Variant ID: vg0326661478 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 26661478 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 108. )
CCCAAACCTGTCTAAACCATTGTTTTTTTAGCCCTTGATGATCCATGAGATGCCAATCACCTCGTTTCCACACACCCGCTCCCTGGCCGAATCCCAAAAG[A/G]
GTGCCACTTCTCCATGCTAGAGGAGTTTGAGCTCCGACACCACTCATTAGCATTTCTTTTCTTTGTTTCTCCTCATACGAGTCGTATTTTGAACTAAAAT
ATTTTAGTTCAAAATACGACTCGTATGAGGAGAAACAAAGAAAAGAAATGCTAATGAGTGGTGTCGGAGCTCAAACTCCTCTAGCATGGAGAAGTGGCAC[T/C]
CTTTTGGGATTCGGCCAGGGAGCGGGTGTGTGGAAACGAGGTGATTGGCATCTCATGGATCATCAAGGGCTAAAAAAACAATGGTTTAGACAGGTTTGGG
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 75.10% | 24.40% | 0.44% | 0.00% | NA |
All Indica | 2759 | 58.70% | 40.50% | 0.76% | 0.00% | NA |
All Japonica | 1512 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 61.50% | 37.80% | 0.67% | 0.00% | NA |
Indica II | 465 | 48.00% | 49.00% | 3.01% | 0.00% | NA |
Indica III | 913 | 63.20% | 36.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 57.80% | 41.90% | 0.38% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 81.10% | 18.90% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0326661478 | A -> G | LOC_Os03g47120.1 | downstream_gene_variant ; 3631.0bp to feature; MODIFIER | silent_mutation | Average:35.033; most accessible tissue: Callus, score: 49.177 | N | N | N | N |
vg0326661478 | A -> G | LOC_Os03g47120-LOC_Os03g47130 | intergenic_region ; MODIFIER | silent_mutation | Average:35.033; most accessible tissue: Callus, score: 49.177 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0326661478 | NA | 8.24E-10 | mr1193_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 |