Run ID: ERR4816702
Sample name:
Date: 2024-04-15T11:41:14.189412
Number of reads: 491390
Percentage reads mapped: 78.04
Median coverage: 13.0
Strain: lineage4.6.2.2
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 1.0 |
lineage4.6.2 | Euro-American | RD726 | 0.99 |
lineage4.6.2.2 | Euro-American (Cameroon) | RD726 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.799C>T | Uncertain significance | Mutation from literature |
gid | c.102delG | Assoc w R | ||
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 |
---|---|---|---|---|---|---|
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 778298 | c.183G>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
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 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471979 | n.134T>C | non_coding_transcript_exon_variant | 0.82 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.92 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.92 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472123 | n.278A>T | non_coding_transcript_exon_variant | 0.71 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.63 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.33 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472558 | n.713G>A | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472569 | n.724G>A | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.94 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472660 | n.815T>C | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.75 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472671 | n.826G>A | non_coding_transcript_exon_variant | 0.65 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472674 | n.829_838delTTCCTTCCTTinsCCCTTCCAC | non_coding_transcript_exon_variant | 0.93 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472687 | n.842A>G | non_coding_transcript_exon_variant | 0.93 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472689 | n.844C>T | non_coding_transcript_exon_variant | 0.68 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.79 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472714 | n.869A>G | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.41 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 0.55 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472982 | n.1137G>A | non_coding_transcript_exon_variant | 0.36 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.52 | streptomycin | Uncertain significance |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473001 | n.1156G>T | non_coding_transcript_exon_variant | 0.36 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473005 | n.1160C>T | non_coding_transcript_exon_variant | 0.41 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473009 | n.1164T>A | non_coding_transcript_exon_variant | 0.36 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.8 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.8 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.88 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473089 | n.1244A>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473122 | n.1277T>A | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473201 | n.1356A>T | non_coding_transcript_exon_variant | 0.44 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.39 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.59 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473283 | n.1439_1445delAACCCTC | non_coding_transcript_exon_variant | 0.64 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473292 | n.1447G>T | non_coding_transcript_exon_variant | 0.43 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473293 | n.1448G>C | non_coding_transcript_exon_variant | 0.43 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473294 | n.1449_1450insT | non_coding_transcript_exon_variant | 0.43 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473294 | n.1449_1450insT | non_coding_transcript_exon_variant | 0.43 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474498 | n.841G>T | non_coding_transcript_exon_variant | 0.75 | capreomycin | |
linezolid | ||||||
rrl | 1474505 | n.848C>G | non_coding_transcript_exon_variant | 0.75 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474507 | n.850G>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474517 | n.860C>G | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
linezolid | ||||||
rrl | 1474537 | n.880G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474913 | n.1256T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475753 | n.2096C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475879 | n.2222T>C | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475902 | n.2245T>C | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.88 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476298 | n.2641C>A | non_coding_transcript_exon_variant | 0.67 | capreomycin | |
linezolid | ||||||
rrl | 1476300 | n.2643G>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
linezolid | ||||||
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476307 | n.2650A>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
linezolid | ||||||
rrl | 1476309 | n.2652G>T | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.77 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2680 | 2996208 | p.Ala35Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
Rv2680 | 2996237 | p.Gly45Ser | missense_variant | 1.0 | capreomycin | |
Rv3083 | 3448567 | p.His22Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
Rv3236c | 3612571 | c.546C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
aftB | 4267272 | p.Lys522Arg | missense_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326739 | c.735C>G | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
ethR | 4328004 | c.456G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |