The following tables are defined in BanzaiDB -
Provides information on a reference used in mapping.
references:
Elements:
---------
id: string
reference_name: string or null
revision: int
reference_id: string or null
Example:
--------
[{"id":"NC_008527","reference_name":"Lactococcus lactis subsp. cremoris SK11, complete genome.","revision":1},{"id":"current_reference","reference_id":"NC_008527","revision":1}]
$ head NC_008527_1.gbk
LOCUS NC_008527 2438589 bp DNA CON 27-AUG-2013
DEFINITION Lactococcus lactis subsp. cremoris SK11, complete genome.
ACCESSION NC_008527
VERSION NC_008527.1 GI:116510843
...
Thus: ACCESSION = reference["id"]
VERSION = reference["id"]+reference["revision"]
DEFINITION = reference["reference_name"]
Note: Primary key 'current_reference' is added to keep track of multiple runs
Provides information on the features of a given reference.
Only supports: CDS, gene and xRNA features
reference_features:
Elements:
---------
end: int
id: string
locus_tag: string
product": string
reference_id: string
sequence: string
start: int
strand: int
translation: string or null
Example:
--------
1) CDS
{
"end": 12450 ,
"id": "NC_008527.1_LACR_0008_CDS" ,
"locus_tag": "LACR_0008" ,
"product": "XRE family transcriptional regulator" ,
"reference_id": "NC_008527.1" ,
"sequence": "ATGGAAATATCCGAAATAATCAAAGAAAATCGTAAACTCAAAAATCTCAGTCAGGAAGAGTTAGCAAAGGAACTACACATCTCTCGTCAATCTATCTTAAAATGGGAGACAGGAAAATCACTTCCCACCACAGACCAACTTATCTTACTCAGTGAAATTTTCGATTGTTCTTTGGACACGTTGCTCAAAGGTGACAAAAAAATGGAAGAAAAAGTAAAACATGAAATTGATGACAAACGGACCTTAAAGTTAATTTATAAGGTTGGTTGGGGTTTTATTGTTCCCTTACTTTTTATTTTGAAATTTGTTTTACATTTGTTTTGA" ,
"start": 12126 ,
"strand": 1 ,
"translation": "MEISEIIKENRKLK
2) gene
{
"end": 24970 ,
"id": "NC_008527.1_LACR_0018_gene" ,
"locus_tag": null ,
"product": null ,
"reference_id": "NC_008527.1" ,
"sequence": "ATGAATAACAACAAACAACCAAGACAAGGAAATTTTGTAAAAAATATCTTAATGTGGGTTATATTGGCTATTGTTGTTGTTGTCGGTTTCAATTTCTTCTTCAGTAGTAATCAATCAGGAGTGGATAAAATTAGCTATTCACAATTGATGACTAAACTTGATGATAATAATATTGAAAACGTCACAATGCAACCATCAGATAGCTTAATTACTGTAACAGGTGAGTATAAAAAACCTGTAAAGGTAAAAGGAAAAAACAATTTCCCACTTTTAGGTAATACTACAAGTGAAGTTAAAAACTTCCAAGCTTATATTATTCCAACTGACAGTGTTGTCAAAGATATCCAAAATGCAGCTAAAAGTAATGATGTAAAACTTAGTGTCGTTCAAGCGTCATCAAGTGGTATGTGGGTTCAAATTCTCTCATATATCATCCCAATGATTTTATTTGTTGGTATCTTCTGGCTCATGATGGGTGGAATGGGCGCTCGTGGCGGAGGCGGCGGTGGAAATCCGATGTCCTTCGGTAAATCTCGTGCTAAACAACAAGATGGTAAAACATCAAAAGTTCGTTTTGCTGATGTTGCCGGTTCTGAAGAGGAAAAACAAGAGCTTGTTGAAGTTGTTGACTTCCTTAAAAATCCGAAAAAATATCACGATTTAGGTGCTCGTATCCCAGCAGGTGTTCTCCTTGAAGGCCCTCCGGGTACAGGGAAAACTTTGCTTGCTAAGGCTGTTGCCGGTGAAGCAGGAGTTCCTTTCTATAGTATCTCAGGTTCTGATTTCGTTGAAATGTTTGTCGGAGTCGGGGCTTCACGTGTTCGTGATTTATTCGAAAATGCGAAGAAAACTGCTCCATCAATCATTTTCATCGATGAAATTGATGCTGTTGGTCGCCAACGTGGTGCAGGTTTAGGTGGGGGTAATGATGAACGTGAACAAACCCTCAACCAATTGCTTGTTGAAATGGATGGATTCCAAGACGATGGAAACTCAGTAATCGTTATCGCTGCAACTAACCGTTCAGATGTGCTTGACCCAGCGCTTTTACGTCCAGGTCGTTTTGACCGTAAAGTCTTGGTCGGAGCACCAGATGTTAAAGGTCGTGAAGCTGTCCTTAAAGTTCATGCTAAAAACAAACCTTTAGCAAGTGATGTTGATTTACACACTGTTGCTACACAAACTCCTGGTTATGTCGGAGCTGATTTGGAAAATGTTTTGAATGAAGCTGCTCTTGTTGCTGCACGTCAAAATAAAAAAGAAATCAATGCTGCTGATATTGATGAAGGAATGGACCGTGCAATGGCTGGTCCTGCTAAGAAAGATCGTATTCAATCAATGCGTGAGCGTGAAATCGTGGCTTATCACGAAGCAGGTCATGCTATTGTTGGTCTCGTTCTTGAAAATGGATCTACTGTTCGTAAAGTTACCGTTGTCCCTCGTGGACGTATCGGTGGTTACATGCTAGCTCTTCCAGATGAAGAAATCATGCAACCAACTAATCTTCATCTTCAAGACCAACTTGCCAGCCTTATGGGTGGACGACTTGGTGAAGAAATTGTCTTTGGTGTAGCTACTCCAGGTGCATCAAATGACATTGAAAAAGCAACACACATTGCTCGTTCAATGGTAACTGAATATGGGATGTCTAAGAAACTTGGTATGGTATCTTATGAAGGAGACCATCAAGTATTTATCGGCCGTGACTATGGTCAGACTAAGACTTACTCAGAAGCTACTGCTGTTATGATTGATGATGAAGTGCGTCGTATTCTTGGTGAAGCTTATGACCGTGCTAAAGAAGCAATTGAAACACATCGTGAACAACATAAAGCAATTGCGCAAGCTCTGCTTAAATACGAAACGCTCGATGCGAAACAAATCATGTCGCTCTTTACAACAGGTAAAATGCCTGATGAAGCAGCTGCATCAGAAGTACCAGAACCAAAAACATTTGAAGAATCTCTCAAAGATGCAAATGCGAATGTTGATGATTTTTCAAACATTAATATCTATAATGGTGAAGAAAAAACAGATTCTAAACCAGAAGAAAATAAGGAAAAATCAGAAGATGAAACAGCCAATTAA" ,
"start": 22882 ,
"strand": 1 ,
"translation": null
}
3) xRNA
{
"end": 25518 ,
"id": "NC_008527.1_25445-25518" ,
"locus_tag": null ,
"product": "tRNA-Phe" ,
"reference_id": "NC_008527.1" ,
"sequence": "GGCTCGGTAGCTCAGTTGGTAGAGCAATGGATTGAAGCTCCATGTGTCGGCGGTTCGATTCCGTCTCGCGCCA" ,
"start": 25445 ,
"strand": 1 ,
"translation": null
}
Provides information on the strains in this study.
strains_under_investigation:
Elements:
---------
StrainID: string
VarCount: int
id: string
Example:
--------
{
"StrainID": "ASCC880397" ,
"VarCount": 40797 ,
"id": "ASCC880397"
}
Provides information on the variants called for a mapping run.
determined_variants:
Elements:
---------
CDSAANum: int
CDSBaseNum: int
CDSRegion: string
ChangeAA: char
ChangeBase: char
Class: string
CorrelatedChange: boolean
Evidence: dict
LocusTag: string
Position: int
Product: string
RefAA: char
RefBase: char
StrainID: string
SubClass: string
UncalledBlock: boolean
id: string
Example:
--------
[{"CDSAANum":null,"CDSBaseNum":null,"CDSRegion":null,"ChangeAA":null,"ChangeBase":"A","Class":"substitution","CorrelatedChange":null,"Evidence":{"A":252,"T":1},"LocusTag":null,"Position":100230,"Product":null,"RefAA":null,"RefBase":"T","StrainID":"ASCC880030","SubClass":null,"UncalledBlock":true,"id":"ASCC880030_NC_008527_100230"}