TB-Profiler result

Run: SAMEA4041354
Summary

Run ID: SAMEA4041354

Sample name:

Date: 2025-05-04T06:08:10.919779

Number of reads: 9252371

Percentage reads mapped: 99.71

Median coverage: 165.0

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
dnaA 902 p.Val301Ala missense_variant 0.13 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.99 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1673357 c.-845G>A upstream_gene_variant 0.16 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1673359 c.-843T>C upstream_gene_variant 0.16 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1673361 c.-841C>G upstream_gene_variant 0.16 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1673380 c.-822C>G upstream_gene_variant 0.24 ethionamide Uncertain significance
isoniazid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.52 pyrazinamide Uncertain significance
PPE35 2170053 p.Thr187Ser missense_variant 0.53 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289461 c.-220T>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin Uncertain significance
thyX 3067570 p.Ala126Thr missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv3083 3448507 c.5_*1407del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
whiB7 3568417 p.Lys88Thr missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3613379 c.-263T>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.22 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.26 ethambutol Uncertain significance
embB 4246556 p.Ala15Pro missense_variant 0.26 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R