| Variant ID: vg0814380695 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14380695 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 126. )
AGTACACTGGGCCTGAAGACTACATGCGGACCCACCAGGGAGCCAGATGGGATTGGGCTCCCGAGGACTTCAAGATCGTGGTCCAAAGGGTGCTGAATCT[T/C]
AGCTCCGTGGAGGCGTCTCGCATTCCTCAGGAGATCCTCCCCCTCTGCAGCGATCCCGACCGCGCCTCCATTCTAACCATTATGATGGGGGTCGGGGCCT
AGGCCCCGACCCCCATCATAATGGTTAGAATGGAGGCGCGGTCGGGATCGCTGCAGAGGGGGAGGATCTCCTGAGGAATGCGAGACGCCTCCACGGAGCT[A/G]
AGATTCAGCACCCTTTGGACCACGATCTTGAAGTCCTCGGGAGCCCAATCCCATCTGGCTCCCTGGTGGGTCCGCATGTAGTCTTCAGGCCCAGTGTACT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.20% | 0.00% | 6.35% | 93.46% | NA |
| All Indica | 2759 | 0.30% | 0.00% | 4.53% | 95.14% | NA |
| All Japonica | 1512 | 0.00% | 0.00% | 5.62% | 94.38% | NA |
| Aus | 269 | 0.00% | 0.00% | 25.65% | 74.35% | NA |
| Indica I | 595 | 0.20% | 0.00% | 1.68% | 98.15% | NA |
| Indica II | 465 | 0.00% | 0.00% | 1.72% | 98.28% | NA |
| Indica III | 913 | 0.50% | 0.00% | 6.02% | 93.43% | NA |
| Indica Intermediate | 786 | 0.40% | 0.00% | 6.62% | 93.00% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 3.65% | 96.35% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 8.73% | 91.27% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 5.39% | 94.61% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 14.58% | 85.42% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0814380695 | T -> C | LOC_Os08g23760.1 | synonymous_variant ; p.Leu271Leu; LOW | synonymous_codon | Average:5.207; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0814380695 | T -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:5.207; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |