<p>The whole chromosomes (All chr), chromosome 10 (Chr10), a 1 Mb fragment of chromosome 10 (Chr10-1M: positions 1000001 to 2000000 of Chr10) from the simulated rice genome were aligned with 75-bp paired-end reads sequenced from the whole rice genome using BWA. The alignments were filtered (+, bars in dark- and middle-red and in dark- and middle-blue) or not filtered (–, bars in light red and in light blue) with Coval-Refine in the basic mode. Two different filtering conditions of Coval-Refine for mismatch reads were applied; one is the default option for removing reads with three or more mismatches (middle-red and middle-blue bars), the other removing the second paired-end mate read when the first mate is filtered and removing a read pair that contained more than two total mismatches (dark red and dark blue bars). The mean coverage of read depth before and after (indicated with parentheses) the Coval-Refine treatment is indicated under the reference chromosome name. Homozygous SNPs and indels were called as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075402#pone-0075402-g001" target="_blank">Figure 1</a>. TPR and FPR for the called SNPs are shown with red and blue bars, respectively.</p
