Run ID: SRR1049023
Sample name:
Date: 2024-04-15T19:30:04.594493
Number of reads: 132184
Percentage reads mapped: 4.34
Median coverage: 2.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 0.94 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.88 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | c.421_423delTTGinsCC | Assoc w R | High-level resistance |
p.Ser140Asn | Uncertain significance | Mutation from literature | ||
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 |
---|---|---|---|---|---|---|---|
katG | 2155689 | c.421_423delTTGinsCC | frameshift_variant&missense_variant | 0.76 | isoniazid | Assoc w R | High-level resistance |
katG | 2155693 | p.Ser140Asn | missense_variant | 0.72 | isoniazid | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.75 | rifampicin | |
rpoC | 762980 | c.-390T>C | upstream_gene_variant | 0.67 | rifampicin | |
rpoC | 764348 | p.Met327Leu | missense_variant | 0.6 | rifampicin | |
rpoC | 764355 | p.Gln329Pro | missense_variant | 0.55 | rifampicin | |
rpoC | 764377 | c.1008C>G | synonymous_variant | 0.55 | rifampicin | Not assoc w R - Interim |
rpoC | 764380 | c.1011G>C | synonymous_variant | 0.55 | rifampicin | Not assoc w R - Interim |
rpoC | 764383 | c.1014C>G | synonymous_variant | 0.55 | rifampicin | |
rpoC | 764387 | c.1018_1020delTTGinsCC | frameshift_variant&missense_variant | 0.55 | rifampicin | |
rpoC | 764398 | c.1029G>C | synonymous_variant | 0.55 | rifampicin | |
rpoC | 764405 | c.1036_1038delAGGinsCC | frameshift_variant&missense_variant | 0.6 | rifampicin | |
rpoC | 764410 | c.1041G>T | synonymous_variant | 0.6 | rifampicin | |
rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 0.8 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.8 | 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 | 0.82 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.75 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.82 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476384 | n.2727G>C | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.88 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.89 | capreomycin | |
linezolid | ||||||
rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.89 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>C | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>G | 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 | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
katG | 2155613 | p.Phe167Leu | missense_variant | 0.8 | isoniazid | |
katG | 2155614 | c.498T>C | synonymous_variant | 0.8 | isoniazid | |
katG | 2155617 | p.Ile165Met | missense_variant | 0.8 | isoniazid | |
katG | 2155626 | c.486G>C | synonymous_variant | 0.91 | isoniazid | |
katG | 2155637 | p.Leu159Ile | missense_variant | 0.91 | isoniazid | |
katG | 2155641 | p.Lys157Arg | missense_variant | 0.91 | isoniazid | |
katG | 2155650 | c.462G>A | synonymous_variant | 0.77 | isoniazid | Not assoc w R - Interim |
katG | 2155655 | p.Lys153Gln | missense_variant | 0.77 | isoniazid | Uncertain significance |
katG | 2155661 | p.Val151Ile | missense_variant | 0.79 | isoniazid | |
katG | 2155668 | c.444G>C | synonymous_variant | 0.83 | isoniazid | |
katG | 2155704 | c.408C>T | synonymous_variant | 0.75 | isoniazid | |
katG | 2155716 | c.396T>C | synonymous_variant | 0.7 | isoniazid | |
katG | 2155722 | c.390G>C | synonymous_variant | 0.68 | isoniazid | |
katG | 2155728 | c.384G>C | synonymous_variant | 0.68 | isoniazid | |
katG | 2155735 | p.Met126Gln | missense_variant | 0.68 | isoniazid | |
katG | 2155737 | c.375C>T | synonymous_variant | 0.68 | isoniazid | |
katG | 2155741 | p.Gly124Ala | missense_variant | 0.65 | isoniazid | Uncertain significance |
katG | 2155743 | c.369G>T | synonymous_variant | 0.65 | isoniazid | |
katG | 2155765 | p.His116Thr | missense_variant | 0.57 | isoniazid |