| Variant ID: vg1215675808 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15675808 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )
GCGTTCTTCAATCCAAAGGGCATGGTGATGTAGCAGTAGGCTCCAAAGGGCGTTATAAACGAGGACTTCAAGCAGTCGGATTCTTTCAGTAGGATCTGAT[G/A]
ATATCCTGAATAGCAGTCCAAGAAACTGAGTAGCTCGCAGCCGGCCGTTGAGTCAACCACCTGGTCAATGCGAGGTAACCCGAAAGGATCTTTAGGGCAA
TTGCCCTAAAGATCCTTTCGGGTTACCTCGCATTGACCAGGTGGTTGACTCAACGGCCGGCTGCGAGCTACTCAGTTTCTTGGACTGCTATTCAGGATAT[C/T]
ATCAGATCCTACTGAAAGAATCCGACTGCTTGAAGTCCTCGTTTATAACGCCCTTTGGAGCCTACTGCTACATCACCATGCCCTTTGGATTGAAGAACGC
| 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 | 73.40% | 25.90% | 0.61% | 0.02% | NA |
| All Indica | 2759 | 70.20% | 28.70% | 1.01% | 0.04% | NA |
| All Japonica | 1512 | 77.90% | 22.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 91.30% | 8.60% | 0.17% | 0.00% | NA |
| Indica II | 465 | 80.00% | 15.30% | 4.52% | 0.22% | NA |
| Indica III | 913 | 46.40% | 53.00% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 76.20% | 23.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 94.90% | 5.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 54.60% | 45.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 72.60% | 27.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 39.60% | 60.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 20.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1215675808 | G -> DEL | LOC_Os12g26750.1 | N | frameshift_variant | Average:25.694; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| vg1215675808 | G -> A | LOC_Os12g26750.1 | missense_variant ; p.His118Tyr; MODERATE | nonsynonymous_codon ; H118Y | Average:25.694; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | unknown | unknown | DELETERIOUS | 0.01 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215675808 | 1.68E-06 | 9.92E-08 | mr1438 | 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 |
| vg1215675808 | NA | 1.19E-07 | mr1093_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1215675808 | NA | 9.65E-06 | mr1243_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |