| Variant ID: vg0424682788 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24682788 |
| Reference Allele: T | Alternative Allele: G,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, G: 0.04, others allele: 0.00, population size: 90. )
GGTTGATCGACTCGTTACCCATGAGATGTTGTCGTAGCCACGCGAGGAAAGTATCAATGTGATGCCGTGTAATCCATGCATCGGACTTACCGATGTTCCT[T/G,A]
GCGCGAACTAGAGCCAAGTGCTCCTCGATGTAAGGAGCTACCAATGAAGAGTGTTGCAGAACAGTGAAATGGGCTTTACGGAATAAATTGTTGTCTACCG
CGGTAGACAACAATTTATTCCGTAAAGCCCATTTCACTGTTCTGCAACACTCTTCATTGGTAGCTCCTTACATCGAGGAGCACTTGGCTCTAGTTCGCGC[A/C,T]
AGGAACATCGGTAAGTCCGATGCATGGATTACACGGCATCACATTGATACTTTCCTCGCGTGGCTACGACAACATCTCATGGGTAACGAGTCGATCAACC
| 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 | 85.30% | 1.80% | 4.46% | 8.40% | A: 0.02% |
| All Indica | 2759 | 99.20% | 0.20% | 0.51% | 0.11% | A: 0.04% |
| All Japonica | 1512 | 61.00% | 4.50% | 10.12% | 24.34% | NA |
| Aus | 269 | 97.40% | 0.00% | 1.86% | 0.74% | NA |
| Indica I | 595 | 98.00% | 0.00% | 1.51% | 0.34% | A: 0.17% |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.30% | 0.51% | 0.13% | NA |
| Temperate Japonica | 767 | 32.10% | 7.30% | 16.95% | 43.68% | NA |
| Tropical Japonica | 504 | 96.60% | 0.60% | 1.79% | 0.99% | NA |
| Japonica Intermediate | 241 | 78.80% | 3.70% | 5.81% | 11.62% | NA |
| VI/Aromatic | 96 | 31.20% | 13.50% | 34.38% | 20.83% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 6.67% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424682788 | T -> G | LOC_Os04g41599.1 | missense_variant ; p.Lys784Gln; MODERATE | nonsynonymous_codon ; K784Q | Average:5.33; most accessible tissue: Zhenshan97 panicle, score: 16.188 | unknown | unknown | DELETERIOUS | 0.04 |
| vg0424682788 | T -> DEL | LOC_Os04g41599.1 | N | frameshift_variant | Average:5.33; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0424682788 | T -> A | LOC_Os04g41599.1 | stop_gained ; p.Lys784*; HIGH | stop_gained | Average:5.33; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |