The Journal of Genomes and Exomes is a new, peer-reviewed, open-access, online publication whose scope comprises reporting of high quality genome, exome, and gene panel sequences with attendant, detailed phenotypes. The intent of this journal is to facilitate comparisons between genome, exome and gene panel sequencing studies in order to assist significance testing of the genotype-phenotype associations, particularly those in uncommon genetic diseases. While there is yet to be a consensus regarding these classifications, the definition of an empiric set is helpful in understanding error models. Herein we have suggested structured templates for submissions and the rationale for the data fields in these templates, as well as examples. The editorial board of the Journal of Genomes and Exomes is keen to receive feedback regarding these structured templates and welcomes submissions.