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All six S. myoti populations showed highly significant deviations from Hardy-Weinberg equilibrium (p < 0.0001), as a result of heterozygote deficiency (FIS: 0.191-0.398).
This finding is consistent with neutrality tests that showed a non-significant signal for population growth in the LimpS and LimpN clades (where only the R2 values were significant), while all tests indicated highly significant deviations from neutrality in the Chefu clade (Table 4).
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Equine PDK4 is located in the genomic region that had the highest inter-population differentiation as well as a highly significant deviation from neutrality in the Ewens-Watterson test and is therefore one of the strongest candidates for selection for exercise adaptation.
Another locus, TpMSAT13, exhibited a highly significant deviation from HWE (χ = 40.23, DF = 8, P = 0.002), which was still significant after Bonferroni correction (corrected α = 0.006).
QC exclusion criteria for SNPs were genotype call rates <0.90, highly significant deviation from Hardy Weinberg equilibrium (P < 5 × 10−7) and minor allele frequency (MAF) < 0.005.
Highly significant deviation from the expected 1 1 segregation ratio on SBI-01 towards the BTx623 allele was also observed by [ 25], which affected almost the entire linkage group.
The G-test for goodness of fit detected a highly significant deviation from a random distribution (G (9) = 61.55; p < 0.001), with all but O7 chromosome segments covered by inversions having a higher than expected number of genes.
By contrast, univalent chromosomes Bj3 and Bj7 both showed highly significant deviation from expected transmission ratios: Bj3 was preferentially retained (~95%% of the time) and Bj7 was preferentially lost (present 25%% of the time) (Additional file 4: Figure S2).
The distribution of the correlation values was skewed towards positive values with a median of 0.17 and a most probable value of 0.4, results that show a highly significant deviation from randomness (Wilcoxon test, p < 0.0001).
Furthermore, the Hudson-Kreitman-Aguade (HKA) test detected a highly significant deviation of OsCIN1 from neutrality for cultivated rice compared with the ADH1 gene (p = 5.89871E-11) [ 36], using O. punctata as an outgroup (Table 3).
SNPs with a call rate lower than 0.9, a minor allele frequency higher than 0.005 and a highly significant deviation (P < 10-5) from the Hardy-Weinberg equilibrium, and SNPs that were not annotated (UMD3) on the autosomes or on the pseudo-autosomal region of the X-chromosome were excluded from the analysis.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com