| Variant ID: vg0817249650 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17249650 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.08, others allele: 0.00, population size: 141. )
CTAAAGGCAAGATTTTTGGACCTGCACTGAAGTTAAGCAGATCTTCCAGGCCTCGTGTTTTCGCATCAACATTTATGGTATTGAAATACTTTTCGAGTAT[T/A]
TGAATGCCTACTTTACATTATGTTCATGTTATATTGAATATACTGCTAGCTTATCTAGGAGATGCTTTGGTGCAGGTATAATGTTTGCATATGCAATTAC
GTAATTGCATATGCAAACATTATACCTGCACCAAAGCATCTCCTAGATAAGCTAGCAGTATATTCAATATAACATGAACATAATGTAAAGTAGGCATTCA[A/T]
ATACTCGAAAAGTATTTCAATACCATAAATGTTGATGCGAAAACACGAGGCCTGGAAGATCTGCTTAACTTCAGTGCAGGTCCAAAAATCTTGCCTTTAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.70% | 11.90% | 1.44% | 52.88% | NA |
| All Indica | 2759 | 5.40% | 10.60% | 2.25% | 81.81% | NA |
| All Japonica | 1512 | 86.80% | 6.40% | 0.26% | 6.48% | NA |
| Aus | 269 | 1.50% | 59.50% | 0.74% | 38.29% | NA |
| Indica I | 595 | 8.60% | 3.00% | 3.53% | 84.87% | NA |
| Indica II | 465 | 4.50% | 4.90% | 1.72% | 88.82% | NA |
| Indica III | 913 | 1.80% | 20.40% | 1.53% | 76.34% | NA |
| Indica Intermediate | 786 | 7.60% | 8.30% | 2.42% | 81.68% | NA |
| Temperate Japonica | 767 | 98.60% | 0.10% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 65.90% | 18.30% | 0.60% | 15.28% | NA |
| Japonica Intermediate | 241 | 93.40% | 1.70% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 90.60% | 1.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 47.80% | 15.60% | 0.00% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817249650 | T -> A | LOC_Os08g28260.1 | downstream_gene_variant ; 357.0bp to feature; MODIFIER | silent_mutation | Average:9.763; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0817249650 | T -> A | LOC_Os08g28260-LOC_Os08g28270 | intergenic_region ; MODIFIER | silent_mutation | Average:9.763; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0817249650 | T -> DEL | N | N | silent_mutation | Average:9.763; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817249650 | 5.79E-07 | 5.79E-07 | mr1108_2 | Jap_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 |
| vg0817249650 | 4.14E-06 | 4.03E-07 | mr1112_2 | Jap_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 |
| vg0817249650 | 5.74E-06 | 5.74E-06 | mr1234_2 | Jap_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 |