Run ID: ERR3957925
Sample name:
Date: 2024-04-15T16:16:53.910158
Number of reads: 2836209
Percentage reads mapped: 97.08
Median coverage: 94.0
Strain: lineage4.3.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.3 | Euro-American (LAM) | None | 1.0 |
| lineage4.3.2 | Euro-American (LAM) | None | 1.0 |
| lineage4 | Euro-American | None | 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 | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| nusG | 734877 | c.624C>G | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | 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 |
| Rv1129c | 1254556 | c.-22A>G | upstream_gene_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.99 | streptomycin | Not assoc w R - Interim |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrl | 1474126 | n.469G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1475877 | n.2220C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475892 | n.2235A>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| inhA | 1673475 | c.-727A>G | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2064472 | p.Val86Ala | missense_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| lpqB | 3623609 | c.1302G>A | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | 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 | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |
