Table 3. Test for predictability of presence of TE excisions based on SNP frequencies in O. sativa and O. glaberrima.

Polymorphism	Test set	Control set	P value
TE excisions	16	2	0.0003
TE insertions	16	27	0.026
Repeat slippage	20	17	0.53
InDel	25	15	0.18

The sequences of the test set were chosen based on the presence of regions with high numbers of SNPs. Gene-containing regions that had a SNP density similar to that of the genome overall served as a control. Differences between test and control sets were tested with a χ²-test.