For those HLA genes with phasing issues, alleles with higher frequency in the public database were assigned over those with lower population frequencies.
In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis.
Thus, in considering individual populations - as opposed to 'species-wide' samples - there is a slight trend toward lower population frequencies of TEs in A. lyrata, consistent with the notion that selection against TEs is stronger in the outcrosser.
FL elements are rare within all Anolis L1 families, comprising about 18% of all L1 in the genome (Novick et al. 2009), and within all natural populations they are found at lower population frequencies relative to TR elements.
As our discovery sample has 80% power to detect around half of the previously implicated CNVs (Fig. 2), we speculate that the remaining 1.2% excess yet to be discovered for CNVs >500 kb will be attributed to CNVs with lower population frequencies and/or smaller ORs than those already identified.
Again there is the consideration that this lower ApoE population frequency may associate with a lower baseline frequency and risk of cardiovascular disease early mortality.
This difference results mainly from a lower normal population frequency for the HFE C282Y allele in the much larger and better age-matched normal control population presented here.
It is also known that ApoE4 frequency is much lower in some areas of the world (Corbo and Scacchi 1999) with a baseline frequency reported of 10%% at age 20 falling to 4%% in the >1990s in Han Chinese, suggesting a similar attrition with age for ApoE4 allele but from a lower baseline population frequency (Jian-Gang et al. 1998; Lu et al. 2014).
Both mechanisms are shown to produce gamma band oscillations at the population level while individual neurons fire at a rate much lower than the population frequency.
To reveal variants with a population frequency lower than 5%%, more markers and new technologies are required.
The frequency of the rs2004640 T allele, which has a central role in IRF5 polymorphisms, was significantly lower in the Korean population (frequency, 0.345) than white populations (frequency, 0.570; Table S2 in Additional file 1).
