| Variant ID: vg0410079379 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079379 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 128. )
ACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTATCAAAACCCAAGAAACCCTGAAGGGGTACCTA[A/G]
CTATATAAATAGGGGTGGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCTGGCTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCC
GGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAGCCAGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCCACCCCTATTTATATAG[T/C]
TAGGTACCCCTTCAGGGTTTCTTGGGTTTTGATAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGT
| 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 | 27.60% | 1.10% | 5.73% | 65.57% | NA |
| All Indica | 2759 | 1.70% | 1.70% | 5.04% | 91.55% | NA |
| All Japonica | 1512 | 77.10% | 0.30% | 6.81% | 15.87% | NA |
| Aus | 269 | 1.10% | 0.40% | 2.97% | 95.54% | NA |
| Indica I | 595 | 1.70% | 2.20% | 4.20% | 91.93% | NA |
| Indica II | 465 | 1.50% | 1.70% | 5.59% | 91.18% | NA |
| Indica III | 913 | 1.40% | 1.20% | 4.93% | 92.44% | NA |
| Indica Intermediate | 786 | 2.00% | 2.00% | 5.47% | 90.46% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.52% | 3.00% | NA |
| Tropical Japonica | 504 | 49.20% | 0.60% | 18.06% | 32.14% | NA |
| Japonica Intermediate | 241 | 73.40% | 0.40% | 3.32% | 22.82% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 15.62% | 33.33% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 6.67% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079379 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0410079379 | A -> G | LOC_Os04g18230.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |