TB-Profiler result

Run: ERR9786048
Summary

Run ID: ERR9786048

Sample name:

Date: 2024-04-16T00:26:14.320616

Number of reads: 4039267

Percentage reads mapped: 98.05

Median coverage: 172.0

Strain: lineage2.2.1;lineage4.3.2

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.38
lineage2 East-Asian RD105 0.65
lineage4.3.2 Euro-American (LAM) None 0.32
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.68
lineage2.2 East-Asian (Beijing) RD105;RD207 0.64
lineage4 Euro-American None 0.35
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid Assoc w R High-level resistance
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 8841 p.Glu514Gln missense_variant 0.32 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.59 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.62 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.72 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.72 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.76 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.37 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 0.72 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.66 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.65 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417932 c.-585G>C upstream_gene_variant 0.63 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.35 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.68 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 0.72 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.64 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
thyA 3073868 p.Thr202Ala missense_variant 0.32 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448486 c.-18C>G upstream_gene_variant 0.32 ethionamide Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.67 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.63 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625453 c.-543G>A upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrB 3626562 p.Pro18Ser missense_variant 0.67 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.47 pyrazinamide 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 0.7 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.67 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.69 ethionamide Uncertain significance
whiB6 4338384 p.Asp46Glu missense_variant 0.42 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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
gid 4407588 c.615A>G synonymous_variant 0.68 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.61 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.31 streptomycin Not assoc w R