TB-Profiler result

Run: SRR5535688
Summary

Run ID: SRR5535688

Sample name:

Date: 2024-10-03T22:49:53.793865

Number of reads: 1333762

Percentage reads mapped: 99.13

Median coverage: 11.0

Strain: lineage4.1.1.1;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 0.48
lineage4.1.1.1 Euro-American (X-type) RD183 0.46
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.69
lineage4.9 Euro-American (H37Rv-like) None 0.61
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
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
sigE 1364205 c.-208G>C upstream_gene_variant 1.0 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
pepQ 2860279 p.Ala47Gly missense_variant 1.0 bedaquiline
clofazimine
fbiD 3339550 p.Gly145Arg missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiA 3641447 p.Thr302Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_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