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As shown in Figure 2, the number of statistically significant tests increases until around ~1.2 Mb, after which the number of statistically significant tests slowly declines due to more stringent significance criteria necessary due to increased hypothesis testing.
With a more stringent significance threshold (false discovery rate q<0.05), 67 genes met criteria for differential expression.
Four loci met the more stringent significance (P<0.01) in the Ewens-Watterson test.
More stringent significance level cutoffs are chosen for the power analyses since power at the 0.10, 0.05, and 0.01 levels is close to or equal to 100% for these parameter specifications.
Deviations from HWE were observed in all three species/sub-species, however, at the more stringent significance level (α0.001), only the deviations observed in the sample of B. bonaerensis remained significant.
Group sequential designs require the adoption of a more stringent significance level to allow for repeated testing.
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The more stringent the significance threshold the more likely it is that real genetic effects of small size will be overlooked due to sampling effects.
With a more stringent 0.5% significance level only the following 10 HLA-C positions: 9, 11, 21, 77, 80, 97, 99, 116, 156, and 163 were identified.
In case of a discrepancy between the two positive selection scores we used the more stringent LRT significance as the indicator of positive selection, the sliding window measure was used as a supporting score.
In large-scale studies, when thousands to millions of loci are measured, the threshold to declare any locus significant is typically based on a more stringent level of significance (e.g. Bonferroni correction or similar) in order to minimize the possibility of false positives, therefore we have displayed the power at two such thresholds.
Thus, any p-value reported less than 0.004 passed a more stringent criterion for significance and is therefore more noteworthy.
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