Fig. 2: The characteristics of human variants with cattle orthologues.
From: The conservation of human functional variants and their effects across livestock species
The association of 1,395,750 human variants with different genomic features is shown (697,875 human variants with orthologues in cattle and an equally sized random sample of 697,875 human variants without known orthologues in cattle). a Number of variants with or without orthologues by their observed allele changes (reference > alternative). The data underlying this plot can be found in Supplementary Data 2. b Number of SNPs with different 5-mer flanking sequences among variants with or without orthologues. Each circle represents a 5-mer flanking sequence with a specific base at a certain position, and the circle color indicates whether the specific base is C/G or A/T. The black dashed line represents parity, i.e., where the number of SNPs with orthologues equals the number of SNPs without known orthologues. All the 5-mer sequences are significantly different between the groups at a P-value less than 2.2 × 10-16 (Chi-Squared test). c Density plots of distances of variants with or without orthologues to processed pseudogenes and snoRNAs (plot restricted to within 10 kb). Distances of variants to processed pseudogenes and snoRNAs are different between groups at P-values less than 3.2 × 10-5 (Two-sample Kolmogorov-Smirnov test). d Density plot of distance between variants with or without orthologues to chromatin regions marked by H3K9ac in the human H9 cell line (plot restricted to within 10 kb). Distance to these regions is different between groups at P-value less than 1.8 × 10-3 (Two-sample Kolmogorov-Smirnov test). The data underlying this plot can be downloaded from https://doi.org/10.6084/m9.figshare.20401851.
