Run ID: SRR13837581
Sample name:
Date: 2024-04-15T02:58:15.625356
Number of reads: 587698
Percentage reads mapped: 100.0
Median coverage: 20.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: RR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Pro439Arg | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
| 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 |
|---|---|---|---|---|---|---|---|
| rpoB | 761122 | p.Pro439Arg | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5192 | c.-48C>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9658 | c.2357_2358insT | frameshift_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 490779 | c.-4A>T | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv0565c | 657379 | p.Arg31His | missense_variant | 1.0 | ethionamide | |
| rpoB | 760041 | p.Gly79Arg | missense_variant | 1.0 | rifampicin | |
| rpoB | 760652 | c.846C>A | synonymous_variant | 1.0 | rifampicin | |
| mmpL5 | 775929 | p.Asn851Ile | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpS5 | 778941 | c.-36A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781149 | c.-411C>T | upstream_gene_variant | 1.0 | streptomycin | |
| rpsL | 781277 | c.-283G>T | upstream_gene_variant | 1.0 | streptomycin | |
| embR | 1417376 | c.-29T>C | upstream_gene_variant | 1.0 | ethambutol | |
| rrl | 1473740 | n.83G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1474574 | n.917A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rpsA | 1834610 | p.Arg357Gly | missense_variant | 1.0 | pyrazinamide | |
| tsnR | 1854354 | p.Leu250Gln | missense_variant | 1.0 | linezolid | |
| ndh | 2101828 | c.1215C>T | synonymous_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| PPE35 | 2168706 | p.Ser636Phe | missense_variant | 1.0 | pyrazinamide | |
| pncA | 2289887 | c.-646A>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| folC | 2746838 | p.Ala254Glu | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2477c | 2783316 | p.Thr243Ala | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| ribD | 2987500 | p.Gly221Asp | missense_variant | 1.0 | para-aminosalicylic_acid | |
| thyX | 3068082 | c.-137T>C | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3338954 | c.-164A>G | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiD | 3339235 | p.Leu40Val | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiD | 3339406 | p.Thr97Ala | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv3083 | 3448625 | p.Leu41Gln | missense_variant | 1.0 | ethionamide | |
| lpqB | 3624203 | c.708C>T | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| mtrB | 3626461 | c.153A>G | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | Not assoc w R - Interim | |||||
| mtrB | 3626554 | c.60A>T | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| mtrA | 3627267 | p.Glu28Val | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| fbiB | 3642247 | p.Asn238Thr | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiB | 3642283 | p.Glu250Ala | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| clpC1 | 4039483 | c.1221_1222insC | frameshift_variant | 1.0 | pyrazinamide | |
| glpK | 4139747 | p.Asp3Glu | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embA | 4243843 | c.613dupG | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4244833 | p.Val534Ala | missense_variant | 1.0 | ethambutol | |
| embA | 4245735 | p.Ala835Ser | missense_variant | 1.0 | ethambutol | |
| aftB | 4267994 | p.Met281Ile | missense_variant | 1.0 | ethambutol |
