Run ID: SRR13861434
Sample name:
Date: 2024-04-15T14:54:25.627269
Number of reads: 445267
Percentage reads mapped: 44.57
Median coverage: 15.0
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 | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | fbiB | c.743delC | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiB | 3642276 | c.743delC | frameshift_variant | 1.0 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| Rv0565c | 656172 | p.Lys433Asn | missense_variant | 1.0 | ethionamide | |
| nusG | 734570 | p.Pro106His | missense_variant | 0.94 | rifampicin | |
| rpoB | 762958 | p.Leu1051Pro | missense_variant | 0.9 | rifampicin | |
| fbiC | 1302962 | p.Ala11Gly | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303706 | p.Leu259Arg | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1305384 | c.2454G>T | synonymous_variant | 0.88 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| sigE | 1364465 | p.Val18Gly | missense_variant | 1.0 | pyrazinamide | |
| Rv1258c | 1406724 | p.Gln206Leu | missense_variant | 1.0 | streptomycin | |
| isoniazid | Uncertain significance | |||||
| pyrazinamide | Uncertain significance | |||||
| embR | 1416800 | p.Ala183Gly | missense_variant | 1.0 | ethambutol | |
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.43 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.38 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.38 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.38 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.33 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| fabG1 | 1673153 | c.-287C>G | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpsA | 1834073 | p.Lys178* | stop_gained | 0.94 | pyrazinamide | Uncertain significance |
| tsnR | 1853807 | p.Val68Leu | missense_variant | 1.0 | linezolid | |
| bacA | 2064191 | p.Thr180Ala | missense_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| Rv2681 | 2996984 | c.246C>G | synonymous_variant | 1.0 | capreomycin | |
| Rv2681 | 2997866 | p.Asp376Glu | missense_variant | 1.0 | capreomycin | |
| Rv2752c | 3066234 | c.-43G>A | upstream_gene_variant | 0.94 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| lpqB | 3624242 | c.669A>C | synonymous_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| rpoA | 3878111 | p.Lys133Gln | missense_variant | 0.87 | rifampicin | |
| embA | 4242703 | c.-530C>T | upstream_gene_variant | 1.0 | ethambutol |
