Table 2.

GBS calls relative to Sequenom MassARRAY genotypes^a

Conventional-primer method
				Concordant			Discordant			Concordance (%)b
Chr	Position	Ref	Alt	MMb	Mmb	mmb	MM	Mm	mm
5	124968560	C	T	0	11	5	0	0	0
6	120556623	T	C	1	8	0	0	0	0
7	25377202	A	G	0	2	1	0	0	0
12	81073590	G	T	5	4	0	0	0	0
17	4536929	G	A	2	8	0	0	0	0
18	11257808	A	G	2	8	0	0	0	0
18	63490716	C	T	6	17	0	0	0	0
23	18485367	C	G	2	8	0	0	0	0
28	1121069	G	T	5	5	0	0	0	0
		Total		23	71	6	0	0	0	100.0
Selective-primer method
5	124968560	C	T	3	13	16	0	9	0
6	120556623	T	C	10	22	12	0	2	0
7	25377202	A	G	5	17	19	0	1	1
11	6123151	T	C	18	13	3	0	8	0
12	81073590	G	T	19	11	3	0	7	0
17	4536929	G	A	11	11	12	0	9	0
18	11257808	A	G	20	16	6	0	3	0
18	63490716	C	T	17	13	4	0	7	0
23	18485367	C	G	18	13	2	0	4	0
24	26394985	G	T	18	13	7	0	5	0
24	26395035	C	T	7	14	18	0	6	0
28	1121069	G	T	24	9	0	0	6	0
X	49928152	C	T	34	8	0	0	0	0
		Total		204	173	102	0	68	0	87.6

^aThe 13 single-nucleotide polymorphisms (SNPs) examined were initially detected in a selective-primer dataset. Only 9 of these 13 SNPs could be retrieved in the corresponding conventional-primer dataset. Variants in these datasets were kept if they qualified based on a read depth ≥ 5, a genotype quality score ≥ 20, no more than one alternative allele, a call rate > 0.2, and a minor allele frequency ≥ 0.025. Chr: chromosome; Ref: reference allele; Alt: alternate allele; MM: homozygous for the reference allele; Mm: heterozygous; mm: homozygous for the alternate allele

^bThe reliability of SNP prediction was based on the reference calls predicted using the Sequenom MassARRAY technology. Discordant SNP reports call conflict by GBS