Table 4.

Summary of the allelic variation observed in the putative Rdm locus region

Region		Modification	SNPs	InDels
Non-Coding		Intergenic region	143	14
		Upstream 5 k	2537	683
		Downstream 5 k	695	204
Coding	UTR	5′ UTR	88	23
		5′ UTR premature start gained	8	–
		3′ UTR	151	46
	Intron	Intron	399	96
		Splice region	19	2
		Splice acceptor site	2	–
		Splice donor site	1	–
	Exon	Disruptive + In-frame Deletion	–	3
		Disruptive + In-frame Insertion	–	2
		Frameshift	–	23
		In-frame Deletion	–	5
		In-frame Insertion	–	4
		Nonsynonymous modification	248	–
		Start lost	1	–
		Stop retained	1	–
		Stop gained	5	–
		Synonymous modification	142	–
Total			4440	1105

Intergenic region: the variant is in an intergenic region; Upstream 5 k: SNPs detected up to 5 kb upstream of the coding region; Downstream 5 k: SNPs detected up to 5 kb downstream of the coding region; 5′ UTR: hits in the 5’UTR; 5′ UTR premature start gained: a variant in the 5’UTR produces a three-base sequence that can be a START codon; 3′ UTR: variant hits in the 3’UTR; Intron: SNPs detected within an intron; Splice region: a sequence variant in which a change has occurred within the region of the splice site, either within 1–3 bases of the exon or 3–8 bases of the intron; Splice acceptor site: the variant hits a splice acceptor site; Disruptive + In-frame Deletion: one codon is changed, and one or more codons are deleted; Disruptive + In-frame Insertion: one codon is changed, and one or many codons are inserted; Frameshift: insertion or deletion causes a frameshift; In-frame Deletion: one or many codons are deleted; In-frame Insertion: one or many codons are inserted; Start lost: variant causes start codon to be mutated into a nonstart codon; Stop G: variant causes a STOP codon; Nonsynonymous modification: SNP variants cause a codon that produces a different amino acid; within the coding region; Synonymous modification: variant causes a codon that produces the same amino acid