Run ID: SRR13837742
Sample name:
Date: 2024-04-16T00:58:40.305754
Number of reads: 2938833
Percentage reads mapped: 95.03
Median coverage: 99.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| 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 | ||||
| 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 | 6027 | p.His263Arg | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 576327 | p.Phe327Tyr | missense_variant | 0.99 | ethionamide | |
| isoniazid | ||||||
| Rv0565c | 656192 | p.Asp427His | missense_variant | 1.0 | ethionamide | |
| rpoB | 759707 | c.-100C>T | upstream_gene_variant | 1.0 | rifampicin | |
| rpoB | 760178 | c.372G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 762284 | c.2478G>A | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 764262 | p.Val298Ala | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 777280 | p.Ala401Ser | missense_variant | 0.99 | clofazimine | |
| bedaquiline | ||||||
| mmpS5 | 778853 | p.Val18Ala | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781277 | c.-283G>C | upstream_gene_variant | 1.0 | streptomycin | |
| rplC | 800213 | c.-596G>T | upstream_gene_variant | 1.0 | linezolid | |
| embR | 1416662 | p.Arg229Pro | missense_variant | 1.0 | ethambutol | |
| rrl | 1476288 | n.2631T>C | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
| linezolid | ||||||
| rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tlyA | 1917545 | c.-395T>A | upstream_gene_variant | 1.0 | capreomycin | |
| katG | 2155675 | p.Arg146Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| Rv1979c | 2222433 | c.732A>G | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv2680 | 2996147 | p.Glu15Gln | missense_variant | 1.0 | capreomycin | |
| Rv2681 | 2996821 | p.Gly28Val | missense_variant | 1.0 | capreomycin | |
| ald | 3086631 | c.-189A>G | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3236c | 3612954 | c.162delC | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv3236c | 3613619 | c.-503T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| alr | 3840284 | p.Trp379* | stop_gained | 1.0 | cycloserine | |
| glpK | 4139736 | p.Gly7Val | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embC | 4239589 | c.-273delA | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4240042 | p.Asn60Lys | missense_variant | 1.0 | ethambutol | |
| embB | 4245806 | c.-708G>A | upstream_gene_variant | 1.0 | ethambutol | |
| embB | 4247075 | c.563dupT | frameshift_variant | 1.0 | ethambutol | |
| embB | 4247839 | c.1326G>A | synonymous_variant | 1.0 | ethambutol | |
| embB | 4249763 | p.Thr1084Pro | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ethA | 4326860 | p.Leu205Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
