| Variant ID: vg0114526611 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526611 |
| 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: 259. )
GAAAAAAAGGCTTCACGTTGATTTTCTGTTTAGGGGAAATTTTAGAGTTGTGTTTTTCTGCTAGGGAATAGATGGTTCTCCAAGTTAGCTCTTATTTGTC[G/A]
GACTGCAGGAATAGTTCTGCAAATAAGAAACACATGATCAAAACTAGAAAAGAAGCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTG
CAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGCTTCTTTTCTAGTTTTGATCATGTGTTTCTTATTTGCAGAACTATTCCTGCAGTC[C/T]
GACAAATAAGAGCTAACTTGGAGAACCATCTATTCCCTAGCAGAAAAACACAACTCTAAAATTTCCCCTAAACAGAAAATCAACGTGAAGCCTTTTTTTC
| 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 | 95.10% | 0.10% | 0.59% | 4.21% | NA |
| All Indica | 2759 | 91.80% | 0.20% | 0.94% | 7.07% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.74% | 0.74% | NA |
| Indica I | 595 | 95.00% | 0.00% | 0.00% | 5.04% | NA |
| Indica II | 465 | 94.80% | 0.20% | 2.15% | 2.80% | NA |
| Indica III | 913 | 91.50% | 0.00% | 0.22% | 8.32% | NA |
| Indica Intermediate | 786 | 88.00% | 0.50% | 1.78% | 9.67% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526611 | G -> A | LOC_Os01g25630.1 | synonymous_variant ; p.Ser1028Ser; LOW | synonymous_codon | Average:41.89; most accessible tissue: Zhenshan97 flower, score: 74.205 | N | N | N | N |
| vg0114526611 | G -> DEL | LOC_Os01g25630.1 | N | frameshift_variant | Average:41.89; most accessible tissue: Zhenshan97 flower, score: 74.205 | N | N | N | N |