Interestingly, mitochondrial genomes of both strains are homogeneous, with no sequence variation detected even at the high resolution employed (>5,600× sequence coverage of the mitochondrial genome).
The amount of between-condition variation detected (by selecting no-variation genes by decreasing p-values) was smaller than with the real dataset, implying that the real dataset had larger differential gene expression.
No coding region variation was found, and all intronic variation detected was either found in unaffected controls or was unlikely to have functional consequences.
c, Circular presentation of different types of structural variation detected in 453 high-coverage rice genomes when compared against the Nipponbare RefSeq.
The expression change was, however, contradictory to the direction of copy number variation detected here.
However, nearly all of the molecular variance was attributed to differences in 'within-site' variation detected for both test statistics.
And finally, another between-condition normalization using only the no-variation genes detected, to calculate the between-condition normalization factors.
The estimation error decreases with the number of no-variation genes detected (Fig. 2), and whenever normalization error is well below biological variation, normalization between samples will be correct and beneficial for downstream analyses.
In contrast, no variation was detected when the competition assay was carried out with nalidixic acid (Table 4).
First, it is suspicious that no variation was detected among individuals A, B, and C. If the Dan06 progenitor was indeed heterozygous at many loci, we would expect greater diversity among its descendants (although the near-clonality of A, B, and C could be explained if these specimens actually trace back to a more recent common ancestor).
