Fig. 2

Intermediate data produced by AFLAP when analyzing an A. thaliana F₂ population. Analysis of parental accession Colombia (Col) is plotted on the left and Landsberg (Ler) on the right. a JELLYFISH histograms were plotted to determine the lower and upper boundaries of single-copy 31-mers (indicated by dotted lines). 31-mers found in both parents were discarded (gray arrows) from further analysis. 31-mers unique to either accession were assembled for each parent (black arrows). b The distribution of the assembled fragments from 31-mers showing that most of these fragments are 61 bp (SNPs). Assembled fragments < 61 bp were discarded (gray arrows). A representative 31-mer marker was extracted from each fragment ≥ 61 bp, verified against the parents, and used for downstream genotyping (black arrows). b Segregation of 31-mer markers in the F₂ population. Markers extracted from fragments > 61 bp segregate at the same frequency as markers derived from fragments exactly = 61 bp, although > 3% of Ler-derived markers from fragments > 61 bp were not observed in the F₂ population and most were found to be contaminants. The modal segregation of Colombia markers was 55%, for Landsberg it was 51%. The black vertical line indicated the expected marker presence of 75% in the F2 (Aa x Aa)