| Variant ID: vg0910529770 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10529770 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
CTTTAAATAACGACGGTTCTGTCCACCATCTATTGTGATCCAAAGGATAGCTTCCCGCCATTGAATCATCGTGGTTTTCTAAGGATGTCCACCTTCCCTC[C/T]
TCTCGGGAAGTGGCTCCATCAGCATAAAATTCATCATGCAATATCCCATCCCCCACAAGTTAAGAATTTAGAGTGTAGCCAAGTGTAATACATGTCCCGG
CCGGGACATGTATTACACTTGGCTACACTCTAAATTCTTAACTTGTGGGGGATGGGATATTGCATGATGAATTTTATGCTGATGGAGCCACTTCCCGAGA[G/A]
GAGGGAAGGTGGACATCCTTAGAAAACCACGATGATTCAATGGCGGGAAGCTATCCTTTGGATCACAATAGATGGTGGACAGAACCGTCGTTATTTAAAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.90% | 0.00% | 1.59% | 22.56% | NA |
| All Indica | 2759 | 88.10% | 0.00% | 2.03% | 9.89% | NA |
| All Japonica | 1512 | 49.70% | 0.00% | 1.06% | 49.21% | NA |
| Aus | 269 | 97.40% | 0.00% | 0.37% | 2.23% | NA |
| Indica I | 595 | 91.10% | 0.00% | 2.69% | 6.22% | NA |
| Indica II | 465 | 80.90% | 0.00% | 1.08% | 18.06% | NA |
| Indica III | 913 | 90.60% | 0.00% | 0.88% | 8.54% | NA |
| Indica Intermediate | 786 | 87.20% | 0.00% | 3.44% | 9.41% | NA |
| Temperate Japonica | 767 | 52.70% | 0.00% | 0.78% | 46.54% | NA |
| Tropical Japonica | 504 | 54.00% | 0.00% | 0.99% | 45.04% | NA |
| Japonica Intermediate | 241 | 31.50% | 0.00% | 2.07% | 66.39% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 2.08% | 17.71% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529770 | C -> T | LOC_Os09g17160.1 | intron_variant ; MODIFIER | N | Average:9.858; most accessible tissue: Callus, score: 36.782 | N | N | N | N |