Hi I'm using Star align and the build in htseq to count gene features. 

however I notice that the final log file, specifically "Uniquely mapped" does not matched the total library size of the count. For example, I could have  sample where the uniquely mapped is 63 million but the the total library size, that is the sum of all the gene count is 54 million? So my question is what is going on here since I though part of the count was to categorized the counts into each gene  so that the sum should be equal? 

thank you. 

A.