Run ID: ERR1035296
Sample name:
Date: 2024-04-14T09:23:09.036452
Number of reads: 10411934
Percentage reads mapped: 99.7
Median coverage: 184.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | katG | c.316dupG | Assoc w R | High-level resistance |
| ahpC | c.-81C>T | Uncertain significance | Mutation from literature | |
| ethambutol | ||||
| pyrazinamide | pncA | p.Ala171Val | Uncertain significance | Mutation from literature |
| c.246delT | Assoc w R | |||
| 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 |
|---|---|---|---|---|---|---|---|
| katG | 2155795 | c.316dupG | frameshift_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2288730 | p.Ala171Val | missense_variant | 0.53 | pyrazinamide | Uncertain significance | Mutation from literature |
| pncA | 2288995 | c.246delT | frameshift_variant | 0.38 | pyrazinamide | Assoc w R | |
| ahpC | 2726112 | c.-81C>T | upstream_gene_variant | 0.99 | isoniazid | Uncertain significance | Mutation from literature |
| 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 | |||||
| Rv0565c | 656195 | p.Gly426Cys | missense_variant | 1.0 | ethionamide | |
| fbiC | 1303257 | c.327C>T | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1473752 | n.95G>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
| linezolid | ||||||
| rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
| linezolid | Uncertain significance | |||||
| rrl | 1473876 | n.219G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
| linezolid | ||||||
| rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473923 | n.266C>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | Uncertain significance | |||||
| rrl | 1473924 | n.267_268insT | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1473944 | n.287G>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
| linezolid | ||||||
| rrl | 1473981 | n.324delGinsAT | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
| linezolid | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| rrl | 1474028 | n.371T>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1474029 | n.372G>A | non_coding_transcript_exon_variant | 0.26 | capreomycin | |
| linezolid | ||||||
| rrl | 1474034 | n.377G>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
| linezolid | ||||||
| rrl | 1474040 | n.383G>A | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1474083 | n.426C>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1474111 | n.454T>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474181 | n.524C>A | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1474266 | n.609T>C | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474291 | n.634_649delTTTCCTCTCCGGAGGAinsC | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
| linezolid | ||||||
| rrl | 1474308 | n.651G>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474310 | n.653T>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
| linezolid | ||||||
| rrl | 1474362 | n.705A>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474374 | n.717T>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1474632 | n.975G>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474716 | n.1059A>G | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475202 | n.1545G>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475252 | n.1595C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1475266 | n.1609T>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475276 | n.1619T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
| linezolid | ||||||
| rrl | 1475289 | n.1632G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
| linezolid | ||||||
| rrl | 1475291 | n.1634A>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475297 | n.1640C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
| linezolid | ||||||
| rrl | 1475315 | n.1658A>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
| linezolid | ||||||
| rrl | 1475333 | n.1676T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475402 | n.1745C>T | non_coding_transcript_exon_variant | 0.1 | capreomycin | |
| linezolid | ||||||
| rrl | 1475429 | n.1772G>A | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475446 | n.1789G>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| glpK | 4138415 | c.1341G>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R - Interim | |||||
| isoniazid | Not assoc w R - Interim | |||||
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R |
