Run ID: 419d2a25-58f2-4171-a055-99c163de2712
Sample name:
Date: 01-11-2023 05:01:24
Number of reads: 343909
Percentage reads mapped: 98.53
Median coverage: 10
Strain: lineage1.1.1.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1.1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1.1.1 | 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 | 5347 | c.108G>A | synonymous_variant | 0.1 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | 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 | 7762 | p.Pro154His | missense_variant | 0.13 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8520 | c.1219C>T | synonymous_variant | 0.15 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9013 | p.Thr571Ile | missense_variant | 0.13 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| 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 | ||||||
| fgd1 | 490972 | p.Arg64Ser | missense_variant | 1.0 | delamanid | Uncertain significance |
| fgd1 | 490984 | c.202C>T | synonymous_variant | 0.15 | delamanid | |
| fgd1 | 491520 | c.738C>T | synonymous_variant | 0.17 | delamanid | |
| rpoB | 759878 | c.72C>T | synonymous_variant | 0.15 | rifampicin | |
| rpoB | 760038 | p.Gly78Ser | missense_variant | 0.15 | rifampicin | |
| rpoB | 760607 | c.801G>T | synonymous_variant | 0.11 | rifampicin | |
| rpoB | 761825 | c.2019C>T | synonymous_variant | 0.17 | rifampicin | |
| rpoB | 762143 | c.2337T>C | synonymous_variant | 0.15 | rifampicin | |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 765379 | c.2010G>A | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 766385 | p.Pro1006Ser | missense_variant | 0.18 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| rplC | 801266 | p.Gly153Ala | missense_variant | 1.0 | linezolid | |
| atpE | 1460860 | c.-185C>T | upstream_gene_variant | 0.17 | bedaquiline | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrs | 1472023 | n.178G>A | non_coding_transcript_exon_variant | 0.12 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 1.0 | linezolid | Uncertain significance |
| rrl | 1476773 | n.3116T>A | non_coding_transcript_exon_variant | 0.18 | linezolid | |
| fabG1 | 1673476 | p.Phe13Ile | missense_variant | 0.18 | ethionamide | |
| isoniazid | ||||||
| katG | 2154351 | c.1761G>A | synonymous_variant | 0.17 | isoniazid | |
| katG | 2156039 | p.His25Tyr | missense_variant | 1.0 | isoniazid | |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.95 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| pncA | 2289583 | c.-342T>C | upstream_gene_variant | 0.18 | pyrazinamide | |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| kasA | 2518906 | c.792A>G | synonymous_variant | 0.17 | isoniazid | |
| eis | 2714830 | p.Pro168Leu | missense_variant | 0.14 | kanamycin | |
| amikacin | ||||||
| eis | 2715064 | p.Thr90Met | missense_variant | 0.12 | kanamycin | |
| amikacin | ||||||
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 | rifampicin | |
| isoniazid | ||||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| fbiD | 3339761 | c.644G>T | stop_lost&splice_region_variant | 0.14 | delamanid | |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | 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 | |||||
| Rv3236c | 3612658 | c.459G>T | synonymous_variant | 0.17 | pyrazinamide | |
| Rv3236c | 3612847 | c.270G>C | synonymous_variant | 0.15 | pyrazinamide | |
| Rv3236c | 3613131 | c.-15A>T | upstream_gene_variant | 0.17 | pyrazinamide | |
| alr | 3840308 | c.1113G>T | synonymous_variant | 0.15 | cycloserine | |
| alr | 3840871 | p.Ala184Thr | missense_variant | 0.14 | cycloserine | |
| rpoA | 3877738 | p.Thr257Met | missense_variant | 0.12 | rifampicin | |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| embC | 4240350 | p.Arg163Gln | missense_variant | 0.11 | ethambutol | |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embA | 4242826 | c.-407G>A | upstream_gene_variant | 0.15 | ethambutol | |
| embA | 4244096 | c.864C>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 |
| aftB | 4266968 | c.1869G>T | synonymous_variant | 0.15 | capreomycin | |
| amikacin | ||||||
| aftB | 4267063 | c.1774T>C | synonymous_variant | 0.11 | capreomycin | |
| amikacin | ||||||
| aftB | 4268970 | c.-134G>A | upstream_gene_variant | 0.14 | capreomycin | Uncertain significance |
| amikacin | ||||||
| whiB6 | 4338242 | p.Gln94Glu | missense_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338316 | p.Ser69Cys | missense_variant | 1.0 | streptomycin | |
| capreomycin | ||||||
| amikacin | ||||||
| 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 | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | |
| gid | 4408021 | p.Arg61His | missense_variant | 0.2 | streptomycin |
