OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

BMC Genomics

Table 3 The types of evidence and levels of support for Nasonia vitripennis gene sets (OGS2 and others). Sequence-level statistics for the different types of evidence are given as proportions of the gene sets that are validated. Gene structure level statistics (ESTgene, Progene, RNAgene) are counts of the number of models that reach three structure level agreements. Homology level statistics are counts of the number of models and proportions matching proteins of reference species and paralogous (same species) proteins. See Methods section for details on the evidence types and the statistics that were measured

Evidence	Available evidence	Statistic	OGS1.2	Evidence-prediction set	OGS2	OGS2 Good genes	NCBI RefSeq	Full-length RNA-Seq assembly
EST	18 Mb	Seq. Overlap	0.506	0.814	0.768	0.715	0.672	0.724
Protein	26 Mb	Seq. Overlap	0.674	0.696	0.729	0.693	0.616	0.612
RNA	46 Mb	Seq. Overlap	0.381	0.551	0.599	0.54	0.468	0.571
RefSeq	17 Mb	Seq. Overlap	1	0.934	0.958	0.908	0.857	0.839
Intron	66,593	Splices Hit	0.846	0.965	0.981	0.969	0.903	0.975
TAR	75 Mb	Seq. Overlap	0.292	0.850	0.533	0.443	0.37	0.386
Transposon	28 Mb	Seq. Overlap	0.168	0.282	0.406	0.099	0.009	0.039
ESTgene	10,194	Perfect	2737	3996	4952	4900	3631	4293
ESTgene	10,194	Equal 66 %	3491	5059	6283	6198	4284	5187
ESTgene	10,194	Some	6263	9940	11,313	11,157	7123	8373
Progene	44,040	Perfect	4808	6713	8048	8010	6215	4935
Progene	44,040	Equal 66 %	7759	12,217	14,046	13,837	9003	8567
Progene	44,040	Some	11,563	18,173	21,759	19,718	10,861	18,457
RNAgene	28,016	Perfect	6004	9531	14,899	13,804	8502	28,016
RNAgene	28,016	Equal 66 %	8173	13,552	18,829	17,608	10,202	28,016
RNAgene	28,016	Some	11,933	19,602	24,936	22,179	12,258	28,016
Homolog	11,683	Matches	16,174	16,669	23,994	17,341	11,950	13,187
Homolog	11,683	Found	10,426	10,593	11,683	11,683	9323	9650
Homolog	11,683	Bits/Amino Acid	0.449	0.424	0.416	0.455	0.562	0.558
Paralog		Matches	12,843	14,503	19,423	12,576	7904	10,520
Paralog		Bits/Amino Acid	0.459	0.45	0.564	0.517	0.554	0.635
Genome		Coding Seq.	28 Mb	31 Mb	36 Mb	29 Mb	10 Mb	16 Mb
Genome		Exon Seq.	29 Mb	52 Mb	70 Mb	45 Mb	24 Mb	24 Mb
Genome		Gene count	18,941	23,605	36,327	24,388	12,989	20,926

ISSN: 1471-2164