TB-Profiler result

Run: SRR13861445
Summary

Run ID: SRR13861445

Sample name:

Date: 2024-10-04T20:50:57.227411

Number of reads: 1700507

Percentage reads mapped: 28.37

Median coverage: 58.0

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
moxifloxacin
hadA 731690 c.-240A>G upstream_gene_variant 1.0 isoniazid
hadA 732094 c.165T>C synonymous_variant 1.0 isoniazid
nusG 734764 p.Ala171Ser missense_variant 0.98 rifampicin
rpoB 761786 c.1980C>T synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoC 764973 p.Asp535Ala missense_variant 1.0 rifampicin
rpsL 781532 c.-28G>T upstream_gene_variant 1.0 streptomycin
rplC 800224 c.-585G>C upstream_gene_variant 1.0 linezolid
fbiC 1302843 c.-88A>C upstream_gene_variant 0.98 pretomanid
delamanid
clofazimine
fbiC 1302887 c.-43delG upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
rrl 1473434 n.-224T>C upstream_gene_variant 1.0 capreomycin
linezolid
rrl 1476368 n.2711T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rpsA 1833260 c.-282G>C upstream_gene_variant 1.0 pyrazinamide
katG 2156364 c.-253T>G upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2221814 p.Leu451Val missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2222030 p.Val379Met missense_variant 0.98 bedaquiline
clofazimine
kasA 2519238 p.Thr375Lys missense_variant 1.0 isoniazid
folC 2747285 p.Val105Ala missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2784556 c.-514A>C upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2859712 p.Thr236Ser missense_variant 1.0 bedaquiline
clofazimine
Rv2681 2996593 c.-146T>C upstream_gene_variant 1.0 capreomycin
Rv2681 2997178 p.Val147Glu missense_variant 1.0 capreomycin
Rv2752c 3065064 c.1128G>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3068085 c.-140T>A upstream_gene_variant 1.0 para-aminosalicylic_acid
ald 3087003 p.Asp62His missense_variant 1.0 cycloserine
Rv3083 3448914 p.Ile137Met missense_variant 1.0 ethionamide
whiB7 3568676 p.Ser2Pro missense_variant 1.0 kanamycin
amikacin
streptomycin
mtrB 3625172 p.Thr481Ser missense_variant 1.0 rifampicin
bedaquiline
fbiA 3641491 p.Ala317Pro missense_variant 1.0 pretomanid
delamanid
clofazimine
alr 3840235 p.Gly396* stop_gained 1.0 cycloserine
alr 3840304 c.1116delT frameshift_variant 0.97 cycloserine
alr 3841263 p.Arg53His missense_variant 1.0 cycloserine
glpK 4139790 c.-35C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4241029 p.Trp389* stop_gained 0.98 ethambutol
embB 4249631 p.Thr1040Pro missense_variant 1.0 ethambutol
ethA 4327197 p.Gly93Arg missense_variant 1.0 ethionamide Uncertain significance