Table 2. Summary of the whole genome sequence variations between wild rice lines and reference genomes.

Reference genome	Sample	SNP	InDel	SV
93–11*	Huaye 1	1,337,698	180,404	6,319
	Huaye 2	1,063,472	148,774	6,489
Nipponbare*	Huaye 1	1,209,308	161,117	4,192
	Huaye 2	1,387,959	180,226	5,305
Total		4,998,437	670,521	22,305

*http://plants.ensembl.org/Oryza_indica/Info/Index (93–11)

http://plants.ensembl.org/Oryza_sativa/Info/Index (Nipponbare)