Run ID: SRR19304109
Sample name:
Date: 2024-03-25T17:03:54.117314
Number of reads: 1894670
Percentage reads mapped: 90.65
Median coverage: 57.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 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 | 9344 | p.Ile681Met | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| fbiC | 1303844 | p.Ala305Val | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| rrl | 1474674 | n.1017_1018delACinsG | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
| linezolid | ||||||
| rrl | 1474677 | n.1020A>G | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474709 | n.1052G>A | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
| linezolid | ||||||
| rrl | 1474734 | n.1077G>T | non_coding_transcript_exon_variant | 0.44 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474749 | n.1092C>T | non_coding_transcript_exon_variant | 0.4 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474753 | n.1097delC | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.33 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474779 | n.1122G>A | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474782 | n.1125G>A | non_coding_transcript_exon_variant | 0.32 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.37 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.17 | 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 | 0.25 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1979c | 2223491 | c.-327C>A | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| Rv2752c | 3065179 | p.Ser338Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
| mtrB | 3625516 | c.1098G>A | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | Not assoc w R - Interim | |||||
| mtrB | 3625645 | c.969C>T | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | Not assoc w R - Interim | |||||
| embC | 4238972 | c.-891C>G | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| gid | 4407678 | c.525G>C | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
