Run ID: ERR11465830
Sample name:
Date: 2024-10-03T14:31:29.271091
Number of reads: 1656433
Percentage reads mapped: 99.62
Median coverage: 34.0
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 |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 575761 | c.414C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
ethionamide | Not assoc w R - Interim | |||||
Rv0565c | 657192 | p.Met93Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
mmaA3 | 737358 | c.792A>C | synonymous_variant | 0.17 | isoniazid | |
rpoB | 759814 | p.Asp3Gly | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoB | 761097 | c.1291_1293delAGCinsTCG | synonymous_variant | 0.19 | rifampicin | |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.19 | rifampicin | |
rpoB | 761579 | c.1773G>C | synonymous_variant | 0.26 | rifampicin | Not assoc w R - Interim |
rpoC | 763483 | c.114G>C | synonymous_variant | 0.17 | rifampicin | |
rpoC | 763486 | c.117T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 763495 | c.126G>A | synonymous_variant | 0.18 | rifampicin | |
rpoC | 763504 | c.135C>G | synonymous_variant | 0.14 | rifampicin | |
rpoC | 763507 | c.138G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 763573 | c.204G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 763594 | c.225C>T | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 763621 | c.252C>T | synonymous_variant | 0.15 | rifampicin | |
rpoC | 763633 | c.264T>C | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rpsL | 781502 | c.-58G>T | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
rpsL | 781793 | c.234G>C | synonymous_variant | 0.18 | streptomycin | |
rpsL | 781796 | p.Met79Ile | missense_variant | 0.17 | streptomycin | |
rpsL | 781802 | c.243G>C | synonymous_variant | 0.15 | streptomycin | |
rpsL | 781808 | c.249C>T | synonymous_variant | 0.14 | streptomycin | |
rpsL | 781811 | c.252C>T | synonymous_variant | 0.14 | streptomycin | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472148 | n.303T>C | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.22 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472379 | n.534T>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.16 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472571 | n.726G>A | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472581 | n.736A>C | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472583 | n.738T>A | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472958 | n.1113A>G | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473026 | n.1181T>C | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473062 | n.1217T>G | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473089 | n.1244A>T | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473091 | n.1246G>A | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473201 | n.1356A>T | non_coding_transcript_exon_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.2 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473315 | n.1470T>C | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473316 | n.1471C>T | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474200 | n.545delT | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474232 | n.575C>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1474239 | n.582G>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474558 | n.901G>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474676 | n.1019T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474677 | n.1020A>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474688 | n.1031G>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474690 | n.1033C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474722 | n.1065T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474734 | n.1077G>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474736 | n.1079C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1474777 | n.1120T>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
linezolid | ||||||
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474801 | n.1144G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474802 | n.1145T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474896 | n.1239A>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474905 | n.1248T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474913 | n.1256T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475508 | n.1851A>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475696 | n.2039T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475883 | n.2226A>G | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475900 | n.2243A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475902 | n.2245T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2169902 | p.Leu237Phe | missense_variant | 0.25 | pyrazinamide | |
PPE35 | 2169910 | p.Asn235Tyr | missense_variant | 0.26 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2752c | 3065873 | p.Phe107Val | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
clpC1 | 4039865 | c.840T>C | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4039875 | p.Asn277Arg | missense_variant | 0.16 | pyrazinamide | |
clpC1 | 4039889 | c.816G>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4040063 | c.642G>C | synonymous_variant | 0.17 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040066 | c.639G>C | synonymous_variant | 0.17 | pyrazinamide | |
clpC1 | 4040644 | c.61A>C | synonymous_variant | 0.21 | pyrazinamide | |
clpC1 | 4040648 | c.57G>A | synonymous_variant | 0.2 | pyrazinamide | |
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 | 4338766 | c.-246delT | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |