In these alignments, the proportion of mismatches was highest at the ends of these alignments where there are typically lower numbers of sequencing reads (Fig. 3).> -wrap-foot> Summary of BLASTN searches of the transcriptome using published sequences from five protein-coding genes as queries.
For all patients, the deviation (continuous variables) from the expected ideal alignment and the proportion of patients with deviations ≤1, 2, 3, and 4° from the expected ideal value was calculated.
The effect was more drastic for Type II New genes; only 0.3% of Type II New genes overlapped a D. melanogaster homolog alignment, while the proportions were 4.9% and 10.9% for Type I New and Previously Known genes, respectively.
Figure 1 provides a summary of the alignment results and the proportion of reads carrying the HpaII sequence tag across the 17 samples.
Polymorphism positions are denoted by the position in our alignment; R% is the proportion of phenotypic variance explained by the detected polymorphisms/LD group; * and ** mean P < 0.05 and P < 0.01, respectively.
We used the protein alignments to calculate the proportion of amino acid differences and indels.
We selected only COSII loci that were identified in two or more of our species, and aligned those sequences in MEGA5 using the MUSCLE alignment tool to assess the proportion of variable sites (Edgar, 2004; Tamura et al., 2011).
The accuracy of the resulting extended alignment was measured as the proportion of true homologies recovered between the QS and the closest human/mouse reference sequence.
We also reported, the number of contigs, coding sequences, and genes that had a significant hit (e-value < 1e-10) independently of the alignment proportion.
