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A position (base in DNA sequence) that is fixed (i.e. fully conserved) in one population, but has a different state (base) compared to another population is treated as diagnostic site or character.
These alignments have been analyzed, along with the phylogenetic tree of the species, by the program phastCons [ 39] to make predictions of discrete conserved genomic elements and to produce conservation level scores for each position (base) in the human genome.
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RC-Seq Sequence Capture Probes, Related to Figure 1 "Position" refers to the first nucleotide position (base 0) in the corresponding retrotransposon consensus sequence.
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