| Variant ID: vg0209334291 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9334291 |
| 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: 286. )
ACGATCCTAGAACTATTTAATATTATTAATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCC[G/A]
ACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTTGTTAAGCAGGTTTGAAGAATTAAAACACTAACTTGGGTACATT
AATGTACCCAAGTTAGTGTTTTAATTCTTCAAACCTGCTTAACAACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGT[C/T]
GGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATTAATAATATTAAATAGTTCTAGGATCGT
| 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 | 51.70% | 0.20% | 3.22% | 44.94% | NA |
| All Indica | 2759 | 27.90% | 0.10% | 4.20% | 67.85% | NA |
| All Japonica | 1512 | 97.20% | 0.10% | 0.20% | 2.51% | NA |
| Aus | 269 | 21.90% | 1.90% | 11.52% | 64.68% | NA |
| Indica I | 595 | 26.60% | 0.00% | 2.52% | 70.92% | NA |
| Indica II | 465 | 33.10% | 0.00% | 3.23% | 63.66% | NA |
| Indica III | 913 | 24.10% | 0.10% | 5.04% | 70.76% | NA |
| Indica Intermediate | 786 | 30.20% | 0.10% | 5.09% | 64.63% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 96.00% | 0.20% | 0.40% | 3.37% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 64.40% | 1.10% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209334291 | G -> A | LOC_Os02g16390.1 | upstream_gene_variant ; 1539.0bp to feature; MODIFIER | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0209334291 | 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 |
| vg0209334291 | G -> DEL | N | N | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |