Reads in NGS Are Distributed over a Sequence Very Inhomogeneously

Abstract

Distribution of read starts over a sequences genetic entity is studied. Key question was whether the starts are distributed uniformly and homogeneously along a sequence, or there exist some spots of the increased local density of the starts. To answer the question, 15 bacterial genomes have been studied. It was found that some genomes exhibit extremely far distribution pattern, from an homogeneity, while others show lower level of the inhomogeneity. The inhomogeneity level was determined through the Kullback-Leibler distance between the real string distribution, and that one bearing the most probable continuations of the shorter strings.