Table II. Impact of using increasing numbers of RNA-seq data sets for annotation.

Ninety-six different RNA-seq data sets were ranked according to the number of Trinity-assembled transcripts they produced. The number (and percentage) of maize chromosome 5 5b+ genes supported by the top one, five, 10, 15, 20, or all transcript collections was calculated (column 2). Column 3 shows the number (and percentage) of 5b+ genes containing a Pfam domain but not supported by any transcript evidence.

RNA-seq Data Sets	Transcript-Supported 5b+ Annotations on Chromosome 5	5b+ Annotations with Pfam Domains But without Transcript Support
Best 1	2,670 (59.7%)	886 (19.8%)
Best 5	3,624 (81.0%)	314 (7.0%)
Best 10	3,924 (87.7%)	159 (3.6%)
Best 15	4,015 (89.8%)	130 (2.9%)
Best 20	4,066 (90.9%)	115 (2.6%)
All assemblies	4,082 (91.3%)	121 (2.7%)