Run ID: SRR13861699
Sample name:
Date: 2024-04-16T10:51:29.058272
Number of reads: 327479
Percentage reads mapped: 32.78
Median coverage: 11.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| 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 | ethA | p.Ser424* | Assoc w R | |
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| ethA | 4326203 | p.Ser424* | stop_gained | 1.0 | ethionamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1057 | c.1057_1059delGTCinsCG | frameshift_variant&missense_variant | 0.8 | isoniazid | Uncertain significance |
| gyrB | 5832 | p.Ala198Gly | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| ccsA | 619735 | c.-156G>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| ccsA | 620100 | c.210G>T | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| rpoB | 759609 | c.-198C>A | upstream_gene_variant | 0.86 | rifampicin | Uncertain significance |
| rpoC | 763050 | c.-320C>T | upstream_gene_variant | 1.0 | rifampicin | |
| mmpS5 | 778642 | p.Trp88* | stop_gained | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1258c | 1407009 | p.Ala111Asp | missense_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.57 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.57 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.54 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.57 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.57 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.54 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.54 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.45 | capreomycin | |
| linezolid | ||||||
| tlyA | 1918625 | p.Pro229Leu | missense_variant | 1.0 | capreomycin | |
| ahpC | 2726345 | p.Phe51Leu | missense_variant | 1.0 | isoniazid | |
| Rv2477c | 2783258 | c.784delC | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| Rv2477c | 2784427 | c.-385T>C | upstream_gene_variant | 0.94 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv3083 | 3448912 | p.Ile137Phe | missense_variant | 1.0 | ethionamide | |
| lpqB | 3624303 | p.Leu203Arg | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| alr | 3840783 | c.637_638insT | frameshift_variant | 1.0 | cycloserine | |
| panD | 4044544 | c.-263G>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| embC | 4241026 | c.1164C>G | synonymous_variant | 1.0 | ethambutol | |
| embA | 4242250 | c.-983C>G | upstream_gene_variant | 1.0 | ethambutol | |
| embB | 4247398 | c.885G>T | synonymous_variant | 0.91 | ethambutol | |
| embB | 4249328 | p.Met939Leu | missense_variant | 1.0 | ethambutol | |
| aftB | 4267490 | c.1347G>C | synonymous_variant | 1.0 | ethambutol |
