| Variant ID: vg0826584274 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26584274 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )
TACTATCGCCATGGTGGGGGTGAGGGAGTTATTTTGTGCTTGTATGTTGATGACATACTGATATTTGGGACAAACCTTGAGGTGATAAATGAGGTTAAAT[C/T]
ATTCTTGTCTCAAAATTTTGATATGAAAGATTTGGGAGTAGCTGATGTTATCTTAAACATTAAGCTAATTAGATGTGAGAATGGGATTACACTCTTGCAG
CTGCAAGAGTGTAATCCCATTCTCACATCTAATTAGCTTAATGTTTAAGATAACATCAGCTACTCCCAAATCTTTCATATCAAAATTTTGAGACAAGAAT[G/A]
ATTTAACCTCATTTATCACCTCAAGGTTTGTCCCAAATATCAGTATGTCATCAACATACAAGCACAAAATAACTCCCTCACCCCCACCATGGCGATAGTA
| 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 | 12.50% | 0.70% | 19.38% | 67.37% | NA |
| All Indica | 2759 | 2.60% | 1.20% | 20.44% | 75.72% | NA |
| All Japonica | 1512 | 27.10% | 0.00% | 15.67% | 57.21% | NA |
| Aus | 269 | 9.70% | 0.00% | 30.11% | 60.22% | NA |
| Indica I | 595 | 2.70% | 0.20% | 15.97% | 81.18% | NA |
| Indica II | 465 | 1.30% | 0.20% | 16.13% | 82.37% | NA |
| Indica III | 913 | 3.30% | 2.50% | 28.70% | 65.50% | NA |
| Indica Intermediate | 786 | 2.70% | 1.00% | 16.79% | 79.52% | NA |
| Temperate Japonica | 767 | 22.80% | 0.00% | 13.56% | 63.62% | NA |
| Tropical Japonica | 504 | 33.90% | 0.00% | 21.63% | 44.44% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.00% | 9.96% | 63.49% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 14.58% | 14.58% | NA |
| Intermediate | 90 | 16.70% | 1.10% | 22.22% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826584274 | C -> T | LOC_Os08g42090.1 | missense_variant ; p.Ser1006Leu; MODERATE | nonsynonymous_codon ; S1006L | Average:5.69; most accessible tissue: Zhenshan97 panicle, score: 20.424 | unknown | unknown | TOLERATED | 0.19 |
| vg0826584274 | C -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:5.69; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |