Run ID: SRR13837877
Sample name:
Date: 2024-04-15T07:52:42.640824
Number of reads: 1469498
Percentage reads mapped: 95.03
Median coverage: 49.0
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 | 5149 | c.-91G>C | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 7090 | p.Asp617Glu | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8436 | p.Tyr379Asn | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
fgd1 | 491701 | p.His307Asn | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
ccsA | 619765 | c.-126G>A | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
hadA | 731718 | c.-212T>C | upstream_gene_variant | 1.0 | isoniazid | |
mmpL5 | 775867 | p.Arg872Gly | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 776710 | p.Cys591Ser | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 777625 | p.Gln286Lys | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
mmpS5 | 778811 | p.Phe32Ser | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
embR | 1416901 | c.447G>C | synonymous_variant | 1.0 | ethambutol | |
rrl | 1474466 | n.810delA | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475224 | n.1567T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476589 | n.2932G>A | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
bacA | 2063516 | p.Val405Ile | missense_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
PPE35 | 2170487 | c.126T>A | synonymous_variant | 1.0 | pyrazinamide | |
Rv1979c | 2221853 | p.Phe438Ile | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
ribD | 2987369 | c.531G>A | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3073975 | p.Arg166Pro | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv3236c | 3612013 | c.1104A>T | synonymous_variant | 1.0 | pyrazinamide | |
Rv3236c | 3612032 | p.Met362Arg | missense_variant | 1.0 | pyrazinamide | |
Rv3236c | 3613624 | c.-508T>A | upstream_gene_variant | 1.0 | pyrazinamide | |
mtrB | 3625654 | c.959delT | frameshift_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Uncertain significance | |||||
mtrB | 3627491 | c.-878G>T | upstream_gene_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
embC | 4240425 | p.Arg188Pro | missense_variant | 1.0 | ethambutol | |
embC | 4240477 | c.615C>A | synonymous_variant | 1.0 | ethambutol | |
embA | 4244214 | p.Ala328Ser | missense_variant | 1.0 | ethambutol | |
embA | 4244849 | c.1617C>G | synonymous_variant | 1.0 | ethambutol | |
embB | 4247198 | p.Thr229Pro | missense_variant | 1.0 | ethambutol | |
embB | 4247381 | p.Trp290Arg | missense_variant | 1.0 | ethambutol | |
aftB | 4268115 | p.Leu241Arg | missense_variant | 1.0 | ethambutol | |
aftB | 4268696 | c.141G>A | synonymous_variant | 1.0 | ethambutol | |
ethA | 4326298 | c.1176G>A | synonymous_variant | 1.0 | ethionamide | |
whiB6 | 4338567 | c.-46C>A | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance |