TB-Profiler result

Run: ERR8975153
Summary

Run ID: ERR8975153

Sample name:

Date: 2024-04-16T10:16:18.035775

Number of reads: 2866749

Percentage reads mapped: 99.73

Median coverage: 114.0

Strain: lineage4.8.1;lineage4.9

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
lineage4.8 Euro-American (mainly T) RD219 0.13
lineage4.8.1 Euro-American (mainly T) RD219 0.16
lineage4.9 Euro-American (H37Rv-like) None 0.86
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 5389 c.150C>A synonymous_variant 0.93 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.11 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.15 pyrazinamide Not assoc w R
PPE35 2170892 c.-280G>A upstream_gene_variant 0.18 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.11 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4040027 c.678C>T synonymous_variant 0.15 pyrazinamide
embA 4246468 p.Ile1079Thr missense_variant 0.92 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R