Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

Table 2 Details of the bi-allelic RAD loci and filtered putative SNPs and PSVs in Family 1 and Family 2

	Family 1	Family 2	Common^a	Total
Total bi-allelic RAD loci	10,238	10,930	6,668	14,500
Bi-allelic RAD loci removed during filtering^b	2,109	3,804	797	5,116
Remaining bi-allelic RAD loci	8,130	7,127	5,871	9,386
Bi-allelic RAD loci with both alleles fixed	3,768	3,491	2,674	4,585
Segregating bi-allelic RAD loci	4,362	3,636	3,197	4,801
Putative SNPs	4,725	3,927	1,940	6,712

^a Common refers to loci where at least one of the RAD alleles at a RAD marker in family 1 matches exactly to one of the RAD alleles at a RAD marker in family 2. In the case of putative SNPs, common refers to the same SNP segregating in both families at the same position in the RAD marker sequence.
^b Filtering criteria given in the ‘Methods’.

ISSN: 1471-2164