TB-Profiler result

Run: SRR22048552
Summary

Run ID: SRR22048552

Sample name:

Date: 2024-10-05T05:05:48.304590

Number of reads: 8685730

Percentage reads mapped: 99.49

Median coverage: 281.0

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 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
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
mshA 575891 p.Ala182Thr missense_variant 0.61 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.39 ethionamide Uncertain significance
Rv0565c 656761 p.Thr237Ile missense_variant 0.6 ethionamide Uncertain significance
mmpL5 775591 p.Val964Leu missense_variant 0.64 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474017 n.360A>G non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155480 p.Ser211Asn missense_variant 0.66 isoniazid Uncertain significance
PPE35 2168076 p.Thr846Met missense_variant 0.42 pyrazinamide Uncertain significance
PPE35 2168149 p.Pro822Ser missense_variant 0.36 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 2995848 c.-257G>A upstream_gene_variant 0.35 capreomycin
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0 ethionamide
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
mtrB 3626251 c.363T>G synonymous_variant 0.61 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
clpC1 4040941 c.-237G>T upstream_gene_variant 0.6 pyrazinamide
glpK 4139908 c.-153T>C upstream_gene_variant 0.66 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242928 c.3066A>G synonymous_variant 0.66 ethambutol Not assoc w R - Interim
embB 4247595 p.Cys361Ser missense_variant 0.58 ethambutol Uncertain significance
aftB 4268040 p.Leu266Pro missense_variant 0.6 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338859 c.-338T>C upstream_gene_variant 0.68 kanamycin
capreomycin
amikacin
gid 4408457 c.-255A>C upstream_gene_variant 0.62 streptomycin