TB-Profiler result

Run: SRR22249944
Summary

Run ID: SRR22249944

Sample name:

Date: 2024-04-16T01:49:17.877341

Number of reads: 8288254

Percentage reads mapped: 99.65

Median coverage: 261.0

Strain: lineage4.1.2.1;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 0.59
lineage4.1 Euro-American None 0.43
lineage4.1.2 Euro-American None 0.41
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.43
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
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 0.59 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
Rv0010c 13394 p.Trp55* stop_gained 0.61 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.48 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.45 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.6 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.33 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.44 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.52 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 781276 c.-284A>C upstream_gene_variant 0.44 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253603 p.Gly311Glu missense_variant 0.39 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiC 1305500 c.2570A>G stop_lost&splice_region_variant 0.56 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833559 c.18C>A synonymous_variant 0.48 pyrazinamide Not assoc w R - Interim
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
ndh 2102875 c.168C>T synonymous_variant 0.39 ethionamide Not assoc w R - Interim
delamanid
isoniazid Not assoc w R - Interim
PPE35 2167768 p.Gly949Ser missense_variant 0.43 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.65 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.41 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.44 cycloserine
fbiD 3339738 c.621C>A synonymous_variant 0.27 clofazimine
pretomanid
delamanid
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 0.6 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.57 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.47 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.41 ethambutol Not assoc w R
embB 4245710 c.-804G>A upstream_gene_variant 0.55 ethambutol
ethR 4327864 p.Gly106Arg missense_variant 0.42 ethionamide Uncertain significance
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