Table 2. Discovery of variants across 52 genotypes in the collection.

Metric	Count
Number of accessions in the Apios collection	52
Total number of reads generated	1,315,730,442
Average number of reads generated per accession	25,302,509
Average % of reads mapped to the assembly per accession	89.5
Average % of reads mapped uniquely to the assembly per accession	61.4
Number of variants (SNP and Indels) identified with base criteria	1,582,730
Number of variants identified (base criteria + read depth ≥ 5)	299,145
Number of SNPs identified (base criteria + read depth ≥ 5)	271,170
Number of SNPs (base criteria + read depth ≥ 5 + MAF ≥ 0.1 + Maximum missing percentage ≤ 10%)	58,154
Average % reproducibility of SNPs (tested using 4 biological replicates)	90.6
Number of components (a.k.a genes) harboring SNPs	9,338
% of components in the assembly harboring SNPs	19.2
Average accessions missing per SNP (%)	1.5
Average heterozygous accessions per SNP (%)	37.5
Number of gene expression markers identified	39,609

Base criteria: At least 2 reads calling variant within at least 1 accession; ≥20% of the reads calling the variant allele in that sample; and average quality of bases calling the variant is ≥10).