Table 2.

Comparison of the three de novo assemblies to the Nipponbare reference (IRGSP-1.0)

	Unaligned reference bases	Unaligned assembly bases	Average ID	SNPs and small indels	Indels > 5 bp	Inversions	Relocations	Translocations
Nipponbare	3.14%	0.31%	99.94%	57,459	3,445	131	252	617
IR64	11.08%	8.94%	98.91%	2,917,780	80,631	1,004	1,721	7,060
DJ123	9.85%	8.55%	98.93%	2,933,257	80,346	1,007	1,615	6,683