| Variant ID: vg1115484688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15484688 |
| Reference Allele: G | Alternative Allele: C,T,A |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.05, others allele: 0.00, population size: 191. )
GGGTTTTGTTTTCCTAGGGTAAGCGAGGTGATAATAAACAATAGTAATGATAAGGCTATAACAAGGATTAATAGGTATTACTAAAAACAGTGATAACGCG[G/C,T,A]
GAATTTAAATAAAGCGATAATGCAATAATTTAAATCAAAATAATTTTATAAACTGGGATTCAATATGCTCAAGGATGATGCGACTTGCCTTGCTCAGAGA
TCTCTGAGCAAGGCAAGTCGCATCATCCTTGAGCATATTGAATCCCAGTTTATAAAATTATTTTGATTTAAATTATTGCATTATCGCTTTATTTAAATTC[C/G,A,T]
CGCGTTATCACTGTTTTTAGTAATACCTATTAATCCTTGTTATAGCCTTATCATTACTATTGTTTATTATCACCTCGCTTACCCTAGGAAAACAAAACCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.90% | 30.30% | 1.59% | 0.17% | A: 0.04% |
| All Indica | 2759 | 52.80% | 44.20% | 2.68% | 0.18% | A: 0.07% |
| All Japonica | 1512 | 98.30% | 1.50% | 0.00% | 0.13% | NA |
| Aus | 269 | 40.50% | 59.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 84.20% | 15.30% | 0.50% | 0.00% | NA |
| Indica II | 465 | 41.10% | 57.20% | 1.72% | 0.00% | NA |
| Indica III | 913 | 39.90% | 55.20% | 4.27% | 0.44% | A: 0.22% |
| Indica Intermediate | 786 | 51.10% | 45.70% | 3.05% | 0.13% | NA |
| Temperate Japonica | 767 | 98.70% | 1.20% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.10% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 3.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 72.20% | 26.70% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115484688 | G -> T | LOC_Os11g26930.1 | upstream_gene_variant ; 1079.0bp to feature; MODIFIER | N | Average:36.367; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg1115484688 | G -> T | LOC_Os11g26920-LOC_Os11g26930 | intergenic_region ; MODIFIER | N | Average:36.367; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg1115484688 | G -> A | LOC_Os11g26930.1 | upstream_gene_variant ; 1079.0bp to feature; MODIFIER | silent_mutation | Average:36.367; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg1115484688 | G -> A | LOC_Os11g26920-LOC_Os11g26930 | intergenic_region ; MODIFIER | silent_mutation | Average:36.367; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg1115484688 | G -> DEL | N | N | silent_mutation | Average:36.367; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg1115484688 | G -> C | LOC_Os11g26930.1 | upstream_gene_variant ; 1079.0bp to feature; MODIFIER | silent_mutation | Average:36.367; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg1115484688 | G -> C | LOC_Os11g26920-LOC_Os11g26930 | intergenic_region ; MODIFIER | silent_mutation | Average:36.367; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1115484688 | NA | 5.67E-08 | mr1097 | 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 |
| vg1115484688 | NA | 1.56E-06 | mr1149 | 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 |
| vg1115484688 | NA | 5.49E-06 | mr1617 | 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 |
| vg1115484688 | NA | 1.78E-07 | mr1072_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 |
| vg1115484688 | NA | 1.24E-06 | mr1092_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 |
| vg1115484688 | 4.91E-08 | NA | mr1097_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 |
| vg1115484688 | 5.20E-06 | 1.31E-09 | mr1097_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 |
| vg1115484688 | NA | 6.38E-07 | mr1152_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 |
| vg1115484688 | 2.91E-09 | NA | mr1154_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 |
| vg1115484688 | 3.01E-08 | 2.20E-13 | mr1154_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 |