TB-Profiler result

Run: ERR9786450
Summary

Run ID: ERR9786450

Sample name:

Date: 2024-10-03T22:24:07.513320

Number of reads: 4365841

Percentage reads mapped: 93.98

Median coverage: 180.0

Strain: lineage4.1.3;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.14
lineage4.1 Euro-American None 0.14
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.87
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 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13638 c.-80A>C upstream_gene_variant 0.14 isoniazid Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.17 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777152 p.Met443Ile missense_variant 0.79 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1304610 c.1680C>T synonymous_variant 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.12 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
ald 3086788 c.-32T>C upstream_gene_variant 0.14 cycloserine
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.17 ethionamide
lpqB 3624660 p.Ala84Gly missense_variant 0.13 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.13 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640343 c.-200A>G upstream_gene_variant 0.9 pretomanid
delamanid
clofazimine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.16 ethambutol Not assoc w R
aftB 4267149 p.Glu563Gly missense_variant 0.92 ethambutol Uncertain significance
aftB 4267155 p.Gln561Arg missense_variant 0.9 ethambutol Uncertain significance
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 0.11 kanamycin
capreomycin
amikacin