| Variant ID: vg0311393570 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 11393570 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )
ATCTTATATAAGGTGGGCAGGAGGCCCTCTAGGGGGCATGACACAAACTGATCGTCAGATCAATATACACCCGGCGGATTCAAATCCCCAAACAGGAGTA[G/A]
GGTATTACCTCTCATCGAGAGGGTCTGAACCTGTCTAAATCCTTTGTCTACGCATCCATCCACTTTTAGGTCTCGTGCGCTACCCCTTTTCATATTGCGA
TCGCAATATGAAAAGGGGTAGCGCACGAGACCTAAAAGTGGATGGATGCGTAGACAAAGGATTTAGACAGGTTCAGACCCTCTCGATGAGAGGTAATACC[C/T]
TACTCCTGTTTGGGGATTTGAATCCGCCGGGTGTATATTGATCTGACGATCAGTTTGTGTCATGCCCCCTAGAGGGCCTCCTGCCCACCTTATATAAGAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.70% | 42.80% | 0.49% | 0.00% | NA |
| All Indica | 2759 | 30.30% | 69.10% | 0.54% | 0.00% | NA |
| All Japonica | 1512 | 99.30% | 0.50% | 0.13% | 0.00% | NA |
| Aus | 269 | 72.50% | 27.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 70.80% | 28.40% | 0.84% | 0.00% | NA |
| Indica II | 465 | 8.00% | 91.60% | 0.43% | 0.00% | NA |
| Indica III | 913 | 12.20% | 87.40% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 34.10% | 65.40% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 5.20% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 34.40% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0311393570 | G -> A | LOC_Os03g20170.1 | upstream_gene_variant ; 2412.0bp to feature; MODIFIER | silent_mutation | Average:78.086; most accessible tissue: Zhenshan97 flower, score: 89.315 | N | N | N | N |
| vg0311393570 | G -> A | LOC_Os03g20150-LOC_Os03g20170 | intergenic_region ; MODIFIER | silent_mutation | Average:78.086; most accessible tissue: Zhenshan97 flower, score: 89.315 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0311393570 | NA | 5.96E-06 | mr1337 | 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 |
| vg0311393570 | NA | 4.75E-11 | mr1524 | 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 |
| vg0311393570 | NA | 5.94E-07 | mr1347_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 |