| Variant ID: vg0321869681 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21869681 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )
TGATTGCTCCAATCAGGGAGAAATTCTCGTCTGAAAACTTTGATAGCTTGTCACATCTGATACAGAAGGTAACCTTGCATGAGCATAGGTCAGCGGAAGT[C/T]
AGGAAAAGCTCTAAGAAGGTTAATCATGTTTGTCCATACATGTATGGGTCGGATGATGAGGAGGACGATTCTGAAATAGCTGCAGCCGAATGGGTGAGGA
TCCTCACCCATTCGGCTGCAGCTATTTCAGAATCGTCCTCCTCATCATCCGACCCATACATGTATGGACAAACATGATTAACCTTCTTAGAGCTTTTCCT[G/A]
ACTTCCGCTGACCTATGCTCATGCAAGGTTACCTTCTGTATCAGATGTGACAAGCTATCAAAGTTTTCAGACGAGAATTTCTCCCTGATTGGAGCAATCA
| 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 | 65.70% | 2.00% | 2.41% | 29.83% | NA |
| All Indica | 2759 | 50.90% | 3.40% | 3.12% | 42.55% | NA |
| All Japonica | 1512 | 98.40% | 0.00% | 0.00% | 1.59% | NA |
| Aus | 269 | 18.60% | 0.40% | 10.04% | 71.00% | NA |
| Indica I | 595 | 89.10% | 4.00% | 0.84% | 6.05% | NA |
| Indica II | 465 | 40.90% | 3.90% | 3.01% | 52.26% | NA |
| Indica III | 913 | 34.50% | 0.30% | 3.94% | 61.23% | NA |
| Indica Intermediate | 786 | 46.90% | 6.40% | 3.94% | 42.75% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.00% | 4.56% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 1.11% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321869681 | C -> T | LOC_Os03g39350.1 | synonymous_variant ; p.Val434Val; LOW | synonymous_codon | Average:44.381; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 | N | N | N | N |
| vg0321869681 | C -> DEL | LOC_Os03g39350.1 | N | frameshift_variant | Average:44.381; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0321869681 | 1.22E-06 | 1.22E-06 | mr1666_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 |
| vg0321869681 | 7.31E-07 | NA | mr1695_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 |
| vg0321869681 | 6.65E-06 | 4.11E-06 | mr1761_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 |
| vg0321869681 | NA | 5.44E-06 | mr1851_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 |