These are described in Table 2. Of these, the five SNPs typed in bold in Table 2 were selected for testing, the selection criterion being based on minor allele frequency and quality control (for details see Genomic region and marker selection, data preparation and genotyping, and Tables S2 and S3).
All values respect suggestion of Affymetrix quality control (for details see simple affy package vignettes).
We, therefore, rigorously evaluated genotyping errors and only included samples that passed our quality control (further details can be found in the supporting information).
Five more series were considered unsuitable for the meta-analysis, for individual reasons, and removed (that is, mislabeled data, high amount of missing data in all samples, multiple arrays grouped together, etcetera; see Additional file 1: Individual Study Quality Control for details of data exclusion justifications).
Phenotypes and genotype data were subjected to rigorous quality control procedures, detailed in Text S2.
After applying the CNV quality control criteria detailed in the "Methods" section, 256 samples (157 German Mutton, 35 Dorper and 64 Sunite sheep) remained for further CNV analyses.
Our quality control steps (detailed in full in the Appendix) sought to exclude suspect samples, poorly genotyped or imputed SNPs, and apparent population outliers.
Yellow perch collected in 1996/97 were pooled within lake according to size, and then wet, whole body homogenates were analyzed for THg using the methods and quality control procedures detailed in the Supporting Information.
The next step handles quality control (for full details, see Supplementary Section S2.2).
Quality control and preprocessing details can be found in the supplementary materials and methods, Supplementary Material online.
