Fig. 1

Example files of PySmooth. (a) Example input genotype file. The first row is the header. Each subsequent row represents a unique marker. The first three columns represent the chromosome name, location, and identification name of the marker, respectively. The fourth and fifth column represent reference/major allele and alternate allele, respectively. These columns can be left blank if not known. A heatmap representing this genotype file is shown in Fig. 2a. (b) Example statistics file corresponding the input genotype file. For each sample the frequency and percentage of each type of genotype call are reported (A: homozygous 1, B: homozygous 2, H: heterozygous, U: missing). A corresponding bar plot is shown in Fig. 2d. (c) Example file indicating the number of singletons detected. In each sample (row), the number and percentage of singletons detected (‘S_count’ and ‘S_count_perc’) are reported. Also reported are the number of original A, B, H genotype calls which were detected as Singletons (S)