TB-Profiler result

Run: SRR998681
Summary

Run ID: SRR998681

Sample name:

Date: 2024-04-16T06:26:39.381846

Number of reads: 4219053

Percentage reads mapped: 99.48

Median coverage: 97.0

Strain: lineage4.6.2.2;lineage4.6.4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.99
lineage4.6.2 Euro-American RD726 0.21
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.19
lineage4.6.4 Euro-American None 0.76
lineage4 Euro-American None 1.0
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 29 p.Thr10Ser missense_variant 0.81 isoniazid Uncertain significance
gyrB 7013 p.Glu592Lys missense_variant 0.72 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 9304 p.Gly668Asp missense_variant 1.0 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 778298 c.183G>A synonymous_variant 0.11 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1305462 c.2532G>T synonymous_variant 0.24 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
sigE 1364407 c.-6A>G upstream_gene_variant 0.75 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472778 n.933C>T non_coding_transcript_exon_variant 0.77 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474750 n.1093C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
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 2063187 c.1542C>T synonymous_variant 0.24 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.15 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222583 c.582A>C synonymous_variant 0.68 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2996208 p.Ala35Asp missense_variant 0.2 capreomycin Uncertain significance
Rv3083 3448567 p.His22Asp missense_variant 0.12 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.19 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.22 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 0.17 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338614 c.-93G>A upstream_gene_variant 0.81 capreomycin
amikacin
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin