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As reads can be aligned to more than one location, the number of alignments may be greater than the number of reads; since some reads may be unaligned, the number of alignments may be less than the number of reads in the bam/sam file (Figure 1).

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• Exonic: A read is labeled exonic if any one of its alignments is completely contained within the respective exon as defined by the database (i.e., even if there is a single base shift of the read relative to the exon, the read will not be called exonic but will fall in the category ‘partially overlaps exon’). If the alignments are strandspecific, then the strand of the alignment must also agree with the strand of the transcript.
• Partially overlaps exon: A read is assigned to partially overlap an exon if any of its alignments overlaps an exon, but at least partly (one base-pair or more) maps out of the exon.
• Intronic: A read is labeled intronic if any one of its alignments maps completely within an intron, but none of the alignments are exonic (either fully or in part). If the alignments are strand-specific, then the strand of the alignment must also agree with the strand of the transcript.
• Reads between genes: A read is labeled ‘between genes’ if none of its alignments overlap a gene.

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