| Variant ID: vg1206299819 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6299819 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 42. )
CGGAAGCTGTCCACTTTGAAGCAACACCCTCGCGGCGGAGGCCATCGCCGGCGCCTCCAGCAGCGCTGCCGCCAAGACGAACATCATCATGACGAGCACC[T/G]
CCGCCAGCCGCCGGCCGCCGGTGGTCCTGAGCGCCGCCGCCATCGCCGATCCTCCGATGATCTTTGCTATCTAAGCTACTAATTAACTGATTTTGAGACA
TGTCTCAAAATCAGTTAATTAGTAGCTTAGATAGCAAAGATCATCGGAGGATCGGCGATGGCGGCGGCGCTCAGGACCACCGGCGGCCGGCGGCTGGCGG[A/C]
GGTGCTCGTCATGATGATGTTCGTCTTGGCGGCAGCGCTGCTGGAGGCGCCGGCGATGGCCTCCGCCGCGAGGGTGTTGCTTCAAAGTGGACAGCTTCCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.50% | 12.70% | 0.11% | 65.68% | NA |
| All Indica | 2759 | 27.50% | 1.40% | 0.11% | 71.04% | NA |
| All Japonica | 1512 | 9.50% | 34.70% | 0.13% | 55.62% | NA |
| Aus | 269 | 1.90% | 9.70% | 0.00% | 88.48% | NA |
| Indica I | 595 | 73.90% | 1.50% | 0.00% | 24.54% | NA |
| Indica II | 465 | 18.30% | 1.70% | 0.00% | 80.00% | NA |
| Indica III | 913 | 2.60% | 0.70% | 0.22% | 96.50% | NA |
| Indica Intermediate | 786 | 26.60% | 1.90% | 0.13% | 71.37% | NA |
| Temperate Japonica | 767 | 15.50% | 37.90% | 0.26% | 46.28% | NA |
| Tropical Japonica | 504 | 2.40% | 23.00% | 0.00% | 74.60% | NA |
| Japonica Intermediate | 241 | 5.40% | 49.00% | 0.00% | 45.64% | NA |
| VI/Aromatic | 96 | 84.40% | 1.00% | 0.00% | 14.58% | NA |
| Intermediate | 90 | 31.10% | 12.20% | 0.00% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206299819 | T -> DEL | LOC_Os12g11610.1 | N | frameshift_variant | Average:68.606; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg1206299819 | T -> G | LOC_Os12g11610.1 | missense_variant ; p.Glu15Ala; MODERATE | nonsynonymous_codon ; E15A | Average:68.606; most accessible tissue: Zhenshan97 panicle, score: 82.888 | unknown | unknown | TOLERATED | 1.00 |