TB-Profiler result

Run: ERR1633888
Summary

Run ID: ERR1633888

Sample name:

Date: 2024-10-05T09:43:09.079706

Number of reads: 3171756

Percentage reads mapped: 99.63

Median coverage: 48.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: HR-TB

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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 0.94
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 katG c.-10145_*20021del Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-38219_*9302del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-18780_*22888del Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid fbiA c.-5250_*20197del Assoc w R - Interim Confers DLM-PMD cross-resistance
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
tlyA 1879720 c.-38219_*9302del transcript_ablation 0.92 capreomycin Assoc w R
katG 2133867 c.-10145_*20021del transcript_ablation 0.92 isoniazid Assoc w R High-level resistance
fbiA 3635292 c.-5250_*20197del transcript_ablation 0.92 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4303115 c.-18780_*22888del transcript_ablation 0.95 ethionamide Assoc w R
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
Rv0010c 13887 c.-329T>C upstream_gene_variant 0.98 isoniazid
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
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 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2164468 c.994_*3180del stop_lost&conservative_inframe_deletion&splice_region_variant 0.93 pyrazinamide
PPE35 2166262 c.2692_*1386del stop_lost&conservative_inframe_deletion&splice_region_variant 0.91 pyrazinamide
PPE35 2166549 c.1198_*1099del stop_lost&conservative_inframe_deletion&splice_region_variant 0.94 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv3236c 3574532 c.1062_*37426del frameshift_variant&stop_lost&splice_region_variant 0.93 pyrazinamide Uncertain significance
embA 4216398 c.-26834_*16207del transcript_ablation 0.95 ethambutol Uncertain significance
embA 4225572 c.-17660_*22218del transcript_ablation 0.93 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.89 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407704 p.Ala167Pro missense_variant 0.9 streptomycin Uncertain significance