Table 1.

Summary statistics characterizing the sets of the GeneMarkS-T gene predictions in assembled transcripts as well as the sets of the high-confidence gene predictions (HC genes).

Species	# of annotated genes	# of genes predicted by GeneMarkS-T	Sn/Sp of GeneMarkS-T predicted genes	# of HC genes (Order excluded DB)	Sn/Sp of HC genes (Order excluded DB)	# of HC genes (Species excluded DB)	Sn/Sp of HC genes (Species excluded DB)
C. elegans	19,969	14,746	46.8/63.4	8,062	35.7/88.4	11,399	51.7/90.6
A. thaliana	27,445	17,589	51.2/79.9	16,008	55.0/94.7	16,551	58.8/97.6
D. melanogaster	13,951	10,163	59.6/81.8	8,109	59.6/81.8	9,223	63.7/96.3
S. lycopersicum	25,158	19,526	67.8/77.8	17,231	74.9/95.2	17,489	75.8/95.1
D. rerio	25,611	22,992	59.6/59.9	16,918	67.0/88.5	16,573	66.9/90.4
G. gallus	17,279	17,381	49.6/47.0	12,473	74.4/89.1	12,564	74.0/88.4
M. musculus	22,611	15,819	49.6/63.2	13,057	63.5/93.2	12,965	63.9/94.5

Two versions of reference protein databases were used for each species: the database called ‘Species excluded’, containing all the proteins from an OrthoDB segment but proteins from the same species, as well as the smaller database called ‘Order excluded’ containing all the proteins from the same OrthoDB segment but proteins from the same taxonomic order (see Materials). Additional data is provided in Supplemental Table S1.