Run ID: e77f366c-4310-439d-85a9-653c365d1939
Sample name:
Date: 19-03-2024 23:51:13
Number of reads: 3905771
Percentage reads mapped: 98.89
Median coverage: 123
Strain: lineage1.2.1.2.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.2.1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.2.1.2 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.2.1.2.1 | 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 | 6112 | p.Met291Ile | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 0.99 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8452 | p.Ala384Val | 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 | 9260 | c.1959G>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 | ||||||
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
| mshA | 575368 | c.21T>C | synonymous_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| mshA | 576116 | p.Ala257Pro | missense_variant | 0.21 | ethionamide | |
| isoniazid | ||||||
| mshA | 576119 | p.Ala258Pro | missense_variant | 0.36 | ethionamide | |
| isoniazid | ||||||
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
| rpoC | 763531 | c.162G>C | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 764809 | c.1440C>T | synonymous_variant | 1.0 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| fbiC | 1302821 | c.-110G>A | upstream_gene_variant | 1.0 | delamanid | Uncertain significance |
| Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 | bedaquiline | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| inhA | 1674162 | c.-40C>T | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2222362 | p.Leu268Trp | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| kasA | 2519048 | p.Gly312Ser | missense_variant | 0.98 | isoniazid | |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
| pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.17 | clofazimine | |
| bedaquiline | ||||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 | delamanid | |
| fbiD | 3339751 | p.Ala212Pro | missense_variant | 0.2 | delamanid | |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.98 | capreomycin | |
| amikacin | ||||||
| fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| whiB7 | 3568428 | c.252A>G | synonymous_variant | 0.33 | streptomycin | |
| kanamycin | ||||||
| amikacin | ||||||
| whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 1.0 | delamanid | |
| rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.18 | rifampicin | |
| clpC1 | 4040235 | p.Gly157Ala | missense_variant | 0.25 | 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 | 4243580 | c.348G>A | synonymous_variant | 1.0 | ethambutol | |
| embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 | ethambutol | |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 | ethambutol | |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| ubiA | 4269864 | c.-32delG | upstream_gene_variant | 0.99 | ethambutol | |
| whiB6 | 4338361 | p.Arg54Gln | missense_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin |
