TB-Profiler result

Run: ERR4814015
Summary

Run ID: ERR4814015

Sample name:

Date: 2025-05-18T06:09:28.817044

Number of reads: 2410404

Percentage reads mapped: 99.75

Median coverage: 74.0

Strain: lineage4.3.4.1;lineage4.7

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.54
lineage4.3.4.1 Euro-American (LAM) RD174 0.49
lineage4.7 Euro-American (mainly T) None 0.47
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.53
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 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 0.49 isoniazid Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.57 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 779352 c.-872C>G upstream_gene_variant 0.45 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.65 pyrazinamide 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 1474294 n.637C>G non_coding_transcript_exon_variant 0.51 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.41 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2101881 p.Ser388Gly missense_variant 0.56 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
Rv1979c 2222854 p.Ile104Thr missense_variant 0.44 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2784413 c.-371C>T upstream_gene_variant 0.49 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.45 para-aminosalicylic_acid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.52 cycloserine Uncertain significance
Rv3083 3449827 p.Gly442Ser missense_variant 0.55 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.62 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.45 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.33 pyrazinamide Not assoc w R
clpC1 4039991 c.714G>A synonymous_variant 0.46 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.55 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 0.42 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.41 streptomycin Not assoc w R