The GENOlist file
Format 733 for Genotyped Animal Lists
This format is designed for uploading information about which animals have been genotyped, usually using whole genome SNP chips. Note that the file has semi-colon field separators (exactly eight) and the column positions allow for these separators.
Column Field description Format Notes 1 Record type Character 3 733 5 Breed of evaluation Character 3 Notes 1 and 3. 9 Population of evaluation Character 3 Notes 2 and 3. 13 International animal ID Character19 Note 4. 33 Genotyping chip code Character10 Note 5. 44 Genotype status code (U/P/A/G/T/) Character 1 Note 6. 46 Share code (right to share genotype (Y/N)) Character 1 Note 7. 48 Tissue code (Availability of tissue for genotyping) Character 1 Note 8. 50 Publish code (right to publish this info (Y/N) Character 1 Note 9.
Notes:
- Breed of evaluation must be one of BSW, GUE, JER, HOL, RDC or SIM if the animal is submitted for Interbull evaluations or UUU otherwise.
The population code must be an upper case population code assigned by the Interbull Centre. It is generally the same as the country code of the organization submitting the data except in the cases of multi-country evaluations (eg. "DEA" and "DFS") or multiple populations within a country participating in the same international evaluation (eg. "CHE"/"CHR", "FRA"/"FRR"/"FRM"). If the animal will not be submitted to Interbull evaluations use code "UUU". i.e., not submitted for MACE
- The breed-population combination must be among the combinations for which your organization is authorized to submit bull evaluations for MACE for dairy production traits, or "UUU;UUU" for animals which will not be submitted to Interbull evaluations.
- The 19-character international animal ID must be valid according to the rules specified for pedigree files (breed*3, country*3, sex*1, id*12). (The animal must exist in the Interbull pedigree database and a pedigree record must have been uploaded.)
The "chip" code must be among the foreseen list present in the DB (eg., None, Parentage, Illu3K, IlluLD, Illu50K, Illu50K2, CRV60K, CRV60K2, IlluHD, AffyHD, Sequence, GGP9K, EUROG10K, Unknown)
- The allowed "status codes" are: U=unavailable, P=genotyping in progress A=available but not yet used for GEBVs, G=used for GEBVs but not yet used in training, T=used for training for protein yield.
- The allowed "share codes" are: Y=yes, the country submitting the data is considering sharing or N=no, the country submitting the data is not considering sharing
- The foreseen "tissue codes" are: N=none, B=blood, S=semen, H=hair bulbs, E=ear punch, M=multiple or U=unknown. This field is available to signal access to biological material on animals which may be of interest to others.
- The allowed "publish codes" are: Y=yes or No. This field indicates whether the information in this specific record may be made available to other organizations (Y) or only to the Interbull Centre (N).
Sample records:
733;BSW;ITA;BSWAUTM012345678900;Illu50K ;G;Y;U;Y 733;BSW;ITA;BSWITAM000123456789;IlluLD ;T;Y;U;Y 733;BSW;ITA;BSWITAM000987654321;Illu50K2 ;G;Y;U;Y 733;BSW;ITA;BSWITAM000987654322;None ;U;N;B;Y 733;BSW;ITA;BSWITAM000987654323;Sequence ;P;Y;S;Y