TB-Profiler result

Run: SRR13861242
Summary

Run ID: SRR13861242

Sample name:

Date: 2024-10-04T02:23:06.018461

Number of reads: 553888

Percentage reads mapped: 55.45

Median coverage: 19.0

Strain: 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 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
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
gyrB 6027 p.His263Arg missense_variant 1.0 levofloxacin
moxifloxacin
mshA 576327 p.Phe327Tyr missense_variant 1.0 isoniazid
ethionamide
Rv0565c 656192 p.Asp427His missense_variant 1.0 ethionamide
rpoB 759707 c.-100C>T upstream_gene_variant 1.0 rifampicin
rpoB 760178 c.372G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>A synonymous_variant 1.0 rifampicin
rpoC 764262 p.Val298Ala missense_variant 0.94 rifampicin
mmpL5 777280 p.Ala401Ser missense_variant 1.0 bedaquiline
clofazimine
mmpS5 778853 p.Val18Ala missense_variant 1.0 bedaquiline
clofazimine
rpsL 781277 c.-283G>C upstream_gene_variant 1.0 streptomycin
rplC 800213 c.-596G>T upstream_gene_variant 1.0 linezolid
embR 1416662 p.Arg229Pro missense_variant 1.0 ethambutol
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
tlyA 1917545 c.-395T>A upstream_gene_variant 1.0 capreomycin
katG 2155675 p.Arg146Leu missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2222433 c.732A>G synonymous_variant 0.91 bedaquiline
clofazimine
Rv2680 2996147 p.Glu15Gln missense_variant 1.0 capreomycin
Rv2681 2996821 p.Gly28Val missense_variant 1.0 capreomycin
ald 3086631 c.-189A>G upstream_gene_variant 1.0 cycloserine
Rv3236c 3612954 c.162delC frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3613619 c.-503T>G upstream_gene_variant 1.0 pyrazinamide
alr 3840284 p.Trp379* stop_gained 1.0 cycloserine
glpK 4139736 p.Gly7Val missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4239589 c.-273delA upstream_gene_variant 1.0 ethambutol
embC 4240042 p.Asn60Lys missense_variant 1.0 ethambutol
embB 4245806 c.-708G>A upstream_gene_variant 0.94 ethambutol
embB 4247075 c.563dupT frameshift_variant 1.0 ethambutol
embB 4247839 c.1326G>A synonymous_variant 1.0 ethambutol
embB 4249763 p.Thr1084Pro missense_variant 1.0 ethambutol Uncertain significance
ethA 4326860 p.Leu205Pro missense_variant 1.0 ethionamide Uncertain significance