TB-Profiler result

Run: ERR4830157
Summary

Run ID: ERR4830157

Sample name:

Date: 2024-10-05T01:58:44.233656

Number of reads: 2201853

Percentage reads mapped: 99.65

Median coverage: 66.0

Strain: lineage4.5;lineage4.8

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
lineage4.5 Euro-American RD122 0.42
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.63
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.Ser315Arg Assoc w R High-level resistance
p.Gly121Val Uncertain significance Mutation from literature
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155167 p.Ser315Arg missense_variant 0.42 isoniazid Assoc w R High-level resistance
katG 2155750 p.Gly121Val missense_variant 0.41 isoniazid Uncertain significance Mutation from literature
ahpC 2726139 c.-54C>T upstream_gene_variant 0.41 isoniazid Uncertain significance Mutation from literature
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 1184 p.Ala395Val missense_variant 0.14 isoniazid Uncertain significance
gyrA 7293 c.-9G>T upstream_gene_variant 0.48 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.52 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8042 c.741C>T synonymous_variant 0.39 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 0.39 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13638 c.-80A>C upstream_gene_variant 0.38 isoniazid Uncertain significance
Rv0010c 13647 c.-89C>A upstream_gene_variant 0.16 isoniazid Uncertain significance
ccsA 620029 c.139C>T synonymous_variant 0.35 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776371 p.Gly704Cys missense_variant 0.51 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253539 p.Ile332Met missense_variant 0.52 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1258c 1406101 p.Pro414Ser missense_variant 0.48 streptomycin Uncertain significance
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1853597 c.-9G>C upstream_gene_variant 0.39 linezolid Uncertain significance
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 2155367 p.Arg249Ser missense_variant 0.16 isoniazid Uncertain significance
PPE35 2170521 p.Trp31* stop_gained 0.39 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.43 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.63 bedaquiline Uncertain significance
clofazimine Not assoc w R
thyA 3074585 c.-118_-115delGACT upstream_gene_variant 0.45 para-aminosalicylic_acid
whiB7 3568581 c.98delC frameshift_variant 0.44 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568734 c.-55G>A upstream_gene_variant 0.33 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.37 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.6 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.42 pyrazinamide Not assoc w R
embC 4238972 c.-891C>G upstream_gene_variant 0.53 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246714 c.201G>T synonymous_variant 0.43 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 0.4 kanamycin
capreomycin
amikacin
gid 4407790 p.Ala138Val missense_variant 0.49 streptomycin Uncertain significance
gid 4407853 p.Gly117Glu missense_variant 0.47 streptomycin Uncertain significance