TB-Profiler result

Run: ERR6865978
Summary

Run ID: ERR6865978

Sample name:

Date: 2024-04-15T02:17:29.654478

Number of reads: 2328283

Percentage reads mapped: 99.71

Median coverage: 68.0

Strain: 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 0.21
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.27
lineage4.3.4.2 Euro-American (LAM) RD174 0.25
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Leu116Pro Assoc w R - Interim
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 0.32 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.24 isoniazid Assoc w R High-level resistance
pncA 2288895 p.Leu116Pro missense_variant 0.25 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.33 ethambutol 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761455 p.Glu550Gly missense_variant 0.29 rifampicin Uncertain significance
rpoB 761889 p.Val695Leu missense_variant 0.77 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.16 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777185 c.1296G>A synonymous_variant 0.78 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.75 linezolid Not assoc w R - Interim
Rv1129c 1254588 c.-54T>G upstream_gene_variant 0.27 moxifloxacin
levofloxacin
rifampicin
isoniazid
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
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.75 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747453 p.Arg49Gln missense_variant 0.12 para-aminosalicylic_acid
Rv2752c 3065517 c.675C>T synonymous_variant 0.72 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.19 para-aminosalicylic_acid
thyA 3074361 c.111T>C synonymous_variant 0.33 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.17 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.31 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878635 c.-128C>T upstream_gene_variant 0.2 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244471 c.1239C>T synonymous_variant 0.75 ethambutol
embB 4248736 c.2223G>T synonymous_variant 0.22 ethambutol Not assoc w R - Interim
ethA 4328317 c.-844C>T upstream_gene_variant 0.79 ethionamide
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 4408054 p.Leu50Arg missense_variant 0.28 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.28 streptomycin Not assoc w R