Morgan et al 2010. Finally if PLINK 2 determines that any samples and covariates are irrelevant to all regressions eg.
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In order to evolve phage resistance bacteria must have sufficient mutation supply which will primarily be determined by population size and gene flow Gandon et al 2008.
. You survey another population and find the following genotype frequencies. --hwes midp modifier applies the mid-p adjustment described in Graffelman J Moreno V 2013 The mid p-value in exact tests for Hardy-Weinberg equilibrium. A covariate could be zero-valued for all but one sample they are removed before any variants are.
Morgan et al 2005. The mid-p adjustment tends to bring the null rejection rate in line with the nominal p-value and also reduces the filters tendency to favor retention of variants with missing data. A07 B049 C042 D021.
If the population is in Hardy-Weinberg equilibrium what proportion of the flies carries both A1 and A2. Pal et al 2007. If your hypothesis is correct what type of natural selection is causing this imbalance.
Hampton et al 2020. By default if this check fails PLINK 2 errors out. Tests show that 70 of the gametes produced in the population contain the A1 allele.
You note that the population is not in Hardy Weinberg equilibrium and propose that natural selection explains the observed imbalance in the genotype frequencies. To just skip the affected regressions instead add the skip-invalid-pheno modifier. A fruit fly population has a gene with two alleles A1 and A2.
Smaller population sizes in vivo may therefore limit resistance.
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