TB-Profiler result

Run: ERR2513553
Summary

Run ID: ERR2513553

Sample name:

Date: 2024-10-04T18:59:36.123655

Number of reads: 1935790

Percentage reads mapped: 99.6

Median coverage: 62.0

Strain: lineage3;lineage4

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.9
lineage4 Euro-American None 0.08
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embB p.Ala313Val Uncertain significance Mutation from literature
pyrazinamide
streptomycin gid p.Gly71* 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
embB 4247451 p.Ala313Val missense_variant 0.15 ethambutol Uncertain significance Mutation from literature
gid 4407992 p.Gly71* stop_gained 0.8 streptomycin 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
dnaA 1186 p.Glu396Lys missense_variant 0.13 isoniazid Uncertain significance
gyrB 5222 c.-18G>T upstream_gene_variant 0.93 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7601 c.300C>G synonymous_variant 0.92 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.79 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.93 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.87 rifampicin Not assoc w R
rpoB 762051 p.His749Tyr missense_variant 0.89 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.93 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.98 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.89 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254595 c.-61A>C upstream_gene_variant 0.88 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473609 n.-49G>C upstream_gene_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.95 pyrazinamide 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
pncA 2289047 c.195C>T synonymous_variant 0.89 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.88 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.93 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.9 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.93 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.85 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.93 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 0.94 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.9 streptomycin Not assoc w R