| Variant ID: vg0125056945 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25056945 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.06, others allele: 0.00, population size: 245. )
ATCCTTTTCTGGACCAGATCTCGTATAATTGATTCAACCTCGTTCTTAATTTGATACATCCTTCGGTTGTTTTTGGTAGGCAAGGACCTGAAAGGGCACA[C/T]
CGCTTCAGATTTTCAGTACAGAGAGGAACTACGAGTACTGAATAACAAACATTTAATTTCGATAGAAATTATGTATAACTGTAAGGTCTGGTTAGTGTTA
TAACACTAACCAGACCTTACAGTTATACATAATTTCTATCGAAATTAAATGTTTGTTATTCAGTACTCGTAGTTCCTCTCTGTACTGAAAATCTGAAGCG[G/A]
TGTGCCCTTTCAGGTCCTTGCCTACCAAAAACAACCGAAGGATGTATCAAATTAAGAACGAGGTTGAATCAATTATACGAGATCTGGTCCAGAAAAGGAT
| 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 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 89.90% | 10.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 84.10% | 15.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 75.90% | 24.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125056945 | C -> T | LOC_Os01g43740.1 | upstream_gene_variant ; 3819.0bp to feature; MODIFIER | silent_mutation | Average:63.496; most accessible tissue: Callus, score: 90.941 | N | N | N | N |
| vg0125056945 | C -> T | LOC_Os01g43720.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.496; most accessible tissue: Callus, score: 90.941 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0125056945 | NA | 3.19E-06 | mr1180 | 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 |
| vg0125056945 | NA | 5.75E-07 | mr1180_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 |
| vg0125056945 | NA | 1.21E-07 | mr1183_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 |