TB-Profiler result

Run: SRR6131515
Summary

Run ID: SRR6131515

Sample name:

Date: 2024-10-04T22:23:15.461745

Number of reads: 23110936

Percentage reads mapped: 69.23

Median coverage: 6.0

Strain: lineage4.1.1.3;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
lineage4.1 Euro-American None 0.81
lineage4.1.1.3 Euro-American (X-type) RD193 0.25
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.19
lineage4.9 Euro-American (H37Rv-like) None 0.56
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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764623 c.1254C>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.43 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764665 c.1296C>G synonymous_variant 0.5 rifampicin
rpoC 764672 p.Gln435Thr missense_variant 0.58 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.46 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473237 n.1392C>T non_coding_transcript_exon_variant 0.31 kanamycin
capreomycin
streptomycin
amikacin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223682 c.-518C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R