Run ID: SRR13861644
Sample name:
Date: 2024-04-15T02:58:47.600111
Number of reads: 1035330
Percentage reads mapped: 51.82
Median coverage: 35.0
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 |
|---|---|---|---|---|---|---|
| gyrB | 6624 | p.Ser462* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| gyrA | 7285 | c.-17T>C | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8798 | c.1497C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| rpoC | 764438 | c.1069_1070insA | frameshift_variant | 1.0 | rifampicin | |
| mmpL5 | 775795 | p.Ala896Ser | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| fbiC | 1303593 | c.663G>A | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1416428 | c.919_920insT | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| rrs | 1471798 | n.-48G>A | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472913 | n.1068G>C | non_coding_transcript_exon_variant | 0.91 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1476167 | n.2510T>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.26 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| inhA | 1674226 | p.Arg9Trp | missense_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpsA | 1833352 | c.-190C>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| rpsA | 1833710 | p.Tyr57Asp | missense_variant | 1.0 | pyrazinamide | |
| rpsA | 1834711 | c.1170C>T | synonymous_variant | 1.0 | pyrazinamide | |
| ndh | 2102326 | c.717G>T | synonymous_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| Rv1979c | 2222739 | c.426C>A | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2222936 | p.Ala77Thr | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| eis | 2714217 | c.1115dupC | frameshift_variant | 1.0 | amikacin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| eis | 2714361 | c.972C>A | synonymous_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| ahpC | 2725906 | c.-287C>G | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2477c | 2782975 | c.1068C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R - Interim | |||||
| kanamycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| pepQ | 2859813 | p.Ile202Met | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| pepQ | 2860286 | p.Val45Leu | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| ribD | 2987503 | p.Gly222Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3087394 | p.Ala192Val | missense_variant | 0.97 | cycloserine | |
| ald | 3087464 | c.645C>T | synonymous_variant | 1.0 | cycloserine | |
| ald | 3087512 | c.693T>A | synonymous_variant | 1.0 | cycloserine | |
| Rv3083 | 3448303 | c.-201G>C | upstream_gene_variant | 1.0 | ethionamide | |
| lpqB | 3623311 | p.Pro534Ser | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3623400 | p.Val504Glu | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3624438 | p.Gln158Leu | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| rpoA | 3879111 | c.-604G>C | upstream_gene_variant | 1.0 | rifampicin | |
| embC | 4241874 | p.Leu671Arg | missense_variant | 1.0 | ethambutol | |
| embC | 4242816 | p.Trp985* | stop_gained | 1.0 | ethambutol | |
| embB | 4248365 | p.Val618Met | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4267893 | p.Ile315Ser | missense_variant | 1.0 | ethambutol | |
| aftB | 4268516 | c.321A>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ethR | 4326691 | c.-858C>A | upstream_gene_variant | 1.0 | ethionamide |
