This page enables to upload the functional variation sets for the update of:
- the Goat_IGGC_65K_v2 Illumina chip. Deadline: 25th of November, 2022.
- the ovine AgR_Ovine_60Kplus chip (AgResearch custom chip with ISGC 50k and 15k base content). Deadline: 28th of February, 2023.
The variants submitted after the deadline will be considered for the next chip updates.
Your email is mandatory and will enable us to inform you which of your variations will be kept in the final set.
The uploaded variation file must have tab separated format including the following columns in this order:
- SNP/INDEL name
- ss name (Submitted SNP (ss) – submitted variant based on asserted location or flanking sequences)
- rs name (Reference SNP (rs) - Non-redundant set of variations based on clustering of SS’es of same variant type and sequence position. Can be found by for example browsing “variant table” menu at Ensembl or looking at the European Variant Archive’s RS Release)
- position (on ARS1 assembly for goat and ARS-UI_Ramb_v2.0 for sheep)
- sequence of the 70 bases pairs on the left
- sequence of the 70 bases pairs on the right
- [ref/alt] alleles separated by a slash
- function (100 characters free text, please indicate here for example the gene in which the SNP is located...)
- remark (500 characters free text, please give as many details as you can, for example the doi of the publication of the variant, if the SNP is already included in another chip with another name, the SNP effect...)
Please check that your spreadsheet program did not autocorrect names.
You will find here an example file.
- ARS1 assembly available on NCBI
and Ensembl sites.
- ARS-UI_Ramb_v2.0 assembly available on NCBI
and Ensembl sites.
If any question, please contact Gwenola Tosser regarding Goat SNPs, Rudiger Brauning and Shannon Clarke for sheep SNPs.