Run ID: SRR13861518
Sample name:
Date: 2024-10-04T22:11:38.225824
Number of reads: 2148896
Percentage reads mapped: 71.7
Median coverage: 74.0
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 | rrs | n.277G>C | Mutation from literature | |
| 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 |
|---|---|---|---|---|---|---|---|
| rrs | 1472122 | n.277G>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5319 | p.Arg27Leu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 575032 | c.-316A>G | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| rpoB | 760867 | p.Gly354Asp | missense_variant | 1.0 | rifampicin | |
| rpoB | 762496 | c.2691delC | frameshift_variant | 1.0 | rifampicin | |
| rpoC | 764793 | p.Met475Arg | missense_variant | 0.99 | rifampicin | |
| rpoC | 766563 | p.Thr1065Ser | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 775976 | c.2505G>C | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 776814 | p.Gln556Arg | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 800623 | c.-186A>C | upstream_gene_variant | 1.0 | linezolid | |
| rplC | 800769 | c.-40A>T | upstream_gene_variant | 1.0 | linezolid | |
| Rv1129c | 1253289 | c.1246C>T | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| fbiC | 1302878 | c.-53C>G | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1303535 | p.Ser202Leu | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv1258c | 1407569 | c.-229C>A | upstream_gene_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| atpE | 1461256 | p.Met71Arg | missense_variant | 1.0 | bedaquiline | |
| rrs | 1471638 | n.-208T>C | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1471836 | n.-10A>G | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.3 | 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 | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.34 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.26 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| bacA | 2063043 | c.1686T>A | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| katG | 2156157 | c.-46C>A | upstream_gene_variant | 1.0 | isoniazid | |
| PPE35 | 2168627 | p.Ile662Met | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2222100 | c.1065T>A | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| pncA | 2289242 | c.-1T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv2477c | 2783664 | c.378delA | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| ribD | 2987205 | p.Ser123Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ribD | 2987347 | p.Pro170Leu | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2680 | 2995859 | c.-246C>A | upstream_gene_variant | 0.99 | capreomycin | |
| Rv2681 | 2997492 | p.Val252Phe | missense_variant | 1.0 | capreomycin | |
| Rv3083 | 3448903 | p.Asp134His | missense_variant | 0.99 | ethionamide | |
| lpqB | 3624372 | p.Val180Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
| bedaquiline | ||||||
| mtrA | 3627051 | p.Asp100Val | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| clpC1 | 4039663 | p.Gly348Ser | missense_variant | 0.99 | pyrazinamide | |
| embC | 4241256 | p.Arg465Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4246449 | p.Val1073Phe | missense_variant | 1.0 | ethambutol | |
| aftB | 4268192 | c.645G>C | synonymous_variant | 1.0 | ethambutol |
