Fig. 3

Genetic map of A. thaliana generated by AFLAP. a 145,330 markers unique to A. thaliana accession Col ordered into five linkage groups. Each horizontal black bar indicates a genetic bin with > 1 marker. The sizes of the blue marks indicate the number of markers in each bin relative to every other genetic bin. Genetic bins with the highest marker densities were near the ends of linkage groups. b Alignment of the genetic map constructed from markers unique to Col against the genome assembly of Col-0. All 31-mers assigned to each genetic bin were aligned to the assembly and plotted. Points are colored by linkage group assignment resulting in a bar depicting the noise for placement of each genetic bin. The average position of each genetic bin is plotted in black, demonstrating that the linkage groups were nearly colinear with the physical assembly. Gray columns indicate centromeric positions. Over 99.99% of the markers were placed on the correct chromosomes and were concordant with the assembly. c 115,810 markers unique to A. thaliana accession Ler ordered into six linkage groups. Sizes of blue marks indicate the number of markers per genetic bin. d Alignment of the genetic map constructed from markers unique to Ler displayed as for Col (B). Arms of Chromosome 3 were generated as independent linkage groups. 98.8% of the markers were placed on the correct chromosomes and were nearly concordant with the assembly. In both b and d, the inexact placement of markers into genetic bins demonstrated by the range of the colored bars is probably due to missing data because of the low coverage of the sequencing data