| Variant ID: vg0910529817 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10529817 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAGCTTCCCGCCATTGAATCATCGTGGTTTTCTAAGGATGTCCACCTTCCCTCCTCTCGGGAAGTGGCTCCATCAGCATAAAATTCATCATGCAATATCC[C/T]
ATCCCCCACAAGTTAAGAATTTAGAGTGTAGCCAAGTGTAATACATGTCCCGGTGCTCAATAACCGCGAGCACGGCTATTCGAATAGATTTGGTTTACTC
GAGTAAACCAAATCTATTCGAATAGCCGTGCTCGCGGTTATTGAGCACCGGGACATGTATTACACTTGGCTACACTCTAAATTCTTAACTTGTGGGGGAT[G/A]
GGATATTGCATGATGAATTTTATGCTGATGGAGCCACTTCCCGAGAGGAGGGAAGGTGGACATCCTTAGAAAACCACGATGATTCAATGGCGGGAAGCTA
| 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% | 2.39% | 22.18% | NA |
| All Indica | 2759 | 88.00% | 0.10% | 2.57% | 9.39% | NA |
| All Japonica | 1512 | 47.30% | 1.40% | 2.45% | 48.88% | 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% | 1.72% | 17.63% | NA |
| Indica III | 913 | 90.60% | 0.00% | 1.53% | 7.89% | NA |
| Indica Intermediate | 786 | 87.20% | 0.10% | 4.07% | 8.65% | NA |
| Temperate Japonica | 767 | 52.30% | 0.30% | 1.17% | 46.28% | NA |
| Tropical Japonica | 504 | 48.60% | 3.80% | 2.98% | 44.64% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 5.39% | 65.98% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529817 | C -> DEL | N | N | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |
| vg0910529817 | C -> T | LOC_Os09g17160.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |