Table 4.

Recovery of removed genes in A. thaliana

	10% annotations removed				90% annotations removed
	OrthoFiller		de novo		OrthoFiller		de novo
No. genes removed	2410		2410		21683		21683
Total genes founda	1233	37.5	13184	426.7	11480	96.2	42504	223.5
Found genes which overlap removed genesa	1107	37.5	4918	130.4	11344	89.0	35609	149.5
Total recovered genesa	1036	31.72	2269	16.4	10380	59.7	20431	33.0
Number of split genesa	67	5.4	1214	23.6	945	34.4	7451	37.7
Mean pF-score of found genesa	0.75	0.01	0.45	(<0.01)	0.70	(<0.01)	0.55	(<0.01)
Mean oF-score of found genesa	0.94	(<0.01)	0.51	(<0.01)	0.89	(<0.01)	0.64	(<0.01)
High-quality found genes (pF-score ≥0.95)a	432.0	29.3	640.8	27.4	3419.8	21.3	9079.6	99.5
Lower-quality found genes (pF-score <0.95)a	674.6	32.1	4277.2	147.8	7923.8	99.5	26529.8	201.3
Mean pF-score of lower-quality genesa	0.61	0.02	0.31	(<0.01)	0.57	(<0.01)	0.33	(<0.01)
% of lower-quality genes with oF-score < 0.95a	34.6	1.9	81.1	0.9	43.4	0.6	73.9	0.1

^aNumbers shown are rounded mean values from ten disjoint removed subsets of genes, with standard deviations bracketed