| Variant ID: vg0823802142 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 23802142 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )
AATCGTTAATAAGATGTTATGAGTTATAAACTTATACGCAATTAGTAATCCATCCGTCCCAAAATATAAGTATTTTAGTTATGAATCTGGACCAAAAGTT[A/G]
ATATATTTTAGTATACGTCAAACGATGGACTGAAACTTGTATTGTTCCAACAAGCGGCTAATCGAATGTCCATTGCGTTTAAAACAAACTGCAGGTTTGT
ACAAACCTGCAGTTTGTTTTAAACGCAATGGACATTCGATTAGCCGCTTGTTGGAACAATACAAGTTTCAGTCCATCGTTTGACGTATACTAAAATATAT[T/C]
AACTTTTGGTCCAGATTCATAACTAAAATACTTATATTTTGGGACGGATGGATTACTAATTGCGTATAAGTTTATAACTCATAACATCTTATTAACGATT
| 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 | 68.70% | 27.50% | 3.75% | 0.00% | NA |
| All Indica | 2759 | 90.50% | 5.90% | 3.59% | 0.00% | NA |
| All Japonica | 1512 | 43.10% | 52.50% | 4.37% | 0.00% | NA |
| Aus | 269 | 11.20% | 88.10% | 0.74% | 0.00% | NA |
| Indica I | 595 | 85.00% | 6.90% | 8.07% | 0.00% | NA |
| Indica II | 465 | 93.50% | 4.30% | 2.15% | 0.00% | NA |
| Indica III | 913 | 95.70% | 4.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 86.90% | 8.10% | 4.96% | 0.00% | NA |
| Temperate Japonica | 767 | 41.20% | 52.20% | 6.65% | 0.00% | NA |
| Tropical Japonica | 504 | 54.80% | 42.90% | 2.38% | 0.00% | NA |
| Japonica Intermediate | 241 | 24.90% | 73.90% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 12.50% | 86.50% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 28.90% | 10.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0823802142 | A -> G | LOC_Os08g37580.1 | downstream_gene_variant ; 1238.0bp to feature; MODIFIER | silent_mutation | Average:64.033; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0823802142 | A -> G | LOC_Os08g37570-LOC_Os08g37580 | intergenic_region ; MODIFIER | silent_mutation | Average:64.033; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0823802142 | NA | 4.20E-06 | mr1398 | 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 |
| vg0823802142 | 5.00E-06 | 4.98E-06 | mr1464 | 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 |
| vg0823802142 | NA | 7.76E-09 | mr1989 | 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 |