| Variant ID: vg1213914611 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13914611 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 272. )
CGCGTGTTCACGGAATCCCGCACCGCCAACATCTTCCTCATGTCCGACGGCAAGCTCGAGGGTAAGACCTCCGGTGACCCGACGCAAGTCAACCCCGGCG[A/G]
GGTCTCCGTCTACACCTTTGGTTTCGGCCATGGCACAGACCACCAGGTATGTATGTACAATTGCTAGTTGCTACTTGCTACTCCAGTTGCTAGCTATTGC
GCAATAGCTAGCAACTGGAGTAGCAAGTAGCAACTAGCAATTGTACATACATACCTGGTGGTCTGTGCCATGGCCGAAACCAAAGGTGTAGACGGAGACC[T/C]
CGCCGGGGTTGACTTGCGTCGGGTCACCGGAGGTCTTACCCTCGAGCTTGCCGTCGGACATGAGGAAGATGTTGGCGGTGCGGGATTCCGTGAACACGCG
| 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213914611 | A -> G | LOC_Os12g24390.1 | missense_variant ; p.Glu186Gly; MODERATE | N | Average:77.316; most accessible tissue: Zhenshan97 young leaf, score: 90.985 | N | N | N | N |
| vg1213914611 | A -> G | LOC_Os12g24400.1 | upstream_gene_variant ; 2800.0bp to feature; MODIFIER | N | Average:77.316; most accessible tissue: Zhenshan97 young leaf, score: 90.985 | N | N | N | N |