Additional file 3.

SNP allele frequencies. Allele frequencies for both alleles and minor allele frequencies (MAF) were shown for DH clonal lines (worksheet 1), INRA-SY (worksheet 2), INRA-SP (worksheet 3), NCCCWA (worksheet 4), all 3 populations (worksheet 5) and for true SNPs (worksheet 6). Allele frequencies were calculated by direct count in the raw genotype data file, expected heterozygosities per locus (He) were estimated by He = 2pq and PIC values were estimated by PIC = H-2p2q2, where p and q are the allele frequencies of the two alternate alleles.

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Boussaha et al. BMC Genomics 2012 13:238   doi:10.1186/1471-2164-13-238