PMC:4502369 / 10993-11734 JSONTXT

{"project":"2_test","denotations":[{"id":"25917919-21478889-43377640","span":{"begin":161,"end":165},"obj":"21478889"},{"id":"25917919-20644199-43377641","span":{"begin":182,"end":186},"obj":"20644199"}],"text":"Gene variant detection\nFor identification of polymorphisms in the Finnish Large White transcriptome, we used the Genome Analysis Toolkit (GATK) (Depristo et al. 2011; McKenna et al. 2010; van der Auwera et al. 2013) program and SNP and Variation Suite v7 (Golden Helix, Inc., Bozeman, MT; www.goldenhelix.com) for filtering and annotation of the identified variants. The data were filtered based on the read depth (\u003e5), genotype quality (\u003e20), and quality score (\u003e80). The possible effect of amino acid substitutions on protein function was analyzed using SIFT (http://www.ensembl.org/Tools/VEP), and the effect on the secondary structure of the protein was analyzed using the CFSSP (http://www.biogem.org/tool/chou-fasman/) prediction tool."}