TB-Profiler result

Run: ERR2229370
Summary

Run ID: ERR2229370

Sample name:

Date: 2024-03-26T13:25:53.565636

Number of reads: 1291217

Percentage reads mapped: 98.7

Median coverage: 26.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: RR-TB

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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 rpoB p.Leu449Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761152 p.Leu449Gln missense_variant 0.27 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
dnaA 845 p.Ile282Thr missense_variant 0.38 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2153970 p.Asp714Glu missense_variant 0.19 isoniazid
PPE35 2168728 p.Gly629Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169269 c.1344A>G synonymous_variant 0.21 pyrazinamide
PPE35 2169272 c.1341C>G synonymous_variant 0.21 pyrazinamide
PPE35 2169278 c.1335T>C synonymous_variant 0.21 pyrazinamide
PPE35 2169281 c.1332T>G synonymous_variant 0.22 pyrazinamide
PPE35 2169725 c.888T>C synonymous_variant 0.12 pyrazinamide
PPE35 2169902 c.709_711delCTGinsTC frameshift_variant&synonymous_variant 0.18 pyrazinamide Uncertain significance
PPE35 2169910 p.Asn235Tyr missense_variant 0.15 pyrazinamide
PPE35 2170048 p.Leu189Val missense_variant 0.64 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.67 pyrazinamide
PPE35 2170189 p.Glu142Gln missense_variant 0.12 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
alr 3841612 c.-193_-192insC upstream_gene_variant 0.21 cycloserine
embB 4246544 p.Thr11Pro missense_variant 0.36 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.56 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.7 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.7 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.56 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.39 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R