TB-Profiler result

Run: SRR10397105
Summary

Run ID: SRR10397105

Sample name:

Date: 2024-10-04T16:44:22.373015

Number of reads: 1358408

Percentage reads mapped: 99.07

Median coverage: 36.0

Strain: lineage3.1.3;lineage4.2.1

Spoligotype:

Drug-resistance: HR-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 0.29
lineage3.1.3 East-African-Indian RD750 0.34
lineage4.2 Euro-American None 0.67
lineage4 Euro-American None 0.68
lineage4.2.1 Euro-American (TUR) None 0.62
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg 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
rpsL 781687 p.Lys43Arg missense_variant 0.76 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid Assoc w R High-level resistance
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
Rv0565c 657081 c.390G>A synonymous_variant 0.35 ethionamide Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.3 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.36 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.79 linezolid
Rv1129c 1253963 p.Asp191Gly missense_variant 0.66 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834159 c.618G>A synonymous_variant 0.43 pyrazinamide Not assoc w R
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
bacA 2063911 p.Ile273Thr missense_variant 0.77 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.26 isoniazid Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.65 pyrazinamide Uncertain significance
Rv1979c 2222732 c.432delT frameshift_variant 0.61 bedaquiline Uncertain significance
clofazimine Uncertain significance
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 0.33 pyrazinamide
Rv2477c 2783731 c.312C>T synonymous_variant 0.74 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
ald 3086742 c.-78A>C upstream_gene_variant 0.82 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448456 c.-48G>A upstream_gene_variant 0.77 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.97 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038932 c.1773G>A synonymous_variant 0.57 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.38 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 0.21 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249195 c.2682C>A synonymous_variant 0.35 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.5 ethambutol Not assoc w R - Interim
ethA 4327118 p.His119Arg missense_variant 0.26 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.76 ethionamide
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 0.49 streptomycin Not assoc w R
gid 4408175 p.Ala10Pro missense_variant 0.32 streptomycin Uncertain significance