Table 2. Summary of the number of candidate SNPs derived from each data source and the number of SNPs from each data source that were included in the final array design.

Data Source	Number included on array	Candidates for array design	Conversion rate
High coverage sequencing & GBS cross validation	3,149	5,451	57.8%
High coverage sequencing & RNA-seq cross validation	368	583	63.1%
High coverage sequencing & RAD-seq cross validation	3,875	8,734	44.36%
GBS	6,046	14,959	40.5%
RNA-seq	10,491	14,922	70.3%
High coverage sequencing	62,568	59,277 + 13,912*	85.5%
sdY markers	6	6	100%
Totals	86,503	117,844*	73.4%

*The initial candidate list was 103,932 SNPs. When this initial set of candidates failed to yield enough SNPs recommended for use on the array 13,912 high coverage SNPs were added to the list of candidates