TB-Profiler result

Run: ERR4813599
Summary

Run ID: ERR4813599

Sample name:

Date: 2024-04-16T04:56:12.393868

Number of reads: 4944173

Percentage reads mapped: 99.83

Median coverage: 156.0

Strain: lineage4.3.3;lineage4.3.4.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.11
lineage4.3.4 Euro-American (LAM) RD174 0.91
lineage4.3.4.2 Euro-American (LAM) RD174 0.89
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA p.Ile21Val Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA p.His51Arg Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.1 rifampicin Assoc w R
inhA 1674262 p.Ile21Val missense_variant 0.11 isoniazid Uncertain significance Mutation from literature
pncA 2289090 p.His51Arg missense_variant 0.11 pyrazinamide 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
dnaA 71 p.Pro24Leu missense_variant 0.12 isoniazid 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.12 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
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Ala missense_variant 0.14 rifampicin Uncertain significance
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
rpsA 1834683 p.Ala381Val missense_variant 0.12 pyrazinamide 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
PPE35 2169041 c.1572G>A synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
PPE35 2169044 c.1569G>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
PPE35 2169047 c.1564_1566delATCinsGT frameshift_variant&missense_variant 0.25 pyrazinamide Uncertain significance
PPE35 2169053 c.1560T>C synonymous_variant 0.57 pyrazinamide Not assoc w R
PPE35 2169056 c.1557A>G synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
PPE35 2169059 c.1554G>A synonymous_variant 0.31 pyrazinamide
PPE35 2169063 p.Met517Thr missense_variant 0.55 pyrazinamide
PPE35 2169065 p.Ala516Ile missense_variant 0.31 pyrazinamide
PPE35 2169068 c.1545G>T synonymous_variant 0.33 pyrazinamide
PPE35 2169071 c.1542A>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2784248 c.-206C>G upstream_gene_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.89 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038824 c.1881C>T synonymous_variant 0.88 pyrazinamide Not assoc w R - Interim
panD 4044682 c.-401C>T upstream_gene_variant 0.88 pyrazinamide
embC 4242176 p.Pro772Ala missense_variant 0.9 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338596 c.-76_-75delAGinsC upstream_gene_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R