TB-Profiler result

Run: ERR7363078
Summary

Run ID: ERR7363078

Sample name:

Date: 2024-04-15T18:03:27.061769

Number of reads: 2388322

Percentage reads mapped: 99.6

Median coverage: 72.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.3
lineage4.1.2 Euro-American None 0.31
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.3
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.7
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 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8971 p.His557Arg missense_variant 0.66 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9016 p.Thr572Asn missense_variant 0.75 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9648 p.Val783Leu missense_variant 0.77 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.3 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.3 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576264 p.Leu306Arg missense_variant 0.34 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 576574 c.1227T>C synonymous_variant 0.73 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.28 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.26 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.21 rifampicin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.65 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.3 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 0.69 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
pncA 2289780 c.-539C>T upstream_gene_variant 0.7 pyrazinamide
kasA 2518076 c.-39C>T upstream_gene_variant 0.27 isoniazid
ahpC 2725912 c.-281T>G upstream_gene_variant 0.46 isoniazid
ribD 2987581 p.Ser248Cys missense_variant 0.7 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.73 capreomycin
Rv2752c 3066299 c.-108C>T upstream_gene_variant 0.25 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.31 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.3 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.22 bedaquiline
rifampicin
embC 4239298 c.-565C>T upstream_gene_variant 0.23 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.25 ethambutol Not assoc w R
embA 4243412 c.180C>T synonymous_variant 0.75 ethambutol Not assoc w R - Interim
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 0.35 capreomycin
amikacin
kanamycin