| Variant ID: vg0814380143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14380143 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 109. )
GGCGGTCCATCTTCTTCCTCCCCTTCGCAATGGCTGGGCTGGTCCCACCATTTTCTTCTTTCTTCATGGATGTCCTGGAGTTCTACGATCTCCAGATGGC[G/T]
CACCTCACCCCCAATGCGGTGATGACATTGGCCATCTTCGCGCACCTGTGCGAGATGTTCATTGGGGTGCGCCCTTCTCTTCAGCTGTTCCGGTGGTTCT
AGAACCACCGGAACAGCTGAAGAGAAGGGCGCACCCCAATGAACATCTCGCACAGGTGCGCGAAGATGGCCAATGTCATCACCGCATTGGGGGTGAGGTG[C/A]
GCCATCTGGAGATCGTAGAACTCCAGGACATCCATGAAGAAAGAAGAAAATGGTGGGACCAGCCCAGCCATTGCGAAGGGGAGGAAGAAGATGGACCGCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.20% | 0.40% | 1.71% | 78.67% | NA |
| All Indica | 2759 | 0.70% | 0.70% | 2.03% | 96.63% | NA |
| All Japonica | 1512 | 56.90% | 0.10% | 1.26% | 41.80% | NA |
| Aus | 269 | 2.20% | 0.00% | 1.12% | 96.65% | NA |
| Indica I | 595 | 0.30% | 1.00% | 3.36% | 95.29% | NA |
| Indica II | 465 | 0.90% | 1.10% | 2.37% | 95.70% | NA |
| Indica III | 913 | 0.30% | 0.00% | 1.42% | 98.25% | NA |
| Indica Intermediate | 786 | 1.10% | 1.00% | 1.53% | 96.31% | NA |
| Temperate Japonica | 767 | 84.70% | 0.00% | 0.00% | 15.25% | NA |
| Tropical Japonica | 504 | 24.40% | 0.20% | 3.37% | 72.02% | NA |
| Japonica Intermediate | 241 | 36.10% | 0.00% | 0.83% | 63.07% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 3.33% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814380143 | G -> T | LOC_Os08g23760.1 | synonymous_variant ; p.Ala87Ala; LOW | synonymous_codon | Average:14.258; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| vg0814380143 | G -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:14.258; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |