| Variant ID: vg0728251572 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 28251572 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, G: 0.11, others allele: 0.00, population size: 263. )
GCTTTGGGTAATAGTCTTCGCCCAGAAGAATATTTGATGATTTGAAATCTCTATATATGACTGGTGGATTTGCCTTATCATGCAGGTACTCCAAACCCTT[C/G]
GCTGCACCAACAGCAATCTTCATCCTTGCATTCCAGTCAAGAGGTTTCTTGCCTGGTGGGCGATCTATTAAGAAAGTGCCCCATGAGTTATAAAATGATA
TATCATTTTATAACTCATGGGGCACTTTCTTAATAGATCGCCCACCAGGCAAGAAACCTCTTGACTGGAATGCAAGGATGAAGATTGCTGTTGGTGCAGC[G/C]
AAGGGTTTGGAGTACCTGCATGATAAGGCAAATCCACCAGTCATATATAGAGATTTCAAATCATCAAATATTCTTCTGGGCGAAGACTATTACCCAAAGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | 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% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0728251572 | C -> G | LOC_Os07g47270.1 | synonymous_variant ; p.Ala187Ala; LOW | synonymous_codon | Average:48.707; most accessible tissue: Callus, score: 75.477 | N | N | N | N |