Variant ID: vg0222686622 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 22686622 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 122. )
GTCCGAGGGGTCCCATCATCGCCTCCTCCCTCGCCGGTGTTGCTTACGCCGCCCATGCCCTCGTTGCTCATGTCTTACTCTGACTTGCACCACATAAATT[G/A]
CATGGGACAATCCTCTAGTTTTATTAAAAGAAAAAAAAAGCTTCATCAATTCCCGTCTCTTGTCCCCGAGTTTTTTTTAACATAAAGAACACTTATCTAT
ATAGATAAGTGTTCTTTATGTTAAAAAAAACTCGGGGACAAGAGACGGGAATTGATGAAGCTTTTTTTTTCTTTTAATAAAACTAGAGGATTGTCCCATG[C/T]
AATTTATGTGGTGCAAGTCAGAGTAAGACATGAGCAACGAGGGCATGGGCGGCGTAAGCAACACCGGCGAGGGAGGAGGCGATGATGGGACCCCTCGGAC
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 88.10% | 8.70% | 3.24% | 0.00% | NA |
All Indica | 2759 | 80.00% | 14.70% | 5.33% | 0.00% | NA |
All Japonica | 1512 | 99.80% | 0.10% | 0.07% | 0.00% | NA |
Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
Indica I | 595 | 62.90% | 20.70% | 16.47% | 0.00% | NA |
Indica II | 465 | 92.50% | 5.80% | 1.72% | 0.00% | NA |
Indica III | 913 | 83.90% | 15.20% | 0.88% | 0.00% | NA |
Indica Intermediate | 786 | 80.90% | 14.90% | 4.20% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.40% | 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% | 2.20% | 4.44% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0222686622 | G -> A | LOC_Os02g37590.1 | upstream_gene_variant ; 656.0bp to feature; MODIFIER | silent_mutation | Average:64.658; most accessible tissue: Minghui63 young leaf, score: 79.549 | N | N | N | N |
vg0222686622 | G -> A | LOC_Os02g37580-LOC_Os02g37590 | intergenic_region ; MODIFIER | silent_mutation | Average:64.658; most accessible tissue: Minghui63 young leaf, score: 79.549 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0222686622 | 6.06E-06 | NA | mr1929 | 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 |
vg0222686622 | NA | 5.45E-08 | mr1124_2 | 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 |
vg0222686622 | NA | 5.59E-06 | mr1222_2 | 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 |
vg0222686622 | 2.01E-07 | NA | mr1918_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 |
vg0222686622 | 1.19E-06 | 8.31E-06 | mr1918_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 |
vg0222686622 | NA | 1.04E-08 | mr1962_2 | 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 |