TB-Profiler result

Run: ERR11243572
Summary

Run ID: ERR11243572

Sample name:

Date: 2024-10-05T12:02:25.409402

Number of reads: 5885384

Percentage reads mapped: 99.71

Median coverage: 133.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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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
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin gid p.His48Gln Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gid 4408059 p.His48Gln missense_variant 1.0 streptomycin 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 13824 c.-266A>T upstream_gene_variant 0.14 isoniazid
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.13 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
Rv1258c 1407062 c.279G>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rpsA 1833641 p.Asn34Asp missense_variant 0.11 pyrazinamide
rpsA 1833651 p.Asp37Ala missense_variant 0.12 pyrazinamide
rpsA 1833658 c.117C>T synonymous_variant 0.12 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223491 c.-327C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518348 c.234A>T synonymous_variant 0.13 isoniazid
folC 2747750 c.-152G>A upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782721 p.Gly441Ala missense_variant 1.0 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
fbiD 3339741 c.624G>T synonymous_variant 0.12 pretomanid
delamanid
clofazimine
fbiD 3339744 c.627A>C synonymous_variant 0.12 pretomanid
delamanid
clofazimine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
rpoA 3878599 c.-92C>G upstream_gene_variant 0.12 rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243331 c.99G>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.32 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.34 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.36 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.36 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.37 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.39 ethambutol Not assoc w R - Interim
aftB 4268078 c.759C>A synonymous_variant 1.0 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R