| Variant ID: vg0315246943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15246943 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.33, others allele: 0.00, population size: 82. )
CAAAATCTTTGAGAACCATATTGGTCTTAATGAGATCATTTGGATTTCTGCCCAACTTCCTGAATGTAGCATATGGCATTAAATTCACAGCAGCTCCTCC[G/A]
TCAACCATCATTTTGGACATCGGCTTCCCATTGGCAAACCCATTAATATACAAAGGCTTGAGATGCCGATTTTCTATCCCTTCTGGCTTCTCAAAAATTG
CAATTTTTGAGAAGCCAGAAGGGATAGAAAATCGGCATCTCAAGCCTTTGTATATTAATGGGTTTGCCAATGGGAAGCCGATGTCCAAAATGATGGTTGA[C/T]
GGAGGAGCTGCTGTGAATTTAATGCCATATGCTACATTCAGGAAGTTGGGCAGAAATCCAAATGATCTCATTAAGACCAATATGGTTCTCAAAGATTTTG
| 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 | 37.40% | 18.00% | 5.99% | 38.66% | NA |
| All Indica | 2759 | 29.70% | 10.10% | 9.75% | 50.38% | NA |
| All Japonica | 1512 | 55.90% | 30.10% | 0.53% | 13.49% | NA |
| Aus | 269 | 2.60% | 27.50% | 1.49% | 68.40% | NA |
| Indica I | 595 | 49.60% | 10.30% | 1.85% | 38.32% | NA |
| Indica II | 465 | 32.90% | 4.90% | 3.87% | 58.28% | NA |
| Indica III | 913 | 13.70% | 12.90% | 19.39% | 54.00% | NA |
| Indica Intermediate | 786 | 31.40% | 9.90% | 8.02% | 50.64% | NA |
| Temperate Japonica | 767 | 85.90% | 4.30% | 0.13% | 9.65% | NA |
| Tropical Japonica | 504 | 19.60% | 64.10% | 1.19% | 15.08% | NA |
| Japonica Intermediate | 241 | 36.10% | 41.10% | 0.41% | 22.41% | NA |
| VI/Aromatic | 96 | 67.70% | 9.40% | 0.00% | 22.92% | NA |
| Intermediate | 90 | 33.30% | 34.40% | 2.22% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315246943 | G -> A | LOC_Os03g26704.1 | synonymous_variant ; p.Asp487Asp; LOW | synonymous_codon | Average:10.171; most accessible tissue: Callus, score: 34.417 | N | N | N | N |
| vg0315246943 | G -> DEL | LOC_Os03g26704.1 | N | frameshift_variant | Average:10.171; most accessible tissue: Callus, score: 34.417 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0315246943 | NA | 2.51E-06 | mr1477_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 |
| vg0315246943 | NA | 3.75E-06 | mr1558_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 |
| vg0315246943 | NA | 3.73E-08 | mr1952_2 | 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 |