Extended Data Fig. 4: Analysis of the LOH regions detected in the gynogenetic pedigree of C. gibelio.
From: Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish
a, Schematic diagram of a LOH region in diploid (left panel) or triploid (right panel). Allele 2 was deleted in a gene deletion event, whereas a gene conversion occurred from Allele 1 to Allele 2. Theoretical ratio of different types of SNPs in a LOH region is shown in the right side of each panel. b, Distribution of average depths of SNP sites in LOH regions. c, Distribution of average minor allele frequencies in LOH regions. d, Ratio distributions of the three types of SNP sites in gene conversion blocks in a 30-SNP sliding window and 1-SNP step. The line in the middle of each boxplot represents the median of the dataset; the upper and lower edges of boxplot indicate the third quartile and first quartile, respectively; and the line extending from the edge is 1.5 times the interquartile range. Small dots indicate outliers. n = 10 individuals.
