Additional file 1: of Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data

Schematic view of the sources of genetic variation identified in KO/KI congenic mice. First, the choice of embryonic stem cells (ESCs) derived from the inbred brown mice is a major source of genetic variation, and genetic characterization of these cells could be unavailable (1). Second, the number of backcrossing with C57BL/6 (substrain N or J) will lead to variable introgression of variants from ESCs into littermates, depending on how many backcrossings were performed (2). Finally, further breeding strategies across generations will determine the final constitution of variants in WT and KO/KI littermates, including the congenic footprint (3). The N of crossings will also determine the number of novel fixed variants in animals. Mice images were designed by the authors. (TIF 338 kb