Run ID: 6f17f958-c64e-4e2f-afde-9c9c572f6bff
Sample name:
Date: 04-08-2023 23:21:53
Number of reads: 353129
Percentage reads mapped: 98.2
Median coverage: 11
Strain: lineage1.1.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1.2 | Indo-Oceanic | RD239 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| moxifloxacin | ||||
| levofloxacin | ||||
| bedaquiline | ||||
| delamanid | ||||
| pretomanid | ||||
| linezolid | ||||
| streptomycin | ||||
| amikacin | ||||
| kanamycin | ||||
| capreomycin | ||||
| clofazimine | ||||
| ethionamide | ||||
| para-aminosalicylic_acid | ||||
| cycloserine |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mmpL5 | 776233 | p.Pro750Ser | missense_variant | 0.12 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 776395 | p.Phe696Leu | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| embR | 1416776 | p.Ile191Thr | missense_variant | 0.17 | ethambutol | |
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| katG | 2156541 | c.-430G>A | upstream_gene_variant | 0.17 | isoniazid | |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
| ribD | 2986844 | c.6C>T | synonymous_variant | 0.15 | para-aminosalicylic_acid | |
| ribD | 2987123 | c.285C>T | synonymous_variant | 0.1 | para-aminosalicylic_acid | |
| thyX | 3067315 | c.631C>T | synonymous_variant | 0.17 | para-aminosalicylic_acid | |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| Rv3236c | 3612680 | p.Arg146Gln | missense_variant | 0.2 | pyrazinamide | |
| clpC1 | 4039513 | p.Lys398Glu | missense_variant | 0.15 | pyrazinamide | |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embA | 4243848 | p.Val206Met | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4245218 | c.1986C>T | synonymous_variant | 1.0 | ethambutol | |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4249702 | c.3189C>T | synonymous_variant | 0.15 | ethambutol | |
| aftB | 4267352 | c.1485C>T | synonymous_variant | 0.14 | capreomycin | |
| amikacin | ||||||
| ubiA | 4269031 | p.Gly268Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | |
| gid | 4408100 | p.Leu35Met | missense_variant | 0.11 | streptomycin | Uncertain significance |
