| Variant ID: vg0132716350 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 32716350 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )
CTGGCATTGATCTCCATCAACCATGCATGCATCTATTGTCTCAGTTATGCAGATGAGAATTAATTTTGTGTGGTTTAACAACAAGTACTACATCCCAAAA[T/TA]
AATAAATTATGTATACGAATCTGAATATATAACAAAATTTGATTTATTTTAGGAGAAGGAGGATTAATTATATATTATTGTTTTTCTTGATTTTCCTTAT
ATAAGGAAAATCAAGAAAAACAATAATATATAATTAATCCTCCTTCTCCTAAAATAAATCAAATTTTGTTATATATTCAGATTCGTATACATAATTTATT[A/TA]
TTTTGGGATGTAGTACTTGTTGTTAAACCACACAAAATTAATTCTCATCTGCATAACTGAGACAATAGATGCATGCATGGTTGATGGAGATCAATGCCAG
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.70% | 25.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 31.50% | 68.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 88.30% | 11.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 7.90% | 92.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 58.90% | 41.10% | 0.00% | 0.00% | NA |