TB-Profiler result

Run: SRR13837653
Summary

Run ID: SRR13837653

Sample name:

Date: 2024-04-15T02:58:15.985233

Number of reads: 293816

Percentage reads mapped: 98.0

Median coverage: 10.0

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
Rv0565c 657081 c.390G>C synonymous_variant 1.0 ethionamide
rpoB 759613 c.-194C>A upstream_gene_variant 1.0 rifampicin
rpoB 759854 p.Ser16Arg missense_variant 1.0 rifampicin
rpoC 766845 p.Arg1159His missense_variant 1.0 rifampicin
mmpR5 778208 c.-782C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
fbiC 1305195 c.2265T>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
katG 2155055 p.Tyr353Asn missense_variant 1.0 isoniazid
eis 2714776 p.Val186Glu missense_variant 1.0 amikacin
kanamycin
Rv2477c 2782646 c.1396delC frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2752c 3065052 p.Glu380Asp missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073902 c.570C>G synonymous_variant 1.0 para-aminosalicylic_acid
lpqB 3623705 c.1205dupA frameshift_variant 1.0 bedaquiline
rifampicin Uncertain significance
panD 4044175 p.Ala36Asp missense_variant 1.0 pyrazinamide
embC 4240583 p.Thr241Ala missense_variant 1.0 ethambutol
whiB6 4338609 c.-88T>G upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407696 c.507C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim