TB-Profiler result

Run: ERR13266813
Summary

Run ID: ERR13266813

Sample name:

Date: 2024-10-03T21:34:38.061404

Number of reads: 5965670

Percentage reads mapped: 99.65

Median coverage: 162.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.66
lineage4.1.2 Euro-American None 0.65
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.64
lineage4 Euro-American None 0.66
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.102delG 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
rpoB 761110 p.Asp435Val missense_variant 0.68 rifampicin Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.63 isoniazid Assoc w R High-level resistance
gid 4408100 c.102delG frameshift_variant 0.64 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
gyrB 6963 p.Arg575His missense_variant 0.38 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.68 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.39 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.69 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.38 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.74 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.32 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.67 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.31 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.65 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 776100 p.Thr794Ile missense_variant 0.39 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776181 p.Asp767Ala missense_variant 0.37 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
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
bacA 2062948 p.Arg594His missense_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.4 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.33 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
pncA 2289365 c.-125delC upstream_gene_variant 0.4 pyrazinamide
kasA 2518076 c.-39C>T upstream_gene_variant 0.66 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.28 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.27 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 0.66 rifampicin
bedaquiline
alr 3841590 c.-170G>A upstream_gene_variant 0.46 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.3 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.59 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.35 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 0.68 ethambutol Not assoc w R
aftB 4268719 p.Asn40Asp missense_variant 0.38 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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.31 streptomycin Not assoc w R