Run ID: ERR2747617
Sample name:
Date: 2024-10-04T21:42:49.207887
Number of reads: 375248
Percentage reads mapped: 10.98
Median coverage: 6.0
Strain: La1.8.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
La1.8 | M.bovis | None | 1.0 |
La1.8.1 | M.bovis | None | 1.0 |
La1 | M.bovis | 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 |
---|---|---|---|---|---|---|
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473165 | n.1320C>T | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.87 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473172 | n.1327T>C | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473193 | n.1348G>T | non_coding_transcript_exon_variant | 0.8 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473200 | n.1355A>C | non_coding_transcript_exon_variant | 0.73 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473204 | n.1359C>A | non_coding_transcript_exon_variant | 0.73 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476353 | n.2696G>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476354 | n.2697A>G | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476388 | n.2731T>C | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
linezolid | ||||||
rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1476451 | n.2794C>A | non_coding_transcript_exon_variant | 0.26 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.83 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv2681 | 2997325 | p.Ala196Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
aftB | 4267858 | p.Ile327Val | missense_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |