Analysing the outcome of CRISPR-aided genome editing in embryos: Screening, genotyping and quality control

•Genome engineering tools such as CRISPR/Cas9 generate mosaic founders.•The type of the desired mutation directs how mutagenesis outcome should be analysed.•Efficient strategies for the analysis of each of these mutant allele types are detailed.•The founder generation can be screened for the presence of the desired mutation.•Mutant genotype can only be established on germ line transmission.