TB-Profiler result

Run: ERR2179748
Summary

Run ID: ERR2179748

Sample name:

Date: 2024-10-05T03:02:49.617413

Number of reads: 4860663

Percentage reads mapped: 97.95

Median coverage: 140.0

Strain: lineage4.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.96
lineage4.4.2 Euro-American None 0.97
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
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 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 1473021 n.1176G>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin 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
PPE35 2169041 c.1572G>A synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
PPE35 2169044 c.1569G>C synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
PPE35 2169047 p.Ile522Val missense_variant 0.53 pyrazinamide Uncertain significance
PPE35 2169053 c.1560T>C synonymous_variant 0.92 pyrazinamide Not assoc w R
PPE35 2169056 c.1557A>G synonymous_variant 0.51 pyrazinamide Not assoc w R - Interim
PPE35 2169059 c.1554G>A synonymous_variant 0.41 pyrazinamide
PPE35 2169063 p.Met517Thr missense_variant 0.89 pyrazinamide
PPE35 2169065 p.Ala516Ile missense_variant 0.39 pyrazinamide
PPE35 2169068 c.1545G>T synonymous_variant 0.41 pyrazinamide
PPE35 2169071 c.1542A>G synonymous_variant 0.44 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ribD 2986964 c.126G>A synonymous_variant 1.0 para-aminosalicylic_acid
Rv2752c 3066099 p.Met31Ile missense_variant 0.97 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 0.99 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.97 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878568 c.-61G>T upstream_gene_variant 0.97 rifampicin
embC 4238963 c.-900C>T upstream_gene_variant 0.99 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 0.98 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.98 ethambutol Uncertain significance
ubiA 4268928 c.906C>T synonymous_variant 0.97 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.98 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