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Indeed, of these 1900 genes (5% of 38,000 contigs), 47.4% were annotated in the low variation group and 33.2% were annotated in the high variation group.
It has to be underlined that a fraction of mitochondrial variants (6.47%) annotated in the low coverage report was not identified by our protocol.
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While the degree of Modularity among the 128 pathways annotated in the ensemble network may be low, it is statistically significant compared to what is expected by chance.
It should be noted that many targets could not be annotated in the GO database due to their low homology to orthologs; thus, the miRNA-target network is likely more complex than the results presented here.
The absence of the type-B2 and type-B3 GmRRs may be due to the following reasons: (i) the sequenced soybean genome comprised of only 950 Mb, representing ∼85% of the predicted 1115-Mb genome; and/or (ii) approximately one-third of 66 400 putative protein-coding loci annotated in the Glyma1 model were predicted with low confidence.
For this purpose we have re-generated the negative sequence set avoiding the low-complexity regions annotated in the Drosophila genome.
The theoretical PATRIC proteome is substantially larger than the standard theoretical RefSeq proteome and it should be pointed out that most of the low molecular weight proteins annotated in the theoretical N. punctiforme PATRIC proteome have to date not been detected in any proteomic analyses.
Thus, the possibility that all genes involved in Sec or SeU utilization have not been sequenced or annotated in the genomes containing orphan SelD is extremely low.
The array contained probes for most exons in the Drosophila genome annotated in the Ensembl database, except for few very short or low-complexity exons.
First, for most groups, only a low fraction of genes are conserved and/or annotated in the same constellation in both species, most genes are found and/or annotated in a species-specific constellation (SG, EE, 5PI-EI, CSS).
The number of porcine miRNAs currently annotated in miRBase is low compared to other higher eukaryotes (i.e. only 211 miRNAs annotated in the pig compared to 1048 in Homo sapiens).
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