| Variant ID: vg0409082025 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9082025 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 331. )
AGGATTTATACTGGGCCAGCTTGCGATGTAATGGTCCAGTAAGCGTGAGGGTTGCTTGTAAACATCCCAGGGAGCTGCACTTCTCAAACTATGTTGTATA[T/A]
CAACTGGGTTGGTTACTTGATTAGATTGTAGAAAGAGCTACCCTACATATGAGAATAGACAAAACCAACCTGTTGATGGCGATGACATGGATGATAAAAA
TTTTTATCATCCATGTCATCGCCATCAACAGGTTGGTTTTGTCTATTCTCATATGTAGGGTAGCTCTTTCTACAATCTAATCAAGTAACCAACCCAGTTG[A/T]
TATACAACATAGTTTGAGAAGTGCAGCTCCCTGGGATGTTTACAAGCAACCCTCACGCTTACTGGACCATTACATCGCAAGCTGGCCCAGTATAAATCCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.40% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.70% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.80% | 2.00% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409082025 | T -> A | LOC_Os04g16680.1 | upstream_gene_variant ; 4137.0bp to feature; MODIFIER | N | Average:55.124; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |
| vg0409082025 | T -> A | LOC_Os04g16700.1 | downstream_gene_variant ; 3039.0bp to feature; MODIFIER | N | Average:55.124; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |
| vg0409082025 | T -> A | LOC_Os04g16690.1 | intron_variant ; MODIFIER | N | Average:55.124; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |