Fig. 5
From: BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data
Schematic representation of alignment of paired-end reads to a reference sequence. Sample 1 has no structural variation w.r.t. the reference; read 1 aligns to the forward strand and read 2 to the reverse. Sample 2 has an inversion with respect to the reference, giving rise to two reads with forward orientation. In order to isolate potential inversion events, we kept kept such alignments, as well as the analogous case with two reverse-mapped reads, by requiring that both reads in an alignment have the same orientation as indicated by the SAM flag 0×10