Table 1.
Classification of SNPs in the 580K SNP Chip after genotyping on 4720 accessions.
| SNP category | Japonica-specific SNPs | Japonica-specific indels | Indica-specific SNPs | Indica-specific indels |
|---|---|---|---|---|
| NoMinorHom | 45,021 | 8,673 | 3,211 | 1,254 |
| MonoHighResolution | 26,363 | 6,202 | 860 | 424 |
| PolyHighResolution | 284,998 | 7,735 | 6,342 | 2,590 |
| CallRateBelowThreshold | 2,196 | 107 | 314 | 216 |
| OTV | 73,259 | 8,783 | 2,040 | 1,148 |
| Other | 68,888 | 6,758 | 10,053 | 5,824 |
| Total | 500,725 | 38,258 | 22,820 | 11,456 |
NoMinorHom: No minor homozygote, MonoHighResolution: Monomorphic high-resolution,
PolyHighResolution: Polymorphic high-resolution, CallRateBelowThreshold: Call rate below threshold, OTV: Off-target variant.