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Table 2 Design and performance characteristics of BOPA1 and BOPA2

From: Development and implementation of high-throughput SNP genotyping in barley

  BOPA1 BOPA2 Both
SNPs represented 1536 1536 3072
Number of unigenes on other BOPA* 77 77 NA
Unigenes represented 1536 1442 2901
Number of unigenes with 1 SNP 1536 1380 2770
Number of unigenes with 2 SNPs 0 43 106
Number of unigenes with 3 SNPs 0 11 16
Number of unigenes with 4 SNPs 0 3 3
Number of unigenes with 5 SNPs 0 5 6
SNPs included in 2943 mapped 1414 1263 2677
SNP unigenes matching Barley1 probe set(s) 1489 1433 2921
MAF ≥ 0.08 in design germplasm 1536 921 2457
MAF ≥ 0.04 and < 0.08 in design germplasm 0 256 256
MAF ≥ 0.005 and < 0.04 in design germplasm 0 345 345
MAF = 0 in design germplasm 0 14 14
MAF = 0 in 2006 BarleyCAP genotypes 99 301 400
MAF > 0 and < 0.05 in 2006 BarleyCAP genotypes 65 284 349
MAF ≥ 0.05 in 2006 BarleyCAP genotypes 1372 951 2323
  1. *Among the 77 unigenes represented by SNPs on both BOPAs, 69 have 1 SNP on BOPA2, 6 have 2 SNPs on BOPA2, 1 has three SNPs on BOPA2, 1 has four SNPs on BOPA2.