| Variant ID: vg0405138328 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 5138328 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 100. )
CTATTTGCTGAAACATTATTTTTATATAGGGTGAAACAACACCCGATTTAAACGAGTGAAACATTTTCGATCTATTTAGTGAAACAATTACGATATACCT[A/G]
GTGGAACATCGTGCAACATTTAAAAATAATTCAATAATAAGCTAAAAAAAATTTCGTCGGAATATATCCATGTGCGGTCTTTTTTTTGAAGATTTAATTG
CAATTAAATCTTCAAAAAAAAGACCGCACATGGATATATTCCGACGAAATTTTTTTTAGCTTATTATTGAATTATTTTTAAATGTTGCACGATGTTCCAC[T/C]
AGGTATATCGTAATTGTTTCACTAAATAGATCGAAAATGTTTCACTCGTTTAAATCGGGTGTTGTTTCACCCTATATAAAAATAATGTTTCAGCAAATAG
| 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 | 85.10% | 12.00% | 0.02% | 2.92% | NA |
| All Indica | 2759 | 96.80% | 0.60% | 0.04% | 2.61% | NA |
| All Japonica | 1512 | 60.20% | 35.60% | 0.00% | 4.17% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 99.00% | 0.30% | 0.00% | 0.67% | NA |
| Indica II | 465 | 92.70% | 0.90% | 0.00% | 6.45% | NA |
| Indica III | 913 | 98.90% | 0.20% | 0.00% | 0.88% | NA |
| Indica Intermediate | 786 | 95.00% | 1.00% | 0.13% | 3.82% | NA |
| Temperate Japonica | 767 | 58.10% | 41.70% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 72.20% | 15.50% | 0.00% | 12.30% | NA |
| Japonica Intermediate | 241 | 41.50% | 58.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 10.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0405138328 | A -> DEL | N | N | silent_mutation | Average:22.031; most accessible tissue: Zhenshan97 panicle, score: 73.605 | N | N | N | N |
| vg0405138328 | A -> G | LOC_Os04g09580.1 | 3_prime_UTR_variant ; 1921.0bp to feature; MODIFIER | silent_mutation | Average:22.031; most accessible tissue: Zhenshan97 panicle, score: 73.605 | N | N | N | N |
| vg0405138328 | A -> G | LOC_Os04g09570.1 | downstream_gene_variant ; 1950.0bp to feature; MODIFIER | silent_mutation | Average:22.031; most accessible tissue: Zhenshan97 panicle, score: 73.605 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0405138328 | 3.45E-06 | NA | mr1602 | 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 |
| vg0405138328 | NA | 5.70E-07 | mr1602 | 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 |
| vg0405138328 | 3.72E-06 | NA | mr1934 | 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 |
| vg0405138328 | NA | 9.36E-06 | mr1154_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 |
| vg0405138328 | 2.42E-06 | NA | mr1631_2 | 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 |