Table 5 Comparison of the three de novo assemblies to the Indica reference (93-11 from [28])
|  | Unaligned reference bases | Unaligned assembly bases | Average ID | SNPs and smal indels | Indels > 5 kbp | Inversions | Relocations | Translocations |
|---|---|---|---|---|---|---|---|---|
Nipponbare | 16.95% | 8.90% | 98.91% | 2,813,076 | 75,944 | 1,162 | 11,627 | 11,030 |
IR64 | 13.29% | 4.31% | 99.52% | 1,228,732 | 35,762 | 644 | 6,985 | 7,101 |
DJ123 | 14.37% | 6.78% | 99.16% | 2,264,541 | 62,191 | 974 | 8,582 | 10,170 |