| Variant ID: vg1213095546 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13095546 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 327. )
CAAACTCCACTCCTGACTTGGCCATGTCCAAAATCAATGTATAAAGGAAAATGGTACACATCGGCCTTCTTTTTGCGGATTGAAGATCAACAGGAGTAGC[G/A]
CAACATACAGAAGAAGCTGTAGATACGGAATCACCAACTACCATTCTATACATATGAAATAGGTGGCGAGTGCTAGTAGGGATCGTAGTTACATCTTTGT
ACAAAGATGTAACTACGATCCCTACTAGCACTCGCCACCTATTTCATATGTATAGAATGGTAGTTGGTGATTCCGTATCTACAGCTTCTTCTGTATGTTG[C/T]
GCTACTCCTGTTGATCTTCAATCCGCAAAAAGAAGGCCGATGTGTACCATTTTCCTTTATACATTGATTTTGGACATGGCCAAGTCAGGAGTGGAGTTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.60% | 0.00% | 0.47% | 10.96% | NA |
| All Indica | 2759 | 81.90% | 0.00% | 0.69% | 17.36% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.20% | 2.38% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.00% | 0.17% | 1.01% | NA |
| Indica II | 465 | 60.60% | 0.00% | 1.72% | 37.63% | NA |
| Indica III | 913 | 81.80% | 0.10% | 0.22% | 17.85% | NA |
| Indica Intermediate | 786 | 81.80% | 0.00% | 1.02% | 17.18% | NA |
| Temperate Japonica | 767 | 95.40% | 0.00% | 0.39% | 4.17% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213095546 | G -> DEL | LOC_Os12g23150.1 | N | frameshift_variant | Average:67.389; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |
| vg1213095546 | G -> A | LOC_Os12g23150.1 | synonymous_variant ; p.Cys193Cys; LOW | synonymous_codon | Average:67.389; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |