Fig. 4

Ploidy of congenic footprint. a Histogram of KO-linked variants for Sall2 KO distinguishing homozygous (red bars) from heterozygous (blue bars) variants. We binned the genomic coordinates of each chromosome every 10 million bases and plotted the variants with each ploidy as frequency histograms according to these positions. b Cartoon depicting the congenic footprinting of each embryo in the Sall2 KO, located on Chr 14. We represented each ploidy with a distinct color (homozygous segment in red, heterozygous segment in blue), marking chromosomal positions above the bars. We performed genotype annotation of KO-linked variants using heterozygous variants from a Sall2 heterozygous littermate. c Histogram of homozygous (red bars) and heterozygous (blue bars) variants from a Sall2 heterozygous embryo on Chr 14. Variants occurring in the WT embryo were previously subtracted from the heterozygous variants. We plotted the variants with each ploidy as in the graph in (A). d Histogram of annotated variants from (A) with heterozygous variants from (B). We plotted the annotated variants as in the graph in (A). e Venn diagram comparing the early prediction of congenic genes for the Sall2 KO (Table S6 in Additional file 5) with annotated variants from (D) showing the overlap. The diagram shows numbers of variants with their corresponding percentages. f Histogram of KO-linked variants for the Stc1 KO differentiating homozygous (red bars) from heterozygous (blue bars) variants. We plotted the variants with each ploidy as in the graph in (A). g Histogram of KO-linked homozygous variants per littermate in the Stc1 KO. We plotted variants from each embryo with a distinct color (KO1 = red, KO2 = blue, KO3 = green). We plotted the variants of each embryo as in the graph in (A). h Histogram of KO-linked heterozygous variants per littermate in the Stc1 KO. We plotted the variants of each embryo as in the graph in (A). i Cartoon depicting the congenic footprinting of each littermate in the Stc1 KO located on Chr 14. We represented each ploidy with a distinct color (homozygous segment in red, heterozygous segment in blue). Chromosomal positions are indicated