Variant ID: vg0705425288 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 5425288 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.25, others allele: 0.00, population size: 232. )
TTCTTTAGATCTTGCAGGTAAGAACATAAATGCCTTATCTCCTGAAATGGATTTGAATTGTTTTGATCAGTTACATTTGCAGGCACTTTGACGACCTATC[T/C]
GGAGTCAAGCTAAAACACATAGAATTTGCTTTATACTGCATTCTTCAAAATGGCGTTATATTCAAACCAAAGCATTTCTTAACCTCTTATTCCGATTTGC
GCAAATCGGAATAAGAGGTTAAGAAATGCTTTGGTTTGAATATAACGCCATTTTGAAGAATGCAGTATAAAGCAAATTCTATGTGTTTTAGCTTGACTCC[A/G]
GATAGGTCGTCAAAGTGCCTGCAAATGTAACTGATCAAAACAATTCAAATCCATTTCAGGAGATAAGGCATTTATGTTCTTACCTGCAAGATCTAAAGAA
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 96.60% | 3.40% | 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 94.50% | 5.50% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0705425288 | T -> C | LOC_Os07g10110.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.833; most accessible tissue: Callus, score: 82.803 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0705425288 | 2.89E-11 | 2.70E-12 | mr1549_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 |
vg0705425288 | 4.88E-10 | 2.04E-10 | mr1550_2 | Jap_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 |
vg0705425288 | 2.06E-09 | 1.11E-10 | mr1757_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 |