Table 2.

Summary statistics on de novo assembly of the RNA-seq data and KLEAT calls. Assembly figures are for contigs longer than 500 nt in length. The total number of cleavage sites called by KLEAT, and the average number of alternative polyadenylation sites per gene, are shown in the last two columns. Two sub-columns for the number of cleavage sites and APA per gene represent total and true positive (TP) calls, at a support threshold of three reads.

Cell Line	Assembler	# Contigs	N50 (nt)	Total Reconstruction (Mnt)	# Cleavage Sites		APA per gene
					All	TP	All	TP
H1-hESC	Trans-ABySS	879,277	1,049	309.1	11,975	8,998	2.54	2.49
	Trinity	159,627	2,250	188.3	9,896	7,565	2.37	2.30
A549	Trans-ABySS	788,688	1,352	299.9	13,984	12,940	2.83	2.80
	Trinity	149,880	2,791	197.4	12,249	11,369	2.62	2.57
MCF-7	Trans-ABySS	1,002,984	1,171	391.5	15,240	13,308	3.09	3.05
	Trinity	237,875	2,925	323.6	12,845	11,387	2.82	2.76