Run ID: SRR6280216
Sample name:
Date: 2024-10-04T06:04:38.708149
Number of reads: 4377141
Percentage reads mapped: 92.53
Median coverage: 134.0
Strain: lineage2.2.2
Spoligotype:
Drug-resistance: RR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage2 | East-Asian | RD105 | 1.0 |
| lineage2.2.2 | East-Asian (Beijing) | RD105;RD207 | 0.99 |
| lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
| isoniazid | ||||
| ethambutol | embB | p.Met306Ile | Assoc w R | |
| 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 |
|---|---|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 6773 | p.Gly512Arg | missense_variant | 0.99 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13479 | p.Ser27Tyr | missense_variant | 1.0 | isoniazid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| Rv0565c | 657142 | p.Arg110His | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 | rifampicin | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.39 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 0.48 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798_2799delCAinsAT | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>A | non_coding_transcript_exon_variant | 0.48 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.48 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476483 | n.2826G>A | non_coding_transcript_exon_variant | 0.33 | capreomycin | |
| linezolid | ||||||
| rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| katG | 2154724 | p.Arg463Leu | missense_variant | 0.99 | isoniazid | Not assoc w R |
| katG | 2155774 | p.Tyr113Cys | missense_variant | 0.99 | isoniazid | |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 | streptomycin | Not assoc w R |
