Run ID: ERR2510790
Sample name:
Date: 2024-04-15T01:44:12.703355
Number of reads: 1005790
Percentage reads mapped: 82.82
Median coverage: 34.0
Strain: lineage4.6.2.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | None | 1.0 |
| lineage4.6.2 | Euro-American | RD726 | 1.0 |
| lineage4.6.2.2 | Euro-American (Cameroon) | RD726 | 1.0 |
| lineage4 | Euro-American | None | 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 |
|---|---|---|---|---|---|---|
| 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 | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 778298 | c.183G>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.32 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.21 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.2 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.36 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.4 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.21 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.3 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472992 | n.1147A>G | non_coding_transcript_exon_variant | 0.11 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473000 | n.1160C>T | non_coding_transcript_exon_variant | 0.19 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.39 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.29 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.21 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.43 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| 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 |
| bacA | 2063187 | c.1542C>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2680 | 2996208 | p.Ala35Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| Rv3083 | 3448567 | p.His22Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4267272 | p.Lys522Arg | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326536 | p.Val313Ala | missense_variant | 1.0 | ethionamide | |
| ethA | 4326578 | p.Gly299Ala | missense_variant | 1.0 | ethionamide | |
| ethA | 4326739 | c.735C>G | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| ethR | 4328004 | c.456G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
