TB-Profiler result

Run: ERR9786062
Summary

Run ID: ERR9786062

Sample name:

Date: 2024-04-16T12:57:30.681530

Number of reads: 1784152

Percentage reads mapped: 99.59

Median coverage: 77.0

Strain: lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.82
lineage4.1 Euro-American None 0.13
lineage4.1.2 Euro-American None 0.17
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.18
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.78
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage4 Euro-American None 0.21
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 rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.72 streptomycin 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 8814 p.Val505Ile missense_variant 0.19 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.14 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.75 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.2 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.74 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.8 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.91 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.12 rifampicin Not assoc w R
rpoB 762878 c.3072C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.28 rifampicin Not assoc w R
rpoC 766089 p.Asp907Gly missense_variant 0.23 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 0.8 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.71 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 778732 c.174C>T synonymous_variant 0.14 clofazimine Not assoc w R - Interim
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.77 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 0.8 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 0.8 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.71 pyrazinamide 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 0.77 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.74 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.22 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.81 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
lpqB 3623972 c.939C>A synonymous_variant 0.21 bedaquiline
rifampicin 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 0.85 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139292 p.Ile155Thr missense_variant 0.69 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4239298 c.-565C>T upstream_gene_variant 0.2 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.2 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.86 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.88 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 0.78 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.64 streptomycin Not assoc w R