These differences were not considered as multiple candidate SNP loci even if the sequence met our quality standard.
In the case of SNPs with multiple candidate best genetic models, the one with the smallest p value derived from the univariate Cox regression analysis was deemed to be the best genetic model [ 13].
Vrabec et al 77 reported a study of a series of SNPs in multiple candidate genes based on a suspected role in MD pathogenesis among patients with MD and selected control individuals.
Third, ESTs from multiple strains permits identification of ~3,400 candidate SNPs [ 14], which have now been validated through additional genome sequencing data that became available in the course of the present study.
The candidate SNPs positive after these stringent multiple testing corrections (22/358 after Bonferroni and 104/358 after Benjamini & Hochberg, n = 10,514) are highlighted in Additional file 1.
The large number of candidate SNPs in these regions identified in multiple analyses indicate these two regions may harbor variants that are locally adaptive, with selection altering the frequency of nearby SNPs through genetic hitchhiking (Nielsen et al. 2005).
GWAS Analyzer served as a valuable tool for managing large amounts of phenotype and PLINK data, integrating and filtering results from multiple PLINK analyses, and performing follow-up research on candidate SNPs.
Sixty-six of the candidate SNPs we identified were seen in multiple fish; these could be orthologous intraspecific polymorphisms (useful for population genetic analyses) or intragenomic polymorphisms due to gene duplications (useful for reconstructing gene trees).
For genes, where multiple SNPs showed P-values <0.05 in the discovery phase, candidate SNPs for follow-up were tested for independence of their association signal in relation to the most strongly associated SNP in each gene (Supplementary Table S4).
Tools such as SNPper (Riva and Kohane, 2002) and SNP Function Portal (Wang et al., 2006) facilitate follow-up research of candidate SNPs and related genes by integrating SNP annotations from multiple public resources.
