Variant ID: vg0317037608 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 17037608 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )
AGCAAGGGAAAGTGCTGGCTTCTCTTAGACCGTTAGACGTCGACCGTTGGGAGAGAACTACGCGTCGGACGTCCGATGTTTTAGGGAAAAATCGGACGCT[G/A]
ACGTCAGCATGACGTCAGCGTCCGATTTACGTGCAAAACTACTTTTAAATTGATTTTTCTCTTAAATTTCTTATCCAAATCATGATTCGATTACACCATT
AATGGTGTAATCGAATCATGATTTGGATAAGAAATTTAAGAGAAAAATCAATTTAAAAGTAGTTTTGCACGTAAATCGGACGCTGACGTCATGCTGACGT[C/T]
AGCGTCCGATTTTTCCCTAAAACATCGGACGTCCGACGCGTAGTTCTCTCCCAACGGTCGACGTCTAACGGTCTAAGAGAAGCCAGCACTTTCCCTTGCT
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 | 49.60% | 48.80% | 0.95% | 0.70% | NA |
All Indica | 2759 | 82.30% | 17.40% | 0.18% | 0.11% | NA |
All Japonica | 1512 | 0.60% | 99.30% | 0.13% | 0.00% | NA |
Aus | 269 | 6.70% | 92.90% | 0.37% | 0.00% | NA |
Indica I | 595 | 94.80% | 5.00% | 0.17% | 0.00% | NA |
Indica II | 465 | 87.10% | 12.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 74.90% | 24.60% | 0.22% | 0.22% | NA |
Indica Intermediate | 786 | 78.60% | 21.00% | 0.25% | 0.13% | NA |
Temperate Japonica | 767 | 0.10% | 99.90% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 0.40% | 98.80% | 0.83% | 0.00% | NA |
VI/Aromatic | 96 | 9.40% | 26.00% | 34.38% | 30.21% | NA |
Intermediate | 90 | 41.10% | 53.30% | 4.44% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0317037608 | G -> A | LOC_Os03g29900.1 | upstream_gene_variant ; 2382.0bp to feature; MODIFIER | silent_mutation | Average:56.322; most accessible tissue: Zhenshan97 flower, score: 79.365 | N | N | N | N |
vg0317037608 | G -> A | LOC_Os03g29910.1 | upstream_gene_variant ; 1690.0bp to feature; MODIFIER | silent_mutation | Average:56.322; most accessible tissue: Zhenshan97 flower, score: 79.365 | N | N | N | N |
vg0317037608 | G -> A | LOC_Os03g29910.2 | upstream_gene_variant ; 1690.0bp to feature; MODIFIER | silent_mutation | Average:56.322; most accessible tissue: Zhenshan97 flower, score: 79.365 | N | N | N | N |
vg0317037608 | G -> A | LOC_Os03g29900-LOC_Os03g29910 | intergenic_region ; MODIFIER | silent_mutation | Average:56.322; most accessible tissue: Zhenshan97 flower, score: 79.365 | N | N | N | N |
vg0317037608 | G -> DEL | N | N | silent_mutation | Average:56.322; most accessible tissue: Zhenshan97 flower, score: 79.365 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0317037608 | NA | 2.71E-34 | mr1026 | 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 |
vg0317037608 | NA | 6.73E-28 | mr1037 | 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 |
vg0317037608 | NA | 3.23E-34 | mr1161 | 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 |
vg0317037608 | NA | 2.03E-10 | mr1180 | 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 |
vg0317037608 | 1.18E-06 | 2.65E-15 | mr1183 | 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 |
vg0317037608 | 8.35E-06 | NA | mr1183 | 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 |
vg0317037608 | 7.87E-06 | 1.96E-14 | mr1503 | 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 |
vg0317037608 | NA | 4.61E-11 | mr1657 | 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 |
vg0317037608 | NA | 3.21E-06 | mr1750 | 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 |
vg0317037608 | NA | 1.43E-09 | 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 |
vg0317037608 | NA | 2.07E-32 | mr1037_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 |
vg0317037608 | NA | 1.64E-16 | mr1180_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 |
vg0317037608 | NA | 2.00E-21 | mr1183_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 |