TB-Profiler result

Run: ERR4809241
Summary

Run ID: ERR4809241

Sample name:

Date: 2024-10-05T12:39:12.202823

Number of reads: 4302296

Percentage reads mapped: 99.56

Median coverage: 138.0

Strain: lineage4.1.2;lineage4.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.13
lineage4.1.2 Euro-American None 0.1
lineage4.2 Euro-American None 0.87
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 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 katG p.Ser315Thr Assoc w R High-level resistance
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
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.85 isoniazid Assoc w R High-level resistance
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
Rv0010c 13519 p.Ala14Ser missense_variant 0.94 isoniazid Uncertain significance
fgd1 491238 c.456C>T synonymous_variant 0.88 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491247 c.465C>T synonymous_variant 0.9 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.12 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.16 ethionamide Uncertain significance
nusG 734817 c.564C>T synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoB 760115 c.309C>T synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 764123 p.Phe252Leu missense_variant 0.87 rifampicin Uncertain significance
rpoC 764263 c.894G>A synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.78 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777320 c.1161C>G synonymous_variant 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.14 linezolid
rplC 800204 c.-605T>C upstream_gene_variant 0.85 linezolid
rrs 1471644 n.-202T>C upstream_gene_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
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
bacA 2063685 c.1044G>A synonymous_variant 0.95 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.89 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.9 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518773 p.Asn220Ser missense_variant 0.86 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.5 capreomycin Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.9 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3611974 c.1143A>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
lpqB 3623770 p.Gly381Ser missense_variant 0.92 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.2 ethambutol Not assoc w R
embA 4243218 c.-15C>G upstream_gene_variant 0.82 ethambutol Uncertain significance
embB 4249594 c.3081G>A synonymous_variant 0.89 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.89 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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin