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Position of variants in the array is fixed, regardless of alterations in the core repeat copy number.
Given the chromosomal position of variants, we designed PCR primers to amplify fragments harboring individual variants by Primer3 [ 36].
Given the position of variants, the PCR primers were designed to encompass the candidate position, ensuring that common SNPs are not covered by the primers.
For exon 4, the position of variants from each subclade within the array is strikingly similar in the three species, as shown in Figure 5B.
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This data gives the most upstream position of variant start sites and the most downstream position of variant end sites.
As is the case for LWS A180 reported here in the Cumaná guppy, the position of variant 5 in the tree based upon the 390 bp alignment depends upon which fragments are used in the phylogenetic analysis (i.e., it would occur in the LWS S180/ A180 clade if only the first 220 bp were utilized).
The sequence positions of variants from the source data were transferred to UniProt protein sequence level [26] and further mapped onto their corresponding locations in terms of three-dimensional structures if available in PDB [27].
Positions of variants identified in different analyses were compared using each of 10-kb, 100-kb and 200-kb windows.
Positions of variants determined in the parental strains were ignored in our analysis regardless of their quality score to reduce false positive calls.
Three major areas that need to be explored for understanding the genetic basis of disease susceptibility are [ 9]: (i) identification of new loci with the genetic variants, (ii) determining the precise position of causal variants and their phenotypic consequences, and (iii) discovery of functional mechanisms of loci and variants, which is the focus of this work.
CTCF has also been proposed to regulate the positioning of variant histones, such as H2A.Z [ 6, 14].
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