TB-Profiler result

Run: ERR2516422
Summary

Run ID: ERR2516422

Sample name:

Date: 2024-10-04T19:00:35.744477

Number of reads: 2115218

Percentage reads mapped: 99.72

Median coverage: 42.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 1.0
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 rpoB p.Ser450Leu Assoc w R
isoniazid katG c.1199dupA Assoc w R High-level resistance
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Gly406Ala Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rrs n.517C>T Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
katG 2154912 c.1199dupA frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>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
embB 4247730 p.Gly406Ala 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
rpoC 764724 p.Phe452Cys missense_variant 0.98 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775715 c.2766G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1304233 p.Trp435Gly missense_variant 1.0 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853578 c.-28G>C upstream_gene_variant 1.0 linezolid Uncertain significance
tsnR 1854014 p.Val137Leu missense_variant 1.0 linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2064364 p.Trp122Ser missense_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518617 p.Val168Gly missense_variant 1.0 isoniazid
Rv2752c 3065201 c.990delT frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
alr 3841071 p.Gly117Asp missense_variant 1.0 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243977 p.Ala249Thr missense_variant 1.0 ethambutol Uncertain significance
embB 4248549 p.Ala679Val missense_variant 1.0 ethambutol Uncertain significance
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.97 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407590 p.Ala205Thr missense_variant 1.0 streptomycin Uncertain significance
gid 4407602 p.Thr201Pro missense_variant 1.0 streptomycin Uncertain significance