Run ID: ERR4407486
Sample name:
Date: 2024-04-14T12:07:00.882832
Number of reads: 1346058
Percentage reads mapped: 99.67
Median coverage: 58.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 1.0 |
| 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 |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 8613 | p.Met438Val | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| 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 | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2064249 | c.480C>T | synonymous_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| PPE35 | 2169071 | c.1463_1541delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2169071 | c.1464_1541delGGCGGTGACGACGCCGGCCAACGTTACCGTGGGTGCGTTTGATTTGCCGGGGTTGACGGTGCCGTCGTTGACGATTCC | disruptive_inframe_deletion | 0.64 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223197 | c.-33T>C | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2477c | 2783267 | p.Asp259Gly | missense_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | ||||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| kanamycin | ||||||
| rifampicin | Uncertain significance | |||||
| amikacin | ||||||
| ald | 3087095 | c.276C>T | synonymous_variant | 1.0 | cycloserine | |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
| clpC1 | 4040021 | c.684A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243905 | p.Asp225Asn | missense_variant | 1.0 | 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 |
