| Variant ID: vg0204059404 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 4059404 |
| Reference Allele: A | Alternative Allele: AC |
| Primary Allele: A | Secondary Allele: AC |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 150. )
TTTGCACCTCCATCTGCATTCTGATGGCATCGTTCACGTTGCGGCTGAGAGAGAGAATTTCACACACAAGCAAACACAAAAATGGAGTTAGGAAAGAACA[A/AC]
AAAAAAAGAGTAACTGAACAAGGACTAAGAAAGAAATTAAAATCTTAAACCGGATTAATTCTACAGTACTAGTGTACTGTTACTAGTGTACTAGTGTAGG
CCTACACTAGTACACTAGTAACAGTACACTAGTACTGTAGAATTAATCCGGTTTAAGATTTTAATTTCTTTCTTAGTCCTTGTTCAGTTACTCTTTTTTT[T/GT]
TGTTCTTTCCTAACTCCATTTTTGTGTTTGCTTGTGTGTGAAATTCTCTCTCTCAGCCGCAACGTGAACGATGCCATCAGAATGCAGATGGAGGTGCAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |