TB-Profiler result

Run: 11fa78c5-1e5b-40c8-901b-b628008b994c
Summary

Run ID: 11fa78c5-1e5b-40c8-901b-b628008b994c

Sample name:

Date: 15-11-2023 13:27:21

Number of reads: 692738

Percentage reads mapped: 98.89

Median coverage: 23

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 1.0
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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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
gyrB 7200 p.Glu654Gly missense_variant 0.1 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
mshA 575316 c.-32C>T upstream_gene_variant 0.12 ethionamide
isoniazid
mshA 575403 p.Val19Asp missense_variant 0.12 ethionamide
isoniazid
ccsA 620195 p.Thr102Asn missense_variant 0.11 capreomycin
amikacin
rpoC 765369 p.Thr667Met missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776921 c.1560C>T synonymous_variant 0.12 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1305197 p.Ala756Val missense_variant 0.1 delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 linezolid Uncertain significance
inhA 1674615 p.Met138Ile missense_variant 0.1 ethionamide
isoniazid
rpsA 1834368 p.Leu276Pro missense_variant 0.12 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
PPE35 2168995 p.Pro540Thr missense_variant 0.11 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
fbiD 3339428 p.Ala104Val missense_variant 0.13 delamanid
rpoA 3878414 p.Tyr32His missense_variant 0.11 rifampicin
rpoA 3878630 c.-123G>C upstream_gene_variant 0.23 rifampicin
clpC1 4040820 c.-117delC upstream_gene_variant 0.13 pyrazinamide
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4246035 p.Glu935* stop_gained 0.12 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338630 c.-109C>A upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide