| Variant ID: vg0409854412 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9854412 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )
GGTGCTGTGACACCTGTAATGGGCCTATGGGCTTGTAACCTCATTTGGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAAGCTGGTGGAGCA[C/T]
GACCCTAGGCACCCCTAGGTCGTCCTCCCACCCCTATATATAGCTAGTTACCCCTTCAGGGTTTCTGGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTA
TAGCAATGGCTAAACTTTAATCTAACAAAACCCCAGAAACCCTGAAGGGGTAACTAGCTATATATAGGGGTGGGAGGACGACCTAGGGGTGCCTAGGGTC[G/A]
TGCTCCACCAGCTTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCCAAATGAGGTTACAAGCCCATAGGCCCATTACAGGTGTCACAGCACC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.90% | 0.10% | 3.60% | 63.42% | NA |
| All Indica | 2759 | 20.20% | 0.00% | 4.93% | 74.81% | NA |
| All Japonica | 1512 | 61.60% | 0.10% | 0.73% | 37.50% | NA |
| Aus | 269 | 11.90% | 0.00% | 4.46% | 83.64% | NA |
| Indica I | 595 | 17.10% | 0.00% | 4.37% | 78.49% | NA |
| Indica II | 465 | 15.70% | 0.00% | 3.66% | 80.65% | NA |
| Indica III | 913 | 25.40% | 0.00% | 6.57% | 68.02% | NA |
| Indica Intermediate | 786 | 19.20% | 0.10% | 4.20% | 76.46% | NA |
| Temperate Japonica | 767 | 96.20% | 0.10% | 0.00% | 3.65% | NA |
| Tropical Japonica | 504 | 5.20% | 0.20% | 0.99% | 93.65% | NA |
| Japonica Intermediate | 241 | 69.70% | 0.00% | 2.49% | 27.80% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 5.21% | 89.58% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 6.67% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409854412 | C -> DEL | N | N | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854412 | C -> T | LOC_Os04g17910.1 | upstream_gene_variant ; 3717.0bp to feature; MODIFIER | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854412 | C -> T | LOC_Os04g17930.1 | downstream_gene_variant ; 1725.0bp to feature; MODIFIER | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854412 | C -> T | LOC_Os04g17920.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |