Genotyping Database

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The genotyping database stores information related to DNA libraries. The core set of tables related to genotyping are:

  • The gbs table stores information about DNA libraries, DNA sequencing orders and DNA Sequence files.
  • The dna table stores information about DNA plates and the samples contained in each well on a plate.
  • The dnaQuant table stores DNA quantification values fluorescence values for each well on a plate.
  • The barcodes table stores information about the barcode sequences used for each plexing scheme for each well on a plate.

In addition to the core tables, the following tables provide details on the tissue and plant DNA sources:

  • The tissue table stores information about the tissue used to prepare a DNA sample.
  • The plant table stores information about the plant that the tissue was extracted from.

The figure below illustrates the table definitions and the key relationships used to formulate queries related to genomic analysis. (PK indicates the primary key for each table.)


Gbs.png


Example Queries

Key Query

The query below shows an example of how to obtain the information used to construct a key file that is required as input to TASSEL.

SELECT gbs.flowcell,
    gbs.lane,
    barcodes.barcode,
    dna.sample_name,
    plant.plant_name,
    dna.plate_id,
    substring(dna.well_A01,1,1),
    substring(dna.well_A01,2,2),
    dna.well_A01,
    dna.notes,
    gbs.plexing,
    gbs.project,
    gbs.enzyme,
    dna.sample_id,
    dna.tissue_id,
    dna.external_id,
    dna.dna_person,
    dna.line_num,
    gbs.gbs_name,
    dna.plate_name,
    dna.well_01A,
    gbs.gbs_id,
    barcodes.`set`
FROM dna LEFT JOIN gbs ON gbs.dna_id = dna.plate_id
     LEFT JOIN plant ON dna.tissue_id = plant.plant_id
     INNER JOIN barcodes ON dna.well_A01 = barcodes.well_A01 AND gbs.plexing LIKE barcodes.`set` 
WHERE gbs.project LIKE "%My_Project%" ORDER BY gbs.gbs_id, dna.well_01A ASC