Run ID: SRR13861713
Sample name:
Date: 2024-04-15T02:58:52.959619
Number of reads: 281823
Percentage reads mapped: 14.1
Median coverage: 9.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
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 | pncA | p.Thr153Asn | Mutation from literature | |
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 |
---|---|---|---|---|---|---|---|
pncA | 2288784 | p.Thr153Asn | missense_variant | 1.0 | pyrazinamide | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 750 | c.750C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
Rv0565c | 657479 | c.-9A>G | upstream_gene_variant | 0.93 | ethionamide | |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.55 | rifampicin | |
rpoB | 762995 | c.3189G>T | synonymous_variant | 0.55 | rifampicin | Not assoc w R - Interim |
rpoC | 767026 | c.3657G>C | synonymous_variant | 1.0 | rifampicin | |
fbiC | 1304225 | p.Gly432Asp | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1305046 | p.Ser706Pro | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
embR | 1416546 | p.Thr268Ser | missense_variant | 1.0 | ethambutol | |
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.43 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.43 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.5 | 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 | 0.47 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.47 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.47 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474652 | n.995T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.73 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.7 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.7 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.7 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.7 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.73 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.73 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.73 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.72 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.72 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.72 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.71 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.68 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.4 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
bacA | 2063152 | p.Arg526Leu | missense_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
katG | 2156722 | c.-611G>A | upstream_gene_variant | 1.0 | isoniazid | |
Rv3236c | 3612913 | p.Leu68Phe | missense_variant | 1.0 | pyrazinamide | |
lpqB | 3624794 | c.117G>C | synonymous_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
ethA | 4327893 | c.-420C>A | upstream_gene_variant | 1.0 | ethionamide | |
gid | 4408070 | p.Trp45Arg | missense_variant | 1.0 | streptomycin | Uncertain significance |