Run ID: SRR28868642
Sample name:
Date: 2025-02-11T19:25:43.303321
Number of reads: 9894251
Percentage reads mapped: 98.91
Median coverage: 312.0
Strain: lineage4.2.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.2.2 | Euro-American (Ural) | None | 0.99 |
| lineage4.2 | Euro-American | None | 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 | |||||
| Rv0010c | 13229 | c.330G>C | synonymous_variant | 1.0 | isoniazid | |
| mshA | 576077 | c.730C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| ethionamide | Not assoc w R - Interim | |||||
| mshA | 576651 | p.Asp435Ala | missense_variant | 0.21 | isoniazid | |
| ethionamide | ||||||
| mmpL5 | 775639 | p.Ile948Val | 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 | 800204 | c.-605T>C | upstream_gene_variant | 1.0 | linezolid | |
| rplC | 800271 | c.-538A>C | upstream_gene_variant | 0.23 | linezolid | |
| Rv1258c | 1407509 | c.-169C>G | upstream_gene_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476149 | n.2492C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tsnR | 1854305 | p.Ser234Ala | missense_variant | 0.22 | linezolid | |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2063685 | c.1044G>A | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R | |||||
| bacA | 2063911 | p.Ile273Thr | missense_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| ndh | 2103331 | c.-289C>T | upstream_gene_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1979c | 2223770 | c.-670_-607delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223770 | c.-669_-607delTGGAAAATTACATCGCCCAGACGCGCGACAAGTTCCTCAGCGCGGCCACATCGTCCACTCCAC | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| pepQ | 2859931 | p.Leu163Arg | missense_variant | 0.21 | bedaquiline | |
| clofazimine | ||||||
| Rv2680 | 2996488 | c.384G>C | synonymous_variant | 0.99 | capreomycin | Not assoc w R - Interim |
| Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.99 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3449811 | p.Phe436Leu | missense_variant | 0.98 | ethionamide | |
| Rv3236c | 3612469 | c.648A>G | synonymous_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 | 4240413 | p.Leu184Arg | missense_variant | 0.33 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4245237 | p.Asp669Asn | missense_variant | 1.0 | ethambutol | |
| embA | 4245835 | p.Leu868Arg | missense_variant | 0.2 | ethambutol | |
| 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 | 4408113 | c.90T>G | synonymous_variant | 0.23 | streptomycin |
