TB-Profiler result

Run: SRR6824605
Summary

Run ID: SRR6824605

Sample name:

Date: 2024-10-04T21:04:10.222216

Number of reads: 7399684

Percentage reads mapped: 99.58

Median coverage: 224.0

Strain: lineage4.4.2;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 0.29
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.7
lineage4.4.2 Euro-American None 0.69
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
gyrB 6716 p.Ile493Leu missense_variant 0.25 levofloxacin
moxifloxacin
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 0.29 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
mshA 575109 c.-239G>A upstream_gene_variant 0.26 isoniazid
ethionamide
ccsA 620029 c.139C>T synonymous_variant 0.32 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
rrs 1471939 n.94C>T non_coding_transcript_exon_variant 0.61 kanamycin
capreomycin
streptomycin
amikacin
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
PPE35 2170568 p.Ile15Met missense_variant 0.26 pyrazinamide Not assoc w R
PPE35 2170856 c.-244G>T upstream_gene_variant 0.65 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2681 2997672 p.Trp312Arg missense_variant 0.72 capreomycin
Rv2752c 3065944 p.His83Pro missense_variant 0.72 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066099 p.Met31Ile missense_variant 0.64 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.77 cycloserine
fbiD 3339480 p.Gln121His missense_variant 0.26 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
ddn 3987001 p.Gly53Asp missense_variant 0.34 pretomanid
delamanid Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 0.3 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.69 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.68 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.72 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.67 ethambutol Not assoc w R
ethA 4327875 c.-402C>A upstream_gene_variant 0.21 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