Coloboma.003 SNPs, micro-indels, and sequence gaps identified in the various linked regions using CA/NGS technology: Number and genomic location.

A<p>The original number of variants identified after bioinformatics analyses, prior to multiple pairwise-line comparisons to identify unique variants.</p>B<p>Unique variants are those specific to Co.003 only after multiple pairwise-line genomic comparisons. See Methods for details as to unique variant identification. Note: Shared variants were ruled out as causative towards the <i>coloboma</i> mutation and submitted to NCBI (Accession No. ss472340674–ss472343089).</p>C<p>CR = causative region. 990,268 bp is the CR identified by the 60<b> </b>K SNP array, which was subsequently utilized for capture array probe creation. 299,860 bp is the size of the CR identified after CA/NGS bioinformatic analysis and further fine-mapping of sample co-275F. 175,915 bp is the CR identified by fine-mapping analysis of recombinant individuals (note that this fine-mapping analysis was ongoing, post-CA/NGS.).</p>D<p>Insertions and deletions range from 1 to 3 nt in length (within the paper referred to as micro-indels).</p>E<p>Gaps (≥4 nt DNA which was not captured for sequencing in the CA/NGS) were identified by alignment to the 990,267 nt RJF reference genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060267#pone.0060267-Bellott1" target="_blank">[61]</a>. Gaps listed are those found to both be unique to Co.003 as well as those shared across all three mutant congenic lines. Although a gap might be present in all three lines, the missing DNA fragment could contain sequence variation compared to the control.