| Variant ID: vg0234178782 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34178782 |
| 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: 386. )
AGCCACCGGCGGGTTCAGAAGCATCCGGCACTATGAGTGGGAGTGCATCGACGAACACCGGCTCAAAGAGATCAAGAACTTCCGGTGTTTGGCAACATTT[C/T]
GATGAGGTGGCCATGACAGGCCCTGATGGAAGGCAGGTAACATTCGCGAGATGTAGAATATGCAAAAATAAGTTATCTGCAAAATCATCTGGTGGAACAG
CTGTTCCACCAGATGATTTTGCAGATAACTTATTTTTGCATATTCTACATCTCGCGAATGTTACCTGCCTTCCATCAGGGCCTGTCATGGCCACCTCATC[G/A]
AAATGTTGCCAAACACCGGAAGTTCTTGATCTCTTTGAGCCGGTGTTCGTCGATGCACTCCCACTCATAGTGCCGGATGCTTCTGAACCCGCCGGTGGCT
| 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 | 77.60% | 0.10% | 7.07% | 15.26% | NA |
| All Indica | 2759 | 67.00% | 0.10% | 9.06% | 23.85% | NA |
| All Japonica | 1512 | 95.90% | 0.00% | 2.65% | 1.46% | NA |
| Aus | 269 | 87.70% | 0.00% | 6.32% | 5.95% | NA |
| Indica I | 595 | 45.20% | 0.00% | 16.13% | 38.66% | NA |
| Indica II | 465 | 60.40% | 0.00% | 9.68% | 29.89% | NA |
| Indica III | 913 | 84.60% | 0.20% | 3.94% | 11.28% | NA |
| Indica Intermediate | 786 | 67.00% | 0.00% | 9.29% | 23.66% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.13% | 1.56% | NA |
| Tropical Japonica | 504 | 92.90% | 0.00% | 6.55% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 2.49% | 2.90% | NA |
| VI/Aromatic | 96 | 64.60% | 2.10% | 19.79% | 13.54% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 8.89% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234178782 | C -> T | LOC_Os02g55830.1 | synonymous_variant ; p.Phe74Phe; LOW | synonymous_codon | Average:5.822; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0234178782 | C -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:5.822; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |