TB-Profiler result

Run: SRR21277407
Summary

Run ID: SRR21277407

Sample name:

Date: 2024-10-04T02:32:47.718768

Number of reads: 20857192

Percentage reads mapped: 99.51

Median coverage: 540.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
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 6892 p.Phe551Leu missense_variant 1.0 levofloxacin
moxifloxacin
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 1.0 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 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
nusG 734680 p.Ala143Ser missense_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1416798 p.Cys184Arg missense_variant 1.0 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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
PPE35 2169041 c.1572G>A synonymous_variant 0.39 pyrazinamide Not assoc w R - Interim
PPE35 2169044 c.1569G>C synonymous_variant 0.45 pyrazinamide Not assoc w R - Interim
PPE35 2169047 p.Ile522Val missense_variant 0.42 pyrazinamide Uncertain significance
PPE35 2169053 c.1560T>C synonymous_variant 1.0 pyrazinamide Not assoc w R
PPE35 2169056 c.1557A>G synonymous_variant 0.42 pyrazinamide Not assoc w R - Interim
PPE35 2169059 c.1554G>A synonymous_variant 0.58 pyrazinamide
PPE35 2169063 p.Met517Thr missense_variant 1.0 pyrazinamide
PPE35 2169065 p.Ala516Ile missense_variant 0.58 pyrazinamide
PPE35 2169068 c.1545G>T synonymous_variant 0.6 pyrazinamide
PPE35 2169071 c.1542A>G synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2715536 c.-204C>T upstream_gene_variant 1.0 kanamycin
amikacin
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.98 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
panD 4044472 c.-191G>T upstream_gene_variant 1.0 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338283 c.234_238dupGGTCG frameshift_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin