We also observe that even if the data were imputed the large proportion of low frequency SNPs was untaggable, which will have deep implications for the efficiency of genotyping low frequency tag SNPs.
When the sampling scheme is biased, there are a large proportion of low-frequency SMPs.
This demonstrated that as the number of newly sampled individuals increases, a large proportion of the low frequency variants in the new dataset cannot be captured by any fixed set of selected tag SNPs.
A large proportion of associations combine a low frequency with a high Jaccard's index.
In addition, although PTEN seems to be downregulated in a large proportion of muscle-invasive tumours, the frequency of genomic loss seems to be much lower, so there is probably a functional difference in outcome between downregulation and deletion (Tsuruta et al., 2006; Sjodahl et al., 2011).
As expected, because selection of SNPs was based on modern domestic breeds, the wild, feral and primitive populations have a lower genetic diversity compared to modern breeds, as suggested by the low values of Ppl and H e [See Additional file 1: Table S1], and by the large proportion of loci that fall in frequency bins between 0.8 and 1 [See Additional file 2: Figure S1].
Predicted deleterious variants may be detrimental, however, these allele frequencies cannot increase in long ROH, as inbred individuals harboring a large proportion of long ROH with a high frequency of deleterious alleles will have reduced fitness, leading to decreased survival.
Poly-A/T made up a large proportion of these, with mean per kb frequencies of 0.27 in hot spots and 0.059 in cold spots.
This showed that a large proportion of the novel variants with low frequency generated by sequencing new individual cannot be covered by the next generation genotyping arrays with a set of fixed variants discovered by the 1000 Genomes Project.
Recent large scale sequencing studies reported that the population frequencies of a large proportion of discovered variants were rare (Minor Allele Frequency (MAF) < 1 %) [ 6– 8].
The genome is in an eroding state, evidenced by a large proportion of pseudogenes (31.2%) and a high frequency of transposable elements (∼600) scattered throughout the genome.
