Run ID: ERR11044338
Sample name:
Date: 2024-04-14T17:55:41.256071
Number of reads: 4731495
Percentage reads mapped: 99.68
Median coverage: 153.0
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 |
|---|---|---|---|---|---|---|
| gyrB | 6317 | p.Val360Met | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 8306 | c.1005C>A | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 491659 | p.Ala293Thr | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.26 | ethionamide | |
| isoniazid | ||||||
| mshA | 576683 | p.Gly446Ser | missense_variant | 1.0 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| 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 |
| tlyA | 1918551 | c.613_687delTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | conservative_inframe_deletion | 1.0 | capreomycin | |
| PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2169192 | p.Ala474Gly | missense_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 | |||||
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
| clpC1 | 4039023 | p.Glu561Ala | missense_variant | 1.0 | pyrazinamide | |
| embC | 4241729 | p.Ala623Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246548 | p.Pro12Gln | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ethR | 4326976 | c.-573G>A | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R |
