Run ID: ERR1140780
Sample name:
Date: 2024-04-15T04:04:53.075993
Number of reads: 14463047
Percentage reads mapped: 92.6
Median coverage: 187.0
Strain: lineage4.2.1.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.2 | Euro-American | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.2.1.1 | Euro-American (TUR) | None | 1.0 |
| lineage4.2.1 | Euro-American (TUR) | 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 | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776536 | p.Lys649Gln | missense_variant | 0.99 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 777451 | p.Val344Leu | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| 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 | ||||||
| rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.17 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.2 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.18 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.32 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.33 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.58 | streptomycin | Uncertain significance |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.57 | streptomycin | Uncertain significance |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.62 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.6 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.55 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.57 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.53 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.53 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.52 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.3 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.45 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.45 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.73 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.2 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | ||||||
| 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 | 2063685 | c.1044G>A | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
| kanamycin | Not assoc w R - Interim | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170813 | c.-201G>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2752c | 3064701 | p.Phe497Leu | missense_variant | 0.99 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| ddn | 3987092 | p.Glu83Asp | missense_variant | 1.0 | delamanid | Uncertain significance |
| pretomanid | ||||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4408213 | c.-11C>T | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
