| Variant ID: vg1225603315 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25603315 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )
GTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATG[C/G]
ACACCGGTGAATTTATCCGGCCTCAGTGCATCGGCAAAACCAGCCATAGTAAAATCACAGTGCCTATAATAAGGTTTTTGGATTGTTGAGATTATAGACA
TGTCTATAATCTCAACAATCCAAAAACCTTATTATAGGCACTGTGATTTTACTATGGCTGGTTTTGCCGATGCACTGAGGCCGGATAAATTCACCGGTGT[G/C]
CATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.10% | 0.40% | 2.05% | 27.42% | NA |
| All Indica | 2759 | 59.50% | 0.70% | 3.19% | 36.64% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 8.20% | 0.00% | 2.23% | 89.59% | NA |
| Indica I | 595 | 90.40% | 0.00% | 0.17% | 9.41% | NA |
| Indica II | 465 | 34.40% | 0.00% | 2.80% | 62.80% | NA |
| Indica III | 913 | 57.70% | 2.00% | 5.48% | 34.83% | NA |
| Indica Intermediate | 786 | 52.90% | 0.10% | 3.05% | 43.89% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 1.04% | 26.04% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 1.11% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225603315 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:17.756; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg1225603315 | C -> G | LOC_Os12g41280.1 | synonymous_variant ; p.Val16Val; LOW | synonymous_codon | Average:17.756; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |