Run ID: SRR13861148
Sample name:
Date: 2024-04-16T10:51:02.566734
Number of reads: 1820344
Percentage reads mapped: 30.37
Median coverage: 61.0
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 | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ethA | p.Ser424* | Assoc w R | |
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| ethA | 4326203 | p.Ser424* | stop_gained | 1.0 | ethionamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1057 | p.Val353Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| gyrB | 5532 | c.295dupG | frameshift_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| gyrB | 5832 | p.Ala198Gly | missense_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 6976 | c.-326A>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| ccsA | 619735 | c.-156G>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| ccsA | 620100 | c.210G>T | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| rpoB | 759609 | c.-198C>A | upstream_gene_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 763050 | c.-320C>T | upstream_gene_variant | 1.0 | rifampicin | |
| mmpL5 | 776796 | p.Val562Ala | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpS5 | 778642 | p.Trp88* | stop_gained | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1258c | 1407009 | p.Ala111Asp | missense_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.19 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.18 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.18 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.18 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.14 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.39 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.46 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.51 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.51 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.51 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.51 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.45 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| inhA | 1674891 | p.Trp230Cys | missense_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| tlyA | 1918625 | p.Pro229Leu | missense_variant | 1.0 | capreomycin | |
| ndh | 2103309 | c.-267C>T | upstream_gene_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| Rv1979c | 2222721 | c.444G>C | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| ahpC | 2726345 | p.Phe51Leu | missense_variant | 1.0 | isoniazid | |
| Rv2477c | 2783258 | c.784delC | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| Rv2477c | 2784427 | c.-385T>C | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2752c | 3066881 | c.-690C>A | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv2752c | 3067095 | c.-904G>C | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv3083 | 3448912 | p.Ile137Phe | missense_variant | 1.0 | ethionamide | |
| whiB7 | 3568676 | p.Ser2Ala | missense_variant | 1.0 | streptomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| lpqB | 3624303 | p.Leu203Arg | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| mtrB | 3626528 | p.Ala29Gly | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| alr | 3840783 | c.637_638insT | frameshift_variant | 1.0 | cycloserine | |
| clpC1 | 4038326 | p.Glu793Asp | missense_variant | 1.0 | pyrazinamide | |
| panD | 4044544 | c.-263G>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4138911 | p.Gly282Val | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embC | 4241026 | c.1164C>G | synonymous_variant | 1.0 | ethambutol | |
| embA | 4242250 | c.-983C>G | upstream_gene_variant | 1.0 | ethambutol | |
| embB | 4247398 | c.885G>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4249328 | p.Met939Leu | missense_variant | 1.0 | ethambutol | |
| aftB | 4267490 | c.1347G>C | synonymous_variant | 1.0 | ethambutol |
