BioSample

C57BL/6J (B6) is the most widely used inbred mouse strain and for that reason it was selected by the Mouse Genome Reference Consortium (MGSC) as the DNA source for the mouse reference genome . However, the origin of the DNA used to sequence it is not well documented, further it is now widely recognized that this mouse reference genome contains a fraction of contaminating non-B6 sequence. In addition, the current reference sequence contains poorly resolved structural information with 686 gaps in the assembly and 961 regions where problems have been noted (Genome Reference Consortium Mouse Build 38, 2012).~The current C57BL/6J colony is now maintained under a genetic stability program, meaning that the colonies are restocked using embryos that are derived from a single male and female (Adam and “Eve”). The current Adam and Eve were F223 and this Eve is the female that we have generated high coverage short read Illumina data, as well as high coverage PacBio data and BioNanoGenomics scaffolding data. Any C57BL/6J mouse ordered from JAX will never be more than 10 generations removed from Eve. In choosing a sample for de novo assembly, we favored Eve over an archival sample from 1998 because the mice that people are using today are closer to Eve.