Table 4.
SNP analysis of GenSeq reads
| Chromosome | Number of SNPs | Number of GenSeq genes with SNP | ||
|---|---|---|---|---|
| Bulks | Parents VER54 (R/R) Ver3939 (S/S) |
In bulks and parents | ||
| 1 | 5 | 252 | 0 | 0 |
| 2 | 6 | 367 | 1 | 1 |
| 3 | 7 | 483 | 0 | 0 |
| 4 | 6 | 239 | 0 | 0 |
| 5 | 4 | 358 | 1 | 1 |
| 6 | 3 | 415 | 0 | 0 |
| 7 | 6 | 588 | 0 | 0 |
| 8 | 5 | 317 | 0 | 0 |
| 9 | 52 | 204 | 36 | 20 |
| 10 | 6 | 409 | 0 | 0 |
| 11 | 2 | 462 | 0 | 0 |
| 12 | 1 | 191 | 0 | 0 |
| 0 | 5 | 37 | 0 | 0 |
| Total | 108 | 4322 | 38 | 22 |
The number of filtered SNPs identified from VarScan that conform to the expected SNP ratio for the bulks, parents and both is shown. The SNPs and the underlying COS and low-copy number genes are organised by potato chromosomes 1–12 and currently unknown positions (chromosome 0)