TB-Profiler result

Run: SRR15316209
Summary

Run ID: SRR15316209

Sample name:

Date: 2024-10-04T09:44:43.427841

Number of reads: 6174014

Percentage reads mapped: 98.17

Median coverage: 189.0

Strain: lineage4.4.2;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 0.89
lineage4.4 Euro-American None 0.13
lineage4.4.2 Euro-American None 0.09
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 1326 p.Gln442His missense_variant 0.9 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmaA3 737591 p.Gly187Ser missense_variant 0.86 isoniazid
rpoB 761631 p.Ala609Ser missense_variant 0.12 rifampicin
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 0.99 streptomycin Not assoc w R
Rv1129c 1254624 c.-90G>A upstream_gene_variant 0.1 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.15 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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 2519001 p.Glu296Ala missense_variant 0.19 isoniazid
Rv2752c 3066099 p.Met31Ile missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3074122 p.Asp117Gly missense_variant 0.88 para-aminosalicylic_acid
ald 3086727 c.-93G>A upstream_gene_variant 0.79 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.2 cycloserine
ald 3086938 p.Gly40Glu missense_variant 0.86 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.12 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840486 p.Ile312Ser missense_variant 0.11 cycloserine
embC 4238963 c.-900C>T upstream_gene_variant 0.16 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.14 ethambutol Not assoc w R
embA 4243072 c.-161C>T upstream_gene_variant 0.89 ethambutol
embB 4248109 c.1596C>G synonymous_variant 0.16 ethambutol
aftB 4268044 p.Ala265Ser missense_variant 0.86 ethambutol
ubiA 4268928 c.906C>T synonymous_variant 0.13 ethambutol Not assoc w R
ethR 4326681 c.-868G>A upstream_gene_variant 0.9 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.16 kanamycin
capreomycin
amikacin