Fig. 6

Analysis of the polymorphic TEs found in this study. Comparison of the number of polymorphic TEs per A LTR family and B DNA TE type found in Tian et al. [38] and in this study. Differences in y- and x-scales are partly explained by the fact that counts for Tian et al. are summed over occurrences in all samples whereas our data counts each SV only once. Note that all scales are logarithmic. C Proportion of matching nucleotides between the two terminal repeats for TE sequences corresponding to 40 different SVs grouped by DNA TE superfamily and by the identifier of the TE sequence they matched in the SoyTEdb database. D Alternate allele frequencies of 156 SNVs located in a ~39-kb linkage disequilibrium block between positions Gm04:2,220,398 and Gm04:2,259,326. Frequencies were computed for three different groups of samples depending on their genotype at the TE insertion site (Gm04:2,257,090). absent: absence of the TE insertion, which corresponds to the reference allele (71 samples); present: presence of the 480-bp Stowaway MITE (9 samples); excised: presence of a 6-bp insertion at the insertion site, putatively left by excision of the TE insertion (14 samples). The locations of three SNVs whose frequency in the “present” and “excised” groups diverge are shown with dotted vertical lines