TB-Profiler result

Run: ERR4811227
Summary

Run ID: ERR4811227

Sample name:

Date: 2024-04-16T00:01:45.004593

Number of reads: 9228918

Percentage reads mapped: 99.61

Median coverage: 286.0

Strain: lineage2.2.1;lineage4.8

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 0.25
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.25
lineage2.2 East-Asian (Beijing) RD105;RD207 0.24
lineage4 Euro-American None 0.76
lineage4.8 Euro-American (mainly T) RD219 0.73
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 gid c.605_606delTG 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
gid 4407596 c.605_606delTG frameshift_variant 0.21 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
gyrB 6432 p.Ala398Val missense_variant 0.73 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 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.28 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.24 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.22 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.25 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.25 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.27 rifampicin Not assoc w R
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 0.26 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.26 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777551 c.930G>A synonymous_variant 0.22 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29 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 0.24 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 0.24 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.3 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 0.29 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.25 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.76 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 2714224 p.Ala370Val missense_variant 0.72 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.77 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.23 cycloserine
whiB7 3568675 p.Ser2Leu missense_variant 0.69 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.29 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.22 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.22 ethambutol Not assoc w R
embA 4245288 p.Ala686Ser missense_variant 0.71 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.23 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 0.28 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.22 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.18 streptomycin Not assoc w R
gid 4408127 c.76T>C synonymous_variant 0.77 streptomycin