Run ID: SRR13837940
Sample name:
Date: 2024-10-04T16:50:24.262688
Number of reads: 1469334
Percentage reads mapped: 97.02
Median coverage: 49.0
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 | 5785 | c.546C>T | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 6314 | c.1076dupC | frameshift_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| gyrA | 7495 | p.Arg65His | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 8780 | p.Asp493Glu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0010c | 13273 | p.Gly96Cys | missense_variant | 1.0 | isoniazid | |
| Rv0010c | 13363 | p.Asp66Tyr | missense_variant | 1.0 | isoniazid | |
| mshA | 574744 | c.-604G>A | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| ccsA | 620129 | p.Gly80Ala | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| rpoB | 761845 | p.Gln680Arg | missense_variant | 1.0 | rifampicin | |
| rpsL | 781185 | c.-375T>G | upstream_gene_variant | 1.0 | streptomycin | |
| rpsL | 781226 | c.-334C>T | upstream_gene_variant | 1.0 | streptomycin | |
| rplC | 800937 | c.129A>G | synonymous_variant | 1.0 | linezolid | |
| embR | 1416298 | c.1050G>C | synonymous_variant | 1.0 | ethambutol | |
| embR | 1417588 | c.-241C>T | upstream_gene_variant | 1.0 | ethambutol | |
| rrl | 1475592 | n.1935A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| tlyA | 1918324 | p.Val129Leu | missense_variant | 1.0 | capreomycin | |
| bacA | 2064860 | c.-132A>G | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| PPE35 | 2168503 | p.Phe704Leu | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168604 | p.Pro670His | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223395 | c.-231G>T | upstream_gene_variant | 0.98 | bedaquiline | |
| clofazimine | ||||||
| ahpC | 2726771 | c.579T>A | synonymous_variant | 1.0 | isoniazid | |
| folC | 2746808 | p.Ala264Gly | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2752c | 3067057 | c.-867_-866insG | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| ald | 3087587 | c.769delC | frameshift_variant | 1.0 | cycloserine | |
| lpqB | 3624686 | p.Glu75Asp | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| fbiA | 3641252 | p.Thr237Ser | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rpoA | 3877496 | p.Glu338* | stop_gained | 1.0 | rifampicin | |
| ddn | 3986684 | c.-160G>C | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| embC | 4238901 | c.-962T>A | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4240480 | c.618G>A | synonymous_variant | 1.0 | ethambutol | |
| embA | 4244410 | p.Trp393Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4249447 | c.2934G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338681 | c.-160A>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
