TB-Profiler result

Run: SRR5485485
Summary

Run ID: SRR5485485

Sample name:

Date: 2024-10-04T15:29:04.105750

Number of reads: 129803

Percentage reads mapped: 96.32

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: RR-TB

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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 rpoB p.Ser431Asn Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.His445Pro Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Lys446Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1484G>T Assoc w R
capreomycin rrs n.1484G>T Assoc w R
kanamycin rrs n.1484G>T Assoc w R
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
rpoB 761098 p.Ser431Asn missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761140 p.His445Pro missense_variant 0.94 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761142 p.Lys446Gln missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 1.0 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
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
rpoB 761138 c.1332C>G synonymous_variant 1.0 rifampicin