Table I. Effects of MAKER-P’s supervision of gene finders on genome-level sensitivity and specificity.

MAKER default, standard, and max refer to different MAKER gene-build options (see “Materials and Methods” and Supplemental Fig. S5).

Parameter	MAKER Default	MAKER Standard	MAKER Max	Augustus Trained for Arabidopsis Run outside of MAKER	SNAP Trained for Arabidopsis Run outside of MAKER	SNAP Trained for Maize Run outside of MAKER	SNAP Trained for Maize Run inside of MAKER
Sensitivity	0.88	0.91	0.93	0.91	0.84	0.47	0.67
Specificity	0.93	0.91	0.81	0.93	0.81	0.92	0.94
Accuracy	0.90	0.91	0.87	0.92	0.82	0.70	0.80