| Variant ID: vg0418069807 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 18069807 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, A: 0.24, others allele: 0.00, population size: 45. )
GGCTGTGGTGGCATGGCACGGATCGAGGCACTTAGCAGCAGCACGGTGCGGATTGAGGCACACGGTGATGGCGCCTGGCAGATGCTTGGTGCGGAGGGAC[T/A]
TCTCTATGACAGTGGGTGCATATTTTACTCTATGGCGTGCAAATGGACTCCATTTTGTTTCTGATATATTTATCTTGTTCTTTCCCTTTGATGCATGCAA
TTGCATGCATCAAAGGGAAAGAACAAGATAAATATATCAGAAACAAAATGGAGTCCATTTGCACGCCATAGAGTAAAATATGCACCCACTGTCATAGAGA[A/T]
GTCCCTCCGCACCAAGCATCTGCCAGGCGCCATCACCGTGTGCCTCAATCCGCACCGTGCTGCTGCTAAGTGCCTCGATCCGTGCCATGCCACCACAGCC
| 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 | 43.80% | 39.00% | 0.74% | 16.50% | NA |
| All Indica | 2759 | 69.00% | 20.00% | 0.87% | 10.15% | NA |
| All Japonica | 1512 | 0.90% | 68.00% | 0.46% | 30.69% | NA |
| Aus | 269 | 44.60% | 50.60% | 1.12% | 3.72% | NA |
| Indica I | 595 | 62.20% | 36.30% | 1.01% | 0.50% | NA |
| Indica II | 465 | 53.80% | 38.30% | 0.86% | 7.10% | NA |
| Indica III | 913 | 77.80% | 1.80% | 0.66% | 19.82% | NA |
| Indica Intermediate | 786 | 72.90% | 18.10% | 1.02% | 8.02% | NA |
| Temperate Japonica | 767 | 0.30% | 97.40% | 0.13% | 2.22% | NA |
| Tropical Japonica | 504 | 1.20% | 35.70% | 0.79% | 62.30% | NA |
| Japonica Intermediate | 241 | 2.10% | 41.90% | 0.83% | 55.19% | NA |
| VI/Aromatic | 96 | 11.50% | 72.90% | 0.00% | 15.62% | NA |
| Intermediate | 90 | 25.60% | 61.10% | 1.11% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0418069807 | T -> DEL | N | N | silent_mutation | Average:61.994; most accessible tissue: Zhenshan97 young leaf, score: 84.814 | N | N | N | N |
| vg0418069807 | T -> A | LOC_Os04g30270.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.994; most accessible tissue: Zhenshan97 young leaf, score: 84.814 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0418069807 | NA | 6.57E-08 | mr1851 | 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 |
| vg0418069807 | 2.11E-06 | 5.92E-09 | mr1851 | 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 |
| vg0418069807 | 4.06E-06 | 2.20E-07 | mr1864 | 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 |
| vg0418069807 | NA | 9.10E-08 | mr1042_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 |
| vg0418069807 | 9.35E-07 | 1.53E-08 | mr1680_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 |
| vg0418069807 | NA | 7.17E-09 | mr1742_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 |