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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)

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

  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
  1. 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