Fig 10.

(a), a gene with three subexons and two isoform are shown. The length of i1 is 260 bp, i2 200 bp. A paired-end read (or read-pair) is represented by light blue boxes intersected by broken lines, which indicates gap sequences. The read length is 50x2 bp. (b) A subexon path {s₁, s₃} applies to both isoform. When on i1, this subexon path implies three subexons with the one in middle shown in gray. Consider a fixed size fragment with gap size 75 bp(shown in gray) and total fragment length 175 bp. This particular fragment can arise from 16 different positions from subexon path {s₁, s₃} on i1 and 26 different positions from subexon path {s₁, s₃} on i2.