Run ID: SRR13861279
Sample name:
Date: 2024-04-15T05:25:10.165021
Number of reads: 2025402
Percentage reads mapped: 33.79
Median coverage: 66.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| 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 | ||||
| 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 |
|---|---|---|---|---|---|---|
| rpoB | 761402 | c.1596C>T | synonymous_variant | 0.98 | rifampicin | |
| rpoC | 762473 | c.-897C>A | upstream_gene_variant | 1.0 | rifampicin | |
| mmpS5 | 778694 | p.Tyr71Ser | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpR5 | 779478 | p.Glu163Asp | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 800969 | p.Tyr54Ser | missense_variant | 1.0 | linezolid | |
| embR | 1417498 | c.-151G>T | upstream_gene_variant | 1.0 | ethambutol | |
| embR | 1417937 | c.-591_-590insA | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1473125 | n.1280A>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1475195 | n.1538G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
| linezolid | ||||||
| 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 | 0.6 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| katG | 2155952 | p.Val54Ile | missense_variant | 1.0 | isoniazid | |
| Rv1979c | 2223817 | c.-653C>A | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| kasA | 2518986 | p.Met291Arg | missense_variant | 1.0 | isoniazid | |
| Rv2752c | 3065218 | p.Ser325Ile | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv3083 | 3448654 | p.Pro51Ala | missense_variant | 1.0 | ethionamide | |
| whiB7 | 3568465 | p.Asp72Val | missense_variant | 1.0 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| mtrB | 3627381 | c.-768G>A | upstream_gene_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| fbiA | 3640597 | p.Val19Leu | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| alr | 3840493 | p.Leu310Val | missense_variant | 1.0 | cycloserine | |
| panD | 4044931 | c.-650C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| embC | 4239802 | c.-61T>A | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4241184 | p.Thr441Lys | missense_variant | 1.0 | ethambutol | |
| embA | 4243518 | p.Gly96Cys | missense_variant | 1.0 | ethambutol | |
| embA | 4244162 | c.931dupC | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4247920 | c.1407T>C | synonymous_variant | 1.0 | ethambutol | |
| ethA | 4327042 | p.Asp144Glu | missense_variant | 1.0 | ethionamide | |
| ethR | 4327865 | p.Gly106Ala | missense_variant | 0.98 | ethionamide |
