Venn diagrams

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       data.addColumn('string', 'Annotation');
       data.addColumn('number', 'All three call the same stop codon index but rast has different start codon');

data.addColumn('number', 'All three call Different stop codon index');

       data.addRows(3);
       data.setValue(0, 0, 'JGI');
       data.setValue(0, 1,650);

data.setValue(0, 2, 290);

       data.setValue(1, 0, 'Rast');
       data.setValue(1, 1,682);

data.setValue(1, 2,472);

       data.setValue(2, 0, 'Manatee');
       data.setValue(2, 1,655);

data.setValue(2, 2,242);

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       chart.draw(data, {width: 800, height: 300, is3D: true,titleX:"Average Gene Size (bp)", title: 'Average Gene Size Comparison'});
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Figure 1: Venn diagram showing the number of exact gene matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same start and stop index for a given gene.

Figure 2: Venn diagram showing the number of stop codon matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same stop index and strand (+/-) for a given gene.

Analysis

The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). This means that the gene calls in Rast significantly differed from the gene calls made by JGI and Manatee. However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the Rast's stop codons calls were usually the same as JGI and Manatee, the start codons that Rast called frequently differed from the other two annotations. This often resulted in Rast predicting longer genes, as can be view in this histogram.