Gene Conservation Laboratory

Statistics Program for Analyzing Mixtures (SPAM) Software

SPAM FAQs Page

Genotype Tolerances

Setting Genotype Tolerances
(in the "*Parameters" section of the control file)

Any mixture individual whose genotype probability is less than the tolerance value will be dropped from the analysis. Specifically, the individual is dropped if, across all baseline populations j, the maximum value of Prob(genotype for individual i| Individual is from Population j) is less than the genotype tolerance.

The user must consider the number of characters (e.g., loci or markers) being used when setting the genotype tolerance parameter. For example, assume you are conducting an analysis with 5 diploid loci in which the lowest-frequency allele of each locus has frequency 0.10 for each population in the baseline. The probability, under Hardy-Weinberg, of a 'low-frequency' homozygote (aabbccddeeffgghhiijj) from any population is then ((.10)^2)^5 or (.10)^10 = 1E-10. If a genotype tolerance of 1E-9 is used, any low-frequency homozygotes in the mixture file will be tossed out as impossible.

The *.log file reports how many observations were actually retained in the analysis (the *.est and *.sim files report how many observations were initially in the mixture file). The dropped mixture individuals will be assigned to a baseline component called 'Unknown', so the *.est file or the *.bot file will contain a contribution estimate for 'Unknown'.