Run ID: ERR11465963
Sample name:
Date: 2024-04-14T20:31:17.922084
Number of reads: 4298576
Percentage reads mapped: 99.45
Median coverage: 88.0
Strain: lineage4.1.1.3;lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.92 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 0.9 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 0.88 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.05 |
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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 4982 | c.-258C>G | upstream_gene_variant | 0.96 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.95 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.94 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 575566 | c.219G>A | synonymous_variant | 0.9 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R - Interim | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.96 | ethionamide | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.88 | rifampicin | 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 |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.89 | linezolid | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.1 | ethionamide | |
isoniazid | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.9 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.98 | capreomycin | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
eis | 2715620 | c.-288C>T | upstream_gene_variant | 0.78 | amikacin | |
kanamycin | ||||||
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.15 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.96 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.89 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiB | 3641298 | c.-237G>A | upstream_gene_variant | 0.79 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
embC | 4242643 | c.2781C>T | synonymous_variant | 0.85 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.94 | ethambutol | Not assoc w R |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.38 | ethambutol | Uncertain significance |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.29 | ethambutol | |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.9 | ethambutol | Not assoc w R |
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 | 0.95 | capreomycin | |
amikacin | ||||||
kanamycin |