| Variant ID: vg0226608559 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 26608559 |
| Reference Allele: A | Alternative Allele: AAACGGAATTGGAAGTTGTTCGGTCAAGTATAGGAAATT |
| Primary Allele: AAACGGAATTGGAAGTTGTT CGGTCAAGTATAGGAAATT | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 245. )
ACAATCGCAGAAAGTGACCTTTTACATGTACCGTGTTTGACAAAAAGAAGGTAAACCGGAAAATACAAAGCCTGTGAACGTATCACACACGACGAATATC[A/AAACGGAATTGGAAGTTGTTCGGTCAAGTATAGGAAATT]
AATCAAGCAAACGTACGATGCATGCAAACTGACACGGATACTTCAATTAATTCGGTTCATCCACTTTTAAGCGTAGTCCTGGTCGGCAACGGGCTGGTAT
ATACCAGCCCGTTGCCGACCAGGACTACGCTTAAAAGTGGATGAACCGAATTAATTGAAGTATCCGTGTCAGTTTGCATGCATCGTACGTTTGCTTGATT[T/AATTTCCTATACTTGACCGAACAACTTCCAATTCCGTTT]
GATATTCGTCGTGTGTGATACGTTCACAGGCTTTGTATTTTCCGGTTTACCTTCTTTTTGTCAAACACGGTACATGTAAAAGGTCACTTTCTGCGATTGT
| Populations | Population Size | Frequency of AAACGGAATTGGAAGTTGTT CGGTCAAGTATAGGAAATT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.40% | 49.30% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 79.80% | 19.70% | 0.51% | 0.00% | NA |
| All Japonica | 1512 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 52.40% | 47.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.40% | 8.90% | 0.67% | 0.00% | NA |
| Indica II | 465 | 76.60% | 23.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 71.50% | 28.00% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 83.30% | 16.00% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 30.00% | 68.90% | 1.11% | 0.00% | NA |