TB-Profiler result

Run: ERR4815695
Summary

Run ID: ERR4815695

Sample name:

Date: 2025-05-11T12:48:50.877061

Number of reads: 1804846

Percentage reads mapped: 99.67

Median coverage: 38.0

Strain: lineage1.2.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.2
lineage4.3 Euro-American (LAM) None 0.78
lineage4 Euro-American None 0.81
lineage1 Indo-Oceanic RD239 0.17
lineage1.2.1.2.1 Indo-Oceanic RD239 0.18
lineage1.2.1 Indo-Oceanic RD239 0.17
lineage4.3.3 Euro-American (LAM) RD115 0.77
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 8040 p.Gly247Ser missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13589 c.-31G>A upstream_gene_variant 0.76 isoniazid Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 763531 c.162G>C synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.79 rifampicin 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
rplC 800357 c.-452C>A upstream_gene_variant 0.21 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.26 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406312 c.1029T>C synonymous_variant 0.24 isoniazid Not assoc w R
pyrazinamide Not assoc w R
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
rpsA 1834836 p.Met432Thr missense_variant 0.66 pyrazinamide Not assoc w R - Interim
tsnR 1853663 p.Gly20Ser missense_variant 0.88 linezolid 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
PPE35 2167926 p.Leu896Ser missense_variant 0.19 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518919 p.Gly269Ser missense_variant 0.84 isoniazid Uncertain significance
Rv2477c 2782724 p.Ala440Val missense_variant 0.82 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783243 p.Thr267Ile missense_variant 0.73 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2680 2996056 c.-49G>C upstream_gene_variant 0.15 capreomycin Uncertain significance
Rv2680 2996107 p.Leu1? start_lost 0.33 capreomycin Uncertain significance
Rv2752c 3065371 p.Arg274Thr missense_variant 0.75 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.78 para-aminosalicylic_acid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
whiB7 3568488 c.191delG frameshift_variant 0.27 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640557 c.15T>C synonymous_variant 0.16 clofazimine Not assoc w R - Interim
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.82 pyrazinamide Not assoc w R
clpC1 4039004 c.1701C>T synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.26 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.26 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.21 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247578 c.1065G>A synonymous_variant 0.3 ethambutol Not assoc w R
embB 4248064 c.1551G>C synonymous_variant 0.81 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.26 ethambutol Not assoc w R
whiB6 4338361 p.Arg54Gln missense_variant 0.19 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin 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 4338603 c.-82C>T upstream_gene_variant 0.17 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
gid 4407588 c.615A>G synonymous_variant 0.28 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.3 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.78 streptomycin Not assoc w R