Schematic diagram representing the distribution of the total population into the 3 subgroups (<i>R. equi</i> pneumonia foals [clinical], subclinical foals, and unaffected foals), and by genome-wide association studies versus PCR genotyping for TRPM2 SNP.

<p>The 3 comparisons among groups are also summarized.</p

Joint analysis of <i>TRPM2</i> SNP UKUL3936.

<p>*Median (range) reported for frequency of allele A, along with the proportion of A alleles among all alleles represented for each group. Joint analysis includes genotypes derived from SNP array and PCR genotyping.</p

CNVs identified in the each clinical group.

<p>CNVs: median (range; sum); Kruskal-Wallis test.</p

Manhattan plots of standard chi-squared significance values for the 3 genome-wide association studies.

<p>Manhattan plots for (A) comparison 1, (B) comparison 2, and (C) comparison 3; (D) Mixed effects-model analysis of comparison 3.</p

Top 5 CNV regions identified using logistic regression for the association of <i>R. equi</i> with either the binary variable presence or absence of a CNV identified in the region (Presence columns) or the log₂ ratio of intensity values of the CNVs (Intensity columns).

<p>CNVR identification numbers are provided in Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098710#pone-0098710-t001" target="_blank">Table 1</a>.</p