TB-Profiler result

Run: ERR230097
Summary

Run ID: ERR230097

Sample name:

Date: 2024-04-16T09:30:40.980204

Number of reads: 2836031

Percentage reads mapped: 99.5

Median coverage: 65.0

Strain: lineage4.1.1.3.1

Spoligotype:

Drug-resistance: Pre-XDR-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 0.95
lineage4.1.1.3 Euro-American (X-type) RD193 0.94
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.93
lineage4.1.1.3.1 Euro-American (X-type) RD193 0.93
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ile491Phe Assoc w R
isoniazid
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Lys96Glu Assoc w R
p.Val7Leu Assoc w R
c.-5delG Assoc w R
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.95 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761277 p.Ile491Phe missense_variant 0.88 rifampicin Assoc w R
pncA 2288956 p.Lys96Glu missense_variant 0.16 pyrazinamide Assoc w R
pncA 2289223 p.Val7Leu missense_variant 0.6 pyrazinamide Assoc w R
pncA 2289245 c.-5delG upstream_gene_variant 0.25 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.92 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.96 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 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.85 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
rplC 800219 c.-590T>C upstream_gene_variant 0.9 linezolid
fbiC 1303601 p.Glu224Gly missense_variant 0.96 clofazimine
pretomanid
delamanid
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 2154695 p.Val473Leu missense_variant 0.97 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223372 c.-208C>G upstream_gene_variant 0.94 clofazimine Uncertain significance
bedaquiline Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.96 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.95 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.97 ethambutol Not assoc w R
ubiA 4269540 c.294C>T synonymous_variant 0.97 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 0.99 capreomycin
amikacin
kanamycin