TB-Profiler result

Run: ERR4830680
Summary

Run ID: ERR4830680

Sample name:

Date: 2024-04-15T18:59:47.595118

Number of reads: 3461515

Percentage reads mapped: 94.6

Median coverage: 92.0

Strain: lineage4.1.2.1;lineage4.3.3

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 0.2
lineage4.1 Euro-American None 0.86
lineage4.1.2 Euro-American None 0.78
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.81
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.17
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
gyrB 7126 c.1887G>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 8040 p.Gly247Ser missense_variant 0.15 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 0.86 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.8 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.84 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.88 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
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
katG 2156553 c.-442G>A upstream_gene_variant 0.11 isoniazid
PPE35 2170294 p.Pro107Ser missense_variant 0.26 pyrazinamide Uncertain significance
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 0.83 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.2 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin
Rv2752c 3065824 p.Pro123Leu missense_variant 0.12 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.11 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 0.88 bedaquiline
rifampicin
rpoA 3879220 c.-713G>A upstream_gene_variant 0.19 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.18 pyrazinamide Not assoc w R
clpC1 4038408 p.Pro766Leu missense_variant 0.87 pyrazinamide Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.79 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 0.74 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
gid 4408156 p.Leu16Arg missense_variant 0.18 streptomycin Not assoc w R