TB-Profiler result

Run: ERR6866849
Summary

Run ID: ERR6866849

Sample name:

Date: 2024-04-15T04:50:54.916840

Number of reads: 2308190

Percentage reads mapped: 99.64

Median coverage: 65.0

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American None 0.24
lineage4.1.2 Euro-American None 0.23
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.24
lineage4 Euro-American None 1.0
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.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Gly406Ser Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
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
inhA 1673423 c.-779G>T upstream_gene_variant 0.78 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
embB 4247729 p.Gly406Ser missense_variant 0.78 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
gyrA 9753 p.Asn818Asp missense_variant 0.23 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.18 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.28 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.17 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.25 rifampicin Not assoc w R
rpoB 761889 p.Val695Leu missense_variant 0.69 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.25 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.22 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.74 linezolid Not assoc w R - Interim
rrs 1471634 n.-212C>T upstream_gene_variant 0.34 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 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
Rv1979c 2222098 p.Thr356Met missense_variant 0.22 clofazimine
bedaquiline
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.77 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.28 isoniazid
Rv2752c 3065517 c.675C>T synonymous_variant 0.83 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.21 cycloserine
Rv3083 3448439 c.-64delA upstream_gene_variant 0.76 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 0.32 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878595 c.-88C>T upstream_gene_variant 0.21 rifampicin
embC 4239298 c.-565C>T upstream_gene_variant 0.14 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.19 ethambutol Not assoc w R
ethA 4328317 c.-844C>T upstream_gene_variant 0.85 ethionamide
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