| Variant ID: vg1225603252 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25603252 |
| 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: 128. )
CGCCAAGAACGCTAAGAATGCATCCCACAAAGAGAGTAGTGGCTTCCTCGAATTGCTTCTGCTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACT[C/T]
ACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACCGGTGAATTTATCCGGCCTCAGTGCATCGGCAA
TTGCCGATGCACTGAGGCCGGATAAATTCACCGGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGT[G/A]
AGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAACAGCAGAAGCAATTCGAGGAAGCCACTACTCTCTTTGTGGGATGCATTCTTAGCGTTCTTGGCG
| 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 | 77.00% | 3.00% | 5.76% | 14.33% | NA |
| All Indica | 2759 | 70.90% | 5.00% | 9.57% | 14.57% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 10.00% | 0.00% | 1.12% | 88.85% | NA |
| Indica I | 595 | 73.80% | 16.10% | 5.88% | 4.20% | NA |
| Indica II | 465 | 55.30% | 1.50% | 16.13% | 27.10% | NA |
| Indica III | 913 | 83.40% | 0.00% | 5.37% | 11.28% | NA |
| Indica Intermediate | 786 | 63.40% | 4.50% | 13.36% | 18.83% | 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% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 1.04% | 22.92% | NA |
| Intermediate | 90 | 78.90% | 1.10% | 4.44% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225603252 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:15.509; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |
| vg1225603252 | C -> T | LOC_Os12g41280.1 | synonymous_variant ; p.Val37Val; LOW | synonymous_codon | Average:15.509; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |