ERR12544387

Sample name:

Date: 2024-03-26T17:50:52.689961

Number of reads: 2120807

Percentage reads mapped: 99.79

Median coverage: 79.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.97
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.96
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 7058 p.Ile607Val missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 8040 p.Gly247Ser missense_variant 0.95 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
Rv0010c 13824 c.-266A>T upstream_gene_variant 0.17 isoniazid
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.19 isoniazid
Rv0010c 13834 c.-276A>T upstream_gene_variant 0.2 isoniazid
rpoC 764995 c.1626C>G synonymous_variant 1.0 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
fbiC 1303095 c.165G>A synonymous_variant 0.98 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474438 n.781A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834836 p.Met432Thr missense_variant 0.98 pyrazinamide Not assoc w R - Interim
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 2156196 c.-85C>T upstream_gene_variant 1.0 isoniazid Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.35 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.34 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518348 c.234A>T synonymous_variant 0.18 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
folC 2746340 p.Ala420Val missense_variant 1.0 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339741 c.624G>T synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiD 3339744 c.627A>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625789 p.Phe275Leu missense_variant 0.2 bedaquiline
rifampicin
rpoA 3878567 c.-60C>G upstream_gene_variant 0.49 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.94 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.27 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.33 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.32 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.32 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.34 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.28 ethambutol Not assoc w R - Interim
aftB 4268566 p.Ser91Ala 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
gid 4408156 p.Leu16Arg missense_variant 0.96 streptomycin Not assoc w R