| Variant ID: vg0329361666 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29361666 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 82. )
CGGCGTCGAGCTCCGCCCGCTCTGCTTGCAGGGCCTCCACCTGGGCACTTAACCCGTCCAACACCGTGGTGTTTGCGATGGCCAAGGCCTGCAGAAGGGG[T/C]
TCTGCGCTCAGTGGAGCAACGGAAGGCGTGGGGAAGAGCCGCCTCGAAGAGGATGCTGCGCGGCTTGGCCCGCCGATGGACGTGCCGGACTCGGGGATGT
ACATCCCCGAGTCCGGCACGTCCATCGGCGGGCCAAGCCGCGCAGCATCCTCTTCGAGGCGGCTCTTCCCCACGCCTTCCGTTGCTCCACTGAGCGCAGA[A/G]
CCCCTTCTGCAGGCCTTGGCCATCGCAAACACCACGGTGTTGGACGGGTTAAGTGCCCAGGTGGAGGCCCTGCAAGCAGAGCGGGCGGAGCTCGACGCCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.60% | 5.20% | 18.83% | 19.36% | NA |
| All Indica | 2759 | 38.30% | 8.80% | 30.74% | 22.18% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.33% | 0.20% | NA |
| Aus | 269 | 1.90% | 0.40% | 2.60% | 95.17% | NA |
| Indica I | 595 | 53.30% | 2.70% | 33.28% | 10.76% | NA |
| Indica II | 465 | 38.70% | 4.50% | 30.75% | 26.02% | NA |
| Indica III | 913 | 28.80% | 15.30% | 28.81% | 27.05% | NA |
| Indica Intermediate | 786 | 37.80% | 8.30% | 31.04% | 22.90% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 54.20% | 1.00% | 19.79% | 25.00% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 12.22% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329361666 | T -> C | LOC_Os03g51320.1 | synonymous_variant ; p.Glu566Glu; LOW | synonymous_codon | Average:32.821; most accessible tissue: Zhenshan97 flower, score: 72.863 | N | N | N | N |
| vg0329361666 | T -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:32.821; most accessible tissue: Zhenshan97 flower, score: 72.863 | N | N | N | N |