TB-Profiler result

Run: ERR4800410
Summary

Run ID: ERR4800410

Sample name:

Date: 2024-04-15T04:33:26.763339

Number of reads: 2310365

Percentage reads mapped: 99.61

Median coverage: 64.0

Strain: lineage3;lineage4.3.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.57
lineage4.3 Euro-American (LAM) None 0.45
lineage4 Euro-American None 0.47
lineage4.3.3 Euro-American (LAM) RD115 0.44
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 gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.55 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.49 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.51 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.48 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.59 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.57 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.53 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.46 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.37 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.47 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472730 n.885A>G non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476197 n.2540T>G non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rpsA 1834836 p.Met432Thr missense_variant 0.55 pyrazinamide Not assoc w R - Interim
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 2154724 p.Arg463Leu missense_variant 0.68 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.44 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.64 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.66 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.55 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.43 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.61 isoniazid Not assoc w R
folC 2746340 p.Ala420Val missense_variant 0.39 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.53 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2681 2997375 p.Glu213Lys missense_variant 0.64 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.61 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.47 pyrazinamide Not assoc w R
clpC1 4039667 p.Gln346His missense_variant 0.56 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.6 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.45 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.42 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.61 streptomycin Not assoc w R
gid 4408010 p.Val65Phe missense_variant 0.38 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.53 streptomycin Not assoc w R