Run ID: SRR13837881
Sample name:
Date: 2024-10-04T11:43:29.292272
Number of reads: 1469386
Percentage reads mapped: 97.02
Median coverage: 49.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| 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 | embR | p.Ser188Arg | Mutation from literature | |
| 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 |
|---|---|---|---|---|---|---|---|
| embR | 1416784 | p.Ser188Arg | missense_variant | 1.0 | ethambutol | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| fgd1 | 490771 | c.-12T>G | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mshA | 575112 | c.-236G>T | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| rpoB | 761125 | c.1320dupG | frameshift_variant | 1.0 | rifampicin | |
| rpoB | 761989 | p.Ala728Val | missense_variant | 1.0 | rifampicin | |
| rpoC | 763884 | p.Ala172Asp | missense_variant | 1.0 | rifampicin | |
| rpoC | 764514 | p.Phe382Tyr | missense_variant | 1.0 | rifampicin | |
| rpoC | 765936 | p.Ala856Gly | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 776303 | c.2178G>C | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 800132 | c.-677C>G | upstream_gene_variant | 1.0 | linezolid | |
| fbiC | 1303334 | p.Gly135Val | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| embR | 1416250 | c.1098C>A | synonymous_variant | 1.0 | ethambutol | |
| rrl | 1474218 | n.561T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1475718 | n.2061T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rpsA | 1833707 | p.Gly56Arg | missense_variant | 1.0 | pyrazinamide | |
| tlyA | 1918168 | p.Phe77Leu | missense_variant | 1.0 | capreomycin | |
| bacA | 2063041 | p.Arg563Pro | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| bacA | 2063427 | c.1302G>T | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| bacA | 2063999 | c.729_730insT | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| ndh | 2103307 | c.-265A>G | upstream_gene_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| kasA | 2518023 | c.-92C>T | upstream_gene_variant | 1.0 | isoniazid | |
| eis | 2715279 | c.54A>G | synonymous_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| folC | 2747689 | c.-91C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3339289 | p.Ser58Ala | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| whiB7 | 3569132 | c.-453C>T | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| Rv3236c | 3613708 | c.-592C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| clpC1 | 4038389 | c.2316G>C | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040326 | p.Leu127Val | missense_variant | 1.0 | pyrazinamide | |
| glpK | 4139633 | c.123C>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| isoniazid | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R - Interim | |||||
| ethambutol | Not assoc w R - Interim | |||||
| embC | 4241920 | p.Asp686Glu | missense_variant | 1.0 | ethambutol | |
| ubiA | 4269209 | p.Ser209Thr | missense_variant | 1.0 | ethambutol |
