| Variant ID: vg0826581362 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26581362 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGGTTTTGCCGATGCACTGAGGCCGGATAAATTCACCGGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTT[C/T]
TGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAACAACAGAAGCAATTCGAGGAAGCTACTACTCTCTTTGTGGGATGCATTCTTAGCGTTC
GAACGCTAAGAATGCATCCCACAAAGAGAGTAGTAGCTTCCTCGAATTGCTTCTGTTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCA[G/A]
AAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACCGGTGAATTTATCCGGCCTCAGTGCATCGGCAAAACCAG
| 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 | 30.70% | 0.60% | 8.06% | 60.66% | NA |
| All Indica | 2759 | 2.50% | 0.40% | 12.98% | 84.12% | NA |
| All Japonica | 1512 | 81.30% | 0.70% | 1.06% | 16.93% | NA |
| Aus | 269 | 8.60% | 0.00% | 0.74% | 90.71% | NA |
| Indica I | 595 | 2.00% | 0.00% | 8.91% | 89.08% | NA |
| Indica II | 465 | 2.60% | 0.20% | 7.74% | 89.46% | NA |
| Indica III | 913 | 2.10% | 1.20% | 19.82% | 76.89% | NA |
| Indica Intermediate | 786 | 3.20% | 0.00% | 11.20% | 85.62% | NA |
| Temperate Japonica | 767 | 94.80% | 0.00% | 0.00% | 5.22% | NA |
| Tropical Japonica | 504 | 70.00% | 2.20% | 2.18% | 25.60% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 2.07% | 36.10% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 43.30% | 6.70% | 5.56% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826581362 | C -> T | LOC_Os08g42090.1 | synonymous_variant ; p.Phe35Phe; LOW | synonymous_codon | Average:6.326; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |
| vg0826581362 | C -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:6.326; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |