TB-Profiler result

Run: ERR10748325
Summary

Run ID: ERR10748325

Sample name:

Date: 2024-10-04T21:35:03.175592

Number of reads: 1421819

Percentage reads mapped: 99.65

Median coverage: 39.0

Strain: lineage2.2.1.1;lineage4.1.2

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
lineage2 East-Asian RD105 0.15
lineage4.1 Euro-American None 0.82
lineage4.1.2 Euro-American None 0.77
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.17
lineage2.2 East-Asian (Beijing) RD105;RD207 0.19
lineage4 Euro-American None 0.78
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.18
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198delG 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
mmpR5 779181 c.198delG frameshift_variant 0.28 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
inhA 1673425 c.-777C>T upstream_gene_variant 0.16 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer 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 8061 p.Arg254Cys missense_variant 0.81 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 491591 p.Lys270Met missense_variant 0.87 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.28 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619612 c.-279G>A upstream_gene_variant 0.79 kanamycin
capreomycin
amikacin
ccsA 620625 p.Ile245Met missense_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.19 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.19 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.82 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 764263 c.894G>A synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.96 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 776182 p.Asp767Asn missense_variant 0.17 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777320 c.1161C>G synonymous_variant 0.9 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.3 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 0.18 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.84 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471644 n.-202T>C upstream_gene_variant 0.79 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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
katG 2154724 p.Arg463Leu missense_variant 0.27 isoniazid Not assoc w R
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.29 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288901 p.Thr114Met missense_variant 0.27 pyrazinamide Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.68 isoniazid
eis 2714846 p.Val163Ile missense_variant 0.16 kanamycin Not assoc w R
amikacin Not assoc w R
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.24 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3611974 c.1143A>C synonymous_variant 0.79 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.97 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.23 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 0.86 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.24 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.16 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 4407927 p.Glu92Asp missense_variant 0.32 streptomycin Not assoc w R