Run ID: ERR2229760
Sample name:
Date: 2024-10-05T00:21:34.736505
Number of reads: 1813935
Percentage reads mapped: 98.35
Median coverage: 47.0
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 | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clofazimine | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1475722 | n.2065G>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | |
| linezolid | ||||||
| rrl | 1475752 | n.2095C>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475758 | n.2101delAinsGG | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1475762 | n.2105G>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475763 | n.2106C>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475764 | n.2107A>C | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475765 | n.2108A>G | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475769 | n.2112_2113insC | non_coding_transcript_exon_variant | 0.55 | capreomycin | |
| linezolid | ||||||
| rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
| linezolid | ||||||
| rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.44 | capreomycin | |
| linezolid | ||||||
| rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 0.44 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475937 | n.2280A>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| inhA | 1673380 | c.-822C>G | upstream_gene_variant | 0.18 | isoniazid | |
| ethionamide | ||||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.35 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.34 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R |
