| Variant ID: vg0409081975 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9081975 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.12, others allele: 0.00, population size: 245. )
TAGAACTGAAGATGCAGTCAAATCAACTGTTGAATTAGTGGGAGAATTTGAGGATTTATACTGGGCCAGCTTGCGATGTAATGGTCCAGTAAGCGTGAGG[G/A]
TTGCTTGTAAACATCCCAGGGAGCTGCACTTCTCAAACTATGTTGTATATCAACTGGGTTGGTTACTTGATTAGATTGTAGAAAGAGCTACCCTACATAT
ATATGTAGGGTAGCTCTTTCTACAATCTAATCAAGTAACCAACCCAGTTGATATACAACATAGTTTGAGAAGTGCAGCTCCCTGGGATGTTTACAAGCAA[C/T]
CCTCACGCTTACTGGACCATTACATCGCAAGCTGGCCCAGTATAAATCCTCAAATTCTCCCACTAATTCAACAGTTGATTTGACTGCATCTTCAGTTCTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.10% | 34.80% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 0.90% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 1.00% | 98.90% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 1.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 14.60% | 85.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 47.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081975 | G -> A | LOC_Os04g16680.1 | upstream_gene_variant ; 4087.0bp to feature; MODIFIER | silent_mutation | Average:55.49; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg0409081975 | G -> A | LOC_Os04g16700.1 | downstream_gene_variant ; 3089.0bp to feature; MODIFIER | silent_mutation | Average:55.49; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg0409081975 | G -> A | LOC_Os04g16690.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.49; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |