TB-Profiler result

Run: SRR2101151
Summary

Run ID: SRR2101151

Sample name:

Date: 2024-10-03T20:42:58.517222

Number of reads: 3667892

Percentage reads mapped: 99.68

Median coverage: 85.0

Strain: lineage3;lineage4.3.4.2.1

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 0.09
lineage4.3 Euro-American (LAM) None 0.88
lineage4 Euro-American None 0.91
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.9
lineage4.3.4 Euro-American (LAM) RD174 0.88
lineage4.3.4.2 Euro-American (LAM) RD174 0.88
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
dnaA 1055 p.Ala352Gly missense_variant 0.91 isoniazid Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8795 c.1494C>T synonymous_variant 0.87 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 0.11 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.92 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779609 c.-704C>T upstream_gene_variant 0.89 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin 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 0.98 capreomycin 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 2289365 c.-125delC upstream_gene_variant 0.15 pyrazinamide
pncA 2289909 c.-668G>A upstream_gene_variant 0.93 pyrazinamide
Rv2477c 2782498 c.1545C>T synonymous_variant 0.13 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
thyA 3073868 p.Thr202Ala missense_variant 0.92 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.86 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.88 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.91 pyrazinamide Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.13 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 0.14 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.89 streptomycin Not assoc w R