| Variant ID: vg0403275975 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3275975 |
| 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: 30. )
TTTTTTTTTGAACCATGTCAGCTGCCACGTGGCAAGCCCTAGGATTTTGTGACAATAAATCAATGTCATATGCTTGTGACAATGAATGTTCAAACGTCAC[A/G]
TGATGAATTTATGACGGTGGCTTTTTGACGTTTGAAATTACGTCATCTGTTTGTCACAAATCTTAATTTTTGACATAATTTTCATATATTATGACATAAT
ATTATGTCATAATATATGAAAATTATGTCAAAAATTAAGATTTGTGACAAACAGATGACGTAATTTCAAACGTCAAAAAGCCACCGTCATAAATTCATCA[T/C]
GTGACGTTTGAACATTCATTGTCACAAGCATATGACATTGATTTATTGTCACAAAATCCTAGGGCTTGCCACGTGGCAGCTGACATGGTTCAAAAAAAAA
| 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 | 30.20% | 2.50% | 8.04% | 59.27% | NA |
| All Indica | 2759 | 20.40% | 4.00% | 12.40% | 63.18% | NA |
| All Japonica | 1512 | 52.40% | 0.30% | 0.79% | 46.56% | NA |
| Aus | 269 | 12.30% | 0.40% | 5.20% | 82.16% | NA |
| Indica I | 595 | 37.00% | 1.50% | 2.18% | 59.33% | NA |
| Indica II | 465 | 17.40% | 4.10% | 21.72% | 56.77% | NA |
| Indica III | 913 | 11.20% | 4.60% | 11.72% | 72.51% | NA |
| Indica Intermediate | 786 | 20.50% | 5.10% | 15.39% | 59.03% | NA |
| Temperate Japonica | 767 | 83.60% | 0.40% | 0.91% | 15.12% | NA |
| Tropical Japonica | 504 | 15.30% | 0.00% | 0.40% | 84.33% | NA |
| Japonica Intermediate | 241 | 30.70% | 0.40% | 1.24% | 67.63% | NA |
| VI/Aromatic | 96 | 12.50% | 0.00% | 0.00% | 87.50% | NA |
| Intermediate | 90 | 30.00% | 2.20% | 13.33% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403275975 | A -> DEL | N | N | silent_mutation | Average:19.52; most accessible tissue: Callus, score: 95.535 | N | N | N | N |
| vg0403275975 | A -> G | LOC_Os04g06280.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.52; most accessible tissue: Callus, score: 95.535 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403275975 | NA | 2.11E-08 | mr1027_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 |
| vg0403275975 | NA | 5.70E-09 | mr1580_2 | 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 |
| vg0403275975 | 4.94E-06 | 1.27E-10 | mr1825_2 | 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 |