I have this single cell RNA-Seq data set prepared by CEL-SEQ 2 protocol (Hashimshony et al. 2016). After I assigned the reads to each cell and did the alignment using Bowtie2, I looked at the reads using Integrative Genome Viewer (IGV). I noticed that a lot of the aligned regions have reads with different start positions and at the same time have the same unique molecular identifier (UMI) sequence. They are in close proximity (usually < 5 nt between adjacent reads) and have equal lengths so it's not due to clipping. Should I regard these reads as separate fragments or are they generated during PCR amplification step and are from the same fragment? What is the possible source of these reads? How are they generated?