Loci with polymorphisms both in the indica-nupt comparison and among sequenced rice pt genomes
–, Absence of nucleotide(s).
| Locus | Coordinates in the indica Rice Plastome | japonica Plastome | 131-kb nuptDNA on Chromosome 10 | O. nivara | indica Plastome |
|---|---|---|---|---|---|
| Linking japonica-nupt | |||||
| 1 | 64,174 | C | C | A | A |
| 2 | 66,410 | A | A | G | G |
| 3 | 62,529–62,536 | CTTGGTCT | CTTGGTCT | AGACCAAG | AGACCAAG |
| 4 | 65,623–65,624 | TT | TT | – | – |
| 5 | 5,015–5,016 | – | – | CCTTTAT | CCTTTAT |
| Linking nivara-nupt | |||||
| 6 | 8,128 | G | A | A | G |
| Linking indica-nupt | |||||
| 7 | 17,785–17,786 | – | 32 nucleotides | – | 32 nucleotides |
| Multiple mutations | |||||
| 8 | 75,989–75,990 | TT | – | TT | T |
| 9 | 77,735–77,736 | – | G | G | TGG |
| 10 | 78,434–78,440 | TTTTTTT | – | TTT | TTTTTT |
| 11 | 80,620 | – | T | T | TT |
| 12 | 134,536–134,545 | A10 | A9 | A11 | A12 |