TB-Profiler result

Run: a0ef3d72-a077-4f7e-adda-30c02a6a8c36
Summary

Run ID: a0ef3d72-a077-4f7e-adda-30c02a6a8c36

Sample name:

Date: 07-01-2023 08:48:10

Number of reads: 2474624

Percentage reads mapped: 99.24

Median coverage: 89

Strain: lineage4.1.1

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
lineage4.1 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) 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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 490751 c.-32T>G upstream_gene_variant 0.3 delamanid
rpoB 759615 c.-192A>C upstream_gene_variant 0.29 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779645 c.-740C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1473084 n.1239T>C non_coding_transcript_exon_variant 1.0 linezolid
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
aminoglycosides
streptomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
PPE35 2169101 c.1512G>A synonymous_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ahpC 2726341 p.Val50Gly missense_variant 0.24 isoniazid
ahpC 2726350 p.Trp53Leu missense_variant 0.32 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
embC 4240655 p.Ala265Pro missense_variant 0.23 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Uncertain significance
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.15 ethambutol
embC 4243092 p.Leu1077Arg missense_variant 0.15 ethambutol
embC 4243095 p.Gly1078Val missense_variant 0.15 ethambutol
embA 4243099 c.-134G>C upstream_gene_variant 0.16 ethambutol
embA 4243102 c.-131G>T upstream_gene_variant 0.16 ethambutol
embC 4243103 p.Thr1081Pro missense_variant 0.16 ethambutol
embC 4243106 p.Arg1082Ser missense_variant 0.16 ethambutol
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.16 ethambutol
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol
aftB 4267799 c.1038G>A synonymous_variant 0.12 capreomycin
amikacin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance