TB-Profiler result

Run: ERR9786407
Summary

Run ID: ERR9786407

Sample name:

Date: 2024-04-15T07:20:21.834843

Number of reads: 1313505

Percentage reads mapped: 98.2

Median coverage: 57.0

Strain: lineage3;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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 0.41
lineage4 Euro-American None 0.56
lineage4.8 Euro-American (mainly T) RD219 0.55
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
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
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
dnaA 371 p.Pro124Leu missense_variant 0.42 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13404 p.Ser52Thr missense_variant 0.66 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.42 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.48 rifampicin Not assoc w R
rpoB 763031 c.3225T>C 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 0.36 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776656 p.Gly609Arg missense_variant 0.58 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777205 p.Pro426Ser missense_variant 0.52 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 0.34 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364383 c.-30C>A upstream_gene_variant 0.42 pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.35 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 0.39 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.5 pyrazinamide Not assoc w R
PPE35 2169662 c.951T>C synonymous_variant 0.59 pyrazinamide Not assoc w R - Interim
PPE35 2169776 c.837C>T synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289365 c.-125delC upstream_gene_variant 0.52 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.66 isoniazid Not assoc w R
ahpC 2726115 c.-78C>T upstream_gene_variant 0.59 isoniazid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.37 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ribD 2986852 p.Gly5Asp missense_variant 0.53 para-aminosalicylic_acid
thyA 3074440 p.Val11Ala missense_variant 0.46 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.52 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.52 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840764 c.657G>C synonymous_variant 0.63 cycloserine
panD 4044905 c.-624C>T upstream_gene_variant 0.33 pyrazinamide
glpK 4139183 c.570_572dupGGG disruptive_inframe_insertion 0.53 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.4 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248803 p.Met764Leu missense_variant 0.33 ethambutol Uncertain significance
embB 4249254 p.Gly914Glu missense_variant 0.26 ethambutol
whiB6 4338471 p.Arg17Ser missense_variant 0.53 capreomycin
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 0.43 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.51 streptomycin Not assoc w R
gid 4407650 p.Asp185Asn missense_variant 0.54 streptomycin Uncertain significance