TB-Profiler result

Run: ERR2510164
Summary

Run ID: ERR2510164

Sample name:

Date: 2024-04-15T16:04:56.621892

Number of reads: 4723135

Percentage reads mapped: 99.58

Median coverage: 100.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.93
lineage4.1.2 Euro-American None 0.91
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.92
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 gid c.115delC Assoc w R
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
gid 4408087 c.115delC frameshift_variant 0.11 streptomycin Assoc w R
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
Rv0010c 13783 c.-225T>A upstream_gene_variant 0.94 isoniazid
fgd1 491591 p.Lys270Met missense_variant 0.91 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.92 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.94 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 778554 p.Val118Ile missense_variant 0.11 clofazimine
bedaquiline
rpsL 781276 c.-284A>C upstream_gene_variant 0.92 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.11 linezolid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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 0.92 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.26 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.94 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.96 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.94 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 0.91 ethambutol Not assoc w R
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