TB-Profiler result

Run: ERR987741
Summary

Run ID: ERR987741

Sample name:

Date: 2024-04-14T21:43:21.358636

Number of reads: 4410877

Percentage reads mapped: 99.69

Median coverage: 93.0

Strain: lineage4.3.4.2;lineage4.6.1.1

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 0.1
lineage4.6 Euro-American None 0.9
lineage4 Euro-American None 1.0
lineage4.6.1.1 Euro-American RD724 0.88
lineage4.6.1 Euro-American (Uganda) RD724 0.89
lineage4.3.4 Euro-American (LAM) RD174 0.09
lineage4.3.4.2 Euro-American (LAM) RD174 0.14
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 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
rpoB 762101 c.2295C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
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
atpE 1461095 p.Met17Ile missense_variant 0.87 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
Rv2681 2996876 c.138A>C synonymous_variant 0.88 capreomycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.18 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.87 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
Rv3236c 3612009 p.Ala370Thr missense_variant 0.12 pyrazinamide Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.14 pyrazinamide Not assoc w R
glpK 4139670 p.Cys29Tyr missense_variant 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4328329 c.-856C>G upstream_gene_variant 0.9 ethionamide
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 4407980 p.Pro75Ala missense_variant 0.12 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.16 streptomycin Not assoc w R