TB-Profiler result

Run: ERR3148038
Summary

Run ID: ERR3148038

Sample name:

Date: 2024-04-16T07:04:24.893147

Number of reads: 7050826

Percentage reads mapped: 99.74

Median coverage: 222.0

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.Asp435Tyr Assoc w R
isoniazid katG p.Arg632Cys Uncertain significance Mutation from literature
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Ile5Thr Uncertain significance Mutation from literature
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Asn499Thr Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Asn499Thr Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid folC p.Ser150Gly Mutation from literature
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 6735 p.Asn499Thr missense_variant 1.0 moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin Assoc w R
katG 2154218 p.Arg632Cys missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
pncA 2289228 p.Ile5Thr missense_variant 1.0 pyrazinamide Uncertain significance Mutation from literature
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
folC 2747151 p.Ser150Gly missense_variant 1.0 para-aminosalicylic_acid Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 760320 p.Gln172Lys missense_variant 1.0 rifampicin Uncertain significance
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
Rv1129c 1253637 p.Arg300Cys missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254623 c.-89C>A upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
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
ahpC 2726151 c.-42T>G upstream_gene_variant 1.0 isoniazid Uncertain significance
ahpC 2726766 p.Lys192Gln missense_variant 0.92 isoniazid Uncertain significance
ald 3087529 p.Gly237Glu missense_variant 1.0 cycloserine
alr 3840278 c.1143T>C synonymous_variant 1.0 cycloserine
embB 4246971 p.Thr153Asn missense_variant 1.0 ethambutol Uncertain significance
embB 4248078 p.Asn522Thr missense_variant 1.0 ethambutol Uncertain significance
ethA 4326219 p.Val419Ile missense_variant 1.0 ethionamide Uncertain significance
ethA 4326631 p.His281Gln missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338594 c.-73T>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
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 4407857 p.Arg116Trp missense_variant 0.93 streptomycin Uncertain significance