TB-Profiler result

Run: ERR2179733

Summary

Run ID: ERR2179733

Sample name:

Date: 2024-04-15T13:33:57.908751

Number of reads: 5369898

Percentage reads mapped: 99.54

Median coverage: 134.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: MDR-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 0.99
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 rpoB p.Leu430Pro Assoc w R
p.Asn437Ser Assoc w R - Interim
isoniazid katG c.551dupG Assoc w R High-level resistance
ahpC c.-81C>T Uncertain significance Mutation from literature
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
rpoB 761095 p.Leu430Pro missense_variant 0.99 rifampicin Assoc w R
rpoB 761116 p.Asn437Ser missense_variant 0.52 rifampicin Assoc w R - Interim
katG 2155560 c.551dupG frameshift_variant 0.98 isoniazid Assoc w R High-level resistance
ahpC 2726112 c.-81C>T upstream_gene_variant 0.97 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
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 7892 c.591G>A synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254134 p.Leu134Pro missense_variant 0.46 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254533 p.Met1? start_lost 0.21 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833734 p.Ala65Thr missense_variant 1.0 pyrazinamide
tsnR 1854216 p.Glu204Gly missense_variant 0.98 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.99 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714211 c.1122G>A synonymous_variant 0.99 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ahpC 2726764 p.Leu191Pro missense_variant 0.45 isoniazid Uncertain significance
Rv2681 2997047 p.Glu103Asp missense_variant 0.99 capreomycin
Rv2752c 3064993 p.Trp400* stop_gained 0.99 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3066294 c.-103C>G upstream_gene_variant 0.99 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878575 c.-68C>T upstream_gene_variant 0.97 rifampicin Not assoc w R
ddn 3986759 c.-85C>T upstream_gene_variant 0.97 delamanid
pretomanid
clpC1 4038318 p.Pro796Leu missense_variant 0.98 pyrazinamide Not assoc w R
clpC1 4040745 c.-41G>A upstream_gene_variant 0.85 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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
gid 4407979 p.Pro75Leu missense_variant 0.99 streptomycin Uncertain significance