Description of columns in data files of "SNPs for thornback ray Raja clavata, validated from genotyped individuals"
Authors : Sabrina Le Cam, Adeline Bidaukt, Grégory Charrier, Florence Cornette, Jean-Baptiste Lamy, Sylvie Lapègue, Pascal Lorance, Verena Trenkel

Convention used for naming SNP (column Locus_Name in data files): RCL_P_xx_yy
xx: continuous number
yy: 5 possibilities
- MAJ_Base, e.g. MAJ_T, for locus with 2 SNP, the major allele "Base" is given for the second SNP
- MIN_Base, e.g. MIN_T, for locus with 2 SNP, the minor allele "Base" is given for the second SNP
- Sex: potentially sex-linked locus based on analysis of RADseq data
- SexMAJ_G/SexMIN_G: potentially sex-linked locus with 2 SNPs

Data file 1 SequencesSNP_Raja_clavata.csv
Locus_Name: Name of SNP
Sequence: nucleotid sequence and SNP from RADSeq analysis; 'N' if several SNPs in flanking sequence
AlleleA_Probe_Sequence: nucleotid sequence  in primer on chip
Assay_Design_Id: unique primer number
Ilmn_Id: Illumina unique primer number
Design_Date: date of primer design with GenomeStudio            
Assay_Type: InfiniumI or InfiniumII
Final_Score: score from in silico analysis with GenomeStudio indicating potential succes rate   

Data file 2 SuccessRateSNP.csv
Locus_Name: Name of SNP 
Call.Freq: proportion of samples (7726) with genotype called  
Minor.Freq: frequency of minor allele
Comment: information on reliability of SNP based on analysis of replicate individuals, etc.