TB-Profiler result

Run: ERR4799172
Summary

Run ID: ERR4799172

Sample name:

Date: 2024-10-04T09:12:42.301005

Number of reads: 3168331

Percentage reads mapped: 99.68

Median coverage: 93.0

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 0.98
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 p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.His1002Arg Uncertain significance Mutation from literature
pyrazinamide pncA c.391dupG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94His Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94His Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.655dupG Assoc w R
c.550_551dupGG 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.Asp94His missense_variant 0.99 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.391dupG frameshift_variant 0.98 pyrazinamide Assoc w R
embB 4249518 p.His1002Arg missense_variant 0.96 ethambutol Uncertain significance Mutation from literature
ethA 4326818 c.655dupG frameshift_variant 0.12 ethionamide Assoc w R
ethA 4326922 c.550_551dupGG frameshift_variant 0.8 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764669 p.Pro434Thr missense_variant 0.85 rifampicin Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 0.1 rifampicin 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
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 2223491 c.-327C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289969 c.-728G>C upstream_gene_variant 1.0 pyrazinamide
ald 3087647 c.830dupG frameshift_variant 1.0 cycloserine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.98 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
ubiA 4269124 p.Ala237Val missense_variant 0.97 ethambutol Uncertain significance
ethA 4326844 c.630C>G synonymous_variant 0.99 ethionamide Not assoc w R - Interim
whiB6 4338362 p.Arg54Gly missense_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4408061 p.His48Asn missense_variant 0.99 streptomycin Uncertain significance