| Variant ID: vg1225600858 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25600858 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )
CGCCTTCTTTCTGAGTATAGCCCTTAGCAACAAGCCGAGCCTTGTACTTTTCAATAGTACCGTCAGGCCTAAGCTTCTTCTTGAACACCCACTTGCACCC[C/A]
ACAGGTTTACACCCATAGGGTCGCTCTGTCACCTCCCAAGTCCCGTTAGCGATAATGGAATCCATTTCACTACGGACAGCCTCCTTCCAGTAGTCTGCAT
ATGCAGACTACTGGAAGGAGGCTGTCCGTAGTGAAATGGATTCCATTATCGCTAACGGGACTTGGGAGGTGACAGAGCGACCCTATGGGTGTAAACCTGT[G/T]
GGGTGCAAGTGGGTGTTCAAGAAGAAGCTTAGGCCTGACGGTACTATTGAAAAGTACAAGGCTCGGCTTGTTGCTAAGGGCTATACTCAGAAAGAAGGCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.50% | 0.30% | 41.32% | 43.91% | NA |
| All Indica | 2759 | 7.60% | 0.10% | 30.99% | 61.22% | NA |
| All Japonica | 1512 | 30.60% | 0.20% | 65.67% | 3.57% | NA |
| Aus | 269 | 0.00% | 0.40% | 0.37% | 99.26% | NA |
| Indica I | 595 | 22.70% | 0.00% | 61.01% | 16.30% | NA |
| Indica II | 465 | 3.20% | 0.00% | 9.89% | 86.88% | NA |
| Indica III | 913 | 1.80% | 0.00% | 23.55% | 74.70% | NA |
| Indica Intermediate | 786 | 5.70% | 0.50% | 29.39% | 64.38% | NA |
| Temperate Japonica | 767 | 46.00% | 0.30% | 47.85% | 5.87% | NA |
| Tropical Japonica | 504 | 15.90% | 0.00% | 83.73% | 0.40% | NA |
| Japonica Intermediate | 241 | 12.00% | 0.40% | 84.65% | 2.90% | NA |
| VI/Aromatic | 96 | 5.20% | 4.20% | 63.54% | 27.08% | NA |
| Intermediate | 90 | 8.90% | 0.00% | 47.78% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225600858 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:8.886; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg1225600858 | C -> A | LOC_Os12g41280.1 | synonymous_variant ; p.Val835Val; LOW | synonymous_codon | Average:8.886; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |