TB-Profiler result

Run: SRR5149238
Summary

Run ID: SRR5149238

Sample name:

Date: 2024-04-15T10:31:50.218278

Number of reads: 494471

Percentage reads mapped: 92.3

Median coverage: 10.0

Strain: lineage2.2.1.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.92
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.84
lineage2.2 East-Asian (Beijing) RD105;RD207 0.92
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.05
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Thr500Pro Uncertain significance Mutation from literature
gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Thr500Pro Uncertain significance Mutation from literature
gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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
gyrB 6737 p.Thr500Pro missense_variant 0.9 moxifloxacin Uncertain significance Mutation from literature
levofloxacin Uncertain significance Mutation from literature
gyrA 7582 p.Asp94Ala missense_variant 1.0 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.91 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.93 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
ahpC 2726145 c.-48G>A upstream_gene_variant 0.54 isoniazid Uncertain significance Mutation from literature
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
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.94 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.94 ethionamide Uncertain significance
rpoC 767123 p.Val1252Met missense_variant 0.92 rifampicin Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9 clofazimine
bedaquiline
Rv1129c 1254614 c.-80C>T upstream_gene_variant 0.85 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.82 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.87 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
katG 2154086 p.Gly676Arg missense_variant 1.0 isoniazid
katG 2154217 p.Arg632His missense_variant 0.85 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.91 pyrazinamide Not assoc w R
pncA 2289028 p.Cys72Gly missense_variant 0.87 pyrazinamide
Rv2752c 3065129 c.1063C>T synonymous_variant 0.92 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.94 cycloserine
mtrB 3625982 p.Val211Ala missense_variant 0.9 bedaquiline
rifampicin
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.73 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