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
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.99 |
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 |
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 |
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 |