Figure 1

Conceptual diagram of sequencing reads mapping to the reference pig genome. White boxes denote an image of the pig reference genome sequence. Blue and red boxes connected with lines denote the 5′ and 3′ ends of a paired-end sequencing read. Most paired-end reads were identified as proper mapping while a small percentage of them were non-proper mapping. One end of the paired-end sequence mapped correctly while the other end was only partially identified at the expected locus on the reference genome. The unidentified sequence could be mapped anywhere else on the reference genome. For singletons, one end of the paired-end sequence mapped correctly while the other end did not map on the reference genome. For unmapped read pairs, neither read mapped to the reference genome.