| Variant ID: vg0230128709 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 30128709 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )
TGATCGACTCGTTACCCATGAGATGTTGTCGTAGCCACGCGGGGAAAGTATCAATGTGATGCCGTGTAATCCATGCATCGGACTTACCGATGTTCTTGGC[G/A]
CGAACTAGAGCCAAGTGCTCCTCGATGTAAGGAGCTACCAATGAAGAGTGTTGCAGAACAGTGAAATGGGCTTTACGGAATAAATTGTTGTCTACCGTCA
TGACGGTAGACAACAATTTATTCCGTAAAGCCCATTTCACTGTTCTGCAACACTCTTCATTGGTAGCTCCTTACATCGAGGAGCACTTGGCTCTAGTTCG[C/T]
GCCAAGAACATCGGTAAGTCCGATGCATGGATTACACGGCATCACATTGATACTTTCCCCGCGTGGCTACGACAACATCTCATGGGTAACGAGTCGATCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.90% | 0.30% | 5.63% | 56.22% | NA |
| All Indica | 2759 | 4.20% | 0.00% | 7.61% | 88.22% | NA |
| All Japonica | 1512 | 97.90% | 0.90% | 0.53% | 0.73% | NA |
| Aus | 269 | 15.20% | 0.00% | 15.99% | 68.77% | NA |
| Indica I | 595 | 2.20% | 0.00% | 11.09% | 86.72% | NA |
| Indica II | 465 | 5.60% | 0.00% | 4.30% | 90.11% | NA |
| Indica III | 913 | 2.40% | 0.00% | 5.70% | 91.89% | NA |
| Indica Intermediate | 786 | 6.90% | 0.00% | 9.16% | 83.97% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.39% | 0.39% | NA |
| Tropical Japonica | 504 | 98.00% | 0.40% | 0.60% | 0.99% | NA |
| Japonica Intermediate | 241 | 93.40% | 4.60% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 5.56% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0230128709 | G -> A | LOC_Os02g49300.1 | synonymous_variant ; p.Arg815Arg; LOW | synonymous_codon | Average:13.318; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0230128709 | G -> DEL | LOC_Os02g49300.1 | N | frameshift_variant | Average:13.318; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |