TB-Profiler result

Run: ERR4811541
Summary

Run ID: ERR4811541

Sample name:

Date: 2025-06-07T21:26:14.693526

Number of reads: 6267286

Percentage reads mapped: 99.59

Median coverage: 180.0

Strain: lineage4.2.2;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.32
lineage4.5 Euro-American RD122 0.66
lineage4.2 Euro-American None 0.31
lineage4 Euro-American None 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.68 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7946 non_coding_transcript_variant 0.36 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13394 p.Trp55* stop_gained 0.69 isoniazid Uncertain significance
Rv0010c 13630 c.-72G>A upstream_gene_variant 0.12 isoniazid Uncertain significance
mshA 576077 c.730C>T synonymous_variant 0.26 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.68 amikacin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
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
rplC 800204 c.-605T>C upstream_gene_variant 0.29 linezolid Uncertain significance
Rv1129c 1254129 p.Gly136Ser missense_variant 0.65 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254591 c.-57C>T upstream_gene_variant 0.66 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918605 non_coding_transcript_variant 0.31 capreomycin Uncertain significance
bacA 2063685 c.1044G>A synonymous_variant 0.31 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
bacA 2063911 p.Ile273Thr missense_variant 0.3 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.7 pyrazinamide 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
ahpC 2726004 c.-189G>C upstream_gene_variant 0.32 isoniazid Uncertain significance
Rv2752c 3065534 p.Pro220Thr missense_variant 0.65 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.28 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.36 cycloserine Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.39 cycloserine Uncertain significance
Rv3236c 3612469 c.648A>G synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
Rv3236c 3612992 p.Ser42Gln missense_variant 0.72 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878575 c.-68C>T upstream_gene_variant 0.69 rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 0.65 rifampicin Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 0.67 pyrazinamide Not assoc w R
embC 4242201 p.Gly780Asp missense_variant 0.33 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance