TB-Profiler result

Run: ERR4829977
Summary

Run ID: ERR4829977

Sample name:

Date: 2024-06-18T07:58:27.218928

Number of reads: 2130618

Percentage reads mapped: 99.31

Median coverage: 62.0

Strain: lineage2.2.1.1;lineage3

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.88
lineage2 East-Asian RD105 0.13
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.11
lineage2.2 East-Asian (Beijing) RD105;RD207 0.12
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.14
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn Assoc w R
isoniazid
ethambutol embB p.Gly406Asp Assoc w R
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 761139 p.His445Asn missense_variant 0.91 rifampicin Assoc w R
mmpR5 779181 c.198dupG frameshift_variant 0.85 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781822 p.Lys88Arg missense_variant 0.14 streptomycin Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.13 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
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 574763 c.-585_-584insG upstream_gene_variant 0.13 ethionamide
isoniazid
mshA 575907 p.Ala187Val missense_variant 0.16 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.19 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.84 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.82 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.19 clofazimine Not assoc w R
bedaquiline Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1407133 p.Gly70Arg missense_variant 0.95 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 0.97 streptomycin
kanamycin
capreomycin
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 2063078 c.1650dupG frameshift_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
katG 2153987 p.Glu709Gln missense_variant 0.19 isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser 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
pncA 2289047 c.195C>T synonymous_variant 0.88 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.87 pyrazinamide
eis 2714846 p.Val163Ile missense_variant 0.16 amikacin Not assoc w R
kanamycin Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.85 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.89 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.87 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.9 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.9 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.77 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.14 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.29 ethambutol Not assoc w R
ubiA 4269024 c.810G>A synonymous_variant 0.88 ethambutol Not assoc w R - Interim
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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407732 c.471G>A synonymous_variant 0.23 streptomycin Not assoc w R - Interim
gid 4407927 p.Glu92Asp missense_variant 0.16 streptomycin Not assoc w R