TB-Profiler result

Run: ERR4024763
Summary

Run ID: ERR4024763

Sample name:

Date: 2024-10-04T10:59:47.717242

Number of reads: 2170585

Percentage reads mapped: 99.75

Median coverage: 65.0

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 0.71
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.72
lineage4.3.4.2 Euro-American (LAM) RD174 0.73
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 0.68 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.7 isoniazid Assoc w R High-level resistance
pncA 2288895 p.Leu116Pro missense_variant 0.62 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.82 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 0.67 rifampicin Uncertain significance
rpoB 761889 p.Val695Leu missense_variant 0.3 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.83 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777185 c.1296G>A synonymous_variant 0.31 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.33 linezolid Not assoc w R - Interim
Rv1129c 1254588 c.-54T>G upstream_gene_variant 0.8 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473645 n.-12delT upstream_gene_variant 0.62 capreomycin Uncertain significance
linezolid
rrl 1474296 n.639T>G non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
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 0.22 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747453 p.Arg49Gln missense_variant 0.74 para-aminosalicylic_acid
Rv2752c 3065517 c.675C>T synonymous_variant 0.43 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.79 para-aminosalicylic_acid
thyA 3074361 c.111T>C synonymous_variant 0.72 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.8 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.71 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.81 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.79 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 0.26 ethambutol
embB 4248736 c.2223G>T synonymous_variant 0.65 ethambutol Not assoc w R - Interim
ethA 4328317 c.-844C>T upstream_gene_variant 0.2 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338600 c.-79T>C upstream_gene_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408054 p.Leu50Arg missense_variant 0.71 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.75 streptomycin Not assoc w R