| Variant ID: vg0208482222 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8482222 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 41. )
GTAGCAATCTCTCGCACCGTAGCTTCCATTAGTGTTTGAAAGATAAGTCTACTCGCTCGCTGGTTCTCGAACCAGTAAAAGGTAGCAATCTCTCGCACCG[C/T]
AGCTTCCGTTGGTGTTCGAGAGATAAGTCTACTCGCTCGCTGGTTCTCGAACCAGTAAATCATAGCAATCTCTCGCACCGCAGCTTCCTTTGGCGTTCGA
TCGAACGCCAAAGGAAGCTGCGGTGCGAGAGATTGCTATGATTTACTGGTTCGAGAACCAGCGAGCGAGTAGACTTATCTCTCGAACACCAACGGAAGCT[G/A]
CGGTGCGAGAGATTGCTACCTTTTACTGGTTCGAGAACCAGCGAGCGAGTAGACTTATCTTTCAAACACTAATGGAAGCTACGGTGCGAGAGATTGCTAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.60% | 33.60% | 10.66% | 18.13% | NA |
| All Indica | 2759 | 50.80% | 11.30% | 16.64% | 21.28% | NA |
| All Japonica | 1512 | 2.60% | 81.10% | 0.93% | 15.41% | NA |
| Aus | 269 | 88.80% | 1.50% | 5.95% | 3.72% | NA |
| Indica I | 595 | 30.90% | 8.40% | 22.86% | 37.82% | NA |
| Indica II | 465 | 46.20% | 25.60% | 13.12% | 15.05% | NA |
| Indica III | 913 | 70.50% | 0.90% | 15.66% | 12.92% | NA |
| Indica Intermediate | 786 | 45.50% | 17.20% | 15.14% | 22.14% | NA |
| Temperate Japonica | 767 | 1.20% | 96.30% | 0.13% | 2.35% | NA |
| Tropical Japonica | 504 | 4.20% | 54.00% | 2.18% | 39.68% | NA |
| Japonica Intermediate | 241 | 3.70% | 89.20% | 0.83% | 6.22% | NA |
| VI/Aromatic | 96 | 60.40% | 13.50% | 8.33% | 17.71% | NA |
| Intermediate | 90 | 42.20% | 38.90% | 7.78% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208482222 | C -> T | LOC_Os02g15200.1 | downstream_gene_variant ; 2615.0bp to feature; MODIFIER | silent_mutation | Average:29.117; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg0208482222 | C -> T | LOC_Os02g15210.1 | downstream_gene_variant ; 449.0bp to feature; MODIFIER | silent_mutation | Average:29.117; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg0208482222 | C -> T | LOC_Os02g15210-LOC_Os02g15220 | intergenic_region ; MODIFIER | silent_mutation | Average:29.117; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg0208482222 | C -> DEL | N | N | silent_mutation | Average:29.117; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0208482222 | 2.57E-06 | 2.57E-06 | mr1398 | 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 |
| vg0208482222 | NA | 3.85E-07 | mr1515 | 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 |
| vg0208482222 | NA | 2.74E-06 | mr1704 | 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 |
| vg0208482222 | NA | 6.13E-07 | mr1815 | 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 |