| Variant ID: vg0420705057 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20705057 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 126. )
TTTTTTTCCTGTTCCGTTGTAATTAGCAATCTTTACTTTCTTAATACAACAAAGATGCGTAAGTTTTTTTTCGTATTCCTGAAAAGAAAATGTAGTTCTT[A/G]
TATGAAGTTGCATGAAAATATATGAATATATAGATGAAGCCACAAAATGAAGTGTCTTAAACTCTTCTATATCATTGAGTTTGTCATATTTCAACAATTT
AAATTGTTGAAATATGACAAACTCAATGATATAGAAGAGTTTAAGACACTTCATTTTGTGGCTTCATCTATATATTCATATATTTTCATGCAACTTCATA[T/C]
AAGAACTACATTTTCTTTTCAGGAATACGAAAAAAAACTTACGCATCTTTGTTGTATTAAGAAAGTAAAGATTGCTAATTACAACGGAACAGGAAAAAAA
| 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 | 81.00% | 6.10% | 5.88% | 7.02% | NA |
| All Indica | 2759 | 76.60% | 10.30% | 9.79% | 3.30% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.13% | 0.07% | NA |
| Aus | 269 | 12.30% | 0.70% | 1.49% | 85.50% | NA |
| Indica I | 595 | 79.00% | 0.30% | 20.67% | 0.00% | NA |
| Indica II | 465 | 75.90% | 13.80% | 9.03% | 1.29% | NA |
| Indica III | 913 | 76.20% | 17.60% | 1.64% | 4.49% | NA |
| Indica Intermediate | 786 | 75.70% | 7.30% | 11.45% | 5.60% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420705057 | A -> DEL | N | N | silent_mutation | Average:43.646; most accessible tissue: Callus, score: 89.046 | N | N | N | N |
| vg0420705057 | A -> G | LOC_Os04g34170.1 | upstream_gene_variant ; 2976.0bp to feature; MODIFIER | silent_mutation | Average:43.646; most accessible tissue: Callus, score: 89.046 | N | N | N | N |
| vg0420705057 | A -> G | LOC_Os04g34170.3 | upstream_gene_variant ; 2976.0bp to feature; MODIFIER | silent_mutation | Average:43.646; most accessible tissue: Callus, score: 89.046 | N | N | N | N |
| vg0420705057 | A -> G | LOC_Os04g34160.1 | downstream_gene_variant ; 1208.0bp to feature; MODIFIER | silent_mutation | Average:43.646; most accessible tissue: Callus, score: 89.046 | N | N | N | N |
| vg0420705057 | A -> G | LOC_Os04g34160-LOC_Os04g34170 | intergenic_region ; MODIFIER | silent_mutation | Average:43.646; most accessible tissue: Callus, score: 89.046 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0420705057 | 4.32E-06 | 5.22E-07 | mr1042_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 |
| vg0420705057 | NA | 6.18E-06 | mr1457_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 |
| vg0420705057 | 8.39E-06 | 3.32E-06 | mr1677_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 |