Selected comparisons of genome measures. Principal component analysis showed expected relationships among the different measures (data not shown). Selected examples are plotted as double y-axis scatterplots. Legends indicate first or second y-axis for blue dots or red crosses, respectively. Linear regression analysis of each y-axes variable independently with respect to the x-axis variable was done and the trend line is drawn on each plot color-coded with respect to each measure. R2 and p-values are shown for each measure. A-B. Numbers of annotated proteins and RNAs with respect to genome size from INSDC and RefSeq annotation sets for complete prokaryotic genomes. Feature counts were obtained from the Complete Microbial Genomes Annotation Report (Aug 10, 2010) and proteins and RNAs from INSDC and RefSeq are plotted with respect to genome length. The count of proteins follows a linear increase with respect to increasing genome size (blue trend line) while the RNA count, which includes all transfer, ribosomal, and non-coding RNAs, shows less of an increase with respect to genome size. Some genomes have extensively annotated RNA features, whereas others do not. A. All INSDC genomes (total of 1218 as of Aug 10, 2010). Those records that have below minimal standards for essential RNAs are encircled (red ellipse). B. RefSeq genomes (total of 1148 genomes as of Aug 10, 2010). Note, not all INSDC genomes are copied into RefSeq records. For the cases where INSDC records were missing essential RNAs, if there was a RefSeq version, the essential RNAs have been added or properly labeled. In all cases where the full set of essential RNAs could not be annotated it appeared that the missing RNA(s) were either non-functional or completely missing from the genome sequence (Table 3; data not shown). C. Protein lengths with respect to coding density for INSDC annotations. As coding density increases (more proteins per Kbp) the average protein length decreases (blue trend line) and the ratio of short proteins increases (red trend line). D. Hypothetical proteins and start codon ratios versus coding density. The ratio of proteins named ‘hypothetical’ increases slightly as the coding density increases whereas the standard start codon ratio decreases. Genomes where ‘hypothetical protein’ ratio is 1 or near 1 (large blue ellipse - every protein is annotated as ‘hypothetical protein’ in the genome) falls below the minimal annotation standards. For these particular cases, if a RefSeq version of the annotation existed, the functional assignment of a number of proteins was improved via curated clusters in the NCBI ProtClustDB (data not shown).