TB-Profiler result

Run: SRR29096676
Summary

Run ID: SRR29096676

Sample name:

Date: 2025-02-11T09:38:46.634626

Number of reads: 461574

Percentage reads mapped: 94.91

Median coverage: 13.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 0.95
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1304748 c.1818T>C synonymous_variant 0.47 pretomanid
delamanid
clofazimine
fbiC 1304757 c.1827A>G synonymous_variant 0.43 pretomanid
delamanid
clofazimine
atpE 1461037 c.-8_-7insT upstream_gene_variant 1.0 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474566 n.909G>A non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rpsA 1833724 c.183C>G synonymous_variant 0.39 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.41 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.43 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.29 pyrazinamide
rpsA 1833793 c.252C>T synonymous_variant 0.29 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.35 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.35 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.35 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.35 pyrazinamide
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide 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
Rv2680 2996084 c.-21A>C upstream_gene_variant 0.4 capreomycin Uncertain significance
rpoA 3877686 c.822A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877737 c.771G>C synonymous_variant 0.47 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3878842 c.-335G>C upstream_gene_variant 0.46 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.6 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.69 rifampicin Uncertain significance
rpoA 3878881 c.-374C>G upstream_gene_variant 0.69 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.4 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R