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The differences can be attributed to sequence effects rather than structural effects.
According to Goicoechea (2009), this seemingly controversial placement of Oryza brachyantha could be attributed to sequence conservation between AA and FF genomes in some of the loci under investigation.
Evidence suggests that the lack of HIV-protective immunity is attributed to sequence divergence between autologous and consensus antigens.
A change in filtering settings would affect both data sets, with the difference remaining, and it is likely that this difference can be attributed to sequence length (average mRNA length 1784 bp).
The large branch found for Myotragus in the phylogenetic tree (Figure 3) could be attributed to sequence changes due to DNA damage or to an accelerated evolution of the Myotragus genome.
Examination of the amino acid sequence alignments suggested that the homology was entirely attributed to sequence similarity in the leucine-rich repeats, which form structural motif involved in protein-protein interactions and are ubiquitously found in all organisms in proteins with unrelated biological functions [27].
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Previously, low levels of intraisolate mtDNA variation (i.e. polymorphism) (Lee and Young 2009) and/or high rates of short indels in reads from 454-sequencing data (Formey et al. 2012) were attributed to sequencing errors.
However, there still remain one half of those differences that can be attributed to sequencing errors.
The G+C content of the enrichment reads demonstrated a principal mode similar to the single cell datasets and N. maritimus (suggesting a large proportion of AOA in the enrichment), as well as a higher G+C component attributed to sequences from the bacteria present in the culture.
Therefore, the observed sequence variations detected within mature miRNAs can be attributed to sequencing errors and/or to sequence variations between the query and the reference genome.
This initial set of 92,814 SNPs and 15,060 InDels was then subjected to filters to eliminate the number of differences that might be attributed to sequencing errors.
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