bThe mean effect of each significant SNP across data subsamples.
This was readily achieved using data subsampled to 25% with no appreciable loss in resolution.
For a given number of clusters, Consensus computes a certain number of clustering solutions (resampling step), each from a sample of the original data (subsampling).
The resample model inclusion probability (RMIP; [ 51]) for each SNP was computed as the frequency across the 50 data subsamples with which the SNP's association test had a p-value less than 10−5.
These two SNPs also had the highest RMIP values among SNPs across the 50 data subsamples; the chromosome 9 SNP had an association with ear rot with p-value < 10−5 in 47 of the 50 data subsamples (Table 3; Figure S1 in Additional file 1; File S6 in Additional file 1).> -wrap-foot> Alleleleffectsts are reported back-transformed to the original 0-100% disease severity scale.
Although surprising, this negative result may be due to a low precision in the estimation of allele frequencies in the temporal subsets of the data (i.e. allelic frequencies were estimated from <50 individuals in approx. 20% of the data subsamples).
RMIP values for each variant are determined based on the proportion of data subsamples in which the variant was selected in a multiple regression model at a given p-value, so RMIP values are subject to stochastic variation in the random sampling of data sets.
Metadata summaries, including details of the references, type of study, data collector, subsample numbers, sampled area, geographical feature, zone, habitat, mesh size, dates of the study and range of depth and position, are accessible before browsing data set domains.
Subsampling: investigating the effect of read depth, data were subsampled to between 10 000 and 240 million read alignments per replicate.
Firstly, a 3 × 3 Gaussian filter is used to remove spikes and noise, and then the range data are subsampled at a 1 4 ratio.
