TB-Profiler result

Run: 53e1cdef-ad01-4b78-962c-4191b668e80d
Summary

Run ID: 53e1cdef-ad01-4b78-962c-4191b668e80d

Sample name:

Date: 15-05-2023 14:31:31

Number of reads: 1265224

Percentage reads mapped: 98.11

Median coverage: 35

Strain: 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
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rpsL p.Lys43Arg Assoc w R
amikacin
kanamycin
capreomycin
clofazimine
ethionamide ethA p.Cys403Gly Uncertain significance
p.Ser329Leu Uncertain significance
para-aminosalicylic_acid
cycloserine
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 1.0 streptomycin Assoc w R
ethA 4326267 p.Cys403Gly missense_variant 1.0 ethionamide Uncertain significance
ethA 4326488 p.Ser329Leu missense_variant 1.0 ethionamide Uncertain significance
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 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 490742 c.-41C>T upstream_gene_variant 1.0 delamanid
mshA 576453 p.Val369Gly missense_variant 0.33 ethionamide
isoniazid
mshA 576456 p.Val370Gly missense_variant 0.33 ethionamide
isoniazid
mshA 576489 p.Val381Gly missense_variant 0.25 ethionamide
isoniazid
mshA 576606 p.Ala420Gly missense_variant 0.27 ethionamide
isoniazid
rpoB 761161 p.Leu452Arg missense_variant 0.22 rifampicin
rpoB 761482 p.Ala559Gly missense_variant 0.25 rifampicin
rpoB 761707 p.Asp634Ala missense_variant 0.25 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777072 p.Lys470Met missense_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
PPE35 2170035 p.Val193Gly missense_variant 0.27 pyrazinamide
PPE35 2170048 p.Leu189Val missense_variant 0.18 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.18 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
eis 2714409 c.924T>G synonymous_variant 0.17 kanamycin
amikacin
folC 2746925 p.Asp225Ala missense_variant 0.2 para-aminosalicylic_acid
pepQ 2860051 p.Arg123Gln missense_variant 1.0 clofazimine
bedaquiline
pepQ 2860159 p.Ala87Gly missense_variant 0.22 clofazimine
bedaquiline
Rv2752c 3067162 c.-971T>G upstream_gene_variant 0.21 rifampicin
isoniazid
thyX 3067944 p.Val1Gly missense_variant 0.2 para-aminosalicylic_acid
fbiD 3339698 p.Asp194Ala missense_variant 0.27 delamanid
fbiD 3339711 c.594A>C synonymous_variant 0.13 delamanid
fprA 3474052 p.Phe16Val missense_variant 0.25 capreomycin
amikacin
clpC1 4038632 c.2073G>A synonymous_variant 1.0 pyrazinamide
embC 4240409 p.Pro183Ala missense_variant 0.15 ethambutol
embC 4240427 p.Ser189Arg missense_variant 0.4 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4244217 p.Thr329Pro missense_variant 0.24 ethambutol
embA 4245835 p.Leu868Arg missense_variant 0.33 ethambutol
embB 4246527 p.Ala5Gly missense_variant 0.29 ethambutol
embB 4247015 p.Ser168Ala missense_variant 0.45 ethambutol
aftB 4268619 p.Val73Gly missense_variant 0.22 capreomycin
amikacin
aftB 4268895 c.-59T>G upstream_gene_variant 0.26 capreomycin
amikacin
whiB6 4338200 p.Asp108His missense_variant 0.17 streptomycin
capreomycin
amikacin
whiB6 4338440 c.81dupT frameshift_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4408003 p.Asp67Gly missense_variant 0.17 streptomycin Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide