| Variant ID: vg0404762368 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4762368 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.59, T: 0.41, others allele: 0.00, population size: 88. )
CACGCAAAACAAAGCTTGTATTATTGCATGATTAATTAAGTATTAACTTTTTTTTTAAAAAAAAATAGATTAATATGATTTTTTAAAACAACTTTCATAT[A/T]
TAATTTTTTTGAATAAATCACACCGTTTAGCAGTTTGAAAAGCGTGCGCGCAAAAAACGAAAGAGTTAGGGTTGGGAAAATAAGGGAATAACACAGCATA
TATGCTGTGTTATTCCCTTATTTTCCCAACCCTAACTCTTTCGTTTTTTGCGCGCACGCTTTTCAAACTGCTAAACGGTGTGATTTATTCAAAAAAATTA[T/A]
ATATGAAAGTTGTTTTAAAAAATCATATTAATCTATTTTTTTTTAAAAAAAAAGTTAATACTTAATTAATCATGCAATAATACAAGCTTTGTTTTGCGTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.20% | 5.80% | 0.97% | 0.02% | NA |
| All Indica | 2759 | 95.50% | 3.40% | 1.05% | 0.04% | NA |
| All Japonica | 1512 | 87.60% | 11.30% | 1.06% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.20% | 8.60% | 0.00% | 0.22% | NA |
| Indica III | 913 | 97.60% | 0.40% | 1.97% | 0.00% | NA |
| Indica Intermediate | 786 | 92.90% | 5.70% | 1.40% | 0.00% | NA |
| Temperate Japonica | 767 | 90.90% | 7.00% | 2.09% | 0.00% | NA |
| Tropical Japonica | 504 | 84.50% | 15.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.80% | 16.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 4.40% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404762368 | A -> DEL | N | N | silent_mutation | Average:55.189; most accessible tissue: Zhenshan97 panicle, score: 79.799 | N | N | N | N |
| vg0404762368 | A -> T | LOC_Os04g08760.1 | upstream_gene_variant ; 1788.0bp to feature; MODIFIER | silent_mutation | Average:55.189; most accessible tissue: Zhenshan97 panicle, score: 79.799 | N | N | N | N |
| vg0404762368 | A -> T | LOC_Os04g08749-LOC_Os04g08760 | intergenic_region ; MODIFIER | silent_mutation | Average:55.189; most accessible tissue: Zhenshan97 panicle, score: 79.799 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404762368 | NA | 8.27E-07 | mr1369_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 |
| vg0404762368 | NA | 1.59E-06 | mr1652_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 |
| vg0404762368 | 3.06E-06 | 3.07E-06 | mr1822_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 |
| vg0404762368 | 4.20E-06 | 4.20E-06 | mr1822_2 | Jap_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 |