TB-Profiler result

Run: SRR13837715
Summary

Run ID: SRR13837715

Sample name:

Date: 2025-03-05T15:34:59.233428

Number of reads: 2936699

Percentage reads mapped: 100.0

Median coverage: 100.0

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
dnaA 1427 p.Ala476Gly missense_variant 1.0 isoniazid Uncertain significance
gyrA 7346 p.Ile15Met missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8335 p.Met345Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9639 p.Gly780Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491505 c.723G>A synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 576310 p.Ile321Met missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657451 p.Ala7Val missense_variant 1.0 ethionamide Uncertain significance
mmpL5 775981 p.Leu834Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776732 c.1749C>T synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777942 p.Pro180Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800343 c.-466G>C upstream_gene_variant 1.0 linezolid Uncertain significance
fbiC 1303422 c.492A>G synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1406592 p.Tyr250Cys missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1416737 p.Arg204Gln missense_variant 1.0 ethambutol Uncertain significance
rrl 1475277 n.1620G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834091 p.Val184Met missense_variant 1.0 pyrazinamide Uncertain significance
tlyA 1918473 c.534T>A synonymous_variant 1.0 capreomycin Uncertain significance
Rv1979c 2221849 p.Leu439Gln missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222231 p.Met312Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222710 p.Asn152Ile missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223809 c.-646_-645insT upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
eis 2714723 p.Cys204Gly missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
folC 2746975 p.Asp208Glu missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2477c 2782420 c.1623T>A synonymous_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2784310 c.-268T>A upstream_gene_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
pepQ 2860233 c.186T>G synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
thyA 3073781 p.Leu231Ile missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv3083 3448420 c.-84_-83insT upstream_gene_variant 1.0 ethionamide Uncertain significance
whiB7 3568689 c.-11delT upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
embC 4240494 p.Gly211Ala missense_variant 1.0 ethambutol Uncertain significance
embC 4241732 p.Ala624Pro missense_variant 1.0 ethambutol Uncertain significance
embA 4245672 p.Gly814Arg missense_variant 1.0 ethambutol Uncertain significance
embB 4247458 p.Tyr315* stop_gained 1.0 ethambutol Uncertain significance
aftB 4268265 p.Leu191Gln missense_variant 1.0 ethambutol Uncertain significance