Rat reference genome selection

Hi, I’m analysing my rat RNA, while when I was using featurecounts, I found there were so many reference genome to choose in USCS main browser. I’ve used ensemble genes as reference, which gave me only 40% assigned reads. I was wondering whether there is any good choice for rat reference genome?

For example, what’s the difference between these NCBI RefSeq tables?

Combined into this topic Very low assigned reads in featureCounts