Factor | cProps | lbProps | Props |
---|
| (Mean ± SD) | (Mean ± SD) | (Mean ± SD) |
---|
shadowMax
| 1.44 ± 0.93 | 1.48 ± 0.70 | 1.80 ± 1.30 |
shadowMean
| -0.05 ± 0.79 | -0.22 ± 0.52 | -0.01 ± 0.82 |
shadowMin
| -2 ± 0.53 | -2.22 ± 1.25 | -1.57 ± 0.91 |
hweOri
| 32.96 ± 1.04 | 39.84 ± 0.73 | 40.33 ± 1.99 |
QUAL
| 98.95 ± 5.12 | 67.83 ± 1.70 | 67.90 ± 1.76 |
Weight
| 131.86 ± 3.56 | 92.78 ± 4.20 | 101.57 ± 4.23 |
FreqOri
| 64.28 ± 2.19 |
110.92 ± 2.79
| 115.02 ± 3.28 |
DEPTH
| 114.21 ± 5.08 | 75.51 ± 1.67 | 114.81 ± 4.81 |
RatioDensity
|
1,182.87 ± 39.82
| 36.68 ± 1.50 |
1,351.57 ± 43.94
|
- Boruta analyses for the different explanatory factors assumed for imputation quality variables Props, cProps and lbProps. Values correspond to averaged effects and their corresponding standard deviations allowing for a ranking of importance of the factors. The maximum value is bolded. Props: proportion of SNPs correctly imputed; cProps: proportion of SNPs correctly imputed corrected by the minor allele frequency; lbProps: lower bound proportion of SNPs correctly imputed based only on the allelic frequency; hweOri: p-value of a Hardy-Weinberg Equilibrium test for each site [47] ; Weight: LD weight estimate 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. “ShadowMean”, “shadowMax” and “ShadowMin” correspond to effects obtained by shuffling the original attributes across objects and used as a reference for deciding which factors are truly important