TB-Profiler result

Run: DRR130193
Summary

Run ID: DRR130193

Sample name:

Date: 2025-03-04T21:04:56.383639

Number of reads: 3523991

Percentage reads mapped: 99.8

Median coverage: 176.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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 rpoB p.His445Asp Assoc w R
isoniazid katG c.580delG Assoc w R High-level resistance
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol embA c.-12C>T Uncertain significance Mutation from literature: doi: 10.1128/AAC.03285-14
embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Val155Met Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide ethA c.752dupG Assoc w R
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
gyrA 7581 p.Asp94Asn missense_variant 0.92 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin Assoc w R
katG 2155531 c.580delG frameshift_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2288779 p.Val155Met missense_variant 1.0 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature: doi: 10.1128/AAC.03285-14
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol Assoc w R
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide Assoc w R
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
dnaA 782 p.Ser261Asn missense_variant 1.0 isoniazid Uncertain significance
gyrB 7103 p.Trp622Arg missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13640 c.-82T>C upstream_gene_variant 0.99 isoniazid Uncertain significance
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
Rv1129c 1254144 p.Thr131Pro missense_variant 0.99 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
Rv1979c 2223724 c.-560C>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
ahpC 2726147 c.-46A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2752c 3065954 p.Thr80Pro missense_variant 0.99 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
thyX 3067954 c.-9G>A upstream_gene_variant 1.0 para-aminosalicylic_acid Uncertain significance
thyA 3074012 c.451_459delCAGTTCTAC conservative_inframe_deletion 1.0 para-aminosalicylic_acid Uncertain significance
ald 3086799 c.-21A>C upstream_gene_variant 0.89 cycloserine Uncertain significance
mtrA 3626710 p.Val214Met missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiB 3642512 c.978G>A synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
gid 4408060 p.His48Pro missense_variant 1.0 streptomycin Uncertain significance