Table 2. The number of SNP positions from the reference panel that was identified in the pooled data set, which could be genotyped in at least 75 percent of individual samples with increasing minimum coverage thresholds.
| Enzyme | No. SNPs predicted at MAF 5%a | Coverage | SNPs genotyped in 75% of samplesb |
| 5X | 18,100 | ||
| 10X | 14,527 | ||
| PstI | 40,621 | 15X | 12,424 |
| 20X | 10,870 | ||
| 25X | 9,593 | ||
| 50X | 5,939 | ||
| 5X | 80,902 | ||
| 10X | 27,067 | ||
| ApeKI | 643,798 | 15X | 12,380 |
| 20X | 7,328 | ||
| 25X | 5,168 | ||
| 50X | 1,975 |
a
Reference SNP panel identified with a MAF of 5 percent in data pooled from equal numbers of reads of all eight varieties.
b
32 samples for ApeKI libraries, and 29 for PstI libraries (three samples were removed due to very low sequencing coverage).