Fig. 3

Dissection of variants linked to targeted genes: the congenic footprint. a A pipeline for the detection of KO-linked variants based on intersected VCF files per genotype as input. We ignored header lines from the inputted VCF file (Filter and Sort program, skipping header lines starting with #). We performed genotype annotation with the VCFAnnotateGenotypes program on null VCF files using the WT counterpart. After selecting lines that not match “Added-genotypes”, we obtained an output with KO-linked variants. b To obtain KO-linked genes from variants in (A), we assessed annotation of variants per genotype with the variant effect predictor program from Ensembl (VEP) and then subtracted KO-linked genes with the aid of Venn diagrams. c Histogram of KO-linked variants for the Gtf2ird1 KO. We binned the genomic coordinates of each chromosome every 10 million bases, and then plotted the variants as frequency histograms according to these positions. The number of congenic genes encompassing these variants is indicated. d The same histogram as in (C) for Mecp2 KO located in Chr X. e The same histogram as in (C) for Sall2 KO located on Chr 14. f The same histogram as in (C) for Stc1 KO located on Chr 14. g The same histogram as in (C) for Itch KO located on Chr 2. This KO presents four chromosomes with KO-linked variants (Chr 2, 9, 10 and 16). The total number of congenic genes encompassing these variants is indicated. h Predicted number of backcrossings with C57BL/6J mice per model. Genomic range of KO-linked variants per model were calculated with the pipeline and translated to centimorgans (cM) with the mouse map converter service (http://cgd.jax.org/mousemapconverter/) according to previously published studies [53, 54]. The extension of KO-linked variants per model in cM is depicted in red