Run ID: SRR13861551
Sample name:
Date: 2024-10-05T06:18:59.595041
Number of reads: 3117212
Percentage reads mapped: 78.01
Median coverage: 105.0
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 |
|---|---|---|---|---|---|---|
| ccsA | 620144 | c.255dupT | frameshift_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| hadA | 731898 | c.-32T>A | upstream_gene_variant | 1.0 | isoniazid | |
| rpoB | 760191 | p.Val129Phe | missense_variant | 1.0 | rifampicin | |
| rpoB | 760311 | p.Val169Leu | missense_variant | 1.0 | rifampicin | |
| rpoB | 762805 | p.Gly1000Asp | missense_variant | 1.0 | rifampicin | |
| rpoB | 762963 | p.Gly1053Arg | missense_variant | 1.0 | rifampicin | |
| rpoC | 763662 | p.Ala98Asp | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 776041 | p.Ala814Thr | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 776070 | c.2410delA | frameshift_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| mmpL5 | 777800 | c.681C>T | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1129c | 1253473 | p.Phe354Leu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| Rv1129c | 1254207 | p.Val110Phe | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| fbiC | 1304996 | p.Leu689Ser | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv1258c | 1407148 | p.Ala65Ser | missense_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| Rv1258c | 1407602 | c.-262G>T | upstream_gene_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| embR | 1416842 | p.Asp169Gly | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embR | 1417911 | c.-564A>T | upstream_gene_variant | 1.0 | ethambutol | |
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| inhA | 1674940 | c.739_740insG | frameshift_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| ndh | 2102694 | p.Val117Ile | missense_variant | 1.0 | isoniazid | Uncertain significance |
| delamanid | Uncertain significance | |||||
| ethionamide | Uncertain significance | |||||
| katG | 2155865 | p.Val83Met | missense_variant | 1.0 | isoniazid | |
| katG | 2156606 | c.-495T>C | upstream_gene_variant | 1.0 | isoniazid | |
| PPE35 | 2168123 | c.2489dupG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170268 | c.345C>A | synonymous_variant | 1.0 | pyrazinamide | |
| kasA | 2518311 | p.Asp66Gly | missense_variant | 1.0 | isoniazid | |
| eis | 2714666 | p.Tyr223Asp | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| ahpC | 2726589 | p.Arg133Ser | missense_variant | 1.0 | isoniazid | |
| Rv2752c | 3066289 | c.-98T>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| thyA | 3074418 | p.Lys18Asn | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3087163 | c.344_345insC | frameshift_variant | 1.0 | cycloserine | |
| Rv3236c | 3612049 | c.1068G>C | synonymous_variant | 1.0 | pyrazinamide | |
| Rv3236c | 3612400 | c.717G>A | synonymous_variant | 1.0 | pyrazinamide | |
| fbiB | 3642445 | p.Ala304Gly | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rpoA | 3879139 | c.-633dupA | upstream_gene_variant | 1.0 | rifampicin | |
| clpC1 | 4038941 | c.1764G>C | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040104 | p.Met201Leu | missense_variant | 0.99 | pyrazinamide | |
| embC | 4241480 | c.1618T>C | synonymous_variant | 1.0 | ethambutol | |
| embB | 4249483 | c.2970C>G | synonymous_variant | 1.0 | ethambutol | |
| aftB | 4268164 | c.672_673insA | frameshift_variant | 0.98 | ethambutol | Uncertain significance |
| ethA | 4327641 | c.-168G>A | upstream_gene_variant | 1.0 | ethionamide |
