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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

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

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