Visual examination by read depth, whole-genome aCGH and digital aCGH around three loci for five representative chicken genomes. The uppermost gene image is generated with the UCSC Genome Browser (http://genome.ucsc.edu/) using the galGal4 assembly. The track below the gene region is depth of coverage for all five individual genomes. Red indicates regions of excess read depth (> mean +3 × STDEV), whereas gray indicates intermediate read depth (mean +2 × STDEV < × < mean +3 × STDEV), and green indicates normal read depth (mean ± 2 × STDEV). All read depth values based on 1 kb non-overlapping windows are corrected by GC content. Whole-genome aCGH and digital aCGH values are depicted as the red-green histograms and correspond to a gain colored in green (>0.5), a loss colored in red (<-0.5) and normal status colored in gray (-0.5 < × <0.5). (A) Two previously reported CNVs (chr20: 11,111,401-11,238,900 and chr20: 11,651,801-11,822,900) associated with dermal hyperpigmentation. The DX and SK genomes show two additional copies of the two regions compared with RJF, and are also validated by whole-genome aCGH. (B) A higher copy number increase for the SOCS2 locus (chr1: 44,764,280-44,765,955) is predicted in LX than in other individuals. (C) The POPDC3 gene (chr3: 68,255,196-68,259,535) is predicted to be duplicated status only in WL.