Table A2.

Comparison of expression level estimates.

Data Set	Replicate	MapA1 > TopHat (%)	MapA1 ∼ TopHat (%)	MapA1 < TopHat (%)
1	1	41.8	45.6	12.6
	2	41.7	45.6	12.7
	3	41.6	45.8	12.6
2	1	38.4	44.7	16.9
	2	39.4	43.6	17.0
	3	40.3	43.1	16.6

For each data set and each replicate, the table shows the number of known splice forms for which MapAl and TopHat yield similar expression levels and for how many splice forms expression levels deviated by more than 20%. The statistics include splice forms without presence call from one or both of the pipelines.