Run ID: SRR13861338
Sample name:
Date: 2024-04-16T00:58:58.535242
Number of reads: 444147
Percentage reads mapped: 11.11
Median coverage: 14.0
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 |
---|---|---|---|---|---|---|
dnaA | 715 | p.Thr239Pro | missense_variant | 1.0 | isoniazid | |
fgd1 | 490955 | p.Met58Arg | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
hadA | 731861 | c.-69G>C | upstream_gene_variant | 1.0 | isoniazid | |
rpsL | 781155 | c.-405G>A | upstream_gene_variant | 1.0 | streptomycin | |
Rv1258c | 1406845 | p.Ala166Pro | missense_variant | 1.0 | streptomycin | |
isoniazid | ||||||
pyrazinamide | ||||||
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.48 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
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 | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.45 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.42 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.42 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.44 | streptomycin | Uncertain significance |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.41 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.41 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.78 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.79 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.84 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.44 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
inhA | 1674607 | p.Pro136Ser | missense_variant | 1.0 | ethionamide | |
isoniazid | ||||||
inhA | 1674778 | p.Pro193Ala | missense_variant | 1.0 | ethionamide | |
isoniazid | ||||||
bacA | 2064115 | p.Ala205Asp | missense_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
PPE35 | 2169081 | p.Leu511Ser | missense_variant | 1.0 | pyrazinamide | |
PPE35 | 2169202 | p.Ser471Pro | missense_variant | 1.0 | pyrazinamide | |
Rv1979c | 2222091 | c.1074G>T | synonymous_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
Rv1979c | 2223306 | c.-142T>A | upstream_gene_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
pncA | 2289228 | p.Ile5Asn | missense_variant | 1.0 | pyrazinamide | |
eis | 2714755 | p.Pro193Gln | missense_variant | 1.0 | amikacin | |
kanamycin | ||||||
ahpC | 2726324 | c.132A>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
ahpC | 2726362 | p.Phe57Ser | missense_variant | 1.0 | isoniazid | |
pepQ | 2859580 | p.Leu280Arg | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
Rv2681 | 2997338 | c.600G>C | synonymous_variant | 1.0 | capreomycin | |
thyX | 3067940 | c.6C>G | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
mtrB | 3626051 | p.Ser188Trp | missense_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
ddn | 3986889 | p.Phe16Val | missense_variant | 1.0 | delamanid | |
pretomanid | ||||||
embC | 4242041 | p.Met727Leu | missense_variant | 1.0 | ethambutol | |
embA | 4244723 | p.Gln497His | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4267979 | c.858G>C | synonymous_variant | 1.0 | ethambutol |