TB-Profiler result

Run: SRR22251315
Summary

Run ID: SRR22251315

Sample name:

Date: 2024-04-15T11:01:58.278431

Number of reads: 1927807

Percentage reads mapped: 99.73

Median coverage: 62.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Asp735Asn Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.His1002Arg Uncertain significance Mutation from literature
pyrazinamide pncA p.Ala143Thr Uncertain significance Mutation from literature
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 765572 p.Asp735Asn missense_variant 1.0 rifampicin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2288815 p.Ala143Thr missense_variant 1.0 pyrazinamide Uncertain significance Mutation from literature
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.92 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289969 c.-728G>C upstream_gene_variant 0.98 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.21 ethambutol
ubiA 4269721 p.Ala38Val missense_variant 0.97 ethambutol Uncertain significance
ethA 4326844 c.630C>G synonymous_variant 0.98 ethionamide Not assoc w R - Interim
whiB6 4338362 p.Arg54Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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
gid 4408061 p.His48Asn missense_variant 0.97 streptomycin Uncertain significance