After the filtering steps, a total of 29,973 variants were identified in the dataset, of which 10,704 were known coding variants (Table 2). These included 1672 nonsynonymous variants, 8 additional stop codons, a loss of 7 stop codons, 3436 unknown variants, and 1194 splicing variants. However, some of the splicing variants arise from mapping errors and therefore require confirmation prior to use in further experiments. Two of the stop loss variations have been previously reported, but 13 appear to be novel (Table 3). After detailed analysis, the variation within MCL1 appears to be an annotation and splicing error. Based on the comparison of the predicted protein sequence translated from our expressed sequences (Figure S3A), the pig MCL1 protein sequence (ENSSSCP00000007094), and human MCL1 protein (ENSP00000358022), the annotation of the pig MCL1 is incomplete and the protein prediction is incorrect (Figure S3B). Furthermore, mapping of the region around the SNRPD3 variation contained a high number of mismatches and unknown bases, and the fact that SNRPD3 is a splicesomal gene diminishes the reliability of this variation. The functional annotation of the rest of the genes containing a stopgain variation revealed several reproduction-related genes. DAZAP1 is expressed most abundantly in the testis, but it does appear necessary for normal growth and development in mice (Hsu et al. 2008). Depletion of DAZAP1 causes male and female sterility, underlining its importance in reproduction. Recent studies in mice have also shown the importance of PPRC1 for early embryonic development (He et al. 2012). Homozygous deficient PPRC1 mice fail to form egg cylinders and die before embryonic day 6.5 (He et al. 2012). CETN2 is a calcium-binding protein and a structural component of the centrosome. In human cells, Centrin 2 depletion results in reduction in ciliogenesis (Graser et al. 2007), which implicates an effect on sperm tail formation and female reproduction through oviduct cilia. Other stopgain variations were found in UNC45, which has a role in HSP90-mediated myosin motor domain folding (Liu, Srikakulam and Winkelmann 2008), and therefore may have an impact on meat quality in pigs. P2RX4 has a role in the response of endothelial cells to changes in blood flow (Yamamoto et al. 2006), and ERCC8 is required for DNA repair (Henning et al. 1995). Mutations within ERCC8 have been shown to cause Cockayne syndrome (Bertola et al. 2006; Cao et al. 2004; Henning et al. 1995; Ridley et al. 2005), which is characterized by growth failure, impaired development of the nervous system, photosensitivity, and premature aging (Knoch et al. 2012). However, understanding the influence of these polymorphisms on phenotype requires further investigation. None of the stopgain variations had the homozygous genotype for the mutated allele, but the stoploss variations allowed homozygosity (Table S6). Thus, the phenotypic effect of these variations is clearly less dramatic.