TB-Profiler result

Run: SRR25207048
Summary

Run ID: SRR25207048

Sample name:

Date: 2024-05-20T10:04:31.532531

Number of reads: 5971707

Percentage reads mapped: 99.49

Median coverage: 219.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American None 1.0
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 gid c.102delG Assoc w R
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 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4408100 c.102delG frameshift_variant 1.0 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 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 1.0 moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rpoC 764918 p.Val517Leu missense_variant 1.0 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
rplC 800780 c.-29C>T upstream_gene_variant 1.0 linezolid Uncertain significance
fbiC 1305446 p.Gly839Ala missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
capreomycin
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 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoA 3878619 c.-112A>C upstream_gene_variant 0.2 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.99 isoniazid Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ethambutol Uncertain significance
levofloxacin Uncertain significance
embC 4240118 p.Val86Ile missense_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4242646 c.-587C>T upstream_gene_variant 1.0 ethambutol
embB 4247028 p.Leu172Arg missense_variant 0.29 ethambutol
embB 4247033 p.Ser174Arg missense_variant 0.23 ethambutol
aftB 4267926 p.Ala304Val missense_variant 1.0 ethambutol Uncertain significance
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