Table 1.
Summary of population genetics parameters in the Korean potato germplasm panel with different single nucleotide polymorphism calling methods.
| Parameter | Range | Value | Type of genotype call software used |
|---|---|---|---|
| Minor allele frequency (MAF) | Mean | 0.28 | diploid genotype calls |
| Lower | 0.05 | snpReady R package | |
| Upper | 0.50 | ||
| Mean | 0.27 | dosage genotype calls | |
| Lower | 0.05 | adegenet R package | |
| Upper | 0.50 | ||
| Polymorphic information content (PIC) | Mean | 0.30 | diploid genotype calls |
| Lower | 0.08 | snpReady R package | |
| Upper | 0.38 | ||
| Informativeness | Mean | 0.64 | dosage genotype calls |
| Lower | 0.01 | this study | |
| Upper | 0.87 | ||
| Ho (observed heterozygosity) | Mean | 0.51 | diploid genotype calls |
| Lower | 0.31 | snpReady R package | |
| Upper | 0.74 | ||
| Mean | 0.63 | dosage genotype calls | |
| Lower | 0.42 | percent heterozygosity | |
| Upper | 0.79 | ||
| Average distances between clones in the same cluster | Namjak group | 0.32 | dosage genotype calls |
| Daeseo group | 0.37 | STRUCTURE2.3.4 | |
| Sumi group | 0.32 | ||
| Mean fixation index (FST) | Namjak group | 0.13 | dosage genotype calls |
| Daeseo group | 0.07 | STRUCTURE2.3.4 | |
| Sumi group | 0.18 | ||
| TajimaD | 3.37 | diploid genotype calls | |
| TASSEL | |||
| 4.04 | dosage calls converted to diploid calls | ||
| TASSEL |