Three dimensional deconvolution and our plane-wise variant reduced artifacts and enhanced the contrast, thus truly improving the resolution in the fused dataset (Fig. 1h and i; Supplementary Fig. S1).
Genomic constitution analysis of rice genotypes based on chromosome-wise physical distribution of variant SNP loci and allele sharing between indica and japonica revealed maximum introgression of japonica in chromosome 12 (average 63%) followed by chromosomes 7 (59%) and 1 (57%); chromosome 6 contained maximum introgression (68%) of indica.
A recent pair-wise analysis of variants related to the IL17-IL23 pathway showed an increasing odds ratio for CD when the 'risk' haplotypes for these genes were combined [ 45].
In a second experimental approach we have used a variant of the WISE (Whole Interactome Scanning Experiment) strategy to probe a large number of naturally occurring and chemically-synthesized peptides arrayed at high density on a glass surface.
Here, we adopt a step-wise approach and exclude one variant in each repetition.
High quality sequence alignment revealed that the size variant alleles showing step-wise distribution contained the expected microsatellite repeat sequences with conserved primer binding sites, but corresponded exactly to the step-wise multiples of the number of repeat units.
Given the fact that filtering significantly reduces the number of TP variants, it might be wise to, with the exception of pipelines using CUSHAW3 and FreeBayes, skip this step when searching for rare, high-impact variants.
Statistical methods as linear or logistic regressions measure marker wise the actual association of the genetic variants with quantitative and binary diseases and traits.
Pair-wise LD between the variants in each gene, haplotype frequencies, and haplotype tags were assessed with Haploview software version 3.32 [47].
The time to first occurrence of at least 50% reduction in CSS total score was used to hierarchically test three hypotheses (H1: HC-ac 2.5% ≥ HC-ac 0.5%, H2: HC-ac 1% ≥ HC-ac 0.5%, and H3: HC-ac 2.5% ≥ HC-ac 1%) using Kaplan-Meier statistics and comparing each of the treatment groups pair-wise with the Cox-variant of the Log-Rank test.
To elucidate interactions between group and DNA variant, t tests for specific contrasts (pair-wise differences) in the least squares means were performed.
