SNP discovery using PolyBayes was performed using 810 k EST sequences generated by the Danish-Chinese Pig Genome Sequencing Initiative. While focusing only on high-quality SNP prediction disregards potentially interesting medium-quality SNPs as candidates we show that, by careful inspection of chromatograms, more than 61% of the bi-allelic candidates were valid and not predicted due to sequencing artifacts. Exemplarily, selected candidate SNPs were genotyped on a breed panel and average minor allele frequencies were calculated to show that candidates derived from medium-quality SNP predictions represent an additional resource for SNP maps or genome-wide QTL scans. Additionally, medium-quality SNPs were compared to the Pig EST Data Explorer database as an independent dataset.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 23.20, 2006
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