Frequency of missing genotypes in Nelore cattle in a total of 1,709 samples tested with the Illumina Bovine HD.

<p>Frequency of missing genotypes in Nelore cattle in a total of 1,709 samples tested with the Illumina Bovine HD.</p

Distribution of SFNBs across bovine chromosomes.

<p>Distribution of SFNBs across bovine chromosomes.</p

Number of non-redundant SFNBs in regions flanking SNPs assayed in the Illumina Bovine HD panel (see S1 Table).

<p>Number of non-redundant SFNBs in regions flanking SNPs assayed in the Illumina Bovine HD panel (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136035#pone.0136035.s001" target="_blank">S1 Table</a>).</p

IGV screenshot image.

<p>The double vertical lines indicate the BovineHD0500032585 SNP position. Colored positions indicate flanking SNPs. There are 6 non-synonymous SNPs and 1 synonymous SNP (4^th column from left).</p

Mean frequency and standard deviation of the nearest Nelore SNPs within 50bp and 100bp size bins.

<p>Mean frequency and standard deviation of the nearest Nelore SNPs within 50bp and 100bp size bins.</p

Functional characterization of 3,183 SNP markers derived from the Illumina Bovine HD panel that consistently generated missing genotypes in the Nelore breed (SFNBs).

<p>Functional characterization of 3,183 SNP markers derived from the Illumina Bovine HD panel that consistently generated missing genotypes in the Nelore breed (SFNBs).</p

Detailed information for 32 SNPs located within coding regions flanking SFNBs which resulted in non-synonymous substitutions.

<p>An extreme case of non-synonymous mutations in gene EP300. Large numbers of olfactory receptor genes were found to contain SNPs that result in non-synonymous substitutions.</p

Functional characterization of 8,837 SNPs and INDELs identified within 100bp regions flanking SNPs assayed in the HD panel.

<p>Functional characterization of 8,837 SNPs and INDELs identified within 100bp regions flanking SNPs assayed in the HD panel.</p

GO annotation of biological processes affected by genes that were identified by SFNBs from the Illumina Bovine HD panel.

<p>GO annotation of biological processes affected by genes that were identified by SFNBs from the Illumina Bovine HD panel.</p

Regions defined for obtaining estimates of genomic variation.

<p>P1 represents the 50bp Illumina probe target sequence. P2 corresponds to the 50bp adjacent to P1 on the distal side of the assayed SNP. S1 and S2 are symmetrical to P1 and P2, respectively.</p