TB-Profiler result

Run: SRR13837569
Summary

Run ID: SRR13837569

Sample name:

Date: 2024-04-16T10:50:48.314935

Number of reads: 587646

Percentage reads mapped: 100.0

Median coverage: 19.0

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
moxifloxacin
gyrB 6314 c.1076dupC frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
gyrA 7495 p.Arg65His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8780 p.Asp493Glu missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13273 p.Gly96Cys missense_variant 1.0 isoniazid
Rv0010c 13363 p.Asp66Tyr missense_variant 1.0 isoniazid
mshA 574744 c.-604G>A upstream_gene_variant 1.0 ethionamide
isoniazid
ccsA 620129 p.Gly80Ala missense_variant 1.0 capreomycin
amikacin
kanamycin
rpoB 761845 p.Gln680Arg missense_variant 1.0 rifampicin
rpsL 781185 c.-375T>G upstream_gene_variant 1.0 streptomycin
rpsL 781226 c.-334C>T upstream_gene_variant 1.0 streptomycin
rplC 800937 c.129A>G synonymous_variant 1.0 linezolid
embR 1416298 c.1050G>C synonymous_variant 1.0 ethambutol
embR 1417588 c.-241C>T upstream_gene_variant 1.0 ethambutol
rrl 1475592 n.1935A>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
tlyA 1918324 p.Val129Leu missense_variant 1.0 capreomycin
bacA 2064860 c.-132A>G upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
PPE35 2168503 p.Phe704Leu missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670His missense_variant 1.0 pyrazinamide
Rv1979c 2223395 c.-231G>T upstream_gene_variant 1.0 clofazimine
bedaquiline
ahpC 2726771 c.579T>A synonymous_variant 1.0 isoniazid
folC 2746808 p.Ala264Gly missense_variant 1.0 para-aminosalicylic_acid
Rv2752c 3067057 c.-867_-866insG upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3087587 c.769delC frameshift_variant 1.0 cycloserine
lpqB 3624686 p.Glu75Asp missense_variant 1.0 bedaquiline
rifampicin
fbiA 3641252 p.Thr237Ser missense_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3877496 p.Glu338* stop_gained 1.0 rifampicin
ddn 3986684 c.-160G>C upstream_gene_variant 1.0 delamanid
pretomanid
embC 4238901 c.-962T>A upstream_gene_variant 1.0 ethambutol
embC 4240480 c.618G>A synonymous_variant 1.0 ethambutol
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 0.96 capreomycin
amikacin
kanamycin