TB-Profiler result

Run: ERR2516334
Summary

Run ID: ERR2516334

Sample name:

Date: 2024-04-16T09:36:20.570858

Number of reads: 11488417

Percentage reads mapped: 99.66

Median coverage: 223.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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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 0.75
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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 1393 p.Ala465Thr missense_variant 0.21 isoniazid Uncertain significance
gyrB 7117 p.Met626Ile missense_variant 0.74 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.28 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
mmpL5 778735 c.-255G>A upstream_gene_variant 0.77 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253934 p.Arg201Trp missense_variant 0.75 moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.81 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854241 c.636C>G synonymous_variant 0.26 linezolid Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.28 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154915 c.1197A>G synonymous_variant 0.26 isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518205 p.Ser31Arg missense_variant 0.68 isoniazid
Rv2752c 3066501 c.-310G>A upstream_gene_variant 0.27 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086767 c.-53A>C upstream_gene_variant 0.77 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.19 cycloserine
fbiD 3338935 c.-183T>C upstream_gene_variant 0.8 clofazimine
pretomanid
delamanid
Rv3236c 3612118 c.999G>A synonymous_variant 0.8 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.23 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640308 c.-235C>T upstream_gene_variant 0.23 clofazimine
pretomanid
delamanid
glpK 4139030 c.726C>T synonymous_variant 0.79 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4239353 c.-510C>T upstream_gene_variant 0.24 ethambutol Uncertain significance
embC 4242161 p.Ala767Thr missense_variant 0.72 ethambutol
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4244000 c.768G>A synonymous_variant 0.72 ethambutol Not assoc w R - Interim
whiB6 4338250 p.Ala91Val missense_variant 0.75 capreomycin
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
whiB6 4338732 c.-211C>T upstream_gene_variant 0.24 capreomycin
amikacin
kanamycin