| Variant ID: vg0608570503 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8570503 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 73. )
TAGAAGGGATTGGGTGAAATTACATGGGCATATAGGGAATTGGCCCTATCATAAAAGTAATTTGTGATTTTTCATCAAAATATAATTATGTGATATCTTG[T/A]
TATAAAGATTTAATTATTATGAACACAACGGTGTAATCGGATCGTAGATCGGATGAGTAATTTAAGAGAAAATTTTATTTAAAGTATAGGTGGATAGAGT
ACTCTATCCACCTATACTTTAAATAAAATTTTCTCTTAAATTACTCATCCGATCTACGATCCGATTACACCGTTGTGTTCATAATAATTAAATCTTTATA[A/T]
CAAGATATCACATAATTATATTTTGATGAAAAATCACAAATTACTTTTATGATAGGGCCAATTCCCTATATGCCCATGTAATTTCACCCAATCCCTTCTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.40% | 4.90% | 5.56% | 46.09% | NA |
| All Indica | 2759 | 6.40% | 8.20% | 9.31% | 76.04% | NA |
| All Japonica | 1512 | 99.00% | 0.00% | 0.20% | 0.79% | NA |
| Aus | 269 | 86.20% | 0.00% | 0.74% | 13.01% | NA |
| Indica I | 595 | 8.10% | 6.60% | 9.75% | 75.63% | NA |
| Indica II | 465 | 6.20% | 12.00% | 11.40% | 70.32% | NA |
| Indica III | 913 | 4.60% | 5.00% | 8.21% | 82.15% | NA |
| Indica Intermediate | 786 | 7.40% | 10.90% | 9.03% | 72.65% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.13% | 0.78% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.40% | 0.40% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 58.90% | 5.60% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0608570503 | T -> A | LOC_Os06g15110.1 | upstream_gene_variant ; 4334.0bp to feature; MODIFIER | silent_mutation | Average:19.098; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0608570503 | T -> A | LOC_Os06g15110-LOC_Os06g15120 | intergenic_region ; MODIFIER | silent_mutation | Average:19.098; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0608570503 | T -> DEL | N | N | silent_mutation | Average:19.098; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608570503 | NA | 6.03E-07 | mr1053 | 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 |
| vg0608570503 | NA | 3.98E-09 | mr1663 | 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 |
| vg0608570503 | NA | 5.46E-13 | mr1377_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 |
| vg0608570503 | NA | 2.32E-06 | mr1377_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 |
| vg0608570503 | NA | 1.96E-10 | mr1649_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 |