Fig 1.
Algorithm stages for the clustering phase.
Fig 2.
Mean contrast and distances between clusters from 1803 random markers (50.000 points on the graph).
Surrounded in blue, clusters that should be merged. Surrounded in green, clusters that should not be merged. The red line represents the separation between clusters that should and should not be merged. BBB/BBA stands for: mean contrast and distance between a supposed BBB cluster and BBA cluster.
Fig 3.
Illustration of genotype determination for 1; 2 or 3; and 4 clusters identified for a given SNP.
Fig 4.
Example of implementation of the additional step to account for highly shifted contrast signal.
Fig 5.
Examples of distribution on the axes of contrast and signal strength of genotypes identified by GenoTriplo for each category of markers.
Table 1.
Number of markers by categories for the different parameters used in clustering phase.
Table 2.
Table with the respective number of SNPs with 1, 2 3 or 4 genotypes identified with GenoTriplo or fitPoly.
Fig 6.
Mean contrast and signal strength values for genotypes of SNP with 1, 2, 3 and 4 different genotypes (from left to right) for fitPoly (above) and GenoTriplo (under) methods.
Table 3.
Number of markers visualized per category, number best genotyped by GenoTriplo, by fitPoly; and corresponding rate of concordant genotypes between methods.
Fig 7.
Number of offspring as a function of the number of mismatches for the best couple (blue) and the second-best couple (red) found by APIS parentage assignment.
Fig 8.
Mean Contrast and SigStren value for each marker genotype given by either GenoTriplo or ploidyClassifier.