| Variant ID: vg0814380656 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14380656 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGATTGCGCCGCTCCAACGGCGCGCCCGGAGCGCCTGGGAGTACACTGGGCCTGAAGACTACATGCGGACCCACCAGGGAGCCAGATGGGATTGGGCTCC[C/T]
GAGGACTTCAAGATCGTGGTCCAAAGGGTGCTGAATCTTAGCTCCGTGGAGGCGTCTCGCATTCCTCAGGAGATCCTCCCCCTCTGCAGCGATCCCGACC
GGTCGGGATCGCTGCAGAGGGGGAGGATCTCCTGAGGAATGCGAGACGCCTCCACGGAGCTAAGATTCAGCACCCTTTGGACCACGATCTTGAAGTCCTC[G/A]
GGAGCCCAATCCCATCTGGCTCCCTGGTGGGTCCGCATGTAGTCTTCAGGCCCAGTGTACTCCCAGGCGCTCCGGGCGCGCCGTTGGAGCGGCGCAATCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.20% | 0.00% | 5.65% | 94.14% | NA |
| All Indica | 2759 | 0.30% | 0.00% | 3.44% | 96.19% | NA |
| All Japonica | 1512 | 0.00% | 0.00% | 5.56% | 94.44% | NA |
| Aus | 269 | 0.00% | 0.00% | 25.28% | 74.72% | NA |
| Indica I | 595 | 0.20% | 0.00% | 1.18% | 98.66% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.65% | 99.35% | NA |
| Indica III | 913 | 0.50% | 0.10% | 4.60% | 94.74% | NA |
| Indica Intermediate | 786 | 0.40% | 0.00% | 5.47% | 94.15% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 3.65% | 96.35% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 8.53% | 91.47% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 5.39% | 94.61% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 13.54% | 86.46% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 7.78% | 92.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814380656 | C -> T | LOC_Os08g23760.1 | synonymous_variant ; p.Pro258Pro; LOW | synonymous_codon | Average:5.207; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0814380656 | C -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:5.207; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |