| Variant ID: vg1219745087 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 19745087 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 73. )
CCGACAGCCACACCTACAAGCTACAGCTGAAGCATCAGATAGGGCAGAGGAGGCATCACAGGTCTGGTTTGGATTAAATTTAATGTTGCACTTTGTATAG[A/C]
TATATGCAGTTTCAATTTCATCTTCTGTTTTCTACCACCTCGCAATGTGACAGTTGGTATGAGGAGATCTCATCAAAGTTCACTGATTTTTTATATTGTT
AACAATATAAAAAATCAGTGAACTTTGATGAGATCTCCTCATACCAACTGTCACATTGCGAGGTGGTAGAAAACAGAAGATGAAATTGAAACTGCATATA[T/G]
CTATACAAAGTGCAACATTAAATTTAATCCAAACCAGACCTGTGATGCCTCCTCTGCCCTATCTGATGCTTCAGCTGTAGCTTGTAGGTGTGGCTGTCGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.80% | 33.40% | 2.03% | 16.76% | NA |
| All Indica | 2759 | 20.50% | 49.80% | 2.86% | 26.79% | NA |
| All Japonica | 1512 | 96.90% | 1.20% | 0.07% | 1.85% | NA |
| Aus | 269 | 28.30% | 62.50% | 5.58% | 3.72% | NA |
| Indica I | 595 | 8.10% | 71.40% | 2.02% | 18.49% | NA |
| Indica II | 465 | 7.30% | 54.40% | 1.29% | 36.99% | NA |
| Indica III | 913 | 32.20% | 32.60% | 5.15% | 30.01% | NA |
| Indica Intermediate | 786 | 24.20% | 50.80% | 1.78% | 23.28% | NA |
| Temperate Japonica | 767 | 98.30% | 0.10% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 96.20% | 1.00% | 0.00% | 2.78% | NA |
| Japonica Intermediate | 241 | 93.80% | 5.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 87.50% | 7.30% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 77.80% | 10.00% | 1.11% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1219745087 | A -> C | LOC_Os12g32690.1 | upstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:14.392; most accessible tissue: Callus, score: 37.925 | N | N | N | N |
| vg1219745087 | A -> C | LOC_Os12g32700.1 | downstream_gene_variant ; 2737.0bp to feature; MODIFIER | silent_mutation | Average:14.392; most accessible tissue: Callus, score: 37.925 | N | N | N | N |
| vg1219745087 | A -> C | LOC_Os12g32690-LOC_Os12g32700 | intergenic_region ; MODIFIER | silent_mutation | Average:14.392; most accessible tissue: Callus, score: 37.925 | N | N | N | N |
| vg1219745087 | A -> DEL | N | N | silent_mutation | Average:14.392; most accessible tissue: Callus, score: 37.925 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1219745087 | NA | 6.61E-09 | mr1575 | 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 |
| vg1219745087 | NA | 1.61E-06 | mr1832 | 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 |
| vg1219745087 | 4.09E-07 | 8.98E-08 | mr1662_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 |
| vg1219745087 | 1.48E-06 | 3.02E-08 | mr1662_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 |