| Variant ID: vg1225600262 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25600262 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 363. )
CAACAAGCTAGGATCATAAGGTGTTGGAGAAGGCTTACTATCAATATAGCCAAAACGATTCAAGATCTTCTCCACATAATGGGACTGCAAGAGTGTAATC[C/T]
CATTCTCACCTCTAATTAGCTTAATGTTTAAGATAACATCAGCTACTCCCAAATCCTTCATATCAAAATTTTGAGACAAGAATGATTTAACCTCATTTAT
ATAAATGAGGTTAAATCATTCTTGTCTCAAAATTTTGATATGAAGGATTTGGGAGTAGCTGATGTTATCTTAAACATTAAGCTAATTAGAGGTGAGAATG[G/A]
GATTACACTCTTGCAGTCCCATTATGTGGAGAAGATCTTGAATCGTTTTGGCTATATTGATAGTAAGCCTTCTCCAACACCTTATGATCCTAGCTTGTTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.00% | 0.10% | 7.74% | 32.12% | NA |
| All Indica | 2759 | 43.30% | 0.00% | 12.07% | 44.65% | NA |
| All Japonica | 1512 | 99.10% | 0.40% | 0.40% | 0.07% | NA |
| Aus | 269 | 3.30% | 0.00% | 7.06% | 89.59% | NA |
| Indica I | 595 | 86.70% | 0.00% | 2.86% | 10.42% | NA |
| Indica II | 465 | 19.10% | 0.00% | 12.47% | 68.39% | NA |
| Indica III | 913 | 30.60% | 0.00% | 18.95% | 50.49% | NA |
| Indica Intermediate | 786 | 39.40% | 0.00% | 10.81% | 49.75% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 1.20% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 2.08% | 25.00% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 6.67% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225600262 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:14.409; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg1225600262 | C -> T | LOC_Os12g41280.1 | missense_variant ; p.Gly1034Glu; MODERATE | nonsynonymous_codon ; G1034E | Average:14.409; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | TOLERATED | 0.13 |