Table 3. χ² test of proportions for predicted exact match introns inferred from RNA-seq mapping data in Arabidopsis.

Pipeline	Predictions Matching RNA-seq	Predictions Not Matching	Predictions Missing	Specificity Less Than Reference Annotationa	Sensitivity Less Than Reference Annotationb
LoReAn	67,064	57,969	4,376	N.S.c	N.S.c
LoReAn-M	66,199	45,073	5,241	<0.001	N.S.c
LoReAn-s	67,003	57,897	4,437	N.S.c	N.S.c
LoReAn-sM	66,133	44,987	5,307	<0.001	N.S.c
BAP	64,444	59,868	6,996	N.S.c	N.S.c
BAPplus	65,037	59,153	6,403	N.S.c	N.S.c
Augustus	63,137	70,107	8,303	N.S.c	N.S.c
GeneMark-ES	61,815	80,017	9,625	N.S.c	N.S.c
MAKER2	60,289	26,238	11,151	<0.001	N.S.c
Reference annotation	69,657	54,910	1,783	Not applicable	Not applicable

^aColumn reports P values for the χ² test of proportions for the specificity metric

^bColumn reports P values for the χ² test of proportions for the sensitivity metric

^cN.S., not significant with a p-value greater than 0.05