| Variant ID: vg0102657456 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 2657456 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 268. )
GGGGGCGGAGATGGTCCTTTCCTTGTCCCCGCTCCCCGCGGAGACCCGAATAGGGGTCCAAGTTTAATATGTCCCTGTCGGTTTGCTGCATGCATGACAC[C/T]
GATTACACCTAGTTACAAGTTTAATATGCAAAATGACTCTCTTGGTGATTTTGAGGGTGATTTTCACCAACGTGGCTCGTTGACCTAGTCCAACCAGTCG
CGACTGGTTGGACTAGGTCAACGAGCCACGTTGGTGAAAATCACCCTCAAAATCACCAAGAGAGTCATTTTGCATATTAAACTTGTAACTAGGTGTAATC[G/A]
GTGTCATGCATGCAGCAAACCGACAGGGACATATTAAACTTGGACCCCTATTCGGGTCTCCGCGGGGAGCGGGGACAAGGAAAGGACCATCTCCGCCCCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.00% | 33.70% | 0.28% | 0.00% | NA |
| All Indica | 2759 | 48.30% | 51.30% | 0.40% | 0.00% | NA |
| All Japonica | 1512 | 91.30% | 8.60% | 0.13% | 0.00% | NA |
| Aus | 269 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 71.80% | 27.70% | 0.50% | 0.00% | NA |
| Indica II | 465 | 15.70% | 83.90% | 0.43% | 0.00% | NA |
| Indica III | 913 | 52.20% | 47.50% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 45.30% | 54.20% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 85.10% | 14.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 2.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 72.20% | 27.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0102657456 | C -> T | LOC_Os01g05570.1 | upstream_gene_variant ; 3366.0bp to feature; MODIFIER | silent_mutation | Average:69.893; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0102657456 | C -> T | LOC_Os01g05560.1 | downstream_gene_variant ; 1817.0bp to feature; MODIFIER | silent_mutation | Average:69.893; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0102657456 | C -> T | LOC_Os01g05560-LOC_Os01g05570 | intergenic_region ; MODIFIER | silent_mutation | Average:69.893; 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 |
|---|---|---|---|---|---|---|
| vg0102657456 | NA | 1.16E-08 | mr1174 | 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 |
| vg0102657456 | NA | 4.44E-07 | mr1970 | 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 |
| vg0102657456 | NA | 2.01E-07 | mr1973 | 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 |
| vg0102657456 | NA | 2.09E-10 | mr1174_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 |
| vg0102657456 | NA | 1.27E-08 | mr1970_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 |
| vg0102657456 | 2.97E-06 | 2.47E-10 | mr1973_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 |