TB-Profiler result

Run: ERR11466504
Summary

Run ID: ERR11466504

Sample name:

Date: 2024-04-16T04:13:24.450935

Number of reads: 796081

Percentage reads mapped: 99.84

Median coverage: 18.0

Strain: lineage4.4.1.1;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
lineage4.9.1 Euro-American (H37Rv-like) None 0.64
lineage4.4.1 Euro-American (S-type) None 0.25
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.35
lineage4.4 Euro-American None 0.26
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 7585 p.Ser95Thr missense_variant 0.41 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8978 c.1677C>T synonymous_variant 0.57 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9138 p.Gln613Glu missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.39 clofazimine Not assoc w R - Interim
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 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2102990 p.Val18Ala missense_variant 0.38 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid 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 0.8 pyrazinamide Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.28 cycloserine
fbiD 3339385 p.Asp90Asn missense_variant 0.74 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.43 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.47 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
clpC1 4040144 c.561G>C synonymous_variant 0.26 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 0.5 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.26 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 0.24 capreomycin
amikacin
kanamycin