Correlation between allele frequency estimates.

<p>Scatter plot matrices between ‘sample replicates’ from the variety Beatrice of the frequency of the variant allele at 1000 randomly selected SNP positions from each of three groupings (a) SNPs with coverage between 5 and 10X in all samples, (b) SNPs with coverage between 10 and 20X in all samples, and (c) SNPs with coverage greater than 20X in all samples. The x and y axis show the frequency of the variant allele. Least squares regression line is shown by solid green line, and Loess smooth is shown by broken red line.