TB-Profiler result

Run: SRR6046130
Summary

Run ID: SRR6046130

Sample name:

Date: 2024-04-15T15:15:51.208280

Number of reads: 766949

Percentage reads mapped: 96.45

Median coverage: 20.0

Strain: lineage4.2.1.1;lineage4.7

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.78
lineage4.7 Euro-American (mainly T) None 0.27
lineage4 Euro-American None 1.0
lineage4.2.1.1 Euro-American (TUR) None 0.76
lineage4.2.1 Euro-American (TUR) None 0.75
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 0.66 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.82 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 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8432 c.1131C>G synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777451 p.Val344Leu missense_variant 0.89 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.61 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.7 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.66 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.67 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290079 c.-838T>C upstream_gene_variant 0.75 pyrazinamide
ald 3086742 c.-78A>C upstream_gene_variant 0.74 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.72 cycloserine
mtrA 3627767 c.-418C>T upstream_gene_variant 0.32 bedaquiline
rifampicin
ddn 3986975 c.132T>C synonymous_variant 0.31 delamanid
pretomanid
ddn 3987092 p.Glu83Asp missense_variant 0.8 delamanid Uncertain significance
pretomanid
embC 4240865 p.Ala335Pro missense_variant 0.38 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.93 capreomycin
amikacin
kanamycin
gid 4408213 c.-11C>T upstream_gene_variant 0.69 streptomycin Uncertain significance