Run ID: SRR7535081
Sample name:
Date: 2024-10-04T00:57:04.722415
Number of reads: 364635
Percentage reads mapped: 6.07
Median coverage: 8.0
Strain: lineage4.6.1.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.6.1.1 | Euro-American | RD724 | 0.97 |
| lineage4.6.1 | Euro-American (Uganda) | RD724 | 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 | 8375 | c.1074G>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | ||||||
| rpoB | 762911 | p.Ile1035Met | missense_variant | 0.74 | rifampicin | |
| rpoB | 762923 | c.3117C>G | synonymous_variant | 0.67 | rifampicin | Not assoc w R - Interim |
| rpoB | 762929 | c.3123G>T | synonymous_variant | 0.7 | rifampicin | Not assoc w R - Interim |
| rpoC | 762932 | c.-438G>T | upstream_gene_variant | 0.7 | rifampicin | |
| rpoB | 762939 | p.Met1045Leu | missense_variant | 0.7 | rifampicin | |
| rpoB | 762942 | p.Ile1046Val | missense_variant | 0.67 | rifampicin | Uncertain significance |
| rpoC | 762947 | c.-423C>G | upstream_gene_variant | 0.67 | rifampicin | |
| rpoB | 762962 | c.3156C>T | synonymous_variant | 0.62 | rifampicin | Not assoc w R - Interim |
| rpoB | 762989 | c.3183G>T | synonymous_variant | 0.67 | rifampicin | Not assoc w R - Interim |
| rpoC | 764905 | c.1536C>T | synonymous_variant | 0.57 | rifampicin | |
| rpoC | 764911 | c.1542A>C | synonymous_variant | 0.53 | rifampicin | |
| rpoC | 764914 | p.Met515Ile | missense_variant | 0.53 | rifampicin | Uncertain significance |
| rpoC | 764918 | p.Val517Ile | missense_variant | 0.57 | rifampicin | |
| rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.85 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472210 | n.365A>T | non_coding_transcript_exon_variant | 0.94 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.94 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.97 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.97 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.97 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1472251 | n.406G>C | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472252 | n.407G>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.96 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.96 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.84 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.79 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472785 | n.940G>T | non_coding_transcript_exon_variant | 0.79 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472786 | n.941C>G | non_coding_transcript_exon_variant | 0.79 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.79 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472814 | n.969G>A | non_coding_transcript_exon_variant | 0.83 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.82 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | ||||||
| amikacin | Uncertain significance | |||||
| rrs | 1473204 | n.1359C>T | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | ||||||
| amikacin | Uncertain significance | |||||
| rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.9 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473226 | n.1381C>T | non_coding_transcript_exon_variant | 0.75 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
| linezolid | ||||||
| rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.92 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.81 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.81 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>A | non_coding_transcript_exon_variant | 0.8 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476483 | n.2826G>A | non_coding_transcript_exon_variant | 0.75 | capreomycin | |
| linezolid | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| panD | 4043882 | p.Pro134Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4328329 | c.-856C>G | upstream_gene_variant | 1.0 | ethionamide | |
| ethA | 4328389 | c.-916C>T | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
