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 |