TB-Profiler result

Run: SRR5818596
Summary

Run ID: SRR5818596

Sample name:

Date: 2025-06-01T19:29:08.473103

Number of reads: 2702506

Percentage reads mapped: 95.54

Median coverage: 56.0

Strain: lineage4.2

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 Euro-American None 0.88
lineage4 Euro-American None 0.93
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
dnaA 1377 c.1377G>A synonymous_variant 0.85 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8475 p.Arg392Cys missense_variant 0.87 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmaA3 737382 non_coding_transcript_variant 0.91 isoniazid Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777178 p.Glu435Gln missense_variant 0.82 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777356 non_coding_transcript_variant 0.75 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.87 linezolid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1833525 c.-17C>G upstream_gene_variant 0.66 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.83 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 0.96 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.33 pyrazinamide Uncertain significance
PPE35 2170053 p.Thr187Ser missense_variant 0.31 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747158 non_coding_transcript_variant 0.92 para-aminosalicylic_acid Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.92 cycloserine Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3626679 p.Lys224Arg missense_variant 0.94 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3640402 c.-141C>G upstream_gene_variant 0.83 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embC 4238938 c.-925T>C upstream_gene_variant 0.9 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
gid 4408160 p.Arg15Trp missense_variant 0.95 streptomycin Uncertain significance