Background: Homology-based taxonomic assignment is impeded by differences between the unassigned read and reference database, forcing a rank-specific classification to the closest (and possibly incorrect) reference lineage.
We first estimated allele substitution effects (ASEs) for birth date for 45,073 SNPs using genomic best linear unbiased prediction (GBLUP) [ 21, 24, 25] applied to 3,570 registered Angus cattle, but we do not report results for the 256 SNPs that map to unassigned contigs in the UMD3.1 reference assembly [ 26].
Among the species-reference reads annotated 'Unassigned' by MEGAN4 (contigs), MetaCluster-TA annotated 4.3% to 'Accurate' and 6.3% to 'Higher'.
One copy of the reference mitochondrial genome and any unassigned contig sequences are added to the merged genome sequence.
For the ETO1 and APT3 amplicons, the positions on the grape genome physical maps were estimated based upon a manual realignment of the unassigned scaffold_233 (chromosome UnRandom of the 12×.0) and the 8× reference sequence version respectively, on the chromosome 2 of the 12×.0 reference sequence version.
Although annotation of bacterial genomes is outside of our area of expertise, another 29 ORFs that were not annotated in the reference genome were added from the Unassigned-ORF table to the target genome based on their similarity to genes in the NCBI nr database.
For all the unassigned conformers, the shape Tanimoto to the most similar reference shape is stored.
Another possible source of dmRNAs are unassigned selenoproteins [ 22].
All ORFs larger than the Cutoff size that have not been matched to a gene in the reference genome are automatically placed in an Unassigned-ORFs table, which is accessed by clicking on the relevant button below the interactive table.
Among the unassigned group, 7 sequences lacked any hit to a viral reference genome.
Secondly, all sequences that remained unassigned as SSU rRNA were analyzed with the Large Subunit rRNA Reference Database (LSUrdb) [34].
