Distribution of read mapping categories. (a) MAQC samples (SRA: SRP000727) contain single-end reads, thus, there are three read mapping categories: uniquely mapped reads, non-uniquely mapped reads, and unmapped reads (b) Thrombin study samples (SRA: SRP008482) contain paired-end reads, thus, five read mapping categories can possibly occur. Cases of uniquely paired reads and non-uniquely paired reads occur when both ends of a read pair are mappable to the genome. Situations of uniquely mapped singletons and non-uniquely mapped singletons occur when only one end of a read pair is mappable to the genome. The RefSeq annotation has the highest percentage of uniquely mapped reads and the lowest non-uniquely mapped reads for both samples.