Additional file 1 of Estimating mutation rate and characterising single nucleotide de novo mutations in pigs

Additional file 1: Table S1. Concordance of heterozygous genotype calls. Summarizes the concordance between genotype calls from the SNPchip and the WGS dataset per trio. Table S2. SNPs overlapping with 50K – pre and post filtering. SNPs in whole genome sequence data overlapping with the 50K SNP Chip before and after filtering criteria for the trios. Table S3. All 704 detected de novo mutations. All DNM detected including their physical position, line, read frequency, pCADD score, VEP, gene annotation, validation and the surrounding 200 base pairs. Table S4. Validation of the DNM. Validation of the DNM using the PlexSeq™ genotyping platform (Agriplex Genomics). Table S5. Summarizing table of DNM results per trio. Table summarizes the DNM results per trio, including the trio number, line number, number of sequenced offspring/half-sibs/full-sibs available, sample type, number of detected DNM, number of validated DNM, SNPs that meet filtering criteria, estimated DNM rate per trio. Table S6. The 42 DNM found in sequenced key boars. The 42 DNM found in sequenced key boars.