TB-Profiler result

Run: ERR7363028
Summary

Run ID: ERR7363028

Sample name:

Date: 2024-04-15T13:18:28.993299

Number of reads: 5339348

Percentage reads mapped: 99.59

Median coverage: 164.0

Strain: lineage4.1.2.1;lineage4.3.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.21
lineage4.3.2 Euro-American (LAM) None 0.22
lineage4.1 Euro-American None 0.8
lineage4.1.2 Euro-American None 0.76
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.78
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 0.81 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.79 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.78 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.8 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
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.27 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.24 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472646 n.801C>T non_coding_transcript_exon_variant 0.72 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 0.81 isoniazid
kasA 2519131 c.1017G>T synonymous_variant 0.21 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.12 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.2 para-aminosalicylic_acid
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
mtrA 3627756 c.-407A>T upstream_gene_variant 0.85 bedaquiline
rifampicin
fbiA 3640838 p.Pro99Arg missense_variant 0.77 clofazimine
pretomanid
delamanid
ddn 3986910 p.Arg23Trp missense_variant 0.23 delamanid Uncertain significance
pretomanid
clpC1 4038287 c.2418C>T synonymous_variant 0.18 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.78 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 0.77 ethambutol Not assoc w R
embB 4248914 p.Ala801Thr missense_variant 0.24 ethambutol Uncertain significance
ubiA 4269974 c.-141C>G upstream_gene_variant 0.39 ethambutol
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
gid 4408156 p.Leu16Arg missense_variant 0.2 streptomycin Not assoc w R