TB-Profiler result

Run: SRR20958082
Summary

Run ID: SRR20958082

Sample name:

Date: 2024-04-14T23:05:57.022531

Number of reads: 11703693

Percentage reads mapped: 99.87

Median coverage: 339.0

Strain: lineage4.3.4.1;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
lineage4.3 Euro-American (LAM) None 0.69
lineage4.3.4.1 Euro-American (LAM) RD174 0.69
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.33
lineage4.3.4 Euro-American (LAM) RD174 0.7
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 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.73 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.71 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 0.74 streptomycin Not assoc w R
fbiC 1304334 p.Ser468Arg missense_variant 0.67 clofazimine
pretomanid
delamanid
sigE 1364434 p.Arg8Trp missense_variant 0.73 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.67 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.69 capreomycin Not assoc w R
Rv1979c 2223123 c.42G>A synonymous_variant 0.7 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.69 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2715333 c.-1T>C upstream_gene_variant 0.7 amikacin
kanamycin
thyA 3073868 p.Thr202Ala missense_variant 0.68 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.69 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.65 pyrazinamide Not assoc w R
lpqB 3623484 p.Phe476Ser missense_variant 0.72 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 0.69 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878614 c.-107A>C upstream_gene_variant 0.12 rifampicin
rpoA 3878619 c.-112A>C upstream_gene_variant 0.13 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.69 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.46 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.72 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.14 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 0.72 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.66 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.73 streptomycin Not assoc w R