| Variant ID: vg0815410433 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15410433 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 126. )
ACTGGTGATAGCCTGACCAAAGGTCTATCTTAGAGAACACAGTAGCTCCTTTCAGCTGATCGAACAGATCATCAATCCTTGGCAAAGGGTACTTGTTCTT[A/G]
ATAGTGACCTCATTGAGTGCGCGGTAGTCCACGCACATCCTCTTGGTTTTGTCTTTCTTTTCCACAAAGATAACCGGAGCACCCCAAGGCGACGTGCTCG
CGAGCACGTCGCCTTGGGGTGCTCCGGTTATCTTTGTGGAAAAGAAAGACAAAACCAAGAGGATGTGCGTGGACTACCGCGCACTCAATGAGGTCACTAT[T/C]
AAGAACAAGTACCCTTTGCCAAGGATTGATGATCTGTTCGATCAGCTGAAAGGAGCTACTGTGTTCTCTAAGATAGACCTTTGGTCAGGCTATCACCAGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.60% | 0.40% | 11.34% | 67.65% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 11.85% | 87.06% | NA |
| All Japonica | 1512 | 60.40% | 1.20% | 6.55% | 31.88% | NA |
| Aus | 269 | 2.20% | 0.00% | 34.94% | 62.83% | NA |
| Indica I | 595 | 0.30% | 0.20% | 0.50% | 98.99% | NA |
| Indica II | 465 | 1.70% | 0.00% | 8.17% | 90.11% | NA |
| Indica III | 913 | 0.30% | 0.00% | 20.48% | 79.19% | NA |
| Indica Intermediate | 786 | 2.00% | 0.00% | 12.60% | 85.37% | NA |
| Temperate Japonica | 767 | 84.20% | 0.00% | 2.61% | 13.17% | NA |
| Tropical Japonica | 504 | 28.40% | 3.40% | 8.93% | 59.33% | NA |
| Japonica Intermediate | 241 | 51.50% | 0.40% | 14.11% | 34.02% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 7.29% | 89.58% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 10.00% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815410433 | A -> G | LOC_Os08g25330.1 | synonymous_variant ; p.Ile651Ile; LOW | synonymous_codon | Average:5.196; most accessible tissue: Callus, score: 12.491 | N | N | N | N |
| vg0815410433 | A -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:5.196; most accessible tissue: Callus, score: 12.491 | N | N | N | N |