SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata 
Ewan Harney, Sébastien Lachambre, Sabine Roussel, Sylvain Huchette, Florian Enez Romain Morvezen, Pierrick Haffray, Pierre Boudry

Data file 1
Information about the 500 SNPs that were genotyped, including position on contig, reference and alternative alleles (base pairs) sense (plus converted reference and alternative alleles for anti-sense contigs), samtools quality scores output by vcftools, genotypes of larval (Trc, Vg1 and Vg2) and adult (Mol and Stm) libraries from Harney et al. (2016), counts of heterozygotes and finally full primer sequences with 50 bp upstream and downstream, and SNPs indicated with square brackets (e.g. “[A/T]”). Acronyms for quality scores from vcftools are as follows: DP = Raw read depth, RPB = Mann-Whitney U test of Read Position Bias (bigger is better), MQB = Mann-Whitney U test of Mapping Quality Bias (bigger is better), BQB = Mann-Whitney U test of Base Quality Bias (bigger is better), MQSB = Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better), MQ0F = Fraction of MQ0 reads (smaller is better), PL = List of Phred-scaled genotype likelihoods, GT = Genotype, AC = Allele count in genotypes for each ALT allele, in the same order as listed, AN = Total number of alleles in called genotypes, DP4 = Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases, MQ = Average mapping quality.

Data file 2
Genotypes of 1065 individual abalone including parents and offspring from mixed cohort families (mix_Cohort) and 5 full sib training families (train_fam_01-05). Genotypes provided for 298 SNPs with >90% genotyping success across all samples.