TB-Profiler result

Run: SRR10809129
Summary

Run ID: SRR10809129

Sample name:

Date: 2024-10-04T02:14:49.962307

Number of reads: 3811273

Percentage reads mapped: 99.71

Median coverage: 124.0

Strain: lineage4.4.1.2;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.26
lineage4.4.1.2 Euro-American None 0.78
lineage4.4.1 Euro-American (S-type) None 0.76
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.76
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 1078 p.Leu360Phe missense_variant 0.23 isoniazid
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 7892 c.591G>A synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9185 c.1884C>T synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13759 c.-201C>T upstream_gene_variant 0.24 isoniazid
mshA 575619 p.Arg91Leu missense_variant 0.74 isoniazid
ethionamide
ccsA 620029 c.139C>T synonymous_variant 0.24 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.74 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2167770 p.Ser948Ile missense_variant 0.71 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.78 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.12 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 2290211 c.-970G>T upstream_gene_variant 0.76 pyrazinamide
pepQ 2860213 p.Pro69Leu missense_variant 0.77 bedaquiline Uncertain significance
clofazimine Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.77 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.76 ethionamide Not assoc w R - Interim
Rv3236c 3613184 c.-68C>T upstream_gene_variant 0.75 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3879070 c.-563G>A upstream_gene_variant 0.29 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.25 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.77 ethambutol Not assoc w R
embC 4242402 p.Arg847His missense_variant 0.73 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247008 c.495G>A synonymous_variant 0.74 ethambutol Not assoc w R - Interim
embB 4249012 c.2499G>A synonymous_variant 0.82 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