Table 1. Total number of SNP markers at different read depths.

	PSPPC	PSPPC+P. fulvum
All filtered markers
SNP number	66 591	67 400
Average read depth	4.1	4.4
Average percent missing taxa/SNP	47	47
Filtered markers with read depth ⩾5
SNP number	16 675	18 097
Average read depth	11.7	12.2
Average percent missing taxa/SNP	18	20

Abbreviations: PSPPC, Pea Single Plant Plus Collection; SNP, single-nucleotide polymorphism.

For both germplasm collections, the numbers represent the UNEAK–Stacks union data set with loci called in at least 20% of individuals and having a minor allele frequency ⩾1%.