TB-Profiler result

Run: ERR4820558
Summary

Run ID: ERR4820558

Sample name:

Date: 2025-05-13T03:33:33.903204

Number of reads: 3561256

Percentage reads mapped: 99.72

Median coverage: 73.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Other

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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 tlyA c.615_688delGCGGTCGGTGCTCGCGGTCGCGCGGCGGGCACAGGAGCTGGGCTGGCACAGCGTCGGCGTCAAGGCCAGCCCGC Assoc w R
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
tlyA 1918551 c.615_688delGCGGTCGGTGCTCGCGGTCGCGCGGCGGGCACAGGAGCTGGGCTGGCACAGCGTCGGCGTCAAGGCCAGCCCGC frameshift_variant 1.0 capreomycin 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
gyrB 6317 p.Val360Met missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8306 non_coding_transcript_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491659 p.Ala293Thr missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 576683 p.Gly446Ser missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
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 0.99 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin 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 2169192 p.Ala474Gly missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv3083 3448507 c.5_*1407del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
clpC1 4039023 p.Glu561Ala missense_variant 1.0 pyrazinamide Uncertain significance
embC 4241729 p.Ala623Thr missense_variant 1.0 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246548 p.Pro12Gln missense_variant 1.0 ethambutol Uncertain significance
ethR 4326976 c.-573G>A upstream_gene_variant 0.99 ethionamide 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