Fig. 4From: Sequence imputation from low density single nucleotide polymorphism panel in a black poplar breeding populationPrincipal Component Analysis of Factors affecting SNP imputation. a Principal Component Analysis factor map of factors calculated at SNP level: Props: proportion of SNPs correctly imputed; cProps: proportion of SNPs correctly imputed and corrected by the minor allele frequency; lbProps: lower bound proportion of SNPs correctly imputed based only on allelic frequency; hweOri: p-value of a Hardy-Weinberg Equilibrium test for each site [47]; Weight: LD weight estimate obtained with the LDAK5 software; FreqOri: original allelic frequency in the sequenced individuals; QUAL: per-site SNP quality from the calling step; DEPTH: sequencing depth per site summed across all individuals ; RatioDensity: ratio between SNPchip density and SNPseq density in a 500kb window. b Correlations between parameters calculated at SNP level and dimension of the ACP from Fig. 3aBack to article page