TB-Profiler result

Run: ERR12544386
Summary

Run ID: ERR12544386

Sample name:

Date: 2024-04-15T18:11:39.508506

Number of reads: 4272713

Percentage reads mapped: 99.58

Median coverage: 191.0

Strain: lineage4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.99
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.99
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
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
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
Rv0010c 13824 c.-266A>T upstream_gene_variant 0.16 isoniazid
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.16 isoniazid
Rv0010c 13834 c.-276A>T upstream_gene_variant 0.16 isoniazid
mshA 576488 c.1141_1143delGTGinsCC frameshift_variant&missense_variant 0.12 ethionamide Uncertain significance
isoniazid Uncertain significance
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
rplC 800204 c.-605T>C upstream_gene_variant 0.99 linezolid
Rv1129c 1254620 c.-86C>T upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1303144 p.Ser72Pro missense_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303155 c.225G>A synonymous_variant 0.16 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.99 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.99 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170035 p.Val193Ala missense_variant 0.17 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.51 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.5 pyrazinamide
PPE35 2170066 p.Ala183Thr missense_variant 0.16 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339741 c.624G>T synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiD 3339744 c.627A>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878567 c.-60C>G upstream_gene_variant 0.43 rifampicin
rpoA 3878578 c.-71C>A upstream_gene_variant 0.25 rifampicin Uncertain significance
rpoA 3878599 c.-92C>G upstream_gene_variant 0.3 rifampicin
rpoA 3878639 c.-132C>G upstream_gene_variant 0.22 rifampicin Uncertain significance
embC 4239281 c.-582C>G upstream_gene_variant 0.18 ethambutol
embC 4239284 c.-579C>G upstream_gene_variant 0.18 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.3 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.33 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.33 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.33 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.34 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.33 ethambutol Not assoc w R - Interim
embB 4249594 c.3081G>A synonymous_variant 0.99 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.99 ethionamide
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