TB-Profiler result

Run: ERR9786445
Summary

Run ID: ERR9786445

Sample name:

Date: 2024-04-15T14:26:07.055877

Number of reads: 1963638

Percentage reads mapped: 93.84

Median coverage: 89.0

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 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 fbiC c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrB 4987 c.-253C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 762131 c.2325C>G synonymous_variant 0.13 rifampicin
rpoB 762317 c.2511A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.15 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.14 rifampicin
rpoC 764489 c.1120C>T synonymous_variant 0.14 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.13 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764554 c.1185C>T synonymous_variant 0.12 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.17 rifampicin
rpoC 765751 c.2382C>G synonymous_variant 0.17 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.17 rifampicin Uncertain significance
rpoC 765772 c.2403C>G synonymous_variant 0.17 rifampicin
rpoC 765784 c.2415C>G synonymous_variant 0.15 rifampicin
rpoC 765787 c.2418C>T synonymous_variant 0.15 rifampicin
rpoC 765793 c.2424C>G synonymous_variant 0.15 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 0.15 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.16 rifampicin
rpoC 766876 c.3507C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766882 c.3513C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766900 c.3531T>C synonymous_variant 0.14 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.15 rifampicin
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
rpsL 781742 c.183C>T synonymous_variant 0.13 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.16 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.16 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.14 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.13 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834303 c.762T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834333 c.792C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.14 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.15 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168813 c.1721_1799delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3065381 p.Arg271Cys missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3074097 c.375C>A synonymous_variant 0.12 para-aminosalicylic_acid
thyA 3074102 p.Asp124Asn missense_variant 0.12 para-aminosalicylic_acid
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
mtrA 3627434 c.-85A>G upstream_gene_variant 1.0 bedaquiline
rifampicin Uncertain significance
fbiA 3640382 c.-161G>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
rpoA 3877962 c.546G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878271 c.237T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.15 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.15 rifampicin
rpoA 3878310 c.198G>C synonymous_variant 0.17 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878334 c.174T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.19 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.16 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.15 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.14 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.14 rifampicin
rpoA 3878388 c.120C>G synonymous_variant 0.14 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.14 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.14 rifampicin
rpoA 3878424 c.84G>C synonymous_variant 0.17 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.14 rifampicin
embC 4238983 c.-880C>G upstream_gene_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248319 c.1806A>G synonymous_variant 0.14 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
gid 4407758 p.Ser149Arg missense_variant 1.0 streptomycin Uncertain significance