Run ID: SRR13861474
Sample name:
Date: 2024-10-03T18:40:00.394157
Number of reads: 1140377
Percentage reads mapped: 22.83
Median coverage: 38.0
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 |
|---|---|---|---|---|---|---|
| gyrA | 7877 | p.His192Gln | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| mshA | 576146 | p.Val267Leu | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| hadA | 732095 | p.Pro56Thr | missense_variant | 1.0 | isoniazid | |
| rpoB | 759869 | c.63C>T | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 763782 | p.Ser138* | stop_gained | 1.0 | rifampicin | |
| rpoC | 764568 | p.Lys400Thr | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 777073 | p.Lys470Glu | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 777311 | c.1170C>T | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 778981 | c.-501C>A | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 801436 | p.Ser210Arg | missense_variant | 1.0 | linezolid | |
| fbiC | 1303686 | c.756C>G | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rrs | 1472605 | n.760G>C | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.31 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.3 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.31 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.31 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.33 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.34 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.35 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.32 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.32 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.32 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.32 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.31 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.32 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.31 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.54 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.57 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.26 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | ||||||
| inhA | 1674376 | p.Pro59Ser | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| tlyA | 1917844 | c.-96C>A | upstream_gene_variant | 1.0 | capreomycin | |
| tlyA | 1918260 | p.His107Gln | missense_variant | 1.0 | capreomycin | |
| bacA | 2064394 | p.Thr112Arg | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| katG | 2154461 | p.Ala551Pro | missense_variant | 1.0 | isoniazid | |
| Rv1979c | 2222535 | c.630C>G | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| kasA | 2518608 | p.Met165Thr | missense_variant | 1.0 | isoniazid | |
| eis | 2714211 | c.1122G>A | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
| amikacin | Not assoc w R - Interim | |||||
| ahpC | 2726250 | p.Gly20Arg | missense_variant | 1.0 | isoniazid | |
| Rv2752c | 3066461 | c.-270C>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv2752c | 3066855 | c.-664T>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| whiB7 | 3568939 | c.-260T>C | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| Rv3236c | 3612518 | p.Tyr200Ser | missense_variant | 1.0 | pyrazinamide | |
| fbiB | 3641684 | p.Ser50Arg | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| glpK | 4139507 | p.Lys83Asn | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embC | 4240263 | p.Val134Ala | missense_variant | 1.0 | ethambutol | |
| embC | 4240920 | p.Leu353Pro | missense_variant | 1.0 | ethambutol | |
| embC | 4241504 | p.Val548Met | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4248000 | p.Asp496Val | missense_variant | 1.0 | ethambutol | |
| aftB | 4268715 | p.Leu41Pro | missense_variant | 1.0 | ethambutol | |
| ethR | 4327704 | p.Lys52Asn | missense_variant | 1.0 | ethionamide |
