TB-Profiler result

Run: ERR11775016
Summary

Run ID: ERR11775016

Sample name:

Date: 2024-05-22T10:44:49.870725

Number of reads: 8766605

Percentage reads mapped: 99.7

Median coverage: 275.0

Strain: lineage4.1.2;lineage4.8

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
lineage4.1 Euro-American None 0.17
lineage4.1.2 Euro-American None 0.16
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.84
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
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
rpoB 761109 p.Asp435Tyr missense_variant 0.62 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.86 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
dnaA 371 p.Pro124Leu missense_variant 0.86 isoniazid Not assoc w R
gyrB 7027 p.Lys596Asn missense_variant 0.13 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.15 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
ccsA 620623 p.Ile245Val missense_variant 0.22 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.18 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.14 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 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473645 n.-12delT upstream_gene_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1853759 p.Val52Ile missense_variant 0.19 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 0.16 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.17 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.17 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840764 c.657G>C synonymous_variant 0.84 cycloserine
alr 3840801 p.Ile207Thr missense_variant 0.83 cycloserine
glpK 4138999 p.Val253Leu missense_variant 0.17 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242497 p.Arg879Gly missense_variant 0.88 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.17 ethambutol Not assoc w R
embA 4245963 p.Val911Ile missense_variant 0.81 ethambutol 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 0.18 capreomycin
amikacin
kanamycin