| Variant ID: vg0112778994 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12778994 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 286. )
CAACTGAATTCCTCCTTGCCCTATAAGCCATGATCTTTGATATGTCAACTCCATATTTTCTCATAACTGCATCCATCATAGAAGTGATTTTTCAGTTTGG[G/A]
TCACTTCTAATGTCCTGTTCATACACTTTACTTAACCATTCACTAGTCACTCTGCTACTGTCCATAGTTGTACCACATGTGTGAGGACCAACCATATTCC
GGAATATGGTTGGTCCTCACACATGTGGTACAACTATGGACAGTAGCAGAGTGACTAGTGAATGGTTAAGTAAAGTGTATGAACAGGACATTAGAAGTGA[C/T]
CCAAACTGAAAAATCACTTCTATGATGGATGCAGTTATGAGAAAATATGGAGTTGACATATCAAAGATCATGGCTTATAGGGCAAGGAGGAATTCAGTTG
| 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 | 59.40% | 40.30% | 0.04% | 0.25% | NA |
| All Indica | 2759 | 35.20% | 64.40% | 0.04% | 0.43% | NA |
| All Japonica | 1512 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 29.20% | 70.60% | 0.00% | 0.17% | NA |
| Indica II | 465 | 41.30% | 58.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 34.20% | 65.20% | 0.11% | 0.55% | NA |
| Indica Intermediate | 786 | 37.20% | 62.10% | 0.00% | 0.76% | NA |
| Temperate Japonica | 767 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 93.70% | 6.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 60.40% | 39.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 23.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112778994 | G -> A | LOC_Os01g22730.1 | upstream_gene_variant ; 25.0bp to feature; MODIFIER | silent_mutation | Average:44.743; most accessible tissue: Zhenshan97 young leaf, score: 67.334 | N | N | N | N |
| vg0112778994 | G -> A | LOC_Os01g22740.1 | upstream_gene_variant ; 2700.0bp to feature; MODIFIER | silent_mutation | Average:44.743; most accessible tissue: Zhenshan97 young leaf, score: 67.334 | N | N | N | N |
| vg0112778994 | G -> A | LOC_Os01g22730-LOC_Os01g22740 | intergenic_region ; MODIFIER | silent_mutation | Average:44.743; most accessible tissue: Zhenshan97 young leaf, score: 67.334 | N | N | N | N |
| vg0112778994 | G -> DEL | N | N | silent_mutation | Average:44.743; most accessible tissue: Zhenshan97 young leaf, score: 67.334 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0112778994 | NA | 2.16E-09 | mr1151 | 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 |
| vg0112778994 | NA | 6.67E-10 | mr1352 | 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 |
| vg0112778994 | NA | 2.69E-09 | mr1881 | 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 |
| vg0112778994 | NA | 1.27E-07 | mr1654_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 |