| Variant ID: vg0409854434 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9854434 |
| 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: 300. )
GCCTATGGGCTTGTAACCTCATTTGGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAAGCTGGTGGAGCACGACCCTAGGCACCCCTAGGTC[G/A]
TCCTCCCACCCCTATATATAGCTAGTTACCCCTTCAGGGTTTCTGGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCG
CGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAACCCCAGAAACCCTGAAGGGGTAACTAGCTATATATAGGGGTGGGAGGA[C/T]
GACCTAGGGGTGCCTAGGGTCGTGCTCCACCAGCTTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCCAAATGAGGTTACAAGCCCATAGGC
| 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 | 32.70% | 0.10% | 5.35% | 61.87% | NA |
| All Indica | 2759 | 20.00% | 0.10% | 7.50% | 72.38% | NA |
| All Japonica | 1512 | 61.20% | 0.10% | 1.12% | 37.57% | NA |
| Aus | 269 | 11.90% | 0.40% | 5.95% | 81.78% | NA |
| Indica I | 595 | 17.30% | 0.00% | 5.71% | 76.97% | NA |
| Indica II | 465 | 17.00% | 0.00% | 6.45% | 76.56% | NA |
| Indica III | 913 | 24.00% | 0.10% | 9.20% | 66.70% | NA |
| Indica Intermediate | 786 | 19.30% | 0.10% | 7.51% | 73.03% | NA |
| Temperate Japonica | 767 | 95.70% | 0.10% | 0.52% | 3.65% | NA |
| Tropical Japonica | 504 | 4.80% | 0.00% | 1.39% | 93.85% | NA |
| Japonica Intermediate | 241 | 69.70% | 0.00% | 2.49% | 27.80% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 6.25% | 88.54% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 7.78% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409854434 | G -> DEL | N | N | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854434 | G -> A | LOC_Os04g17910.1 | upstream_gene_variant ; 3739.0bp to feature; MODIFIER | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854434 | G -> A | LOC_Os04g17930.1 | downstream_gene_variant ; 1703.0bp to feature; MODIFIER | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854434 | G -> A | LOC_Os04g17920.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |