Run ID: SRR19303808
Sample name:
Date: 2024-04-15T05:33:19.953862
Number of reads: 6510039
Percentage reads mapped: 97.38
Median coverage: 169.0
Strain: lineage4.1.2.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 1.0 |
| lineage4.1.2 | Euro-American | None | 1.0 |
| lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 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 |
|---|---|---|---|---|---|---|
| gyrB | 7240 | c.2001C>G | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| 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 | |||||
| fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 | ethionamide | Not assoc w R |
| isoniazid | Not assoc w R | |||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.25 | ethionamide | |
| isoniazid | ||||||
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoB | 759494 | c.-313G>A | upstream_gene_variant | 1.0 | rifampicin | |
| rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| 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 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472414 | n.569C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2063733 | p.Ile332Met | missense_variant | 0.99 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| PPE35 | 2165264 | c.1024_*2384del | stop_lost&conservative_inframe_deletion&splice_region_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| pncA | 2290199 | c.-958C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.99 | isoniazid | |
| Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.17 | capreomycin | Uncertain significance |
| Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.13 | capreomycin | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| embC | 4239298 | c.-565C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242803 | p.Val981Leu | missense_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 | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
