TB-Profiler result

Run: SRR19428597
Summary

Run ID: SRR19428597

Sample name:

Date: 2024-10-04T05:56:17.197904

Number of reads: 429770

Percentage reads mapped: 99.69

Median coverage: 23.0

Strain: lineage3.1.1;lineage4.3.3

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.74
lineage4.3 Euro-American (LAM) None 0.32
lineage3.1.1 East-African-Indian RD750 0.73
lineage4.3.3 Euro-American (LAM) RD115 0.22
lineage3.1 East-African-Indian RD750 0.8
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser441Gln Assoc w R
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
rpoB 761127 p.Ser441Gln missense_variant 0.77 rifampicin 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 0.71 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656507 p.Asp322Asn missense_variant 0.88 ethionamide
rpoB 759746 c.-61C>T upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.7 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 0.67 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 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 0.64 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.82 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.59 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 0.71 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.74 pyrazinamide
eis 2714899 p.Arg145Pro missense_variant 0.76 kanamycin
amikacin
ahpC 2726105 c.-88G>A upstream_gene_variant 0.88 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 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
ddn 3986714 c.-130C>T upstream_gene_variant 0.32 pretomanid
delamanid
panD 4044872 c.-591C>T upstream_gene_variant 0.81 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.53 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 0.6 streptomycin Not assoc w R