| Variant ID: vg1225603349 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25603349 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )
ACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACCGGTGAATTTATCCGGCCTCAGTGCATCG[G/A]
CAAAACCAGCCATAGTAAAATCACAGTGCCTATAATAAGGTTTTTGGATTGTTGAGATTATAGACATATAATGATTTAATCTATTCTATAAATAAATCAT
ATGATTTATTTATAGAATAGATTAAATCATTATATGTCTATAATCTCAACAATCCAAAAACCTTATTATAGGCACTGTGATTTTACTATGGCTGGTTTTG[C/T]
CGATGCACTGAGGCCGGATAAATTCACCGGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGT
| 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 | 68.60% | 0.10% | 3.20% | 28.08% | NA |
| All Indica | 2759 | 58.30% | 0.10% | 3.77% | 37.84% | NA |
| All Japonica | 1512 | 97.80% | 0.30% | 1.92% | 0.00% | NA |
| Aus | 269 | 6.70% | 0.00% | 4.09% | 89.22% | NA |
| Indica I | 595 | 89.40% | 0.20% | 0.84% | 9.58% | NA |
| Indica II | 465 | 35.50% | 0.00% | 1.29% | 63.23% | NA |
| Indica III | 913 | 56.00% | 0.00% | 6.35% | 37.68% | NA |
| Indica Intermediate | 786 | 50.90% | 0.30% | 4.45% | 44.40% | NA |
| Temperate Japonica | 767 | 96.00% | 0.50% | 3.52% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 2.08% | 25.00% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 5.56% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225603349 | G -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:17.317; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg1225603349 | G -> A | LOC_Os12g41280.1 | missense_variant ; p.Ala5Val; MODERATE | nonsynonymous_codon ; A5V | Average:17.317; most accessible tissue: Zhenshan97 panicle, score: 36.038 | unknown | unknown | DELETERIOUS | 0.02 |