| Variant ID: vg1200352586 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 352586 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 300. )
TACTCTTGCTTCAACATAAGTTCTCTATACAACCTACACAGGATTCACCGATGCGTATACCAGCTGAGCAATTCCTTACTTTAAGGGCATATGGTGCACC[G/A]
CCAGTCATAGTAGCGCTTGCAGCACAAGGTGCTTTTCGTGGATTCATGGATACAAAGACACCGTTGTTTGCTGTGGGTAAGACAATGTATGCAAACTCTT
AAGAGTTTGCATACATTGTCTTACCCACAGCAAACAACGGTGTCTTTGTATCCATGAATCCACGAAAAGCACCTTGTGCTGCAAGCGCTACTATGACTGG[C/T]
GGTGCACCATATGCCCTTAAAGTAAGGAATTGCTCAGCTGGTATACGCATCGGTGAATCCTGTGTAGGTTGTATAGAGAACTTATGTTGAAGCAAGAGTA
| 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 | 81.30% | 18.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 68.40% | 31.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 52.80% | 47.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 65.80% | 34.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 69.50% | 30.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1200352586 | G -> A | LOC_Os12g01580.1 | synonymous_variant ; p.Pro252Pro; LOW | synonymous_codon | Average:56.908; most accessible tissue: Minghui63 flag leaf, score: 74.955 | N | N | N | N |
| vg1200352586 | G -> A | LOC_Os12g01580.2 | synonymous_variant ; p.Pro41Pro; LOW | synonymous_codon | Average:56.908; most accessible tissue: Minghui63 flag leaf, score: 74.955 | N | N | N | N |