Run ID: SRR5074711
Sample name:
Date: 2024-10-05T09:08:29.504058
Number of reads: 4319157
Percentage reads mapped: 86.14
Median coverage: 174.0
Strain: lineage4.3.3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.3 | Euro-American (LAM) | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.3.3 | Euro-American (LAM) | RD115 | 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 | 6408 | p.Glu390Gly | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| 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 | 8040 | p.Gly247Ser | 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 | |||||
| ccsA | 619640 | c.-251G>C | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| 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 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472438 | n.593T>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472447 | n.602C>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472448 | n.603T>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472450 | n.605A>C | non_coding_transcript_exon_variant | 0.14 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472451 | n.606C>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472462 | n.617T>G | non_coding_transcript_exon_variant | 0.17 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472464 | n.619A>G | non_coding_transcript_exon_variant | 0.21 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472673 | n.828_830delTTTinsGTC | non_coding_transcript_exon_variant | 0.25 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472677 | n.832C>A | non_coding_transcript_exon_variant | 0.23 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | ||||||
| amikacin | Uncertain significance | |||||
| rrs | 1472682 | n.837T>A | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472683 | n.838_842delTGGGAinsCGGGT | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472707 | n.862A>T | non_coding_transcript_exon_variant | 0.2 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
| linezolid | ||||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.99 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.17 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.15 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 | isoniazid | |
| Rv2752c | 3065824 | p.Pro123Leu | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4239441 | c.-422G>A | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| ubiA | 4269300 | c.534G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338312 | c.209_210insT | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| 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 | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |
