Run ID: SRR13861733
Sample name:
Date: 2024-04-16T05:50:14.357972
Number of reads: 3389181
Percentage reads mapped: 56.54
Median coverage: 115.0
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 | 5922 | p.Glu228Gly | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 7242 | p.Lys668Thr | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| ccsA | 620360 | p.Tyr157Ser | missense_variant | 0.99 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| hadA | 732060 | p.Gly44Val | missense_variant | 1.0 | isoniazid | |
| hadA | 732292 | c.363C>T | synonymous_variant | 1.0 | isoniazid | |
| nusG | 734239 | c.-14delG | upstream_gene_variant | 1.0 | rifampicin | |
| rpoB | 761356 | c.1550_1551insA | frameshift_variant | 1.0 | rifampicin | |
| rpoC | 763347 | c.-23C>G | upstream_gene_variant | 1.0 | rifampicin | |
| rpoC | 766025 | p.Val886Met | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 776145 | p.Ala779Gly | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 776954 | p.Lys509Asn | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 801231 | c.423C>A | synonymous_variant | 1.0 | linezolid | |
| sigE | 1364454 | c.42G>A | synonymous_variant | 1.0 | pyrazinamide | |
| atpE | 1460916 | c.-129G>A | upstream_gene_variant | 1.0 | bedaquiline | |
| rrl | 1476201 | n.2544C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.3 | 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 | 0.31 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| katG | 2155137 | c.975G>C | synonymous_variant | 1.0 | isoniazid | |
| PPE35 | 2168892 | p.Thr574Lys | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| ribD | 2987259 | p.Leu141Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2752c | 3065161 | p.Asn344Thr | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv2752c | 3065830 | p.Ile121Thr | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv2752c | 3067100 | c.-909G>A | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| fbiD | 3339117 | c.-1C>T | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv3083 | 3448661 | p.Val53Ala | missense_variant | 1.0 | ethionamide | |
| Rv3236c | 3612041 | p.Val359Glu | missense_variant | 1.0 | pyrazinamide | |
| lpqB | 3623964 | p.Gly316Val | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3624582 | p.Ala110Gly | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| fbiA | 3640418 | c.-125C>A | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rpoA | 3877877 | p.Ala211Ser | missense_variant | 1.0 | rifampicin | |
| clpC1 | 4039250 | c.1455C>G | synonymous_variant | 1.0 | pyrazinamide | |
| embC | 4242113 | c.2251C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4246367 | c.-147C>T | upstream_gene_variant | 1.0 | ethambutol | |
| whiB6 | 4338567 | c.-46C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4408302 | c.-101delC | upstream_gene_variant | 1.0 | streptomycin |
