TB-Profiler result

Run: ERR234634
Summary

Run ID: ERR234634

Sample name:

Date: 2025-05-18T21:45:07.820631

Number of reads: 5729448

Percentage reads mapped: 99.62

Median coverage: 126.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.98
lineage4.1.2 Euro-American None 0.98
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 ethR p.Phe110Leu Uncertain significance Mutation from literature
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
ethR 4327876 p.Phe110Leu missense_variant 0.98 ethionamide Uncertain significance Mutation from literature
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13639 c.-81C>G upstream_gene_variant 0.98 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.98 clofazimine Not assoc w R
delamanid Uncertain significance
pretomanid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.96 ethionamide Uncertain significance
rpoB 759841 p.Ser12Thr missense_variant 0.99 rifampicin Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.95 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 800200 c.-609C>G upstream_gene_variant 0.99 linezolid Uncertain significance
rplC 800889 c.81C>A synonymous_variant 0.97 linezolid Not assoc w R - Interim
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
PPE35 2168303 c.2310G>T synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
PPE35 2169776 p.Phe279Leu missense_variant 0.98 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.97 isoniazid Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.48 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.15 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840263 non_coding_transcript_variant 0.94 cycloserine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.97 ethambutol Not assoc w R
embB 4247086 c.573C>T synonymous_variant 0.96 ethambutol Not assoc w R - Interim
ubiA 4269847 c.-14A>G upstream_gene_variant 0.98 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance