| Variant ID: vg0823066777 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 23066777 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCGCTGCCGCCGACGAACGACACCGAGATCGGCCTGGAGACGTGCTTCCCGTGGCCGCCGCCGCCGAGCGTGGCCGTGACGGTCCCGGACATGGAGCTC[C/T]
ACTTCGACGGCGGCGCCAACATGACCGTGCCGCCGGAGAACTACATGCTGATCGACGGCGCCACCGGGTTCCTGTGCCTGGCGATGATCCGCTCCGGCGA
TCGCCGGAGCGGATCATCGCCAGGCACAGGAACCCGGTGGCGCCGTCGATCAGCATGTAGTTCTCCGGCGGCACGGTCATGTTGGCGCCGCCGTCGAAGT[G/A]
GAGCTCCATGTCCGGGACCGTCACGGCCACGCTCGGCGGCGGCGGCCACGGGAAGCACGTCTCCAGGCCGATCTCGGTGTCGTTCGTCGGCGGCAGCGGC
| 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 | 99.90% | 0.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0823066777 | C -> T | LOC_Os08g36530.1 | missense_variant ; p.His382Tyr; MODERATE | N | Average:72.4; most accessible tissue: Minghui63 root, score: 82.511 | N | N | N | N |
| vg0823066777 | C -> T | LOC_Os08g36520.1 | upstream_gene_variant ; 3551.0bp to feature; MODIFIER | N | Average:72.4; most accessible tissue: Minghui63 root, score: 82.511 | N | N | N | N |
| vg0823066777 | C -> T | LOC_Os08g36540.1 | upstream_gene_variant ; 2526.0bp to feature; MODIFIER | N | Average:72.4; most accessible tissue: Minghui63 root, score: 82.511 | N | N | N | N |