| Variant ID: vg0814380086 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14380086 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 77. )
CCACCGGTCGGGAGATAGTGATGCTGGGCGAGGGGCGCCCGGCACCAGACTACCCGGGGCGGTCCATCTTCTTCCTCCCCTTCGCAATGGCTGGGCTGGT[C/T]
CCACCATTTTCTTCTTTCTTCATGGATGTCCTGGAGTTCTACGATCTCCAGATGGCGCACCTCACCCCCAATGCGGTGATGACATTGGCCATCTTCGCGC
GCGCGAAGATGGCCAATGTCATCACCGCATTGGGGGTGAGGTGCGCCATCTGGAGATCGTAGAACTCCAGGACATCCATGAAGAAAGAAGAAAATGGTGG[G/A]
ACCAGCCCAGCCATTGCGAAGGGGAGGAAGAAGATGGACCGCCCCGGGTAGTCTGGTGCCGGGCGCCCCTCGCCCAGCATCACTATCTCCCGACCGGTGG
| 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 | 23.60% | 0.10% | 16.55% | 59.75% | NA |
| All Indica | 2759 | 6.60% | 0.00% | 22.47% | 70.93% | NA |
| All Japonica | 1512 | 59.30% | 0.10% | 4.03% | 36.57% | NA |
| Aus | 269 | 1.10% | 1.50% | 27.14% | 70.26% | NA |
| Indica I | 595 | 5.40% | 0.00% | 21.01% | 73.61% | NA |
| Indica II | 465 | 7.70% | 0.00% | 15.91% | 76.34% | NA |
| Indica III | 913 | 6.50% | 0.00% | 25.96% | 67.58% | NA |
| Indica Intermediate | 786 | 7.00% | 0.00% | 23.41% | 69.59% | NA |
| Temperate Japonica | 767 | 85.00% | 0.00% | 0.78% | 14.21% | NA |
| Tropical Japonica | 504 | 30.20% | 0.20% | 9.92% | 59.72% | NA |
| Japonica Intermediate | 241 | 38.60% | 0.00% | 2.07% | 59.34% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 17.71% | 76.04% | NA |
| Intermediate | 90 | 30.00% | 0.00% | 12.22% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814380086 | C -> T | LOC_Os08g23760.1 | synonymous_variant ; p.Val68Val; LOW | synonymous_codon | Average:13.775; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| vg0814380086 | C -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:13.775; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |