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Fig. 2 | BMC Genomics

Fig. 2

From: Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data

Fig. 2

Genome-wide detection and distribution of variants from GEM mice. a Interleaved bar graph showing the percentage of novel (black bars) and existing (grey bars) variants characterized by the variant effect predictor (VEP) in each KO. The total number of variants is depicted above each bar. b Percentage of frameshift variants (red), missense variants (green) and other variants (grey) characterized in every KO. c The ratio between homozygous (black) and heterozygous variants (grey) expressed as percentages in every KO. d Histogram of 129P2OlaHsd private variants per chromosome in Sall2 WT and null embryos. We binned the genomic coordinates of each chromosome every 10 million bases and plotted the variants of each genotype as frequency histograms according to these positions. Blue bars represent variants from one WT embryo and red bars represent the average variants from three Sall2-null embryos. e Sashimi plots from three biological replicates of WT and KO RNA sequencing samples from Hnrnpd KO. Per-base expression is plotted on the y-axis of Sashimi plot; genomic coordinates on the x-axis, and the gene structure are represented on the bottom (in blue, obtained from the USCS server). We obtained the genotypes of the Casp4 gene from each replicate with Freebayes based on at least one SNP call. We highlighted the expression of exon 7 in a black rectangle to denote its absence in Casp4 null samples

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