Table 2 Annotation of the accession-specific single nucleotide polymorphisms (SNPs) that were identified from the B. rapa core collection
Annotation of variants | Type | Accession-specific SNPs (No.) | KASP markers (No.) |
|---|---|---|---|
Variant causes a codon that produces a different amino acid | Exon | 456 | 72 |
Variant causes a codon that produces the same amino acid | Exon | 189 | 18 |
Variant causes a STOP codon | Exon | 17 | 2 |
Variant causes start codon to be mutated into a non-start codon | Exon | 1 | 0 |
Variant causes stop codon to be mutated into a non-stop codon | Exon | 1 | 0 |
Variant causes stop codon to be mutated into another stop codon | Exon | 3 | 1 |
The variant hits a splice acceptor site | Intron | 5 | 0 |
The variant hits a Splice donor site | Intron | 4 | 0 |
Variant hits intron | Intron | 122 | 1 |
Downstream of a gene (default length: 5Â K bases) | Non-coding | 459 | 0 |
The variant is in an intergenic region | Non-coding | 119 | 0 |
Upstream of a gene (default length: 5Â K bases) | Non-coding | 1549 | 6 |
Total | - | 2,925 | 100 |