| Variant ID: vg0906286694 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6286694 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACTGGCCCTGTTCGGCTGAACACATGCAGCTGCGGTGTAGCCAACTGGAACAGTGATATCTGTAAGTAGCTGCTGTGACACCCCACACTTTTACCAAGGA[C/T]
GGGCCCTCTCTACATCACATCAACACTACATCAGCACTTTTACCAAGGCTGACGCCCCACACTTTTACTAAGGTCTAGTAGGAAGGCTGAACACATGCAG
CTGCATGTGTTCAGCCTTCCTACTAGACCTTAGTAAAAGTGTGGGGCGTCAGCCTTGGTAAAAGTGCTGATGTAGTGTTGATGTGATGTAGAGAGGGCCC[G/A]
TCCTTGGTAAAAGTGTGGGGTGTCACAGCAGCTACTTACAGATATCACTGTTCCAGTTGGCTACACCGCAGCTGCATGTGTTCAGCCGAACAGGGCCAGT
| 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 | 44.50% | 0.20% | 6.60% | 48.67% | NA |
| All Indica | 2759 | 18.20% | 0.10% | 5.76% | 75.90% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 0.07% | 1.79% | NA |
| Aus | 269 | 20.40% | 0.70% | 39.41% | 39.41% | NA |
| Indica I | 595 | 26.20% | 0.00% | 6.39% | 67.39% | NA |
| Indica II | 465 | 14.60% | 0.20% | 2.58% | 82.58% | NA |
| Indica III | 913 | 12.70% | 0.20% | 6.90% | 80.18% | NA |
| Indica Intermediate | 786 | 20.60% | 0.10% | 5.85% | 73.41% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 91.70% | 0.00% | 0.00% | 8.30% | NA |
| VI/Aromatic | 96 | 13.50% | 3.10% | 37.50% | 45.83% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 11.11% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0906286694 | C -> DEL | N | N | silent_mutation | Average:37.133; most accessible tissue: Minghui63 flag leaf, score: 64.867 | N | N | N | N |
| vg0906286694 | C -> T | LOC_Os09g11320.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.133; most accessible tissue: Minghui63 flag leaf, score: 64.867 | N | N | N | N |