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Second, variants with low MAF are on average highly correlated with multiple SNPs throughout the genome.
Meaningful second variants may not have been identified because they were large indels or located in an untranslated region.
Second, variants in the same gene regulatory element (e.g. enhancers, insulators, silencers and non-coding RNAs) would be physically clustered in the DNA sequence (Raab and Kamakaka, 2010).
Second, variants were called with the Nesoni high-throughput sequencing data analysis toolkit (http://www.vicbioinformatics.com/software.nesoni.shtml, last accessed November 19, 2013), using SHRiMP (David et al. 2011) as the aligner and Freebayes as the caller.
Second, variants were not forwarded to the next step if (i) more than 5% of reads had mapping quality 0, (ii) coverage was more than six fold higher compared to the mean coverage, or (iii) a SNP quality score was below 100.
Variants, which belonged to any other class without inbred correction, but changed to PHR after inbred correction received a weight of 5, and all remaining variants not fulfilling the previous criteria obtained a weight of 0. Second, variants were weighted regarding the concordance of their calls with the in silico variant calls from sequencing.
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