Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation

Table 2 GBS calls relative to Sequenom MassARRAY genotypes^a

^aThe 13 single-nucleotide polymorphisms (SNPs) examined were initially detected in a selective-primer dataset. Only 9 of these 13 SNPs could be retrieved in the corresponding conventional-primer dataset. Variants in these datasets were kept if they qualified based on a read depth ≥ 5, a genotype quality score ≥ 20, no more than one alternative allele, a call rate > 0.2, and a minor allele frequency ≥ 0.025. Chr: chromosome; Ref: reference allele; Alt: alternate allele; MM: homozygous for the reference allele; Mm: heterozygous; mm: homozygous for the alternate allele
^bThe reliability of SNP prediction was based on the reference calls predicted using the Sequenom MassARRAY technology. Discordant SNP reports call conflict by GBS

ISSN: 2730-6844