PSE Submission File Formats v1.1

Submissions must uploaded as a ZIP-archive containing two files meta.csv and snps.csv.

Every SNP specific record in snps.csv file must have a corresponding record in meta.csv file and the information regarding country and breed for given individual must be in agreement in both files.

The fields in both files should be comma separated and no blank fields are allowed.

meta.csv

This file contains information related to animals and the genotyping. There must be one line in this file for each animal in the snps.csv.

Field Name

Description

Allowed Values

Record Type

Numeric

702

Service User

Alphanumeric

Any organization abbreviation

Source Country of Animals

Numeric

Any country code

Animal ID - Breed Code

Alphabetic

Any breed code

Animal ID - Nation Code

Numeric

Any country code

Animal ID - Sex Code

Alphabetic

M or F

Animal ID - Registration

Alphanumeric

Example: A1234567890

Genotyping Laboratory Identification

Alphanumeric

Any lab ISAG code

Sample ID

Alphanumeric

Example: R1234567890

Scan Date

Numeric

Any valid date in the format yyyymmdd

Platform

Alphanumeric

Any SNP Platform code

No. SNPs in Genotype

Total number of SNPs in the animal's full genotype used to create the SNP record for GenoEx-PSE

Example: 55647

Genotype Call Rate

Percent call rate of the animal's full genotype used to create the SNP record for GenoEx-PSE

Example: 99.9

snps.csv

This file contains genotype data one or more animals. Four each animal in this file, identified by the four Animal ID fields, there must be a corresponding record in the meta.csv file.

Field Name

Description

Allowed Values

Record Type

Numeric

704-AB or 704-TOP

Animal ID - Breed Code

Alphabetic

Any breed code

Animal ID - Nation Code

Numeric

Any country code

Animal ID - Sex Code

Alphabetic

M or F

Animal ID - Registration

Alphanumeric

Example: A1234567890

SNP Name

Alphanumeric

Any SNP name in CAPITALS

Allele 1

Alphabetic

A or B for 704-AB; A, C G or Tfor 704-TOP

Allele 2

Alphabetic

A or B for 704-AB; A, C G or Tfor 704-TOP