Variant ID: vg0412128903 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 12128903 |
Reference Allele: G | Alternative Allele: T |
Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 116. )
TCCCCGCCAACGGCGCCAGAATTGCTTGTTGGTATTTCTTAACGGCATTACAAGAAATATAATTCCCAACAATGGCGCAGAAATATTTCTGGTATATTAT[G/T]
GTTACAGAGTTCATCCGCAAGCGCATGGATATACCATTGTAGCATTTCACCTTAGAGTATTCCAATGGTATCGTATTTATTTTATCCCGTGGGAAGATCA
TGATCTTCCCACGGGATAAAATAAATACGATACCATTGGAATACTCTAAGGTGAAATGCTACAATGGTATATCCATGCGCTTGCGGATGAACTCTGTAAC[C/A]
ATAATATACCAGAAATATTTCTGCGCCATTGTTGGGAATTATATTTCTTGTAATGCCGTTAAGAAATACCAACAAGCAATTCTGGCGCCGTTGGCGGGGA
Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 57.60% | 41.50% | 0.89% | 0.00% | NA |
All Indica | 2759 | 92.10% | 6.50% | 1.41% | 0.00% | NA |
All Japonica | 1512 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
Aus | 269 | 48.00% | 51.70% | 0.37% | 0.00% | NA |
Indica I | 595 | 98.80% | 0.80% | 0.34% | 0.00% | NA |
Indica II | 465 | 94.40% | 4.70% | 0.86% | 0.00% | NA |
Indica III | 913 | 86.60% | 10.50% | 2.85% | 0.00% | NA |
Indica Intermediate | 786 | 91.90% | 7.30% | 0.89% | 0.00% | NA |
Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 41.10% | 56.70% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0412128903 | G -> T | LOC_Os04g21450.1 | upstream_gene_variant ; 580.0bp to feature; MODIFIER | silent_mutation | Average:22.258; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
vg0412128903 | G -> T | LOC_Os04g21450-LOC_Os04g21460 | intergenic_region ; MODIFIER | silent_mutation | Average:22.258; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0412128903 | 1.07E-06 | 1.54E-07 | mr1071 | 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 |
vg0412128903 | NA | 2.75E-06 | mr1080 | 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 |
vg0412128903 | NA | 8.06E-06 | mr1140 | 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 |
vg0412128903 | NA | 4.01E-16 | mr1156 | 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 |
vg0412128903 | NA | 8.26E-16 | mr1700 | 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 |
vg0412128903 | NA | 2.46E-53 | mr1795 | 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 |
vg0412128903 | NA | 1.15E-07 | mr1804_2 | 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 |