Run ID: SRR13861255
Sample name:
Date: 2024-10-04T09:42:10.123602
Number of reads: 453194
Percentage reads mapped: 22.68
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 | embB | p.Met482Ile | Mutation from literature | |
| 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 |
|---|---|---|---|---|---|---|---|
| embB | 4247959 | p.Met482Ile | missense_variant | 1.0 | ethambutol | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| fgd1 | 491360 | p.Ile193Ser | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mshA | 576396 | p.Ser350Ile | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| rpoB | 760225 | p.Glu140Ala | missense_variant | 1.0 | rifampicin | |
| rpoC | 767186 | p.Gln1273* | stop_gained | 0.93 | rifampicin | |
| rplC | 800933 | p.Pro42His | missense_variant | 1.0 | linezolid | |
| fbiC | 1305306 | c.2376A>T | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.42 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.63 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.63 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.63 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.3 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tlyA | 1918560 | c.621G>T | synonymous_variant | 1.0 | capreomycin | |
| bacA | 2063120 | c.1609C>T | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Not assoc w R - Interim | |||||
| amikacin | ||||||
| ndh | 2102402 | p.Leu214Arg | missense_variant | 1.0 | isoniazid | Uncertain significance |
| delamanid | ||||||
| ethionamide | ||||||
| katG | 2156175 | c.-64T>G | upstream_gene_variant | 1.0 | isoniazid | |
| PPE35 | 2170540 | p.Leu25Val | missense_variant | 1.0 | pyrazinamide | |
| pncA | 2288999 | p.Phe81Leu | missense_variant | 1.0 | pyrazinamide | |
| fbiD | 3339660 | c.543C>G | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv3236c | 3612627 | p.Ala164Thr | missense_variant | 1.0 | pyrazinamide | |
| fbiA | 3640219 | c.-324C>T | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| embA | 4244119 | p.Tyr296Phe | missense_variant | 1.0 | ethambutol | |
| embB | 4247417 | p.Tyr302Asn | missense_variant | 1.0 | ethambutol | |
| embB | 4248036 | p.Val508Gly | missense_variant | 1.0 | ethambutol | |
| embB | 4248325 | c.1812G>C | synonymous_variant | 1.0 | ethambutol | |
| aftB | 4267894 | p.Ile315Phe | missense_variant | 1.0 | ethambutol | |
| ethA | 4327388 | p.Thr29Ile | missense_variant | 0.95 | ethionamide | |
| ethR | 4328162 | p.His205Pro | missense_variant | 1.0 | ethionamide | |
| whiB6 | 4338518 | c.4C>A | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
