CS-DCC Climate-Smart Data Collaboration Centre

Leveraging Genomics To Achieve Dairy Net-Zero: Genotype File Layout

Description

Data schema for the pedigree file layout for the Net-Zero Dairy Genome Project.

Schema

AttributeUnitLabelInformationDatatypeFormat
ANIMAL_IDANIMAL_IDINTERBULL REGISTRATION CODE WHICH HAS EXACTLY 19 CHARACTERS. MADE UP OF FOUR COMPONENTS: BREED (3), COUNTRY (3), SEX(1), REGISTRATION NUMBER(12)Text
SAMPLE_IDSAMPLE_IDUNIQUELY IDENTIFIES GENOTYPE (ie. SENTRIX CODE); DO NOT USE THE ANIMAL_ID (REGISTRATION NUM) TO ALLOW FOR MULTIPLE GENOTYPES PER ANIMAL IF REQUIREDText
TRANSACTION_TYPETRANSACTION_TYPEText
SNP_CHIP_PANEL_TYPESNP_CHIP_PANEL_TYPEText
IMPUTATION_USED_TO_GENERATE_DATAIMPUTATION_USED_TO_GENERATE_DATAYES or NOText
PANEL_TYPE_BEFORE_IMPUTATIONPANEL_TYPE_BEFORE_IMPUTATIONText
DATE_OF_GENOTYPE_TESTDATE_OF_GENOTYPE_TESTDateTime
FILE_TYPEFILE_TYPEText
GENOTYPEGENOTYPEUSING THE CDCB FORMAT ; THE GENOTYPE IS A VARIABLE LENGTH STRING OF 0,1,2,5 INDICATING SNP GENOTYPES OF BB, AB, AA, \\-\\- (1 BYTE PER SNP, NO COMMAS BETWEEN SNPS). FOR EXAMPLE \'01252010250211110025.......\'.Text
SOURCE_OF_DATASOURCE_OF_DATASee contacts list under \'Source of Data\' columnText
PROJECTPROJECTText