| Variant ID: vg1206302047 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6302047 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 51. )
CGGCGGAGGCCATCACCGGCGCCTCCTGCAGCGCCGCCGCCATGACGAACAGCATCAGGACGAGCAGCGCCGCCAGCCGCCGCCGGCCACCGGTGGCCCT[G/A]
AGCGCCGCCGCCATCGCCGATCCTCCGATGATCCTTACTAACTAATTAAGCTACTTAACTGATTTGTCACAGATGTTTGGGTTAATCTGAATTTGCTGAA
TTCAGCAAATTCAGATTAACCCAAACATCTGTGACAAATCAGTTAAGTAGCTTAATTAGTTAGTAAGGATCATCGGAGGATCGGCGATGGCGGCGGCGCT[C/T]
AGGGCCACCGGTGGCCGGCGGCGGCTGGCGGCGCTGCTCGTCCTGATGCTGTTCGTCATGGCGGCGGCGCTGCAGGAGGCGCCGGTGATGGCCTCCGCCG
| 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 | 62.90% | 2.90% | 7.24% | 26.96% | NA |
| All Indica | 2759 | 74.60% | 4.80% | 10.15% | 10.47% | NA |
| All Japonica | 1512 | 48.80% | 0.10% | 2.51% | 48.54% | NA |
| Aus | 269 | 14.50% | 0.00% | 3.72% | 81.78% | NA |
| Indica I | 595 | 90.30% | 0.00% | 0.84% | 8.91% | NA |
| Indica II | 465 | 75.30% | 5.80% | 14.41% | 4.52% | NA |
| Indica III | 913 | 66.40% | 8.80% | 14.90% | 9.97% | NA |
| Indica Intermediate | 786 | 71.90% | 3.20% | 9.16% | 15.78% | NA |
| Temperate Japonica | 767 | 59.10% | 0.00% | 3.78% | 37.16% | NA |
| Tropical Japonica | 504 | 29.80% | 0.40% | 1.19% | 68.65% | NA |
| Japonica Intermediate | 241 | 56.00% | 0.00% | 1.24% | 42.74% | NA |
| VI/Aromatic | 96 | 86.50% | 1.00% | 8.33% | 4.17% | NA |
| Intermediate | 90 | 60.00% | 3.30% | 6.67% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206302047 | G -> DEL | LOC_Os12g11620.1 | N | frameshift_variant | Average:79.691; most accessible tissue: Zhenshan97 flag leaf, score: 87.661 | N | N | N | N |
| vg1206302047 | G -> A | LOC_Os12g11620.1 | synonymous_variant ; p.Leu5Leu; LOW | synonymous_codon | Average:79.691; most accessible tissue: Zhenshan97 flag leaf, score: 87.661 | N | N | N | N |