Novel transfrag annotation. (a) Using stage specific sequence data we were able to show that approximately 60% of the novel transfrags have sequenced reads mapping to them. We also show that 60% of these transfrags with sequence information can be connected to known gene annotation using paired-ended sequence reads, where one read of the pair is anchored on the transfrag while the other overlaps a gene annotation. Examples of novel regions identified from our analysis, show (b) a new 5' exon and (c) a novel transcript. (d) Transfrags identified as novel in our tiling data based on WS150 of the genome annotation were compared against WS160, WS170, WS180 and WS190 models. We see that >30% of the transfrags that were novel based on WS150 are predicted to be exonic in later annotations (grey bars). Almost 50% of novel transfrags that also have sequence reads overlapping them are predicted to be exonic in later annotations (black bars). We can show annotation overlap for a further 15% (tiling alone - gray) or 25% (tiling with sequence data - black) when we compare the transfrags to TwinScan models.