The phrase "alignment in reference" is correct and usable in written English.
It can be used in contexts where you are discussing the consistency or agreement of information or ideas in relation to a specific point or standard.
Example: "The alignment in reference to the project's goals is crucial for its success."
Alternatives: "consistency in relation" or "agreement in context".
In each breed, roughly 0.1% of the mapping read pairs had no concordant alignment in the reference genome, referred to as discordant paired-end reads [ 2, 17], indicating a potential SV.
The output is given in a tab-separated format containing the reference and query sequence names, the start and end position of the alignment in the reference sequences, as well as the strand and the number of mismatches per read.
Socrates works by efficiently identifying clusters of soft clipped alignments in the reference genome as candidate break points.
This function prints a coloured RC-MSA representation of the sections of the alignment in which the reference alignment and the alignment to be inspected differ.
Sequencing errors, choice in alignment algorithm, and choice in reference genome used, all have the potential of contributing to alignment artifacts.
Figure 5A and C shows the alignment sensitivity, and Figure 5B and D shows precision for various sequence identity bins in reference alignments.
Relative entropy at each position (or column) of a multiple sequence alignment followed the definition used in reference [ 24]: (1) where X i is a random variable for A, C, G, or T, P(X i ) represents the frequencies of four types of nucleotides in each column of a sequence alignment (see Figure 1 for an example), and Q(X i ) is the background distribution of X i in sequences.
We optimized the parameters for SP5 (with new profile-based gap model) by maximizing the percent of matches between the reference alignment in PREFAB and the alignment made SP5.
While some have mistakenly used such masks prior to performing other analyses [4], [6], [22] [25], a better practice would be to manually curate the reference alignment in these regions and to include all of the data.
Figure 1b shows the alignment found after Phase II using the reference alignment in Figure 1a.
