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Table 2 Annotation of the accession-specific single nucleotide polymorphisms (SNPs) that were identified from the B. rapa core collection

From: Identification of accession-specific variants and development of KASP markers for assessing the genetic makeup of Brassica rapa seeds

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: 5 K bases) Non-coding 459 0
The variant is in an intergenic region Non-coding 119 0
Upstream of a gene (default length: 5 K bases) Non-coding 1549 6
Total - 2,925 100