TB-Profiler result

Run: ERR036248
Summary

Run ID: ERR036248

Sample name:

Date: 2024-10-05T00:16:49.460079

Number of reads: 6587602

Percentage reads mapped: 99.54

Median coverage: 111.0

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 0.92
lineage4.3.4.2 Euro-American (LAM) RD174 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
gyrB 6140 p.Val301Leu missense_variant 0.1 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.89 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.93 rifampicin 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
fbiC 1302634 c.-297C>T upstream_gene_variant 0.95 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.92 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 2168149 p.Pro822Ser missense_variant 0.95 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714787 p.Trp182* stop_gained 0.93 kanamycin Uncertain significance
amikacin Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.91 capreomycin
ald 3086750 c.-70A>C upstream_gene_variant 0.87 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.11 cycloserine
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.5 ethionamide
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.92 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.96 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.11 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.92 pyrazinamide Not assoc w R
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