Imax for SNP marker genotyping. We called genotypes of clones at SNPs based on the raw signal intensities obtained from Illumina genotyping system. A number (Nneg) of SNPs showed very low intensities for both alleles in the goat (panel A). Specifically, the statistic used for genotype calling of a given SNP in a given clone was the maximum observed intensity over the two possible alleles (herein called Imax). The distribution of Imax in a given clone can be seen as a mixture of two underlying distributions, where one for the non-retained SNPs in the clone and one for the retained SNPs (e.g. panel B).