| Variant ID: vg0409586505 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586505 |
| 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: 304. )
TGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAACCCGAGAAACCCTGAAGGGGTAACTAGCTATATATAGGGGTGGGAGGACGACCTAGGGGT[G/A]
CCTAGGGTCGTGCTCCACCAGCTTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCCAAATGAAGTTACAAGCCCATAGGCCCATTATAGGTG
CACCTATAATGGGCCTATGGGCTTGTAACTTCATTTGGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAAGCTGGTGGAGCACGACCCTAGG[C/T]
ACCCCTAGGTCGTCCTCCCACCCCTATATATAGCTAGTTACCCCTTCAGGGTTTCTCGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCA
| 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 | 28.80% | 3.50% | 23.11% | 44.58% | NA |
| All Indica | 2759 | 8.40% | 0.20% | 24.94% | 66.51% | NA |
| All Japonica | 1512 | 68.50% | 10.20% | 21.03% | 0.33% | NA |
| Aus | 269 | 4.80% | 0.40% | 6.69% | 88.10% | NA |
| Indica I | 595 | 11.10% | 0.00% | 23.53% | 65.38% | NA |
| Indica II | 465 | 10.10% | 0.00% | 21.51% | 68.39% | NA |
| Indica III | 913 | 5.40% | 0.00% | 23.99% | 70.65% | NA |
| Indica Intermediate | 786 | 8.80% | 0.60% | 29.13% | 61.45% | NA |
| Temperate Japonica | 767 | 96.90% | 0.40% | 2.61% | 0.13% | NA |
| Tropical Japonica | 504 | 22.20% | 27.60% | 50.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 74.70% | 5.00% | 19.09% | 1.24% | NA |
| VI/Aromatic | 96 | 50.00% | 1.00% | 37.50% | 11.46% | NA |
| Intermediate | 90 | 37.80% | 5.60% | 35.56% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586505 | G -> DEL | N | N | silent_mutation | Average:10.262; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0409586505 | G -> A | LOC_Os04g17510.1 | upstream_gene_variant ; 1814.0bp to feature; MODIFIER | silent_mutation | Average:10.262; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0409586505 | G -> A | LOC_Os04g17530.1 | downstream_gene_variant ; 1733.0bp to feature; MODIFIER | silent_mutation | Average:10.262; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0409586505 | G -> A | LOC_Os04g17540.1 | downstream_gene_variant ; 4192.0bp to feature; MODIFIER | silent_mutation | Average:10.262; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0409586505 | G -> A | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.262; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |