Run ID: SRR13837939
Sample name:
Date: 2024-10-03T16:14:57.723719
Number of reads: 1474062
Percentage reads mapped: 97.34
Median coverage: 49.0
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 |
|---|---|---|---|---|---|---|
| gyrA | 8827 | p.Asp509Gly | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| nusG | 734793 | c.540C>G | synonymous_variant | 1.0 | rifampicin | |
| mmpR5 | 779201 | p.Ala71Val | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 800119 | c.-690G>C | upstream_gene_variant | 1.0 | linezolid | |
| rplC | 800522 | c.-287C>A | upstream_gene_variant | 0.98 | linezolid | |
| Rv1129c | 1253232 | p.Asp435His | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| Rv1129c | 1253562 | p.Gln325Lys | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| Rv1129c | 1254726 | c.-192C>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| fbiC | 1305062 | p.Gly711Glu | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| sigE | 1364621 | p.Ala70Val | missense_variant | 1.0 | pyrazinamide | |
| rrs | 1472361 | n.516C>G | non_coding_transcript_exon_variant | 0.98 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1475981 | n.2324G>A | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rpsA | 1834620 | p.Leu360Ser | missense_variant | 1.0 | pyrazinamide | |
| tlyA | 1918366 | p.Ala143Pro | missense_variant | 0.98 | capreomycin | |
| bacA | 2064408 | c.321C>T | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| ndh | 2101701 | c.1341delG | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
| delamanid | Uncertain significance | |||||
| ethionamide | Uncertain significance | |||||
| ndh | 2103327 | c.-285C>A | upstream_gene_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2170109 | c.504C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| kasA | 2518676 | p.Gly188Cys | missense_variant | 1.0 | isoniazid | |
| eis | 2714749 | p.Val195Ala | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| eis | 2715045 | c.288G>A | synonymous_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| Rv2752c | 3067080 | c.-889G>C | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| lpqB | 3624325 | p.Thr196Pro | missense_variant | 0.98 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625849 | p.His255Gln | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| clpC1 | 4039055 | p.Ile550Met | missense_variant | 0.98 | pyrazinamide | |
| embC | 4242797 | p.Asp979His | missense_variant | 1.0 | ethambutol | |
| embB | 4247936 | p.Thr475Ala | missense_variant | 1.0 | ethambutol |
