Run ID: SRR1172844
Sample name:
Date: 2024-10-03T22:30:21.090297
Number of reads: 166105
Percentage reads mapped: 50.66
Median coverage: 3.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 0.99 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.76 |
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 |
---|---|---|---|---|---|---|
rpoB | 760328 | c.522G>C | synonymous_variant | 0.6 | rifampicin | |
rpoC | 763702 | c.333C>G | synonymous_variant | 0.46 | rifampicin | Not assoc w R - Interim |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.54 | rifampicin | |
rpoC | 764131 | c.762T>C | synonymous_variant | 0.67 | rifampicin | |
rpoC | 764215 | c.846A>G | synonymous_variant | 0.55 | rifampicin | |
rplC | 800867 | p.Ser20Asn | missense_variant | 0.7 | linezolid | |
rplC | 800874 | c.66A>G | synonymous_variant | 0.7 | linezolid | |
rplC | 800875 | p.Val23Ile | missense_variant | 0.7 | linezolid | |
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.67 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472970 | n.1125C>G | non_coding_transcript_exon_variant | 0.67 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 0.7 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473105 | n.1260G>A | non_coding_transcript_exon_variant | 0.71 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473123 | n.1278delAinsTT | non_coding_transcript_exon_variant | 0.62 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.81 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.77 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474823 | n.1166C>T | non_coding_transcript_exon_variant | 0.73 | capreomycin | |
linezolid | ||||||
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475369 | n.1712G>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | |
linezolid | ||||||
rrl | 1475402 | n.1745C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.75 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475429 | n.1772G>A | non_coding_transcript_exon_variant | 0.77 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475483 | n.1826C>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.54 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476583 | n.2926G>A | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.7 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.7 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476603 | n.2946G>A | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476608 | n.2951C>G | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.75 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
inhA | 1674582 | c.381T>C | synonymous_variant | 0.7 | isoniazid | |
ethionamide | ||||||
inhA | 1674601 | p.Leu134Thr | missense_variant | 0.7 | isoniazid | |
ethionamide | ||||||
rpsA | 1833661 | c.120A>G | synonymous_variant | 0.62 | pyrazinamide | |
rpsA | 1833727 | c.186G>C | synonymous_variant | 0.6 | pyrazinamide | |
rpsA | 1834000 | c.459G>C | synonymous_variant | 0.82 | pyrazinamide | |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.6 | pyrazinamide | Not assoc w R - Interim |
embA | 4245137 | c.1905T>C | synonymous_variant | 0.6 | ethambutol | |
embA | 4245146 | c.1914G>A | synonymous_variant | 0.55 | ethambutol | |
embA | 4245149 | c.1917C>G | synonymous_variant | 0.55 | ethambutol | |
embA | 4245153 | p.Ile641Val | missense_variant | 0.58 | ethambutol |