TB-Profiler result

Run: ERR221644
Summary

Run ID: ERR221644

Sample name:

Date: 2024-04-15T18:24:04.457183

Number of reads: 8047043

Percentage reads mapped: 99.75

Median coverage: 177.5

Strain: lineage4.3.4.2.1;lineage4.9

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 0.11
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.1
lineage4.9 Euro-American (H37Rv-like) None 0.88
lineage4.3.4 Euro-American (LAM) RD174 0.11
lineage4.3.4.2 Euro-American (LAM) RD174 0.12
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
gyrB 6140 p.Val301Leu missense_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 574906 c.-442G>A upstream_gene_variant 0.92 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoB 759906 p.Ser34Ala missense_variant 0.84 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.12 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.11 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 0.11 streptomycin Not assoc w R
rplC 801355 p.His183Tyr missense_variant 0.9 linezolid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2170036 p.Val193Met missense_variant 0.9 pyrazinamide Uncertain significance
Rv2752c 3066026 p.Gly56Ser missense_variant 0.88 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.12 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.1 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.12 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.12 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 0.16 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.12 streptomycin Not assoc w R