If the insert size is small, just few bases (5-8 in average) longer than a single read length, the reads overlap with 135 bases out of 150. Can this cause low mapping rate? Like if the paired reads are overlapping as if they are one single read, could this be a reason for low mapping? I am having ~70 alignment, changed the alignment algorithm, still ~70%. reads quality are ok, and no contamination when I checked. I checked adapters are removed. Could the insert size short length affect the mapping?