TB-Profiler result

Run: SRR18715380
Summary

Run ID: SRR18715380

Sample name:

Date: 2024-04-15T15:02:29.531819

Number of reads: 2507509

Percentage reads mapped: 99.77

Median coverage: 51.0

Strain: lineage4.3.3;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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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 0.64
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.36
lineage4.3.3 Euro-American (LAM) RD115 0.65
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.6 isoniazid Assoc w R High-level resistance
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
dnaA 434 p.His145Arg missense_variant 0.43 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.58 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.7 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.37 ethionamide Uncertain significance
Rv0565c 657449 p.Gly8Ser missense_variant 0.63 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.75 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.65 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
embR 1417942 c.-595G>T upstream_gene_variant 0.89 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.66 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.54 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.58 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.45 pyrazinamide Not assoc w R
PPE35 2168343 p.Gly757Val missense_variant 0.6 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.76 isoniazid
ahpC 2726066 c.-127G>A upstream_gene_variant 0.36 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.64 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.37 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.57 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.65 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.67 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.64 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.58 pyrazinamide Not assoc w R - Interim
glpK 4139015 c.741G>T synonymous_variant 0.75 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244728 p.Phe499Cys missense_variant 0.34 ethambutol Uncertain significance
embA 4245131 c.1899G>A synonymous_variant 0.35 ethambutol Not assoc w R - Interim
embB 4247395 c.882C>T synonymous_variant 0.42 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.6 capreomycin
amikacin
kanamycin
gid 4408016 p.Asp63Tyr missense_variant 0.71 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.67 streptomycin Not assoc w R