TB-Profiler result

Run: ERR351926
Summary

Run ID: ERR351926

Sample name:

Date: 2024-10-04T20:23:31.685661

Number of reads: 3576399

Percentage reads mapped: 99.56

Median coverage: 82.0

Strain: lineage3;lineage4.4

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
lineage3 East-African-Indian RD750 0.85
lineage4 Euro-American None 0.14
lineage4.4 Euro-American None 0.14
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
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 1673425 c.-777C>T upstream_gene_variant 0.87 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9596 c.2295G>T synonymous_variant 0.8 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13277 c.282T>C synonymous_variant 0.88 isoniazid Not assoc w R
fgd1 491367 c.585G>A synonymous_variant 0.24 pretomanid
delamanid
clofazimine
fgd1 491742 c.960T>C synonymous_variant 0.88 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
nusG 734354 p.Pro34Leu missense_variant 0.77 rifampicin Not assoc w R
nusG 734753 p.Thr167Met missense_variant 0.8 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.85 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.84 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.74 rifampicin Not assoc w R
rpoC 764181 p.Asp271Gly missense_variant 0.81 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 776100 p.Thr794Ile missense_variant 0.83 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 1254039 p.Asn166Asp missense_variant 0.83 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.64 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475357 n.1700C>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
tsnR 1854300 p.Leu232Pro missense_variant 0.98 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 0.82 isoniazid Not assoc w R
katG 2155351 p.Arg254Leu missense_variant 0.84 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.83 pyrazinamide Not assoc w R
PPE35 2170769 c.-157C>T upstream_gene_variant 0.85 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.86 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.86 pyrazinamide
eis 2714523 p.His270Gln missense_variant 0.16 kanamycin Uncertain significance
amikacin Uncertain significance
eis 2714879 p.Asp152Asn missense_variant 0.86 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726105 c.-88G>A upstream_gene_variant 0.88 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.82 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3066452 c.-261T>G upstream_gene_variant 0.13 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087118 p.Ser100Leu missense_variant 0.21 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.84 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139528 p.Asn76Lys missense_variant 0.8 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.9 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247548 c.1035C>T synonymous_variant 0.14 ethambutol Not assoc w R - Interim
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 0.86 streptomycin Not assoc w R