TB-Profiler result

Run: SRR28868654
Summary

Run ID: SRR28868654

Sample name:

Date: 2025-02-11T16:55:37.559653

Number of reads: 10309671

Percentage reads mapped: 98.74

Median coverage: 343.0

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
mshA 576347 p.Thr334Ala missense_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 576618 p.His424Pro missense_variant 0.18 isoniazid
ethionamide
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 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155433 c.679C>T synonymous_variant 1.0 isoniazid
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 0.96 bedaquiline Uncertain significance
clofazimine Not assoc w R
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0 ethionamide
Rv3083 3448508 c.6_*1407del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
whiB7 3568425 c.255T>G synonymous_variant 0.37 kanamycin
amikacin
streptomycin
whiB7 3568428 c.252A>C synonymous_variant 0.33 kanamycin
amikacin
streptomycin
whiB7 3568492 p.Trp63* stop_gained 0.99 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
embC 4240413 p.Leu184Arg missense_variant 0.23 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol