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Table 6 Putative functional annotations of predicted SVs

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

    Coding Repeats
aamq n % genes % within exons % exons % CR1 1 % GGLTR 2 % other 3 % TR 4 % dust 5 %! 6
35 280 43.9 0.36 5 19.6 5.3 5.0 25.0 36.1 42.9
60 186 43.0 0.54 3.8 18.8 4.3 3.2 26.9 36.6 41.9
  1. SVs of data subsets aamq 35 and aamq 60 were annotated based on their mapping location on the chicken genome. SVs were analyzed to determine whether they mapped within genes, within exons, or partially overlapped exons.
  2. 1CR1 = chicken repeat 1 [36]
  3. 2GGLTR = Gallus gallus long terminal repeat
  4. 3other = other specific repeat classes
  5. 4SVs that mapped in repetitive sequences were analyzed for signatures of common repeats in the chicken genome and scanned for tandem repeats identified by Tandem Repeat Finder [37];
  6. 5SVs that mapped in repetitive sequences were analyzed for signatures of simple repeats identified by the DUST algorithm [38];
  7. 6The fraction of SVs that mapped in intronic and intergenic regions not identified as repetitive or low complexity are given in column "%!".