TB-Profiler result

Run: ERR11466164
Summary

Run ID: ERR11466164

Sample name:

Date: 2024-04-16T01:43:44.193575

Number of reads: 2019272

Percentage reads mapped: 99.71

Median coverage: 64.0

Strain: lineage4.1.1.3;lineage4.9.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.14
lineage4.9.1 Euro-American (H37Rv-like) None 0.82
lineage4.1.1.3 Euro-American (X-type) RD193 0.15
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.17
lineage4.9 Euro-American (H37Rv-like) None 0.84
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 8978 c.1677C>T synonymous_variant 0.8 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.18 rifampicin Not assoc w R
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
rplC 800219 c.-590T>C upstream_gene_variant 0.2 linezolid
embR 1417416 c.-69G>A upstream_gene_variant 0.89 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.24 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
pncA 2289138 p.Leu35Arg missense_variant 0.77 pyrazinamide Not assoc w R - Interim
eis 2715179 p.Ala52Ser missense_variant 0.17 amikacin
kanamycin
ald 3086788 c.-32T>C upstream_gene_variant 0.11 cycloserine
fbiD 3339385 p.Asp90Asn missense_variant 0.97 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
clpC1 4038201 p.Ala835Val missense_variant 0.89 pyrazinamide
embB 4249408 c.2895G>A synonymous_variant 0.16 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 0.21 capreomycin
amikacin
kanamycin