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The first two columns contain total number of reads (Total reads) and total number of alignments (Total alignments). Theoretically, for single-end chemistry, total number of reds reads equals total number of alignments.  For double-end reads, theoretical result is to have twice as many alignments as reads (the term “read” refers to the fragment being sequenced, and since each fragment is sequenced from two directions, one can expect to get two alignments per fragment). When counting the actual number of alignments (Total alignments), however, reads that align more than once (multimappers) are also taken into account. Next, the Aligned column contains the fraction of all the reads that were aligned to the reference assembly.

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