TB-Profiler result

Run: ERR2513438
Summary

Run ID: ERR2513438

Sample name:

Date: 2024-04-15T13:42:29.639216

Number of reads: 625172

Percentage reads mapped: 81.02

Median coverage: 20.0

Strain: lineage4.1.2.1

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 0.99
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 1.0
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.93 rifampicin Not assoc w R
rpoB 762959 c.3153G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 762983 c.-387C>T upstream_gene_variant 0.26 rifampicin
rpoB 762989 c.3183G>A synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 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
rpsL 781706 c.147T>G synonymous_variant 0.15 streptomycin
rpsL 781715 c.156T>G synonymous_variant 0.12 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1833928 c.387G>C synonymous_variant 0.25 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.28 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.23 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.28 pyrazinamide
rpsA 1833991 c.450C>G synonymous_variant 0.31 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.31 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.28 pyrazinamide
rpsA 1834012 c.471G>T synonymous_variant 0.28 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.3 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.3 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834033 c.492C>T synonymous_variant 0.26 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 1.0 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 1.0 ethambutol Not assoc w R
aftB 4267194 p.Pro548Gln missense_variant 1.0 ethambutol Uncertain significance
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 1.0 capreomycin
amikacin
kanamycin