Figure 2– Distribution of ultraconserved elements (UCEs) and their mutation impact scores (CADD scores). (A) Karyotype plot of the chicken genome with the distribution of UCEs (black bars) and density of UCEs (green peaks). (B) Karyotype plot of chicken chromosome 1 showing the distribution of UCE-dense regions. Green peaks above the 1% horizontal line are significantly enriched for UCEs (p<0.01). At the bottom of Panel B, zoomed in at a single UCE and its 2000bp flanking regions (i.e., UCE2729), the CADD scores of every possible substitution at each site. The UCE is shown in blue. The CADD scores in flanking regions are shown in red. Distribution of all CADD scores for (C) the entire chromosome 1 of the chicken genome, and (D) 620 UCEs in chromosome 1 and their 2000bp flanking regions. (E) The CADD score distribution of the flanking regions and the UCEs within the six pink pigeon genomes. (F) SNP frequency at flanking regions and the UCEs. (See main text for test results).