Table 2. Numbers of contigs in different size categories where θ is lower than the cutoff.

Contig size (kb)	Number of contigs (% genome)
	japonica (J)	indica (I)	overlapping regions (I and J)	O. rufipogon
<100	64	60	40	77
100∼200	96	44	27	31
200∼300	49	28	11	4
300∼400	22	17	6	0
400∼500	33	5	2	0
500∼600	9	2	2	0
≥600	53	7	2	0
<200 kb	160 (4.90%)	104 (2.75%)	67 (1.60%)	108 (2.45%)
≥200 kb	166 (26.38%)	59 (6.15%)	23 (2.35%)	4 (0.25%)

Common regions are windows overlapping between indica and japonica. The cutoff is determined for each subspecies by whole-genome random shuffling of 1 kb segments (see Materials and Methods). The cutoff values (θ per kb) are 0.215 for japonica, 2.153 for indica and 2.343 for O. rufipogon.