TB-Profiler result

Run: ERR12546193
Summary

Run ID: ERR12546193

Sample name:

Date: 2024-04-15T11:03:05.285063

Number of reads: 3120391

Percentage reads mapped: 99.7

Median coverage: 117.0

Strain: lineage4.3.3;lineage4.8

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 0.13
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.89
lineage4.3.3 Euro-American (LAM) RD115 0.1
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 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.93 ethionamide Uncertain significance
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 0.15 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 1474001 n.344C>T non_coding_transcript_exon_variant 0.91 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rpsA 1834836 p.Met432Thr missense_variant 0.17 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.15 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.9 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.36 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.89 capreomycin
ald 3086997 p.Thr60Gly missense_variant 0.14 cycloserine
fbiD 3339744 c.627A>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
mtrB 3625065 p.Met517Leu missense_variant 0.23 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878567 c.-60C>G upstream_gene_variant 0.29 rifampicin
rpoA 3878599 c.-92C>G upstream_gene_variant 0.39 rifampicin
rpoA 3878639 c.-132C>G upstream_gene_variant 0.18 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.12 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.54 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.57 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.54 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.54 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.57 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.54 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.17 streptomycin Not assoc w R