TB-Profiler result

Run: SRR13837746
Summary

Run ID: SRR13837746

Sample name:

Date: 2025-03-06T13:44:12.553881

Number of reads: 2936500

Percentage reads mapped: 100.0

Median coverage: 99.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 embB p.Arg460Cys Mutation from literature
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
embB 4247891 p.Arg460Cys missense_variant 1.0 ethambutol Mutation from literature
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 6088 c.849C>A synonymous_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
hadA 731690 c.-240A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
hadA 732094 c.165T>C synonymous_variant 1.0 isoniazid Uncertain significance
nusG 734764 p.Ala171Ser missense_variant 1.0 rifampicin Uncertain significance
rpoB 761786 c.1980C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764973 p.Asp535Ala missense_variant 1.0 rifampicin Uncertain significance
rpsL 781532 c.-28G>T upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800224 c.-585G>C upstream_gene_variant 1.0 linezolid Uncertain significance
fbiC 1302843 c.-88A>C upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1302887 c.-43delG upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrl 1473434 n.-224T>C upstream_gene_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833260 c.-282G>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
katG 2156364 c.-253T>G upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2221814 p.Leu451Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222030 p.Val379Met missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
kasA 2519238 p.Thr375Lys missense_variant 1.0 isoniazid Uncertain significance
folC 2747285 p.Val105Ala missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2477c 2784556 c.-514A>C 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 2859712 p.Thr236Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2681 2996593 c.-146T>C upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv2681 2997178 p.Val147Glu missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065064 c.1128G>T synonymous_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
thyX 3068085 c.-140T>A upstream_gene_variant 1.0 para-aminosalicylic_acid Uncertain significance
ald 3087003 p.Asp62His missense_variant 1.0 cycloserine Uncertain significance
Rv3083 3448914 p.Ile137Met missense_variant 1.0 ethionamide Uncertain significance
whiB7 3568676 p.Ser2Pro missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3625172 p.Thr481Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3641491 p.Ala317Pro missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
alr 3840235 p.Gly396* stop_gained 1.0 cycloserine Uncertain significance
alr 3840304 c.1116delT frameshift_variant 1.0 cycloserine Uncertain significance
alr 3841263 p.Arg53His missense_variant 1.0 cycloserine Uncertain significance
glpK 4139790 c.-35C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4241029 p.Trp389* stop_gained 1.0 ethambutol Uncertain significance
embB 4249631 p.Thr1040Pro missense_variant 1.0 ethambutol Uncertain significance
ethA 4327197 p.Gly93Arg missense_variant 1.0 ethionamide Uncertain significance