| Variant ID: vg1220961255 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20961255 |
| 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: 395. )
ACTGTCATGCCCCATGAGCACTTTGCACCGATAGAACACAATGATCAAACGCCTGAGGAAAATCCTGAGGAGGACAACATTGTAGATACTCGCAAGAGTA[A/G]
GAGACAAAGGGTTGCAAAATCCTTTGGAGATGACTACATTGTATACCTCGTGGATGACACCCCAAGAACCATAGAAGAGGCATATTCATCTCCTGACGCT
AGCGTCAGGAGATGAATATGCCTCTTCTATGGTTCTTGGGGTGTCATCCACGAGGTATACAATGTAGTCATCTCCAAAGGATTTTGCAACCCTTTGTCTC[T/C]
TACTCTTGCGAGTATCTACAATGTTGTCCTCCTCAGGATTTTCCTCAGGCGTTTGATCATTGTGTTCTATCGGTGCAAAGTGCTCATGGGGCATGACAGT
| 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 | 3.30% | 1.00% | 6.14% | 89.57% | NA |
| All Indica | 2759 | 4.40% | 1.30% | 6.42% | 87.86% | NA |
| All Japonica | 1512 | 1.90% | 0.40% | 6.15% | 91.60% | NA |
| Aus | 269 | 1.10% | 1.10% | 4.09% | 93.68% | NA |
| Indica I | 595 | 1.00% | 0.00% | 1.68% | 97.31% | NA |
| Indica II | 465 | 1.70% | 3.00% | 7.31% | 87.96% | NA |
| Indica III | 913 | 8.40% | 1.30% | 10.51% | 79.74% | NA |
| Indica Intermediate | 786 | 3.90% | 1.30% | 4.71% | 90.08% | NA |
| Temperate Japonica | 767 | 2.20% | 0.10% | 4.95% | 92.70% | NA |
| Tropical Japonica | 504 | 1.20% | 0.80% | 5.16% | 92.86% | NA |
| Japonica Intermediate | 241 | 2.10% | 0.40% | 12.03% | 85.48% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 4.40% | 1.10% | 10.00% | 84.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220961255 | A -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220961255 | A -> G | LOC_Os12g34580.1 | missense_variant ; p.Lys880Arg; MODERATE | nonsynonymous_codon ; K880R | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |