TB-Profiler result

Run: ERR4813371
Summary

Run ID: ERR4813371

Sample name:

Date: 2024-03-25T23:10:53.302249

Number of reads: 4284155

Percentage reads mapped: 99.61

Median coverage: 145.0

Strain: lineage2.2.1;lineage4.3.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.44
lineage2 East-Asian RD105 0.6
lineage4.3.2 Euro-American (LAM) None 0.42
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.59
lineage2.2 East-Asian (Beijing) RD105;RD207 0.61
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Thr160Pro Assoc w R
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 761101 p.Gln432Pro missense_variant 0.44 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid Assoc w R High-level resistance
pncA 2288764 p.Thr160Pro missense_variant 0.4 pyrazinamide Assoc w R
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
fgd1 491742 c.960T>C synonymous_variant 0.72 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.68 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.56 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.56 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.56 ethionamide Uncertain significance
nusG 734420 p.Ala56Val missense_variant 0.47 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 765926 p.Thr853Ala missense_variant 0.44 rifampicin Uncertain significance
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 0.6 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.54 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.63 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 0.71 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.44 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.34 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
tsnR 1854169 c.564A>C synonymous_variant 0.52 linezolid Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 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 0.62 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.71 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 2715727 c.-395G>A upstream_gene_variant 0.31 amikacin
kanamycin
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.46 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.38 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
ald 3087755 c.936G>T synonymous_variant 0.63 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.5 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.65 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.53 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.33 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.44 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.49 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 4407588 c.615A>G synonymous_variant 0.7 streptomycin Not assoc w R
gid 4407721 p.Ala161Gly missense_variant 0.4 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.6 streptomycin Not assoc w R
gid 4408050 p.Asn51Lys missense_variant 0.46 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.44 streptomycin Not assoc w R