TB-Profiler result

Run: ERR2020072
Summary

Run ID: ERR2020072

Sample name:

Date: 2024-04-15T18:23:42.068694

Number of reads: 2263376

Percentage reads mapped: 95.76

Median coverage: 59.0

Strain: lineage4.4.2

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 Euro-American None 1.0
lineage4.4 Euro-American None 0.97
lineage4.4.2 Euro-American None 0.98
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.Ser315Asn Assoc w R High-level resistance
p.Val1Ala Mutation from literature
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.Ser315Asn missense_variant 0.75 isoniazid Assoc w R High-level resistance
katG 2156110 p.Val1Ala missense_variant 0.16 isoniazid Mutation from literature
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 8798 c.1497C>T synonymous_variant 0.95 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
fgd1 491251 p.Leu157Phe missense_variant 0.94 clofazimine
pretomanid
delamanid
rpoB 759894 p.Pro30Ala missense_variant 0.91 rifampicin Uncertain significance
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
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673903 p.Ala155Gly missense_variant 0.16 ethionamide
isoniazid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3066099 p.Met31Ile missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.97 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.91 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039873 p.Thr278Ser missense_variant 0.98 pyrazinamide Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.97 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244975 c.1743C>T synonymous_variant 0.97 ethambutol
embA 4246508 c.3276G>A synonymous_variant 0.91 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.93 ethambutol Uncertain significance
ubiA 4268928 c.906C>T synonymous_variant 0.98 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.99 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