TB-Profiler result

Run: ERR2600431
Summary

Run ID: ERR2600431

Sample name:

Date: 2024-10-04T14:37:34.055433

Number of reads: 7708290

Percentage reads mapped: 99.6

Median coverage: 224.0

Strain: lineage4.8

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 0.98
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
rpoC 765369 p.Thr667Met missense_variant 0.99 rifampicin Uncertain significance
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
Rv1129c 1254557 c.-23C>A upstream_gene_variant 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.99 capreomycin Not assoc w R
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 0.26 pyrazinamide Not assoc w R - Interim
PPE35 2169044 c.1569G>C synonymous_variant 0.34 pyrazinamide Not assoc w R - Interim
PPE35 2169047 p.Ile522Val missense_variant 0.33 pyrazinamide Uncertain significance
PPE35 2169053 c.1560T>C synonymous_variant 0.9 pyrazinamide Not assoc w R
PPE35 2169056 c.1557A>G synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
PPE35 2169059 c.1554G>A synonymous_variant 0.59 pyrazinamide
PPE35 2169063 p.Met517Thr missense_variant 0.93 pyrazinamide
PPE35 2169065 p.Ala516Ile missense_variant 0.59 pyrazinamide
PPE35 2169068 c.1545G>T synonymous_variant 0.62 pyrazinamide
PPE35 2169071 c.1542A>G synonymous_variant 0.27 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
Rv3083 3448500 c.-3_*1408del transcript_ablation 0.97 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 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 4338630 c.-109C>A upstream_gene_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance