Run ID: ERR5865968
Sample name:
Date: 2024-10-05T03:21:50.491124
Number of reads: 4650315
Percentage reads mapped: 89.77
Median coverage: 73.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: MDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 0.99 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embB | p.Met306Ile | Assoc w R | |
| pyrazinamide | pncA | p.Trp68Gly | Assoc w R | |
| streptomycin | gid | c.115delC | Assoc w R | |
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | rrs | n.1401A>G | Assoc w R | |
| capreomycin | rrs | n.1401A>G | Assoc w R | |
| kanamycin | rrs | n.1401A>G | Assoc w R | |
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.98 | rifampicin | Assoc w R | |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.97 | amikacin | Assoc w R | |
| capreomycin | Assoc w R | ||||||
| kanamycin | Assoc w R | ||||||
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2289040 | p.Trp68Gly | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.97 | ethambutol | Assoc w R | |
| gid | 4408087 | c.115delC | frameshift_variant | 0.99 | streptomycin | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5499 | p.Ala87Asp | 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 | 7724 | p.Met141Ile | missense_variant | 0.97 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| Rv0010c | 13262 | c.297G>A | synonymous_variant | 0.99 | isoniazid | |
| fgd1 | 490829 | p.Ala16Val | missense_variant | 0.99 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mmaA3 | 737324 | p.Ala276Thr | missense_variant | 0.99 | isoniazid | |
| rpoC | 767123 | p.Val1252Met | missense_variant | 0.96 | rifampicin | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 775677 | p.Lys935Thr | missense_variant | 0.99 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.28 | 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 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| 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 | 0.99 | capreomycin | Not assoc w R |
| ndh | 2103202 | c.-160C>T | upstream_gene_variant | 0.15 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv3083 | 3448444 | c.-59_*1408del | transcript_ablation | 0.96 | ethionamide | Uncertain significance |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.99 | ethionamide | Uncertain significance |
| glpK | 4138698 | p.Val353Gly | missense_variant | 0.19 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| glpK | 4138930 | p.Glu276Lys | missense_variant | 0.36 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4269546 | c.-710G>C | upstream_gene_variant | 0.96 | ethambutol | |
| ubiA | 4269864 | c.-31C>T | upstream_gene_variant | 0.95 | ethambutol | Uncertain significance |
| ethA | 4327006 | p.Asp156Glu | missense_variant | 0.99 | ethionamide | |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R |
