| Variant ID: vg0209334297 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9334297 |
| 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: 281. )
CTAGAACTATTTAATATTATTAATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCT[G/A]
GGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTTGTTAAGCAGGTTTGAAGAATTAAAACACTAACTTGGGTACATTGCTCGG
CCGAGCAATGTACCCAAGTTAGTGTTTTAATTCTTCAAACCTGCTTAACAACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACC[C/T]
AGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATTAATAATATTAAATAGTTCTAG
| 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 | 45.50% | 1.40% | 15.62% | 37.52% | NA |
| All Indica | 2759 | 16.80% | 2.40% | 21.24% | 59.62% | NA |
| All Japonica | 1512 | 97.50% | 0.00% | 0.26% | 2.25% | NA |
| Aus | 269 | 26.00% | 0.00% | 48.70% | 25.28% | NA |
| Indica I | 595 | 23.70% | 0.20% | 7.39% | 68.74% | NA |
| Indica II | 465 | 23.20% | 2.20% | 24.30% | 50.32% | NA |
| Indica III | 913 | 7.00% | 3.70% | 28.37% | 60.90% | NA |
| Indica Intermediate | 786 | 19.10% | 2.50% | 21.63% | 56.74% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.26% | 1.56% | NA |
| Tropical Japonica | 504 | 96.60% | 0.00% | 0.20% | 3.17% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 9.38% | 2.08% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 8.89% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209334297 | G -> A | LOC_Os02g16390.1 | upstream_gene_variant ; 1533.0bp to feature; MODIFIER | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0209334297 | G -> A | LOC_Os02g16380.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0209334297 | G -> DEL | N | N | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |