| Variant ID: vg0609451875 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9451875 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, A: 0.11, others allele: 0.00, population size: 70. )
TACTTTTTTGGATCGGACTTATTTTTTTTCTTTTTTTGCCGGTTTTTCCCCCTCTTTCGCCCTTTTTGATCTGACATGTTTTGTTTTTTTTTTCACACGG[T/A]
TTTTTTTCGCGTGTGGATTTTTTTTCGTTTGTTTCGTCTATTTTTTTATCGGACATAGTTTTTTGTTCGTCTGGTTTTTTTCGCATGGTTTTTTTCTCTC
GAGAGAAAAAAACCATGCGAAAAAAACCAGACGAACAAAAAACTATGTCCGATAAAAAAATAGACGAAACAAACGAAAAAAAATCCACACGCGAAAAAAA[A/T]
CCGTGTGAAAAAAAAAACAAAACATGTCAGATCAAAAAGGGCGAAAGAGGGGGAAAAACCGGCAAAAAAAGAAAAAAAATAAGTCCGATCCAAAAAAGTA
| 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 | 44.70% | 12.20% | 0.08% | 43.04% | NA |
| All Indica | 2759 | 73.80% | 4.10% | 0.04% | 22.00% | NA |
| All Japonica | 1512 | 2.10% | 29.60% | 0.07% | 68.25% | NA |
| Aus | 269 | 1.90% | 1.10% | 0.00% | 97.03% | NA |
| Indica I | 595 | 82.50% | 1.50% | 0.00% | 15.97% | NA |
| Indica II | 465 | 82.40% | 0.60% | 0.00% | 16.99% | NA |
| Indica III | 913 | 61.10% | 10.20% | 0.11% | 28.59% | NA |
| Indica Intermediate | 786 | 77.00% | 1.10% | 0.00% | 21.88% | NA |
| Temperate Japonica | 767 | 1.80% | 54.60% | 0.00% | 43.55% | NA |
| Tropical Japonica | 504 | 2.00% | 1.20% | 0.20% | 96.63% | NA |
| Japonica Intermediate | 241 | 3.30% | 9.10% | 0.00% | 87.55% | NA |
| VI/Aromatic | 96 | 4.20% | 2.10% | 0.00% | 93.75% | NA |
| Intermediate | 90 | 38.90% | 10.00% | 2.22% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609451875 | T -> A | LOC_Os06g16460-LOC_Os06g16470 | intergenic_region ; MODIFIER | silent_mutation | Average:26.907; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0609451875 | T -> DEL | N | N | silent_mutation | Average:26.907; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0609451875 | NA | 3.67E-06 | mr1096 | 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 |
| vg0609451875 | NA | 6.16E-08 | mr1090_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 |
| vg0609451875 | NA | 3.70E-06 | mr1094_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 |
| vg0609451875 | NA | 3.04E-06 | mr1096_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 |
| vg0609451875 | NA | 9.76E-07 | mr1211_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 |
| vg0609451875 | NA | 4.85E-10 | mr1570_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 |