| Variant ID: vg0409586482 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586482 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )
GACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAACCCGAGAAACCCTGAAGGGGTAACTAGCTATATATAG[G/A]
GGTGGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCAGCTTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCCAAATGAAGTTACA
TGTAACTTCATTTGGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAAGCTGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCCACC[C/T]
CTATATATAGCTAGTTACCCCTTCAGGGTTTCTCGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTC
| 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 | 46.90% | 0.10% | 11.91% | 41.13% | NA |
| All Indica | 2759 | 16.40% | 0.10% | 19.54% | 63.94% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Aus | 269 | 34.20% | 0.00% | 5.95% | 59.85% | NA |
| Indica I | 595 | 15.50% | 0.00% | 18.32% | 66.22% | NA |
| Indica II | 465 | 17.20% | 0.20% | 13.98% | 68.60% | NA |
| Indica III | 913 | 13.80% | 0.00% | 19.82% | 66.37% | NA |
| Indica Intermediate | 786 | 19.60% | 0.40% | 23.41% | 56.62% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 3.12% | 4.17% | NA |
| Intermediate | 90 | 82.20% | 0.00% | 5.56% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586482 | G -> DEL | N | N | silent_mutation | Average:9.709; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0409586482 | G -> A | LOC_Os04g17510.1 | upstream_gene_variant ; 1791.0bp to feature; MODIFIER | silent_mutation | Average:9.709; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0409586482 | G -> A | LOC_Os04g17530.1 | downstream_gene_variant ; 1756.0bp to feature; MODIFIER | silent_mutation | Average:9.709; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0409586482 | G -> A | LOC_Os04g17540.1 | downstream_gene_variant ; 4215.0bp to feature; MODIFIER | silent_mutation | Average:9.709; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0409586482 | G -> A | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.709; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |