TB-Profiler result

Run: ERR4830048
Summary

Run ID: ERR4830048

Sample name:

Date: 2024-10-05T11:23:22.524020

Number of reads: 4429178

Percentage reads mapped: 99.55

Median coverage: 140.0

Strain: lineage4.3.3;lineage4.5

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.89
lineage4.3 Euro-American (LAM) None 0.08
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.11
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 0.15 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.94 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.92 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 766667 p.Ser1100Ala missense_variant 0.1 rifampicin 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
Rv1258c 1406101 p.Pro414Ser missense_variant 0.92 streptomycin Uncertain significance
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853597 c.-9G>C upstream_gene_variant 0.92 linezolid Uncertain significance
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
katG 2155087 p.Glu342Ala missense_variant 0.89 isoniazid Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.91 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
eis 2715271 p.Ala21Glu missense_variant 0.86 kanamycin Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.13 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.94 rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.13 pyrazinamide Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.88 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248316 c.1803C>T synonymous_variant 0.19 ethambutol Not assoc w R - Interim
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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408009 p.Val65Ala missense_variant 0.14 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.16 streptomycin Not assoc w R