| Variant ID: vg0333760698 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 33760698 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, T: 0.14, A: 0.01, others allele: 0.00, population size: 93. )
TGATGCACCGCTCATCGACCATACCTAGAGATGGACACATACACTTACGGGATAGTGTGTACTACTATTTATTACTAGTTGCTACCTGACATAAACTCCG[G/A]
CCGTCCGAGAAAACCCTAACATAAAATGATAGCAGACATAACCTAGTATAATAAATCTAGACAGATTTCTATTAAATTATAATATGCTTTTTATAGTTCT
AGAACTATAAAAAGCATATTATAATTTAATAGAAATCTGTCTAGATTTATTATACTAGGTTATGTCTGCTATCATTTTATGTTAGGGTTTTCTCGGACGG[C/T]
CGGAGTTTATGTCAGGTAGCAACTAGTAATAAATAGTAGTACACACTATCCCGTAAGTGTATGTGTCCATCTCTAGGTATGGTCGATGAGCGGTGCATCA
| 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 | 65.70% | 31.60% | 2.73% | 0.00% | NA |
| All Indica | 2759 | 42.60% | 53.00% | 4.46% | 0.00% | NA |
| All Japonica | 1512 | 99.30% | 0.60% | 0.13% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 22.50% | 68.10% | 9.41% | 0.00% | NA |
| Indica II | 465 | 28.80% | 66.50% | 4.73% | 0.00% | NA |
| Indica III | 913 | 62.30% | 36.90% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 43.00% | 52.20% | 4.83% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 22.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0333760698 | G -> A | LOC_Os03g59290.1 | upstream_gene_variant ; 1402.0bp to feature; MODIFIER | silent_mutation | Average:45.38; most accessible tissue: Callus, score: 89.748 | N | N | N | N |
| vg0333760698 | G -> A | LOC_Os03g59300.1 | upstream_gene_variant ; 4762.0bp to feature; MODIFIER | silent_mutation | Average:45.38; most accessible tissue: Callus, score: 89.748 | N | N | N | N |
| vg0333760698 | G -> A | LOC_Os03g59280.1 | downstream_gene_variant ; 4926.0bp to feature; MODIFIER | silent_mutation | Average:45.38; most accessible tissue: Callus, score: 89.748 | N | N | N | N |
| vg0333760698 | G -> A | LOC_Os03g59290-LOC_Os03g59300 | intergenic_region ; MODIFIER | silent_mutation | Average:45.38; most accessible tissue: Callus, score: 89.748 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0333760698 | NA | 3.56E-08 | mr1707 | 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 |
| vg0333760698 | NA | 2.82E-06 | mr1346_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 |
| vg0333760698 | NA | 2.95E-10 | mr1834_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 |
| vg0333760698 | NA | 5.43E-06 | mr1834_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 |