TB-Profiler result

Run: ERR1633849
Summary

Run ID: ERR1633849

Sample name:

Date: 2024-10-05T08:23:19.834432

Number of reads: 3866014

Percentage reads mapped: 99.65

Median coverage: 86.0

Strain: lineage3;lineage4.7

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.15
lineage4.7 Euro-American (mainly T) None 0.85
lineage4 Euro-American None 0.87
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
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
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 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8056 p.Arg252Leu missense_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13887 c.-329T>C upstream_gene_variant 0.78 isoniazid
fgd1 491742 c.960T>C synonymous_variant 0.11 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656114 p.Ser453Ala missense_variant 0.13 ethionamide Uncertain significance
hadA 732145 c.216C>T synonymous_variant 0.14 isoniazid Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.13 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.15 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 776100 p.Thr794Ile missense_variant 0.14 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.89 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.11 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.19 isoniazid 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
pncA 2289047 c.195C>T synonymous_variant 0.12 pyrazinamide Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.22 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
thyA 3074424 c.48G>T synonymous_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.1 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.14 rifampicin Not assoc w R
bedaquiline Uncertain significance
glpK 4138622 c.1134C>T synonymous_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138654 c.1102C>T synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.9 ethambutol Not assoc w R
ethA 4328212 c.-740delC upstream_gene_variant 0.21 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 0.14 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.12 streptomycin Not assoc w R
gid 4407704 p.Ala167Pro missense_variant 0.84 streptomycin Uncertain significance