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Also, the distribution of Tajima's D statistic (Tajima, 1989) in maize inbreds and teosintes revealed the expected shift towards a higher frequency of rare variants as expected after a recent bottleneck.
To define variants as "expected pathogenic" we used the criteria previously described.
We find additional support that we are calling variants as expected, particularly those positions with ≥15-fold coverage.
The findings of this study indicate that this is likely to involve not only exonic variants, as expected, but also variants in regulatory regions and noncoding RNA genes typically not detectable by WES technologies.
The homozygous Sod3 KG06029 line has much lower expression of the SOD3 variants as expected in both sexes (n=5, P<0.01 and <0.001; Figures 7A and 7B), but with a suggestion of associated lower expression of SOD1 in males and a low but significant up-regulation of the mitochondrial Mn SOD2 in females (n=5, P<0.01; Figure 7B).
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The relationship was strong in the group of infants lacking the 7-repeat variant; as expected, mothers showing a low level of anomalous behaviour had infants displaying a low level of disorganisation, and conversely, infants of highly atypical mothers showed a high level of disorganised attachment behaviour.
Variants were genetically mapped with R/qtl, and variants segregating as expected in these calls were used to create a Family Reference Variant Resource that contained 6849 SNPs and 2164 indels (Broman et al. 2003).
Genotypes were submitted to further analysis after verifying that the distribution of homozygous and heterozygous carriers of variants was as expected from the Hardy-Weinberg [13] law (χ2 goodness-of-fit tests: p>0.05).
The genotype distribution for the UCP2 866G>A variants was as expected from Hardy-Weinberg equilibrium (P = 0.743 for case subjects and P = 0.066 for control subjects).
The genotype distribution for both the −866G>A and the A55V variants was as expected from Hardy Weinberg equilibrium (χ = 0.50, p = 0.48 and χ = 0.06, p = 0.30, respectively).
This suggests the existence of positive selection pressure for some variants, as might be expected for genes coding for proteins that interact with host cells such as the P1 adhesin.
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