TB-Profiler result

Run: SRR13837942
Summary

Run ID: SRR13837942

Sample name:

Date: 2025-03-05T07:04:54.352361

Number of reads: 1468254

Percentage reads mapped: 100.0

Median coverage: 50.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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
gyrB 5785 c.546C>T synonymous_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6314 c.1076dupC frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7495 p.Arg65His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8780 p.Asp493Glu missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13273 p.Gly96Cys missense_variant 1.0 isoniazid Uncertain significance
Rv0010c 13363 p.Asp66Tyr missense_variant 1.0 isoniazid Uncertain significance
mshA 574744 c.-604G>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
ccsA 620129 p.Gly80Ala missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
rpoB 761845 p.Gln680Arg missense_variant 1.0 rifampicin Uncertain significance
rpsL 781185 c.-375T>G upstream_gene_variant 1.0 streptomycin Uncertain significance
rpsL 781226 c.-334C>T upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800937 c.129A>G synonymous_variant 1.0 linezolid Uncertain significance
embR 1416298 c.1050G>C synonymous_variant 1.0 ethambutol Uncertain significance
embR 1417588 c.-241C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
rrl 1475592 n.1935A>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1918324 p.Val129Leu missense_variant 1.0 capreomycin Uncertain significance
bacA 2064860 c.-132A>G upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2168503 p.Phe704Leu missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670His missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223395 c.-231G>T upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
ahpC 2726771 c.579T>A synonymous_variant 1.0 isoniazid Uncertain significance
folC 2746808 p.Ala264Gly missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2752c 3067057 c.-867_-866insG upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3087587 c.769delC frameshift_variant 1.0 cycloserine Uncertain significance
lpqB 3624686 p.Glu75Asp missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3641252 p.Thr237Ser missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3877496 p.Glu338* stop_gained 1.0 rifampicin Uncertain significance
ddn 3986684 c.-160G>C upstream_gene_variant 1.0 delamanid Uncertain significance
pretomanid Uncertain significance
embC 4238901 c.-962T>A upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4240480 c.618G>A synonymous_variant 0.99 ethambutol Uncertain significance
embA 4244410 p.Trp393Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4249447 c.2934G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338681 c.-160A>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance