Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

Table 7 Annotation of confirmed deletions and DNA signatures at breakpoints

Deletions were annotated based on their mapping position on the chicken genome and deleted sequences were analyzed for common and more chicken-specific repeats. trf = repeats identified by Tandem Repeat Finder [37]; dust = simple repeats identified by the DUST algorithm [38]; CR1, = chicken repeat 1 [36]; Z-REP = macrosatellite family on chicken chromosome Z [39]; GG = repeats on the chicken genome identified by RECON [40]. We also analyzed the DNA sequence at SV breakpoints for signatures indicating the mechanism by which the SVs are formed, and we identified microhomology (MH) in some cases.

ISSN: 1471-2164