BanzaiDB tables schema
The following tables are defined in BanzaiDB
Mapping
reference_genome_features
strains_under_investigation
reference_genomes
determined_variants
Key |
Value (type) |
Comments |
id |
string |
Primary (StrainID_RefID_Position) |
StrainID | string |
|
Positiion |
int |
|
LocusTag |
string |
Of reference |
Class |
string |
substitution, insertion, deletion |
SubClass |
string or None |
synonymous, non-synonymous |
RefBase |
char |
A T C or G (N) ? |
ChangeBase |
char |
A T C G or (N) ? |
CDSBaseNum |
int |
|
CDSAANum |
int |
|
CDSRegion |
string or None |
x..y |
RefAA |
char or None |
|
ChangeAA |
char of None |
|
Product |
string |
|
CorrelatedChange |
boolean |
If up/down-stream change effects |
Evidence |
string |
|
strains_under_investigation
Key |
Value (type) |
Comments |
StrainID |
string |
|
VarCount |
int |
total number of parsed (CDS) variants |
REF
REF_FEATURES
Key |
Value (type) |
Comments |
LocusTag |
string |
|
Sequence |
int |
|
Translation |
string |
|
Start |
int |
|
End |
int |
|
Strand |
int |
1/-1 |
Product |
string |
Should be equal to VARIANT[‘CDS’] |