| Variant ID: vg0114587506 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587506 |
| 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: 268. )
CTGAAGAGTACATTAATTTAAGTGTTGCATTCATGGTAAGAACAAGAACAACTATACAGAGTTTTTGTATGTACGAAGTTGAGTACTCACATATGTCAAC[G/A]
TCATTTACCTAGACAAATTTGAAGAATTCAGCAGAAGAAAGATTATGTTCTTGGTTTTCCATAGTCCACATCATGGTCCACATTTGGAGGGAAAATGAAA
TTTCATTTTCCCTCCAAATGTGGACCATGATGTGGACTATGGAAAACCAAGAACATAATCTTTCTTCTGCTGAATTCTTCAAATTTGTCTAGGTAAATGA[C/T]
GTTGACATATGTGAGTACTCAACTTCGTACATACAAAAACTCTGTATAGTTGTTCTTGTTCTTACCATGAATGCAACACTTAAATTAATGTACTCTTCAG
| 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 | 78.70% | 0.90% | 0.49% | 19.95% | NA |
| All Indica | 2759 | 65.50% | 0.10% | 0.80% | 33.64% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.00% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 50.90% | 0.00% | 0.84% | 48.24% | NA |
| Indica II | 465 | 71.00% | 0.00% | 0.00% | 29.03% | NA |
| Indica III | 913 | 70.20% | 0.20% | 1.10% | 28.48% | NA |
| Indica Intermediate | 786 | 67.70% | 0.10% | 0.89% | 31.30% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 60.40% | 39.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 1.10% | 1.11% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587506 | G -> A | LOC_Os01g25730.1 | downstream_gene_variant ; 4128.0bp to feature; MODIFIER | silent_mutation | Average:62.436; most accessible tissue: Zhenshan97 young leaf, score: 77.422 | N | N | N | N |
| vg0114587506 | G -> A | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.436; most accessible tissue: Zhenshan97 young leaf, score: 77.422 | N | N | N | N |
| vg0114587506 | G -> DEL | N | N | silent_mutation | Average:62.436; most accessible tissue: Zhenshan97 young leaf, score: 77.422 | N | N | N | N |