TB-Profiler result

Run: ERR13290903
Summary

Run ID: ERR13290903

Sample name:

Date: 2025-02-11T17:20:53.521905

Number of reads: 5980938

Percentage reads mapped: 99.66

Median coverage: 174.0

Strain: lineage2.1

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.97
lineage2.1 East-Asian (non-Beijing) 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.Asn138His Uncertain significance Mutation from literature
ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Leu Assoc w R
pyrazinamide pncA p.Lys96Gln Assoc w R
streptomycin gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Pro378Leu Uncertain significance Mutation from literature
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 0.99 rifampicin Assoc w R
katG 2155700 p.Asn138His missense_variant 0.88 isoniazid Uncertain significance Mutation from literature
pncA 2288956 p.Lys96Gln missense_variant 0.91 pyrazinamide Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 0.89 isoniazid Uncertain significance Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.88 ethambutol Assoc w R
ethA 4326341 p.Pro378Leu missense_variant 0.89 ethionamide Uncertain significance Mutation from literature
gid 4407851 c.351delG frameshift_variant 0.89 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 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 13635 c.-77C>T upstream_gene_variant 0.88 isoniazid
Rv0010c 13636 c.-78A>G upstream_gene_variant 0.87 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.98 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.12 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.98 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 765113 p.Val582Leu missense_variant 0.89 rifampicin Uncertain significance
rpoC 765121 c.1752G>A synonymous_variant 0.89 rifampicin Not assoc w R - Interim
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 0.96 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1304443 p.Ala505Thr missense_variant 0.9 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.96 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
katG 2154724 p.Arg463Leu missense_variant 0.96 isoniazid Not assoc w R
katG 2156484 c.-373A>G upstream_gene_variant 0.92 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.96 pyrazinamide Not assoc w R
PPE35 2170819 c.-207C>A upstream_gene_variant 0.92 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726468 c.276G>A synonymous_variant 0.91 isoniazid Not assoc w R - Interim
Rv2477c 2783790 p.Val85Ile missense_variant 0.9 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Not assoc w R
amikacin Uncertain significance
Rv2752c 3065992 p.Val67Ala missense_variant 0.88 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
whiB7 3568759 c.-80A>C upstream_gene_variant 0.85 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040841 c.-138delG upstream_gene_variant 0.92 pyrazinamide
glpK 4139183 c.569_572dupGGGG frameshift_variant 0.68 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246088 c.2856A>G synonymous_variant 0.85 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.25 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.92 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 4407588 c.615A>G synonymous_variant 0.94 streptomycin Not assoc w R