Run ID: SRR13861360
Sample name:
Date: 2024-10-05T06:18:51.325929
Number of reads: 450234
Percentage reads mapped: 45.07
Median coverage: 15.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
| 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 | katG | c.1313_1314insT | Assoc w R | High-level resistance |
| 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 |
|---|---|---|---|---|---|---|---|
| katG | 2154798 | c.1313_1314insT | frameshift_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5906 | p.Val223Leu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 6011 | p.Val258Met | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 6678 | p.Pro480Arg | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 490676 | c.-107G>C | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| ccsA | 620028 | c.138G>C | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| rpoB | 759638 | c.-169T>A | upstream_gene_variant | 1.0 | rifampicin | |
| rpoB | 760454 | c.650delG | frameshift_variant | 1.0 | rifampicin | |
| rpoC | 765487 | p.Met706Ile | missense_variant | 1.0 | rifampicin | |
| rpsL | 781409 | c.-151T>A | upstream_gene_variant | 1.0 | streptomycin | |
| Rv1129c | 1254013 | p.Met174Ile | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| Rv1129c | 1254452 | p.Glu28Ala | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| fbiC | 1302873 | c.-58A>T | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rrs | 1471874 | n.29A>C | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.33 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.33 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.36 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.38 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.4 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.38 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.4 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.4 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.38 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.38 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| bacA | 2063125 | p.Ala535Asp | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| bacA | 2064843 | c.-115C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| katG | 2154654 | p.Ser486Arg | missense_variant | 1.0 | isoniazid | |
| katG | 2154882 | c.1230G>A | synonymous_variant | 1.0 | isoniazid | |
| katG | 2155857 | c.255C>A | synonymous_variant | 1.0 | isoniazid | |
| PPE35 | 2170198 | p.Ala139Ser | missense_variant | 1.0 | pyrazinamide | |
| pncA | 2290069 | c.-828C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| eis | 2714922 | c.411G>A | synonymous_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| thyA | 3074067 | c.405C>G | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
| lpqB | 3624738 | p.Ala58Val | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625436 | p.Ile393Asn | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrA | 3626728 | p.Asp208Tyr | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| alr | 3840223 | c.1198A>C | synonymous_variant | 1.0 | cycloserine | |
| alr | 3840711 | p.Ser237Leu | missense_variant | 1.0 | cycloserine | |
| clpC1 | 4039648 | p.Glu353Gln | missense_variant | 1.0 | pyrazinamide | |
| embC | 4242023 | p.Val721Leu | missense_variant | 1.0 | ethambutol |
