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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 |