| Variant ID: vg0206387400 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6387400 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 54. )
ATTACATATTTGGATAATTTTACCATCCTTTAATTTAGACGATACCGATAAATACTATATTTTTCTAATATCAAATTTTAATATCTACGTGTACTTTCTT[A/G]
AGAACTATAAAATTTCTCAATATATTTAGTTACACACAAGCTAGCACTGTGTACGTATCATAGCCACAGTAGTGAGTAGTACACTGGGACTTCACCGAAT
ATTCGGTGAAGTCCCAGTGTACTACTCACTACTGTGGCTATGATACGTACACAGTGCTAGCTTGTGTGTAACTAAATATATTGAGAAATTTTATAGTTCT[T/C]
AAGAAAGTACACGTAGATATTAAAATTTGATATTAGAAAAATATAGTATTTATCGGTATCGTCTAAATTAAAGGATGGTAAAATTATCCAAATATGTAAT
| 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 | 67.10% | 22.80% | 2.62% | 7.43% | NA |
| All Indica | 2759 | 49.90% | 38.10% | 4.31% | 7.65% | NA |
| All Japonica | 1512 | 98.40% | 0.30% | 0.00% | 1.26% | NA |
| Aus | 269 | 72.90% | 1.10% | 0.74% | 25.28% | NA |
| Indica I | 595 | 55.10% | 30.10% | 9.08% | 5.71% | NA |
| Indica II | 465 | 62.20% | 24.30% | 3.23% | 10.32% | NA |
| Indica III | 913 | 42.80% | 49.30% | 0.99% | 6.90% | NA |
| Indica Intermediate | 786 | 47.10% | 39.30% | 5.22% | 8.40% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.00% | 0.20% | 0.00% | 2.78% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.80% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 38.50% | 10.40% | 2.08% | 48.96% | NA |
| Intermediate | 90 | 81.10% | 11.10% | 1.11% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206387400 | A -> G | LOC_Os02g12250.1 | downstream_gene_variant ; 4473.0bp to feature; MODIFIER | silent_mutation | Average:69.794; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0206387400 | A -> G | LOC_Os02g12260.1 | downstream_gene_variant ; 257.0bp to feature; MODIFIER | silent_mutation | Average:69.794; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0206387400 | A -> G | LOC_Os02g12270.1 | downstream_gene_variant ; 118.0bp to feature; MODIFIER | silent_mutation | Average:69.794; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0206387400 | A -> G | LOC_Os02g12280.1 | downstream_gene_variant ; 2514.0bp to feature; MODIFIER | silent_mutation | Average:69.794; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0206387400 | A -> G | LOC_Os02g12260-LOC_Os02g12270 | intergenic_region ; MODIFIER | silent_mutation | Average:69.794; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0206387400 | A -> DEL | N | N | silent_mutation | Average:69.794; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206387400 | 5.02E-07 | 4.98E-07 | mr1197_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 |
| vg0206387400 | NA | 8.99E-07 | mr1197_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 |
| vg0206387400 | NA | 5.58E-06 | mr1277_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 |