| Variant ID: vg0910529769 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10529769 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACTTTAAATAACGACGGTTCTGTCCACCATCTATTGTGATCCAAAGGATAGCTTCCCGCCATTGAATCATCGTGGTTTTCTAAGGATGTCCACCTTCCCT[C/T]
CTCTCGGGAAGTGGCTCCATCAGCATAAAATTCATCATGCAATATCCCATCCCCCACAAGTTAAGAATTTAGAGTGTAGCCAAGTGTAATACATGTCCCG
CGGGACATGTATTACACTTGGCTACACTCTAAATTCTTAACTTGTGGGGGATGGGATATTGCATGATGAATTTTATGCTGATGGAGCCACTTCCCGAGAG[G/A]
AGGGAAGGTGGACATCCTTAGAAAACCACGATGATTCAATGGCGGGAAGCTATCCTTTGGATCACAATAGATGGTGGACAGAACCGTCGTTATTTAAAGT
| 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 | 74.90% | 0.50% | 2.01% | 22.58% | NA |
| All Indica | 2759 | 87.90% | 0.10% | 2.17% | 9.86% | NA |
| All Japonica | 1512 | 47.40% | 1.40% | 1.98% | 49.27% | NA |
| Aus | 269 | 97.40% | 0.00% | 0.37% | 2.23% | NA |
| Indica I | 595 | 90.90% | 0.00% | 2.86% | 6.22% | NA |
| Indica II | 465 | 80.40% | 0.20% | 1.29% | 18.06% | NA |
| Indica III | 913 | 90.60% | 0.00% | 0.99% | 8.43% | NA |
| Indica Intermediate | 786 | 86.90% | 0.10% | 3.56% | 9.41% | NA |
| Temperate Japonica | 767 | 52.40% | 0.30% | 0.65% | 46.68% | NA |
| Tropical Japonica | 504 | 48.40% | 3.80% | 2.78% | 45.04% | NA |
| Japonica Intermediate | 241 | 29.00% | 0.00% | 4.56% | 66.39% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 4.17% | 18.75% | NA |
| Intermediate | 90 | 70.00% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529769 | C -> DEL | N | N | silent_mutation | Average:9.858; most accessible tissue: Callus, score: 36.782 | N | N | N | N |
| vg0910529769 | C -> T | LOC_Os09g17160.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.858; most accessible tissue: Callus, score: 36.782 | N | N | N | N |