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Table 7 Annotation of confirmed deletions and DNA signatures at breakpoints

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

Breakpoints Gene Exons Repeats Signatures
4_43663736-43663781 ENSGALG00000010719 ENSGALE00000116074   MH
2_46860428-46860509 ENSGALG00000012116    
10_1627991-1628223 ENSGALG00000001729   trf1 MH
7_28561048-28561407 ENSGALG00000011699   dust  
1_44948882-44949390    dust  
3_110574268-110574832 ENSGALG00000016679   CR1-F0, Z-REP, trf, dust  
1_188914114-188915200    dust, trf  
2_55356006-55357163 ENSGALG00000012402   dust, trf  
4_23256240-23257477 ENSGALG00000020249   dust, trf  
2_112569238-112574924    CR1-Y4, dust, trf  
1_61836457_61844398 ENSGALG00000012956   CR1-D2, Mariner1, GG, dust MH
  1. 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.