> > Population structure was analysed with GenAlEx 6.5 (Peakall and Smouse 2012), to obtain mean values per population of the total number of alleles, the number of alleles with a minimum allele frequency of 5%%, the number of effective alleles, the Shannon's Information Index, the number of private alleles, the expected heterozygosity, Rst and the estimation of gene flow.
Comparison between the genetic profiles allowed the identification of low frequency alleles and those with a minimum allele frequency (MAF) below 5%% were removed, then originating a panel of 1713 SNPs evenly distributed along the genome at a mean distance of 215,223 pb.
Since we were dealing with a haploid genome, and since heterozygous sites were unexpected, we used a minimum allele frequency threshold of 80% to call the alleles.
In the case where the minimum allele frequency is low, the difference between the frequencies of the two alleles at one locus is large and disparate, while the differences are much smaller when the minimum allele frequency is high.
All SNPs had a minimum allele frequency >5%, displayed less than 5% of missing values, and were in HWE (p > 0.05).
Minimum allele frequency (MAF) for the 1713 SNPs panel in japonica and indica groups of our collection and for those from 3KRGP were calculated using Tassel (Tassel 5.2.26, Bradbury et al. 2007).
Increasing the effect size reduced the minimum allele frequency at which an association could be detected.
Haplotype reconstruction was performed using Bayesian statistical method implemented in PHASE [8], version 2.1.1, using single nucleotide polymorphism (SNP) with a minimum allele frequency (MAF) of 2%.
In our biallelic loci, by convention we specify the smaller of the two allele frequencies and call this the minimum allele frequency.
Eleven SNPs which mark the HMIP-2 block define two complementary haplotypes in European expatriates (Figure 1A); each SNP's minimum allele frequency (MAF) is approximately 30% in this population of European descent (Table 1).
The SNPs were included only if they met the following criteria; call rate >90%, minimum allele frequency >5%, and did not have extreme Hardy Weinberg (HWE) χ2 values (>600).
