| Variant ID: vg0817015495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015495 |
| Reference Allele: A | Alternative Allele: T,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: 300. )
GTTCCAACGGAGAGAAGCATCAAGGAAACACAAATCCTCGCCAAGATTCCAGTTTCAGCCTAACTCCAGTGCCAGGACAGAGGAATCAAAATGAGAAAAG[A/T,G]
AAATGCCGAGTCCGGGAAGATATCTGTTGCTTCAATTGTCAAGGAATGGGTCATTTCGCCGACAAGTGCCCAAAACCGAGAAACGTAGCTGCCAGCACGT
ACGTGCTGGCAGCTACGTTTCTCGGTTTTGGGCACTTGTCGGCGAAATGACCCATTCCTTGACAATTGAAGCAACAGATATCTTCCCGGACTCGGCATTT[T/A,C]
CTTTTCTCATTTTGATTCCTCTGTCCTGGCACTGGAGTTAGGCTGAAACTGGAATCTTGGCGAGGATTTGTGTTTCCTTGATGCTTCTCTCCGTTGGAAC
| 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 | 46.30% | 0.00% | 7.32% | 46.30% | T: 0.04% |
| All Indica | 2759 | 34.80% | 0.00% | 9.68% | 55.56% | NA |
| All Japonica | 1512 | 66.90% | 0.10% | 0.86% | 32.14% | NA |
| Aus | 269 | 34.60% | 0.00% | 23.42% | 41.64% | T: 0.37% |
| Indica I | 595 | 11.90% | 0.00% | 10.25% | 77.82% | NA |
| Indica II | 465 | 23.90% | 0.00% | 9.25% | 66.88% | NA |
| Indica III | 913 | 57.80% | 0.00% | 8.43% | 33.73% | NA |
| Indica Intermediate | 786 | 31.70% | 0.00% | 10.94% | 57.38% | NA |
| Temperate Japonica | 767 | 81.10% | 0.00% | 0.52% | 18.38% | NA |
| Tropical Japonica | 504 | 45.00% | 0.20% | 1.39% | 53.37% | NA |
| Japonica Intermediate | 241 | 67.60% | 0.00% | 0.83% | 31.54% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 3.33% | 41.11% | T: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015495 | A -> G | LOC_Os08g27910.1 | synonymous_variant ; p.Arg301Arg; LOW | synonymous_codon | Average:6.76; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0817015495 | A -> T | LOC_Os08g27910.1 | missense_variant ; p.Arg301Ser; MODERATE | nonsynonymous_codon ; R301S | Average:6.76; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0817015495 | A -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:6.76; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |