Run ID: SRR2082763
Sample name:
Date: 2024-10-03T22:42:45.636598
Number of reads: 65697683
Percentage reads mapped: 97.96
Median coverage: 6.0
Strain: lineage1.2.2.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage1.2.2 | Indo-Oceanic | RD239 | 0.5 |
| lineage1.2.2.2 | Indo-Oceanic | RD239 | 0.35 |
| lineage1 | Indo-Oceanic | RD239 | 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 |
|---|---|---|---|---|---|---|
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7268 | c.-34C>T | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| 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 | 7685 | c.384G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R | |||||
| nusG | 734116 | c.-138T>C | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 763690 | c.321C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoC | 763884 | p.Ala172Val | missense_variant | 0.99 | rifampicin | Not assoc w R |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 800357 | c.-452C>A | upstream_gene_variant | 1.0 | linezolid | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1475363 | n.1706C>A | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
| linezolid | ||||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Not assoc w R | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3626467 | c.147G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| ethA | 4326148 | c.1326G>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| whiB6 | 4338840 | c.-319T>C | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4408180 | p.Ala8Val | missense_variant | 1.0 | streptomycin | Uncertain significance |
