| Variant ID: vg0910529774 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10529774 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAATAACGACGGTTCTGTCCACCATCTATTGTGATCCAAAGGATAGCTTCCCGCCATTGAATCATCGTGGTTTTCTAAGGATGTCCACCTTCCCTCCTCT[C/T]
GGGAAGTGGCTCCATCAGCATAAAATTCATCATGCAATATCCCATCCCCCACAAGTTAAGAATTTAGAGTGTAGCCAAGTGTAATACATGTCCCGGTGCT
AGCACCGGGACATGTATTACACTTGGCTACACTCTAAATTCTTAACTTGTGGGGGATGGGATATTGCATGATGAATTTTATGCTGATGGAGCCACTTCCC[G/A]
AGAGGAGGGAAGGTGGACATCCTTAGAAAACCACGATGATTCAATGGCGGGAAGCTATCCTTTGGATCACAATAGATGGTGGACAGAACCGTCGTTATTT
| 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 | 75.80% | 0.10% | 1.88% | 22.20% | NA |
| All Indica | 2759 | 88.00% | 0.10% | 2.50% | 9.39% | NA |
| All Japonica | 1512 | 49.70% | 0.10% | 1.12% | 49.07% | NA |
| Aus | 269 | 97.40% | 0.00% | 0.37% | 2.23% | NA |
| Indica I | 595 | 90.90% | 0.20% | 2.69% | 6.22% | NA |
| Indica II | 465 | 80.60% | 0.20% | 1.51% | 17.63% | NA |
| Indica III | 913 | 90.50% | 0.10% | 1.53% | 7.89% | NA |
| Indica Intermediate | 786 | 87.30% | 0.00% | 4.07% | 8.65% | NA |
| Temperate Japonica | 767 | 52.80% | 0.00% | 0.78% | 46.41% | NA |
| Tropical Japonica | 504 | 53.80% | 0.20% | 1.19% | 44.84% | NA |
| Japonica Intermediate | 241 | 31.50% | 0.00% | 2.07% | 66.39% | NA |
| VI/Aromatic | 96 | 81.20% | 0.00% | 1.04% | 17.71% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 1.11% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529774 | C -> DEL | N | N | silent_mutation | Average:9.858; most accessible tissue: Callus, score: 36.782 | N | N | N | N |
| vg0910529774 | C -> T | LOC_Os09g17160.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.858; most accessible tissue: Callus, score: 36.782 | N | N | N | N |