| Variant ID: vg0316205466 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 16205466 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTAGAGCGCCACGTGGTGACTTAGGAACGTTTATAGGAGTCACATGTGGCGGTTTGAGAGCGTTTGTAGGAAATTTAATGTGCTTTTAATATATAATAA[T/C]
GGATGTTCGATCCATTGTTTCTATTTTCTTAAGAAACCTCGCGAAACATTTACTACTGACAAATGTATATTATTTGTACCATCGTCATCACTTTAATTGG
CCAATTAAAGTGATGACGATGGTACAAATAATATACATTTGTCAGTAGTAAATGTTTCGCGAGGTTTCTTAAGAAAATAGAAACAATGGATCGAACATCC[A/G]
TTATTATATATTAAAAGCACATTAAATTTCCTACAAACGCTCTCAAACCGCCACATGTGACTCCTATAAACGTTCCTAAGTCACCACGTGGCGCTCTAAT
| 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 | 75.90% | 24.10% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.70% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 37.60% | 62.30% | 0.13% | 0.00% | NA |
| Aus | 269 | 79.90% | 20.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.80% | 3.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 9.00% | 90.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 70.20% | 29.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 60.20% | 39.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 25.00% | 75.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 24.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0316205466 | T -> C | LOC_Os03g28160.2 | upstream_gene_variant ; 3668.0bp to feature; MODIFIER | silent_mutation | Average:57.219; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| vg0316205466 | T -> C | LOC_Os03g28160.1 | upstream_gene_variant ; 3666.0bp to feature; MODIFIER | silent_mutation | Average:57.219; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| vg0316205466 | T -> C | LOC_Os03g28140-LOC_Os03g28160 | intergenic_region ; MODIFIER | silent_mutation | Average:57.219; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0316205466 | NA | 1.53E-09 | mr1063 | 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 |
| vg0316205466 | NA | 6.07E-06 | mr1521 | 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 |
| vg0316205466 | NA | 1.27E-06 | mr1531 | 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 |