Functional SNP panel for parentage assessment and assignment in worldwide goat breeds

Table 1 Performance of the 195-SNP panel on the cleaned dataset using the full 195-SNP panel (left column) and using the panel without the SNPs on the sex chromosomes (right column)

	Performances including the sex chromosome markers	Performances excluding the sex chromosome markers
Pair number
Related pairs	802	802
Unrelated pairs	7,551,639	7,551,639
Total number of pairs	7,552,441	7,552,441
Assignment
True positive (a)	628	798
False negative (b)	174	4
False positive (c)	2	4
True negative (d)	7,551,637	7,551,635
Diagnostic parameter
Sensitivity	78.30%	99.50%
Specificity	100.00%	100.00%
Positive predictive value	99.68%	99.50%
Negative predictive value	2.30408E−05	0.999999735
Accuracy	0.999976696	0.999999204

The inclusion of X-linked markers in the direct assignment led to the exclusion of a large number of related pairs, whereas several are correctly assigned using the autosomal SNPs. This is because almost all these pairs involve a male-male comparison, highlighting how these SNPs cannot be used to perform a proper hemizygous evaluation, and is consistent with the higher Pe values found for the SNPs on the sex chromosomes

ISSN: 1297-9686