Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee
Jones, Julia C. et al. (2020), Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee, Dryad, Dataset, https://doi.org/10.5061/dryad.gxd2547gp
The file lists all 103'270 SNPs included on the HDHB chip. The individual columns state the SNP's local ID, linkage group, base position, flanking sequences, and the polymorphisms.
The file lists all 3'272 samples available for the publication. The data includes the Beebreed ID (www.beebreed.eu) of the colony whose queen was genotyped, as well as its location, and the tissue type of the sample.
This is a large file to be opened with special editors (e.g. "vim" or "Notepad++") or custom scripts (e.g. in languages R or Python). The first line gives the local IDs of the SNPs. Each line starts with the sample number in Supp_Table_2.xlsx with an additional "S" in front of it. The row proceeds giving the sample's genotyping results. Genotypes "AA", "AB", and "BB" are coded as "0", "1", and "2", respectively, while "0" states that the location could not be called for this sample.
German Federal Ministry of Food and Agriculture with the Landwirtschaftliche Rentenbank, Award: 742 397