Run ID: ERR1633888
Sample name:
Date: 2024-04-14T14:06:28.732520
Number of reads: 3171756
Percentage reads mapped: 99.63
Median coverage: 48.0
Strain: lineage4.7
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.7 | Euro-American (mainly T) | None | 0.94 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | c.-10145_*20021del | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | tlyA | c.-38219_*9302del | Assoc w R | |
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.-18780_*22888del | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | fbiA | c.-5250_*20197del | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
tlyA | 1879720 | c.-38219_*9302del | transcript_ablation | 0.92 | capreomycin | Assoc w R | |
katG | 2133867 | c.-10145_*20021del | transcript_ablation | 0.92 | isoniazid | Assoc w R | High-level resistance |
fbiA | 3635292 | c.-5250_*20197del | transcript_ablation | 0.92 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
ethA | 4303115 | c.-18780_*22888del | transcript_ablation | 0.95 | ethionamide | Assoc w R |
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 | |||||
Rv0010c | 13887 | c.-329T>C | upstream_gene_variant | 0.98 | isoniazid | |
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 | 1474294 | n.637C>G | non_coding_transcript_exon_variant | 0.93 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2164468 | c.994_*3180del | stop_lost&conservative_inframe_deletion&splice_region_variant | 0.93 | pyrazinamide | |
PPE35 | 2166262 | c.2692_*1386del | stop_lost&conservative_inframe_deletion&splice_region_variant | 0.91 | pyrazinamide | |
PPE35 | 2166549 | c.1198_*1099del | stop_lost&conservative_inframe_deletion&splice_region_variant | 0.94 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv3236c | 3574532 | c.1062_*37426del | frameshift_variant&stop_lost&splice_region_variant | 0.93 | pyrazinamide | Uncertain significance |
embA | 4216398 | c.-26834_*16207del | transcript_ablation | 0.95 | ethambutol | Uncertain significance |
embA | 4225572 | c.-17660_*22218del | transcript_ablation | 0.93 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249732 | c.3219C>G | synonymous_variant | 0.89 | 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 | |||||
gid | 4407704 | p.Ala167Pro | missense_variant | 0.9 | streptomycin | Uncertain significance |