Figure 3

The impact of a gene model on RNA- Seq read mapping (read length  =  75 bp). (A) composition of mapped reads: roughly 23% are junction reads, and the rest 77% are non-junction reads; (B) effect on mapping of non-junctions reads: on average, 95% remain mapped to exactly the same genomic location, whilst 3–9% of reads become multiple-mapped reads; (C) effect on mapping of junctions reads: an average of 53% of reads remain mapped to the same genomic regions without the assistance of a gene model. About 30% of junction reads fail to be mapped, while 10–15% map alternatively. (Note: the 16 tissue sample names are denoted as follows: a: adipose; b: adrenal, c: brain; d: breast; e: colon; f: heart; g: kidney; h: leukocyte; i: liver; j: lung; k: lymph node; l: ovary; m: prostate; n: skeletal muscle; o: testis; and p: thyroid).