TB-Profiler result

Run: SRR1723919
Summary

Run ID: SRR1723919

Sample name:

Date: 2024-04-15T12:41:15.717729

Number of reads: 3160375

Percentage reads mapped: 99.46

Median coverage: 36.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.98
lineage4 Euro-American None 0.99
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.97 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
ccsA 620029 c.139C>T synonymous_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 0.97 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778121 c.360C>T synonymous_variant 0.97 clofazimine
bedaquiline Not assoc w R - Interim
mmpL5 778301 p.Gln60His missense_variant 0.9 clofazimine
bedaquiline
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
rpsA 1833734 p.Ala65Thr missense_variant 0.9 pyrazinamide
tsnR 1854216 p.Glu204Gly missense_variant 1.0 linezolid
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
PPE35 2170568 p.Ile15Met missense_variant 0.94 pyrazinamide 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
eis 2714211 c.1122G>A synonymous_variant 0.97 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
thyX 3068084 c.-139T>G upstream_gene_variant 0.88 para-aminosalicylic_acid
ald 3087695 p.Asp292Glu missense_variant 0.29 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840415 p.Pro336Ser missense_variant 0.91 cycloserine
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
ddn 3986759 c.-85C>T upstream_gene_variant 0.97 delamanid
pretomanid
clpC1 4038318 p.Pro796Leu missense_variant 0.97 pyrazinamide Not assoc w R
clpC1 4040745 c.-41G>A upstream_gene_variant 0.98 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 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