PT - JOURNAL ARTICLE AU - Shweta Ramdas AU - Ayse Bilge Ozel AU - Katie Holl AU - Myrna Mandell AU - Leah Solberg Woods AU - Jun Z. Li TI - Extended regions of suspected mis-assembly in the rat reference genome AID - 10.1101/332932 DP - 2018 Jan 01 TA - bioRxiv PG - 332932 4099 - http://biorxiv.org/content/early/2018/05/29/332932.1.short 4100 - http://biorxiv.org/content/early/2018/05/29/332932.1.full AB - We performed whole-genome sequencing for eight inbred rat strains commonly used in genetic mapping studies, and they are the founders of the NIH heterogeneous stock (HS) outbred colony. We provide their sequences and variant calls to the rat genomics community. When analyzing the variant calls we identified regions with unusually high heterozygosity. We show that these regions are consistent across the eight inbred strains, including the BN strain, which was the basis of the rat reference genome. These regions show significantly higher read depth than other regions in the genome. The evidence suggests that these regions may contain segmental duplications that are incorrectly overlaid in the reference genome. We provide masks for these suspected regions of mis-assembly as a resource for the community to flag potentially false interpretations of mapping results or functional data.