TB-Profiler result

Run: SRR25340804
Summary

Run ID: SRR25340804

Sample name:

Date: 2024-10-03T14:39:38.044529

Number of reads: 6281926

Percentage reads mapped: 99.52

Median coverage: 194.0

Strain: lineage3.1.2;lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.3
lineage4.3 Euro-American (LAM) None 0.67
lineage3.1.2 East-African-Indian RD750 0.32
lineage4 Euro-American None 0.7
lineage4.3.3 Euro-American (LAM) RD115 0.7
lineage3.1 East-African-Indian RD750 0.29
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
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 8040 p.Gly247Ser missense_variant 0.69 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 0.3 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.29 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.32 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.25 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764757 p.Leu463Arg missense_variant 0.36 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.69 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 0.28 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 0.34 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
rpsA 1834836 p.Met432Thr missense_variant 0.82 pyrazinamide Not assoc w R - Interim
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
tlyA 1918104 c.165G>A synonymous_variant 0.28 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.31 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.63 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.21 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.27 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 0.29 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.33 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.64 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.36 isoniazid Not assoc w R
folC 2746340 p.Ala420Val missense_variant 0.76 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.31 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
Rv2752c 3065236 p.Ser319Trp missense_variant 0.62 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.65 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.72 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.32 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.35 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 4242075 p.Arg738Gln missense_variant 0.3 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
whiB6 4338518 c.3delG frameshift_variant&start_lost 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.24 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.71 streptomycin Not assoc w R