Variant ID: vg0302609274 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 2609274 |
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: 318. )
GCCTATAGAGCGTGGGCTAATGGTGGCCATGGAGGCTAGCTAAGCTACTTCTTCTTGGGGAGGAATGGCTATGCATGGCCTCCATAGTCGACGACTTTTA[C/T]
CTCTACTAAGGTAGGGCAACTTGTATCCTTTGGCAATTATTCGGTGGATGTCTGTTGGTGGTGGTGTTAGGGATTGGAGCCGGATGAATCTTGAGTTTGA
TCAAACTCAAGATTCATCCGGCTCCAATCCCTAACACCACCACCAACAGACATCCACCGAATAATTGCCAAAGGATACAAGTTGCCCTACCTTAGTAGAG[G/A]
TAAAAGTCGTCGACTATGGAGGCCATGCATAGCCATTCCTCCCCAAGAAGAAGTAGCTTAGCTAGCCTCCATGGCCACCATTAGCCCACGCTCTATAGGC
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 | 90.30% | 8.40% | 1.33% | 0.00% | NA |
All Indica | 2759 | 83.60% | 14.10% | 2.25% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 86.20% | 9.40% | 4.37% | 0.00% | NA |
Indica II | 465 | 98.30% | 0.60% | 1.08% | 0.00% | NA |
Indica III | 913 | 75.80% | 23.90% | 0.33% | 0.00% | NA |
Indica Intermediate | 786 | 82.10% | 14.40% | 3.56% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0302609274 | C -> T | LOC_Os03g05334.1 | 5_prime_UTR_variant ; 48.0bp to feature; MODIFIER | silent_mutation | Average:67.523; most accessible tissue: Callus, score: 89.682 | N | N | N | N |
vg0302609274 | C -> T | LOC_Os03g05330.1 | downstream_gene_variant ; 3772.0bp to feature; MODIFIER | silent_mutation | Average:67.523; most accessible tissue: Callus, score: 89.682 | N | N | N | N |
vg0302609274 | C -> T | LOC_Os03g05340.1 | downstream_gene_variant ; 766.0bp to feature; MODIFIER | silent_mutation | Average:67.523; most accessible tissue: Callus, score: 89.682 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0302609274 | NA | 5.67E-07 | mr1155 | 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 |
vg0302609274 | 3.98E-07 | 3.98E-07 | mr1449 | 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 |