Run ID: SRR13837655
Sample name:
Date: 2024-04-16T10:50:49.040254
Number of reads: 294762
Percentage reads mapped: 97.33
Median coverage: 10.0
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 |
---|---|---|---|---|---|---|
mshA | 575032 | c.-316A>G | upstream_gene_variant | 1.0 | ethionamide | |
isoniazid | ||||||
rpoB | 762496 | c.2691delC | frameshift_variant | 1.0 | rifampicin | |
rpoC | 764793 | p.Met475Arg | missense_variant | 0.94 | rifampicin | |
mmpL5 | 775976 | c.2505G>C | synonymous_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 776814 | p.Gln556Arg | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
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 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
fbiC | 1303535 | p.Ser202Leu | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
atpE | 1461256 | p.Met71Arg | missense_variant | 1.0 | bedaquiline | |
rrs | 1471638 | n.-208T>C | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
Rv1979c | 2222100 | c.1065T>A | synonymous_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
ribD | 2987205 | p.Ser123Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
ribD | 2987347 | p.Pro170Leu | missense_variant | 1.0 | para-aminosalicylic_acid | |
mtrA | 3627051 | p.Asp100Val | missense_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
embC | 4241256 | p.Arg465Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4268192 | c.645G>C | synonymous_variant | 1.0 | ethambutol |