| Variant ID: vg0206930782 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6930782 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 78. )
GCTCTCAACGTATACTCCTTCCGCCTCATAAAAAACAATCTAGTGCCGAATGTAACACATGCTAGTACCATGAATTTGGACGTAGGCATGTACAGATTTC[G/A]
TAATAGAAATATATCACATCTTATCTTAAAATTGGTTTTCATGGGACGGAGGGAGTACGTACCAATTAGCATTTGTGGTGCCATGAATGATTCTGCATAA
TTATGCAGAATCATTCATGGCACCACAAATGCTAATTGGTACGTACTCCCTCCGTCCCATGAAAACCAATTTTAAGATAAGATGTGATATATTTCTATTA[C/T]
GAAATCTGTACATGCCTACGTCCAAATTCATGGTACTAGCATGTGTTACATTCGGCACTAGATTGTTTTTTATGAGGCGGAAGGAGTATACGTTGAGAGC
| 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 | 71.50% | 22.90% | 1.65% | 4.02% | NA |
| All Indica | 2759 | 91.00% | 2.70% | 1.16% | 5.15% | NA |
| All Japonica | 1512 | 31.70% | 63.40% | 2.38% | 2.51% | NA |
| Aus | 269 | 95.50% | 1.10% | 2.23% | 1.12% | NA |
| Indica I | 595 | 93.80% | 3.00% | 0.84% | 2.35% | NA |
| Indica II | 465 | 89.50% | 3.00% | 2.15% | 5.38% | NA |
| Indica III | 913 | 90.00% | 1.90% | 0.99% | 7.12% | NA |
| Indica Intermediate | 786 | 90.80% | 3.30% | 1.02% | 4.83% | NA |
| Temperate Japonica | 767 | 9.80% | 89.30% | 0.52% | 0.39% | NA |
| Tropical Japonica | 504 | 56.30% | 32.70% | 5.56% | 5.36% | NA |
| Japonica Intermediate | 241 | 50.20% | 44.80% | 1.66% | 3.32% | NA |
| VI/Aromatic | 96 | 72.90% | 22.90% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 66.70% | 25.60% | 2.22% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206930782 | G -> A | LOC_Os02g13080-LOC_Os02g13090 | intergenic_region ; MODIFIER | silent_mutation | Average:70.761; most accessible tissue: Zhenshan97 panicle, score: 79.071 | N | N | N | N |
| vg0206930782 | G -> DEL | N | N | silent_mutation | Average:70.761; most accessible tissue: Zhenshan97 panicle, score: 79.071 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206930782 | NA | 1.47E-08 | mr1866 | 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 |
| vg0206930782 | 7.07E-07 | NA | mr1563_2 | 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 |
| vg0206930782 | NA | 4.29E-06 | mr1730_2 | Jap_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 |