BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 Table 2: Design and performance characteristics of BOPA1 and BOPA2 BOPA1 BOPA2 1536 77 1536 1536 0 0 0 0 1414 1489 1536 0 0 0 99 65 1372 1536 77 1442 1380 43 11 3 5 1263 1433 921 256 345 14 301 284 951 Both 3072 2901 2770 106 16 3 6 2677 2921 2457 256 345 14 400 349 2323 SNPs represented Number of unigenes on other BOPA* Unigenes represented Number of unigenes with 1 SNP Number of unigenes with 2 SNPs Number of unigenes with 3 SNPs Number of unigenes with 4 SNPs Number of unigenes with 5 SNPs SNPs included in 2943 mapped SNP unigenes matching Barley1 probe set(s) MAF ≥ 0.08 in design germplasm MAF ≥ 0.04 and < 0.08 in design germplasm MAF ≥ 0.005 and < 0.04 in design germplasm MAF = 0 in design germplasm MAF = 0 in 2006 BarleyCAP genotypes MAF > 0 and < 0.05 in 2006 BarleyCAP genotypes MAF ≥ 0.05 in 2006 BarleyCAP genotypes *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. Data production for map construction and MAF estimation DNA concentrations were re-checked using Quant-iT PicoGreen (Invitrogen, Carlsbad, CA) and standardized to 80 ng/μl in TE buffer in preparation for the GoldenGate assay and 5 μl (400 ng) were used for each assay. Data were generated from each progeny line in the OWB, SxM and MxB doubled haploid populations using POPA1 and POPA2. Data were also produced using POPA3 from the complete OWB and MxB sets of DNA samples, but from only 92 SxM doubled haploids. Data from 95 HxO dou- bled haploids using BOPA1 were also generated. For each of these four mapping populations, extensive integration of SNP data with other types of marker data will be described elsewhere (for example OWB marker integra- tion in Szűcs et al. [10]). Data used for the determination of allele frequency (see below) came from 125 germplasm samples for POPA1, 195 germplasm samples for POPA2, and 189 germplasm samples for POPA3. Data processing Raw data were transformed to genotype calls, initially using Illumina GenCall and subsequently using Illumina BeadStudio version 3 with the genotyping module. For each OPA, the data from all samples were visually inspected to manually set 1536 archetypal clustering pat- terns. The cluster positioning was guided by knowledge that heterozygotes are nearly non-existent in doubled haploids and rare in highly inbred parental genotypes and germplasm samples. Several "synthetic heterozygote" DNA samples were made by mixing parental DNAs in a 1:1 mass ratio (Figure 2A, green dots), and included to anchor heterozygote cluster positions to enable the iden- tification of true heterozygotes which occur at a significant Page 10 of 13 (page number not for citation purposes)