| Variant ID: vg0128509535 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509535 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.29, others allele: 0.00, population size: 49. )
GCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGAAGCT[T/C]
AGGGCGAACGACGCGGCCAAGGCACCGAACAACATCATGGTGCTGCAGCATCCGGAGGCCGAGCTCGCCTGACGTCCGATCCGCCCGCCGCTCGCATCCG
CGGATGCGAGCGGCGGGCGGATCGGACGTCAGGCGAGCTCGGCCTCCGGATGCTGCAGCACCATGATGTTGTTCGGTGCCTTGGCCGCGTCGTTCGCCCT[A/G]
AGCTTCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.90% | 16.00% | 5.90% | 53.26% | NA |
| All Indica | 2759 | 1.40% | 17.90% | 9.53% | 71.19% | NA |
| All Japonica | 1512 | 72.00% | 16.20% | 0.53% | 11.31% | NA |
| Aus | 269 | 3.30% | 0.00% | 0.74% | 95.91% | NA |
| Indica I | 595 | 1.70% | 6.90% | 5.88% | 85.55% | NA |
| Indica II | 465 | 3.00% | 8.60% | 8.39% | 80.00% | NA |
| Indica III | 913 | 0.40% | 35.30% | 15.22% | 49.07% | NA |
| Indica Intermediate | 786 | 1.40% | 11.50% | 6.36% | 80.79% | NA |
| Temperate Japonica | 767 | 92.70% | 0.30% | 0.00% | 7.04% | NA |
| Tropical Japonica | 504 | 32.50% | 44.80% | 1.59% | 21.03% | NA |
| Japonica Intermediate | 241 | 88.40% | 7.10% | 0.00% | 4.56% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 3.12% | 83.33% | NA |
| Intermediate | 90 | 30.00% | 17.80% | 3.33% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509535 | T -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:32.218; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| vg0128509535 | T -> C | LOC_Os01g49570.1 | synonymous_variant ; p.Leu13Leu; LOW | synonymous_codon | Average:32.218; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |