Run ID: SRR7070315
Sample name:
Date: 2024-05-20T09:29:01.693171
Number of reads: 2257642
Percentage reads mapped: 96.7
Median coverage: 65.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.888G>A | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
capreomycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
kanamycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.58 | streptomycin | Uncertain significance | Mutation from literature |
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.28 | amikacin | Uncertain significance | Mutation from literature |
capreomycin | Uncertain significance | Mutation from literature | |||||
kanamycin | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
capreomycin | ||||||
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.56 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.53 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.4 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.44 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.44 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473081 | n.1236C>T | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.41 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.39 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.35 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.35 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.35 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.27 | kanamycin | Not assoc w R |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.27 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473270 | n.1425G>A | non_coding_transcript_exon_variant | 0.27 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | ||||||
capreomycin | ||||||
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.27 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473290 | n.1445C>T | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | ||||||
capreomycin | Uncertain significance | |||||
rrs | 1473291 | n.1446G>T | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | ||||||
capreomycin | Uncertain significance | |||||
rrs | 1473301 | n.1456T>C | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1473305 | n.1460G>T | non_coding_transcript_exon_variant | 0.18 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
capreomycin | ||||||
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475937 | n.2280A>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.57 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.47 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.43 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.48 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.45 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
Rv3083 | 3448497 | c.-6_*1408del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
Rv3236c | 3613379 | c.-263T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R |