| Variant ID: vg0332982053 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 32982053 |
| Reference Allele: A | Alternative Allele: G |
| 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: 277. )
AACTCACTCGTAAGCAACTCATTTTCCGCTACGGGATTGGTAGAACTAGAACATCGATCAAATTCAGCTTGAAGATTGTATAGCAAATCAGCAAGTGACT[A/G]
TTTGACACTAAAAAATTATGTGCAAGCCGGTAAGCAGGGATTGAACCAGAGCCTGCTTGTGTCAATTTGTACTATTTGATGCGTGCATCAATCAACAACA
TGTTGTTGATTGATGCACGCATCAAATAGTACAAATTGACACAAGCAGGCTCTGGTTCAATCCCTGCTTACCGGCTTGCACATAATTTTTTAGTGTCAAA[T/C]
AGTCACTTGCTGATTTGCTATACAATCTTCAAGCTGAATTTGATCGATGTTCTAGTTCTACCAATCCCGTAGCGGAAAATGAGTTGCTTACGAGTGAGTT
| 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 | 62.20% | 37.70% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 94.50% | 5.50% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 0.90% | 99.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.00% | 7.80% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.60% | 98.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 45.60% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0332982053 | A -> G | LOC_Os03g57900.1 | 3_prime_UTR_variant ; 340.0bp to feature; MODIFIER | silent_mutation | Average:54.893; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
| vg0332982053 | A -> G | LOC_Os03g57910.1 | downstream_gene_variant ; 2461.0bp to feature; MODIFIER | silent_mutation | Average:54.893; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
| vg0332982053 | A -> G | LOC_Os03g57920.1 | downstream_gene_variant ; 4990.0bp to feature; MODIFIER | silent_mutation | Average:54.893; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |