. Author manuscript; available in PMC: 2019 Apr 1.

Published in final edited form as: Nat Genet. 2018 Oct 1;50(11):1574–1583. doi: 10.1038/s41588-018-0223-8

Table 1. Genome Reference Consortium (GRCm38) and GENCODE annotation updates informed by the strain assemblies.

Updates indicate known GRC issues solved based on C57BL/6NJ de novo assembly. GENCODE update is based on comparative Augustus predictions with 75% novel introns and includes annotation and predictions which occur on chromosomes 1-12.

Genome Reference Consortium (GRCm38) Update
GRC issue solved	11	Genes completed	10
GRC issue solved	11	Genes improved	1
GENCODE Update
Annotated new locus	62	Protein coding	19
		lncRNA	37
		Pseudogene	6
Annotated updated annotation	272	new coding transcript	105
		new transcript	31
		new NMD transcript	6
		other	130