TB-Profiler result

Run: ERR11081047
Summary

Run ID: ERR11081047

Sample name:

Date: 2024-10-04T19:49:57.607219

Number of reads: 2796157

Percentage reads mapped: 99.55

Median coverage: 80.0

Strain: lineage4.1

Spoligotype:

Drug-resistance: Pre-XDR-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 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.Ser315Ile Assoc w R - Interim High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.38 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.6 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Ile missense_variant 1.0 isoniazid Assoc w R - Interim High-level resistance
embB 4247429 p.Met306Val missense_variant 1.0 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 8694 c.1393C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 0.25 rifampicin Uncertain significance
rpoC 764916 p.Leu516Pro missense_variant 0.81 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
embR 1417369 c.-22C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834348 c.807T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ribD 2987146 p.Arg103Leu missense_variant 0.3 para-aminosalicylic_acid
Rv2752c 3066129 c.63G>A synonymous_variant 0.26 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568713 c.-34C>T upstream_gene_variant 0.14 kanamycin Uncertain significance
amikacin
streptomycin
Rv3236c 3612515 p.Arg201His missense_variant 1.0 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.98 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 1.0 ethambutol Not assoc w R
embA 4245250 p.His673Arg missense_variant 0.3 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol Not assoc w R
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
gid 4407991 p.Gly71Glu missense_variant 0.27 streptomycin Uncertain significance
gid 4408031 p.Leu58Phe missense_variant 0.99 streptomycin Uncertain significance