Variant ID: vg0805209698 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 5209698 |
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: 286. )
TATATCAATTGAGAAAAAAAAAAGTTTGCTTCGCTAGGATATATTTATTATGAGAAATATCAAGCAATTAACTTAATCAAAACGTAGCTACTAGTTTTAG[C/T]
TTTTCCGGCAGCATACTTTAACCCTCAACACCCTTCCATGATCACTCTTTTCTTGAAAAGAAACCTTTCACCTTTTCCCTGAGCTATTCTCTGCTCTATA
TATAGAGCAGAGAATAGCTCAGGGAAAAGGTGAAAGGTTTCTTTTCAAGAAAAGAGTGATCATGGAAGGGTGTTGAGGGTTAAAGTATGCTGCCGGAAAA[G/A]
CTAAAACTAGTAGCTACGTTTTGATTAAGTTAATTGCTTGATATTTCTCATAATAAATATATCCTAGCGAAGCAAACTTTTTTTTTTCTCAATTGATATA
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 | 96.20% | 3.80% | 0.02% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 88.20% | 11.70% | 0.07% | 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 | 81.20% | 18.60% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 87.60% | 12.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 2.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0805209698 | C -> T | LOC_Os08g08950.1 | downstream_gene_variant ; 3619.0bp to feature; MODIFIER | silent_mutation | Average:40.986; most accessible tissue: Callus, score: 79.646 | N | N | N | N |
vg0805209698 | C -> T | LOC_Os08g08960.1 | downstream_gene_variant ; 129.0bp to feature; MODIFIER | silent_mutation | Average:40.986; most accessible tissue: Callus, score: 79.646 | N | N | N | N |
vg0805209698 | C -> T | LOC_Os08g08960-LOC_Os08g08970 | intergenic_region ; MODIFIER | silent_mutation | Average:40.986; most accessible tissue: Callus, score: 79.646 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0805209698 | NA | 3.49E-06 | mr1062 | 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 |
vg0805209698 | 8.98E-07 | NA | mr1631_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 |
vg0805209698 | NA | 4.07E-08 | mr1631_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 |