| Variant ID: vg0823069973 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 23069973 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGACGAGGCCGATCCAAACCACCGCGATAGTGAGCAATCCGGTGGAGACCGTCTACTACTACGTGCCGCTGGTTGGCATCTCGCTCGGGCACAAGCGGCT[C/T]
GCCGTGCCGGCGGCGAGCCTCGCAATGAGGCCCGACGGCGGCGGCGGCACGATCGTCGACTCTGGCAGCACGGTGGCGTACCTCGTGGAGGCGGCGTTCG
CGAACGCCGCCTCCACGAGGTACGCCACCGTGCTGCCAGAGTCGACGATCGTGCCGCCGCCGCCGTCGGGCCTCATTGCGAGGCTCGCCGCCGGCACGGC[G/A]
AGCCGCTTGTGCCCGAGCGAGATGCCAACCAGCGGCACGTAGTAGTAGACGGTCTCCACCGGATTGCTCACTATCGCGGTGGTTTGGATCGGCCTCGTCG
| 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 | 87.80% | 9.40% | 2.79% | 0.00% | NA |
| All Indica | 2759 | 79.50% | 15.90% | 4.57% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 88.60% | 0.20% | 11.26% | 0.00% | NA |
| Indica II | 465 | 94.40% | 4.10% | 1.51% | 0.00% | NA |
| Indica III | 913 | 60.00% | 38.60% | 1.42% | 0.00% | NA |
| Indica Intermediate | 786 | 86.40% | 8.70% | 4.96% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 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 | 91.10% | 4.40% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0823069973 | C -> T | LOC_Os08g36540.1 | synonymous_variant ; p.Leu223Leu; LOW | synonymous_codon | Average:79.718; most accessible tissue: Zhenshan97 young leaf, score: 89.226 | N | N | N | N |