TB-Profiler result

Run: ERR2229367
Summary

Run ID: ERR2229367

Sample name:

Date: 2024-04-15T01:41:19.830970

Number of reads: 1307107

Percentage reads mapped: 96.53

Median coverage: 27.0

Strain: 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 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
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
Rv0565c 657612 c.-142C>T upstream_gene_variant 0.16 ethionamide
Rv0565c 657621 c.-151A>G upstream_gene_variant 0.18 ethionamide
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303747 p.Thr273Ala missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2167965 p.Ala883Gly missense_variant 0.19 pyrazinamide
PPE35 2167967 c.2646A>C synonymous_variant 0.19 pyrazinamide
PPE35 2168728 p.Gly629Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169902 c.709_711delCTGinsTC frameshift_variant&synonymous_variant 0.17 pyrazinamide Uncertain significance
PPE35 2169910 p.Asn235Tyr missense_variant 0.15 pyrazinamide
PPE35 2170048 p.Leu189Val missense_variant 0.66 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.66 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv3083 3448473 c.-30_*1408del transcript_ablation 1.0 ethionamide Uncertain significance
alr 3841612 c.-193_-192insC upstream_gene_variant 0.18 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.42 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.62 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.67 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.67 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 0.98 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R