Fig 3. Accuracy analysis for candidate aligners.

(A) Categories of aligned deletions. (B) Analysis of performance of a representative set of aligners on synthetic read datasets, designed to represent JuMP data. Alignments were performed using two sets of synthetic data: containing deletions and deletion-insertions. The deletions set consists of reads with a randomly placed deletion whereas the deletion-insertions dataset also contained a 1–9 nucleotide sequence insertion at the deletion site. Both synthetic datasets contain point mutations reflective of those observed in experimental reads. Each synthetic dataset contained one million reads generated from an RNase P reference sequence. Match categories reported as percentage of total reads in each category.