| Variant ID: vg1214660699 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14660699 |
| 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: 263. )
TATTAAAGTATGCATTGAGGTTGCCATAGAACTATTTGAGCTTCTTGGTATTAAATCTGGGAGGTACTTGTATGAGCTAGATTCGCATTTGGATATTCGT[A/G]
CTTGTATGTGCAGATGAGCGCACGTACGGGTTGGTGTGGGTCCTCGAGACCGGGGGCGTAGCTGAGAGACTGATGATGAACGTGGTGCTTTTTATGGGCG
CGCCCATAAAAAGCACCACGTTCATCATCAGTCTCTCAGCTACGCCCCCGGTCTCGAGGACCCACACCAACCCGTACGTGCGCTCATCTGCACATACAAG[T/C]
ACGAATATCCAAATGCGAATCTAGCTCATACAAGTACCTCCCAGATTTAATACCAAGAAGCTCAAATAGTTCTATGGCAACCTCAATGCATACTTTAATA
| 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 | 84.70% | 0.20% | 3.49% | 11.62% | NA |
| All Indica | 2759 | 74.30% | 0.30% | 5.94% | 19.43% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 82.70% | 0.00% | 1.34% | 15.97% | NA |
| Indica II | 465 | 71.20% | 1.30% | 14.19% | 13.33% | NA |
| Indica III | 913 | 65.80% | 0.10% | 6.46% | 27.60% | NA |
| Indica Intermediate | 786 | 79.60% | 0.30% | 3.94% | 16.16% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1214660699 | A -> DEL | N | N | silent_mutation | Average:37.74; most accessible tissue: Minghui63 flag leaf, score: 60.569 | N | N | N | N |
| vg1214660699 | A -> G | LOC_Os12g25409.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.74; most accessible tissue: Minghui63 flag leaf, score: 60.569 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214660699 | NA | 7.29E-06 | Grain_weight | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1214660699 | NA | 1.87E-10 | Grain_width | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1214660699 | 2.21E-06 | 2.21E-06 | mr1926 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |