Run ID: SRR7535077
Sample name:
Date: 2024-04-15T13:08:18.255615
Number of reads: 1036028
Percentage reads mapped: 10.4
Median coverage: 18.0
Strain: lineage4.6.1.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | None | 1.0 |
| lineage4.6.1.2 | Euro-American | RD724 | 0.98 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.6.1 | Euro-American (Uganda) | RD724 | 0.99 |
| 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 |
|---|---|---|---|---|---|---|
| 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 |
| embR | 1416410 | p.Leu313Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
| rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.86 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472210 | n.365A>T | non_coding_transcript_exon_variant | 0.95 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.9 | streptomycin | Uncertain significance |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.9 | streptomycin | Uncertain significance |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472251 | n.406G>C | non_coding_transcript_exon_variant | 0.89 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472252 | n.407G>A | non_coding_transcript_exon_variant | 0.89 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.93 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
| linezolid | ||||||
| rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.93 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.8 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | |
| linezolid | ||||||
| inhA | 1674465 | c.264C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| isoniazid | Not assoc w R - Interim | |||||
| 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 |
| Rv2681 | 2996876 | c.138A>C | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Not assoc w R | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4245055 | p.Thr608Asn | missense_variant | 1.0 | ethambutol | Uncertain significance |
| 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 | 4338635 | c.-114A>C | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
