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While the '''LooRsq''' statistic completely ignores experimental genotypes, '''EmpR''' is calculated by calculating the correlation between the true genotyped values and the imputed dosages that were calculated by hiding all known genotyped for the given SNP (see [[ #LooDosage | '''LooDosage''']]). A negative correlation between imputed and experimental genotypes can indicate allele flips. This statistic also can only be provided for genotyped sites. '''EmpRsq''' is the square of this correlation.
While the '''LooRsq''' statistic completely ignores experimental genotypes, '''EmpR''' is calculated by calculating the correlation between the true genotyped values and the imputed dosages that were calculated by hiding all known genotyped for the given SNP (see [[ #LooDosage | '''LooDosage''']]). A negative correlation between imputed and experimental genotypes can indicate allele flips. This statistic also can only be provided for genotyped sites. '''EmpRsq''' is the square of this correlation.
==='''Dose1'''===
==='''Dose0'''===
Average [[ #LooDosage | '''LooDosage''']] at haplotypes with alternate allele at this site. A value of 0.97 denotes that out of all the haplotypes with an alternate allele at this site, 97% of them would get imputed accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 1.0, more accurately has that site been imputed.
Average [[ #LooDosage | '''LooDosage''']] at haplotypes with alternate allele at this site. A value of 0.97 denotes that out of all the haplotypes with an alternate allele at this site, 97% of them would get imputed accurately to the alternate allele, if this site was assumed to be not genotyped. The closer the value is to 1.0, more accurately has that site been imputed.
