A visual examination of a spurious gene (<i>CDC27</i>).

<p>The top panels show visualization of read alignment in good (a) and bad (b) conditions using the software IGV <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038470#pone.0038470-Robinson1" target="_blank">[29]</a>. The top part of each figure shows the coverage. Each grey bar represents one read, with the color grey indicating it is matched well with the reference and other colors indicating mismatches. Panel (c) shows the distribution of mapping quality (MAPQ) of all the reads in a representative sample. MAPQ is defined as -10×log₁₀<i>Pr(mapping position is wrong)</i>, rounded to the nearest integer. As shown on the x-axis in (c), MAPQ ranges between 0 and 60 in this sample, with 60 indicating the best mapping. Y-axis in (c) is the number of reads in this sample. Panel (d) shows the distribution of MAPQ of all the reads in a sample and the reads mapped to <i>CDC27</i> exon regions. Y-axis in (d) is the proportion of reads in each MAPQ range (x-axis).