Run ID: SRR13861478
Sample name:
Date: 2024-10-05T10:19:33.871167
Number of reads: 3822074
Percentage reads mapped: 76.52
Median coverage: 130.0
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 |
|---|---|---|---|---|---|---|
| dnaA | 375 | p.Asp125Glu | missense_variant | 1.0 | isoniazid | |
| gyrB | 4996 | c.-244A>C | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 5258 | p.Lys7* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| gyrB | 7122 | c.1883_1884insA | frameshift_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| Rv0010c | 13577 | c.-19G>T | upstream_gene_variant | 1.0 | isoniazid | |
| mmaA3 | 738206 | c.-57G>T | upstream_gene_variant | 1.0 | isoniazid | |
| mmpL5 | 776374 | p.Arg703Cys | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpR5 | 779126 | p.Cys46Phe | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 801447 | p.Lys213Asn | missense_variant | 1.0 | linezolid | |
| Rv1129c | 1253197 | c.1338C>A | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| Rv1129c | 1253317 | c.1218G>A | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| Rv1129c | 1253639 | p.Leu299* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| fbiC | 1303004 | p.Ala25Glu | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1303171 | p.Arg81Trp | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1303517 | p.Met196Thr | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv1258c | 1407597 | c.-257C>G | upstream_gene_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476268 | n.2611A>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476275 | n.2618T>A | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476279 | n.2622G>A | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.33 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.33 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rpsA | 1834640 | p.Glu367* | stop_gained | 1.0 | pyrazinamide | Uncertain significance |
| bacA | 2064395 | p.Thr112Pro | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| bacA | 2064589 | c.139delT | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| ndh | 2103004 | c.39T>G | synonymous_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2170453 | p.Gly54Ser | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223326 | c.-162C>T | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223365 | c.-201C>A | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| pncA | 2288748 | p.Ala165Asp | missense_variant | 1.0 | pyrazinamide | |
| kasA | 2518474 | p.Glu120Asp | missense_variant | 1.0 | isoniazid | |
| thyX | 3067529 | c.417C>G | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
| thyA | 3073764 | c.708T>C | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
| thyA | 3073862 | p.Gly204Ser | missense_variant | 1.0 | para-aminosalicylic_acid | |
| thyA | 3073963 | p.Leu170Gln | missense_variant | 0.99 | para-aminosalicylic_acid | |
| fbiD | 3339357 | c.240G>T | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv3083 | 3448352 | c.-152G>C | upstream_gene_variant | 1.0 | ethionamide | |
| Rv3083 | 3449624 | p.Lys374Met | missense_variant | 1.0 | ethionamide | |
| Rv3083 | 3449919 | c.1416C>A | synonymous_variant | 1.0 | ethionamide | |
| fbiB | 3642227 | p.Gln231His | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiB | 3642581 | c.1047A>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| embA | 4244641 | p.Val470Gly | missense_variant | 1.0 | ethambutol | |
| embA | 4245197 | c.1965C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R - Interim |
| embB | 4246641 | p.Ala43Glu | missense_variant | 1.0 | ethambutol | |
| embB | 4247233 | p.Asp240Glu | missense_variant | 1.0 | ethambutol | |
| ethA | 4327035 | p.Tyr147Asp | missense_variant | 1.0 | ethionamide | |
| ethR | 4327923 | p.Gln125His | missense_variant | 1.0 | ethionamide |
