Quantitative analysis of low-density SNP data for parentage assignment and estimation of family contributions to pooled samples

Table 1 Estimated counts of G10 offspring for which both sire and dam, only sire or only dam, or neither parent appeared to be present, depending on the method for parentage assignment used

Counts are for the quantitative genotype method and perturbed genotype maximum likelihood method using either an estimated error ( $\hat{ε}$ ) or an assumed error ( $\tilde{ε}$ ), and exclusion with a threshold of either zero or three mismatches. For sire+dam, the trio LOD is greater than 0, the sire LOD and the dam LOD. For sire+missing, the sire LOD is greater than both 0 and the trio LOD, and the dam LOD is less than the trio LOD or less than 0. For dam+missing, the dam LOD is greater than both 0 and the trio LOD, and the sire LOD is less than the trio LOD or less than 0. For (sire or dam)+missing, the sire LOD and dam LOD are both greater than 0, and both greater than the trio LOD. If all LOD scores are less than 0, it is assumed that genotypes for both parents are missing. Equivalent conditions are applied for the exclusion method.

ISSN: 1297-9686