If I am looking at a specific gene that is comprised of 3 exons or 2 protein coding regions, and I find that some of my reads being aligned are very small proportionally to to the entire protein coding region and located only in one of those protein coding regions. Should I consider this a "bad quality" alignment generally speaking? Similarly if the read spans the entirety of one protein coding region, but is largely absent in the other (1/2), how should I classify these alignments?