TB-Profiler result

Run: ERR9285802

Summary

Run ID: ERR9285802

Sample name:

Date: 2024-03-24T16:23:59.279785

Number of reads: 4655673

Percentage reads mapped: 99.64

Median coverage: 146.0

Strain: lineage4.4.1.1;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
lineage4.4.1 Euro-American (S-type) None 0.11
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.9
lineage4.4.1.1 Euro-American None 0.08
lineage4.4 Euro-American None 0.07
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 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.92 ethionamide Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.13 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid 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 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.11 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
ndh 2103202 c.-160C>A upstream_gene_variant 0.91 ethionamide
delamanid
isoniazid
PPE35 2168149 p.Pro822Ser missense_variant 0.86 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.11 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223601 c.-437C>G upstream_gene_variant 0.88 clofazimine
bedaquiline
folC 2746923 p.Gly226Ser missense_variant 0.14 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.93 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.92 ethionamide Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.1 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243692 p.Gly154Ser missense_variant 0.12 ethambutol Uncertain significance
embB 4247395 c.882C>T synonymous_variant 0.87 ethambutol Not assoc w R - Interim
ethA 4328252 c.-779T>G upstream_gene_variant 0.13 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.14 capreomycin
amikacin
kanamycin